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1,855 results for “Framework”
Database of NGS results of IGF-2 gene of intensive fattening lambs of sheep breeds raised in Latvia in 2022 within the framework of project of the Latvian Council of Science LZP-2021/1-0489 project
<p>Project of The Latvian Council of Science (LCS) - LZP-2021/1-0489 project: “<strong>Development of an innovative approach to identify biological determinants involved in the between-animal variation in feed efficiency in sheep farming</strong>.”</p> <p><strong>The aim of the project</strong> is to determine whether the feed efficiency status of Latvian meat sheep breeds could be predicted using a panel of genetic and molecular markers previously found to be associated with divergent Feed efficiency status in a training population of lambs when fed the same diet.</p> <p><strong>Novelty</strong>: to determine the parameters predicting the most productive result of lamb rearing, we set out to develop the cheapest and most effective method for determining markers of feed efficiency - based on molecular and genetic markers obtained from the blood of live lambs.</p> <p><strong>About the project:</strong></p> <p>The costs associated with lambing (buying or keeping sheep) and preparing or purchasing feed are the two largest components of variable costs in sheep raising. Feed costs are high due to poor grain growing conditions in major producing countries, the use of feed grains in ethanol production, and increased competition for land in crop production compared to urban development. Feed efficiency in growing lambs (i.e. the animal ability to reach a market or adult body weight (BW) with the least amount of feed intake), is a key factor in the sheep industry. Improving Feed efficiency reduces production costs. Improving Feed efficiency by 5% can bring economic benefits that are up to four times higher than a 5% increase in average daily gain (ADG).</p> <p>Traditionally, meat breeding programs have focused on outputs, due mainly to the routine availability of phenotypic data on outputs or correlated traits. Currently no marker has successfully explained enough of the variability in feed efficiency that they were used as part of a routine improvement program, as well as, according to our data, no genetic parameters for performance and feed efficiency traits are available for sheep. The physiological determinants of feed efficiency or putative biomarkers used to analyze animal-to-animal variation in live lambs could be used as a cost-effective and rapid tool for genetic selection or management decisions.</p> <p>As with other complex traits (also referred to as quantitative or polygenic traits), Feed efficiency is controlled by many genes which are involved in several molecular mechanisms and pathways causing animal-to-animal genetic variation in different biological functions. GWAS results suggested genes impacting lipid and energy metabolism as markers of Feed efficiency. Detection of a large number of variants in these genes is necessary in order to accurately predict or identify efficient animals.</p> <p>A major role of insulin-like growth factors (IGFs) is considered to be the regulation of tissue growth and differentiation. Insulin-like growth factor 2 (IGF2), also known as growth regulator A or somatomedin A, plays an important role in regulating fetal development, tumor proliferation and skeletal muscle growth. IGF2 also functions as a major growth factor that promotesand as an autocrine signal in muscle cell growth. The proportion of skeletal muscle in various animal taxa ranges from 40 - 60%. As an essential factor for muscle cell differentiation. IGF2 can promote sheep muscle cell proliferation and differentiation by increasing the expression of <em>MyoD</em> and <em>myogenin</em></p> <p><strong>About the data of the project:</strong></p> <p>LZP-2021/1-0489 project data on lamb samples of the year 2022, or the A22 group, which consists of 76 intensively fattened lambs from six breeds.</p> <p>Exons (5) of the IGF-2 gene and their flanking intron regions were sequenced using Illumina NGS technology (AmpliSeq). The IGF-2 gene has been sequenced in lambs of Latvia (in sheep research in Latvia) for the first time.</p> <p>Information about 16 loci was found compared with the last reference sequences ARS_UI_Ramb_v2.0. Six (6) loci form three groups with complete linkage disequilibrium between polymorphisms. Six new SNP (without ID number) were found.</p> <p>The database contains information on each locus for each lamb and the distribution of alleles and genotypes for each locus across all 76 samples. The data will be used in (1) analysis of Latvian sheep and (2) analysis of association with feed efficiency.</p> <p> </p> <p>The data is the<strong> joint property</strong> of the participants of the LCS project: the University of Latvia and the Latvian University of Life Sciences and Technologies.</p>
