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3,121 results for “Resources”
Data from: Resequencing of common bean identifies regions of inter-gene pool introgression and provides comprehensive resources for molecular breeding
Common bean is the most important grain legume for human consumption and a main nutrition source in the tropics. Because bean production is reduced by both abiotic and biotic constraints, current breeding efforts are focused on the development of improved varieties with tolerance to these stresses. We characterized materials from different breeding programs spanning three continents to understand their sequence diversity and advance the development of molecular breeding tools. For this, 37 varieties belonging to P. vulgaris, P. acutifolius, and P. coccineus were sequenced by whole-genome sequencing (WGS), identifying more than 40 million genomic variants. Evaluation of nuclear DNA content and analysis of copy number variation revealed important differences in genomic content not only between P. vulgaris and two other domesticated Phaseolus species, but also within P. vulgaris, affecting hundreds of protein-coding genomic regions. A large number of inter-gene-pool introgressions were identified. Furthermore, interspecific introgressions for disease resistance in breeding lines were mapped. Evaluation of newly developed SNP markers within previously discovered QTL for common bacterial blight and angular leaf spot provide improved specificity to tag sources of resistance to these diseases. We expect that this dataset will provide a deeper molecular understanding of breeding germplasm and deliver molecular tools for germplasm development, aiming to increase the efficiency of bean breeding programs.
Data from: "Transcriptome sequence identity between Lyme disease tick vectors, Ixodes scapularis and Ixodes ricinus" in Genomic Resources Notes accepted 1 April 2014 to 31 May 2014
Ixodes scapularis and I. ricinus transmit the Lyme disease agent Borrelia burgdorferi in the U.S. and Europe, respectively. The only tick genome sequence available is that of I. scapularis, which constitutes a limitation for tick research. Recent evidences suggest that I. ricinus and I. scapularis transcriptomes share some degree of sequence identity. However, only the global transcriptome comparison reported here demonstrated that I. ricinus and I. scapularis share a 99.232±0.005 percent sequence identity with a very low frequency of INDELs. However, due to limitations of the current I. scapularis genome assembly, the number of aligned reads was only 26-27%. These results support the use of I. scapularis genome sequence as a reference for the analysis of I. ricinus transcriptomics and proteomics data, but addressing the limitations associated with the I. scapularis genome assembly.
Data from: The implicitome: a resource for rationalizing gene-disease associations
High-throughput experimental methods such as medical sequencing and genome-wide association studies (GWAS) identify increasingly large numbers of potential relations between genetic variants and diseases. Both biological complexity (millions of potential gene-disease associations) and the accelerating rate of data production necessitate computational approaches to prioritize and rationalize potential gene-disease relations. Here, we use concept profile technology to expose from the biomedical literature both explicitly stated gene-disease relations (the explicitome) and a much larger set of implied gene-disease associations (the implicitome). Implicit relations are largely unknown to, or are even unintended by the original authors, but they vastly extend the reach of existing biomedical knowledge for identification and interpretation of gene-disease associations. The implicitome can be used in conjunction with experimental data resources to rationalize both known and novel associations. We demonstrate the usefulness of the implicitome by rationalizing known and novel gene-disease associations, including those from GWAS. To facilitate the re-use of implicit gene-disease associations, we publish our data in compliance with FAIR Data Publishing recommendations [https://www.force11.org/group/fairgroup] using nanopublications. An online tool (http://knowledge.bio) is available to explore established and potential gene-disease associations in the context of other biomedical relations.
Data from: Whole genome sequencing of elite rice cultivars as a comprehensive information resource for marker assisted selection
Current advances in sequencing technologies and bioinformatics revealed the genomic background of rice, a staple food for the poor people, and provided the basis to develop large genomic variation databases for thousands of cultivars. Proper analysis of this massive resource is expected to give novel insights into the structure, function, and evolution of the rice genome, and to aid the development of rice varieties through marker assisted selection or genomic selection. In this work we present sequencing and bioinformatics analyses of 104 rice varieties belonging to the major subspecies of Oryza sativa. We identified repetitive elements and recurrent copy number variation covering about 200 Mbp of the rice genome. Genotyping of over 18 million polymorphic locations within O. sativa allowed us to reconstruct the individual haplotype patterns shaping the genomic background of elite varieties used by farmers throughout the Americas. Based on a reconstruction of the alleles for the gene GBSSI, we could identify novel genetic markers for selection of varieties with high amylose content. We expect that both the analysis methods and the genomic information described here would be of great use for the rice research community and for other groups carrying on similar sequencing efforts in other crops.
