cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15482/usda.adc/1529203
title: Rock Chute Design

description: This Excel spreadsheet is included as a tool to design rock chutes for conservation practices. Median size for rock is determined along with the chute hydraulics and dimensions. This spreadsheet is based on "Design of Rock Chutes" by Robinson, Rice, and Kadavy, ASAE Vol. 41(3), pp. 621-626, 1998. One Spreadsheet version is included. Rock_Chute.xls is intended for Excel in Microsoft Office 97. The program was developed by the Iowa design staffa nd modified by the WI-engineering staff. The Excel file (.xls) is password protected. A Glossary is included.
Rock chute design information is consolidated from several sources to provide a comprehensive design tool. The rock slope stability, boundary roughness, and outlet stability of rock chutes are each discussed. Tests were performed in three rectangular flumes and in two full size structures. Angular riprap with a median stone size ranging from 15 to 278 mm was examined on rock chutes with slopes ranging from 2 to 40%. The typical mode of channel failure is described. An empirical prediction equation is presented relating the highest stable discharge on a rock chute to the median stone size and the bed slope. A boundary roughness relationship is also presented that relates the Manning roughness coefficient to the median stone size and bed slope. These tests also suggest that the riprap size required for stability on the slope will remain stable in the outlet reach even with minimal tailwater. This article contains information needed to perform a rock chute design. Rock chutes or loose-riprap-lined channels are used to safely convey water to a lower elevation. These structures provide an alternative method of protecting the soil surface to maintain a stable slope and to dissipate a portion of the flow energy. Watershed management applications for this type of structure are numerous such as channel stabilization, grade control, and embankment overtopping. Depending on the availability and quality of accessible rock materials, rock chutes may offer economic advantages over more traditional structures. Flow cascading down a rock chute is visually pleasing, and these structures offer aesthetic advantages for sensitive locations. Construction of these chutes can be performed with unskilled labor and a comparatively small amount of equipment. A typical rock chute profile is shown in figure 1.
DOI: 10.15482/usda.adc/1529204
title: WinSRFR

description: WinSRFR is a hydraulic analysis tool for surface irrigation systems. The software combines simulation, evaluation, operational analysis, and design functionalities. Intended users are irrigation specialists, extension agents, researchers, consultants, students, and farmers with moderate to advanced knowledge of surface irrigation hydraulics. WinSRFR 5.1 is the fifth major release of the software. The new version offers a reprogrammed simulation engine, an application programming interface, batch simulation capabilities, and enhancements to the user interface.
DOI: 10.5281/zenodo.8156115
title: Dataset for "EuroMod: Modelling European power markets with improved price granularity"

description: Raw and derived results to support the paper "EuroMod: Modelling European power markets with improved price granularity". Description and readme at https://github.com/carlamtmendes/EuroMod.
DOI: 10.5281/zenodo.8156116
title: Dataset for "EuroMod: Modelling European power markets with improved price granularity"

description: Raw and derived results to support the paper "EuroMod: Modelling European power markets with improved price granularity". Description and readme at https://github.com/carlamtmendes/EuroMod.
DOI: 10.15482/usda.adc/1529206
title: USDA Agricultural Research Service- Available Biological Materials

description: The biological materials in this section are unpatented, proprietary intellectual property, available for licensing under a Biological Materials License Agreement: Hybridoma Cell Lines; Microbial Isolates; Cloned Genetic Material; Cell Lines; Viruses; Plasmids. Updated June 2018.
DOI: 10.15482/usda.adc/1529207
title: Data from: Genome-Wide Association Mapping of Loci Associated with Plant Growth and Forage Production under Salt Stress in Alfalfa (Medicago sativa L.)