Database of NGS results of MSTN gene of intensive fattening lambs of sheep breeds raised in Latvia in 2022 within the framework of project of the Latvian Council of Science LZP-2021/1-0489 project
<p>Project of The Latvian Council of Science (LCS) - LZP-2021/1-0489 project: “<strong>Development of an innovative approach to identify biological determinants involved in the between-animal variation in feed efficiency in sheep farming</strong>.”</p> <p><strong>The aim of the project</strong> is to determine whether the feed efficiency status of Latvian meat sheep breeds could be predicted using a panel of genetic and molecular markers previously found to be associated with divergent Feed efficiency status in a training population of lambs when fed the same diet.</p> <p><strong>Novelty</strong>: to determine the parameters predicting the most productive result of lamb rearing, we set out to develop the cheapest and most effective method for determining markers of feed efficiency - based on molecular and genetic markers obtained from the blood of live lambs.</p> <p><strong>About the project:</strong></p> <p>The costs associated with lambing (buying or keeping sheep) and preparing or purchasing feed are the two largest components of variable costs in sheep raising. Feed costs are high due to poor grain growing conditions in major producing countries, the use of feed grains in ethanol production, and increased competition for land in crop production compared to urban development. Feed efficiency in growing lambs (i.e., the animal’s ability to reach a market or adult body weight (BW) with the least amount of feed intake) is a key factor in the sheep industry. Improving Feed efficiency reduces production costs. Improving Feed efficiency by 5% can bring economic benefits that are up to four times higher than a 5% increase in average daily gain (ADG).</p> <p>Traditionally, meat breeding programs have focused on outputs due mainly to the routine availability of phenotypic data on outputs or correlated traits. Currently, no marker has successfully explained enough of the variability in feed efficiency that they were used as part of a routine improvement program, as well as, according to our data, no genetic parameters for performance and feed efficiency traits are available for sheep. The physiological determinants of feed efficiency or putative biomarkers used to analyze animal-to-animal variation in live lambs could be used as a cost-effective and rapid tool for genetic selection or management decisions.</p> <p>As with other complex traits (also referred to as quantitative or polygenic traits), Feed efficiency is controlled by many genes which are involved in several molecular mechanisms and pathways causing animal-to-animal genetic variation in different biological functions. GWAS results suggested genes impacting lipid and energy metabolism as markers of Feed efficiency. Detection of many variants in these genes is necessary to predict or identify efficient animals accurately.</p> <p>Myostatin (MSTN), a highly conserved member of the transforming growth factor-beta (TGF-b) superfamily, also known as growth/differentiation factor 8 (GDF8), the major regulator of myogenesis, functions as a negative regulator of muscle growth and development in mammals. Myostatin is a transforming growth factor (TGF)-β superfamily member and cannot be classified into the existing TGF-β subfamilies, such as inhibins or bone morphogenic proteins. Mutations of <em>MSTN</em> produce a “double-muscle” phenotype, making it commercially invaluable for improving livestock meat production and providing high-quality human protein. However, mutations at different loci of the <em>MSTN</em> often produce a variety of different phenotypes.</p> <p><strong>About the data of the project:</strong></p> <p>LZP-2021/1-0489 project data on lamb samples of the year 2022, or the A22 group, which consists of 76 intensively fattened lambs from six breeds.</p> <p>Full MSTN gene were sequenced using Illumina NGS technology (AmpliSeq). The MSTN gene has been fully sequenced in lambs of Latvia (in sheep research in Latvia) for the first time.</p> <p>Information about 23 loci were found comparing with the last reference sequences ARS_UI_Ramb_v2.0. Nine (9) loci form three groups with complete linkage disequilibrium between polymorphisms. One new SNP (without ID number) were found.</p> <p>The database contains information on each locus for each lamb and the distribution of alleles and genotypes for each locus across all 76 samples. The data will be used in (1) analysis of Latvian sheep and (2) analysis of association with feed efficiency.</p> <p> </p> <p>The data is the<strong> joint property</strong> of the participants of the LCS project: the University of Latvia and the Latvian University of Life Sciences and Technologies.</p>
