cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.16595999.v2
title: ML tree of 456 mapped 7PET genomes

description: Maximum-likelihood phylogeny of the 456 mapped 7PET genomes.<br>For variant calling, Illumina short reads were mapped against the novel reference strain CNRVC190243 genome. We mapped all 242 short read sets from 2018-2019 Yemeni <i>V. cholerae </i>isolates, provided read mapping were mapped at a sufficient depth (see below); we also mapped read sets from 218 contextual <i>V. cholerae</i> isolates linked to 7PET-T13 sublineage. Reads were trimmed with Trimmomatic, mapped to both CNRVC190243 reference chromosomes with BWA-MEM. Mapped genomes with an average read depth below 5x over the two chromosomes (n = 4, all from the novel Yemen read sets) were deemed of insufficient read depth and were excluded, for a final set of 456 mapped <i>V. cholerae</i> 7PET genomes. We used the software suite samtools/bcftools v1.9 to call variants with a minimum coverage of 10x read depth, excluding indels. Resulting consensus sequences were combined and processed with snp-sites (Page et al., 2016) to produce a single nucleotide polymorphism (SNP) alignment featuring 2,092 positions. <br>Alternative hypotheses of tolpologies were formulated based on the distribution of branch supports. The topology of the ML tree ouput by RaxML-NG (file with suffix tag "full.rooted") was compared to topologies featured in files with the tags "full.rooted.H9hsisterH9g" and "full.rooted.H9hsisterH9guniteH9c". Shimodaira-Hasegawa test were conducted, showing that the "full.rooted.H9hsisterH9guniteH9c" had better likelihood, and this topology was retained for further analyses.<br>The tree in files which names include the keyword *full* include the 456 genomes; the tree in files which names include the keyword *subcladeH9* is a subtree of the former and include only 352/456 genomes corresponding to the 7PET-T13<b> </b>sublineage and close relatives.<br>BactDating v1.1 was used to estimate a timed phylogeny (using 100,000 Monte-Carlo Markov chain iterations and otherwise default parameters) of the Yemen 2016-2019 genomes and relatives using the ML mapped genome tree (restricted to the 7PET-T13 genome tips) and day-resolved dates as input; median day of the year of isolation was used for isolates where these data were missing.
DOI: 10.6084/m9.figshare.7485665.v2
title: Data related to "On-demand serum-free media formulations for human hematopoietic cell expansion using a high dimensional search algorithm”

description: This is the data presented in the manuscript <i>"On-demand serum-free media formulations for human hematopoietic cell expansion using a high dimensional search algorithm”</i> by Kim and Audet, to be published in Communications Biology (accepted Nov 28, 2018)<br><br>The file named "TF-1 data table" is the primary data related to Figure 2 and Figure 5 and is available in JMP or Excel file format.<br>The file named "T cell data table" is the primary data related to Figure 3, Figure 4 and Figure 5 and is available in JMP or Excel file format.<br>The file named "Supplementary Data 1" is related to Figure 1b in the manuscript.<br>The file named Supplementary Data 2 is related to Figure 4.<br>The file named Supplementary Data 3 is related to Figure 5.<br>The code is available on GitHub https://github.com/julieaudet/cell-manufacturing<br><br><br>
DOI: 10.17632/h92rc2tj4m
title: EVO—Evolutionary algorithm for crystal structure prediction

description: This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2018) Abstract We present EVO—an evolution strategy designed for crystal structure search and prediction. The concept and main features of biological evolution such as creation of diversity and survival of the fittest have been transferred to crystal structure prediction. EVO successfully demonstrates its applicability to find crystal structures of the elements of the 3rd main group with their different spacegroups. For this we used the number of atoms in the conventional cell and multiples of it. Running ... Title of program: EVO Catalogue Id: AEOZ_v1_0 Nature of problem Crystal structure search is a global optimisation problem in 3N+3 dimensions where N is the number of atoms in the unit cell. The high dimensional search space is accompanied by an unknown energy landscape. Versions of this program held in the CPC repository in Mendeley Data AEOZ_v1_0; EVO; 10.1016/j.cpc.2013.02.007
DOI: 10.17632/xj67ctfpkw
title: Drug-target-MR-analysis