description: Salinity tolerance is highly desirable to sustain alfalfa production in marginal lands that have been rendered saline. In this study, we used a diverse panel of 198 alfalfa accessions for mapping loci associated with plant growth and forage production under salt stress using genome-wide association studies (GWAS). The plants were genotyped using genotyping-by-sequencing (GBS). A greenhouse procedure was used for phenotyping four agronomic and physiological traits affected by salt stress, including dry weight (DW), plant height (PH), leaf chlorophyll content (LCC), and stomatal conductance (SC). For each trait, a stress susceptibility index (SSI) was used to evaluate plant performance under stressed and non-stressed conditions. Marker-trait association identified a total of 42 markers significantly associated with salt tolerance. They were located on all chromosomes except chromosome 2 based on the alignment of their flanking sequences to the reference genome (Medicago truncatula). Of those identified, 13 were associated with multiple traits. Several loci identified in the present study were also identified in previous reports. BLAST search revealed that 19 putative candidate genes linked to 24 significant markers. Among them, B3 DNA-binding protein, Thiaminepyrophosphokinase and IQ calmodulin-binding motif protein were identified among multiple traits in the present and previous studies. With further investigation, these markers and candidates would be useful for developing markers for marker-assisted selection in breeding programs to improve alfalfa cultivars with enhanced tolerance to salt stress.
DOI: 10.15482/usda.adc/1529208
title: Data from: Identification of Single-Nucleotide Polymorphic Loci Associated with Biomass Yield under Water Deficit in Alfalfa (Medicago sativa L.) Using Genome-Wide Sequencing and Association Mapping

description: Alfalfa is a worldwide grown forage crop and is important due to its high biomass production and nutritional value. However, the production of alfalfa is challenged by adverse environmental factors such as drought and other stresses. Developing drought resistance alfalfa is an important breeding target for enhancing alfalfa productivity in arid and semi-arid regions. In the present study, we used genotyping-by-sequencing and genome-wide association to identify marker loci associated with biomass yield under drought in the field in a panel of diverse germplasm of alfalfa. A total of 28 markers at 22 genetic loci were associated with yield under water deficit, whereas only four markers associated with the same trait under well-watered condition. Comparisons of marker-trait associations between water deficit and well-watered conditions showed non-similarity except one. Most of the markers were identical across harvest periods within the treatment, although different levels of significance were found among the three harvests. The loci associated with biomass yield under water deficit located throughout all chromosomes in the alfalfa genome agreed with previous reports. Our results suggest that biomass yield under drought is a complex quantitative trait with polygenic inheritance and may involve a different mechanism compared to that of non-stress. BLAST searches of the flanking sequences of the associated loci against DNA databases revealed several stress-responsive genes linked to the drought resistance loci, including leucine-rich repeat receptor-like kinase, B3 DNA-binding domain protein, translation initiation factor IF2, and phospholipase-like protein. With further investigation, those markers closely linked to drought resistance can be used for MAS to accelerate the development of new alfalfa cultivars with improved resistance to drought and other abiotic stresses.
DOI: 10.15482/usda.adc/1529209
title: Data from: Chondroitin sulfate disaccharides modified the structure and function of the murine gut microbiome under healthy and stressed conditions

description: Chondroitin sulfate (CS) has been widely used for medical and nutraceutical purposes due to its roles in maintaining tissue structural integrity. We investigated if CS disaccharides may act as a bioactive compound and modulate gut microbial composition in mice. Our data show that CS disaccharides supplementation for 16 days significantly reduced blood LPS in the mice experiencing exhaustive exercise stress. CS disaccharides partially restored total fecal short-chain fatty acids from the level significantly repressed in mice under the stress. Our findings demonstrated that CS was likely butyrogenic and resulted in a significant increase in fecal butyrate concentration. CS disaccharides had a profound impact on gut microbial composition, affecting the abundance of 13.6% and 7.3% Operational Taxonomic Units in fecal microbial communities in healthy and stressed mice, respectively. CS disaccharides reduced the prevalence of inflammatory Proteobacteria. Together, our findings demonstrated that CS may ameliorate stress-induced intestinal inflammation. Furthermore, CS significantly increased intestinal Bacteroides acidifaciens population, indirectly exerting its immunomodulatory effect on the intestine. CS disaccharides had a significant impact on a broad range of biological pathways under stressed condition, such as ABC transporters, two-component systems, and carbohydrate metabolism. Our results will facilitate the development of CS as a bioactive nutraceutical.
DOI: 10.5519/qd.d3749bkn
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (44 records)
DOI: 10.15482/usda.adc/1529210
title: Data from: Fine mapping of the soybean aphid-resistance genes Rag6 and Rag3c from Glycine soja 85-32