Database of NGS results of CAST gene of intensive fattening lambs of sheep breeds in Latvia within the framework of project of the Latvian Council of Science LZP-2021/1-0489 project
<p>Project of The Latvian Council of Science (LCS) - LZP-2021/1-0489 project: “<strong>Development of an innovative approach to identify biological determinants involved in the between-animal variation in feed efficiency in sheep farming</strong>.”</p> <p><strong>The aim of the project</strong> is to determine whether the feed efficiency status of Latvian meat sheep breeds could be predicted using a panel of genetic and molecular markers previously found to be associated with divergent feed efficiency status in a training population of lambs when fed the same diet.</p> <p><strong>Novelty</strong>: to determine the parameters predicting the most productive result of lamb rearing, we set out to develop the cheapest and most effective method for determining markers of feed efficiency - based on molecular and genetic markers obtained from the blood of live lambs.</p> <p><strong>About the project:</strong></p> <p>The costs associated with lambing (buying or keeping sheep) and preparing or purchasing feed are the two largest components of variable costs in sheep raising. Feed costs are high due to poor grain growing conditions in major producing countries, the use of feed grains in ethanol production, and increased competition for land in crop production compared to urban development. Feed efficiency in growing lambs (i.e., the animal's ability to reach a market or adult body weight (BW) with the least amount of feed intake) is a key factor in the sheep industry. Improving feed efficiency reduces production costs. Improving Feed efficiency by 5% can bring economic benefits that are up to four times higher than a 5% increase in average daily gain (ADG).</p> <p>Traditionally, meat breeding programs have focused on outputs due mainly to the routine availability of phenotypic data on outputs or correlated traits. Currently, no marker has successfully explained enough of the variability in feed efficiency that they were used as part of a routine improvement program, as well as according to our data, no genetic parameters for performance and feed efficiency traits are available for sheep. The physiological determinants of feed efficiency or putative biomarkers used to analyze animal-to-animal variation in live lambs could be used as a cost-effective and rapid tool for genetic selection or management decisions.</p> <p>As with other complex traits (also referred to as quantitative or polygenic traits), Feed efficiency is controlled by many genes which are involved in several molecular mechanisms and pathways causing animal-to-animal genetic variation in different biological functions. GWAS results suggested genes impacting lipid and energy metabolism as markers of Feed efficiency. Detection of many variants in these genes is necessary to predict or identify efficient animals accurately.</p> <p>Calpastatin (CAST) plays a key role in skeletal muscle development and is involved in myoblast migration, protein metabolism, apoptosis, muscle growth and development, and fat deposition.</p> <p><strong>About the data of the project:</strong></p> <p>LZP-2021/1-0489 project data on lamb samples of the year 2022, or the A22 group, which consists of 76 intensively fattened lambs from six breeds.</p> <p>Exons (29) of the CAST gene and their flanking intron regions were sequenced using Illumina NGS technology (AmpliSeq). The CAST gene has been sequenced in lambs of Latvia (in sheep research in Latvia) for the first time.</p> <p>Information about 89 loci were found, from which eight were monozygotic or were found only for the rear allele compering with the last reference sequences ARS_UI_Ramb_v2.0. Forty (40) loci form five groups with complete linkage disequilibrium between polymorphisms. Four new SNP (without ID number) were found, and three SNPs were determined to be a single polymorphism.</p> <p>The database contains information on each locus for each lamb and the distribution of alleles and genotypes for each locus across all 76 samples. The data will be used in (1) an analysis of Latvian sheep and (2) an analysis of the association with feed efficiency.</p> <p> </p> <p>The data is the<strong> joint property</strong> of the participants of the LCS project: the University of Latvia and the Latvian University of Life Sciences and Technologies.</p>
