Author: ecogrow

Additionally, clinical studies are needed, since in vitro and animal studies, while potentially relevant as preclinical models, do not directly assess outcomes such as the vascular effects in humans. Clinical and mechanistic data on the biological effects of polyphenols derived from dates are limited . Such evidence is crucial for agriculture, health professionals and consumers, particularly as the concept of personalized nutrition grows more popular. In addition to randomized clinical trials on the fruit in general, more data is needed to identify which polyphenols are the most vasculoprotective and then determine how best to cultivate, harvest and process the fruit for maximum bio-activity. The efficacy of date consumption also needs further interrogation in various at-risk groups such as those with lipid disorders, hypertension, obesity or diabetes. Since all fruits are not equal in composition, identification of unique bio-active compounds or fractions in dates would help define benefits that may not be obtained from other fruits or plant-based foods. Beyond polyphenols, dates contain cardiovascular-protective nutrients including potassium, magnesium, folate, selenium, fiber, and vitamin C . Most date varieties are rich in potassium and low in sodium, both of which are important dietary factors that help maintain blood pressure in the normal range.Dates contain folic acid and vitamin C. Folic acid is required to metabolize homocysteine to methionine. Elevated levels of serum homocysteine have been associated with increased risk for CVD . Although the mechanisms by which increased homocysteine promotes CVD are incompletely defined,blueberry packaging box suggested alterations include impaired vascular tone due to decreases in NO bio-availability and increases in ET-1, promotion of damaging ROS, and endothelial inflammation and the activation of the coagulation cascade.

The vitamin C in dates, while modest in amount compared to most citrus fruits, can nonetheless help to scavenge free radicals via enzymatic and non-enzymatic activities, and help protect lipoproteins from oxidative damage. In addition, vitamin C can improve measures such as arterial stiffness and endothelial function, and low serum concentrations of vitamin C have been linked to increased CVD risk and mortality. Some of the cardioprotective effects of dates have been ascribed to dietary fibers, which have a well-established lipid-lowering effect. Serum triacylglycerol, total cholesterol, and LDL-C levels were significantly lowered in rats given 100 g/kg of date dietary fibers. Most of the fibers in dates are insoluble. These fibers can bind to cholesterol and triacylglycerols in the intestine and facilitate their excretion, which helps lower circulating cholesterol levels. As a result, less lipoprotein is also susceptible to oxidation, thus reducing the impact on atherogenesis. Further, fiber-rich foods can promote production of beneficial commensal bacteria while limiting the growth of known opportunistic pathogens. A high-fiber diet was reported to increase acetateproducing micro-biota, lower blood pressure and decrease cardiac hypertrophy and fibrosis in hypertensive mice. Bacterial fermentation of prebiotic soluble fiber generates short chain fatty acids, which are thought to exert several beneficial effects including differentiation of immune regulatory T cells, and decreasing the expression and activation of peroxisome proliferator-activated receptor-γ . Downregulation of PPAR-γ activates a mitochondrial uncoupling protein 2 and an AMP-activated protein kinase network, shifting metabolism in adipose and liver tissue from lipogenesis to fatty acid oxidation. Conversely, activation of PPAR-γ has been shown to have anti-inflammatory effects, promote the expression of genes for fatty acid oxidation, and decrease lipotoxicity in macrophages .

The gut micro-biota are critical for enhanced bio availability and activity of ingested polyphenols, as most parent compounds are not well absorbed in the small intestine. Following the ingestion of polyphenols, typically in their glycosylated forms, bacteria in the gastrointesti-nal tract metabolize these molecules to low-molecular-weight phenolic compounds that are then absorbed by intestinal epithelial cells. Polyphenols have been shown to undergo a variety of enzymatic processes by bacterial populations in the gastrointestinal tract, including the hydrolysis of glycosylated flavonoids, acylation of flavanol-3-ols and esterification of hydroxycinnamic acids . A detailed description of these mechanisms can be found elsewhere. While the health promoting cardiovascular benefits of a number of fruits, nuts and berries rich in select polyphenols have been characterized through animal and human studies, no such data exists for dates to our knowledge. Given the polyphenol and fiber content of dates, vascular function and gut micro-biome studies would be useful. Vascular function is commonly assessed by two noninvasive techniques: flow-mediated dilation of the brachial artery and peripheral arterial tonometry in the fingertip. Both methods have demonstrated prognostic value for the assessment of cardiovascular risk factor burden. High dietary intakes of select polyphenols, such as the flavanols and PACs found in berries, tea, red grapes, and cocoa have been reported to significantly improve FMD and PAT in various population groups. Importantly, no data exists with respect to the impact of date products and their polyphenols on vascular dysfunction via measurement of FMD and PAT. An inherent challenge with most nutrition studies is the identification of suitable controls. This is particularly difficult when examining the potential health effects of whole foods that contain a multitude of compounds that are bio-active either separately or through their interaction with other constituents in the food matrix.

One model for testing foods or extracts is to use a control product that is closely matched in calories, macro- and micronutrients, taste, and color, but devoid of the test fraction or compound. This model has been used successfully in studies that assess the effects of a dietary strawberry powder and a flavanol-rich cocoa drink . Another model is to employ a no-intervention control group, although operationally, this may skew the results since a number of those assigned to the control group may withdraw from the study prior to its completion, and those remaining may not fully represent the population initially enrolled. Future human research on dates must select the study population carefully, and focus mainly on groups at risk for CVD. Accordingly, hormonal status, age and sex are factors that can produce significant interindividual variability in cardiometabolic responses to phenolic compounds and must be considered. Factors such as microbial metabolism and genetic polymorphisms may be other contributors to outcome variability. Recent attention has also emphasized the challenge of reproducibility and accuracy in human nutrition research. As noted above, more complete compositional profiles of dates are needed rather than simply recognizing the total amount of GAEs, a gross index of flavonoid content. A more detailed characterization of products, reagents, and model systems used, as well as better rigor and reporting of experimental designs, protocols, and data analysis, will help achieve this goal. Worthy of note, many of these elements were limiting factors in the in vitro and in vivo animal reports discussed above. While dates have positive biological effects, concerns have been raised about their potential concentrations of heavy metals. Exposure to heavy metals can result in cardiovascular diseases, encephalopathy, renal dysfunction, dementia, and certain cancers. A recent study of seven date varieties collected from different locations in Saudi Arabia noted that aluminum, chromium, and antimony were within a safe range based on the maximum allowable levels set by the World Health Organization, while arsenic, lead, and cadmium exceeded the upper limit in some of the date cultivars. Numerous environmental factors can increase concentrations of heavy metals such as mining, fertilizer applications and industrial emissions,blueberry packaging containers as well as naturally occurring amounts normally found in some soils. An increasing body of evidence suggests that the gut micro-biota has a profound impact on human health. While the micro-biome of a healthy individual is relatively stable, gut microbial dynamics can be influenced by host lifestyle and dietary choices. An acute change in dietary pattern from animal-based to plant-based diet alters gut microbial populations within 24 h and then reverts to baseline within 48 h of returning to the baseline dietary pattern. Studies that involve intake of a specific dietary component demonstrate how certain micro-biota tend to respond to nutrient-specific challenges. Protein, fats, digestible and non-digestible carbohydrates, probiotics, and dietary polyphenols all induce shifts in the micro-biome with secondary effects on host immunological and metabolic markers. An emerging and rapidly growing scientific literature is implicating the micro-biome in a number of conditions and disorders including inflammatory bowel disease, obesity, type 2 diabetes mellitus, cardiovascular disease, cancer, autism, mood and neurodegenerative disorders. The consumption of polyphenol-rich foods, including fruits and vegetables, has been reported to reduce pathogenic Clostridia and to enrich beneficial bacteria such as Bifidobacterium and Lactobacillus species in human studies. In conjunction with these changes, reductions in plasma triglycerides and C-reactive protein have been noted. Dietary polyphenols have been shown to help maintain intestinal health by preserving the gut microbial balance through the stimulation of the growth of beneficial bacteria and the inhibition of pathogenic bacteria, exerting prebiotic-like effects.

We have previously demonstrated the effect of water extract of culinary spices, including cinnamon, Mediterranean oregano, ginger, rosemary, black and cayenne pepper, on the growth of 33 Bifidobaterium and Latobacillus spp., and its antimicrobial activity against 88 intestinal, pathogenic, and toxigenic bacterial strains in an in vitro model. These spices promoted the growth of Bifidobaterium and Latobacillus spp. Cinnamon, ginger, oregano, black pepper, and cayenne pepper showed activity against several pathogenic Fusobaterium and Ruminococcus spp. and selected Clostridium difficile strains. The present pilot study was designed to investigate the effects of mixed spices at culinary doses consumed over 2 weeks in a standardized 5 g capsule on the production of gut micro-biota and short-chain fatty acids in healthy subjects compared to a placebo maltodextrin capsule in a parallel randomized controlled clinical trial. The pilot study was conducted in accordance with the guidelines of the Office of the Human Research Protection Programs of the University of California, Los Angeles. The clinical protocol was approved by the UCLA Internal Review Board and the study was registered at the NIH Clinical Trial Registry . A total of 66 healthy women and men aged 18 to 65 were screened in 2017 through local advertisement. Participants with a history of gastrointestinal surgery, diabetes mellitus, or other serious medical conditions such as chronic hepatic or renal disease, bleeding disorder, congestive heart disease, chronic diarrhea, myocardial infarction, coronary artery bypass graft, angioplasty within 6 months prior to screening, current diagnosis of uncontrolled hypertension or chronic gastrointestinal disorders, bulimia, anorexia, laxative abuse, or endocrine disorders were excluded. Participants who were consuming a high-fiber/polyphenol diet; taking any medication or dietary supplement interfering with the absorption of polyphenols; pregnant or breastfeeding; frequently using prebiotics, probiotics, yogurt, or fiber supplements; taking antibiotics or laxatives within the previous 3 months; or currently using tobacco products were also excluded. Thirty-one subjects meeting enrollment criteria were recruited and provided written informed consent before the study began. A randomized, placebo-controlled, double-blind pilot study was conducted. Subjects were randomized according to an algorithm modified from a previous publication. The study was divided into two periods: an initial run-in period of 1 week and an intervention period of 2 weeks. After the run-in period, 31 subjects were randomly allocated to consume either 5 g capsules of spice mixture containing 1 g cinnamon, 1.5 g oregano, 1.5 g ginger, 0.85 g black pepper, and 0.15 g cayenne pepper, or 5 g capsules containing maltodextrin daily for 2 weeks. The individual spices were purchased from local grocery stores. At the start of study, participants received a diet instructional handout and were counseled by a registered dietitian on compliance. During the run-in and intervention period, all participants consumed a beige diet . The beige diet handout advised participants to eat foods beige in color and rich in simple carbohydrates like white breads/bagels, crackers, granola bars, rice, macaroni/pasta, yogurt, dairy, poultry, cereal, and bananas and to avoid foods high in polyphenols and/or fiber. Participants were also provided with weekly checklists to track their fruit and vegetable intake throughout the study with a limit of three servings per day. This checklist included a list of higher fiber/polyphenol foods to avoid as well as a list of lower fiber/polyphenol fruits and vegetables theycould consume as a part of their three servings per day, with a serving size estimation tool included. At the baseline and final visits, participants also completed and returned 3-day food records that were evaluated by the dietitian for compliance with the beige diet.

There is a growing interest in better understanding factors affecting agroecosystem functions and services. One key property of agroecosystems that has received much attention in recent years is the diversity of crop species. National crop species diversity has been associated with the stability of food production and used as a proxy for pollination services partly because local crop diversity enhances associated biodiversity . However, it is unclear how national crop diversity is related to local-scale diversity, and assuming that inferences made at one scale are maintained at other scales can be misleading. Crop species diversity also has a temporal dimension of great importance resulting from farmers’ crop rotations. These crop rotations can reduce pressure from pathogens, pests, and weeds and improve soil quality and yield stability . Yet, the temporal dimension of crop diversity is frequently ignored in most diversity assessments, mainly because it is hard to measure , and it is not clear how diversity in space and time relates. Therefore, a better understanding and treatment of the scale dependency of spatial crop species diversity and its relation with temporal diversity is needed to develop comprehensive theories of crop diversity effects on agroecosystem function. Most calls for more diverse farming systems do not consider regional differences that might limit farmers’ diversification opportunities or demand-side constraints . Moreover,wholesale grow bags most studies on crop species diversity used variation in diversity to explain other phenomena but there has been less progress in understanding factors that shape crop diversity .

Thus, to gain a quantitative understanding of diversity patterns and processes and improve comparisons between regions and countries, environmental and crop demand constraints to crop diversity must be identified. The first two chapters of this dissertation deal with some fundamental aspects of crop species diversity. The first chapter explores how crop diversity can be measured, depending on the dimension and scale considered and how these relate, using data for the conterminous United States. The second chapter examines which factors define and limit crop diversity. It outlines a framework for quantifying potential and attainable levels of crop species diversity, which is then applied at the global level. Crop species diversity in the USA increased during the first half of the 20th century, but it has gradually declined over the past 50 years in most of the country . This specialization, together with increasing use of inputs, allowed substantial yield gains, but it was also associated with important negative environmental impacts . Consequently, there is an interest in developing more diverse and sustainable cropping systems . Most studies on diversified cropping systems consider crop rotation diversification a key management practice to be developed and implemented . However, there have been no comprehensive efforts to analyze crop rotation diversity across the US, probably because it needs to be observed at a very high spatial resolution . The first chapter analyzes temporal and spatial crop species diversity patterns in the conterminous US and how they relate. It shows that crop rotation diversity is tightly associated with local diversity at a spatial resolution close to typical US farm size. It also shows that this diversity is lower for rotations that include major crops. The observable patterns in the spatial distribution of crop species and their subsequent diversity are realizations of underlying processes that need to be elucidated .

