cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/bhxn64ytnn.1
title: Inbreeding coefficients and runs of homozygosity islands in Brazilian water buffalo - Supplementary material

description: Supplementary material from the paper "Inbreeding coefficients and runs of homozygosity islands in Brazilian water buffalo" published in the Journal of Dairy Science (https://doi.org/10.3168/jds.2020-18397). ABSTRACT - Characterization of autozygosity is relevant to monitor genetic diversity and manage inbreeding levels in breeding programs. Identification of autozygosity hotspots can unravel genomic regions targeted by selection for economically important traits and can help identify candidate genes for selection. In this study, we estimated the inbreeding levels of a Brazilian population of Murrah buffalo undergoing selection for milk production traits, particularly milk yield. We also studied the distribution of runs of homozygosity (ROH) islands and identified putative genes and quantitative trait loci (QTL) under selection. We genotyped 422 Murrah buffalo for 51,611 SNP; 350 of these had ROH longer than 10 Mb, indicating the occurrence of inbreeding in the last 5 generations. The mean length of the ROH per animal was 4.28 ± 1.85 Mb. Inbreeding coefficients were calculated from the genomic relationship matrix, the pedigree, and the ROH, with estimates varying between 0.242 and 0.035. Inbreeding estimates from the pedigree had a low correlation with the genomic estimates, and estimates from the genomic relationship matrix were much higher than those from the pedigree or the ROH. Signatures of selection were identified in 6 genomic regions, located on chromosomes 1, 2, 3, 5, 16, and 18, encompassing a total of 190 genes and 174 QTL. Many of the genes (e.g., APRT and ACSF3) and QTL identified are related to milk production traits, such as milk yield, milk fat yield and percentage, and milk protein yield and percentage. Other genes are associated with reproduction and immune response traits as well as morphological aspects of the buffalo species. Inbreeding levels in this population are still low but are increasing due to selection and should be managed to avoid future losses due to inbreeding depression. The proximity of genes linked to milk production traits with genes associated with reproduction and immune system traits suggests the need to include these latter genes in the breeding program to avoid negatively affecting them due to selection for production traits.
DOI: 10.17632/64snbt988z.1
title: UNRAVELLING CITIZENS' STORYLINES THROUGH A SOCIO-HYDROLOGICAL OBSERVATORY FOR WATER SECURITY: FROM CONCEPTUALIZATION TO A BRAZILIAN CASE STUDY– SUPPLEMENTARY MATERIAL

description: This document provides a broad description regarding the paper Unravelling Citizens' Storylines Through A Socio-Hydrological Observatory for Water Security: From conceptualization to a Brazilian case study (Souza et al, 2020). First, a description of the employed variables allows readers to understand how the task in this experiment was developed and how each question quantifies respective variables. Then, a table with results is provided.
DOI: 10.17632/87zz9hytp7.1
title: Computer Designed PRC2 Inhibitor, EBdCas9, Reveals Functional TATA boxes in Distal Promoter Regions

description: This is Raw Data Omics, star methods and supplemental table.
DOI: 10.17632/cg2ys63ps2.1
title: Data S1 and Data S2: Labyrinthula sp. genome

description: Supplementary Datasets associated with the paper "First genome of Labyrinthula sp., an opportunistic seagrass pathogen, reveals novel insight into marine protist phylogeny, ecology and CAZyme cell-wall degradation", Microbial Ecology, DOI: 10.1007/s00248-020-01647-x. Data S1: Assembled genome, transcriptome, gene model and sequences of predicted proteins/transcripts, and ortholog annotation output. The genome contains contig IDs that match those in the GFF annotation file. Data S2: Super-alignment of mitochondrial genes and phylogenetic tree in Newick format.
DOI: 10.17632/scj72c967f.1
title: scripts for YJCPH_110030

description: These scripts are used for Enriched Galerkin Discretization for Modeling Poroelasticity and Permeability Alteration in Heterogeneous Porous Media It has been tested only in the Linux operating system, and the main dependencies are Numpy (≥ 1.16.5), FEniCS (≥ 2018.1.0) with PETSc (≥ 3.10.5) and petsc4py (≥ 3.10), and multiphenics (≥ 0.2.0).
DOI: 10.17632/b2wvnbnpj9.1
title: The Impact of Covid-19 Pandemic on the Global Economy: Emphasis on Poverty Alleviation and Economic Growth

