cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/5zdrppdc3j.1
title: “pyGDM” - new functionalities and major improvements to the python toolkit for nano-optics full-field simulations

description: pyGDM is a python toolkit for electro-dynamical simulations of individual nano-structures, based on the Green Dyadic Method (GDM). pyGDM uses the concept of a generalized propagator, which allows to solve cost-efficiently monochromatic problems with a large number of varying illumination conditions such as incident angle scans or focused beam raster-scan simulations. We provide an overview of new features added since the initial publication [Wiecha, Comput. Phys. Commun. 233 (2018) 167–192]. The updated version of pyGDM is implemented in pure python, removing the former dependency on fortran-based binaries. In the course of this re-write, the toolkit's internal architecture has been completely redesigned to offer a much wider range of possibilities to the user such as the choice of the dyadic Green's functions describing the environment. A new class of dyads allows to perform 2D simulations of infinitely long nanostructures. While the Green's dyads in pyGDM are based on a quasistatic description for interfaces, we also provide as new external python package “pyGDM2_retard” a module with retarded Green's tensors for an environment with two interfaces. We have furthermore added functionalities for simulations using fast-electron excitation, namely electron energy loss spectroscopy and cathodoluminescence. Along with several further new tools and improvements, the update includes also the possibility to calculate the magnetic field and the magnetic LDOS inside nanostructures, field-gradients in- and outside a nanoparticle, optical forces or the chirality of nearfields. All new functionalities remain compatible with the evolutionary optimization module of pyGDM for nano-photonics inverse design.
DOI: 10.5519/qd.abfz89ra
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (209 records)
DOI: 10.17632/sv5m953vjj.1
title: Dataset: "Deep learning with digital holographic microscopy discriminates apoptosis and necroptosis"

description: In this repository you will find all data, models and MATLAB code used with this publication; DOI: (pending). This is used for cell death detection on DHM (Digital holographic microscopy) data using deep learning in MATLAB.
This processing pipeline consists of a few different parts.
1) SAD.m
Supervised Anomaly Detection in order to remove all Alive cells from cell death experiments and vice versa. This since cell death induction (like any other biological process) is happening not at the same time; the cell population is heterogeneous. SAD filters and homogenizes the dataset, the SAD filter is stored in Models/SAD_filter.mat
2) CropFromCaptureAndFilter.m
This script takes the captures (whole field of view, from folder Captures) of the DHM camera snaps and crops out the cells from each capture. The single cells are stored in CroppedImages
3) These CroppedImages are split in HoldoutSet and TrainingSet
4) MakeModelViaTransferLearning.m
Uses Transfer learning to reuse the VGG-19 network and repurpose this to predict cell death on these data. This script relearns the model on the trainingset from the folder TrainingSet and saves the model under Models/convnet.mat
5) UseModelOnHoldoutSet.m
Opens ConvNet model (created by MakeModelViaTransferLearning.m) and the HoldoutSet (independent experiments) and runs the model on these images. Later on the overall accuracy is measured (total correct predictions/total samples *100%)  and a confusion matrix is made. Finally an ROC plot is made.
DOI: 10.5519/qd.2e6kk8t6
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (3086 records)
DOI: 10.21223/uioc0t/o8tjvm
title: SimplifiedCropGrowthModelBasedOnNDVIImages.rar

description: :unav
DOI: 10.21223/uioc0t
title: Simplified Crop Growth Model Based On NDVI Images

description: It is a 2D crop growth model that utilizes NDVI images, incident photosynthetically active radiation (PAR), and physiological crop data, in order to simulate C3 plants net biomass starting from an adaptation model of instantaneous foliage photosynthesis proposed by Thronley 2002*.
DOI: 10.5519/qd.odpvwwl5
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (1 records)
DOI: 10.5519/qd.rdvvrpu7
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (1 records)
DOI: 10.5519/qd.5tcyk0ps
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (135 records)
DOI: 10.5281/zenodo.5470831
title: Epimenia babai SPAdes preassembly

description: .
DOI: 10.5281/zenodo.5470830
title: Epimenia babai SPAdes preassembly

description: .
DOI: 10.5519/qd.n0y6svoy
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (1049 records)
DOI: 10.5519/qd.u8hx9hmf
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (21900 records)
DOI: 10.6084/m9.figshare.14425760
title: Table_S2.xlsx - "Examination of gene loss in the DNA mismatch repair pathway and its mutational consequences in a fungal phylum"

