cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.12082035.v1
title: The codon usage pattern of the novel coronavirus

description: <b> </b>The current outbreak of a novel coronavirus (severe acute respiratory syndrome coronavirus 2, SARS-CoV-2) is spreading rapidly across the whole world. The World Health Organization has declared the coronavirus diseases (COVID-19) to be a global pandemic. COVID-19 is milder, less fatal than SARS and MERS, but SARS-CoV-2 poses more serious threats to public health, because it is highly contagious and has a high potential of causing severe-acute, life-threatening pneumonia. Here we analyzed the similarities of codon usages between humans and different viruses, including human immunodeficiency virus (HIV), highly pathogenic avian influenza (HPAI), and coronavirus (CoV). The codon usages of HPAIs are highly similar to that of humans. In contrast, the codon usage of HIVs and CoVs is less and the codon usage of SARS-CoV-2 is the least similar to that of humans among all viruses tested. Besides, human-preferred codons are adopted to substitute less-preferred ones in SARS-CoV; in SARS-CoV-2, however, human-preferred codons are replaced by less-preferred ones. The unique codon usage pattern suggests that SARS-CoV-2 was probably formed by evolving in an unusual intermediate host over a long period, in which its codon usage became drastically different from that of humans and those of other pathogenic viruses. Moreover, its pathogenicity is weakened compared with SARS-CoV, but it becomes more potent and may gain higher potentials in the future. Therefore, there is an urgent need to block the transmission routes among humans, search for the origin and intermediate hosts of the coronaviruses, and prevent any future outbreaks.<br>
DOI: 10.6084/m9.figshare.12082011
title: Supplementary tables

description: These material contains supplemental tables of the manuscript entitles "A New Insight Into The Treatment of Primary Macronodular Adrenal Hyperplasia".
DOI: 10.6084/m9.figshare.12082020
title: Supplementary file

description: List of organisms used in the phylogenetic analyses.; General features of mitogenomes of Ocypodidae species.
DOI: 10.6084/m9.figshare.12081978
title: MiSeq_Run1_fastqfiles

description: Fastq R1 and R2 files of a MiSeq run of freshwater mesocosm bacterioplankton from an experiment developed at the LEAP (Quebec, Canada) platform in 2016.
DOI: 10.6084/m9.figshare.12081984
title: MiSeq_Run2_fastqfiles

description: Fastq R1 and R2 files of a MiSeq run of freshwater mesocosm bacterioplankton from an experiment developed at the LEAP (Quebec, Canada) platform in 2016.
DOI: 10.6084/m9.figshare.12082011.v1
title: Supplementary tables

description: These material contains supplemental tables of the manuscript entitles "A New Insight Into The Treatment of Primary Macronodular Adrenal Hyperplasia".
DOI: 10.6084/m9.figshare.12081984.v1
title: MiSeq_Run2_fastqfiles

description: Fastq R1 and R2 files of a MiSeq run of freshwater mesocosm bacterioplankton from an experiment developed at the LEAP (Quebec, Canada) platform in 2016.
DOI: 10.6084/m9.figshare.12081978.v1
title: MiSeq_Run1_fastqfiles

description: Fastq R1 and R2 files of a MiSeq run of freshwater mesocosm bacterioplankton from an experiment developed at the LEAP (Quebec, Canada) platform in 2016.
DOI: 10.6084/m9.figshare.12082020.v3
title: Supplementary file

description: List of organisms used in the phylogenetic analyses.; General features of mitogenomes of Ocypodidae species.
DOI: 10.6084/m9.figshare.12081795
title: Fruit transect species richness by site and season

description: Fruit transect species compositions by site and season.<br>Analysed in: Climatic and resource determinants of forest elephant movements<br>
DOI: 10.6084/m9.figshare.12081837
title: All data from the publication "Climatic and resource determinants of forest elephant movements"

description: All of the data relating to the publication "Climatic and resource determinants of forest elephant movements" in Frontier in Ecology and Evolution. For more information contact john.poulsen@duke.edu<br>
DOI: 10.6084/m9.figshare.12081798
title: Monthly movement behaviour data

description: The monthly movement behaviour characteristics from forest elephants. <br><br>Analysed in: Climatic and resource determinants of forest elephant movements<br>
DOI: 10.6084/m9.figshare.12081777
title: Follow level movement behaviour data