description: Non-steroidal anti-inflammatory drug target gene associations with major depressive disorders: a Mendelian randomisation study integrating GWAS, eQTL and mQTL Data
DOI: 10.6084/m9.figshare.1040417.v1
title: Dorsal ROI

description: Dorsal ROI from Lancet Psychiatry paper
DOI: 10.6084/m9.figshare.24487616.v1
title: Circular Dichroism (CD) and FRET data from Interaction of gallium, indium and vanadyl diacetylcurcumin complexes with lysozyme: mechanistic aspects and evaluation of antiamyloidogenic activity

description: This file includes the near-UV and visible CD data and also Fluorescence resonance Energy Transfer (FRET) data upon interaction of lysozyme with diacetylcurcumin metal complexes in this wor
DOI: 10.6084/m9.figshare.28578614.v1
title: fcs files for neutrophil FACS analysis.

description: Neutrophils were separated using Polymorphprep and used for FACS analysis.Neutrophils were cultured in RPMI-1640 with or without 100 U/mL IFN-γ and 5 ng/mL TNF supplementation for 16 hr.Neutrophils were stained with Live/Dead, anti-CD15 antibody, anti-MPO antibody, anti-FcgR1 antibody, anti-FcgR2 antibody, and anti-FcgR3 antibody.
DOI: 10.17632/8rvtr3zybx
title: Life history parameters of crustaceans

description: The data corresponds to life-history parameters recorded from different articles published in different scientific journals.
DOI: 10.17632/j5z57k64tw
title: Uropathogens and Antimicrobial Susceptibility Trends in Ghana (2019-2022).

description: This data was collected from the Greater Accra Regional Hospital in Accra, Ghana with the aim to assess the burden and trends of UTIs, explore variations in prevalence across age groups and months, and evaluate the distribution and antimicrobial susceptibility patterns of these uropathogens to provide evidence-based insights for improving clinical and public health interventions.
DOI: 10.6084/m9.figshare.11788794.v1
title: Molecular dynamics simulations of coronavirus 2019-nCoV protease model in complex with G75 and G82 ligands (covalently bound)

description: Molecular dynamics simulations (500 ps MD at 310 K) of comparative model of novel coronavirus 2019-nCoV protease Mpro in complex with the covalently bound ligands G75 and G82. The starting position of the ligands has been respectively taken from 3SZN and 3TIU PDB structures.<br>The archives contain also an heatmap representing the protein-ligand contact frequencies. Green-boxed occurrences in the heatmap represent hydrogen bond formation during the simulation.
DOI: 10.6084/m9.figshare.14538084.v2
title: A System-GMM Approach to Investigating the Agricultural Producer Price – Agricultural Sustainability Nexus towards Sustainable Food Security in Africa

description: This file describe the computational models and their input commands employed to produce required results for this study.
DOI: 10.6084/m9.figshare.19539085.v2
title: Global models and predictions of plant diversity based on advanced machine learning techniques

description: Data, code and vascular plant diversity predictions from Cai et al. 2022
DOI: 10.6084/m9.figshare.21601029.v1
title: A cross-sectional study on assessment of spiritual health and its associated factors among undergraduate students in a medical college in Mangalore, Karnataka. Informed Consent form.docx

description: Informed Consent Form
DOI: 10.6084/m9.figshare.6016106.v1
title: Etanercept glycoform assignment

description: ZIP archive containing raw spectra (in RAW and mzML format); MoFi parameter and output files; processed results and the corresponding processing scripts; glycopeptide data. See the readme file for further details.
DOI: 10.17632/nb26v3mx3x
title: Inherited PD-1 deficiency: single-cell RNA sequencing (scRNASeq) of PBMCs

