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5,510 results for “Foods”
Data from: Improving accuracy of DNA diet estimates using food tissue control materials and an evaluation of proxies for digestion bias
Ecologists are increasingly interested in quantifying consumer diets based on food DNA in dietary samples and high-throughput sequencing of marker genes. It is tempting to assume that food DNA sequence proportions recovered from diet samples are representative of consumer's diet proportions, despite the fact that captive feeding studies do not support that assumption. Here, we examine the idea of sequencing control materials of known composition along with dietary samples in order to correct for technical biases introduced during amplicon sequencing and biological biases such as variable gene copy number. Using the Ion Torrent PGM©, we sequenced prey DNA amplified from scats of captive harbour seals (Phoca vitulina) fed a constant diet including three fish species in known proportions. Alongside, we sequenced a prey tissue mix matching the seals' diet to generate tissue correction factors (TCFs). TCFs improved the diet estimates (based on sequence proportions) for all species and reduced the average estimate error from 28 ± 15% (uncorrected) to 14 ± 9% (TCF-corrected). The experimental design also allowed us to infer the magnitude of prey-specific digestion biases and calculate digestion correction factors (DCFs). The DCFs were compared with possible proxies for differential digestion (e.g. fish protein%, fish lipid%) revealing a strong relationship between the DCFs and percent lipid of the fish prey, suggesting prey-specific corrections based on lipid content would produce accurate diet estimates in this study system. These findings demonstrate the value of parallel sequencing of food tissue mixtures in diet studies and offer new directions for future research in quantitative DNA diet analysis.
Data from: Innovative consumers: ecological, behavioral and physiological predictors of responses to novel food
Consumer innovation, i.e. the acquisition and consumption of novel food types, has received little attention despite its predominance among animal innovations, and its potential implications for the ecology and evolution of species in a changing world. Results of the few studies that have investigated individual responses to novel foods suggest that various ecological, behavioral, and physiological variables may impact individual propensity for consumer innovation, but further work is needed to clarify these relationships. We investigated if urbanization, social rank, exploratory personality, and baseline levels of corticosterone predict food neophobia and consumer innovation responses of wild-caught black-capped chickadees (N=170) from 14 sites along an urbanization gradient. Our analyses do not support a link between food neophobia or consumer innovation and urbanization, dominance or exploratory personality. However, birds with higher levels of baseline corticosterone were quicker to contact novel food types, and more likely to consume novel foods than individuals with lower levels of the hormone. This finding suggests that physiological states that promote foraging behavior might drive individual responses to novel food. Additionally, we found that chickadees tested later in autumn were less neophobic than those tested earlier in the season, perhaps reflecting seasonal changes in food availability. Together, the ability of baseline corticosterone and date of capture to predict responses to novel food suggest that necessity may drive consumer innovation in chickadees.
Data from: Relative preference and localized food affect predator space use and consumption of incidental prey
Abundant, localized foods can concentrate predators and their foraging efforts, thus altering both the spatial distribution of predation risk and predator preferences for prey that are encountered incidentally. However, few investigations have quantified the spatial scale over which localized foods affect predator foraging behavior and consumption of incidental prey. In spring 2010, we experimentally tested how point-source foods altered how generalist predators (white-footed mice, Peromyscus leucopus) utilized space and depredated two incidental prey items: almonds (Prunus dulcis; highly profitable) and maple seeds (Acer saccharum; less profitable). We estimated mouse population densities with trapping webs, quantified mouse consumption rates of these incidental prey items, and measured local mouse activity with track plates. We predicted that 1) mouse activity would be elevated near full feeders, but depressed at intermediate distances from the feeder, 2) consumption of both incidental prey would be high near feeders providing less-preferred food and, 3) consumption of incidental prey would be contingent on predator preference for prey relative to feeders providing more-preferred food. Mouse densities increased significantly from pre- to post-experiment. Mean mouse activity was unexpectedly greatest in control treatments, particularly <15 m from the control (empty) feeder. Feeders with highly preferred food (sunflower seeds) created localized refuges for incidental prey at intermediate distances (15 to 25m) from the feeder. Feeders with less-preferred food (corn) generated localized high risk for highly preferred almonds <10 m of the feeder. Our findings highlight the contingent but predictable effects of locally abundant food on risk experienced by incidental prey, which can be positive or negative depending on both spatial proximity and relative preference.