Connecting Microscale And Macroscale Damage Models In A Bayesian Framework for Fatigue Damage Prognostics Of CFRP Composites
Composites offer unique advantages for aerospace structures and are increasingly being adopted into newer designs. However, it is also acknowledged that given current understanding of damage mechanisms in composites there is a significant risk with the extensive use of composites materials in aerospace applications. On one hand the uncertainty in damage evolution along lifetime is extremely large, and on the other hand there is a lack of knowledge about the mechanics of the onset, posterior growth, and interactions between several micro-scale damage modes. All these factors lead to the adoption of high safety margins in the design and costly inspection schedules along the service to mitigate the risks. Structural health monitoring for onboard damage diagnosis and prognosis of structural failures has the potential to reduce maintenance costs and improve the safety of the structure through a condition based maintenance scheduling. In this scheme the current damage state of a specific structural element is estimated and further used as the input for a prognostic algorithm that predicts the propagation of damage through time using updated models and based on some knowledge of the future load conditions. A novel damage prognostics framework for composites FRP under fatigue loadings is proposed in this work. The proposed methodology is grounded on physics-based models for evolution of damage at (1) micro-scale, i.e. micro-cracks and delamination, and (2) macro-scale such as stiffness reduction induced by micro-scale damage modes. Through stochastic embedding, these apriori deterministic models are converted to probabilistic models by introducing a modeling error term. This error term is controlled by a probability density function whose parameters are estimated in addition to the rest of "physical" parameters. The probabilistic damage models are then incorporated in a Bayesian filtering algorithm that sequentially updates both, a damage state variable and the set of model parameters, as fresh damage data become available along the fatigue cycling process. Next, these damage models are used to simulate fault propagation with this updated state information to generate a prognostic estimate of the remaining useful life of the structure in a probabilistic sense. The proposed methodology is demonstrated using experimental NDE damage data for micro-crack density, delamination area, and stiffness reduction from an extensive post-impact tension-tension fatigue test performed over several CFRP [0,90]4s laminates.
Online Companion - A Distributionally Robust Framework for Improving the Provision of Passive Balancing Services
<p>Passive balancing refers to the intentional deviations of market actors from their position in energy markets to support the real-time system balancing. Such a service is typically incentivized in a single imbalance pricing mechanism, where all imbalances are settled at a unique price. In this context, this paper presents a novel distributionally robust decision support tool, based on a bi-level model, for a market actor providing passive balancing services. The uncertainty related to the imbalance price is characterized by a Wasserstein metric-based ambiguity set, collecting all distributions in the neighborhoud of a central empirical one. In addition, the bi-level structure of the model allows capturing the interaction between the intentional imbalance position of the actor and the imbalance pricing mechanism. The proposed approach provides optimal passive balancing services in expectation over a worst-case imbalance price distribution, ensuring performance guarantees even if the probability distribution is not perfectly known. With a realistic case study using real-world market data from the Belgian power system, we validate and compare the proposed approach w.r.t. the performance of stochastic programming and robust optimization models. </p>
Trees and Alignments for: A species-level phylogenetic framework and infrageneric classification for the genus Maesa (Primulaceae)
<p>Alignments, gene trees and species trees from phylogenomic analyses in Sumanon et al. (in prep.), A species-level phylogenetic framework and infrageneric classification for the genus Maesa (Primulaceae).</p> <p>Raw sequence data are deposited in Sequence Read Archive (SRA) data available on NCBI servers under BioProject number PRJNA774956. Scripts for all phylogenetic analyses are available at https://github.com/pebgroup/Maesa_sptree.</p>
Dataset related to article "Modifications to the framework regions eliminate chimeric antigen receptor tonic signaling"