description: Data for 170 countries in respect to the impact of covid-19 on the global economy
DOI: 10.17632/k6ykcjjh7z.1
title: Vaccine Files

description: Design of epitope-based vaccines from tRNA peptides. The Vaccine Data Used And Download Paths to Intermediate Results are available. We initially obtained all available sequences of tRNA nucleotides from GtRNAdb from various species. It was then translated from the EMBOSSTranseq tool into equivalent peptide sequences tREP’s. These tREPs were subsequently screened for complete structural peptide selection via VaxiJen v2.0 to predict antigenic peptides. Depending on T-cell epitope prediction, these antigenic peptides are further screened based on major histocompatibility complex (MHC) class I binding, proteasomal C terminal cleavage, and TAP transport efficiency using NetCTL1.2 Server. The promising epitopes were then selected, based on cell penetration (CellPPD), toxicity (ToxinPred), antigenicity (VaxiJen v2.0), allergenicity (AllerTop v.2.0), conservancy (ECA IEDB Suite), and higher immunogenicity (C1I IEDB Suite) filtration. These epitopes should then be identified by (MHC) I alleles which are present in the endoplasmic reticulum, so that it can bind to them, and can be brought to the surface of the cell, where a T-cell or a B-cell can identify to produce an antibody. In order to bind these epitopes with alleles, the 3D structures of epitopes were generated and the corresponding allele was retrieved from RCSB to perform docking. The stability and conformational changes of these two bindings along with their dynamic interactions are then analyzed, through molecular dynamics.
DOI: 10.17632/y7c54rmh84.1
title: Elemental Adsorption and Interface Reaction in Direct Active Bonding of GaAs to GaAs using Sn-Ag-Ti Solder filler

description: In this work, there are three research hypothesizes: First, the active element Ti only adsorbs at the interface of the joint but not involved in chemical reactions to form new substances; Second, Titanium does not form obvious adsorption at the interface, but takes part in reaction with GaAs substrate to form new phases; Third, at the bonding interface, there are both obvious titanium adsorption and new phases formation, which may be continuous or intermittent. It is very necessary to analyze the experimental data to understand the way and role of titanium in low temperature bonding. Although disrupt opinions have been given on the role of Ti in active bonding of filler alloys on ceramics, most of these experimental data are obtained from the samples welded at high temperature and the mechanism of wetting and welding is discussed at high temperature. However, first of all, the bonding temperature is a key parameter of the active solder wetting the substrate, whether the active solder following the high temperature wetting mechanism to achieve wetting with the substrate at low temperature needs to be further studied and analyzed; secondly, the reaction environment temperature between the active solder and the substrate at low temperature is also different from high temperature. Therefore, the behavior of active elements in the interface may be affected, which may cause some difference from that of high temperature brazing. And there will also be great differences in welding dynamic process. All of these are needed to be analyzed and discussed in detail both experimentally and theoretically. In our experimental data, titanium element is found to obviously take part in the active bonding between GaAs substrate and Sn3.5Ag4Ti(Ce,Ga) alloy filler. According to the transmission electron microscopy (TEM) analysis, the titanium elements segregate successively at the interface and the element gallium included in GaAs is dissolved into the molten alloy strongly. In addition, there is a resultant formed discontiniously along the interface which is identified as Ga4Ti5, but no arsenic compounds were found. Underlying wetting and reaction mechanism were elucidated based on the thermodynamics theories and the molecular dynamic (MD) model. The fitted results analyzed are all based on theoretical basis and experimental data which show that the chemical reaction and the adsorption of active elements may control the reactive wetting of Sn3.5Ag4Ti(Ce,Ga) filler alloy on Gallium arsenide together. The wetting behavior should be the result of the interaction of titanium adsorption and chemical reaction together.
DOI: 10.17632/f4ysyn9t58.3
title: Alternative Lengthening of Telomeres is a Self-Perpetuating Process in ALT-Associated PML Bodies