While drivers of current crop genetic diversity patterns have been studied , there is very little knowledge on processes shaping the diversity of crop species. However, some concepts from macroecology and bio geography might be applicable . For instance, one of the most established patterns in Ecology, latitudinal biodiversity gradients , can also be expected to regulate crop species diversity. But crop diversity depends on both natural and human-mediated processes. Thus, while some tropical regions might be suitable for many crop species , current diversity patterns are also affected by individual and structural factors shaping farming decisions and resulting in different specialization levels . The second chapter sets a theoretical framework of hierarchical levels of crop diversity that considers crop-specific environmental requirements and the demand for agricultural products. This framework is then used to analyze the environmental drivers of potential and attainable crop diversity and quantify diversity gaps. The results show that potential and attainable crop diversity are lower in temperate and continental areas than in tropical and coastal regions. Although current diversity follows these patterns to some extent, other processes also affect it, resulting in high spatial variability in diversity gaps. The third chapter of this dissertation is on a different topic. It contributes to a project to better understand the opportunities for improved management of acid soils in Africa. One of the initial steps of the project is developing a spatially-explicit analysis of the costs and benefits of liming in Africa. This analysis is founded on models for lime requirement estimation. However, the literature on lime requirement estimation methods is sparse and inconsistent, particularly for acid tropical soils. Thus, the third chapter focused on a comparison of lime requirement models. Acid tropical soils can have several problems affecting crop growth, such as aluminum and manganese toxicity and calcium and magnesium deficiencies .

These issues can be addressed by applying liming materials . The amount of agricultural lime required is often estimated with locally calibrated soil tests . Both soil testing and liming might be relatively cheap and easy to access for intensive commercial farmers, but that is not the case for most smallholder farmers in tropical developing countries . Lime application is relatively expensive in many tropical regions, and the experimental evidence on lime response is also limited. Furthermore, soil tests that work elsewhere cannot be assumed to work for these places and must be re-calibrated. Therefore, general models to estimate lime requirements from generally available soil data could be useful as a starting point in developing locally optimal liming recommendations and for strategic research on future lime use. The third chapter compares and evaluates different models for lime requirement estimation that can be used in acid tropical soils with readily available soil data and introduces an outperforming model developed based on past experiences and clear principles. It shows that there are important differences in model accuracy and prediction values and that liming estimates largely depend on the target soil chemical property of the model. Therefore, the most important soil acidity problems affecting crop yields must be identified to formulate liming recommendations in acid tropical soils. However,grow bags for gardening models for other acidity problems than aluminum toxicity still need to be developed.Low soil pH is associated with a high concentration of toxic elements in the soil solution, such as aluminum and manganese, and with low availability of phosphorus, calcium, and other plant nutrients . Soil acidity problems can be addressed with liming, the application of calcium or magnesium-rich materials that react as a base . Liming has been practiced for centuries , and its use is still expanding, particularly in tropical areas with acid soils. For example, it played a key role in the recent expansion of agriculture in the Brazilian Cerrado region . The amount of lime required to adjust soil acidity depends on the soil, the target crop, and the liming material used. In temperate regions, lime requirements are commonly estimated with locally calibrated quick tests using buffer solutions . These tests can be developed by comparing the buffer’s response to the soil with the soil response to lime in field or incubation studies or by slow titrations. Both the soil testing and the lime application may be a relatively small expense in intensively managed commercial farms, partly because lime is cheap and partly because the use of lime, when needed, increases the use efficiency of other inputs . Moreover, applying a bit more lime than needed means its benefits will last longer . Thus, blanket applications that err on the higher side are not very risky , so there is no need for a highly accurate determination of the amount of lime to apply. This situation is different for smallholder farmers in sub-Saharan Africa and other tropical regions . Lime may be relatively expensive, and its benefit may be relatively small if fertilizer use is low. Under these circumstances, it would be helpful to have accurate estimates of lime requirements. However, empirical evidence from these tropical regions is limited, and laboratory-based soil testing is often inaccessible. Furthermore, methods that depend on direct measurements of soil acidity in each field with buffer solutions cannot be assumed to work elsewhere and would have to be redeveloped. Models to estimate lime requirements from generally available soil data are needed for strategic research of potential lime use across tropical regions.

They can be particularly useful for subSaharan Africa, where the impact of soil acidity on crop productivity and nutrient-use efficiency is poorly understood . Lime requirement models could serve as a starting point to develop locally optimal liming recommendations for farmers and development practitioners and provide strategic information to national governments and the private sector on potential market sizes for lime for a region of interest. The latter is now possible thanks to the availability of high-resolution spatial products for most soil properties across the continent . Here we provide a comprehensive review of general lime requirement models for tropical acid soils that can be used with readily available soil data. We first introduce key concepts related to estimating lime requirements that have been a source of confusion and inconsistency. We then describe and discuss published lime requirement models for tropical soils and introduce a new model to estimate lime requirements. Finally, we show substantial differences in the estimated lime requirement for acid tropical soils when using these models and discuss their implications. Soils can be naturally acidic or become acidic because of agricultural practices such as the use of acidifying fertilizer and the removal of elements with harvested products. In the tropics, many soils in humid areas are inherently acidic because intense weathering processes have resulted in the displacement and leaching of basic exchangeable cations and the accumulation of exchangeable acidity . The main problem with soil acidity in the tropics is not the low pH as such, but rather the associated aluminum toxicity that constrains crop growth . The purpose of liming should be, therefore, to remove Al toxicity, considering the sensitivity of the target crops, together with other possible constraints such as Ca and Mg deficiencies , but not to increase pH for its own sake . Acidity saturation is the fraction of the effective cation exchange capacity of the soil occupied by exchangeable acid cations . In tropical soils, nearly all exchangeable acidity comprises exchangeable Al3+ and, thus, Al saturation approximates acidity saturation . For that reason, acidity saturation is often used as a proxy for Al toxicity . Many lime requirement models estimate the lime rate required to lower the acidity saturation to a target level that does not affect crop yield . The terms exchangeable acidity and exchangeable Al3+ have been used interchangeably in tropical soil literature, with the term exchangeable Al3+ more commonly used in older literature . Indeed, several authors of the lime requirement models reviewed here measured acidity saturation but referred to it as Al saturation . Consequently, some models were originally formulated for exchangeable Al3+ but derived from exchangeable acidity measurements. Some highly weathered acid soils can have very low ECEC and, thus, low exchangeable Ca2+ and Mg2+ but low acidity saturation, resulting in Ca and Mg deficiencies without Al toxicity problems . Therefore, some lime requirement models based on acidity saturation also estimate the lime rate needed to cover such deficiencies . Such mineral deficiencies can also be addressed with compost or inorganic fertilizers such as calcium nitrate, which might be more convenient in soils with no Al toxicity problems. An alternative approach to alleviating soil acidity problems aims to raise the “base saturation” to a certain level rather than focusing on acidity saturation . Base saturation is the sum of all exchangeable bases divided by the Cation Exchange Capacity at pH 7 . CEC7 is different from ECEC, especially in acid soils, where CEC7 ≫ ECEC. For ECEC, exchangeable acid cations are extracted with a neutral unbuffered salt. In contrast, a pH 7 buffer solution is used for CEC7, which extracts both exchangeable and non-exchangeable acidity , comprising the potential acidity.

In non Western samples, we might find that categorical information might have an indirect effect , because people in non-Western cultural contexts could potentially see the inter connectedness with other categories. To be sure, our finding does not necessarily mean that emphasizing categorical information in language does not have a long term effect in fostering a holistic thinking style. Future research should implement training studies across different cultures to test this hypothesis. Interestingly, our Study 2 observed that females, more than males, are influenced by the verbal labels during the verbal triad task. First of all, this cannot be attributed to the fact that females are generally more susceptible to categorical associations, since there was no difference in the control condition in Study 2 and no difference in both pictorial and verbal triad tasks in Study 1. Although there were some studies showing gender differences in thinking styles, we do not have a strong theory to explain the gender differences observed in the current study. We could only speculate that females may be more receptive to verbal information than males, given some evidence on gender differences in verbal skills . One caveat is that our sample size in Study 2 was small and unbalanced in gender so future studies should examine the potential gender differences with a larger and balanced sample. There are a couple of limitations of the current studies. First, due to the global COVID-19 pandemic, both studies were conducted online so the testing environment and the attentional state of participants were not controlled. Since the studies were self-paced, the priming influence in our Study 2 could vary across individuals. Second, we only focused on a young adult sample in a Western culture so the generalizability of the current findings awaits the tests from future studies examining different ages and cultures. In conclusion,square black flower bucket wholesale our research provided some new evidence that verbal labels could influence thinking styles measured in the triad task.

The way language might influence thinking styles however , might depend on the language context. Our results add on the evidence that language could mediate the impact of culture on thinking styles. More importantly, thinking styles should be considered a contextually-dependent concept which could vary across individuals, tasks, and cultures. Cultivation and consumption of pomegranate can be dated back to at least 3000 BC. Historically, pomegranate has served as a symbol of fertility and prosperity. In addition, various parts of the pomegranate have been used in traditional medicine for treating a wide variety of illness. Pomegranate fruits have purported use for expelling parasites, seeds and fruit peels for treating diarrhea, flowers for managing diabetes, tree barks and roots for stopping bleeding and healing ulcers, and leaves for controlling inflammation and treating digestive system disorders. Due to its reported benefits to human health, the pomegranate has drawn great interest from the consumers in recent years. Nowadays, the pomegranate is used for functional food ingredients and dietary supplements in various forms, such as fresh fruit and juice, powdered capsules and tablets that contain extracts of different pomegranate tissues, tea brewed from pomegranate leaves, jam, jelly, juice and wine produced from pomegranate fruits, as well as spices prepared from dried seeds. With the advancement of technologies and the expansion of experimental inquiries into the bio-activities of pomegranate phytochemicals, many new discoveries have been made in this ancient fruit within the last decade. To date, over 1500 articles have been published on the subject“pomegranate”, of which 1259 articles were published between 2006 and 2016. Although the pomegranate produces and accumulates a wide variety of phytochemicals with diverse structures in different tissues , investigative efforts thus far have been given mainly to the bio-activities of polyphenols in pomegranate fruits, in particular anthocyanins and hydrolyzable tannins , which are assessed in this review. Specifically, various health-promoting activities of urolithins, a group of phenolic metabolites transformed from ellagic acid by the human gut micro-biota, will be reviewed.

Development of cutting-edge analytical techniques has enabled the acquisition of large-scale metabolic datasets, which requires careful analysis and interpretation. To facilitate characterization of metabolite profiling data in pomegranate, we examine the phytochemicals that have been identified in pomegranate, including detailed information on the chemical structures, molecular formulas, molecular weights, analytical methods , and tissues of identification . Knowledge of phytochemicals present in different pomegranate tissues will also help assess the structural determinants of their bio-activities as well as the additive, antagonistic or synergistic interactions of these phytochemicals in complex mixtures. Numerous phytochemicals have been identified in different pomegranate tissues using diode array detection , electron spin resonance , fluorescence detection , flame ionization detection , infrared spectroscopy , mass spectrometry , nuclear magnetic resonance , and thin layer chromatography . It should be noted that disparities regarding the presence/absence of phytochemicals in specific tissues have been observed in different pomegranate cultivars. In addition, the quantities of phytochemicals vary among the pomegranate cultivars. HTs are among the most studied phytochemicals in pomegranate; they can be further grouped into ETs and gallotannins based on the different phenolic acids that are esterified to the core cyclic polyol molecule . Overall, more than 60 HTs have been identified from pomegranate using MS and/or NMR . Pomegranate fruit peel is rich in HTs, particularly ETs. Punicalagin isomers constitute up to 85% of total tannins extracted from pomegranate fruit peel. EA, methylated EA, and their glycosidic derivatives have also been found in fruit peel and other pomegranate tissues . Although punicalagin isomers represent the major ETs in pomegranate roots, they accumulate at much lower levels in roots than fruit peel. Besides fruit peel, pomegranate stem barks are also abundant in HTs and have been used historically in tanneries for making leather. In addition to the HTs identified in fruit peel, stem barks also contain ET C-glycosides, punicacorteins A–D , and punigluconin.

