cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4806619.v1
title: Dataset 1: Genotyping results for 111 single nucleotide polymorphisms (SNPs) typed in 2486 Plasmodium falciparum samples collected from primary school children during a parasitological survey in western Kenya in 2009 and 2010.

description: The columns contain the following information: sample_id, unique sample identifier; admin1, provincial location of school; district_name, district location of school; date_visit, date of sample collection; assay_code, name of assay; allele1 and allele2, alternative alleles at a specific SNP position; result, genotype call after processing; allele_ratio1, proportion of allele 1; allele_ratio2, proportion of allele 2; pass_fail, coding of SNP based on availability of valid genotype (pass=1) or lack of a valid genotype (fail=0). Geospatial data for individual school locations is considered sensitive data and therefore cannot be made open access. However, it can be accessed through a request to our data governance committee at dgc@kemri-wellcome.org. The criteria for such access is specified in detail in the data sharing guidelines under which the DGC operates, and relates to a) addressing health research, b)operating within the bounds of informed consent, c)complying with confidentiality procedures, d) mitigating potential harm to participants in research.
DOI: 10.6084/m9.figshare.4806616.v1
title: The effect of initial treatment on hearing prognosis in idiopathic sudden sensorineural hearing loss: a nationwide survey in Japan

description: <b>Objective:</b> To investigate the hearing prognosis of idiopathic sudden sensorineural hearing loss (SSNHL) treated with different initial therapies. <b>Methods:</b> Subjects consisted of patients diagnosed with idiopathic SSNHL within 7 days from onset and showing severe hearing loss (≥60 dB), who were registered in a Japanese multicenter database between April 2014 and March 2016. Subjects were divided into four groups according to initial therapy: (1) steroids, (2) steroids + Prostaglandins (PGs), (3) intratympanic steroids (ITS), and (4) no steroids. Hearing outcomes were compared among the groups. <b>Results:</b> In total, 1305 patients were enrolled. The final hearing level and hearing gain of patients treated with steroids + PGs were significantly higher than those of patients treated with steroids alone or no steroids. The ratio of good prognosis (complete recovery or marked improvement) in patients treated with steroids + PGs was higher than that in patients treated with steroids alone or no steroids. There was no difference in the prognosis of patients treated with steroids alone or no steroids. <b>Conclusion:</b> A large number of patients with idiopathic SSNHL were registered in a multicenter database. PG use in combination with steroid administration was associated with a good hearing prognosis in patients with severe hearing loss.
DOI: 10.6084/m9.figshare.4806598
title: Supplementary Material for: Determinants of Advanced Bone Age in Childhood Obesity

description: <i>Background:</i> Childhood obesity is associated with advanced bone age (BA). Previous studies suggest that androgens, oestrogens, sex hormone-binding globulin, and insulin are responsible for this phenomenon, but results are contradictory and might be biased by confounders. We aim to elucidate this matter by applying a multivariate approach. <i>Method:</i> We performed a correlation analysis of BA standard deviation score (SDS) with age- and sex-specific SDS for androgens, oestrogens, and with indicators of insulin secretion derived from oral glucose tolerance testing, in a group of obese children. A multivariate analysis was performed to investigate which parameters were independently predictive of BA SDS. <i>Results:</i> In this cohort (<i>n</i> = 101; mean age 10.9 years; mean BA 11.8 years; mean BMI SDS 3.3), BMI SDS was significantly correlated to BA SDS (<i>r</i> = 0.55, <i>p</i> &lt; 0.001). In a regression analysis in the total cohort (<i>B</i> = 0.27, <i>p</i> &lt; 0.001) as well as in females (<i>B</i> = 0.34, <i>p</i> = 0.042), males (<i>B</i> = 0.31, <i>p</i> = 0.006), and pubertal children (<i>B</i> = 0.32, <i>p</i> = 0.046), dehydroepiandrosterone sulphate (DHEAS) showed a positive, independent association with BA SDS. No association with indicators of insulin secretion was found. <i>Conclusion:</i> BMI SDS is highly correlated to BA SDS in obese children. Increased DHEAS has a central role in advanced BA in obese children.
DOI: 10.6084/m9.figshare.4806598.v2
title: Supplementary Material for: Determinants of Advanced Bone Age in Childhood Obesity

