cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.6243644
title: Additional file 2: of Ouroboros resembling competitive endogenous loop (ORCEL) in circular RNAs revealed through transcriptome sequencing dataset analysis

description: A complete list of ORCEL (Ouroboros Resembling Competitive Endogenous Loop) reported in this article. (XLSX 59 kb)
DOI: 10.6084/m9.figshare.6243629
title: Additional file 1: of Ouroboros resembling competitive endogenous loop (ORCEL) in circular RNAs revealed through transcriptome sequencing dataset analysis

description: A detail list of these circRNAs, as well as their corresponding SRPBM and FPKM values within the samples. (XLSX 528 kb)
DOI: 10.6084/m9.figshare.6243629.v1
title: Additional file 1: of Ouroboros resembling competitive endogenous loop (ORCEL) in circular RNAs revealed through transcriptome sequencing dataset analysis

description: A detail list of these circRNAs, as well as their corresponding SRPBM and FPKM values within the samples. (XLSX 528 kb)
DOI: 10.6084/m9.figshare.6243545
title: Additional file 1: of Clinical decision making in cancer care: a review of current and future roles of patient age

description: Appendix Details on identified references. Full references, year of publication, country of publication, type of article, subject of article and type of cancer investigated. (XLSX 45Â kb)
DOI: 10.6084/m9.figshare.6243545.v1
title: Additional file 1: of Clinical decision making in cancer care: a review of current and future roles of patient age

description: Appendix Details on identified references. Full references, year of publication, country of publication, type of article, subject of article and type of cancer investigated. (XLSX 45Â kb)
DOI: 10.6084/m9.figshare.6243539
title: Additional file 1: of Predicting response to checkpoint inhibitors in melanoma beyond PD-L1 and mutational burden

description: Table S1 Clinical characteristics of the melanoma cohort. Table S2 Survival analyses for studied biomarkers. Table S3 Comprehensive gene expression and mutational profile of melanoma cohort. Table S4 Over representation test results of categorical variables for gene expression clusters. Table S5 Over representation test results of gene ranks for gene expression clusters. Table S6 ORR for all biomarker groups studied. Table S7 Objective response rates for studied biomarkers. Table S8 Objective response counts for melanoma cohort. Table S9 ORR for training set response score groups. (XLSX 1378 kb)
DOI: 10.6084/m9.figshare.6243539.v1
title: Additional file 1: of Predicting response to checkpoint inhibitors in melanoma beyond PD-L1 and mutational burden

description: Table S1 Clinical characteristics of the melanoma cohort. Table S2 Survival analyses for studied biomarkers. Table S3 Comprehensive gene expression and mutational profile of melanoma cohort. Table S4 Over representation test results of categorical variables for gene expression clusters. Table S5 Over representation test results of gene ranks for gene expression clusters. Table S6 ORR for all biomarker groups studied. Table S7 Objective response rates for studied biomarkers. Table S8 Objective response counts for melanoma cohort. Table S9 ORR for training set response score groups. (XLSX 1378 kb)
DOI: 10.6084/m9.figshare.6243533
title: Additional file 2: Tables S2, S3, and S5. of Delineation of condition specific Cis- and Trans-acting elements in plant promoters under various Endo- and exogenous stimuli

description: Top 10 significant entries of overrepresented 3-mer and 4-mer sequences for heat stress specific TFsÂ andÂ ABA-CsTFs, respectively, and CsTFs lists in three condition datasets. (XLS 143Â kb)
DOI: 10.6084/m9.figshare.6243533.v1
title: Additional file 2: Tables S2, S3, and S5. of Delineation of condition specific Cis- and Trans-acting elements in plant promoters under various Endo- and exogenous stimuli

description: Top 10 significant entries of overrepresented 3-mer and 4-mer sequences for heat stress specific TFsÂ andÂ ABA-CsTFs, respectively, and CsTFs lists in three condition datasets. (XLS 143Â kb)
DOI: 10.6084/m9.figshare.6243254
title: PM25.data.China

description: This is a minimal PM2.5 dataset from 2013 to 2017 for China cites and all these data is from a third party, that is “ PM2.5 in”, whose link is "http://www.pm25.in/". More comprehensive and up-to-date data can be downloaded from this site for free.
DOI: 10.6084/m9.figshare.6243254.v1
title: All the available PM2.5 data during 2013 to 2017 for China cities

description: This is a minimal PM2.5 dataset and all this data is from a third party, that is “ PM2.5 in”, whose link is "http://www.pm25.in/". More comprehensive and up-to-date data can be downloaded from this site for free.
DOI: 10.6084/m9.figshare.12894149.v1
title: Dataset of 'MODIS FIRMS and Maximum entropy method-based forest fire prediction mapping of Sikkim Himalaya.'