Data from: Reduced tillage, but not organic matter input, increased nematode diversity and food web stability in European long-term field experiments
Soil nematode communities and food web indices can inform about the complexity, nutrient flows and decomposition pathways of soil food webs, reflecting soil quality. Relative abundance of nematode feeding and life-history groups are used for calculating food web indices, i.e. maturity index (MI), enrichment index (EI), structure index (SI) and channel index (CI). Molecular methods to study nematode communities potentially offer advantages compared to traditional methods in terms of resolution, throughput, cost and time. In spite of such advantages, molecular data have not often been adopted so far to assess the effects of soil management on nematode communities and to calculate these food web indices. Here, we used high-throughput amplicon sequencing to investigate the effects of tillage (conventional vs reduced) and organic matter addition (low vs high) on nematode communities and food web indices in ten European long-term field experiments and we assessed the relationship between nematode communities and soil parameters. We found that nematode communities were more strongly affected by tillage than by organic matter addition. Compared to conventional tillage, reduced tillage increased nematode diversity (23% higher Shannon diversity index), nematode community stability (12% higher MI), structure (24% higher SI), and the fungal decomposition channel (59% higher CI), and also the number of herbivorous nematodes (70% higher). Total and labile organic carbon, available K and microbial parameters explained nematode community structure. Our findings show that nematode communities are sensitive indicators of soil quality and that molecular profiling of nematode communities has the potential to reveal the effects of soil management on soil quality.
Data from: Using risk of bias domains to identify opportunities for improvement in food- and nutrition-related research: an evaluation of research type and design, year of publication, and source of funding
Purpose: This retrospective cross-sectional study aimed to identify opportunities for improvement in food and nutrition research by examining risk of bias (ROB) domains. Methods: Rating were extracted from critical appraisal records for 5675 studies used in systematic reviews conducted by three organizations. Variables were as follows: ROB domains defined by the Cochrane Collaboration (Selection, Performance, Detection, Attrition, and Reporting), publication year, research type (intervention or observation) and specific design, funder, and overall quality rating (positive, neutral, or negative). Appraisal instrument questions were mapped to ROB domains. The kappa statistic was used to determine consistency when multiple ROB ratings were available. Binary logistic regression and multinomial logistic regression were used to predict overall quality and ROB domains. Findings: Studies represented a wide variety of research topics (clinical nutrition, food safety, dietary patterns, and dietary supplements) among 15 different research designs with a balance of intervention (49%) and observation (51%) types, published between 1930 and 2015 (64% between 2000-2009). Duplicate ratings (10%) were consistent (k=0.86-0.94). Selection and Performance domain criteria were least likely to be met (57.9% to 60.1%). Selection, Detection, and Performance ROB ratings predicted neutral or negative quality compared to positive quality (p<0.001). Funder, year, and research design were significant predictors of ROB. Some sources of funding predicted increased ROB (p<0.001) for Selection (Interventional: industry only and none/not reported; Observational: other only and none/not reported) and Reporting (Observational: university only and other only). Reduced ROB was predicted by combined and other-only funding for intervention research (p<0.005). Performance ROB domain ratings started significantly improving in 2000; others improved after 1990 (p<0.001). Research designs with higher ROB were nonrandomized intervention and time series designs compared to RCT and prospective cohort designs respectively (p<0.001). Conclusions: Opportunities for improvement in food and nutrition research are in the Selection, Performance, and Detection ROB domains.
Data from: Individual variation in winter supplementary food consumption and its consequences for reproduction in wild birds.
The provision of wild birds with supplementary food has increased substantially over recent decades. While it is assumed that provisioning birds is beneficial, supplementary feeding can have detrimental 'carry-over' effects on reproductive traits. Due to difficulties in monitoring individual feeding behaviour, assessing how individuals within a population vary in their exploitation of supplementary food resources has been limited. Quantifying individual consumption of supplementary food is necessary to understand the operation of carry-over effects at the individual level. We used Radio Frequency Identification (RFID) technology and automated feeders to estimate individual consumption of supplementary winter food in a large wild population of great tits Parus major and blue tits Cyanistes caeruleus. Using these data, we identified demographic factors that explained individual variation in levels of supplementary food consumption. We also tested for carry-over effects of supplementary food consumption on recruitment, reproductive success and a measure of survival. Individual variation in consumption of supplementary food was explained by differences between species, ages, sexes and years. Individuals were consistent across time in their usage of supplementary resources. We found no strong evidence that the extent of supplementary food consumption directly influenced subsequent fitness parameters. Such effects may instead result from supplementary food influencing population demographics by enhancing the survival and subsequent breeding of less competitive individuals, which reduce average breeding parameters and increase density-dependent competition. Carry-over effects of supplementary feeding are not universal and may depend upon the temporal availability of the food provided. Our study demonstrates how RFID systems can be used to examine individual-level behaviour with minimal effects on fitness.