description: <i>Background:</i> Childhood obesity is associated with advanced bone age (BA). Previous studies suggest that androgens, oestrogens, sex hormone-binding globulin, and insulin are responsible for this phenomenon, but results are contradictory and might be biased by confounders. We aim to elucidate this matter by applying a multivariate approach. <i>Method:</i> We performed a correlation analysis of BA standard deviation score (SDS) with age- and sex-specific SDS for androgens, oestrogens, and with indicators of insulin secretion derived from oral glucose tolerance testing, in a group of obese children. A multivariate analysis was performed to investigate which parameters were independently predictive of BA SDS. <i>Results:</i> In this cohort (<i>n</i> = 101; mean age 10.9 years; mean BA 11.8 years; mean BMI SDS 3.3), BMI SDS was significantly correlated to BA SDS (<i>r</i> = 0.55, <i>p</i> &lt; 0.001). In a regression analysis in the total cohort (<i>B</i> = 0.27, <i>p</i> &lt; 0.001) as well as in females (<i>B</i> = 0.34, <i>p</i> = 0.042), males (<i>B</i> = 0.31, <i>p</i> = 0.006), and pubertal children (<i>B</i> = 0.32, <i>p</i> = 0.046), dehydroepiandrosterone sulphate (DHEAS) showed a positive, independent association with BA SDS. No association with indicators of insulin secretion was found. <i>Conclusion:</i> BMI SDS is highly correlated to BA SDS in obese children. Increased DHEAS has a central role in advanced BA in obese children.
DOI: 10.6084/m9.figshare.4806559
title: Data set: Decision-related pupil dilation reflects upcoming choice and individual bias.

description: This is the data from de Gee JW, Knapen T & Donner TH. 2014. Decision-related pupil dilation reflects upcoming choice and individual bias. Proceedings of the National Academy of Sciences USA, 111(5), E618-E625.<br>See https://github.com/jwdegee/2014_PNAS for the analysis code.
DOI: 10.6084/m9.figshare.4806562
title: Data set: Dynamic modulation of decision biases by brainstem arousal systems

description: This is the data from de Gee JW, Colizoli O, Kloosterman NA, Knapen T, Nieuwenhuis S & Donner TH. 2017. Dynamic modulation of decision biases by brainstem arousal systems. eLife.<br>See https://github.com/jwdegee/2017_eLife for the analysis code.
DOI: 10.6084/m9.figshare.4806544
title: MD simulations of P-glycoprotein started from three different crystal strucures: 3G5U, 4M1M and 4KSB

description: Molecular simulations of mouse P-glycoprotein started from three different crystal structures with PDB IDs corresponding to 3G5U, 4KSB and 4M1M. The protein was transferred to POPC/cholesterol bilayer, followed by energy minimization and 10 ns equilibration period. All the simulations were performed in Gromacs 3.3.3 in conjunction with GROMOS54a7 force field at 300 K and pressure of 1 bar. Each system was run in triplicates for 200 ns. <br><br>The uploaded fileset contains:<br> - MD protocol used to run simulations for 3G5U, 4M1M and 4KSB systems; <br><br> - Example input file for a production run for each system (3G5U_run1.mdp, 4M1M_run1.mdp, 4KSB_run1.mdp);<br><br> - System topologies (3G5U_memb.top, 4M1M_memb.top, 4KSB_memb.top) and relevant parameter files (3g5u.itp, 4m1m.itp, 4ksb.itp, CLR.itp, POPC.itp, vdw_OML_CH3L.itp); <br> <br> - Set of three trajectories containing membrane-embedded P-glycoprotein with 1000 frames for each simulated system (snapshots printed every 200 ps);<br><br> - Movies generated from each trajectory with a more detailed description provided in <i>Movie_Legends.pdf</i>;<br><br> - Model data calculated using principal component analysis method, including the covariance matrices, for each replica (<i>3G5U1-3.eda.npz, 4KSB1-3.eda.npz, 4M1M1-3.eda.npz</i>) and for the concatenated trajectory containing all 9 replicas (<i>3G5U_4KSB_4M1M.eda.npz</i>). The files containing data for the transmembrane domain only have the <i>tmd </i>prefix. These models can be further explored in ProDy package by using <i>loadModel() </i>function. <br><br> - Figures representing cholesterol distributions in the upper (dark violet) and lower leaflets (light violet) in all three systems at the beginning and at the end of each simulation.<br><br><br> <br><br><br>
DOI: 10.6084/m9.figshare.4806559.v2
title: Data set: Decision-related pupil dilation reflects upcoming choice and individual bias.