description: Globally incidents of forest fire events are in the rise due to human encroachment into wilderness and climate change. Likewise, Sikkim suffers seasonal instances of frequent forest fire during the dry winter months. To address this issue, a GIS-aided and MaxEnt machine learning-based forest fire prediction map has been prepared using forest fire inventory database and maps of environmental features. The study indicates that amongst the environmental features, population density and proximity to roads are the major determinants of the forest fire. This indicates the role of human activities on the incidences of a forest fire. Model validation criteria like ROC curve, correlation coefficient and Cohen’s Kappa show a good predictive capability (AUC = 0.95, COR = 0.78, κ = 0.78). The outcomes of this study in the form of a forest fire prediction map can aid the stakeholders of the forest in taking informed mitigation measures.
DOI: 10.6084/m9.figshare.12894149
title: Dataset of 'MODIS FIRMS and Maximum entropy method-based forest fire prediction mapping of Sikkim Himalaya.'

description: Globally incidents of forest fire events are in the rise due to human encroachment into wilderness and climate change. Likewise, Sikkim suffers seasonal instances of frequent forest fire during the dry winter months. To address this issue, a GIS-aided and MaxEnt machine learning-based forest fire prediction map has been prepared using forest fire inventory database and maps of environmental features. The study indicates that amongst the environmental features, population density and proximity to roads are the major determinants of the forest fire. This indicates the role of human activities on the incidences of a forest fire. Model validation criteria like ROC curve, correlation coefficient and Cohen’s Kappa show a good predictive capability (AUC = 0.95, COR = 0.78, κ = 0.78). The outcomes of this study in the form of a forest fire prediction map can aid the stakeholders of the forest in taking informed mitigation measures.
DOI: 10.6084/m9.figshare.6242015
title: bow shock simulation

description: bow shock brakout<br>
DOI: 10.6084/m9.figshare.6242015.v1
title: bow shock simulation

description: bow shock brakout<br>
DOI: 10.6084/m9.figshare.6241799.v1
title: Mosaic heterogeneity case

description: IF and FISH data of a HER2 mosaic heterogeneity case
DOI: 10.6084/m9.figshare.6241796
title: cancer heterogeneity cases

description: Immunofluorescence and fluorescence in situ hybridization signals in cluster and mosaic heterogeneous cases
DOI: 10.6084/m9.figshare.6241796.v2
title: cancer heterogeneity cases

description: Immunofluorescence and fluorescence in situ hybridization signals in cluster and mosaic heterogeneous cases
DOI: 10.6084/m9.figshare.6241796.v1
title: Cluster heterogeneity case

description: Immunofluorescence and fluorescence in situ hybridization signals in a cluster heterogeneous case
DOI: 10.15131/shef.data.6241694
title: High Purcell factor generation of coherent on-chip single photons

description: Data from the manuscript "High Purcell factor generation of coherent on-chip single photons".<br>Abstract:<br>On-chip single-photon sources are key components for integrated photonic quantum technologies. Semiconductor quantum dots can exhibit near-ideal single-photon emission but this can be significantly degraded in on-chip geometries owing to nearby etched surfaces. A long-proposed solution to improve the indistinguishablility is by using the Purcell effect to reduce the radiative lifetime. However, until now only modest Purcell enhancements have been observed. Here we use pulsed resonant excitation to eliminate slow relaxation paths, revealing a highly Purcell-shortened radiative lifetime (22.7 ps) in a waveguide-coupled quantum dot–photonic crystal cavity system. This leads to near-lifetime-limited single-photon emission which retains high indistinguishablility (93.9%) on a timescale in which 20 photons may be emitted. Nearly background-free pulsed resonance fluorescence is achieved under π-pulse excitation, enabling demonstration of an on-chip, on-demand single-photon source with very high potential repetition rates.
DOI: 10.6084/m9.figshare.6241070
title: TENS dataset for selective nerve stimulation