The dense inner part of pomegranate tree trunk contains brevifolin carboxylic acid, EA rutinoside, diellagic acid rutinoside, methyl-EA, methyl-EA rutinoside, punicalin, galloylpunicalin, and galloylpunicacortein D. The composition of HTs in pomegranate leaves is largely different from that in fruit peel. In leaves, the major HTs are granatins A and B, whereas punicalagins and punicalins are present at negligible levels. Additional ETs with galloyl and/or hexahydroxydiphenoyl substitutions have also been identified in leaves. Interestingly, derivatives of EA and ETs, including urolithin M-5, brevifolin, and brevifolin carboxylic acid, have been isolated from pomegranate leaves. In pomegranate flowers, EA and two oxidized derivatives of EA, pomegranatate and phyllanthusiin E, were discovered. Punicatannins A and B, two ETs that contain an unusual 3-oxol,3,3a,8b-tetrahydrofuro[3,4-b]benzofuran functional group, together with a structurally relatedcompound isocorilagin, were also found in pomegranate flowers. In addition, brevifolin carboxylic acid, ethylbrevifolin carboxylate, as well as glucose with various galloyl and/or HHDP substitutions, including hippomanin A, gemin D, digalloyl-diHHDP-glucose, trigalloyl glucose, and gallic acid 3-O-β-D–glucopyranoside showed measurable accumulations in pomegranate flowers.Pomegranate fruit peel, aril, and juice are abundant in flavonoids of diverse structures, including the aglycones and glycosides of chalcones, flavanones, flavones, flavonols, ATs, flavan-3-ols, and procyanidins . Two flavones, luteolin and tricetin, were found in a methanolic extract of pomegranate flowers. Structures of two flavanones, punicaflavanol and granatumflavanyl xyloside, were elucidated by NMR, while hovetrichoside C and phlorizin were identified by IR in pomegranate flowers. Similar to other plants, leaves of pomegranate also accumulate high levels of flavone glycosides. Two flavanone diglycosides and one flavonol diglycoside isolated from pomegranate stem barks were shown to be eriodictyol-7-O-α-L-arabinofuranosyl-β-D-glucoside,plastic square flower bucket naringenin-40 methyl ether 7-O-α-L-arabinofuranosyl-β-D-glucoside, and quercetin-3,40 -dimethyl ether 7-O-α-L-arabinofuranosyl-β-D-glucoside, respectively, by NMR analysis. High performance liquid chromatography -DAD studies revealed that two isoflavones, genistein and daidzein, as well as a flavonol quercetin, are present in pomegranate seeds. Plant lignans are a group of phytoestrogens that can be metabolized into mammalian lignans by the gut micro-biota. Furofuran-, dibenzylbutane-, and dibenzylbutyrolactone-type lignans have been identified in different pomegranate tissues based on liquid chromatography -MSn studies , while isolariciresinol is the most abundant lignan present in pomegranate fruit peel. In addition to the above-mentioned lignans, pomegralignan, a dihydrobenzofuran-type neolignan glycoside, was discovered in the aril and fruit peel of pomegranate. Another neolignan, punnicatannin C, was isolated from pomegranate flowers and structurally characterized by NMR analysis. Triterpenoids are the biosynthetic precursors of steroids in plants and animals . Triterpenoids and phytosterols have been found in pomegranate seed, leaf, flower, fruit peel, and bark tissues . The presence of human steroid hormones, including estrone, estriol, estradiol, and testosterone, in pomegranate seeds was reported previously based on TLC separations and colorimetric assays. However, HPLC-DAD- and gas chromatography -MS-based analysis showed that these steroid hormones could not be identified in pomegranate seeds using the more sensitive analytical methods. Pelletierine, pseudopelletierine, and N-methylpelletierine comprise the major alkaloids in pomegranate stem and root barks. Sedridine, 2–∆ 1piperideine, 2–∆ 1piperideine, norpseudopelletierine, and the pyrrolidine alkaloids hygrine and norhygrine, were also found in root barks at low quantities. In addition to the alkaloids that accumulate in root and stem barks, N-pyridinium chloride was identified in pomegranate leaves, and a pyrrolidine-type alkaloid punigratane was recently characterized in pomegranate fruit peel. Besides alkaloids, low levels of indolamines , including tryptamine, melatonin, and serotonin, were present in the extract of pomegranate fruit.Fatty acids of medium , long , and very long chain length have been identified from pomegranate seeds, juice, and fruit using GC-FID, MS, or NMR analysis .

The polyunsaturated FA punicic acid represents the most abundant FA in pomegranate seeds, accounting for over 60% of seed oil. Triacylglycerols containing 9E, 11Z, 13E-octadecatrienoic acid, 3-O-octadec-2-enoic acid, 9Z, 11E, 13Z-octadecatrienoic acid, and 8Z, 11Z, 13E-octadecatrienoic acid are produced in pomegranate seeds and their structures were determined by NMR. In addition, a glycosphingolipid N-palmitoyl cerebroside was identified from pomegranate seed oil by TLC and GC-FID analyses. The major organic acids in pomegranate juice are citric acid and malic acid. Pomegranate juice also contains ascorbic acid, fumaric acid, oxalic acid, quinic acid, succinic acid, and tartaric acid, some of which have also been identified in the leaf, fruit peel, and seed tissues. Phenolic acids , primarily benzoic acid and cinnamic acid derivatives, are usually found in pomegranate fruit peel, juice, and flowers . In addition, the structure of a substituted coumarin, 7,8-dihydroxy-3-carboxymethylcoumarin-5-carboxylic acid, was characterized in pomegranate flowers by NMR. The synergy principle of phytochemicals has long been employed in traditional herbal medicine. Multi-target drugs derived from mixtures of plant natural products have increasingly been pursued nowadays to contradict drug tolerance and resistance in cancer therapy. Although several studies have suggested synergistic interactions among pomegranate phytochemicals, this is a promising, but currently under-explored topic. Fresh arils and juice products of pomegranate fruit, as well as seeds of the soft-seeded cultivars, are mostly consumed. Phytochemicals in pomegranate fruit peel extracts, fermented pomegranate juice, and pomegranate seed oil exhibited cooperative interactions toward limiting the proliferation, metastasis, and invasiveness of human prostate cancer cells in vitro. A subsequent analysis with pure phytochemicals, including EA, caffeic acid, luteolin, and punicic acid, also showed synergistic interactions on suppressing the invasion of prostate cancer cells. Interestingly, commercial pomegranate juice demonstrated more antioxidant and anti-proliferative activities than the purified pomegranate polyphenols in colon cancer cells, suggesting that inherent synergies exist among polyphenols and other phytochemicals in pomegranate juice. When the commercial pomegranate-nectarine juice was separated into predominately sugar, organic acid, neutral phenol, and AT fractions, complex antagonistic or synergistic effects were observed among different fractions on the total phenol or total antioxidant content. The antagonistic or synergistic interactions depended on the concentrations of the chemical constituents in the juice product . The polyphenol extracts of pomegranate fruit also synergistically interacted with the antibacterial drug ciprofloxacin, though various bacterial strains responded differently to the phytochemical-drug synergy, and the underlying mechanism of such synergy remains unknown .ATs are colorful, water-soluble polyphenol pigments that are found in many plant foods, such as berries and pomegranate fruits. Plant ATs are often investigated collectively as a group of phytochemicals for their bio-activities, and have been linked to many aspects of human disease prevention and treatment. The anti-inflammatory and cardioprotective activities of ATs are attributed by their antioxidant properties via various underlying mechanisms. ATs can quench free radicals, inhibit the activity of xanthine oxidase that generates free radicals, and chelate metal ions that are involved in oxidation of low-density lipoproteins. In addition, ATs induce the expression of nuclear factor-erythroid 2-related factor-2 that regulates the expression of endogenous antioxidant enzymes, such as hemeoxygenase-1.

Employers are assigned to the NAICS code that represents the majority of their sales, so grape vineyards can be distinguished from strawberry, other berry, and non-citrus tree fruit farms. These four types of farms account for almost three-fourths of direct-hire crop employment. Between 1990 and 2020, average direct-hire employment in grapes fell by almost half; strawberry employment doubled; employment in other berries such as blueberries and raspberries tripled; and average employment in non-citrus tree fruits such as peaches, nectarines, and plums fell by a third . Note that there is no commodity information for workers brought to farms by labor contractors.The gaps between peak and trough months of agricultural employment are shrinking. Between 1990 and 2000, average agricultural employment rose by almost 10%, from 367,000 to 400,000, and rose especially fast during the winter and spring months, reducing the peak-trough ratio from 1.8 in 1990 to 1.6 in 2000 . Between 2000 and 2010, average employment fell from 400,000 to 380,000, and the peak-trough ratio remained at 1.6. Between 2010 and 2020, average employment rose above 400,000,flower harvest buckets and the peak-trough employment ratio fell to 1.4. Average employment rose during the winter months and was stable during the summer months. Declining seasonality was accompanied by a rising share of farm labor contractor employment; the farm labor contractor share of the state’s average agricultural employment rose from 20% to 35% between 1990 and 2020 .

The largest jump in the FLC share of agricultural employment occurred in the 1990s, when there was an influx of undocumented Mexican workers seeking jobs at a time of low U.S. unemployment. The FLC share of California agricultural employment was stable between 2000 and 2010, but jumped between 2010 and 2020. The FLC share of the state’ saverage agricultural employment is highest during the summer months of May through August. Three regions account for over 90% of the state’s average agricultural employment: the San Joaquin Valley, the Central Coast region centered on Monterey, and the South Coast, which includes Santa Barbara and Ventura counties. Monterey County was the leading producer of hand-harvested fruits and vegetables in 1990, and was joined in 2000 by Fresno, Kern, and Tulare counties . Monterey continued to lead in hand-harvested fruits and vegetables in 2020 with over 4 million tons, but Fresno, Kern, and Tulare also expanded to each produce more than 2 million tons of hand-harvested fruits and vegetables. This helps explain rising farm employment and reduced seasonality.The San Joaquin Valley, from San Joaquin in the north to Kern County in the south, accounts for half of the state’s average agricultural employment. SJV average agricultural employment rose from 170,000 in 1990 to 200,000 in 2000, dipped to 185,000 in 2010, and was almost 200,000 in 2020. Seasonality often increases in smaller geographic areas, but the peak-trough employment ratio fell more in the SJV than it did statewide. The SJV peak-trough ratio fell from 2.2 in 1990 to 1.4 in 2020, more than the drop in the California peak-trough ratio, which fell from 1.8 to 1.4 over these three decades . Almost half of average agricultural employment in the San Joaquin Valley is with farm labor contractors, which explains why the SJV has a higher share of the state’s FLC employment than of overall agricultural employment. The SJV had over 60% of California’s FLC employment in 2020, versus 50% of the state’s agricultural employment.

Average FLC employment in the SJV rose sharply between 1990 and 2000, was stable between 2000 and 2010, and rose between 2010 and 2020, when FLC employment was 45% of the SJV’s average agricultural employment. The FLC share of SJV agricultural employment is highest during the summer months and lowest in April .This region includes Monterey County — the U.S. salad and berry bowl. Average employment in Central Coast agriculture rose from 54,000 in 1990 and 2000 to 70,000 by 2020, or a sixth of California’s agricultural employment, reflecting more strawberry acreage. Seasonality is more pronounced in the Central Coast than in the SJV, peaking in July 2020 at 89,000 and reaching a low of 46,000 in January 2020 for a peak-trough ratio of 1.9 . This is significantly higher than the 1.4 peak-trough ratio in the SJV. The farm labor contractor share of Central Coast agricultural employment rose sharply between 1990 and 2020. In 1990, FLC average employment was one sixth of Central Coast agricultural employment; by 2020, the FLC share was a third. Peak FLC employment in the Central Coast was 31,000 in June and July 2020, while trough employment was 15,000 in December 2020, a FLC peak-trough ratio of 2.1 .The South Coast region, which includes the six coastal counties from San Luis Obispo in the north to San Diego in the south, had average agricultural employment of 70,000 in 2020, the same as the Central Coast. However, growth in average agricultural employment was slower in the South Coast than in the Central Coast over the past three decades . The FLC share of average agricultural employment rose from less than 10% in 1990 to almost a quarter by 2020. FLC seasonality in the South Coast is similar to FLC seasonality in other regions. There were 180 workers employed by FLCs in June 2020 for each 100 workers employed by FLCs in December .Strawberries and other berries are among the most labor-intensive commodities grown in California.

Their production doubled and tripled over the past three decades . The state’s strawberries were worth $2 billion in 2020, raspberries were worth $405 million, and blueberries were worth $215 million, for total berry sales of over $2.6 billion. California’s average employment in berries more than doubled from 16,000 to 36,000 between 1990 and 2020, while seasonality as measured by employment peak-trough ratios declined from 5.9 to 2.5 . In 1990, berry employment was lowest at 5,000 in January and highest at 28,000 in May. In 2020, January was still the trough month; just under 20,000 workers were employed, compared with 49,000 in June. Berry employment in January tripled between 1990 and 2020 and doubled in May and June. The upsurge in winter and total berry employment is evident in a comparison of the largest sectors of employment in fruit and nut agriculture. In 1990, California fruit and nut employment peaked at 139,000 in September, including 67,000 in grapes, 34,000 in tree fruit, and 16,000 in berries. By 2020, California fruit and nut employment peaked at 108,000 in June, including 49,000 in berries, 20,000 in grapes, and 19,000 in tree fruit. There were four workers in grapes for each berry worker in 1990, and 2.5 workers in berries for each grape worker in 2020. Note that some of the decline in grape and tree fruit employment may be due to employers switching from hiring workers directly to hiring them via FLCs; no data are collected on the commodities where FLC employees work. The Central Coast and South Coast regions accounted for 98% of average berry employment in 2020, including 60% in the South Coast and 38% in the Central Coast. The South Coast share of average berry employment rose from 50% in 1990 to 60%, in 2020, in part due to the expansion of berry production in the Santa Maria area of Santa Barbara County.Over the past three decades, average employment in California agriculture rose by 10% to 404,000, while seasonality declined due to more employment during the winter months. The ratio of monthly peak to monthly trough employment fell from 1.8 in 1990 to 1.4 in 2020, reflecting 474,000 workers employed in September 1990 and 270,000 in February 1990,round flower buckets compared with 470,000 workers employed in May 2020 and 346,000 in March 2020. Many farming operations that hire large numbers of workers have year-round work forces comprised of local workers; they turn to contractors to bring local and H-2A workers to their farms to perform specific seasonal tasks. The FLC share of California agricultural employment rose from 20% in 1990 to 35% in 2020. FLC employment is more seasonal, with a statewide peak-trough employment ratio of 1.6 in 2020, higher than the 1.4 employment ratio for all agricultural employment. The San Joaquin Valley accounts for half of California’s agricultural employment, and seasonality in the valley declined faster than statewide. The SJV has over 60% of California’s FLC employment, and FLC employment in the SJV is slightly more seasonal than statewide. There were 170 workers employed by FLCs in the SJV in September 2020 for each 100 employed in April 2020. The Central Coast, centered on Monterey County, accounts for one-sixth of California’s agricultural employment, and its farm employment is more seasonal than in the SJV. For each 190 workers employed in June and July 2020 in the Central Coast, 100 were employed in January 2020.