description: This is the data from de Gee JW, Knapen T & Donner TH. 2014. Decision-related pupil dilation reflects upcoming choice and individual bias. Proceedings of the National Academy of Sciences USA, 111(5), E618-E625.<br>See https://github.com/jwdegee/2014_PNAS for the analysis code.
DOI: 10.6084/m9.figshare.4806562.v2
title: Data set: Dynamic modulation of decision biases by brainstem arousal systems

description: This is the data from de Gee JW, Colizoli O, Kloosterman NA, Knapen T, Nieuwenhuis S & Donner TH. 2017. Dynamic modulation of decision biases by brainstem arousal systems. eLife.<br>See https://github.com/jwdegee/2017_eLife for the analysis code.
DOI: 10.6084/m9.figshare.4806559.v1
title: Data set: Decision-related pupil dilation reflects upcoming choice and individual bias.

description: This is the data from de Gee JW, Knapen T & Donner TH. 2014. Decision-related pupil dilation reflects upcoming choice and individual bias. Proceedings of the National Academy of Sciences USA, 111(5), E618-E625.<br>See https://github.com/jwdegee/2014_PNAS for the analysis code.
DOI: 10.6084/m9.figshare.4806562.v1
title: Data set: Dynamic modulation of decision biases by brainstem arousal systems

description: This is the data from de Gee JW, Colizoli O, Kloosterman NA, Knapen T, Nieuwenhuis S & Donner TH. 2017. Dynamic modulation of decision biases by brainstem arousal systems. eLife.<br>See https://github.com/jwdegee/2017_eLife for the analysis code.
DOI: 10.6084/m9.figshare.4806544.v3
title: MD simulations of P-glycoprotein started from three different crystal strucures: 3G5U, 4M1M and 4KSB

description: Molecular simulations of mouse P-glycoprotein started from three different crystal structures with PDB IDs corresponding to 3G5U, 4KSB and 4M1M. The protein was transferred to POPC/cholesterol bilayer, followed by energy minimization and 10 ns equilibration period. All the simulations were performed in Gromacs 3.3.3 in conjunction with GROMOS54a7 force field at 300 K and pressure of 1 bar. Each system was run in triplicates for 200 ns. <br><br>The uploaded fileset contains:<br> - MD protocol used to run simulations for 3G5U, 4M1M and 4KSB systems; <br><br> - Example input file for a production run for each system (3G5U_run1.mdp, 4M1M_run1.mdp, 4KSB_run1.mdp);<br><br> - System topologies (3G5U_memb.top, 4M1M_memb.top, 4KSB_memb.top) and relevant parameter files (3g5u.itp, 4m1m.itp, 4ksb.itp, CLR.itp, POPC.itp, vdw_OML_CH3L.itp); <br> <br> - Set of three trajectories containing membrane-embedded P-glycoprotein with 1000 frames for each simulated system (snapshots printed every 200 ps);<br><br> - Movies generated from each trajectory with a more detailed description provided in <i>Movie_Legends.pdf</i>. <br><br><br>
DOI: 10.6084/m9.figshare.4806496
title: 100% Renewable Power Generation in 2040: The Case of Java-Bali Region, Indonesia

description: A sustainable and dependable electricity is needed to continue the economic significance of Java-Bali (JB) region in the future. This paper summarizes the renewable resources in JB region from literatures available in peer-reviewed journals, publicly available government documents, and international agencies reports, then projects it to meet current and 2040 system stability.Renewable energy resources in the region are identified in the form of geothermal, hydropower, biomass, solar PV, and wind energy. If it is available by now, renewable energy resources can reach 2016 system stability, but extensive increase in solar PV capacity and efficiency measures in all sector is needed to meet 2040 demand. Political commitment from national to subnational level is also needed for the transition to happen.<br>The datasets for the graphs and tables are available in the supplied Excel file.
DOI: 10.6084/m9.figshare.4805848
title: MSR 2017 Attractiveness replication package

description: Replication package for the MSR project titled "The Impact of the Adoption of Continuous Integration on Developer Attraction and Retention".
DOI: 10.6084/m9.figshare.4805842
title: TRACULA tract profiles for each of the 18 identified fiber tracts in old (age &gt; 13.0 yrs.) and young (age &lt;= 13.0 yrs.) participants

description: <pre>Shown are the TRACULA tract profiles for each of the 18 identified fiber tracts in old (age &gt; 13.0 yrs.) and young (age &lt;= 13.0 yrs.) participants. Plotted is FA (±SE) along the core of the fiber tract (y-axis) at equidistant points (x-axis). Shaded regions represent locations in which p &lt; 0.05, FDR-corrected.</pre>
DOI: 10.6084/m9.figshare.4805839
title: TRACULA tract profiles for each of the 18 identified fiber tracts in girls and boys