Resource allocation effects on the timing of reproduction in an avian habitat specialist
<p>Variation in nutrient allocation can influence the timing of breeding and ultimately reproductive output. Time and space constraints might exist, however, if fewer food resources are available to meet the costs of reproduction early during the reproductive season. Here, for the first time, we test whether nutrient allocation strategies for reproduction in a shrub-dependent avian species differs with timing of breeding in different ecoregions: a high-elevation landscape, containing spatially complex vegetation (Rocky Mountains) versus a low-elevation, more homogenous landscape (Great Plains). We analyzed data collected from radio-telemetry and stable isotopes to assess the degree to which endogenous (body) reserves are used for reproduction and whether variation in allocation strategies was associated with time of year, ecoregion, habitat quality (including sagebrush type and plant greenness), or maternal characteristics. Using a Bayesian statistical framework, we found that females relied on a similar amount of endogenous reserves for reproduction in first nesting and renesting attempts. Additionally, endogenous contributions declined more rapidly throughout the nesting season in the Rocky Mountains than in the Great Plains. Individuals in high- and intermediate-elevation sagebrush types in the Rocky Mountains used similar amounts of endogenous reserves, whereas females nesting in low-elevation sagebrush used less. Females nesting at intermediate elevations, which experience the greatest flush of new green vegetation during the nesting season, switched their reliance from endogenous to exogenous sources for reproduction as green vegetation became available during spring. Our study highlights adaptations of a nutrient-allocation strategy across areas with varying levels of resources in time and space in a habitat specialist bird. Nutrient allocation by individuals residing in high-elevation areas favors a strategy that mainly uses nutrients gained from wintering habitats, whereas individuals residing in low-elevation areas mainly use exogenous sources for reproduction.</p>
Data for: Larval environmental conditions influence plasticity in resource use by adults in the burying beetle, Nicrophorus vespilloides
<p><span><span><span><span><span><span><span><span><span><span><span>Recent studies have shown that intraspecific patterns of phenotypic plasticity can mirror patterns of evolutionary diversification among species. This appears to be the case in <i>Nicrophorus </i>beetles. Within species, body size is positively correlated with the size of carrion used to provision larvae and parental performance. Likewise, among species, variation in body size influences whether species exploit smaller or larger carrion and the extent to which larvae depend on parental care. However, it is unclear whether developmental plasticity in response to carcass size, parental care, or both underlie transitions to new carcass niches. We examined this by testing whether variation in the conditions experienced by <i>N. vespilloides </i>larvae influenced their ability to breed efficiently upon differently sized carcasses as adults. We found that the conditions experienced by larvae during development played a critical role in determining their ability to use large carcasses effectively as adults. Specifically, individuals that developed with parental care and on large carcasses were best able to convert the resources on a large carcass into offspring when breeding themselves. Our results suggest that parentally-induced plasticity can be important in the initial stages of niche expansion.</span></span></span></span></span></span></span></span></span></span></span></p> <p> </p>
Data from: Genomic evidence that resource-based trade-offs limit host-range expansion in a seed beetle
Trade-offs have often been invoked to explain the evolution of ecological specialization. Phytophagous insects have been especially well studied, but there has been little evidence that resource-based trade-offs contribute to the evolution of host specialization in this group. Here, we combine experimental evolution and partial genome resequencing of replicate seed beetle selection lines to test the trade-off hypothesis and measure the repeatability of evolution. Bayesian estimates of selection coefficients suggest that rapid adaptation to a poor host (lentil) was mediated by standing genetic variation at multiple genetic loci and involved many of the same variants in replicate lines. Sublines that were then switched back to the ancestral host (mung bean) showed a more gradual and variable (less repeatable) loss of adaptation to lentil. We were able to obtain estimates of variance effective population sizes from genome-wide differences in allele frequencies within and between lines. These estimates were relatively large, which suggests that the contribution of genetic drift to the loss of adaptation following reversion was small. Instead, we find that some alleles that were favored on lentil were selected against during reversion on mung bean, consistent with the genetic trade-off hypothesis.