FLCs accounted for one-third of the 70,000 average agricultural jobs in the Central Coast in 2020, up from 20% in 1990. The South Coast region from San Luis Obispo to San Diego has the same average employment as the Central Coast, about 70,000, and experienced less growth between 1990 and 2020, up 12% versus a 30% increase in the Central Coast. The FLC share of agricultural employment in the South Coast more than doubled from 1990 to 2020, reaching almost a quarter of farm employment. The SJV, Central Coast, and South Coast accounted for 49%, 17%, and 17% of the state’s average agricultural employment of 404,000 in 2020, respectively, or a total of 83%. These three regions accounted for 63%, 17%, and 11%, respectively, of the state’s average FLC employment of 142,500, or 91% of the state’s total FLC employment. The trends highlighted by this analysis — stable farm employment, decreased seasonality, and more workers brought to farms by labor contractors — seem poised to continue. A growing share of the workers brought to farms by labor contractors are H-2A guest workers , whose costs are higher because H-2A workers must be provided transportation and housing at no cost and paid an Adverse Effect Wage Rate of $18.65 an hour in 2023, when the minimum wage was $15.50 an hour. A major challenge for the state’s agriculture is to ensure that H-2A workers are productive enough to justify their higher costs, which are offset in part by payroll tax savings and by the fact that H-2A workers ensure that farm work is done on time.Categorization processes are fundamental in making sense of the world. Not surprisingly, the study of categorization is of central importance in cognitive science; researchers have long sought to characterize the nature of the conceptual structures that best support classification decisions. There is general agreement that some parts of a concept are more important—more conceptually central— than others for categorization . For example, as Medin and Shoben demonstrated, the property of “curvedness” is more central for the category of boomerangs than for the category of bananas. That is, “straight bananas” are better examples of bananas than “straight boomerangs” are of boomerangs, because “curvedness” plays a more central role in the theoretical principles supporting one’s knowledge of boomerangs. We argue here that conceptual centrality is closely related to the goodness of an explanation: specifically, that the centrality of a conceptual component derives from its role in the best explanation of what holds category members together. On this view, a good conceptual structure is one that contains important explanatory information. The study of explanation spans several disciplines, ranging from philosophy and computer science to psychology . In psychology, the view that category knowledge comprises important explanatory information is not new; and our proposal takes off from the theory- or knowledge-based framework of conceptual structure . We also draw on a specific instantiation of this view, the causal status hypothesis . Murphy and Medin argued persuasively that categorization can be viewed as an inference to the best explanation . On the relationship between theoretical knowledge and centrality, Murphy and Medin defined the weight associated with features as “[d]etermined in part by importance in the underlying principles” . This characterization is best viewed as a starting point, for it leaves open the critical question of how to define “importance.” One prominent answer to this question is the causal status hypothesis, according to which the role that a feature plays in a concept—either as a cause or as an effect—partly determines its centrality; and causal features are more important than effect features for categorization judgments: e.g., a potential category members’ possession of causal features is more diagnostic of category membership than possession of effect features. This hypothesis has received support in a variety of contexts and for several cognitive tasks .

We also found that BB supplementation preserves levels of hippocampal CaMKII phosphorylation after TBI, and changes in CaMKII correlated negatively with latency to locate the escape hole in the Barnes maze memory test. CaMKII, the main protein of the postsynaptic density and key BDNF signaling element, upon autophosphorylation increases synaptic efficacy and long-term synaptic memory.In fact, CaMKII dysregulation has been associated with several neuropsychiatric diseases.It is possible that the effects of BB on the BDNF levels results in autophosphorylation of tyrosine residues that rise intracellular calcium levels leading to CaMKII activation.Elevated levels of free radical formation are a common sequel of TBI pathology that can result in lipid peroxidation.In particular, lipid peroxidation has negative consequences for the function of the plasma membrane. It has been reported that optimal maintenance of membrane function is essential to support neuronal signaling that underlie synaptic plasticity, and that membrane function loss following TBI may be associated with cognitive deficits.Phospholipids are components of the plasma membrane that are particularly important for regulating cellular signaling and neuronal excitability.The fatty acids residues in phospholipids are sensitive targets to oxidative free radical attack to induce lipid peroxidation. Lipid peroxidation products can impair the barrier function, ion-channel activity,black plastic plant pots bulk and neurotransmitter release associated synaptic activity.Higher 4-HNE formation causes ionic disruption and membrane disturbance which contributes to additional reactive oxygen species production.

We presently found that TBI caused a marked increase in 4-HNE levels indicative of decreased neuronal excitability. Elevated levels of 4-HNE can form adducts with proteins, promotes oxidative stress,and contributes to membrane damage following TBI.BB is considered to have strong antioxidant capacity, important in its ability to attenuate oxidative stress.The fact that BB reduced the levels of 4-HNE supports the notion that BB attenuated TBI-related oxidative damage with positive consequences for neuronal excitability and plasma membrane function. Further, our reported positive correlation of spatial memory performance with 4-HNE levels suggest that a reduction of 4-HNE is important for behavioral outcome, in agreement with behavioral impact of 4-HNE on spatial memory performance.Interestingly, BB powder supplementation showed a positive effect on various aspects of brain function and plasticity in spite of the fact that the powder contains several components with recognized unhealthy effects. For example, the BB powder has high contents of sugars, particularly fructose, which upon consumption reduced levels of the same plasticity markers being decreased by BB supplementation in our study.It is important to note that in the present study, we matched the two diets for sugars and vitamin C. Therefore, it is likely that the flavonoid components are largely responsible for the observed positive effects of the BB powder possessing antioxidant property.These results seem to indicate that the combination of fructose with flavonoids in natural foods has an overall healthy action, which further suggests the importance of consuming natural foods. Also, the protective effects of BB against TBI pathology may be attributed to the presence of other bio-active compounds present in the powder such as β-carotenes and anthocyanins.

Anthocyanins, the important class of flavonoids has reported to be effective in promoting cognitive performance in animals through changes in synaptic plasticity via protein kinase signaling components such as c-Jun N-terminal kinase /Akt and phosphatidylinositol-3 kinase /Akt.Similarly, human intervention studies with anthocyanins have shown to promote a range of cognitive domains that include attention, visuospatial memory and executive function.Additionally, previous reports with anthocyanins have also reported hippocampal localization of glycosylated derivatives.In turn, β-carotenes and vitamins have strong potential to promote neuronal plasticity as reviewed by ref.70 and to delay cognitive decline.In the natural environment, the sense of smell, or olfaction, serves to detect toxins and judge nutritional content by taking advantage of the associations between compounds as they are created in biochemical reactions. This suggests that the nervous system can classify odors based on statistics of their co-occurrence within natural mixtures rather than from the chemical structures of the ligands themselves. We show that this statistical perspective makes it possible to map odors to points in a hyperbolic space. For example, these coordinates approximate the distance between species computed along dendrograms and, more generally, between points within hierarchical tree–like networks. We find that both natural odors and human perceptual descriptions of smells can be described using a three-dimensional hyperbolic space. This match in geometries can avoid distortions that would otherwise arise when mapping odors to perception. The reason that the sense of smell can be used to avoid poisons or estimate a food’s nutrition content is because biochemical reactions create many by-products. Thus, the emission of certain sets of volatile compounds will accompany the production of a specific poison by a plant or bacteria.

An animal can therefore judge the presence of poisons in the food by how the food smells. Other specific examples include the use of smell by bees when judging whether a flower has more pollen or nectar. Fruit flies select places to lay eggs based on odors. These examples suggest that, from a practical perspective, it would be useful for the nervous system to classify odors based on statistics of their co-occurrence. For example, if odor components that are strongly correlated are represented nearby within the nervous system, then detection of one component could be quickly used as an indicator for the likely existence of another component that is strongly correlated with it. With this perspective in mind, we set out to study the structure of the olfactory space based on odor co-occurrence. Before we describe the results, we review the reasons for why one might expect to find hyperbolic coordinates to be relevant for olfaction and biological systems in general. Biological data are often represented using dendrograms or hierarchical tree structures . These data can be equivalently represented using Venn diagrams, where larger circles correspond to broader classifications. For example, before Darwin, these Venn diagrams were used to classify species based on their properties . Darwin used the mapping from Venn diagrams to trees to infer the likely tree for speciation based on available descriptions of species properties . There is a deep mathematical reason underlying the equivalence between these two representations, and it involves hyperbolic spaces. Specifically, starting with the Venn diagram , one can assign points to a three- dimensional space whose horizontal x and y coordinates equal to center coordinates of the Venn circles, whereas the vertical coordinate equals to the circle radius. In this manner, larger circles get assigned to higher heights, which would then correspond to positions closer to the tip of the tree . Sometimes, the presence of partially overlapping circles leads to a structure that is not precisely a tree because it contains loop. Nevertheless, the resulting 3D space has a hyperbolic metric and can be described by the Poincare half-space model for the hyperbolic space. The fact that the metric is non-Euclidean can be ob- served from the fact that the shortest distance between two points goes up in the z-direction before descending back to the tar- get node. In Fig. 1D, we show an example shortest path between two points in a 2D half-space model and its discrete approximation. To foreshadow the results on olfactory odor classification, we note that 3D hyperbolic space is the lowest dimensional space where the descriptor sets are not 1D, as in Fig. 1D, but are 2D circles as in Fig. 1 . At least two axes have been described for the human odorant perception.Together,procona system these mathematical and biological observations point to the relevance of 3D hyperbolic geometry for odor perception.To analyze which space best describes the statistics of co-occurrence within natural odor mixtures, we used a recently developed a statistical method that can identify the presence of a geometric structure in data based on observed correlations between data components. This method is unaffected by linear or nonlinear monotonic transformations of inputs and therefore can be used to determine the overall geometry of the data without worrying at first about the precise scaling of the axes. The analysis starts by taking a set of measurements of concentrations of individual monomolecular odors, as they occur in the natural environment.

Our analyses will be based on four data sets of odors measured from samples of strawberries, tomatoes, blueberries, and mouse urine. To give an overview of the data, 69 monomolecular odors were measured across 50 different mouse urine samples, 66 monomolecular odors across 79 tomato samples, 45 monomolecular odors across 101 blueberry samples, and 78 monomolecular odors across 54 samples of strawberries. For high thresholds, the number of cycles will be low because most units are not connected. Similarly, at low thresholds, the number of cycles is also low because units form fully connected networks. Plotting the number of cycles as a function of density of edges, or equivalently the number of connected nodes, yields the so-called Betti curves. It turns out that the shapes of these Betti curves are quite sensitive to the statistics of correlations. This sensitivity makes it possible to infer the geometry of the space that can produce these correlations if we sample points from this space and assume that stronger correlations imply closer distances. Applying this statistical approach to each of the four data sets separately, we found the data in each case to be consistent with being drawn from a neighborhood of a sphere positioned within a 3D hyperbolic space together with a small amount of multiplicative noise added to the distances . The fact that hyperbolic space approximates hierarchical tree–like networks motivated this choice of the model, with odors reflecting leaves of the network—the neighborhood of the surface . Quantitatively, one can compare Betti curves derived from a model geometrical space and from a data set by computing the integral of the curve, the quantity referred to as the integrated Betti value. To find the best-fitting geometry, we optimized parameters of the model such that the noise magnitude and the range of radii within the space from which the sample points were drawn provided the best match to the first integrated Betti value. Then, we examined how these optimized parameters could account for the second and third integrated Betti values. For all four data sets, we found the measurements to be consistent with sampling from a 3D hyperbolic space . The first three Betti curves were also sufficient to show that Euclidean spaces could not account for the data, even when dimensionality and other parameters were optimized . As a control, we verified that shuffling odor concentrations between samples, which destroys correlations between odors, produced Betti curves that canbe fully ex- plained by random matrices . These matrices would not be consistent with the hyperbolic space plus the small amount noise that fits the real data . As additional controls, we verified that evaluating differences between Betti curves using L1 distances instead of the integrated Betti values or applying logarithm to concentration values before computing their correlations led to the same conclusions . In particular, hyperbolic 3D is consistent with measurements for all three Betti curves, whereas the best-fitting Euclidean model can be ruled out according to these measures. The corresponding P values are provided in tables S1 to S4. Note that hyperbolic spaces of dimensions higher than three cannot be ruled out . However, the 3D hyperbolic space remains the best-fitting model across the four data sets. This is true whether one uses either the integrated Betti value or the L1 distances between model and experimental Betti curves . To visualize how the points consistent with odorant correlation statistics might be distributed within the hyperbolic space, we used non- metric multidimensional scaling. The non-metric MDS algorithm embeds a set of points into the N-dimensional space while attempting to preserve the rank ordering of distances as best as possible . Traditionally, MDS is applied to the Euclidean space, but we modified it to work with hyperbolic distances. After testing the algorithm on synthetic data , we applied the modified algorithm to the four data sets. In Fig. 3, we show results for the four data sets. Because the points are located near a surface of a sphere , we present the points on a sphere using the two angles of latitude and longitude. The results show approximately uniform sampling in all four data sets. Notably, the points do not cluster based on functional chemical properties of the individual components . One can understand the absence of clustering from the fact that monomolecular odors with different functional properties are produced together in biochemical pathways.