description: Rag6 and Rag3c were delimited to a 49-kb interval on chromosome 8 and a 150-kb interval on chromosome 16, respectively. Structural variants in the exons of candidate genes were identified.
The soybean aphid, an invasive species, has significantly threatened soybean production in North America since 2000. Host-plant resistance is known as an ideal management strategy for aphids. Two novel aphid-resistance loci, Rag6 and Rag3c, from Glycine soja 85-32, were previously detected in a 10.5-cM interval on chromosome 8 and a 7.5-cM interval on chromosome 16, respectively. Defining the exact genomic position of these two genes is critical for improving the effectiveness of marker-assisted selection for aphid resistance and for identification of the functional genes. To pinpoint the locations of Rag6 and Rag3c, four populations segregating for Rag6 and Rag3c were used to fine map these two genes. The availability of the Illumina Infinium SoySNP50K/8K iSelect BeadChip, combined with single-nucleotide polymorphism (SNP) markers discovered through the whole-genome re-sequencing of E12901, facilitated the fine mapping process. Rag6 was refined to a 49-kb interval on chromosome 8 with four candidate genes, including three clustered nucleotide-binding site leucine-rich repeat (NBS–LRR) genes and an amine oxidase encoding gene. Rag3c was refined to a 150-kb interval on chromosome 16 with 11 candidate genes, two of which are a LRR gene and a lipase gene. Moreover, by sequencing the whole-genome exome-capture of the resistant source (E12901), structural variants were identified in the exons of the candidate genes of Rag6 and Rag3c. The closely linked SNP markers and the candidate gene information presented in this study will be significant resources for integrating Rag6 and Rag3c into elite cultivars and for future functional genetics studies.
DOI: 10.15482/usda.adc/1529211
title: Data from: Development and Validation of KASP Markers for Wheat Streak Mosaic Virus Resistance Gene Wsm2

description: Wheat streak mosaic virus (WSMV) can cause significant yield loss in wheat (Triticum aestivum L.) in the Great Plains of North America. A recently identified WSMV resistance gene, Wsm2, was mapped to chromosome 3BS in germplasm line 'CO960293–2'. Effective genetic markers tightly linked to the gene will enhance the selection of WSMV-resistant lines through marker-assisted selection. We have mapped Wsm2 using a high-density map developed from the wheat 90K Infinium iSelect single-nucleotide polymorphism (SNP) array with recombinant inbred lines from the cross between CO960293–2 and susceptible cultivar 'TAM 111'. Array-based SNPs that mapped within 4 cM of Wsm2 on chromosome 3BS were converted to Kompetitive Allele Specific Polymerase Chain Reaction (KASP) assays in this study. Six KASP SNPs were validated in two doubled haploid populations developed from crosses of 'RonL' × 'Ripper' and 'Snowmass' × 'Antero'. RonL and Snowmass possess the Wsm2 gene from CO960293–2. Three closely linked KASP SNPs, converted from IAAV6442, BS00018764_51, and wsnp_Ra_c16264_24873670, showed high sensitivity and specificity (0.83 ≤ sensitivity ≤ 0.97, 0.89 ≤ specificity ≤ 0.99). The latter two were also validated in six F2 breeding populations. These three KASP SNPs were effective in differentiating resistant and susceptible genotypes. Comparative mapping was performed using sequences of SNPs flanking Wsm2 and identified candidate genes and regions in Brachypodium and rice (Oryza sativa L. ssp. japonica). The KASP SNPs developed in this study should be useful for marker-assisted selection of Wsm2 in wheat breeding programs, and the newly constructed map will also facilitate map based cloning of Wsm2.
DOI: 10.15482/usda.adc/1529212
title: Data from: Key molecular processes of the diapause to post‐diapause quiescence transition in the alfalfa leafcutting bee Megachile rotundata identified by comparative transcriptome analysis

