cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11872176
title: Code and data to reproduce "The abundant-centre is not all that abundant: a comment to Osorio-Olvera et al. 2020 "

description: Code and data to reproduce our re-analysis of:<br>Osorio‐Olvera, Luis, et al. "Relationships between population densities and niche‐centroid distances in North American birds." <i>Ecology Letters</i>.<br><br><br>The re-analysis and comment can be cited as: <br>Dallas, T, L Santini, S Pironon. The abundant-centre is not all that abundant: a comment on Osorio-Olvera et al. 2020. doi: https://doi.org/10.1101/2020.02.27.968586<br><br>Dallas.Rmd is the main code file to reproduce the analyses. <br><br>d_omr, d_omr1, d_omr2 are the output csv files in case the user does not want to run the entire re-analysis (which will require that you download Osorio-Olvera et al (2020) data repo).<br>boxplot_rhos_by_methodPanel.pdf is a figure.<br>
DOI: 10.6084/m9.figshare.11872227
title: Extracellular recording of cerebellar Purkinje cells and labels of complex spikes from expert

description: 159 extracellular recordings of cerebellar Purkinje cells and labels of complex spikes from expert.
DOI: 10.6084/m9.figshare.11872176.v1
title: Code and data to reproduce "The abundant-centre is not all that abundant: a comment to Osorio-Olvera et al. 2020 "

description: Code and data to reproduce our re-analysis of:<br>Osorio‐Olvera, Luis, et al. "Relationships between population densities and niche‐centroid distances in North American birds." <i>Ecology Letters</i>.<br><br><br>The re-analysis and comment can be cited as: <br>Dallas, T, L Santini, S Pironon. The abundant-centre is not all that abundant: a comment on Osorio-Olvera et al. 2020. doi: https://doi.org/10.1101/2020.02.27.968586<br><br>Dallas.Rmd is the main code file to reproduce the analyses. <br><br>d_omr, d_omr1, d_omr2 are the output csv files in case the user does not want to run the entire re-analysis (which will require that you download Osorio-Olvera et al (2020) data repo).<br>boxplot_rhos_by_methodPanel.pdf is a figure.<br>
DOI: 10.6084/m9.figshare.11872110
title: Forner-Phillips, Mills, Ross (2020) Source Memory Task EEG Data

description: This data set was used for analysis in Forner-Phillips, Mills, and Ross (2020) "Tendency to Ruminate and Anxiety are Associated with Altered Alpha and Beta Oscillatory Power Dynamics During Memory for Contextual Details". Participants completed a source memory task while their brain activity was recorded with EEG. The task included a study phase followed by a test phase. During study, participants were shown non-nameable objects that appeared either on the right or left side of the computer screen. Participants were instructed to remember both the item and the side of the screen. During test, the studied objects were mixed in with unstudied objects and all were presented in the center of the screen. For each item the participant made a judgement of old right, old left, or new. Event markers in the data are as follows: S1: Fixation cross encoding, S2: Test object encoding, S3: Fixation cross retrieval, S4: Test object retrieval
DOI: 10.6084/m9.figshare.11872113
title: Effects of artificial light at night (ALAN) on European hedgehog activity at supplementary feeding stations.

description: Data from our controlled lighting experiment. Each activity or feeding block is made up of 10 minute time periods and whether one or more hedgehog were recorded in it.
DOI: 10.6084/m9.figshare.11872089
title: Complete Datasets from Prevalence, infected density or individual probability of infection? Assessing vector infection risk in the wild transmission of Chagas disease

description: Vector-borne infectious disease dynamics result mainly from the intertwined effect of the diversity, abundance and behaviour of hosts and vectors. Most studies, however, have analysed the relationship between host–species diversity and infection risk, focusing on vector population instead of individuals, probably dismissing the level at which the transmission process occurs. In this paper, we examine the importance of the host community in accounting for infection risk, at both population and individual levels, using the wild transmission of the protozoan that causes Chagas disease as a vector-borne disease model. Chagas disease is caused by <i>Trypanosoma cruzi</i>, transmitted by triatomine insects to mammals. We assessed if <i>T. cruzi</i> infection in vectors is explained by small mammal diversity and their densities (total and infected), when infection risk is measured at population level as infection prevalence (under frequency-dependent transmission approach) and as density of infected vectors (density-dependent transmission approach), and when measured at individual level as vector infection probability. We analysed the infection status of 1974 vectors and co-occurring small mammal hosts in a semiarid-Mediterranean ecosystem. Results revealed that regardless of the level of analysis, only one host rodent species accounted for most variation in vector infection risk, suggesting a key role in the transmission cycle. To determine the factors explaining vector-borne disease dynamics, infection risk should be assessed at different scales, reflecting the factors meaningful from the vector's perspective and considering vector class-specific features.
DOI: 10.6084/m9.figshare.11872113.v1
title: Effects of artificial light at night (ALAN) on European hedgehog activity at supplementary feeding stations.