Data from: Predictable food supplies induce plastic shifts in avian scaled body mass
Urbanization constitutes one of the most profound forms of land-use change and strongly affects global biodiversity and ecosystem functioning. Expansion of urban areas typically leads to species loss but may also induce more subtle changes in species dynamics through selection or plasticity. Using a dual correlative (field) and experimental (aviary) approach, we here show that free-ranging urban house sparrows in southern France were smaller and lighter than their rural counterparts after allometric scaling, whereas 2 independent indices of nutritional (feather growth rates) and developmental (feather asymmetry) stress did not vary with urbanization. When subjecting these individuals to urban or rural diets in a highly predictable, controlled setting, rural but not urban sparrows decreased their body mass, independent of diet type, to the extent that initial scaled mass differences between urban and rural birds disappeared by the end of the captive period. By integrating field- and aviary measurements of body size and mass with indices of nutritional and developmental stress, we conclude that the lower scaled body masses of urban birds likely reflect a plastic response to predictable food supplies, possibly mediated through predation. Urban environments therefore do not necessarily constitute nutritionally stressful environments for species that typically cohabit with humans, such as house sparrows.
Data from: Feed or fight: testing the impact of food availability and intraspecific aggression on the functional ecology of an island lizard
Body size often varies among insular populations relative to continental conspecifics – the 'island rule' – and functional, context-dependent morphological differences tend to track this body size variation on islands. Two hypotheses are often proposed as potential drivers of insular population differences in morphology: one relating to diet and the other involving intraspecific competition and aggression. We directly tested whether differences in morphology and maximum bite capacity were explained by interisland changes in hardness of both available and consumed prey, and levels of lizard-to-lizard aggression among small-island populations. Our study included 11 islands in the Greek Cyclades and made use of a gradient in island area spanning five orders of magnitude. We focused on the widespread lizard Podarcis erhardii. We found that on smaller islands, P. erhardii body size was larger, head height was larger relative to body size, and maximum bite capacity became proportionally stronger. This pattern in morphology and performance was not related to differences in diet, but was highly correlated with proxies of intraspecific aggression – bite scars and missing toes. Our findings suggest that critical functional traits such as body size and bite force in P. erhardii follow the predictions of the island rule and are changing in response to changes in the competitive landscape across islands of different sizes.
Data from: Exploring the temporal variability of a food web using long-term biomonitoring data
Ecological communities are constantly being reshaped in the face of environmental change and anthropogenic pressures. Yet, how food webs change over time remains poorly understood. Food web science is characterized by a trade-off between complexity (in terms of the number of species and feeding links) and dynamics. Topological analysis can use complex, highly resolved empirical food web models to explore the architecture of feeding interactions but is limited to a static view, whereas ecosystem models can be dynamic but use highly aggregated food webs. Here, we explore the temporal dynamics of a highly resolved empirical food web over a time period of 18 years, using the German Bight fish and benthic epifauna community as our case study. We relied on long-term monitoring ecosystem surveys (from 1998 to 2015) to build a metaweb, i.e. the meta food web containing all species recorded over the time span of our study. We then combined time series of species abundances with topological network analysis to construct annual food web snapshots. We developed a new approach, "node-weighted" food web metrics by including species abundances to represent the temporal dynamics of food web structure, focusing on generality and vulnerability. Our results suggest that structural food web properties change through time; however, binary food web structural properties may not be as temporally variable as the underlying changes in species composition. Further, the node-weighted metrics enabled us to detect that food web structure was influenced by changes in species composition during the first half of the time series and more strongly by changes in species dominance during the second half. Our results demonstrate how ecosystem surveys can be used to monitor temporal changes in food web structure, which are important ecosystem indicators for building marine management and conservation plans.