Consumption of the HFD caused an increased lipid deposition in the liver that was not observed in HFA40 mouse liver. The NAFLD activity score was significantly higher in the liver from HF compared to C, CA, and HFA40 mice . Several proteins involved in the inflammatory response were measured in liver by Western blot . The chemokine MCP-1, the cytokine TNFα, the macrophage marker F4/80, and the enzyme NOS2 were all upregulated in the liver of HF mice. No significant differences were observed between C and CA in markers of steatosis and liver inflammation.Chronic consumption of a HFD by mice led to the development of obesity, adiposity, dyslipidemia, steatosis, liver inflammation and insulin resistance. Simultaneous consumption of a diet rich in AC, i.e. cyanidins and delphinidins, attenuated all these adverse effects. In addition, the AC-associated improvement of inflammation, oxidative stress, and insulin sensitivity was in part associated with their capacity to modulate NF-κB and JNK. Diets rich in fat and carbohydrates are in part responsible for the increasing global burden of overweight and obesity. The dietary consumption of a HFD by mice mimics the consequences of Western style diets in humans. The amount of ACs provided are comparable in quality and amount to that achievable through food consumption and/or rational amounts of dietary supplements in humans. We observed that mice eating the HFD and AC gained less weight than those fed the HFD alone, despite consuming similar amounts of calories.

In line with these results, AC at the highest amount provided, i.e. 40 mg/kg body weight,plastic growers pots led to lower weight of brown, visceral, and retroperitoneal fat pads, but not epididymal or subcutaneous fat, compared to the non-supplementedHFD-fed mice. AC-mediated decrease in visceral fat is particularly relevant given the role of this fat pad in the development of systemic adverse effects through the release of adipokines, growth factors and inflammatory molecules. Thus, visceral fat accumulation is associated with the development of metabolic syndrome and associated diseases, e.g., NAFL and cardiovascular disease. AC supplementation also attenuated the hyperlipidemia and steatosis associated with HFD consumption. These results disagree with previous reports that pure AC but not AC in berry extracts have the capacity to improve dyslipidem. These differences may be related to differences in experimental design, but stress the relevance of the overall food matrix in AC absorption and metabolism, and subsequently on their biological actions. Part of the mentioned effects on obesity and steatosis could be due to the actions of AC at the gastrointestinal tract. In this regard, factors that can contribute to the capacity of AC to mitigate body weight gain and excess tissue lipid deposition may include the modulation of GLP-1, a hormone known to reduce adiposity, and/or a decreased fat absorption associated to the inhibition of pancreatic lipase, which is essential for dietary triglyceride absorption in the intestine. With regard to the latter, both cyanidin and cyanidin-3,5- diglucoside were shown to inhibit the enzyme in vitr. Pancreatic lipase inhibition would also be consistent with the current finding of high fecal triglyceride levels in the AC-supplemented and HFD-fed mice. The increasing incidence of T2D worldwide has paralleled that of overweight and obesity. As previously reported. HFD consumption by C57BL/6J mice led to insulin resistance as evidenced by high fasted plasma glucose and insulin levels, and impaired ITT and GTT tests. At the highest concentration tested, the AC blend improved all these parameters.

Accordingly, an AC-rich blueberry extract was found to improve parameters of insulin sensitivity in HFD-fed mice, although under the tested conditions the ITT and GTT were not affected by fat consumption. The above beneficial effects could be in part related to the capacity of AC to modulate hormones that regulate different aspects of glucose homeostasis. Adipokines and incretins contribute to the regulation of satiety and/or glucose homeostasis. While plasma adiponectin levels were not affected, plasma leptin was increased because of HFD consumption, as it is observed in diet-induced obesity, The attenuation of hyperleptinemia by AC supplementation in HFD-fed mice may in part reflect a decreased fat pad mass and an improved capacity to modulate food intake and energy balance. In terms of the incretins, GIP and GLP- 1 increase insulin secretion after food consumption influencing glucose control. Furthermore, GLP-1 promotes satiety and improves basal and postprandial lipidemia. The prevention by AC of HFD-mediated GIP increase may reflect AC-mediated improved capacity to regulate glucose homeostasis. While AC supplementation did not affect HFD-mediated increase in plasma GLP-1, it increased GLP-1 plasma levels in mice fed the control diet. Consistently with the latter, delphinidin was found to increase GLP-1 secretion in GLUTag cells. The capacity of cyanidin and/or delphinidin to increase plasma GLP-1 may be an important mechanism underlying, in part, their anti-obesity and anti-T2D actions. In fact, GLP-1 is a relevant therapeutic target for the control of T2D. The liver is one of the central organs in the maintenance of glucose and lipid homeostasis. HFD consumption disrupted this homeostasis, and in parallel caused liver fat deposition and inflammation. The coordinated AC-mediated improvement of HFD-induced liver steatosis, inflammation, and systemic insulin resistance can be explained through the interplay among these adverse conditions. In terms of biochemical mechanisms, inflammation, oxidative stress and the activation of NF-κB are events that establish a self-feeding cycle that can be initiated by excess nutrient consumption.

The capacity of AC to mitigate HFD-triggered hepatic inflammation and NF-κB/JNK activation can be in part due to AC capacity to modulate liver oxidative stress. AC cannot exert direct antioxidant actions except at the gastrointestinal tract where they can reach high enough concentrations that allow to scavenge oxidants at a significant extent. On the other hand, in the liver and other organs, the regulation of oxidative stress is mainly due to indirect antioxidant actions exerted by AC, mainly their metabolites, through the modulation of the production of superoxide anion and nitric oxide. In fact, we observed that AC supplementation prevented HFD-mediated upregulation of NOX3 and NOX4, and of the pro-in- flammatory inducible nitric oxide synthase, NOS2. AC supplementation also prevented the high levels of 4-HNE-protein adducts in HFD-mouse liver. Consistently, nutrient overload can cause increased formation of 4-HNE which irreversibly form adducts with macromolecules , which can modify cell function, and contribute to T2D and NAFLD development. Inactivation of the redox sensitive transcription NF-κB can be central to AC beneficial actions. We observed that AC supplementation inhibited in the liver HFD-induced NF-κB activation, as evidenced by both decreased IKK phosphorylation, and NF-κB-DNA binding. Accordingly, we previously observed that cyanidin and delphinidin 3- O-glucosides inhibited TNFα-induced NF-κB activation and downstream loss of monolayer integrity in Caco-2 intestinal cells. Cyanidin inhibited the inflammatory response and redox imbalance triggered by TNFα in Caco-2 cells, which was attributed in part to NF-κB inhibition and Nrf2 upregulation. NF- κB and JNK pathways are key players in the development of insulin resistance. Activation of the NF-κB upstream kinase IKK and of JNK leads to the phosphorylation in serine residues of the insulin receptor substrate-1 causing a downregulation of the insulin cascade. In addition, NF-κB activation also induces the transcription of PTP1B, a tyrosine phosphatase which dephosphorylates and inactivates the insulin receptor and IRS1. Thus, disruption of the high fatdiet induced cycle of inflammation, oxidative stress and NF-κB/JNK activation can be central in the capacity of AC to mitigate HFD-induced insulin resistance. Furthermore, it can be argued that the effects of AC on insulin resistance are in part derived from an upstream regulation of oxidant levels and/or inflammation. In summary, blueberry in pot supplementation with a cyanidin and delphinidin-rich blend, mitigated the adverse consequences of HFD consumption, i.e. obesity, dyslipidemia, steatosis, and insulin resistance. Inhibition of inflammation, oxidative stress and NF-κB/JNK activation emerge as mechanisms underlying those AC-mediated benefits. In addition, AC could also act in part by inhibiting pancreatic lipase and subsequently dietary lipid absorption, and by modulating incretins involved in glucose and lipid homeostasis. Increased AC cyanidin/delphinidin consumption either through diet or by supplementation could be a plausible strategy to control the adverse effects of Western style diets.While the health benefits of fruits and vegetables are widely acknowledged, consumption of these foods among children and youth is at a low level. Fewer than 11% of school-aged children eat fruits and vegetables at the recommended levels ; as many as one-third of high school students eat vegetables less than once a day, and 28% eat fruit less than once a day .

Further, data collected by the Centers for Disease Control and Prevention’s National Health and Nutrition Examination Survey shows that the fruits and vegetables adolescents consume tend to be the less nutritious forms: Fruit juices and fried potatoes are major contributors . Children’s low consumption of fruits and vegetables has been documented in numerous studies. It is clearly addressed in the 2010 USDA Dietary Guidelines , which note that intakes of fried potatoes and fruit beverages have seen recent growth, while intakes of fresh fruits and vegetables have not.The United States is confronting an epidemic of poor nutrition among children. Schools can play an important role in addressing this epidemic, both by serving food directly to students and by using the power of role modeling to demonstrate healthy diets to students and their families. Despite educational efforts, at the population level fruit and vegetable intakes have changed very little, prompting some to suggest that alternative individual-, community- and population-level interventions are necessary . One promising approach is to provide more servings of fruits and vegetables in schools and youth-serving programs . Findings suggest that if children are provided with healthful, appealing foods, they will eat them. A European review of the literature found that availability and accessibility of fruits and vegetables and taste preferences were the determinants most consistently and positively related to consumption . Furthermore, a combination of increased access to fruits and vegetables at school with nutrition education in the curriculum has a considerably greater impact than nutrition education alone, although both are important . The USDA Fresh Fruit and Vegetable Program, which provides an extra serving of a fruit or vegetable as a between-meal snack to children at schools in low-income communities that apply for the program, is being evaluated and shows promise for increasing children’s consumption . The greatest room for improvement in children’s fruit and vegetable consumption is at school, where children consume up to half of their calories . The National Academy of Sciences Institute of Medicine has urged school action to increase fruit and vegetable intake , and federal policies resulting from the Healthy, Hunger-Free Kids Act of 2010 mandate this increase.The California Fresh Start Program was a pilot school breakfast program that informed state and federal policymakers about the opportunities, challenges and benefits of programs to increase produce consumption in schools. Lessons from the program are especially important now for two reasons: School districts will be increasing offerings of fruits and vegetables in the School Breakfast Program in July 2014 to meet the new school nutrition guidelines in the Healthy, Hunger-Free Kids Act; and childhood obesity has escalated, with the consequent risk of serious chronic conditions including type 2 diabetes and heart disease. Here, we highlight the results of the California Fresh Start Program, which was conducted during the 2006-2007 school year, and recommend promising strategies for increasing produce consumption by children in the school setting. The barriers we identify to program implementation can provide guidance to policymakers and administrators in school districts nationwide. Responding to the critical state of children’s nutritional health, California enacted Senate Bill 281, commonly known as the California Fresh Start Program , which was signed into law in 2005. It was the first statewide legislation to specifically address fresh and local produce in schools. The innovative pilot program offered a 10-cent per meal reimbursement to schools to increase the servings of fruits and vegetables they offered in the School Breakfast Program. Priority was given to serving fresh fruits and vegetables and, where possible, California-grown produce. The program goals were to promote the consumption of fresh fruits and vegetables, increase school breakfast participation and ultimately improve children’s lifelong eating habits and decrease the incidence of obesity. Supplementing fruits and vegetables in the breakfast program, which serves more than a million California students each day, was an important first step in reaching school-age children, nearly all of whom are at nutritional risk due to low produce consumption. Of California public school students who eat breakfast at school, 78% were reached by the California Fresh Start Program during the 2006-2007 school year.

Nocturnal transpiration due to incomplete closure of stomata or high vapour pressure deficits can create and maintain high water potential gradients between the soil and leaves and thus limit water movement to other parts of the root system. In addition,rehydration of roots in dry soil layers may be slower where there are significant constraints to water movement, including embolisms, small-diameter and curved xylem vessels with extensive branching , high frequency of pits and endplate membranes , and the presence of heartwood, latewood, and rays . Lateral water movement may also be limited by the high resistances that form at the stem base–root junction . Vaccinium corymbosum has been reported to be a species that does not effectively distribute water laterally . Using a split-root water application, Abbott and Gough found that dyes did not move laterally from one stem to another and observed root mortality in the unwatered root container. The main objective of this study was to quantify patterns of nocturnal internal hydraulic redistribution and conductances among the first seven orders of V. corymbosum roots under severe drought conditions and its implications for root tissue rehydration. Vaccinium corymbosum was selected due to its unique root anatomy and morphology and its reported limited ability to redistribute water. It was hypothesized that root tissue rehydration at night would be delayed,collection pot especially in the distal root orders because of their greater hydraulic constraints .The V. corymbosum root system is characterized as being very efficient in terms of biomass allocation for the production of a large amount of root surface area.