description: List and function of MMR genes used in "Examination of gene loss in the DNA mismatch repair pathway and its mutational consequences in a fungal phylum." Columns indicate model organism the genes were selected from.
DOI: 10.6084/m9.figshare.14410646
title: Table_S4.txt - "Examination of gene loss in the DNA mismatch repair pathway and its mutational consequences in a fungal phylum"

description: HLT & LLT microsatellite length analysis for "Examination of gene loss in the DNA mismatch repair pathway and its mutational consequences in a fungal phylum" <br>
DOI: 10.6084/m9.figshare.14410706
title: Tables_S5-8.xlsx - "Examination of gene loss in the DNA mismatch repair pathway and its mutational consequences in a fungal phylum"

description: Statistical analysis accompanying Fig. 5 of "Examination of gene loss in the DNA mismatch repair pathway and its mutational consequences in a fungal phylum"<br>
DOI: 10.6084/m9.figshare.14410643
title: Table_S3.txt - "Examination of gene loss in the DNA mismatch repair pathway and its mutational consequences in a fungal phylum"

description: HLT & LLT microsatellite count analysis for "Examination of gene loss in the DNA mismatch repair pathway and its mutational consequences in a fungal phylum" <br>
DOI: 10.6084/m9.figshare.14410697
title: README.txt - "Examination of gene loss in the DNA mismatch repair pathway and its mutational consequences in a fungal phylum"

description: README file for "Examination of gene loss in the DNA mismatch repair pathway and its mutational consequences in a fungal phylum" <br>
DOI: 10.6084/m9.figshare.14410538
title: File_S1.txt - "Examination of gene loss in the DNA mismatch repair pathway and its mutational consequences in a fungal phylum"

description: Matrix of MMR gene presence/absence in Ascomycota for "Examination of gene loss in the DNA mismatch repair pathway and its mutational consequences in a fungal phylum" <br>
DOI: 10.6084/m9.figshare.14410643.v4
title: Table_S3.txt - "Examination of gene loss in the DNA mismatch repair pathway and its mutational consequences in a fungal phylum"

description: HLT & LLT microsatellite count analysis for "Examination of gene loss in the DNA mismatch repair pathway and its mutational consequences in a fungal phylum" <br>
DOI: 10.6084/m9.figshare.14410697.v4
title: README.txt - "Examination of gene loss in the DNA mismatch repair pathway and its mutational consequences in a fungal phylum"

description: README file for "Examination of gene loss in the DNA mismatch repair pathway and its mutational consequences in a fungal phylum" <br>
DOI: 10.6084/m9.figshare.14410994
title: Examination of gene loss in the DNA mismatch repair pathway and its mutational consequences in a fungal phylum

description: Supplementary data for "Examination of gene loss in the DNA mismatch repair pathway and its mutational consequences in a fungal phylum"<br>
DOI: 10.6084/m9.figshare.14410706.v6
title: Tables_S5-8.xlsx - "Examination of gene loss in the DNA mismatch repair pathway and its mutational consequences in a fungal phylum"

description: Statistical analysis accompanying Fig. 5 of "Examination of gene loss in the DNA mismatch repair pathway and its mutational consequences in a fungal phylum"<br>
DOI: 10.6084/m9.figshare.14425760.v2
title: Table_S2.xlsx - "Examination of gene loss in the DNA mismatch repair pathway and its mutational consequences in a fungal phylum"

description: List and function of MMR genes used in "Examination of gene loss in the DNA mismatch repair pathway and its mutational consequences in a fungal phylum." Columns indicate model organism the genes were selected from.
DOI: 10.6084/m9.figshare.14410538.v3
title: File_S1.txt - "Examination of gene loss in the DNA mismatch repair pathway and its mutational consequences in a fungal phylum"

description: Matrix of MMR gene presence/absence in Ascomycota for "Examination of gene loss in the DNA mismatch repair pathway and its mutational consequences in a fungal phylum" <br>
DOI: 10.6084/m9.figshare.14410646.v4
title: Table_S4.txt - "Examination of gene loss in the DNA mismatch repair pathway and its mutational consequences in a fungal phylum"