description: <pre>Shown are the TRACULA tract profiles for each of the 18 identified fiber tracts in girls and boys. Plotted are FA, RD, AD, and MD (± SE) along the core of the fiber tract (y-axis) at equidistant points (x-axis). Shaded regions represent locations in which p &lt; 0.05, FDR-corrected.</pre>
DOI: 10.6084/m9.figshare.4805836
title: Automated Fiber Quantification (AFQ) tract profiles for the 8 corpus callosum segments in old (age &gt; 13.0 yrs.) and young (age &lt;= 13.0 yrs.) participants

description: <pre>Shown are the Automated Fiber Quantification (AFQ) tract profiles for the 8 corpus callosum segments in old (age &gt; 13.0 yrs.) and young (age &lt;= 13.0 yrs.) participants. Plotted are FA, RD, AD, and MD (± SE) along the core of the fiber tract (y-axis) at 100 equidistant points (x-axis). The left hemisphere is on the left (location 0 - 49) and the right hemisphere is on the right (location 51 - 100) with midsagittal at location 50.</pre>
DOI: 10.6084/m9.figshare.4805848.v1
title: attractiveness.r

description: Replication package fore the MSR project titled "The Impact of the Adoption of Continuous Integration on Developer Attraction and Retention<br>"
DOI: 10.6084/m9.figshare.4805827
title: Automated Fiber Quantification (AFQ) tract profiles for each of the 20 identified fiber tracts in old (age &gt; 13.0 yrs.) and young (age &lt;= 13.0 yrs.) participants

description: <pre>Shown are the Automated Fiber Quantification (AFQ) tract profiles for each of the 20 identified fiber tracts in old (age &gt; 13.0 yrs.) and young (age &lt;= 13.0 yrs.) participants. Plotted are FA, RD, AD, and MD (± SE) along the core of the fiber tract (y-axis) at 100 equidistant points (x-axis). Shaded regions represent locations in which p &lt; 0.05, FDR-corrected.</pre>
DOI: 10.6084/m9.figshare.4805830
title: Automated Fiber Quantification (AFQ) tract profiles for the 8 corpus callosum segments in girls and boys

description: <pre>Shown are the Automated Fiber Quantification (AFQ) tract profiles for the 8 corpus callosum segments in girls and boys. Plotted is FA (± SE) along the core of the fiber tract (y-axis) at 100 equidistant points (x-axis). The left hemisphere is on the left (location 0 - 49) and the right hemisphere is on the right (location 51 - 100) with midsagittal at location 50. Shaded regions represent locations in which p &lt; 0.05, FDR-corrected.</pre>
DOI: 10.6084/m9.figshare.4805797
title: Supplemental file 3 4 5.fasta

description: <em>Supplemental file 3 De novo</em> assembly of clean readSupplemental file 4 The sequences of the 105,222 genesSupplemental file 4, 5 The annotation of the 105,222 genes
DOI: 10.6084/m9.figshare.4805809
title: Automated Fiber Quantification (AFQ) tract profiles for each of the 20 identified fiber tracts in girls and boys

description: <pre>Shown are the Automated Fiber Quantification (AFQ) tract profiles for each of the 20 identified fiber tracts in girls and boys. Plotted are FA, RD, AD, and MD (± SE) along the core of the fiber tract (y-axis) at 100 equidistant points (x-axis). Shaded regions represent locations in which p &lt; 0.05, FDR-corrected.</pre>
DOI: 10.6084/m9.figshare.4805761
title: Texas Bombus Records

description: This dataset contains 3,500+ bumble bee (<i>Bombus spp.) </i>records from the state of Texas, spanning 1897-2016. These data come from natural history collections, citizen science repositories, and field research.
DOI: 10.6084/m9.figshare.4805737
title: Dorsal root ganglia neurite outgrowth measured as a function of changes in microelectrode array resistance

description: cultured DRG on a microelectrode array. Please see PLOS ONE publication for specific details.
DOI: 10.6084/m9.figshare.4805737.v1
title: Dorsal root ganglia neurite outgrowth measured as a function of changes in microelectrode array resistance

description: cultured DRG on a microelectrode array. Please see PLOS ONE publication for specific details.
DOI: 10.6084/m9.figshare.4805719
title: Structural Equation Models for Dealing With Spatial Confounding

description: In regression analyses of spatially structured data, it is common practice to introduce spatially correlated random effects into the regression model to reduce or even avoid unobserved variable bias in the estimation of other covariate effects. If besides the response the covariates are also spatially correlated, the spatial effects may confound the effect of the covariates or vice versa. In this case, the model fails to identify the true covariate effect due to multicollinearity. For highly collinear continuous covariates, path analysis and structural equation modeling techniques prove to be helpful to disentangle direct covariate effects from indirect covariate effects arising from correlation with other variables. This work discusses the applicability of these techniques in regression setups, where spatial and covariate effects coincide at least partly and classical geoadditive models fail to separate these effects. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.4805713
title: Improved Statistical Methods for Evaluation of Stability of In Vitro Diagnostic Reagents