description: Insect diapause (dormancy) synchronizes an insect's life cycle to seasonal changes in the abiotic and biotic resources required for development and reproduction. Transcription analysis of diapause to post‐diapause quiescent transition in the alfalfa leafcutting bee Megachile rotundata Fabricius identifies 643 post‐diapause up‐regulated gene transcripts and 242 post‐diapause down‐regulated transcripts. The log2 fold change in gene expression levels ranges from −5 to 7. Transcripts from several pivotal diapause‐related processes, including chromatin remodelling, cellular signalling pathways, microRNA processing, anaerobic glycolysis, cell cycle arrest and neuroendocrine control, are identified as being differentially expressed during the diapause to post‐diapause transition. In conjunction with studies from other insect species, the data indicate that there are several common mechanisms of diapause control and maintenance.
DOI: 10.15482/usda.adc/1529213
title: Data from: The Majority of Genotypes of the Virulence Gene inlA Are Intact among Natural Watershed Isolates of Listeria monocytogenes from the Central California Coast

description: Internalin A is an essential virulence gene involved in the uptake of the foodborne pathogen Listeria monocytogenes into host cells. It is intact in clinical strains and often truncated due to Premature Stop Codons (PMSCs) in isolates from processed foods and processing facilities. Less information is known about environmental isolates. We sequenced the inlA alleles and did Multi Locus Variable Number Tandem Repeat Analysis (MLVA) on 112 L. monocytogenes isolates from a 3-year period from naturally contaminated watersheds near a leafy green growing area in Central California. The collection contained 14 serotype 1/2a, 12 serotype 1/2b, and 86 serotype 4b strains. Twenty-seven different inlA alleles were found. Twenty-three of the alleles are predicted to encode intact copies of InlA, while three contain PMSCs. Another allele has a 9-nucleotide deletion, previously described for a clinical strain, indicating that it is still functional. Intact inlA genes were found in 101 isolates, and 8 isolates contained the allele predicted to contain the 3-amino acid deletion. Both allele types were found throughout the 3-year sampling period. Three strains contained inlA alleles with PMSCs, and these were found only during the first 3 months of the study. SNP analysis of the intact alleles indicated clustering of alleles based on serotype and lineage with serotypes 1/2b and 4b (lineage I strains) clustering together, and serotype 1/2a (lineage II strains) clustering separately. The combination of serotype, MLVA types, and inlA allele types indicate that the 112 isolates reflect at least 49 different strains of L. monocytogenes. The finding that 90% of environmental L. monocytogenes isolates contain intact inlA alleles varies significantly from isolates found in processing plants. This information is important to public health labs and growers as to the varieties of L. monocytogenes that could potentially contaminate fresh produce in the field by various means.
DOI: 10.6084/m9.figshare.23696367
title: <strong>Figure 3.</strong> <strong>Depolymerization of actin filaments has no effect on the decline in the level of ATP induced by blockade of ATP production in either growth cones or cell bodies.</strong>

description: The growth cone was defined as the distal 10 microns of the axon shaft. If a growth cone exhibited lamellipodia then the distal most extent of the lamellipodium was taken as the distal most point on the growth cone, if not the distal most extent of the axon shaft was used as the defining distal point. Quantitative analysis of images was performed using Zeiss AxioVision software. The region of interest encompassing the growth cone was outlined and measurements of mean pixel fluorescence intensity in all relevant channels was determined for generation of ratios. For each channel, the mean intensity value obtained from the background of the image not containing any cells was subtracted from the mean intensity in the growth cone region of interest prior to determination of the ratio. Acquisition settings were chosen to generate maximum pixel values between 20-30% of the dynamic range to allow for detection of both decreases and increases in intensity in response to experimental treatments.
DOI: 10.6084/m9.figshare.23696367.v1
title: <strong>Figure 3.</strong> <strong>Depolymerization of actin filaments has no effect on the decline in the level of ATP induced by blockade of ATP production in either growth cones or cell bodies.</strong>