description: To identify transcriptional modules perturbed by inherited PD-1 deficiency, single-cell RNA sequencing was performed on PBMCs obtained from the ten-year-old PD-1-deficient patient and his healthy six-year-old brother (wild-type for the PDCD1 allele). The preparation was enriched in viable cells by resuspending 1×10^6 cells in 200 μL of 2% FBS and 1 mM calcium chloride in PBS and passing the suspension through a strainer with 40 µm pores, before removing dead cells with the EasySep Dead Cell Removal Kit (StemCell Technologies, Cat: 17899). The initial viability of ~50% was increased to 79% and 75% for the samples of the patient and his brother, respectively. The samples were loaded onto a 10X Genomics Chromium chip for single-cell capture. Libraries were prepared with the Chromium Single Cell 3’ Reagent Kit (v3.1). Library quality was assessed with a Bioanalyzer DNA chip. The libraries were sequenced on one lane (S4 flowcell) of an Illumina NovaSeq 6000 sequencer. Sequences were processed with Cell Ranger 3.1.0. The filtered feature-cell matrix was used for subsequent analyses. Separately, PBMCs from four healthy controls were processed and sequenced as described above (i.e., historical controls), and the data were analyzed simultaneously. Publicly available control PBMC datasets were downloaded from the 10X Genomics website (https://support.10xgenomics.com/single-cell-gene-expression/datasets). The filtered feature-cell matrix was retrieved for the following datasets: frozen PBMCs (Donors A to C) from Zheng et al.64, 33,000 PBMCs from a healthy donor from the Chromium demonstration (v1 Chemistry, processed by Cell Ranger 1.1.0), 8,000 PBMCs from a healthy donor from the Chromium demonstration (v2 Chemistry, processed by Cell Ranger 2.1.0), 10,000 PBMCs from a healthy donor from the Chromium demonstration (v3 Chemistry, processed by Cell Ranger 3.0.0) with or without cell surface protein levels determined by TotalSeq, 5,000 PBMCs from a healthy donor from the Chromium Next GEM demonstration (v3.1 Chemistry, processed by Cell Ranger 3.0.2) with or without cell surface protein levels determined by TotalSeq, and a total of 66,000 PBMCs from an aggregate of eight Chromium connect channels and eight manual channels (v3.1 Chemistry, processed by Cell Ranger 3.1.0). These 10 datasets were used as the baseline for subsequent analyses.
DOI: 10.6084/m9.figshare.12723404.v1
title: PAD meta-analysis van Zuydam et al. 2020

description: There are 6 files that include summary statistics from the analysis of PAD:<br>1. pad_primary.txt.gz2. pad_diabetes.txt.gz 3. pad_nodiabetes.txt.gz4. pad_diabetesvsnodiabetes.txt.gz 5. pad_neversmoker.txt.gz6. pad_eversmoker.txt.gz 7. pad_eversmokervsneversmoker.txt.gz<br>Each file contains the following columns:<br>1) "chr" - Chromosome 2) "bp" - base pair position 3) "or_allele" - the allele which the odds ratio refers to 4) "nonor_allele" - the other allele 5) "snp" - refsnp id 6) "eaf" - effect allele frequency of the or allele 7) "or" - odds ratio 8) "or_se" - standard error of the odds ratio 9) "p" - p value of significance 10) "ncases" - number of cases 11) "ncontrols" - number of controls <br>The ever smoker vs never smoker / diabetes vs no diabetes files contain extra columns:<br>12) "pint" - the interaction p value for differences in odds ratios between strata13) "NEFF" - effective sample size. In the final meta-analyses NEFF&gt;=4000 was used to filter variants. For the interaction summary statistics we included the variant in both strata even if it only passed QC in one. N.B. treat variants with NEFF&lt;4000 with caution.<br>Any issues with these summary statistics please contact nvanzuydam@gmail.com<br>
DOI: 10.6084/m9.figshare.9585350.v1
title: AJP Endo Hormone Supplement.08-01-19.Final.docx

description: The online document contains further details of methodologies and supplemental data.
DOI: 10.17632/c35zbmn7j8
title: Data for: Accelerated Cycle Life Testing and Capacity Degradation Modeling of LiCoO2-graphite Cells
DOI: 10.6084/m9.figshare.26124052.v1
title: ETHICS_TAX_3.xlsx

description: <b>A Questionnaire-Based Approach Regarding Tax Compliance Patterns in Romania</b>
DOI: 10.6084/m9.figshare.28373330.v1
title: <i>Neuropsychological Teleintervention</i> <i>for</i> <i>Executive Functions in Children with Williams Syndrome</i>