Specialized metabolites in floral resources: effects and detection in buff-tailed bumblebees
<p>The selection of appropriate food resources by bees is a critical aspect for the maintenance of their populations, especially in the current context of global change and pollinator decline. Wild bees have a sophisticated ability to forage selectively on specific resources, and can assess the quality of pollen using contact chemosensory perception (taste). While numerous studies have investigated the detection of pollen macronutrients in bees and their impact on bee health and reproductive success, only a few studies have described the gustatory responses of bees towards specialized metabolites. In addition, these studies mostly focused on the response to nectar and neglected pollen, which is the main food resource for both bee imagines and larvae. Whether bees have the ability to detect specialized toxic metabolites in pollen and then rapidly adapt their foraging behavior to avoid them is very little studied. In this study, we tested whether pollen specialized metabolites affect bumblebees at both the micro-colony and individual levels (<i>i.e. </i>bioassays using supplemented pollen), and whether foragers detect these specialized metabolites and potentially display an avoidance behavior (<i>i.e. </i>preference tests using supplemented syrup). Bumblebees were fed with either amygdalin-, scopolamine- or sinigrin-supplemented pollen diets in ratios that mimic 50%, 100% and 200% of naturally occurring concentrations. We found no effect of these specialized metabolites on resource collection, reproductive success and stress response at the micro-colony level. At the individual level, bumblebees fed on 50%-amygdalin or 50%-scopolamine diets displayed the highest scores for damage to their digestive systems. Interestingly, during the preference tests, the solution with 50%-scopolamine displayed a phagostimulatory activity, whereas solution with 50%-amygdalin had a deterrent effect and could trigger an active avoidance behavior in bumblebees, with a faster proboscis retraction. Our results suggest that regulation of toxin intake is not as well-established and effective as the regulation of nutrient intake in bees. Bees are therefore not equally adapted to all specialized pollen metabolites that they can come into contact with.</p>
FIG. 5. A in Resource defence mating system in two ¯ies from Sulawesi: Gymnonerius fuscus Wiedemann and Telostylinus sp. near duplicatus Wiedemann (Diptera: Neriidae)
FIG. 5. A male Telostylinus standing guard over an egg-laying female.
FIG. 1. A female G in Resource defence mating system in two ¯ies from Sulawesi: Gymnonerius fuscus Wiedemann and Telostylinus sp. near duplicatus Wiedemann (Diptera: Neriidae)
FIG. 1. A female G. fuscus dabbing her labellum against an active beetle boring.
Fig. 3 in Activity pattern and resource use of two Callosciurus species in different habitats in northeastern Thailand
Fig. 3. Proportion of observed behaviours of (a) Callosciurus finlaysonii and (b) C. caniceps throughout the day.
Fig. 2 in Aquatic insects as the main food resource of fish the community in a Neotropical reservoir
Fig. 2. Alimentary Index (%) of food categories consumed by the fish community of the Nova Avanhandava Reservoir. AI = Aquatic insect; TI = Terrestrial insects; CR = Crustaceans; FI = Fish; MA = Macroinvertebrates; MI = Microcrustaceans; AL = Algae; VM = Vegetal matter; DS = Detritus/sediment; SC = Scales. The acronyms of species are in Table 1.
Fig. 9 in Is fish passage technology saving fish resources in the lower La Plata River basin?
Fig. 9. Comparison between fish biomass in the upper and lower chambers across different operation flows over three different months (adapted from Espinach Ros et al., 1997).