description: Set of files regarding a simulation environment for a transcutaneous electrical nerve stimulation (TENS) system.This set contains the following:- Files to create Matlab nerve models from a FEM of a human finger- Four main Matlab nerve models.- Matlab scripts to evaluate different stimulation cases for the modelled nerves.
DOI: 10.6084/m9.figshare.6241070.v1
title: case2.sif

description: Set of files regarding a simulation environment for a transcutaneous electrical nerve stimulation (TENS) system.This set contains the following:- Files to create Matlab nerve models from a FEM of a human finger- Four main Matlab nerve models.- Matlab scripts to evaluate different stimulation cases for the modelled nerves.
DOI: 10.6084/m9.figshare.6241070.v2
title: case2.sif

description: Set of files regarding a simulation environment for a transcutaneous electrical nerve stimulation (TENS) system.This set contains the following:- Files to create Matlab nerve models from a FEM of a human finger- Four main Matlab nerve models.- Matlab scripts to evaluate different stimulation cases for the modelled nerves.
DOI: 10.6084/m9.figshare.6239573
title: Perineum status

description: Tabla de datos del método SWEP para el estado del periné
DOI: 10.6084/m9.figshare.6239573.v1
title: Perineum status

description: Tabla de datos del método SWEP para el estado del periné
DOI: 10.6084/m9.figshare.6239573.v3
title: Perineum status

description: Tabla de datos del método SWEP para el estado del periné
DOI: 10.6084/m9.figshare.6239573.v2
title: Perineum status

description: Tabla de datos del método SWEP para el estado del periné
DOI: 10.6084/m9.figshare.6239021
title: Using the Latent Correlations to Measure the Association Between Continuous and Binary Markers With Repeated Measurements

description: This study was motivated by one of the important challenges in sleep research: estimating not only an overall association between objective and subjective sleep measures but at within- and between-subject levels as well. Comparing to the literature on the association between two continuous or two binary outcomes, to our knowledge, fewer works were published for the case when one outcome is continuous and the other is binary while both are measured repeatedly. We address this problem by considering a latent correlation (LC) that is the correlation between two continuous outcomes. The first is the original observed continuous outcome while the second is an underlying latent variable, dichotomization of which produces the original binary outcome. Building upon a flexible Bayesian generalized linear mixed model fitted by the MCMC, our proposal allows estimation of the total correlation, and the between- and within-subject correlations simultaneously. The goal of joint estimation of all these correlations, to our knowledge, was not fulfilled in previous proposals (either the between- or within-subject correlation needed to be fixed at zero). Moreover, the approach avoids bias of a two-step procedure and does not rely on approximation of the covariance matrix and hence the correlations. It provides accurate estimates covering a wide range of values. We can also incorporate the cases of missing data, covariate adjustment, and comparison between subgroups. Furthermore, these advantages are achieved at a low computational cost. We demonstrate properties and implementation of our proposal with a large simulation study and with real data from two clinical trials of an insomnia drug where one of the questions is how continuous biomarkers derived from the polysomnographic measurements are associated with the binary patient-reported sleep quality. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.6239021.v1
title: Using the Latent Correlations to Measure the Association Between Continuous and Binary Markers With Repeated Measurements

