cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.k5s20
title: Data from: Water quality assessment of Australian ports using water quality evaluation indices

description: Australian ports serve diverse and extensive activities, such as shipping,
 tourism and fisheries, which may all impact the quality of port water. In
 this work water quality monitoring at different ports using a range of
 water quality evaluation indices was applied to assess the port water
 quality. Seawater samples at 30 stations in the year 2016–2017 from six
 ports in NSW, Australia, namely Port Jackson, Botany, Kembla, Newcastle,
 Yamba and Eden, were investigated to determine the physicochemical and
 biological variables that affect the port water quality. The large
 datasets obtained were designed to determine the Water Quality Index,
 Heavy metal Evaluation Index, Contamination Index and newly developed
 Environmental Water Quality Index. The study revealed medium water quality
 index and high and medium heavy metal evaluation index at three of the
 study ports and high contamination index in almost all study ports. Low
 level dissolved oxygen and higher level of total dissolved solids,
 turbidity, fecal coliforms, copper, iron, lead, zinc, manganese, cadmium
 and cobalt are mainly responsible for the poor water qualities of the port
 areas. Good water quality at the background samples indicated that various
 port activities are the likely cause for poor water quality inside the
 port area.
description: S1 Table Sample site
 identificationTable S1 Table.: Sample
 site identification.S2 Table Standards for
 Marine water ecosystemS2 Table.: Australian
 and international standards and guidelines for marine water
 ecosystem.S3 Table Original data
 for water quality parametersS3 Table.: Original data
 for water quality parameters.S4 Table EWQI
 calculationS4 Table.: Calculation
 data for Environmental Water Quality Index (EWQI).
DOI: 10.5061/dryad.7gp1f
title: Data from: No gene flow across the Eastern Pacific Barrier in the reef-building coral Porites lobata

description: The expanse of deep water between the Central Pacific islands and the
 continental shelf of the Eastern Tropical Pacific is regarded as the
 world’s most potent marine biogeographic barrier. During recurrent
 climatic fluctuations (ENSO - El Niño Southern Oscillation), however,
 changes in water temperature and the speed and direction of currents
 become favorable for trans-oceanic dispersal of larvae from central
 Pacific to marginal Eastern Pacific reefs. Here we investigate the
 population connectivity of the reef building coral Porites lobata across
 the Eastern Pacific Barrier (EPB). Patterns of recent gene flow in samples
 (n=1173) from the Central Pacific and the Eastern Tropical Pacific (ETP),
 were analyzed with 12 microsatellite loci. Results indicated that P.
 lobata from the ETP are strongly isolated from those in the central
 Pacific and Hawaii (F’CT=0.509; P&lt;0.001). However, samples from
 Clipperton Atoll, an oceanic island on the eastern side of the EPB,
 grouped with the Central Pacific. Within the Central Pacific, Hawaiian
 populations were strongly isolated from three co-occurring clusters found
 throughout the remainder of the Central Pacific. No further substructure
 was evident in the ETP. Changes in oceanographic conditions during ENSO
 over the past several thousand years thus appear insufficient to support
 larval deliveries from the central Pacific to the ETP or strong
 post-settlement selection acts on ETP settlers from the central Pacific.
 Recovery of P. lobata populations in the frequently disturbed ETP thus
 must depend on local larval sources.
description: DRYAD_BaumsEtAl_2012_Plobata_GenotypesDRYAD_BaumsEtAl_2012_StructureInputInput file for Structure v 2.3.3. First line contains locus names. One line per individual. Missing data is encoded by -9. Column1: Sample ID; Column2: Population; Column3: Population Flag; Column 4ff: allele sizesDRYAD_BaumsEtAl_2012_StructureParametersParameters for Structure v 2.3.3.
DOI: 10.6084/m9.figshare.14992434.v1
title: N. fowleri TY functional gene annotations

description: Functional gene annotations of N. fowleri TY predicted genes
DOI: 10.6084/m9.figshare.26906593.v1
title: <b>Light-harvesting by antenna-containing rhodopsins in pelagic Asgard archaea. Bioinformatic Data</b>