description: HLT & LLT microsatellite length analysis for "Examination of gene loss in the DNA mismatch repair pathway and its mutational consequences in a fungal phylum" <br>
DOI: 10.6084/m9.figshare.16574576
title: Table_S1.xlsx - "Examination of gene loss in the DNA mismatch repair pathway and its mutational consequences in a fungal phylum"

description: High loss taxa (HLT) and low loss taxa (LLT) genome information<br>
DOI: 10.6084/m9.figshare.14410697.v3
title: README.txt - "Examination of gene loss in the DNA mismatch repair pathway and its mutational consequences in a fungal phylum"

description: README file for "Examination of gene loss in the DNA mismatch repair pathway and its mutational consequences in a fungal phylum" <br>
DOI: 10.6084/m9.figshare.14410706.v5
title: Tables_S4-7.xlsx - "Examination of gene loss in the DNA mismatch repair pathway and its mutational consequences in a fungal phylum"

description: Statistical analysis accompanying Fig. 5 of "Examination of gene loss in the DNA mismatch repair pathway and its mutational consequences in a fungal phylum"<br>
DOI: 10.6084/m9.figshare.16574576.v1
title: Table_S1.xlsx - "Examination of gene loss in the DNA mismatch repair pathway and its mutational consequences in a fungal phylum"

description: High loss taxa (HLT) and low loss taxa (LLT) genome information<br>
DOI: 10.6084/m9.figshare.14425760.v1
title: Table_S1.xlsx - "Examination of gene loss in the DNA mismatch repair pathway and its mutational consequences in a fungal phylum"

description: List and function of MMR genes used in "Examination of gene loss in the DNA mismatch repair pathway and its mutational consequences in a fungal phylum." Columns indicate model organism the genes were selected from.
DOI: 10.6084/m9.figshare.14410538.v2
title: File_S1.txt - "Examination of gene loss in the DNA mismatch repair pathway and its mutational consequences in a fungal phylum"

description: Matrix of MMR gene presence/absence in Ascomycota for "Examination of gene loss in the DNA mismatch repair pathway and its mutational consequences in a fungal phylum" <br>
DOI: 10.6084/m9.figshare.14410643.v3
title: Table_S2.txt - "Examination of gene loss in the DNA mismatch repair pathway and its mutational consequences in a fungal phylum"

description: HLT & LLT microsatellite count analysis for "Examination of gene loss in the DNA mismatch repair pathway and its mutational consequences in a fungal phylum" <br>
DOI: 10.6084/m9.figshare.14410646.v3
title: Table_S3.txt - "Examination of gene loss in the DNA mismatch repair pathway and its mutational consequences in a fungal phylum"

description: HLT & LLT microsatellite length analysis for "Examination of gene loss in the DNA mismatch repair pathway and its mutational consequences in a fungal phylum" <br>
DOI: 10.6084/m9.figshare.14410994.v2
title: Examination of gene loss in the DNA mismatch repair pathway and its mutational consequences in a fungal phylum

description: Supplementary data for "Examination of gene loss in the DNA mismatch repair pathway and its mutational consequences in a fungal phylum"<br>
DOI: 10.6084/m9.figshare.16574693
title: Dexmedetomidine Equine Endotoxemia Study Data

description: Data set comparing 390 minutes of anesthesia in experimentally endotoxemic horses receiving or not receiving a dexmedetomidine constant rate infusion.
DOI: 10.6084/m9.figshare.16574693.v1
title: Dexmedetomidine Equine Endotoxemia Study Data

description: Data set comparing 390 minutes of anesthesia in experimentally endotoxemic horses receiving or not receiving a dexmedetomidine constant rate infusion.
DOI: 10.5281/zenodo.5153507
title: Dataset: Quantitative Evaluation of Enhanced multi-plane clinical fetal diffusion MRI with a crossing-fiber phantom

description: This dataset provides MRI acquisitions of a customized crossing phantom for fetal brain. It contains:<br> <br> 1) High Resolution acquisitions of 1.5 mm<sup>3</sup> isotropic and 61 directions (with b-vectors/b-values) 2) Six low resolution acquisitions of 1x1x4 mm<sup>3</sup> and 9-16-25 directions (with respective b-vectors/b-values) 3) A structural T2-w acquisition
DOI: 10.5281/zenodo.5153506
title: Dataset: Quantitative Evaluation of Enhanced multi-plane clinical fetal diffusion MRI with a crossing-fiber phantom