description: Follow-level movement behaviour traits of forest elephants.<br>Analysed in: Climatic and resource determinants of forest elephant movements<br>
DOI: 10.6084/m9.figshare.12081780
title: Fruit availability transect data

description: The fruit availability data from fruit transects conducted during focal forest elephant follows.<br>Analysed in: Climatic and resource determinants of forest elephant movements<br>
DOI: 10.6084/m9.figshare.12081774
title: Dung seed species by site and season

description: The seed species composition of dungs search in two different survey sites, in two different seasons.<br>Analysed in: Climatic and resource determinants of forest elephant movements
DOI: 10.6084/m9.figshare.12081774.v1
title: Dung seed species by site and season

description: The seed species composition of dungs search in two different survey sites, in two different seasons.<br>Analysed in: Climatic and resource determinants of forest elephant movements
DOI: 10.6084/m9.figshare.12081777.v1
title: Follow level movement behaviour data

description: Follow-level movement behaviour traits of forest elephants.<br>Analysed in: Climatic and resource determinants of forest elephant movements<br>
DOI: 10.6084/m9.figshare.12081780.v1
title: Fruit availability transect data

description: The fruit availability data from fruit transects conducted during focal forest elephant follows.<br>Analysed in: Climatic and resource determinants of forest elephant movements<br>
DOI: 10.6084/m9.figshare.12081771
title: Dung composition data

description: Data set detailing the proportion of fruit matter within forest elephant dungs in relation to herbaceous material.<br><br>Analysed in: Climatic and resource determinants of forest elephant movements
DOI: 10.6084/m9.figshare.12081771.v1
title: Dung composition data

description: Data set detailing the proportion of fruit matter within forest elephant dungs in relation to herbaceous material.<br><br>Analysed in: Climatic and resource determinants of forest elephant movements
DOI: 10.6084/m9.figshare.12081624
title: SPSS master file

description: Full data set saved as an SPSS data file and Excel file. Raw data from all
DOI: 10.6084/m9.figshare.12081405
title: Enhancement of Visual Biological Motion Recognition in Early-Deaf Adults: Functional and Behavioral Correlates

description: Deafness leads to brain modifications that are generally associated with a cross-modal activity of the auditory cortex, particularly for visual stimulations. In the present study, we explore the cortical processing of biological motion that conveyed either non-communicative (pantomimes) or communicative (emblems) information, in early-deaf and hearing individuals, using fMRI analyses. Behaviorally, deaf individuals showed an advantage in detecting communicative gestures relative to hearing individuals. Deaf individuals also showed significantly greater activation in the superior temporal cortex (including the planum temporale and primary auditory cortex) than hearing individuals. The activation levels in this region were correlated with deaf individuals’ response times. This study provides neural and behavioral evidence that cross-modal plasticity leads to functional advantages in the processing of biological motion following lifelong auditory deprivation.
DOI: 10.6084/m9.figshare.12081708
title: Diffraction tomography with a deep image prior - raw data

description: This repository contains the raw multi-angle datasets for the experimental results in Figs. 7-10 in our paper, <i>Diffraction tomography with a deep image prior</i> (https://www.osapublishing.org/oe/abstract.cfm?uri=oe-28-9-12872). The 3D reconstruction python/tensorflow code that uses this data is available at https://github.com/kevinczhou/deep-prior-diffraction-tomography.
DOI: 10.6084/m9.figshare.12081405.v1
title: Enhancement of Visual Biological Motion Recognition in Early-Deaf Adults: Functional and Behavioral Correlates

description: Deafness leads to brain modifications that are generally associated with a cross-modal activity of the auditory cortex, particularly for visual stimulations. In the present study, we explore the cortical processing of biological motion that conveyed either non-communicative (pantomimes) or communicative (emblems) information, in early-deaf and hearing individuals, using fMRI analyses. Behaviorally, deaf individuals showed an advantage in detecting communicative gestures relative to hearing individuals. Deaf individuals also showed significantly greater activation in the superior temporal cortex (including the planum temporale and primary auditory cortex) than hearing individuals. The activation levels in this region were correlated with deaf individuals’ response times. This study provides neural and behavioral evidence that cross-modal plasticity leads to functional advantages in the processing of biological motion following lifelong auditory deprivation.
DOI: 10.6084/m9.figshare.12081144
title: PanSTARRS DR1 Broad Morphology Catalog