description: This data include the original images of western blots and microscopy for the paper titled "Alternative Lengthening of Telomeres is a Self-Perpetuating Process in ALT-Associated PML Bodies" Alternative lengthening of telomeres (ALT) is mediated by break-induced replication (BIR), but how BIR is regulated at telomeres is poorly understood. Here, we show that telomeric BIR is a self-perpetuating process. By tethering PML-IV to telomeres, we induced telomere clustering in ALT-associated PML bodies (APBs) and a POLD3-dependent ATR response at telomeres, showing that BIR generates replication stress. Ablation of BLM helicase activity in APBs abolishes telomere synthesis but causes multiple chromosome bridges between telomeres, revealing a function of BLM in processing inter-telomere BIR intermediates. Interestingly, the accumulation of BLM in APBs requires its own helicase activity and POLD3, suggesting that BIR triggers a feedforward loop to further recruit BLM. Enhancing BIR induces PIAS4-mediated TRF2 SUMOylation, and PIAS4 loss deprives APBs of repair proteins and compromises ALT telomere synthesis. Thus, a BLM-driven and PIAS4-mediated feedforward loop operates in APBs to perpetuate BIR, providing a critical mechanism to extend ALT telomeres.
DOI: 10.17632/rrdc4xsk2h.3
title: Phylogenomics identifies a new major subgroup of apicomplexans, Marosporida class. nov., with extreme apicoplast genome reduction

description: - Nuclear and Plastid multi-protein matrices for phylogenomics analyses - Apicoplast genomes of Rhytidocystis sp1 and sp2, Siedleckia nematoides, and Eleutheroschizon dubosqi - Transcriptome & WGS assemblies
DOI: 10.17632/g7mnwgx6bh.1
title: Five tea samples; UV and MS raw data and processed data

description: UV acquisition data (275 and 365 nm), mass acquisition data, the processed data obtained from the Python script.
DOI: 10.17632/jysv6g942s.1
title: LINF_040005000

description: calcium-translocating P-type ATPase; Leishmania infantum
DOI: 10.17632/jx49rrv75r.1
title: LINF_040005100

description: pteridine transporter; Leishmania infantum
DOI: 10.17632/c3f7p377zp.1
title: LINF_040005200

description: cAMP-specific phosphodiesterase; Leishmania infantum
DOI: 10.17632/4njcc9tfdn.1
title: LINF_040005400

description: CCCH/Zn finger-containing protein; Leishmania infantum
DOI: 10.17632/bbbgynbyn3.1
title: LINF_040005600

description: hypothetical protein - conserved; Leishmania infantum
DOI: 10.17632/gv78x64n23.1
title: LINF_040005700

description: DNA topoisomerase type IB small subunit; Leishmania infantum
DOI: 10.17632/xd22vrrd3t.1
title: LINF_040006600

description: hypothetical protein - conserved; Leishmania infantum
DOI: 10.17632/2btx6vzp4w.1
title: LINF_040006700

description: hypothetical protein - conserved; Leishmania infantum
DOI: 10.17632/s3h3nhf4p8.1
title: LINF_040006800

description: hypothetical protein - conserved; Leishmania infantum
DOI: 10.17632/47nzf6ffcg.3
title: Economic impacts of adoption of fall armyworm management practices on household welfare of smallholder maize farmers in Ghana

description: This study analyzed the factors influencing adoption of fall armyworm management practices (FAW MPs) and the impacts of the adoption of these management practices on maize yield and household maize income. The findings show that relative to non-adoption, the joint adoption of a combination of early planting and pesticide application had greater impacts on both maize yield and household maize income. Our findings indicate that efforts should be geared towards training farmers to practice different combination of the FAW MPs in controlling fall armyworm on their farms while improving their access to support services such as extension and input supply. The dataset is a primary data with most of the variables coded in the binary form and some as dummy variables. The data can be analyzed and interpreted using the multinomial endogenous switching regression model in STATA through the usage of the selmlog command.
DOI: 10.17632/k2mv2xbgk5.1
title: Geochronological and geochemical data of rocks from Offshore Islands, East China Sea

description: Table 1. Zircon LA–ICP–MS isotopic analyses of volcanic samples. Table 2. Major (wt.%) and trace element (ppm) compositions of volcanic rocks from Fuying and Dayushan Islands. Table 3. Whole-rock Sr–Nd–Pb isotopic compositions of rhyolitic rocks from Fuying and Dayushan Islands.
DOI: 10.17632/rrn32wbtfg.1
title: Review of ZIKV production with Brazilian researchers from 1945 to 2017

description: This document presents a massive review of ZIKV production with Brazilian researchers from 1945 to 2017. It contains the year and month of release, plus companies and institutions implicated in these productions, such as Universities, Labs and Government Agencies.
DOI: 10.17632/ws9pwxkbb2.2
title: Case Studies for Optimal Placement and Control of Valves and Chlorine Boosters in Water Networks