description: <i>Objective</i>s: The aim of this study was to analyze the effect of two teleintervention programs on executive functions in children with WS. <i>Methods:</i> Twelve children with WS were randomly assigned to one of two intervention programs, NeuronUP or Pirate Adventure, and evaluated in a double-blind TeleNp assessment before and after the intervention. The NeuronUP program consisted of daily 20-minute sessions of restoration activities, while the Pirate Adventure program was adapted for administration via Zoom and mediated by anexpert neuropsychologist in weekly one-hour sessions. Both programs were administered over 12 weeks. <i>Results</i>: The results revealed an improvement in executive functions in both groups. Those who received the NeuronUP intervention showed improved semantic fluency and social interaction, and those receiving the Pirate Adventure intervention had better FIQ scores and working memory. <i>Conclusions</i>: These findings provide evidence that TeleNp could be a reliable modality for intervention and follow-up with people with WS who live at a distance from mental health services
DOI: 10.17632/7c6kktxg2s
title: Corporate ESG performance and the capital market information environment

description: Since China began to disclose ESG performance in 2011, we selected A-share listed companies on the Shanghai and Shenzhen stock exchanges from 2011 to 2022 as the research sample. The samples were further excluded from special treatment companies, companies in the financial industry, and those with missing data. The final sample contained 17,752 firm-year observations. All continuous variables are winsorized at the 1% level to avoid outlier effects. ESG data are from the Wind database, and financial data are from the China Securities Market and Accounting Research database.
DOI: 10.17632/dnzykbrzxk
title: Swan: A tool for porting CUDA programs to OpenCL

description: This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2018) Abstract The use of modern, high-performance graphical processing units (GPUs) for acceleration of scientific computation has been widely reported. The majority of this work has used the CUDA programming model supported exclusively by GPUs manufactured by NVIDIA. An industry standardisation effort has recently produced the OpenCL specification for GPU programming. This offers the benefits of hardware-independence and reduced dependence on proprietary tool-chains. Here we describe a source-to-source tr... Title of program: Swan Catalogue Id: AEIH_v1_0 Nature of problem Graphical Processing Units (GPUs) from NVIDIA are preferentially programed with the proprietary CUDA programming toolkit. An alternative programming model promoted as an industry standard, OpenCL, provides similar capabilities to CUDA and is also supported on non-NIVIDA hardware (including multicore x86 CPUs, AMD GPUs and IBM Cell processors). The adaptation of a program from CUDA to OpenCL is relatively straightforward but laborious. The Swan tool facilitates this conversion. Versions of this program held in the CPC repository in Mendeley Data AEIH_v1_0; Swan; 10.1016/j.cpc.2010.12.052
DOI: 10.17632/jm2f2cw634
title: LINF_190010700

description: Tubulin binding cofactor C; Leishmania infantum (strain JPCM5)
DOI: 10.17632/rxd4z2x67d
title: Qualitative dataset of stunting problem solving based on mothers needs

description: This data set is based on the results of coding, indexing and categorization of transcripts from a focused discussion group with several mothers who have children with stunting indications at the age of less than two years. This dataset was created using the Nvivo 12 software.
DOI: 10.6084/m9.figshare.14459598.v2
title: A genome wide association study for hematological traits in Murciano-Granadina goats

description: Genotypes and phenotypes of Murcino-Granadina goats<br>
DOI: 10.6084/m9.figshare.21919410.v1
title: Raw Data.zip

description: Digital elevation models (DEMs) and orthomosaics for ten Acropora palmata colonies. In 2018, we conducted photogrammetric surveys and captured the images used to construct 3D models for DEM and orthomosaic creation.
DOI: 10.17632/3jbfpgnc25
title: Single-cell dissection of the human blood-brain barrier and glioma blood-tumor barrier

description: In our study entitled 'Single-cell Dissection of the Human Blood-Brain Barrier and glioma Blood-Tumor Barrier' (manuscript submitted in April 2024), we analyzed protein level of collagen expression in two murine glioma models (RCAS tumor and CT2A tumor) following PXS-5153A treatment (Figure S9A and S9C).
DOI: 10.17632/bz3yr67j87
title: PLEC Promotes Bone Formation Via Phase Separation And Sequestering ANXA2

description: The original data of PLEC promotes bone formation via phase separation and sequestering ANXA2.
DOI: 10.17632/4tmb8dm9j9
title: DoNOF: An open-source implementation of natural-orbital-functional-based methods for quantum chemistry