Data from: Age-specific offspring mortality economically tracks food abundance in a piscivorous seabird
Earlier offspring mortality prior to independence saves resources for kin, which should be more beneficial when food is short. Using 24 years of data on age-specific common tern (Sterna hirundo) chick mortality, best described by the Gompertz function, and estimates of energy consumption per age of mortality, we investigated how energy wasted on non-fledged chicks depends on brood size, hatching order and annual abundance of herring (Clupea harengus), the main food source. We found mortality directly after hatching (Gompertz baseline mortality) to be high and to increase with decreasing herring abundance. Mortality declined with age, at a rate relatively insensitive to herring abundance. The sensitivity of baseline mortality to herring abundance reduced energy wasted on non-fledged chicks when herring was short. Among chicks that did not fledge, last-hatched chicks were less costly than earlier hatched chicks, due to their earlier mortality. However, per hatchling produced, the least energy was wasted on chicks without siblings, due to their baseline mortality being most sensitive to herring abundance. We suggest that earlier mortality of offspring when food is short facilitates economic adjustment of post-hatching parental investment to food abundance, but that such economic brood reduction may be constrained by sibling competition.
Data from: Outlier SNPs enable food traceability of the southern rock lobster, Jasus edwardsii
Recent advances in next-generation sequencing have enhanced the resolution of population genetic studies of non-model organisms through increased marker generation and sample throughput. Using double digest restriction site-associated DNA sequencing (ddRADseq), we investigated the population structure of the commercially important southern rock lobster, Jasus edwardsii, in Australia and New Zealand with the aim of identifying a panel of SNP markers that could be used to trace country of origin. Four ddRADseq libraries comprising a total of 88 individuals were sequenced on the Illumina MiSeq platform, and demultiplexed reads were used to create a reference catalog of loci. Individual reads were then mapped to the reference catalog, and variant calling was performed. We have characterized two single-nucleotide polymorphism (SNP) panels comprised in total of 656 SNPs. The first panel contained 535 neutral SNPs and the second, 121 outlier SNPs that were characteristic of being putatively under selection. Both neutral and outlier SNP panels showed significant differentiation between the two countries, with the outlier loci demonstrating much larger FST values (FST outlier SNP panel = 0.134, P < 0.0001; FST neutral SNP panel = 0.022, P < 0.0001). Assignment tests performed with the outlier SNP panel allocated 100 % of the individuals to country of origin, demonstrating the usefulness of these markers for food traceability of J. edwardsii.
Data from: Food restriction and chronic stress alter energy use and affect immunity in an infrequent feeder
Glucocorticoids are important mediators of energy utilization for key physiological processes, including immune function. Much work has focused on the effects of energy limitation and stress for key physiological processes such as reproduction and immunity. However, it is unclear how stress alters energy use across different energy states, and the physiological ramifications of such effects are even less clear. In this study, we altered energy and stress states of an infrequent feeder, the Terrestrial Gartersnake (Thamnophis elegans), using fasting and repeated restraint stress (Chronic Stressors) to test how these challenges interacted to affect immune function, energy metabolites, and glucocorticoid reactivity (a traditional indicator of stress state) to restraint stress, a standardized, acute stressor. After this acute stressor, the snakes which had received chronic stress had increased glucocorticoid reactivity, and both treatments altered energy metabolite use and storage. Evidence of interaction of food restriction and chronic stress treatments on innate immune function and energy metabolites (triglycerides and glycerol) suggests that stress alters energy use in a manner dependent on the energy state of the animal. Snakes have a remarkable ability to maintain functionality of key physiological processes under stressful conditions but are still susceptible to multiple simultaneous stressors, a situation increasingly prevalent in our ever-changing environment.
Figure 5 in Invertebrate communities, sediment parameters and food availability of intertidal soft-sediment ecosystems on the north coast of British Columbia, Canada
Figure 5. Non-metric multidimensional scaling (nMDS) plots showing infaunal invertebrate community at three intertidal sandy shore sites on the north coast of British Columbia, Canada during the summer of 2017. (a) the infaunal community by sandy shore site and sampling round and (b) the vector overlay indicates the direction of increased density, with correlations>0.3 shown. BO: Boulder Beach. GU: Coast Guard Beach. PI: Prescott Inlet. Round A: 23 May–1 June. Round B: 21–26 June. Round C: 19–25 July. Round D: 18–24 August.
Figure 6 in Invertebrate communities, sediment parameters and food availability of intertidal soft-sediment ecosystems on the north coast of British Columbia, Canada
Figure 6. Non-metric multidimensional scaling (nMDS) plots of (a) sediment parameters (depth to the aRPD, water content, particle size, penetrability, % macrophyte coverage, % Zostera marina cover, and % wood cover) by site and round and (b) the food availability (chlorophyll a and organic matter content) at three intertidal sandy shore sites on the north coast of British Columbia, Canada during the summer of 2017. Vector overlays for sediment and food variables show the correlation between variables and nMDS axes, with each vector showing the direction of increased value. BO: Boulder Beach. GU: Coast Guard Beach. PI: Prescott Inlet. Round A: 23 May 23–1 June. Round B: 21–26 June. Round C: 19–25 July. Round D: 18–24 August.