description: EPANET models and corresponding information needed to formulate the problem of optimal placement and control of valves and chlorine boosters in water networks for case studies used in - "Tightened Polyhedral Relaxations of a Non-Convex Mixed Integer Program for Optimal Placement and Control of Valves and Chlorine Boosters in Water Networks" by Filippo Pecci, Ivan Stoianov and Avi Ostfeld (2020) - "Convex Heuristic for Optimal Placement and Control of Valves and Chlorine Boosters in Water Networks" by Filippo Pecci, Ivan Stoianov and Avi Ostfeld (2020) Acknowledgments: Filippo Pecci and Ivan Stoianov are supported by EPSRC (EP/P004229/1, Dynamically Adaptive and Resilient Water Supply Networks for a Sustainable Future). Avi Ostfeld is supported by the Israel Science Foundation (grant No. 555/18).
DOI: 10.17632/87y543y3rm.1
title: Omics and transgenic analyses reveal that salvianolic acid B exhibits its anti-inflammatory effects through inhibiting Mincle-Syk related pathway in macrophages

description: The data are supplemental Figures and Tables for "Omics and transgenic analyses reveal thatsalvianolic acid B exhibits its anti-inflammatory effects through inhibiting Mincle-Syk related pathway in macrophages".
DOI: 10.15129/18d9dfa4-d356-4d21-97d9-4a890dad7eca
title: Data for: "Resonant very low- and ultra low frequency digital signal reception using a portable atomic magnetometer"

description: Dataset for "Resonant very low- and ultra low frequency digital signal reception using a portable atomic magnetometer". Data is recorded in post-analysis xlsx and csv formats with explanatory file headers and plotted data.
DOI: 10.17632/mn7x93562v.2
title: Measurement of a corpus of business process models designed in existing business process modelling approaches

description: This document contains the measurements for the redundancy, complexity and the minimal number of change operations for 12 business processes modelled in several business processes modelling approaches. The BPPLE approach is not included.
DOI: 10.17632/whtc75rj55.1
title: An open-source parallel code for computing the spectral fractional Laplacian on 3D complex geometry domains

description: We present a spectral element algorithm and open-source code for computing the fractional Laplacian defined by the eigenfunction expansion on finite 2D/3D complex domains with both homogeneous and nonhomogeneous boundaries. We demonstrate the scalability of the spectral element algorithm on large clusters by constructing the fractional Laplacian based on computed eigenvalues and eigenfunctions using up to thousands of CPUs. To demonstrate the accuracy of this eigen-based approach for computing the factional Laplacian, we approximate the solutions of the fractional diffusion equation using the computed eigenvalues and eigenfunctions on a 2D quadrilateral, and on a 3D cubic and cylindrical domain, and compare the results with the contrived solutions to demonstrate fast convergence. Subsequently, we present simulation results for a fractional diffusion equation on a hand-shaped domain discretized with 3D hexahedra, as well as on a domain constructed from the Hanford site geometry corresponding to nonzero Dirichlet boundary conditions. Finally, we apply the algorithm to solve the surface quasi-geostrophic (SQG) equation on a 2D square with periodic boundaries. Simulation results demonstrate the accuracy, efficiency, and geometric flexibility of our algorithm and that our algorithm can capture the subtle dynamics of anomalous diffusion modeled by the fractional Laplacian on complex geometry domains. The included open-source code is the first of its kind.
DOI: 10.17632/3cp24349jx.1
title: AlgerianChidrenCAPT_1_4

description: The contains pronunciations from nine pupils aging from 5 to 8 years; each of them uttered a set of 16 sequences (words or group of words). The chosen words included some difficulties for the young learners such as the long vowels and the words written with more than one connected component.
DOI: 10.17632/ttmgw6rjct.1
title: COL7A1 Ex3 RNP HDR approach NGS data

description: NGS data for primary WT as wells as primary and immortalized RDEB keratinocytes treated with RNPs in combination with HDR templates. Also includes off-target analysis data and hypothermic treatment data.
DOI: 10.17632/pf9x7375vd.1
title: Additional Data for "Advanced analysis of satellite data reveals ground deformation precursors to the Brumadinho Tailings Dam collapse".