Its highly branched root system is composed of very fine roots that usually proliferate in the top 20–30 cm of the soil . Water and nutrient uptake presumably occurs mostly in the first three root orders, which correspond to the mycorrhizal and non-woody, ephemeral section of the root system . These non-woody roots have very few and small-diameter vessels. Such root anatomical characteristics may lead to a high cavitation vulnerability of the distal roots during severe drought, especially when water is available to only a fraction of the root system such as might occur with drip irrigation or when there are only a few deeper roots. Plants may cope with drought under conditions of heterogeneous soil moisture conditions by internally redistributing water from roots in moist soil to those in dry soil during the night, such as in grape , but to a much more limited extent in blueberry. In the present work, patterns of root water potentials measured throughout the night revealed how water redistributes internally within the root system of Vaccinium. Vaccinium rehydrated the distal first five root orders in dry soil from 60% to 70% in a period of 11 h when well irrigated in another portion of the root system. No other work has previously quantified the rate or magnitude of change of tissue rehydration over the night as water moved through different branch orders in the root system. Root rehydration at night was influenced by several factors, including root hydraulic constraints, duration of the nocturnal period, water availability in the wet-side, and water potential gradients among roots. The overall final rehydration achieved by the distal root orders in dry soil served as an indicator of how efficiently or inefficiently water was hydraulically redistributed through the root system.

As suspected, the distal, finest root orders experienced the lowest water potentials at the onset of the nocturnal period, followed by medium and coarse roots. Although water was readily available to roots in the wet soil and transpiration was minimal, it took the whole night-time period of 12 h for the distal finest roots under dry soil conditions to reach the same water potentials as fine roots in wet soil. Even though roots in dry soil equilibrated with roots in wet soil, the equilibrium point reached before sunrise was still approximately –1.2 MPa, indicating that the tissues were not fully rehydrated, i.e. not fully in equilibrium with the soil water potential in the wettest portion of the rooted soil. Even with an additional hour and a half of no transpiration, water potentials for all root orders were predicted to range between –0.6 MPa to –0.7 MPa . Therefore, even with the additional time, roots in dry soil would not be predicted to reach values greater than –0.5 MPa, suggesting that the duration of the nocturnal period was not sufficient for roots in dry soil to be fully rehydrated. The main factors influencing water transport were the hydraulic properties of the conductive system. In very fine roots, internal water movement was probably delayed by either very high hydraulic resistances due to small diameter vessels in these roots or by additional resistances caused by the occurrence of xylem embolisms associated with severe water stress conditions . With the single-branch model, it was possible to estimate the water potential of each of the seven root orders over the night and to identify those orders with the highest hydraulic resistance. As expected, the magnitude of hydraulic resistance per individual root was highest in 1st-order roots due to these roots having the fewest number of vessels and the smallest vessel diameters.

However, it was found that in a root branch composed of seven root orders, 3rd-, 4th-, and 5th-orders , exhibited the highest overall hydraulic resistances within the root branch . Thus, when many resistances are arranged in parallel , the total resistance added to the system was not highest in the 1st- and 2nd-order roots but in the medium root orders, which had fewer individuals within the root branch . In the case of root orders greater than five, although the number of these roots was small, numerous and wider vessels helped to compensate for the limited length and number of roots . Therefore, the high hydraulic resistances exhibited by 3rd-, 4th-, and 5th-order roots may contribute considerably to delayed rehydration of the finest root orders. Interestingly, these roots represented the transition from the more permanent roots with secondary development to the more ephemeral roots without secondary development . The possibility of intermediate-order roots serving as hydraulic controllers has important implications for the function of the whole root system. The observed pattern of hydraulic resistances in Vaccinium roots is consistent with the segmentation concept proposed by Zimmermann for above-ground hydraulic architecture. Similar to the occurrence of embolism within stem junctions, which may cause the sacrifice of minor branches and leaves during severe water stress conditions, hydraulic failure in 5th- or 4th-order roots may lead to the sacrifice of the lower root orders under drought conditions, but the maintenance of higher order roots. In summary, it has been found that under severe water stress conditions the root system of V. corymbosum did not fully redistribute water from roots in wet soil to roots in dry soil. This was mainly attributed to anatomical constraints on water movement and because of the severe degree of water stress of roots in dry soil. Root orders with the highest hydraulic resistances corresponded to the lowest orders of the permanent root system , indicating the possible location of a hydraulic safety control in the root system of this species.Human-altered landscapes are expanding globally and are often associated with declining natural habitat, non-native species, fragmentation, and transformations in structure, inputs, climate, and connectivity. These changes collectively have resulted in shifts in both spatial distributions and species diversity across many taxa including birds, mammals, reptiles, amphibians, invertebrates, and plants. One common driver of global change is urbanization, which in the extreme is associated with a reduction in biodiversity compared to habitats in their more natural state. However,10 plastic plant pots in moderately urbanized areas, the effects of urban impacts on species distribution and diversity can vary greatly and depends on region, type of change, and taxonomic group, among other factors.

Documenting the effects of urbanization compared to natural communities has proven problematic, making predictions of community change associated with urbanization difficult. Human-altered landscapes are often associated with many non-native species which add to species diversity but also can obscure changes in community dynamics. Thus, to assess accurately the complex impacts of land use change on ecological communities, one must look beyond species richness to investigate ecological processes themselves. Ecological processes are the links between organisms in a functioning ecosystem, and are critical in understanding how altered biodiversity can lead to changes in ecosystem functioning. Global environmental change has been found to have a wide variety of impacts on ecological processes in different systems. Pollinator-plant relationships in particular are found to be particularly vulnerable to land use change, resulting in decreases in interaction strength and frequency. Pollination services are crucial ecosystem processes in natural systems, but also in agricultural and urban areas. Bees provide the majority of animal-mediated pollination services on which it is estimated 87.5% of flowering plants depend. The value of pollination in agriculture is estimated at $200 billion worldwide, largely due to many foods that are essential for food security and a healthy human diet, including numerous fruits, vegetables, and nuts that require bee pollination. As urban areas expand, there has been increasing interest in urban agriculture to ensure food security and access to healthy foods for growing populations, and these systems also depend on pollination. For example, Kollin estimated that the economic value of urban fruit trees to be worth $10 million annually in San Jose, California. Despite the important role of pollinators and concerns about bee declines, there remain many uncertainties regarding the impact of land use change on pollinators. Urbanization has resulted in more interfaces with both natural and agricultural landscapes, creating new transitional zones of peri-urbanization. While there has been extensive pollinator research in agricultural and natural systems, less attention has focused on pollination in neighboring urban areas and how the changing landscape has impacted pollination. In addition, very few studies of urban areas have looked beyond changes in bee diversity to understand explicitly the effect of urbanization on pollinator-plant interactions. Here, we investigate the effect of land use change on pollinatorplant ecosystem processes. We make use of a ‘‘natural experimental design’’ in which urban, agricultural, and natural areas intersect. Bees visit flowers for both pollen and nectar resources, and floral visitation is a commonly used as an index of pollination services. However, depending on the flower, certain bee groups are much more effective pollinators than others. Thus, while visitation is important, it alone does not definitively indicate whether pollination services were received by the plant. When pollen is limited by other factors, consequences for plant fitness can include failure to set seed, production of smaller fruits, and even complete lack of reproduction. By looking at rates of bee visitation and comparing this with other measures of plant fitness, such as seed set, we can develop a more complete understanding of how shifts in bee distributions between areas that differ in land use are impacting pollination services. To study the impact of changing land use on pollinator-plant interactions, we focus on bee pollination of a widespread plant, yellow starthistle , a common weed found in natural, agricultural, and urban habitats. Using standardized observations of floral visitation and seed set measurements of yellow starthistle, we test the hypotheses that increasing urbanization decreases 1) rates of bee visitation, 2) viable seed set, and 3) the efficiency of pollination . In addition to contributing to a better understanding of how change in landscape use, particularly urbanization, affects pollination-plant interactions, the study illustrates the importance of use of neighboring lands for pollination services.Yellow starthistle has composite flowers, which are aggregations of anywhere from 20–80 florets. At each site, 12 yellow star thistle buds were randomly selected from different plants and covered with a mesh bag. Yellow starthistle blooming cycles have been described in detail in other publications. We selected buds at stage BU-4, when buds had no yellow petals exposed, but had well-developed straw-colored spines. When in full flowering, 10 bags were opened for a 4 hour period from 10 am to 2 pm, while 2 were kept closed as controls to verify that self-pollination was not occurring. At the opening and re-closing of the bags, the number of florets that had their stigmas extended were counted. Later, when flowers were fully mature , seed heads were collected, and later dissected in the lab.

Other authors have explored whether ethanol refineries have an effect on land use. Fatal and Thurman use county-level data to estimate the corn acreage effect of ethanol re- fineries. They find that a typical ethanol refinery increases corn acreage in its home county by over 500 acres and has effects that can persist for up to 300 miles. Miao also uses county-level data and finds a significant effect of ethanol refineries on corn acreage, as well as a differential effect between locally-owned and non-locally-owned refineries. Turnquist et al. , in contrast to more recent studies, fail to find any significant agricultural land conversion in areas near Wisconsin ethanol refineries. Finally, Feng and Babcock explore the full general equilibrium effect of increased ethanol production and find an unambiguous increase in corn acreage. Several researchers have focused on how ethanol production affects water quality and nitrate runoff. Donner and Kucharik highlight how the aggregate impact of the EISA will likely make achieving nitrate level goals in the Mississippi impossible. Thomas et al. use hydrologic models to estimate the water quality impacts of corn production caused by increased demand due to bio-fuel mandates. They find significant negative results. While it is likely true that “refineries cause corn,” it is also likely true that “corn causes refineries.” Ethanol refineries are not located at random,blueberries in pots and several researchers have explored the topic of ethanol refinery placement.

A series of papers have shown, unsurprisingly, that ethanol refineries are more likely to locate near areas with large corn production, near transportation infrastructure, and not near existing ethanol refineries . This finding is important because it highlights that ethanol refinery placement cannot be treated as truly random in econometric analyses without accounting for the underlying drivers of this placement. In my analysis, I argue that field-level fixed effects appropriately account for the major determinants of refinery placement. In particular, I study how distance-to-nearest-refinery affects the probability of a field being planted to corn. Whenever a new refinery is built, its presence differentially affects fields close to it relative to fields slightly farther away. However, due to the spatial characteristics of soil quality and topology, “more-treated” and “less-treated” fields are qualitatively comparable. My project improves upon previous work by leveraging new sources of field-level land use data and exploiting a finer-scaled panel of observations than previous authors. I exploit both the Cropland Data Layer and Common Land Unit to create annual observations of field-level land use. These agricultural micro-data allow for much more nuanced econometric estimation than in previous studies. Other authors have exploited similar micro-data in agricultural research to great effect . I also highlight the locality effect of ethanol refineries rather than the general equilibrium effect, focusing on small-scale heterogeneous effects that have not been well identified in previous work. The remainder of this paper is divided into a theoretical framework , a summary of my data, an overview of my econometric methods, a discussion of my results, and a conclusion. According to the Farm Service Agency of the USDA, a Common Land Unit is “an individual contiguous farming parcel, which is the smallest unit of land that has a permanent, contiguous boundary, common land cover and land management, a common owner, and/or a common producer association” .

Practically, a CLU represents a single agricultural field. Polygon shapefiles of CLUs are maintained by the FSA, but are not currently publicly available. I obtain CLU data for Illinois, Indiana, Iowa, and Nebraska from the website Geo Community . These data contain shapefiles from the mid 2000s, before CLU data were removed from the public domain. In this research, I implicitly assume that individual CLUs do not change over time: a reasonable assumption given the FSA definition. In reality, the FSA does adjust individual CLU definitions on a case-by-case basis if necessary, but I assume these adjustments to be negligible as in previous similar studies . Using the geospatial software ArcGIS, I overlay the CDL raster data with CLU polygons as shown in Figure 3.4. Upon visual inspection, the fit is quite good: CLU boundaries line up with crop changes in the CDL, roads appear clearly in both datasets, and geographical features such as waterways and elevation changes are visible. One concern is that many CLUs are quite small and appear to outline geographical features such as gullies, rather than larger constituent fields. This is particularly pronounced in areas near urban sprawl. Therefore, to maintain confidence that the fields I study are actually “fields” in the way we think of them, I drop all CLUs from my dataset with areas of less than 10 acres. I also drop CLUs with areas of greater than 10,000 acres, based on an assumption that these CLUs are incorrect.4 To assign each CLU a single crop cover, I calculate the modal value of the raster pixels contained within each CLU polygon. I then assign that modal value to the entire CLU. This procedure enforces the assumption that each field is planted to a single crop – an assumption strongly supported by a visual examination of the data. To my knowledge, this is the first instance of using modal statistics to interact the CDL and CLU datasets.