<p>Dataset of raw data related to article mentioned at title </p>
Video Recordings of the Research "Roadmap for an Islamic Poverty Framework and Measurement: Stakeholders' Perspectives on the Proposed Model"
<p>The uploaded videos are the data for the research paper "Roadmap for an Islamic Poverty Framework and Measurement: Stakeholders’ Perspectives on the Proposed Model".</p>
A multi-objective Bayesian optimization framework for the synthesis of methanol from syngas using interpretable Gaussian process models
<p>The data sets are synthesized with two reactors (1) Recycle reactor (2) Once through reactor. These reactors have a typical fixed bed of catalysts. The inlet parameter values are varied, and output parameter readings are recorded.</p> <p> </p>
Table S2. Enhancer-gene correlation framework
<p>Outcome of all enhancer-gene correlations with FDR < 0.05</p>
Code and data for the anaylsis of Case study #1 and #2 - Attitudinal Space Framework
<p>This is a folder that contains all the necessary material to replicate the analysis of the manuscript entitled "The Attitudinal Space Framework: Embracing the multidimensionality of attitudinal diversity" (Arbieu, U., Albrecht, J., Böhning-Gaese, K., Lehnen, L., Schleuning, M. & Mueller, T.).</p> <p>Case Study #1 is an analysis of affective polarization in the American electorate based on the ANES dataset (publicly available). "Traits_ANES_Pol2_88-08_V2.csv" contains the answers to the questionnaire (see supporting information of the manuscript for more details) and "Communities_ANES_Pol2_88-08_V2.csv" includes the distribution of respondents in the two partisan groups, twenty years apart. "US_Case_Study.R" is the R code used to conduct the analysis and produce the figures included in the manuscript and the supporting information.</p> <p>Case Study #2 is an analysis of attitudes towards wolves in Germany in regions with and without wolves (data previously published in Arbieu et al., 2019, see manuscript). "DE_Wolf_orig.csv" contains the answers to the questionnaire (see supporting information of the manuscript for more details) and "Communities_DE_Wolforig.csv" includes the distribution of respondents in the two regions. "Wolf_Case_Study.R" is the R code used to conduct the analysis and produce the figures included in the manuscript and the supporting information.</p> <p>Both scripts need the functions in the "multidimFD.R", which was produced by Sébastien Villéger, and downloaded from his website.</p>
A Hydrodynamic-Based Physical Unified Modelling Framework for Simulating Shallow Landslide Local Failures, Mass Release and Debris Flow Run-out Extent Behaviour
<p>Simulation results for manuscript "A Hydrodynamic-Based Physical Unified Modelling Framework for Simulating Shallow Landslide Local Failures, Mass Release and Debris Flow Run-out Extent Behaviour", submitted to Water Resources Research.</p>
A Framework for Designing Efficient Deep Learning-Based Genomic Basecallers
<p>Trained models and basecalled reads.</p>
Data for the metaRegulon framework
<p>The original data for the metaRegulon framework</p>
Habitat loss alters effects of intransitive higher-order competition on biodiversity: a new metapopulation framework
Recent studies have suggested that intransitive competition, as opposed to hierarchical competition, allow more species to coexist. Furthermore, it is recognized that the prevalent paradigm, which assumes that species interactions are exclusively pairwise, may be insufficient. More importantly, whether and how habitat loss, a key driver of biodiversity loss, can alter these complex competition structures and therefore species coexistence remain unclear. We thus present a new simple yet comprehensive metapopulation framework which can account for any competition pattern and more complex higher-order interactions (HOIs) among species. We find that competitive intransitivity increases community diversity and that HOIs generally enhance this effect. Essentially, intransitivity promotes species richness by mitigating competitive exclusion, while HOIs facilitate species coexistence through stabilizing community dynamics. However, variation in species vital rates and habitat loss can weaken or even reverse such higher-order effects, as their interaction can lead to a more rapid decline in competitive intransitivity under HOIs. Thus, it is essential to correctly identify the most appropriate interaction model for a given system before models are used to inform conservation efforts. Overall, our simple model framework provides a more parsimonious explanation for biodiversity maintenance than existing theory.
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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.