description: See the preprint here. The files are as follows:<br><code>ACA references.faa</code> - reference Archaea clade A proteorhodopsins used for phylogeny and searching for homologs<code>ACB references.faa</code> - reference Archaea clade B rhodopsins<code>HeimdallR references.faa</code> - reference HeimdallR rhodopsins<code>Rhodopsins metadata.xlsx</code> - rhodopsin metadata<code>HeimdallRs MAFFT alignment.fasta</code> - (near-)complete HeimdallR sequences used for NJ phylogeny<code>HeimdallRs MEGA NJ tree.newick</code> - the HeimdallR NZ phylogeny<code>Kariarchaeaceae metadata.xlsx</code> - metadata for Kariarchaeaceae genomes<code>Kari_Gs0128817 scaffold (HeimdallR3).gbk</code> - annotated scaffold containing HeimdallR3<code>K_pelagium pangenome.gbk</code> - annotated pangenome of Ca. Kariarchaeum pelagium (scaffolds which include intervals assigned to the core pangenome)<code>Rhodopsins SplitsTree.nex</code> - phylogenetic network of representative rhodopsins from the proteorhodopsin-xanthorhodopsin clade<code>Metagenomic profiles.xlsx</code> - metagenomic profiles of archaeal rhodopsin outward proton pumps<code>Kariarchaeaceae phylogeny - phylophlan alignments.zip -</code> alignments of individual phylophlan markers<code>Kariarchaeaceae</code><code> phylogeny - concatenated alignment.fasta</code> - concatenated and trimmed alignment used for the reconstruction of the Kariarchaeaceae phylogeny<code>Kariarchaeaceae phylogeny - pplacer alignment for Kari_Gs0128817.fasta</code> - alignment used for phylogenetic placement of the HeimdallR3 scaffold<code>Kariarchaeaceae phylogeny - genes per genome.txt</code> - distribution of marker genes (<code>phylophlan_marker</code>) and genes appearing on the HeimdallR3 scaffold (<code>Gs0128817_gene</code>) among the Kariarchaeaceae<code>Kariarchaeaceae phylogeny - RAxML.newick</code> - RAxML phylogenetic tree of the family <code>Kariarchaeaceae phylogeny - pplacer.newick</code> - phylogenetic tree of the family with the best placement of the HeimdallR3 scaffold (support values are rapid bootstraps from the RAxML tree and the branch length are based on the extended alignment).
DOI: 10.6084/m9.figshare.5121568.v1
title: Supplementary Material for: Mobile Intimal Flap in the Brachiocephalic Artery Diagnosed by Ultrasonography

description: Medicine
DOI: 10.6084/m9.figshare.7710494.v1
title: Drought monitoring in the Brazilian Semiarid region

description: ABSTRACT Drought is a natural and recurrent phenomenon. It is considered ‘a natural disaster’ whenever it occurs in an intensive manner in highly populated regions, resulting in significant damage (material and human) and loss (socioeconomic). This paper presents the efforts developed to monitor the impact of drought in the semiarid region of Northeast Brazil. In this scope, information from different sources is compiled to support the evaluation and identification of impacted municipalities, with the main objective of supporting emergency actions to mitigate their impact. In the semiarid region of Brazil there are frequent occurrences of dry periods during the rainy season, which, depending on the intensity and duration, can cause significant damage to family-farmed crops, with a farming system characterized by low productivity indices. However, rain-fed agriculture has great economic expression and high social importance due to the region is densely occupied, and contributes to the establishment of communities in the countryside. Specifically, in the present study, the methodology adopted to monitor the impact of agricultural droughts, including an analysis of the hydrological year 2015-2016, is presented, considering different water stress indicators for the identification of the affected municipalities and assessment of the methods and tools developed.
DOI: 10.17632/3sjjtjfhx7
title: Van Gogh Paintings dataset 

description: Vincent Willem van Gogh was a Dutch post-Impressionist painter whose work had far-reaching influence on 20th-century art. His paintings include portraits, self portraits, landscapes, still lifes of cypresses, wheat fields and sunflowers.
DOI: 10.6084/m9.figshare.22358050.v1
title: Data Collection.xlsx

description: The listing of the papers analyzed for the prevalence study
DOI: 10.17632/mn9fb7xdx6
title: DIB_Data

description: Contains the full set of test data for the battery degradation and state of health estimation
DOI: 10.6084/m9.figshare.27859329.v1
title: Data used to plot Figure 2

description: Near surface electric field measured during thunderstorm registered at Nor Amberd station. Uploaded files include also simultaneous time series registered by Geiger-Muller flux.
DOI: 10.6084/m9.figshare.28342367.v1
title: Embryo data summary raw.xlsx

description: Embryo data summary raw
DOI: 10.17632/hd9nnhrttg
title: Ancestral Library Identifies Conserved Reprogrammable Liver Motif on AAV Capsid

description: Raw, Unprocessed Data from the Manuscript titled "Ancestral Library Identifies Conserved Reprogrammable Liver Motif on AAV Capsid", Zinn et al., Cell Reports Medicine, 2022.