description: This study was motivated by one of the important challenges in sleep research: estimating not only an overall association between objective and subjective sleep measures but at within- and between-subject levels as well. Comparing to the literature on the association between two continuous or two binary outcomes, to our knowledge, fewer works were published for the case when one outcome is continuous and the other is binary while both are measured repeatedly. We address this problem by considering a latent correlation (LC) that is the correlation between two continuous outcomes. The first is the original observed continuous outcome while the second is an underlying latent variable, dichotomization of which produces the original binary outcome. Building upon a flexible Bayesian generalized linear mixed model fitted by the MCMC, our proposal allows estimation of the total correlation, and the between- and within-subject correlations simultaneously. The goal of joint estimation of all these correlations, to our knowledge, was not fulfilled in previous proposals (either the between- or within-subject correlation needed to be fixed at zero). Moreover, the approach avoids bias of a two-step procedure and does not rely on approximation of the covariance matrix and hence the correlations. It provides accurate estimates covering a wide range of values. We can also incorporate the cases of missing data, covariate adjustment, and comparison between subgroups. Furthermore, these advantages are achieved at a low computational cost. We demonstrate properties and implementation of our proposal with a large simulation study and with real data from two clinical trials of an insomnia drug where one of the questions is how continuous biomarkers derived from the polysomnographic measurements are associated with the binary patient-reported sleep quality. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.6238991
title: Multidimensional Scaling With Very Large Datasets

description: Multidimensional scaling has a wide range of applications when observations are not continuous but it is possible to define a distance (or dissimilarity) among them. However, standard implementations are limited when analyzing very large datasets because they rely on eigendecomposition of the full distance matrix and require very long computing times and large quantities of memory. Here, a new approach is developed based on projection of the observations in a space defined by a subset of the full dataset. The method is easily implemented. A simulation study showed that its performance are satisfactory in different situations and can be run in a short time when the standard method takes a very long time or cannot be run because of memory requirements.
DOI: 10.6084/m9.figshare.6238991.v2
title: Multidimensional Scaling With Very Large Datasets

description: Multidimensional scaling has a wide range of applications when observations are not continuous but it is possible to define a distance (or dissimilarity) among them. However, standard implementations are limited when analyzing very large datasets because they rely on eigendecomposition of the full distance matrix and require very long computing times and large quantities of memory. Here, a new approach is developed based on projection of the observations in a space defined by a subset of the full dataset. The method is easily implemented. A simulation study showed that its performance are satisfactory in different situations and can be run in a short time when the standard method takes a very long time or cannot be run because of memory requirements.
DOI: 10.6084/m9.figshare.6238991.v1
title: Multidimensional scaling with very large data sets

description: Multidimensional scaling has a wide range of applications when observations are not continuous but it is possible to define a distance (or dissimilarity) among them. However, standard implementations are limited when analyzing very large data sets because they rely on eigendecomposition of the full distance matrix and require very long computing times and large quantities of memory. Here, a new approach is developed based on projection of the observations in a space defined by a subset of the full data set. The method is easily implemented. A simulation study showed that its performance are satisfactory in different situations and can be run in a short time when the standard method takes a very long time or cannot be run because of memory requirements.
DOI: 10.6084/m9.figshare.6238901
title: Survival in the dark: strategies adopted by <i>Tetraselmis indica</i> (Chlorodendrophyceae, Chlorophyta)

description: The adaptive strategy of <i>Tetraselmis indica</i> to survive darkness was evaluated over a period of 182 days. Resting cells formation and reduction in catabolic activity facilitated dark survival and their rejuvenation. The occurrence of thick-walled cells (type 1) and thin-walled cells with the condensed chloroplast (type 2) in light-dark and dark conditions respectively indicated differential resting cell formation. The dissolved organic carbon remained nearly constant throughout the dark period signifying <i>T. indica</i> did not favour heterotrophy. Upon re-illumination of dark-adapted cells, the lag phase lengthened from 2 to 28 days when darkness period increased from 8 to 182 days, respectively. However, this negative influence on growth was compensated by an increase in growth rate from 0.35 to 0.95 d<sup>−1</sup>. This resurgence capability of <i>T. indica</i> after six months of dark exposure and distinctive resting cell formation indicate a differential population sustenance mechanism. Further elucidation of dark adaptability and survival strategies in <i>T. indica</i> may have significance in ecological and evolutionary processes.
DOI: 10.6084/m9.figshare.6238901.v1
title: Survival in the dark: strategies adopted by <i>Tetraselmis indica</i> (Chlorodendrophyceae, Chlorophyta)