description: This is a broad morphology (spiral or elliptical) catalog of images identified as galaxies from the first data release of PanSTARRS (PS1 DR1). Annotations were produced by a deep neural network based on the LeNet-5 architecture, and training labels were obtained using "superclean" Galaxy Zoo annotations.<br>The catalog contains labels for 1,662,190 images and has approximately 95% overall accuracy. The dataset is a csv file (with headers) containing the following columns:<b>objid</b> (string): The object ID of the image assigned by PanSTARRS.<b>ra</b> (float): The object's right ascension.<b>dec</b> (float): The object's declination.<b>prob_sp</b> (float): The probability of the galaxy being spiral.<b>prob_el</b> (float): The probability of the galaxy being elliptical.<b>spiral</b> (integer): If prob_sp is greater than prob_el, this is 1; otherwise, it is 0.<b>elliptical</b> (integer): If prob_el is greater than prob_sp, this is 1; otherwise, it is 0.
DOI: 10.6084/m9.figshare.12080964
title: Tag Recommendation Dataset - Elo7 Products

description: Elo7 dataset - Files and formats<br>*.test*: test sets*.train.*: train sets<br>wordmap: Contain all words in the dataset's vocabulary and their corresponding integer identifiers. Format: each line contains a pair <br>*.ids: product identifiers*.ground_truth: relevant tags for each object (one product per line, aligned with .ids file) titledesc.csv: title and descriptions of products*.feats (available after the review process of our article): tag quality attributes, in RankLib format, that is:<br> RelevanceLabel qid:number attribute1:value1 attribute2:value ... #TagID<br> Example:<br> 0 qid:1 1:2 2:10 #10 1 qid:1 1:3 2:10 #42<br> In the above example, there are two candidate tags associated with product 1 (qid:1). The first (ID=10) is non relevant (label=0) while the second (ID=42) is relevant (label=1)<br>
DOI: 10.6084/m9.figshare.12080964.v1
title: Tag Recommendation Dataset - Elo7 Products

description: Elo7 dataset - Files and formats<br>*.test*: test sets*.train.*: train sets<br>wordmap: Contain all words in the dataset's vocabulary and their corresponding integer identifiers. Format: each line contains a pair <br>*.ids: product identifiers*.ground_truth: relevant tags for each object (one product per line, aligned with .ids file) titledesc.csv: title and descriptions of products*.feats (available after the review process of our article): tag quality attributes, in RankLib format, that is:<br> RelevanceLabel qid:number attribute1:value1 attribute2:value ... #TagID<br> Example:<br> 0 qid:1 1:2 2:10 #10 1 qid:1 1:3 2:10 #42<br> In the above example, there are two candidate tags associated with product 1 (qid:1). The first (ID=10) is non relevant (label=0) while the second (ID=42) is relevant (label=1)<br>
DOI: 10.6084/m9.figshare.12078519
title: How reliable are species identifications in biodiversity big data? Evaluating the records of a neotropical fish family in online repositories

description: The increase of free and open online biodiversity databases is of paramount importance for current research in ecology and evolution. However, little attention is paid to using updated taxonomy in these “biodiversity big data” repositories and the quality of their taxonomic information is often questioned. Here we assess how reliable is the current use of nomenclatural classification in the distributional information available from two biodiversity information networks: GBIF and the Brazilian SpeciesLink. We use as a study case the records of Auchenipteridae, a Neotropical fish family that has been subject to recent taxonomical reviews. A data filtering procedure was applied to identify and quantify the inaccuracies in the taxonomical status of the records in three steps: assessment of identification accuracy at the family, genus or species level; current validity of species name; and assignation of inaccurate species records to different categories of classification quality. Synonyms, nonexistent combinations, and outdated combinations were reassigned to currently valid species. A total of 9148 records of Auchenipteridae fishes were analyzed, of which 4165 were from GBIF and 4983 from SpeciesLink, deriving from 46 and 31 sources, respectively. After correcting all possible records following the taxonomic data filtering steps, 6988 records (76.4% of the original) were adequate for describing species distributions, while 2160 remained inaccurate. The most inaccurate records at the species level were due to the use of outdated nomenclatures, resulting in non-valid combinations of species and genus, and synonymy. Our results evidence a large taxonomic inconsistency among records, and, most importantly, that taxonomic information obtained from repositories should be used with caution. Many inaccuracy issues may be embedded in the biodiversity databases’ records, which could lead researchers to provide an incomplete or even mistaken perspective of the variations in the natural world.
DOI: 10.6084/m9.figshare.12078549
title: Deep genetic divergence and paraphyly in cryptic species of <i>Mugil</i> fishes (Actinopterygii: Mugilidae)