Folder Contents Follow:

Figure 1 (Approach and Substrate)
   |- Circos Diagram Data Files 
      -Contains data to make Fig 1C
   |- Shanon Entropy Calculation 
      -Contains data to make Entropy component of Fig 1C

Figure 2 (Vector Production and Huh7 Cell Selection)
   |- Huh7 Selection 
       -Contains data from in vitro selection
   |- Vector Production
      -Contains data from the +/- AAP vector production screening

Figure 3 (Liver Toggle in Detail)
   |- Mouse Data
      -Contains liver-derived DNA/RNA barcode counts organized by biological replicate (from mouse data)
   |- NHP Data
      -Contains liver-derived DNA/RNA barcode counts organized by biological replicate (from NHP data)

Figure 4 (Parallel Pharmacokinetics)
   |- Mouse
      -Contains DNA barcode counts from Liver, Quadricep, Spleen, and Serum (mouse) organized by biological replicate
   |- NHP
      -Contains DNA barcode counts from liver, Quadricep, Spleen, and Serum (NHP) organized by biological replicate 

Figure 5 (Summary of In Vivo Tropism Studies)
   |- Data
      -Contains csv files comprised of normalized regularized regression coefficients relating positions of variation within the Anc80 library to log-transformed fold-change of barcode across experimental conditions for mouse (ASP102) and NHP (MSP2) experiments.
      -Heatmap Subtraction.ipynb
         -A python notebook detailing the subtractive logic underpinning Figure 5C

Figure 6 (Clonal confirmation of P3 "liver toggle"...)
      - Contains CSV files of DNA/RNA abundances following biodistribution studies comparing AAV9, AAV9-GA, and AAV9-GAST as well as those comparing Anc80L1533 and Anc80L1093

Figure 7 (In vivo transduction of re-programmed AAVs)
   |- Dose Escalation Data
      - Raw data from biodstribution study comparing AAV9 and AAV9-GAST at escalating doses across a variety of tissues.
   |- Histology Data
      - Raw micrscopy data from histological sections of mice injected with AAV9 or AAV9-GAST expressing eGFP in Liver, Quadricep, and Heart
   |- IVIS Data
      - Raw Data from IVIS studies comparing AAV9, AAV3B, and AAV3b-AG

BaBUSHKA Code
   |- Python Scripts for conversion of fastq data to mapped barcodes
DOI: 10.6084/m9.figshare.14888907.v1
title: Review_Figshare_File.xlsx

description: This contains information about the studies included in a review where the search took place in 2018.
DOI: 10.6084/m9.figshare.25633875.v1
title: DEAP Dataset Feature Extraction

description: DEAP dataset feature extraction
DOI: 10.6084/m9.figshare.5745729.v1
title: Student Survey (Responses).xlsx

description: Online survey assessing mentorship needs for undergraduate medical students at an Irish medical school
DOI: 10.17632/24kp3t95cp
title: Safety of guselkumab and ustekinumab treatment in patients with moderate-to-severe plaque psoriasis combined with latent tuberculosis or inactive hepatitis B virus infection: A retrospective multicenter observational study

description: The supplemental material of this article, which includes 3 figures (1.Patient Flowcharts and Follow-up Data Treated with Guselkumab 2.Patient Flowcharts and Follow-up Data Treated with Guselkumab 3.The certificate of english language editing) and 1 table (Hepatitis B screening outcomes at week 0 and 52 of patients combined with inactive HBV infection at baseline).
DOI: 10.17632/s2k7hbb8jc
title: Environmental Sustainability in Mining Industry: A Systematic Review of Economy Perspective for Achieving Sustainability Development Goals

description: Environmental Sustainability in Mining Industry: A Systematic Review of Economy Perspective for Achieving Sustainability Development Goals Data
DOI: 10.17632/sb79nrs48t
title: Loci alignments of 446 anchored hybrid enrichment generated markers of Lepanthes horrida group

description: Loci alignments of 446 anchored hybrid enrichment generated markers evaluated in the paper Bogarín et al.
DOI: 10.6084/m9.figshare.28784090.v2
title: <b>Single-nucleus profiling of the left ventricle of the mouse heart after chronic stress</b>

description: This folder contains gene expression matrix files for 8 samples (4 control samples, 4 chronic stress group samples), all stored under "filtered_feature-bc_matrix. h5", which includes cell barcodes, genes, and corresponding expression values.
DOI: 10.6084/m9.figshare.19989395.v2
title: Whole genome alignments of Drosophila species