Previous research has used an off-center centroid to sample a single point of the underlying raster data. My procedure is preferable in that it reduces the chance of idiosyncratic mis-measurement of the field’s true land cover.In this paper, I have demonstrated that ethanol refineries exert a statistically significant effect on the land use of surrounding fields. Increases in corn acreage and nitrogen application occur within 30 miles of ethanol refineries, suggesting a highly localized effect. These findings are consistent with a model of ethanol refineries lowering corn basis for nearby farmers. Within a sample of almost 114 million acres, I find nearly 300,000 acres of the corn grown in 2014 can be attributed to ethanol placement effects accumulated over the years between 2002 and 2014. This project makes several important contributions to the existing literature and improves upon previous research. Most importantly, I leverage field-level observations of land use to create a thirteen year panel of over two million observations. This allows me to estimate a highly nonlinear relationship between distance to a field’s nearest ethanol refinery and that field’s probability of growing corn. My panel also allows me to include field-level fixed effects that control for time-invariant characteristics of each field such as soil type. In three econometric specifications that condition on the previous year’s land use, I find interesting patterns. Ethanol refineries seem to strongly incentivize nearby fields to grow corn-after-corn, while the effect appears opposite for corn-after-soy. The result for cornafter-soy is puzzling and is not predicted by my model. Future work may attempt to better understand this result. Nonetheless, the net effect of these two individual effects is that farmers appear to be growing more corn near ethanol refineries in the way the most stresses crop rotations and most exacerbates the use of nitrate-producing fertilizer. There is considerable room for further work on these questions. First, this analysis treats all refineries as identical. In reality, different refineries have different production capacities and ownership structures, and may have heterogeneous effects on surrounding land. Second, there is room to explore a wider range of econometric specifications beyond the linear probability model estimated in this paper. Finally, future work should explore data from the US Geological Survey to test whether water nitrate levels directly reflect the effect derived in the current project. While the findings of this paper appear relatively small in the context of the entire US Corn Belt, they are strongly statistically significant and demonstrate a real and important localized effect of ethanol refinery placement. My results are useful for anyone interested in a fuller understanding of the spatial forces driving land use change and nitrogen application in agriculture. Managing urban runoff and its associated pollutants is one of the most challenging environmental issues facing urban landscape management. The conversion of naturally pervious land surfaces to buildings, roads, parking lots,growing berries in containers and other impervious surfaces results in a rapid surface runoff response for both time of concentration and peak flow. Impervious land surfaces adversely impact the quantity and quality of surface runoff because of their effects on surface water retention, infiltration, and contaminant fate and transport. Large volumes of storm runoff from urbanized areas cause flooding, sewer system overflows, water pollution, groundwater recharge deficits, habitat destruction, beach closures, toxicity to aquatic organisms, and groundwater contamination.

Traditional urban runoff management focuses on removing the surface runoff from urban areas as soon as possible to protect public safety. However, as excess surface water is quickly drained from urban areas, it is no longer available for recharging groundwater, irrigating urban landscapes, sustaining wildlife habitat and other uses. Green infrastructure uses natural or engineered systems that mimic natural processes to control storm water runoff . For example, traditional detention ponds have been widely used to treat storm runoff and permeable paving promotes infiltration of rain where it falls. Importantly, decentralized green infrastructure strategies control runoff and contaminants at their source . Vegetation is a green infrastructure strategy that can play an important role in surface runoff management. Large-scale tree planting programs have been established in many cities to mitigate the urban heatis land effect, improve urban air quality, and reduce and treat urban runoff . There are municipal storm water credit programs in a growing number of cities that promote retaining existing tree canopy, as well as planting new trees. Although these programs encourage planning and management of urban forests to reduce runoff impacts, fertilizer is required to promote plant growth, and these added nutrients may contribute to contamination of surface runoff. Thus, reducing nutrients in storm runoff is a challenging task for landscape and water managers. Bioswales are shallow drainage courses that are filled with vegetation, compost, and/or riprap. As a part of the surface runoff flow path, they are designed to maximize the time water spends in the swale, which aids in the trapping and breakdown of certain pollutants. Bioswales have been widely recognized as an effective decentralized storm water BMP to control urban runoff. Their effects are threefold; vegetation intercepts rainfall reducing net precipitation; plant uptake of water via transpiration reduces soil moisture, thereby increasing subsurface water storage capacity, and root channels improve infiltration. Traditional bioswales are designed to remove silt and other pollutants from surface runoff waters. New bioswales are being developed for harvesting surface runoff and supporting urban tree growth . Bioswales that integrate engineered soil mixes and vegetation are being used to enhance treatment and storage of surface runoff . The composition of ESMs varies widely, from simple mixtures of stones and native soil to patented commercial products. Highly porous ESM mixes provide ample infiltration and pore space for temporary storage of surface runoff. Also, they support tree growth by providing more water and aeration to roots than compacted native soil alone. ESMs can reduce conflicts between surface roots and sidewalks by promoting deeper rooting systems. In California alone, over $70 million is spent annually to remediate damage by shallow tree roots to sidewalks, curbs and gutters, and street pavement. In Davis, California, a bioswale installed next to a parking lot reduced runoff from the parking lot by 88.8% and the total pollutant loading by 95.4% during the nearly two year monitoring period. Furthermore, a bioswale installed next to a turf grass patch at the University of California-Davis campus eliminated dry weather runoff from an irrigated urban landscape The ESM used in these studies offered several advantages over other ESMs because the main structural element was locally quarried and relatively inexpensive lava rock . This ESM had a high porosity, high infiltration rate, and a high water storage capacity . It effectively fostered the growth of biofilms that retain nutrients and degrade organic pollutants. Because vegetated bioswale research is in its infancy, very few studies have monitored vegetation growth and its impacts on bioswale performance. Moreover, evaluation of system performance is generally conducted before vegetation is fully established. In contrast, this study evaluated the effectiveness of two bioswales on surface runoff reduction, pollutant reduction, and tree growth eight years after construction.

This strategy is being employed by members of a European initiative, Meta Explore, who are screening fosmid clones from a variety of environmental samples to access enzymes of interest to industry, including chitinases and dehalogenases: . Another approach is to sequence subsets of the metagenome, such as collections of ribosomal RNA signature sequences. For example, based on 16S rRNA gene sequence data, we have developed a relatively good understanding of the species diversity and distribution of specific bacterial and archaeal phyla in different soils. Further, based on work from Noah Fierer, Rob Knight, and their colleagues at the University of Colorado, Boulder, we know that pH and salinity are major drivers of microbial biogeography. From these and other studies, we also know that soils contain high abundances of Acidobacteria, whose 26 subgroups vary in abundance from one soil type to another. Also, some phyla are more prevalent in a given soil type than in others. More generally, databases of 16S sequences are yielding insights into how chemical and physical parameters correlate with microbial distributions in soils. Here, I use the term metagenome to refer to sequencing of total community DNA, including both phylogenetic and functional genes, while taking a shotgun-sequencing approach. Although few shotgun soil metagenome studies are published, more are anticipated during the next year as investigators take advantage of recent advances in sequencing instruments, for example, using 454 pyrosequencing and Illumina technologies. These 2nd-generation sequencing approaches generate megabases to gigabases of sequence data, respectively,blueberry pot in single runs with relatively short read lengths of approximately 400 to 100 bp, respectively.

Other sequencing technologies recently developed, including the Pacific Biosciences platform for sequencing single molecules of DNA, holdpromise for generating longer sequencing read lengths.In a project involving my group at the Lawrence Berkeley National Laboratory, James Tiedje and his colleagues at Michigan State University, and the Joint Genome Institute , we are using a combination of second-generation platforms to sequence DNA from microbes in soil samples from the Great Prairie of the United States, including native prairie and adjacent cultivated soils from Wisconsin, Iowa, and Kansas . This project aims to determine the impact of land management on soil microbial communities and their functions, including cycling of carbon and nitrogen. One of the sites, Kansas native prairie, is also the focus of another project that is specifically addressing the impact of altered rainfall patterns due to climate change on carbon cycling processes in the Great Prairie . The Kansas prairie metagenome that was sequenced at JGI currently has the largest amount of sequence data of any soil metagenome to date, approaching 400 Gb of Illumina sequence, and will serve as a resource for this project. Also in collaboration with JGI, we sequenced DNA extracted from Alaskan permafrost soil samples collected by Mark Waldrop from the U.S. Geological Survey . The aim is to use metagenomics to gain an understanding of the impact of climate warming-induced thaw on the microbial degradation of carbon reserves that have been trapped in permafrost for thousands of years and that have potential to contribute large amounts of greenhouse gases to the atmosphere. Other ongoing soil metagenome sequencing projects include several that focus on field sites for which there is substantial temporal environmental and climate data. For example, the UK Rothamsted Field Station is one of the longest running field stations in the world and has served as the site for several metagenome sequencing projects.

One of these projects, “DeepSoil” , is sequencing DNA from a longterm grassland and an adjacent fallow site at Rothamsted. The overarching goal of this sequencing effort is to establish the long-term impact of plants on the soil microbiota. Another project at Rothamsted is a French metagenome sequencing project, Metasoil, coordinated by Tim Vogel and Pascal Simonet of the Ecole Centrale de Lyon, France. The Metasoil project is sequencing DNA from the Park Grass site at Rothamsted that was established in 1856. Their strategy relies on constructing and sequencing a fosmid library in addition to shotgun metagenome sequencing. Cheryl Kuske and coworkers at the Department of Energy Los Alamos National Laboratory, in collaboration with JGI, are sequencing soils from selected free air-carbon dioxide enrichment sites in the United States. These sites were established to determine the influence of increases in atmospheric CO2 levels due to climate change on terrestrial ecosystems. In addition, Folker Meyer and coworkers at the DOE Argonne National Laboratory are sequencing metagenomes from several different U.S. soils that were collected across a range of habitats to determine which microorganisms and functional processes predominate in different soil ecosystems. Together these soil metagenomics projects will be a tremendous resource to the scientific community and will provide a much greater understanding of microbial diversity and functions in soil.Although the sequencing of DNA is no longer a bottleneck, large amounts of sequence data generated from analyzing highly diverse soil communities are proving a challenge to accommodate. This issue is exacerbated by the need to cope with short reads—for example, 75–125 bp—that arise from analyses using the Illumina instrument. Thus, better algorithms, new bio-informatics tools, and “terabytes” of computer storage are required. Increased access to supercomputers, such as the National Energy Research Scientific Computing Center at the Lawrence Berkeley National Laboratory, can help.

For instance, we used NERSC to perform BLASTX of our permafrost metagenome data . This analysis took approximately 800,000 core hours, or the equivalent of more than 85 computer years, which lasted 2 weeks using the NERSC supercomputer and nodes at JGI. Cloud computing will further help to reduce this bottleneck. Another challenge is the large numbers of errors that different sequencing platforms generate. How can we differentiate sequencing errors from microheterogeneity within DNA samples from soil microbial communities? Also, there can be difficulties with different steps in sample processing. For example, each DNA extraction procedure can introduce its own bias with respect to sample loss or preferential lysis of some members of the microbial community over others. The most commonly used extraction procedures rely on beating with microscopic beads to lyse cells, although pressure lysis is another attractive option. Ideally, different laboratories should each use the same extraction protocol. However, despite the availability of commercial kits, laboratories typically follow their own favorite DNA extraction methods. Another problem lies with soil samples that have low biomass or high levels of contaminants such as humic acids that result in low DNA yields. For example, permafrost soils yield relatively little DNA in our experience. However, amplifying DNA before preparing a library might help. Two DNA-amplifying methods are used: multiple displacement amplification and emulsion PCR . Of the two, the MDA approach is subject to considerable bias, whereas emPCR should be less biased because each template is separately amplified. However, to my knowledge, no one has directly compared the two methods. Sometimes the volume of data falls short for conducting a metagenome analysis. For instance, when Susannah Tringe and coworkers at JGI first assembled soil metagenome data, their efforts failed because the 100 Mbp of sequence data that they collected proved insufficient. They estimated that they would need 2–5 Gbp to obtain draft genome assemblies of the most dominant organisms in soil, and current estimates from analysis of the Great Prairie metagenome data suggest that probably closer to 2 Tbp of data are needed! However, even a relatively low level of coverage was sufficient for some initial comparisons of the soil metagenome from a Minnesota farm to other available metagenome sequence datasets. Recently Etienne Yergeau and colleagues at the National Research Council of Canada produced 1 Gbp of sequence data from permafrost soil after amplifying their sample via MDA, which introduced considerable bias. Nevertheless,nursery pots when these data were compared to other metagenome data, DNA extracts from Minnesota farm soil—but not data from marine or other habitats—proved to be most closely related to the permafrost sample.Although we are learning a great deal about dominant bacteria and archaea in soils based on 16S rRNA gene sequence data, many of the dominant operational taxonomic units that we detect in soil have no close representatives in culture collections. Researchers are addressing these deficiencies through initiatives such as the Genomic Encyclopedia for Bacteria and Archaea project that Jonathan Eisen of the University of California, Davis and JGI coordinates. The long-term goal is to fill in the phylogenetic tree of life by sequencing genomes from underrepresented phyla. Another project, “Microbial Earth,” being coordinated by Nikos Kyrpides at JGI, calls for sequencing microbial type strains in culture collections. Meanwhile, the Earth Microbiome Project is an initiative that aims to sequence what some call the “dark matter” of biology, the full microbial diversity on Earth . The EMP will begin sequencing 10,000 metagenomes from various collections and habitats, and eventually will cover hundreds of thousands of such samples, pending dedicated support.