description: The growth cone was defined as the distal 10 microns of the axon shaft. If a growth cone exhibited lamellipodia then the distal most extent of the lamellipodium was taken as the distal most point on the growth cone, if not the distal most extent of the axon shaft was used as the defining distal point. Quantitative analysis of images was performed using Zeiss AxioVision software. The region of interest encompassing the growth cone was outlined and measurements of mean pixel fluorescence intensity in all relevant channels was determined for generation of ratios. For each channel, the mean intensity value obtained from the background of the image not containing any cells was subtracted from the mean intensity in the growth cone region of interest prior to determination of the ratio. Acquisition settings were chosen to generate maximum pixel values between 20-30% of the dynamic range to allow for detection of both decreases and increases in intensity in response to experimental treatments.
DOI: 10.15482/usda.adc/1529214
title: Data from: Metabolic Coevolution in the Bacterial Symbiosis of Whiteflies and Related Plant Sap-Feeding Insects

description: Genomic decay is a common feature of intracellular bacteria that have entered into symbiosis with plant sap-feeding insects. This study of the whitefly Bemisia tabaci and two bacteria (Portiera aleyrodidarum and Hamiltonella defensa) cohoused in each host cell investigated whether the decay of Portiera metabolism genes is complemented by host and Hamiltonella genes, and compared the metabolic traits of the whitefly symbiosis with other sap-feeding insects (aphids, psyllids, and mealybugs). Parallel genomic and transcriptomic analysis revealed that the host genome contributes multiple metabolic reactions that complement or duplicate Portiera function, and that Hamiltonella may contribute multiple cofactors and one essential amino acid, lysine. Homologs of the Bemisia metabolism genes of insect origin have also been implicated in essential amino acid synthesis in other sap-feeding insect hosts, indicative of parallel coevolution of shared metabolic pathways across multiple symbioses. Further metabolism genes coded in the Bemisia genome are of bacterial origin, but phylogenetically distinct from Portiera, Hamiltonella and horizontally transferred genes identified in other sap-feeding insects. Overall, 75% of the metabolism genes of bacterial origin are functionally unique to one symbiosis, indicating that the evolutionary history of metabolic integration in these symbioses is strongly contingent on the pattern of horizontally acquired genes. Our analysis, further, shows that bacteria with genomic decay enable host acquisition of complex metabolic pathways by multiple independent horizontal gene transfers from exogenous bacteria. Specifically, each horizontally acquired gene can function with other genes in the pathway coded by the symbiont, while facilitating the decay of the symbiont gene coding the same reaction.
DOI: 10.6084/m9.figshare.23696385
title: <strong>Figure 1.</strong> <strong>Actin filament depolymerization has no effect on the decrease in the cytosolic ATP level induced by blockade of ATP production in forebrain neurons.</strong>

description: The growth cone was defined as the distal 10 microns of the axon shaft. If a growth cone exhibited lamellipodia then the distal most extent of the lamellipodium was taken as the distal most point on the growth cone, if not the distal most extent of the axon shaft was used as the defining distal point. Quantitative analysis of images was performed using Zeiss AxioVision software. The region of interest encompassing the growth cone was outlined and measurements of mean pixel fluorescence intensity in all relevant channels was determined for generation of ratios. For each channel, the mean intensity value obtained from the background of the image not containing any cells was subtracted from the mean intensity in the growth cone region of interest prior to determination of the ratio. Acquisition settings were chosen to generate maximum pixel values between 20-30% of the dynamic range to allow for detection of both decreases and increases in intensity in response to experimental treatments.
DOI: 10.6084/m9.figshare.23696385.v1
title: <strong>Figure 1.</strong> <strong>Actin filament depolymerization has no effect on the decrease in the cytosolic ATP level induced by blockade of ATP production in forebrain neurons.</strong>

description: The growth cone was defined as the distal 10 microns of the axon shaft. If a growth cone exhibited lamellipodia then the distal most extent of the lamellipodium was taken as the distal most point on the growth cone, if not the distal most extent of the axon shaft was used as the defining distal point. Quantitative analysis of images was performed using Zeiss AxioVision software. The region of interest encompassing the growth cone was outlined and measurements of mean pixel fluorescence intensity in all relevant channels was determined for generation of ratios. For each channel, the mean intensity value obtained from the background of the image not containing any cells was subtracted from the mean intensity in the growth cone region of interest prior to determination of the ratio. Acquisition settings were chosen to generate maximum pixel values between 20-30% of the dynamic range to allow for detection of both decreases and increases in intensity in response to experimental treatments.