Interplay of above- and belowground resource limitations: a competition-facilitation shift maintains species coexistence
<p>Forest ecosystems are commonly characterised by a hierarchy of resources. During a disturbance of a forest community, increased light availability in the understorey can support competitive interactions at the expense of facilitation. This may overwhelm the role of belowground resource heterogeneity in maintaining species coexistence and so result in biotic homogenisation of a site. We re-surveyed species composition while estimating interspecific interactions along a microtopographic (moisture) gradient of a temperate swamp forest after increasing the availability of light into the undergrowth. We measured temporal changes in species diversity, compositional dissimilarity measures and functional traits, while belowground resource heterogeneity remained unchanged over time. To explain observed changes in terms of prevailing interspecific interactions, we evaluated temporal changes in the competition-facilitation balance. The productivity of understorey vegetation increased strongly over the five years of the study. This was accompanied by an increase in species diversity and the maintenance of compositional dissimilarity. The relative importance of competitive and facilitative interactions along the microtopographic gradient did not change over time. Rather than an overall biotic homogenisation of a site, we observed a spread of resource acquisitive species within the resource-rich sites and of stress-tolerant species within the resource-limited sites. We have shown that the temporary increase in productivity did not mitigate the effects of belowground resource heterogeneity on plant species turnover, which is likely maintained by contrasting interspecific interactions prevalent in different parts of the resource gradient. This suggests contrasting community assembly processes maintain diversity and productivity even in a local community.</p>
Results and further resources concerning our pre-studies concerning revealing biases in news articles
<p>Slanted news coverage strongly affects public opinion. This is especially true for coverage on politics and related issues, where studies have shown that bias in the news may strongly influence elections and other collective decisions. Due to its viable importance, news coverage has long been studied in the social sciences, resulting in comprehensive models to describe it and effective yet costly methods to analyze it, such as content analysis. We present an in-progress system for news recommendation that is the first to automate the manual procedure of content analysis to reveal person-targeting biases in news articles reporting on policy issues. In a large-scale user study, we find very promising results regarding this interdisciplinary research direction. Our recommender detects and reveals substantial frames that are actually present in individual news articles. In contrast, prior work rather only facilitates the visibility of biases, e.g., by distinguishing left- and right-wing outlets. Further, our study shows that recommending news articles that differently frame an event significantly improves respondents' awareness of bias.</p>
Dataset of the paper: "POLICIER: Pareto-OptimaL allocatIon of Continuous IntEgration Resources"
<p>This repository contains the dataset of the paper "POLICIER: Pareto-OptimaL allocatIon of Continuous IntEgration Resources"</p>
Patterns of pollination interactions at community-level are related to the type and quantity of floral resources
<p>1. A fundamental question in community ecology is how the quantity of floral resources affects pollinator activity and how this relates to the structure and robustness of pollination networks. The issue has been mainly addressed at species level, while at community level several questions are still open.</p> <p>2. Using a species-rich semi-natural grassland as model ecosystem, we explored the relationship between community-level quantity of floral resources, the number of flower visits at community-level and descriptors of the structure and robustness of pollination networks. To assess whether patterns of pollination interactions were consistent when using different types of floral resources, we measured three types of floral resources, namely the volume of nectar, the number of pollen grains and the number of flowers.</p> <p>3. Community-level pollinator visitation rate showed a hump-shaped relationship with the quantity of floral resources. Results were consistent among models employing different measures of floral resources as independent variables. The relationship between the quantity of floral resources and the structure and robustness of the network was not consistent among different types of floral resources; only intermediate levels of nectar volume were associated with high levels of network robustness.</p> <p>4. The pattern we found is in contrast with some former studies which reported positive linear relationships between the community-level visitation rate of pollinators and the quantity of floral resources. Rather, the observed hump-shaped pattern resembles the relationship previously found between the quantity of floral resources of a given plant species and its visitation rate per flower. Our results highlighted that, by using specific types of floral resources (e.g., the volume of nectar and the number of pollen grains) it is possible to reveal ecological processes that would be masked by using the number of flowers as the sole measure of floral resource.</p>
Figure 5 from: Ziegler A, Mirantsev G, Jangoux M, Kroh A (2014) Historical aspects of meetings, publication series, and digital resources dedicated to echinoderms. Zoosystematics and Evolution 90(1): 45-56. https://doi.org/10.3897/zse.90.7201
Figure 5 - Conference logos from selected national, regional, and international echinoderm meetings held from 1978 to 2013. (A) 3rd International Echinoderm Conference, Sydney, Australia, 1978. (B) 5th Florida Echinoderm Festival, Tampa, Florida, USA, 1999. (C) 1. Arbeitstreffen deutschsprachiger Echinodermenforscher, Greifswald, Germany, 2001. (D) International Conference on Sea-Urchin Fisheries and Aquaculture, Puerto Varas, Chile, 2003. (E) 3. Arbeitstreffen deutschsprachiger Echinodermenforscher, Ingelfingen, Germany, 2004. (F) ACIAR-SPC Asia-Pacific Tropical Sea Cucumber Aquaculture Symposium, Nouméa, New Caledonia, 2011. (G) 2° Congreso Latinoamericano de Equinodermos, São Sebastião, Brazil, 2013. (H) 5. Arbeitstreffen deutschsprachiger Echinodermenforscher, Stuttgart, Germany, 2013.