description: Files in this dataset
<br>
<strong>Acalyptratae20.hal</strong>
Whole genome alignments of 20 Drosophila species by progressive cactus
<br>
<strong>supplementary_file_unannotated_alignments.txt</strong>
the alignments of lineage-specific de novo gene candidates, with orthologs in close species and nongenic ortholog regions in outgroup speces.
DOI: 10.6084/m9.figshare.20454435.v1
title: RSmDB: a global database of rodents and shrews-associated microbial communities from metagenomes

description: The rodent- and shrew-associated microbial communities database (RSmDB) is a metagenomic resource to investigate the microbial communities of rodents and shrews.
DOI: 10.6084/m9.figshare.28806992.v1
title: <i>Sideroxydans lithotrophicus </i>ES-1 Compare Flux with Expression Table

description: A novel template for generating stoichiometric metabolic models of iron-oxidizing bacteria was generated using the ModelSEED2 toolkit in KBase. Flux balance analysis (FBA) was performed and FBA models were compared to transcriptome data from cultures on the same media during mid-log growth.
DOI: 10.6084/m9.figshare.7849268.v2
title: Domestication of Campylobacter jejuni NCTC 11168

description: While the model organism allows basic comparison within and between labs, it is important to remember the effect even small differences in isolate genomes can have on the validity and reproducibility of experimental work. We quantify differences in 23 reference <i>Campylobacter </i>genomes and compare them with observable differences in common laboratory phenotypes.<b><br></b><b>Supplementary data</b>Table S1: Isolate listTable S2: Isolates used for genomic contextFile S1: wgMLST output for all isolatesFile S2: Alignment file: NCTC11168 isolates only.File S3: Alignment file: NCTC11168 isolates and 83 previously published genomes.File S4: SNP matrixFile S5: Summary of Gubbins output.<br>
DOI: 10.17632/bfd7gft38s
title: Complete database for neonatal pain

description: The database includes all the data collected during our studies on neonatal pain in 100 full term newborns. The Neonatal Infant Pain Scale and a multichannel near-infrared spectroscopy device (Hitachi ETG -00) were used to assess, respectively, the infant behavioural response and cortical response to a painful stimulation (a routine heel prick for metabolic screening). Such data wer published in 2015 (Bembich S, Cont G, Baldassi G, Bua J, Demarini S. Maternal holding vs oral glucose administration as nonpharmacologic analgesia in newborns: a functional neuroimaging study. JAMA Pediatr. 2015 Mar;169(3):284-5) and 2018 (Bembich S, Cont G, Causin E, Paviotti G, Marzari P, Demarini S. Infant Analgesia With a Combination of Breast Milk, Glucose, or Maternal Holding. Pediatrics. 2018 Sep;142(3):e20173416).
DOI: 10.6084/m9.figshare.27708315.v2
title: Genomic ancestry and GUSB gene expression data

description: Analysis of <i>GUSB</i> gene expression profile and genomic ancestry for MPS VII. The analysis of <i>GUSB</i> gene expression is a case-control study in which the sample consisted of 23 individuals divided into two groups: a control group of 20 individuals without the disease and an MPS VII group of one patient with the new variant and his parents (heterozygotes). The study of genomic ancestry of MPS VII is a retrospective cohort study in which samples for ancestry analysis consisted of 5 of the 13 patients with MPS VII.
DOI: 10.6084/m9.figshare.28615955.v1
title: Data and R code for the paper "<b>Coevolutionary patterns between coloration and diel activity in moths</b>"

description: This is data for the paper "<b>Coevolutionary patterns between coloration and diel activity in moths</b>"
DOI: 10.6084/m9.figshare.5442229.v3
title: Datasets used in "Antibody interface prediction with 3D Zernike descriptors and SVM"