description: Morphological conservatism among closely related species often results in incongruent taxonomic classification between studies, leading to disagreements about the inferred evolutionary history of the species. This is the case in <i>Mugil</i> fishes, where extreme morphologic conservatism contrasts with wide distributions and high genetic divergence. To understand how these morphologically similar species evolved, it is necessary to 1) test whether taxonomically recognized species are independently evolving lineages, and 2) evaluate the timing and geographic context of the diversification of these lineages. Based on three mitochondrial genes and fossil data, we estimated a comprehensive time-calibrated phylogeny for 13 out of the 16 valid species of <i>Mugil</i> and tested the monophyly of each species. Our results indicate that the diversification of <i>Mugil</i> began nearly 30 MYA, during a period of large temperature fluctuations. <i>Mugil cephalus</i>, <i>M. curema</i> and <i>M. rubrioculus</i> all form relatively old groups (between 5 and 10 MYA) and form paraphyletic entities. Our study reinforces the general finding that morphologically and ecologically similar species may have long and independent evolutionary histories, which must be considered when assessing the evolution and conservation of such ecologically and economically important species.
DOI: 10.6084/m9.figshare.12078519.v1
title: How reliable are species identifications in biodiversity big data? Evaluating the records of a neotropical fish family in online repositories

description: The increase of free and open online biodiversity databases is of paramount importance for current research in ecology and evolution. However, little attention is paid to using updated taxonomy in these “biodiversity big data” repositories and the quality of their taxonomic information is often questioned. Here we assess how reliable is the current use of nomenclatural classification in the distributional information available from two biodiversity information networks: GBIF and the Brazilian SpeciesLink. We use as a study case the records of Auchenipteridae, a Neotropical fish family that has been subject to recent taxonomical reviews. A data filtering procedure was applied to identify and quantify the inaccuracies in the taxonomical status of the records in three steps: assessment of identification accuracy at the family, genus or species level; current validity of species name; and assignation of inaccurate species records to different categories of classification quality. Synonyms, nonexistent combinations, and outdated combinations were reassigned to currently valid species. A total of 9148 records of Auchenipteridae fishes were analyzed, of which 4165 were from GBIF and 4983 from SpeciesLink, deriving from 46 and 31 sources, respectively. After correcting all possible records following the taxonomic data filtering steps, 6988 records (76.4% of the original) were adequate for describing species distributions, while 2160 remained inaccurate. The most inaccurate records at the species level were due to the use of outdated nomenclatures, resulting in non-valid combinations of species and genus, and synonymy. Our results evidence a large taxonomic inconsistency among records, and, most importantly, that taxonomic information obtained from repositories should be used with caution. Many inaccuracy issues may be embedded in the biodiversity databases’ records, which could lead researchers to provide an incomplete or even mistaken perspective of the variations in the natural world.
DOI: 10.6084/m9.figshare.12078549.v1
title: Deep genetic divergence and paraphyly in cryptic species of <i>Mugil</i> fishes (Actinopterygii: Mugilidae)

description: Morphological conservatism among closely related species often results in incongruent taxonomic classification between studies, leading to disagreements about the inferred evolutionary history of the species. This is the case in <i>Mugil</i> fishes, where extreme morphologic conservatism contrasts with wide distributions and high genetic divergence. To understand how these morphologically similar species evolved, it is necessary to 1) test whether taxonomically recognized species are independently evolving lineages, and 2) evaluate the timing and geographic context of the diversification of these lineages. Based on three mitochondrial genes and fossil data, we estimated a comprehensive time-calibrated phylogeny for 13 out of the 16 valid species of <i>Mugil</i> and tested the monophyly of each species. Our results indicate that the diversification of <i>Mugil</i> began nearly 30 MYA, during a period of large temperature fluctuations. <i>Mugil cephalus</i>, <i>M. curema</i> and <i>M. rubrioculus</i> all form relatively old groups (between 5 and 10 MYA) and form paraphyletic entities. Our study reinforces the general finding that morphologically and ecologically similar species may have long and independent evolutionary histories, which must be considered when assessing the evolution and conservation of such ecologically and economically important species.
DOI: 10.6084/m9.figshare.12078168
title: Results