description: This dataset provides MRI acquisitions of a customized crossing phantom for fetal brain. It contains:<br> <br> 1) High Resolution acquisitions of 1.5 mm<sup>3</sup> isotropic and 61 directions (with b-vectors/b-values) 2) Six low resolution acquisitions of 1x1x4 mm<sup>3</sup> and 9-16-25 directions (with respective b-vectors/b-values) 3) A structural T2-w acquisition
DOI: 10.6084/m9.figshare.16574609
title: Suppl_Data_Female polyandry dilutes inbreeding in a solitary fast-living hibernator.xlsx

description: Supplementary Material: Research Data from relatedness and parentage analyses for Batova et al. "Female polyandry dilutes inbreeding in a solitary fast-living hibernator"
DOI: 10.5281/zenodo.4904779
title: CSCoV: Computational Studies about COVID-19

description: CSCoV (Computational Studies about COVID-19) is a dataset containing filtered computational studies related with COVID-19.
DOI: 10.5281/zenodo.4988350
title: Fighting COVID-19 with computational tools: an AI guided review of 17,000 studies - The CSCoV database.

description: CSCoV (Computational Studies about COVID-19) is a dataset containing COVID-19 related studies extracted from PubMed, bioRxiv, medRxiv, and arXiv, together with article and author related metrics obtained from Semantic Scholar (plus page views from bioRxiv and medRxiv). Using machine learning, the articles are categorized in six topics (Pharmacology, Genomics, Epidemiology, Healthcare, Clinical Medicine, Clinical Imaging) and prioritized. The database is periodically updated.
DOI: 10.5281/zenodo.5471437
title: dataset related to article "Multiple Genetic Rare Variants in Autism Spectrum Disorders: A Single-Center Targeted NGS Study"

description: dataset contains: NGS data (.vcf; .bam; .bam.bai) of all 40 ASD patients analysed in the study at title
description: This study was funded by a grant from Fondazione Mariani (CM 22) and Banca d'Italia (RM19).021-09-06
DOI: 10.5281/zenodo.5471436
title: dataset related to article "Multiple Genetic Rare Variants in Autism Spectrum Disorders: A Single-Center Targeted NGS Study"

description: dataset contains: NGS data (.vcf; .bam; .bam.bai) of all 40 ASD patients analysed in the study at title
description: This study was funded by a grant from Fondazione Mariani (CM 22) and Banca d'Italia (RM19).021-09-06
DOI: 10.5281/zenodo.4988445
title: Fighting COVID-19 with computational tools: an AI guided review of 17,000 studies - The CSCoV database.

description: CSCoV (Computational Studies about COVID-19) is a dataset containing COVID-19 related studies extracted from PubMed, bioRxiv, medRxiv, and arXiv, together with article and author related metrics obtained from Semantic Scholar (plus page views from bioRxiv and medRxiv). Using machine learning, the articles are categorized in six topics (Pharmacology, Genomics, Epidemiology, Healthcare, Clinical Medicine, Clinical Imaging) and prioritized. The database is periodically updated.
DOI: 10.5281/zenodo.5136684
title: Fighting COVID-19 with computational tools: an AI guided review of 17,000 studies - The CSCoV database.

description: CSCoV (Computational Studies about COVID-19) is a dataset containing COVID-19 related studies extracted from PubMed, bioRxiv, medRxiv, and arXiv, together with article and author related metrics obtained from Semantic Scholar (plus page views from bioRxiv and medRxiv). Using machine learning, the articles are categorized in six topics (Pharmacology, Genomics, Epidemiology, Healthcare, Clinical Medicine, Clinical Imaging) and prioritized. The database is periodically updated.
DOI: 10.15131/shef.data.15134709
title: Commensal bacteria augment Staphylococcus aureus infection by inactivation of phagocyte-derived reactive oxygen species