description: <b>Background:</b> In this work we present a novel method for antibody interface prediction from their experimentally-solved structures based on 3D Zernike Descriptors. Roto-translationally invariant descriptors are computed from circular patches of the antibody surface enriched with a chosen subset of physicochemical properties from the AAindex1 amino acid index set, and are used as samples for a binary classification problem. An SVM classifier is used to distinguish interface surface patches from non-interface ones. The proposed method was shown to outperform other antigen-binding interface prediction software.<b><br><br>seq_descriptors_4.5.tar.gz -</b> Contains the sequence descriptors generated from the antibody structures in the development/validation set which were used for feature selection with the Randomized Logistic Regression algorithm.<br><br><b>development_set_structures_descriptors.tar.gz -</b> Contains the PDB structures of the antibody-antigen complexes in the development/validation set; the 3D Zernike Descriptors for each antibody; the predicted patch scores for each antibody; other supplementary files.<br><br><b>training_set_structures_descriptors.tar.gz -</b> Contains the PDB structures of the antibody-antigen complexes in the training set and the 3D Zernike Descriptors (rebalanced) for each antibody.<br><b><br>test_set_protein_ag_structures_descriptors.tar.gz - </b>Contains the PDB structures of the antibody-antigen complexes in the test set of antibodies complexed with protein antigens; the 3D Zernike Descriptors for each antibody; the predicted patch scores for each antibody; other supplementary files. <br><br><b>homology_modelled_test_set_protein_ag_structures_descriptors.tar.gz - </b>Contains the PDB structures of the homology modelled antibody structures in the test set of antibodies complexed with protein antigens; the 3D Zernike Descriptors for each antibody; the predicted patch scores for each antibody; other supplementary files. <br><br><br><br><br>
DOI: 10.17632/4yk8v93vpn
title: Clearance of multiple cutaneous warts by targeting a single lesion: a randomized comparative evaluation of mild local hyperthermia versus cryotherapy

description: Supplement I. Protocol of the trial
Supplement II. Medical Instruments
A plantar wart patient is receiving treatment with a hyperthermia medical instrument, and a 2 cm diameter red facula is the treatment spot.
Supplement III. Time course of the treatment and evaluation points.
Participants were randomly assigned to receive hyperthermia at a temperature of 44±2°C for 30 min on days 1, 2, 3, 17, 18, 25, and 32 and cryotherapy on days 1, 14, and 28 on a single target lesion. At each time visit, the patient was assigned to a blinded evaluator to evaluate the status of all the lesions.
Supplement V. Representative clinical pictures of multiple plantar warts cleared in the two groups.
The red circles show target lesions, and the blue arrows delineate nontarget lesions. The blue rectangle that is highlighting pictures in the cryotherapy group shows a remote subungual wart under the patient's thumbnail.
DOI: 10.17632/fxvyvt84gf
title: Hedgehog inhibitor in scGVHD Supplement

description: Supplement material for Efficacy of Hedgehog Pathway Inhibitors as Adjuvant in Treating Steroid-Refractory Sclerodermatous Chronic Graft-Versus-Host Disease: Methods and Supplement Table
DOI: 10.6084/m9.figshare.13270802.v1
title: Nestorowa 2016 scRNA-seq

description: scRNA-seqblood cellsNestorowa 2016AnnDatah5ad
DOI: 10.6084/m9.figshare.1603456.v2
title: A multi-region community model for inference about geographic variation in species richness

description: Data used in the application of the multi-region community model (MRCM) to detection non-detection data collected from bird assemblages in R=8 geographically distinct areas (regions) in northern Italy. We augmented the data for all regions such that M = M_r = 200, i.e., by 200-n_r species for each region. The data file contains the following six objects: dataREG: region-specific covariates; K_tot: number of sampling occasions for each site in each region; M: total number of species in the augmented data set; nsites: total number of sites per region; nspecies: total number of observed species for each region; Yaug_tot: augmented species-by-sites-by-region detection frequency matrix.
DOI: 10.6084/m9.figshare.19684047.v2
title: Priorities for rheumatic and musculoskeletal disease research in Ireland_Dataset_Dorris et al

description: Dataset from the study <em><strong>Priorities for rheumatic and musculoskeletal disease research in Ireland</strong></em> published in BMC Rheumatology in 2022. <br> Dataset contains survey data from the exploratory survey into what topics/areas stakeholders in Ireland thought needed to be researched to improve quality of life for people living with RMD in Ireland.
DOI: 10.6084/m9.figshare.20284713.v11
title: Data availability for Mirusviricota and the GOEV database

description: Data availability includes supplemental tables, FASTA files corresponding to the GOEV genomic database, genes, proteins, predicted 3D protein structure, and phylogenetic trees with theiur associated metadata. This data availability also includes a folder for all to Mirusviricota MAGs.
DOI: 10.6084/m9.figshare.21835014.v1
title: File 7

description: Species annotation information at family level
DOI: 10.17632/zhbhxpnx5r
title: Data for: Mantle source to near-surface emplacement of enriched and intermediate poikilitic shergottites in Mars

description: Mineral, bulk rock, quantitative textural analyses, and ƒO2 of all poikilitic shergottites.
DOI: 10.6084/m9.figshare.10282724.v1
title: Mesocosms_data

description: These are the results of a mesocosm experiment with artificial plant communities that was held at the botanical gardens in Jerusalem, Israel.More data can be found in: https://www.pnas.org/content/early/2020/02/14/1911540117<br><br>