description: In Vitro diagnostic (IVD) reagent stability is typically evaluated using regression analysis of measurand drift across time following CLSI guideline EP25-A. The corresponding stability duration establishment has several limitations. The stability duration conclusion is based on a two-stage acceptance criteria using the p-value of the regression slope followed by the 95% confidence interval (CI) on the fitted regression line if the p-value &lt; 0.05. This analysis technique is based on traditional statistical hypothesis testing; however, the statistical equivalence testing framework better represents the goals of IVD reagent stability evaluation. The resulting stability duration CI does not achieve 95% coverage probability and the statistical properties of the estimated stability duration are substantially impacted by presence of common variance components not accounted for during power analysis and by not accounting for variability in the baseline estimate. The current proposal based on the equivalence testing framework uses a one-stage acceptance criteria based on the 95% CI for proportional measurand drift derived from the regression fit. The proposed methodology was applied to automated immunoassay data (Akbas et al., 2016). Monte Carlo simulation studies are presented to illustrate the improved statistical properties of the current proposal along with an example power analysis for study design.
DOI: 10.6084/m9.figshare.4805749.v1
title: Bengalese Finch song repository

description: This is a collection of song from four Bengalese finches recorded in the Sober lab at Emory University. The song has been hand-labeled by two of the authors. We share it as a means of testing different machine learning algorithms for classifying the elements of birdsong, known as syllables. A Python package, hybrid-vocal-classifier (HVC), has been tested using this dataset: https://github.com/NickleDave/hybrid-vocal-classifier. <br>The actual sound files have the extension .cbin and were collected using the program EvTAF. They can be loaded with the `load_cbin` function in the `evfuncs` module of HVC. Each .cbin file has an associated .cbin.not.mat file that contains song syllable onsets, offsets, labels, etc. These files can be opened with the `load_notmat` function in the `evfuncs` module. Each .cbin file also has associated .tmp and .rec files also created by EvTAF. Those files are not strictly required to work with this dataset but are included for completeness.<br>
DOI: 10.6084/m9.figshare.4805707
title: The Wilcoxon–Mann–Whitney Procedure Fails as a Test of Medians

description: To illustrate and document the tenuous connection between the Wilcoxon–Mann–Whitney (WMW) procedure and medians, its relationship to mean ranks is first contrasted with the relationship of a <i>t</i>-test to means. The quantity actually tested: Pr ^(X1&lt;X2)+ Pr ^(X1=X2)/2 is then described and recommended as the basis for an alternative summary statistic that can be employed instead of medians. In order to graphically represent an estimate of the quantity: Pr(<i>X</i><sub>1</sub> &lt; <i>X</i><sub>2</sub>) + Pr(<i>X</i><sub>1</sub> = <i>X</i><sub>2</sub>)/2, use of a bubble plot, an ROC curve and a dominance diagram are illustrated. Several counter-examples (real and constructed) are presented, all demonstrating that the WMW procedure fails to be a test of medians. The discussion also addresses another, less common and perhaps less clear cut, but potentially even more important misconception: that the WMW procedure requires continuous data in order to be valid. Discussion of other issues surrounding the question of the WMW procedure and medians is presented, along with the authors' teaching experience with the topic. SAS code used for the examples is included as supplementary material.
DOI: 10.6084/m9.figshare.4805713.v1
title: Improved Statistical Methods for Evaluation of Stability of In Vitro Diagnostic Reagents

description: In Vitro diagnostic (IVD) reagent stability is typically evaluated using regression analysis of measurand drift across time following CLSI guideline EP25-A. The corresponding stability duration establishment has several limitations. The stability duration conclusion is based on a two-stage acceptance criteria using the p-value of the regression slope followed by the 95% confidence interval (CI) on the fitted regression line if the p-value &lt; 0.05. This analysis technique is based on traditional statistical hypothesis testing; however, the statistical equivalence testing framework better represents the goals of IVD reagent stability evaluation. The resulting stability duration CI does not achieve 95% coverage probability and the statistical properties of the estimated stability duration are substantially impacted by presence of common variance components not accounted for during power analysis and by not accounting for variability in the baseline estimate. The current proposal based on the equivalence testing framework uses a one-stage acceptance criteria based on the 95% CI for proportional measurand drift derived from the regression fit. The proposed methodology was applied to automated immunoassay data (Akbas et al., 2016). Monte Carlo simulation studies are presented to illustrate the improved statistical properties of the current proposal along with an example power analysis for study design.