description: File contains second level contrasts and ROIs used for time course analysis (cf. manuscript)<br>
DOI: 10.6084/m9.figshare.12078201
title: Stratified_SEIR_DEMO_BMC_Infecious_Diseases

description: The data and code used in the paper submitted to BMC Infectious Diseases.
DOI: 10.6084/m9.figshare.12078201.v1
title: Stratified_SEIR_DEMO_BMC_Infecious_Diseases

description: The data and code used in the paper submitted to BMC Infectious Diseases.
DOI: 10.6084/m9.figshare.12078042
title: S3 AMSTAR Quality Data Turmeric VRolfe 3Apr2020.xlsx

description: Quality evaluation using R-AMSTAR scoring of turmeric systematic reviews for inclusion into a meta-review.
DOI: 10.6084/m9.figshare.12078060
title: S4 Data Extraction Table Turmeric VRolfe 3Apr2020.xlsx

description: Extracted data and analyses, including meta-analysis results for turmeric meta-review.
DOI: 10.6084/m9.figshare.12078168.v1
title: Results

description: File contains second level contrasts and ROIs used for time course analysis (cf. manuscript)<br>
DOI: 10.6084/m9.figshare.12078060.v1
title: S4 Data Extraction Table Turmeric VRolfe 3Apr2020.xlsx

description: Extracted data and analyses, including meta-analysis results for turmeric meta-review.
DOI: 10.6084/m9.figshare.12077898
title: Supp 1 Search strategy for turmeric

description: Search strategy doc.
DOI: 10.6084/m9.figshare.12077985
title: S2 Inclusion Exclusion Data VRolfe 3Apr2020.xlsx

description: Dataset of inclusion and exclusion criteria and process for turmeric overview of systematic reviews.
DOI: 10.6084/m9.figshare.12077985.v1
title: S2 Inclusion Exclusion Data VRolfe 3Apr2020.xlsx

description: Dataset of inclusion and exclusion criteria and process for turmeric overview of systematic reviews.
DOI: 10.6084/m9.figshare.12077259
title: ROR Data Dump 4.0 (April 2020)

description: ROR data download. Based on GRID release 10.6084/m9.figshare.12022722
DOI: 10.6084/m9.figshare.12077259.v1
title: ROR Data Dump 4.0 (April 2020)

description: ROR data download. Based on GRID release 10.6084/m9.figshare.12022722
DOI: 10.6084/m9.figshare.12081147.v11
title: Data for research on "Effect of plate length on subduction kinematics and slab geometry: Insights from buoyancy-driven analog subduction models".

description: Data for research on "Effect of plate length on subduction kinematics and slab geometry: Insights from buoyancy-driven analog subduction models".
DOI: 10.5522/04/12076719
title: Primary studies evaluating school lotteries: data used for the meta-analysis of the effect of schools under these admission policies on student academic outcomes

description: The file consists of three spreadsheets. This first one is the dataset. It contains information extracted from primary studies that were part of the quantitative synthesis of a systematic review of school randomised admissions. The second tab is the codebook, including a brief description of each variable extracted or assessed from the primary studies, and its corresponding values. The third sheet shows the APA bibliographic reference and access link for each of the primary studies included in the meta-analysis.These data were used for one of the research chapters of the author's PhD thesis, available here https://discovery.ucl.ac.uk/id/eprint/10096351<br>
DOI: 10.6084/m9.figshare.12076704
title: Data from Biological archives reveal contrasting patterns in trace element concentrations in pelagic seabird feathers over more than a century

description: Data from Bond & Lavers 2020. Biological archives reveal contrasting patterns in trace element concentrations inpelagic seabird feathers over more than a century. Environmental Pollution
DOI: 10.5522/04/12076719.v1
title: Primary studies evaluating school lotteries: data used for the meta-analysis of the effect of schools under these admission policies on student academic outcomes

description: The file consists of three spreadsheets. This first one is the dataset. It contains information extracted from primary studies that were part of the quantitative synthesis of a systematic review of school randomised admissions. The second tab is the codebook, including a brief description of each variable extracted or assessed from the primary studies, and its corresponding values. The third sheet shows the APA bibliographic reference and access link for each of the primary studies included in the meta-analysis.These data were used for one of the research chapters of the author's PhD thesis, available here https://discovery.ucl.ac.uk/id/eprint/10096351<br>