Figure 6 from: Ziegler A, Mirantsev G, Jangoux M, Kroh A (2014) Historical aspects of meetings, publication series, and digital resources dedicated to echinoderms. Zoosystematics and Evolution 90(1): 45-56. https://doi.org/10.3897/zse.90.7201
Figure 6 - Flyer announcing an informal gathering of the Friends of the Echinoderms during the 2010 Meeting of the Geological Society of America in Denver, Colorado, USA. Image courtesy Ronald L. Parsley.
Figure 3 from: Ziegler A, Mirantsev G, Jangoux M, Kroh A (2014) Historical aspects of meetings, publication series, and digital resources dedicated to echinoderms. Zoosystematics and Evolution 90(1): 45-56. https://doi.org/10.3897/zse.90.7201
Figure 3 - Group photo of the participants of the 1st European Conference on Echinoderms, held 1979 in Brussels. 1 Chantal De Ridder, 2 Michel Jangoux, 3 Claude Massin, 4 Anneliese Strenger, 5 Charles W. Walker, 6 Mrs. Hulbert, 7 Alan W. Hulbert, 8 David Nichols, 9 Mrs. Vasserot, 10 Robert F. O'Brien, 11 Anke Burkhardt, 12 Helge Hilgers, 13 Alfred Goldschmid, 14 Mrs. Goldschmid, 15 Richard M. Pagett, 16 Alan M. Raymond, 17 Raimundo Pidal, 18 Jean Le Menn, 19 Michel Huet, 20 Jean-Michel Vasserot, 21 Maria de Natividade Albuquerque, 22 Konrad Märkel, 23 Sebastian Bachmann, 24 Heinz Splechtna, 25 F. Jensenius Madsen, 26 Mrs. Guille, 27 Alain Guille, 28 Hubert Caspers, 29 Henri Termier, 30 Genevieve Termier, 31 Mrs. Roman, 32 Jean Roman, 33 Edwin Van Impe, 34 Jean-Guy Ferrand, 35 Robert Delavault, 36 Mrs. Huet, 37 Yulin Liao, 38 Jovanka Mitrović, 39 Norman Millott, 40 Mrs. Millott, 41 Ricard Martínez, 42 John E. Binyon, 43 Edward P. F. Rose, 44 Duncan Heddle, 45 Michel Philippe, 46 Jean-Pierre Féral, 47 Daniel Fournier, 48 Solveig Sjögren, 49 Monique Guillou, 50 Ms. Bacallado-Aranega, 51 Jacques Guillou, 52 Mrs. David, 53 Juan Jose Bacallado-Aranega, 54 Bruno David, 55 Celso Rodriguez Babio, 56 Mrs. Monteiro Marques, 57 Myriam Sibuet, 58 Enrico Tortonese, 59 Michel Roux, 60 Peter A. Voogt, 61 Gustave Cherbonnier, 62 Reimund Haude, 63 Mrs. Paterson, 64 Mrs. Durkin, 65 Ailsa M. Clark, 66 Radu Sukarno, 67 Michael K. Durkin, 68 Richard P. S. Jefferies, 69 Lesley I. Messer, 70 Ester Ryberg, 71 David G. Stephenson, 72 Edith Bricourt, 73 Guy Coppois, 74 Michel Demargne, 75 Christopher R. C. Paul, 76 Erhard Höbaus, 77 Pierre Magniez, 78 Alain Bidar, 79 Geoffrey Q. Case, 80 Lydie Dupont, 81 M. De Waal, 82 Wolfram P. Tertschnig, 83 Unidentified person, 84 Gerardo Gustato, 85 Aagje J. Van der Plas, 86 Anna Villari, 87 Derek E. G. Briggs, 88 Vasco M. A. Monteiro Marques, 89 Megumi F. Strathmann, 90 Rob C. H. M. Oudejans, 91 Peter M. Jost, 92 Unidentified person, 93 Gordon L. J. Paterson, 94 Paula F. Dehn, 95 Hussein Kamel Badawi, 96 Roland H. Emson, 97 Paul A. Tyler, 98 Grace S. Y. Lim, 99 John M. Lawrence, 100 Andrew B. Smith, 101 Ilana Ferber, 102 Haruo Kanatani, 103 Desmond B. Johnson, 104 Iain C. Wilkie, 105 Jaume Gallemi Paulet, 106 Kurt Traer, 107 Bent Hansen, 108 Jan J. S. Broertjes, 109 Richard R. Strathmann, 110 Tine Valentinčič.
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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.