description: The natural orbital functional theory (NOFT) has emerged as an alternative formalism to both density functional (DF) and wavefunction methods. In NOFT, the electronic structure is described in terms of the natural orbitals (NOs) and their occupation numbers (ONs). The approximate NOFs have proven to be more accurate than those of the density for systems with a significant multiconfigurational character, on one side, and scale better with the number of basis functions than correlated wavefunction methods, on the other side. A challenging task in NOFT is to efficiently perform orbital optimization. In this article we present DoNOF, our open source implementation based on diagonalizations that allows to obtain the resulting orbitals automatically orthogonal. The one-particle reduced-density matrix (1RDM) of the ensemble of pure-spin states provides the proper description of spin multiplets. The capabilities of the code are tested on the water molecule, namely, geometry optimization, natural and canonical representations of molecular orbitals, ionization potential, and electric moments. In DoNOF, the electron-pair-based NOFs developed in our group PNOF5, PNOF7 and PNOF7s are implemented. These JKL-only NOFs take into account most non-dynamic effects plus intrapair-dynamic electron correlation, but lack a significant part of interpair-dynamic correlation. Correlation corrections are estimated by the single-reference NOF-MP2 method that simultaneously calculates static and dynamic electron correlations taking as a reference the Slater determinant formed with the NOs of a previous PNOF calculation. The NOF-MP2 method is used to analyze the potential energy surface (PES) and the binding energy for the symmetric dissociation of the water molecule, and compare it with accurate wavefunction-based methods.
DOI: 10.17632/63tkvzcnfj
title: Lubbe_2023_https://doi.org/10.1007/s12224-023-09429-2

description: Lubbe, F.C., Hrouda, A., Bartoš, M. et al. Creating a root architecture model: taprooted or adventitious-rooted Plantago lanceolata. Folia Geobotanica (2023). https://doi.org/10.1007/s12224-023-09429-2

Herbaceous plants can form root systems by investing in one main taproot or many adventitious roots. While monocots have adventitious systems, eudicots can have either type in different species and even within a single species depending on its age, environment, or injury. Although clearly different, we know little about their relationship to ecological functions and response. We used Plantago lanceolata, a species that can have either root system and forms adventitious buds on roots, to test methods to form plants with a taproot, adventitious roots, or that grow from a root fragment, to obtain individuals of comparable size. We first evaluated injury response and root traits, then used selected models in a pilot study. For the pilot study, we selected an adventitious root model procedure with root removal from approximately 5-day-old seedlings at 1-2 mm below the stem base (hypocotyl) and rootsprout model of the topmost 4 cm of the taproot from 4-week-old plants. We planted adventitious and taprooted plants in three urban lawns and harvested them after three months. Adventitious and tap-rooted plants were similarly affected by competition, producing lower biomass of leaves and stem in more competitive lawns. Root and leaf traits were consistent regardless of architecture type. Plantago lanceolata fully compensated early loss of the taproot when injured at about 10 days old, and in mesic conditions both root architectures perform similarly. These model systems can be used for investigating the role of root architecture in a variety of ecological topics, for example, its function along a moisture gradient.
DOI: 10.17632/bcv9vsxkyc
title: Physical Action Dataset

description: Thousands of people around the globe are limited in their daily activities due to physical or mental disability, which hinders in their daily tasks. All such individuals can get a boost in their lives by introduction of computer aided assistive applications that help them by classifying the muscle movements. Designing of such systems gets further uplifts by availability of non-invasive sensors, like Surface Electromyography (sEMG), which can be mapped onto the routine activities using machine learning. In this dataset, sEMG signature against routine activities such as typing, resting, lifting and exercise (push up) has been acquired. The sEMG data is coupled with information from a 9-DoF inertial measurement unit (IMU) in the form of accelerometer, gyro and derived orientation signals. Fusion of sEMG with IMU data can lead us to get better classification results especially while segregating abnormal data from normal or routine actions. This data can be of particular value to the researchers working on computer-aided systems for subjects with physical or mental disabilities.
DOI: 10.17632/mms8p8py38
title: Moral Intensity

description: Data file for the study of moral intensity and ethical decision-making: cIPMA study