description: The adaptive strategy of <i>Tetraselmis indica</i> to survive darkness was evaluated over a period of 182 days. Resting cells formation and reduction in catabolic activity facilitated dark survival and their rejuvenation. The occurrence of thick-walled cells (type 1) and thin-walled cells with the condensed chloroplast (type 2) in light-dark and dark conditions respectively indicated differential resting cell formation. The dissolved organic carbon remained nearly constant throughout the dark period signifying <i>T. indica</i> did not favour heterotrophy. Upon re-illumination of dark-adapted cells, the lag phase lengthened from 2 to 28 days when darkness period increased from 8 to 182 days, respectively. However, this negative influence on growth was compensated by an increase in growth rate from 0.35 to 0.95 d<sup>−1</sup>. This resurgence capability of <i>T. indica</i> after six months of dark exposure and distinctive resting cell formation indicate a differential population sustenance mechanism. Further elucidation of dark adaptability and survival strategies in <i>T. indica</i> may have significance in ecological and evolutionary processes.
DOI: 10.6084/m9.figshare.6238433.v1
title: Improvement of Mycobacterium tuberculosis detection by Xpert MTB/RIF Ultra: a head to head comparison on Xpert-negative samples

description: Sixty-eight decontaminated frozen samples (36 respiratory and 32 non-respiratory) collected over a 4-year period which were smear-negative, Xpert-negative but MTB culture-positive, were tested with Xpert MTB/RIF Ultra at the Unit of Microbiology of the S. Orsola-Malpighi University Hospital in Bologna (Italy). Database reports smear microscopy, mycobacterial culture, Xpert and Xpert Ultra results, Rif detection,semi-quantitative load and Ct results of IS1081, IS6110 and rpoB genes.<br>
DOI: 10.6084/m9.figshare.6238424
title: Net-Net AutoML of Ecosytems

description: AutoML prediction of ANN topologies able to predict complex ecological networks using shannon information theory
DOI: 10.6084/m9.figshare.6237608
title: Brazil road mortality rates for birds and mammals

description: Data and R scripts related to publication González-Suárez, M; Zanchetta Ferreira, F; Grilo, C (2018) Spatial and species-level predictions of road mortality risk using trait data Global Ecology and Biogeography. https://doi.org/10.1111/geb.12769<br>Data include: - 783 empirical road mortality rates from Brazil, representing 170 bird and 73 mammalian species ("Brazil_Roadkill_data.csv").- predicted road mortality rates for 1775 birds and 623 mammals from Brazil ("Predicted_roadkill_rates_for_Brazil.csv").- trait data for 1775 birds and 623 mammals from Brazil ("Aves_trait_data.csv", "Mammalia_trait_data_csv").<br>R scripts used for all analyses and figures in the mentioned paper.
DOI: 10.6084/m9.figshare.6237518
title: Are some individuals generally more behaviorally plastic than others? An experiment with sailfin mollies

description: Reversal learning, personality and mating tactic scores measured in male sailfin mollies <br>
DOI: 10.6084/m9.figshare.6237518.v2
title: Are some individuals generally more behaviorally plastic than others? An experiment with sailfin mollies

description: Reversal learning, personality and mating tactic scores measured in male sailfin mollies <br>
DOI: 10.6084/m9.figshare.6237518.v1
title: DataPlasticityRepeatabilityShare.txt

description: Reversal learning, personality and mating tactic scores measured in male sailfin mollies <br>
DOI: 10.6084/m9.figshare.6237197
title: Rediscovering a forgotten rodent of Patagonia and its phylogenetic implications

description: Cephalomyidae is an enigmatic caviomorph ‘family’ recorded in the Deseadan–Colhuehuapian SALMAs (South American Land Mammal Age) of Bolivia and Argentina. The validity and phylogenetic relationships of this group remain unconfirmed. <i>Litodontomys chubutensis</i> is one of the most poorly known cephalomyids, recorded only by a partial mandible with the complete dental series. Here we present a new specimen of <i>Litodontomys</i> from the same Deseadan locality as the holotype (Cabeza Blanca, Chubut, Argentina). It is a more complete and better preserved specimen from a larger and older individual. A phylogenetic analysis, performed to test the position of the genus and the validity and relationships of the family Cephalomyidae, recovered <i>Litodontomys</i> as the sister taxon of <i>Cephalomys</i> and confirmed the monophyly of the clade for the first time in an updated matrix and broader phylogenetic context.