Figure 2 in Invertebrate communities, sediment parameters and food availability of intertidal soft-sediment ecosystems on the north coast of British Columbia, Canada
Figure 2. Flow chart demonstrating statistical analysis conducted on the biotic and abiotic variables sampled at intertidal mudflats (n = 3) and intertidal sandy shores (n = 3) on the north coast of British Columbia, Canada during the summer of 2017.
Figure 1 in Invertebrate communities, sediment parameters and food availability of intertidal soft-sediment ecosystems on the north coast of British Columbia, Canada
Figure 1. Map of intertidal mudflats and sandy shore study sties around Prince Rupert, and on Prescott Island, British Columbia, sampled during summer of 2017. Figure 1(a) shows mudflats close to the Skeena River (CC: Cassiar Cannery 54.1747, 130.1721; TB: Tyee Banks 54.2000, 129.9634; WC: Wolfe Cove 54.2424, 130.2730). Figure 1(b) shows sandy shores on Prescott Island (BO: Boulder Beach 54.0871, 130.5970; PI: Prescott Inlet 54.0709, 130.5950; GU: Coast Guard Beach 54.0659, 130.5757).
Figure 3 in Invertebrate communities, sediment parameters and food availability of intertidal soft-sediment ecosystems on the north coast of British Columbia, Canada
Figure 3. Non-metric multidimensional scaling (nMDS) graphs showing infaunal invertebrate community at three intertidal mudflats on the north coast of British Columbia, Canada during the summer of 2017. (a) the infaunal community by mudflat and sampling round and (b) the vector overlay indicates the direction of increased density, with correlations>0.3 shown. CC: Cassiar Cannery. TB: Tyee Banks. WC: Wolfe Cove. Round A: 23 May–June 1. Round B: 21–26 June. Round C: 19–25 July. Round D: 18–24 August.
Figure 4 in Invertebrate communities, sediment parameters and food availability of intertidal soft-sediment ecosystems on the north coast of British Columbia, Canada
Figure 4. Non-metric multidimensional scaling (nMDS) plots of (a) sediment parameters (depth to the aRPD [apparent redox potential discontinuity], water content, particle size, penetrability, % macrophyte coverage, and % wood cover) by site and round and (b) the food availability (chlorophyll a and organic matter content) at three intertidal mudflats on the north coast of British Columbia, Canada during the summer of 2017. Vector overlays for sediment and food variables show the correlation between variables and nMDS axes, with each vector showing the direction of increased value. CC: Cassiar Cannery. TB: Tyee Banks. WC: Wolfe Cove. Round A: 23 May–1 June. Round B: 21–26 June. Round C: 19–25 July. Round D: 18–24 August.
High Throughput Multispectral Image Processing with applications in Food Science
<p>Raw image samples for the PLoS ONE paper entitled "High Throughput Multispectral Image Processing with applications in Food Science".</p> <p>Segmented images for the PLoS ONE paper entitled "High Throughput Multispectral Image Processing with applications in Food Science".</p>
Adult picky eaters with symptoms of Avoidant/Restrictive Food Intake Disorder: Comparable distress and comorbidity but different eating behaviors compared to those with disordered eating symptoms
<p>Picky eaters are people who avoid many new and familiar foods because they dislike the taste, smell, texture, or appearance of many foods. When it is severe, picky eating can lead to weight loss or difficulty maintaining a healthy weight, nutritional deficiencies, dependence on supplements to get adequate nutrition or calories, or shame, anxiety, or difficulty engaging in daily life. When severe picky eating leads to these consequences, it can be diagnosed as Avoidant/Restrictive Food Intake Disorder (ARFID). People who restrict the amount of food they consume (or engage in exercise, purging, or fasting behaviors to get rid of calories after eating) because they are afraid of gaining weight or being fat are diagnosed with anorexia or bulimia when their eating leads to weight loss, nutritional problems, or interferes with life. ARFID is a new diagnosis, and in this paper, we show that 1) adults with ARFID symptoms are just as distressed, and just as likely to have symptoms of depression, anxiety, and obsessive compulsive disorder, as those with anorexia or bulimia, but that 2) adults with ARFID show very different types of eating behavior from adults with symptoms of anorexia or bulimia.</p>
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.