The soil microbial ecology research community has established an international consortium, the International TerraGenome Consortium . The consortium recognizes the high complexity of the soil environment and is focused on determining “the soil metagenome.” TerraGenome is a clearinghouse for information about funding for soil metagenomics research, for development and provision of bioinformatics tools, for metadata standards, and for workshops and meetings on these topics. For example, TerraGenome set forth criteria for metadata obtained from analyzing soil samples that researchers must meet before their sequence data may be deposited into centrally held databases. This effort to set the minimum information about an environmental marker sequence was coordinated through the Genome Standards Consortium .Through soil metagenomics research, we can address fundamental questions about soil microbial ecology. For example, is there functional microbial redundancy in soil? Soil microbial community compositions differ in different soils in terms of dominant populations, according to 16S rRNA gene surveys. Although soil pH is a Table 1. Examples of ongoing soil metagenome sequencing projects Sequencing project Strategy Status Principal Investigators Funding “Metasoil”: Rothamsted Park Grass permanent grassland, started 1856 454–FLX and Titanium 24 Gigabases Pascal Simonet & Tim Vogel France “DeepSoil”: Rothamsted Highfield permanent grassland and permanent bare-fallow plots, started 1959 Illumina paired end sequencing 80 Gigabases Dirk Evers , Tim Vogel, , Janet Jansson , James Tiedje Illumina Great Prairie Grand Challenge pilot study. Native prairie and adjacent cultivated corn sites in Wisconsin, Iowa and Kansas 454 Titanium and Illumina paired end sequencing  1.6 Terabase James Tiedje ; Janet Jansson, Susannah Tringe & Eddy Rubin DOE-JGI Alaskan permafrost, thermokarst bog and active layer samples Illumina paired end sequencing  80 Gigabases Janet Jansson, Eddy Rubin, Rachel Mackelprang & Jenni Hultman , Mark Waldrop DOE-JGI 24 Sites across continental US 454-FLX & Titanium 1.2 Gigabases Folker Meyer DOE-Argonne laboratory DOE FACE sites- impact of elevated CO2–5 sites 454–FLX & Titanium 5 Gigabases Cheryl Kuske DOE-JGI 314 Y Microbe / Volume 6, Number 7, 2011 6key driver of soil community composition, biogeography also plays a role. As an illustration, we can compare soil microbial diversity to the diversity of microbial communities in the human gut. The gut microbiota from one individual to another differs at the 16S rRNA gene level, but at the broad functional level the communities are rather homogenous in healthy individuals. This pattern suggests that several different bacterial species can carry out the same functional roles in the human intestine. The situation in soil might be similar, but we have yet to explore and compare many soil metagenomes in depth to determine whether that possibility holds. Metagenomics can help us determine whether microorganisms in soils embody a specialized cache of gene functions. Available metagenome sequence datasets are already providing clues as to what functions are predominant in soils. For example, genes for cellobiose phosphorylase, an enzyme that degrades plant carbohydrates, were identified in a Minnesota farm soil metagenome, but not in one from the Sargasso Sea. When we screened permafrost for other functional genes specifically involved in cycling carbon and nitrogen, the samples included several genes that were more or less prevalent after thaw. For example, although methanogens may not be numerically dominant in permafrost, they play a key role in producing methane, which is 21 times more potent as a greenhouse gas than carbon dioxide. With deep sequencing, it should be possible to obtain genomes of some of the dominant species in soil and even some species of relatively low abundance, provided that they do not have large amounts of strain heterogeneities.

Given that the full word meaning remains activated, the picture is thus judged as being less related to the full word. To a first approximation, it seems that cascading processes cannot account for the preferential access of the first “constituent” over the second. However, the activation of embedded constituents can be triggered by initially identifying the leftmost constituent . Thus, the meaning of the first followed by the second “constituent” can be quickly accessed and integrated with the full word meaning resulting in an inhibition for semantically unrelated “constituents”. Our results seem to be at odds with the predictions of models positing a prelexical parser that is entirely blind to the semantics of morpho-orthographic segments. A semantically blind system wouldn’t distinguish between compounds and pseudocompounds, not at least when scanning one of its constituents. If the system reads left-to-right, a semantically blind morpho-orthographic mechanism should treat both compounds and pseudocompounds as yielding potential morphemes. If the system is morphologically savvy and a “head hunter” it should treat the second morpho-orthographic sequence as a potential morpheme. But our results show significant differences in RTs and accuracy between compounds and pseudocompounds at both segments. However, it is possible that the lexical parsing mechanism first identifies the leftmost constituent but with semantic information quickly ruling out misparses. That would be the case of a pseudocompound whose “constituent” fan is accessed but quickly ruled-out upon accessing the full word fanfare. The whole word meaning can be accessed via a postlexical route or following a semantically anomalous composition of parsed “constituents”.

This in effect would reflect in faster and more accurate judgements for compounds given that the full word meaning is related to the meaning of the head,plant pot with drainage even if the referent picture stands for the head only . It is clear that the time-course of visual word recognition is faster than the time it takes to make a semantic judgement about a word and a picture. With our method, we aimed to capture the early moments of visual word recognition and lexical access by relying on a short presentation of words and pictures dichoptically, that is, without foveation. So, it is possible that the lexical targets—and thus their morpho-orthographic parsing—were degraded, limiting the scope of our results. However, it is important to note that the judgement accuracy for single constituents at the same spatial position as their embedded counterparts yielded high accuracy suggesting that parafoveal viewing was sufficiently clear to enable morpho-orthographic parsing. Taken together, our findings support a model whereby the visual word recognition system produces left-to-right constituent recognition, with these constituents accessing their lexical entries, but with morpho-semantic processes rapidly ruling out misparses. In other words, “constituent” meanings are accessed, though only the representation of semantically related “constituents” remain active. Our suggestion is that both constituents and full words token their concepts; but while the concept BED is compatible with the complex word bedroom , the concept FAN is incompatible with the monomorphemic word fanfare and is rapidly suppressed. This view is compatible with a model of visual word recognition that produces multiple parses that are initially insensitive to the semantics of morpho-orthographic sequences, but which are quickly evaluated by semanticcomposition processes.

With innovations and advancements in analytical instruments and computer technology, omics studies based on statistical analysis, such as phytochemical omics, oilomics/lipidomics, proteomics, metabolomics, and glycomics, are increasingly popular in the areas of food chemistry and nutrition science. Clear graphical representation and visual communication are effective ways to present large datasets and dense information to learners. Heatmaps with hierarchical clustering analysis and principal component analysis are commonly used cluster analysis methods for omics studies. Wang et al. investigated the interaction of fruity aromas with polyphenols by the use of heatmap cluster analysis by Origin Pro 9.0; Varunjikar et al. analyzed proteomics from tandem mass spectrometry by the use of heatmap cluster analysis through Omics Explorer V 3.6 software for food-grade insect protein analysis; Lin et al. analyzed the glycome profile of blueberry using a heatmap via R software. Yang et al. combined head space-gas chromatography-ion mobility spectrometry with PCA to detect the flavor compounds of fermented soybean products by the use of a software package with a dynamic PCA plug-in. Green & Selina employed both PCA and hierarchal cluster analysis without a heatmap to classify fatty acid and sterol profiles for analyzing avocado oil quality by the use of OriginPro2016 software. Zhao et al. implemented PCA in R software and machine learning algorithms in Python to classify up to ten types of major edible oils based on fatty acid profiles and Raman spectra datasets; Zhao et al. also applied PCA based on R software to analyze phenolic compound profiles of different cultivars of the US midwestern grapes with selenium and lithium fertilizer treatments. Richter et al. used PCA and heatmap cluster analysis to analyze inductively coupled plasma mass spectrometry data in R software for identifying food authentication of German asparagus. Zou et al. analyzed a multidimensional dataset of HS-SPMEGC×GC-TOFMS of coffee using ChromaTOF® , ChromaTOF Tile , R version 4.0.2, and MATLAB® .

However, processing high-dimensional data from raw food omics datasets is time consuming and remains a challenging task for data mining and untargeted foodomics studies. To achieve multiple data analysis methods, different software or code packages may be needed. For instance, by the use of R software, packages ‘ggbiplot’ and ‘ggplot’ are usually used for PCA analysis, while another package ‘heatmap20 is usually applied for heatmap cluster analysis. However, it takes time for researchers to learn and operate different software and code packages with confidence. The objective of the study is to develop an integrated code basis program based on MATLAB® software to give a 3D heatmap, heatmap hierarchical clustering analysis, and PCA all at once by directly reading datasets from Excel® files. The code has been optimized for figure qualities such as resolution, color code, and label font size. The code also adjusts the size of the 3D bars of the heatmap in accordance with the values, which gives readers better data visualization and differentiation. In addition, we have provided proper code annotations and completed user guidance in the supplementary materials for future learning and educational proposes. The original dataset of our previous publication about the US California olive pomace phenolics was used as an example dataset in this study. As can be seen from Table S1, the data matrix contained 7 extracts * 22 olive pomace phenolic compounds. Data were saved in an ‘.xlsx’ file format by the use of Microsoft® Excel; in this case, the full file name was ‘olive phenolics.xlsx’. Here, Hadley Wickham’s ‘Tidy Data’ conceptwas referred, where each variable was a column and each sample observation was a row, because the input data must be tidy for the best results. It can be seen from Figure S1a that the names of 7 olive pomace extracts were listed in the first column from A2 to A8,growing blueberries in pots and the names of 22 olive pomace phenolic compounds were listed in the first row from B1 to W1. The text ‘NAME’ was placed in cell A1. The file was saved as ‘olive phenolics.xlsx’ in a MATLAB work folder. The data area in the excel file can be expanded in both rows and columns; however, there should be no blank cells in any places in the data area. The sample observation name should also be listed in the first column and the compound variables names should be listed in the first row. Omics data of each sample must be listed in each row, and variables/compounds must be listed in columns; otherwise, the program will still run, but output meaningless results. The excel data file and ‘.m’ code in the MATLAB files have been uploaded to the file exchange website as a secondary way to obtain the dataset and code. Readers can download from there in the MATLAB software, as shown in the ‘screenshot’ in Figure S1b, or via the MATLAB file exchange website.In perennial plants, masting marks one extreme end of the spectrum of population-level variation, and constant yield marks the opposite end. To date, much of the research on synchronous seed production has been focused on mast-seeding by wind-pollinated trees in temperate regions. It may be that mast-seeding is more common in wind-pollinated taxa; theory suggests selection for enhanced pollination efficiency through synchronous flowering with conspecifics is more likely in wind-pollinated species .

In insect-pollinated species, synchronous flowering may saturate insect pollinators and high pollination efficiency at low flowering density may select for a more constant production of flowers . An alternative explanation of the over representation of wind-pollinated species in the synchronous seeding literature is that much of the masting work, and indeed the bulk of ecological and evolutionary research, has been done in temperate regions where wind is the predominant pollination syndrome among forest trees. Early reviews on whether pollination syndrome predicts the tendency for masting had difficulty gathering sufficient data on insect pollinated and animal-dispersed taxa. A recent meta-analysis included data with approximately equal numbers of animal- and wind pollinated species, but there were more time series per species for the wind- than animal-pollinated ones . To help to fill this gap, we make use of an analogous pattern of highly variable reproduction in perennial crop plants which, unlike mast-seeding forest trees, are biased toward insect-pollinated taxa and span tropical, Mediterranean and temperate climates . Alternate bearing in fruit and nut crops is an intermediate pattern of perennial reproductive variability in which a year of high reproduction is followed by a year of low reproduction. While media and trade reports have cited alternate bearing in discussions of national crop yield, literature on the extent and drivers of synchrony among alternate-bearing individuals is scarce. Despite evidence of similar plant-level mechanisms in masting and alternate bearing, ecological research on the synchrony of mast-seeding has largely ignored, or explicitly excluded, alternate-bearing crops . This may be because breeding and management actions are generally assumed to outweigh any natural conditions that could result in alternate bearing at farm-, region- or nationwide scales. Similarly, agricultural research on yield and alternate bearing rarely integrates insights from masting literature. Such insights include the possibility that factors which increase yield in one year may result in a more severe reduction in the following year and the expectation that wind-pollinated taxa may be more prone to synchronous fluctuations in yield at larger spatial scales than insect-pollinated taxa . Here, we use global crop production data for plants known to be alternate bearing at an individual level to evaluate patterns of seed production at the national level. Specifically, we assess whether these crops are alternate bearing at national scales and whether patterns differ across pollination syndromes and are consistent with findings in masting systems. For this analysis, we use data from the Food and Agriculture Organization of the United Nations. The global, long-term nature of the FAO data offers a unique opportunity to study reproductive patterns in perennial plants, but also poses some limitations that could mask a signal of alternate bearing even if one exists. First, the FAO reports data at the national level, and while the total area under production is included, it is not spatially explicit and thus cannot serve as a proxy for the extent of cultivation. As such, we cannot directly test for synchrony among individuals or populations using these data. While a signal of alternate bearing in national-scale data would require synchrony at smaller scales, a lack of a signal does not preclude synchrony at the farm or regional level. Studies of synchrony in mast-seeding species suggest that we might expect signals of alternate bearing to be weaker in data at national compared to local scales. In that sense, our analysis is likely to underestimate the magnitude of alternate bearing at more local scales and thus their potential impact on farmer livelihoods. Furthermore, multiple crops are sometimes grouped together into a single FAO crop category , which could mask a species-specific signal. Finally, there is no information on the genetic variety or cultivation practices employed in each country that could influence the tendency toward alternate bearing within taxa. These features make any observed patterns in these data particularly salient. The presence of alternate bearing at national scales would highlight its ecological and socio-ecological importance.