description: <i>Staphylococcus aureus </i>is a human commensal organism and opportunist pathogen, causing potentially fatal disease. The presence of non-pathogenic microflora or their components, at the point of infection, dramatically increases <i>S. aureus</i> pathogenicity, a process termed augmentation. Augmentation is associated with macrophage interaction but by a hitherto unknown mechanism. Here, we demonstrate a breadth of cross-kingdom microorganisms can augment <i>S. aureus</i> disease and that pathogenesis of <i>Enterococcus faecalis </i>can also be augmented. Co-administration of augmenting material also forms an efficacious vaccine model for <i>S. aureus</i>. <i>In vitro</i>, augmenting material protects<i> S. aureus </i>directly<i> </i>from reactive oxygen species (ROS), which correlates with <i>in vivo </i>studies where augmentation restores full virulence to the ROS-susceptible, attenuated mutant <i>katA ahpC</i>. At the cellular level, augmentation increases bacterial survival within macrophages via amelioration of ROS, leading to proliferation and escape. We have defined the molecular basis for augmentation that represents an important aspect of the initiation of infection. <br>Animal work in the UK was performed in accordance with the Animal (Scientific Procedures) Act 1986. At the University of Sheffield, work was completed under project licences P3BFD6DB9 and PPL 40/3699 for murine work, or P1A4A7A5E for zebrafish work, with ethical approval from the University of Sheffield Local Ethical Review Panel. At Imperial College London, work was conducted under licence P4C824899 with approval from the Imperial ethical review board. At INRAE, animal work was approved by the local ethics committee (COMETHEA or “Comité d’Ethique en Expérimentation Animale”, Centre de Recherche Ile de France - Jouy en Josas – Antony) under the registration numbers 15_08, and by the French Ministry of Higher Education and Research APAFIS #480-2015041518048149v1, where all animal experiments were performed in accordance with European directive 2010/63/EU. Animal experiments in Calgary were approved by the University of Calgary Animal Care Committee and were in compliance with the Canadian Council for Animal Care Guidelines (protocol nr. AC16-0148). MDMs were derived, with informed consent, from the blood of healthy volunteers, in accordance with guidelines from the South Sheffield Research Ethics Committee (07/Q2305/7). <br><br>
DOI: 10.15131/shef.data.15134709.v1
title: Commensal bacteria augment Staphylococcus aureus infection by inactivation of phagocyte-derived reactive oxygen species

description: <i>Staphylococcus aureus </i>is a human commensal organism and opportunist pathogen, causing potentially fatal disease. The presence of non-pathogenic microflora or their components, at the point of infection, dramatically increases <i>S. aureus</i> pathogenicity, a process termed augmentation. Augmentation is associated with macrophage interaction but by a hitherto unknown mechanism. Here, we demonstrate a breadth of cross-kingdom microorganisms can augment <i>S. aureus</i> disease and that pathogenesis of <i>Enterococcus faecalis </i>can also be augmented. Co-administration of augmenting material also forms an efficacious vaccine model for <i>S. aureus</i>. <i>In vitro</i>, augmenting material protects<i> S. aureus </i>directly<i> </i>from reactive oxygen species (ROS), which correlates with <i>in vivo </i>studies where augmentation restores full virulence to the ROS-susceptible, attenuated mutant <i>katA ahpC</i>. At the cellular level, augmentation increases bacterial survival within macrophages via amelioration of ROS, leading to proliferation and escape. We have defined the molecular basis for augmentation that represents an important aspect of the initiation of infection. <br>Animal work in the UK was performed in accordance with the Animal (Scientific Procedures) Act 1986. At the University of Sheffield, work was completed under project licences P3BFD6DB9 and PPL 40/3699 for murine work, or P1A4A7A5E for zebrafish work, with ethical approval from the University of Sheffield Local Ethical Review Panel. At Imperial College London, work was conducted under licence P4C824899 with approval from the Imperial ethical review board. At INRAE, animal work was approved by the local ethics committee (COMETHEA or “Comité d’Ethique en Expérimentation Animale”, Centre de Recherche Ile de France - Jouy en Josas – Antony) under the registration numbers 15_08, and by the French Ministry of Higher Education and Research APAFIS #480-2015041518048149v1, where all animal experiments were performed in accordance with European directive 2010/63/EU. Animal experiments in Calgary were approved by the University of Calgary Animal Care Committee and were in compliance with the Canadian Council for Animal Care Guidelines (protocol nr. AC16-0148). MDMs were derived, with informed consent, from the blood of healthy volunteers, in accordance with guidelines from the South Sheffield Research Ethics Committee (07/Q2305/7). <br><br>