description: 1. ISBAS InSAR time-series data for locations on the Brumadinho tailings dam. 2. Brumadinho tailings dam failure prediction data. 3. Daily rainfall data for the Cercadinho-F501 meteorological station. 4. Daily rainfall data for the Rola Moça-A555 meteorological station. 5. ISBAS InSAR time-series data for locations on the Sul Superior tailings dam.
DOI: 10.17632/2ww38jd2db.1
title: GOHAI instituzionalized elderly

description: The dataset was used in a cross-sectional study aimed to assess the Oral Health status and the impact on quality on life among the institutionalized elderly in Southern Italy and to analyzed the Oral Health Related Quality of Life (OHRQoL). From July 2018 to June 2019, a face to face interview was conducted with institutionalized elderly of 10 long-term care facilities randomly selected from a public available frame of all facilities accredited by Regional Health System in Southern Italy. The questionnaire covered a broad range of issues related to sociodemographic characteristics of the participants (gender, age, marital status, education level, residential area and previous occupation), smoking habits, health status (chronic disease), dental attendance and oral hygiene behavior. It was retrieved from patient medical records eventual cognitive impairments evaluated by clinical using tests of cognitive function such as Mini-Mental State Exam (MMSE) and Short Portable Mental Status Questionnaire (SPMSQ). Participants were also questioned about their feelings about their need for dental treatment. The dental health status was assessed recording the decayed, missing or filled dental elements due to carious lesions (DMFT) index, the presence of visible plaque (PI) index and gingival condition (GI) index and the use of any prosthesis. The influence of dental health status self-perceived value of life was assessed using the Geriatric Oral Health Assessment Index (GOHAI). Multivariate analyses were conducted using stepwise multivariate logistic regression modelling techniques to investigate the following outcomes: GOHAI about self-perceived need of dental care, GOHAI abut the use of a prosthesis and about DMFT index. To assess QHRQoL, the participants were asked to respond to 12 different statements of GOHAI. The GOHAI score was calculated by summing the scores to each statement. The total score ranged from 12 to 60. It was divided into three categories: good (57-60), fair (51-56) and poor (less than 50) rating of oral health, indicating, respectively, good, moderate and very compromised QHRQoL. The response rate was 84.5%. In the sample, 18.4% reported frequent tooth-brushing and 39.9% reported the need of dental care. Less than a third of the participants had a GOHAI score 50 that is suggestive of very compromised Oral Health Related Quality of Life. The DMFT index was 26.4. The GOHAI score was significantly better for elderly individuals who no self-perceived need of dental care, who use a removable complete denture and with lower DMFT index. The findings of this study highlighted the burden of oral condition of long-term facility residents, the high impact of its on their OHRQoL and the need to improve oral health in this context by enhancing multidisciplinary approach.
DOI: 10.17632/tnx2fdn2hc.1
title: ADB_IE_MP_2015_NEERMAN

description: Data related to "Divide and Prosper? Impacts of power-distribution feeder separation on household energy-use, irrigation, and crop production" article is published here.
DOI: 10.17632/6h4xrydwfb.2
title: ADG: Automated generation and evaluation of many-body diagrams II. Particle-number projected Bogoliubov many-body perturbation theory

description: We describe the second version (v2.0.0) of the code ADG that automatically (1) generates all valid off-diagonal Bogoliubov many-body perturbation theory diagrams at play in particle-number projected Bogoliubov many-body perturbation theory (PNP-BMBPT) and (2) evaluates their algebraic expression to be implemented for numerical applications. This is achieved at any perturbative order p for a Hamiltonian containing both two-body (four-legs) and three-body (six-legs) interactions (vertices). All valid off-diagonal BMBPT diagrams of order p are systematically generated from the set of diagonal, i.e.,unprojected, BMBPT diagrams. The production of the latter were described at length in Arthuis et al. (2019) dealing with the first version of ADG. The automated evaluation of off-diagonal BMBPT diagrams relies both on the application of algebraic Feynman’s rules and on the identification of a powerful diagrammatic rule providing the result of the remaining p-tuple time integral. The new diagrammatic rule generalizes the one already identified in Arthuis et al. (2019) to evaluate diagonal BMBPT diagrams independently of their perturbative order and topology. The code ADG is written in Python3 and uses the graph manipulation package NetworkX. The code is kept flexible enough to be further expanded throughout the years to tackle the diagrammatics at play in various many-body formalisms that already exist or are yet to be formulated.