description: Data from our controlled lighting experiment. Each activity or feeding block is made up of 10 minute time periods and whether one or more hedgehog were recorded in it.
DOI: 10.6084/m9.figshare.11872047
title: MOB-suite: Universal whole-sequence based plasmid typing and utility to prediction of host-range and epidemiological surveillance

description: Supplemental figure and tables from the manuscript: Universal whole-sequence based plasmid typing and utility to prediction of host-range and epidemiological surveillance<br><b></b>
DOI: 10.6084/m9.figshare.11872077
title: Lipidomics from Skm and WAT from mice with restrained OXPHOS

description: Lipidomics from skeletal muscle (SKM) and white adipose tissue (WAT) of mice with restrained OXPHOS in Skm and fed with high fat diet (HDF). Data obtained by Lipotype (https://www.lipotype.com/gclid=EAIaIQobChMIyeG1jK_g5wIVgvhRCh3KbgZuEAAYASAAEgIi0vD_BwE) and analized by Laura Formentini (PI in de Department of Molecular Biology in Centro de Biología Molecular ‘“Severo Ochoa’” (CBMSO)- Universidad Autónoma de Madrid (UAM), leading the project "Role of mitochondrial bioenergetics in skeletal muscle secretrome)during exercise and pathology".
DOI: 10.6084/m9.figshare.11872089.v2
title: Complete Datasets from Prevalence, infected density or individual probability of infection? Assessing vector infection risk in the wild transmission of Chagas disease

description: Vector-borne infectious disease dynamics result mainly from the intertwined effect of the diversity, abundance and behaviour of hosts and vectors. Most studies, however, have analysed the relationship between host–species diversity and infection risk, focusing on vector population instead of individuals, probably dismissing the level at which the transmission process occurs. In this paper, we examine the importance of the host community in accounting for infection risk, at both population and individual levels, using the wild transmission of the protozoan that causes Chagas disease as a vector-borne disease model. Chagas disease is caused by <i>Trypanosoma cruzi</i>, transmitted by triatomine insects to mammals. We assessed if <i>T. cruzi</i> infection in vectors is explained by small mammal diversity and their densities (total and infected), when infection risk is measured at population level as infection prevalence (under frequency-dependent transmission approach) and as density of infected vectors (density-dependent transmission approach), and when measured at individual level as vector infection probability. We analysed the infection status of 1974 vectors and co-occurring small mammal hosts in a semiarid-Mediterranean ecosystem. Results revealed that regardless of the level of analysis, only one host rodent species accounted for most variation in vector infection risk, suggesting a key role in the transmission cycle. To determine the factors explaining vector-borne disease dynamics, infection risk should be assessed at different scales, reflecting the factors meaningful from the vector's perspective and considering vector class-specific features.
DOI: 10.6084/m9.figshare.11872047.v1
title: MOB-suite: Universal whole-sequence based plasmid typing and utility to prediction of host-range and epidemiological surveillance

description: Supplemental figure and tables from the manuscript: Universal whole-sequence based plasmid typing and utility to prediction of host-range and epidemiological surveillance<br><b></b>
DOI: 10.6084/m9.figshare.11872077.v1
title: Lipidomics from Skm and WAT from mice with restrained OXPHOS

description: Lipidomics from skeletal muscle (SKM) and white adipose tissue (WAT) of mice with restrained OXPHOS in Skm and fed with high fat diet (HDF). Data obtained by Lipotype (https://www.lipotype.com/gclid=EAIaIQobChMIyeG1jK_g5wIVgvhRCh3KbgZuEAAYASAAEgIi0vD_BwE) and analized by Laura Formentini (PI in de Department of Molecular Biology in Centro de Biología Molecular ‘“Severo Ochoa’” (CBMSO)- Universidad Autónoma de Madrid (UAM), leading the project "Role of mitochondrial bioenergetics in skeletal muscle secretrome)during exercise and pathology".
DOI: 10.6084/m9.figshare.11872047.v3
title: MOB-suite: Universal whole-sequence based plasmid typing and utility to prediction of host-range and epidemiological surveillance

description: Supplemental figure and tables from the manuscript: Universal whole-sequence based plasmid typing and utility to prediction of host-range and epidemiological surveillance<br><b></b>
DOI: 10.6084/m9.figshare.11872077.v2
title: Lipidomics from Skm and WAT from mice with restrained OXPHOS

description: Lipidomics from skeletal muscle (SKM) and white adipose tissue (WAT) of mice with restrained OXPHOS in Skm and fed with high fat diet (HDF). Data obtained by Lipotype (https://www.lipotype.com/gclid=EAIaIQobChMIyeG1jK_g5wIVgvhRCh3KbgZuEAAYASAAEgIi0vD_BwE) and analized by Laura Formentini (PI in de Department of Molecular Biology in Centro de Biología Molecular ‘“Severo Ochoa’” (CBMSO)- Universidad Autónoma de Madrid (UAM), leading the project "Role of mitochondrial bioenergetics in skeletal muscle secretrome)during exercise and pathology".
DOI: 10.6084/m9.figshare.11872077.v3
title: Lipidomics from Skm and WAT from mice with restrained OXPHOS

description: Lipidomics from skeletal muscle (SKM) and white adipose tissue (WAT) of mice with restrained OXPHOS in Skm and fed with high fat diet (HDF). Data obtained by Lipotype (https://www.lipotype.com/gclid=EAIaIQobChMIyeG1jK_g5wIVgvhRCh3KbgZuEAAYASAAEgIi0vD_BwE) and analized by Laura Formentini (PI in de Department of Molecular Biology in Centro de Biología Molecular ‘“Severo Ochoa’” (CBMSO)- Universidad Autónoma de Madrid (UAM), leading the project "Role of mitochondrial bioenergetics in skeletal muscle secretrome)during exercise and pathology".
DOI: 10.6084/m9.figshare.11871999
title: SupplementalTable - Closed Genomes

description: Supplemental table listing the closed genomes used in the benchmarking of the MOB-suite and derivation of the valid clustering threshold range.
DOI: 10.6084/m9.figshare.11872047.v2
title: MOB-suite: Universal whole-sequence based plasmid typing and utility to prediction of host-range and epidemiological surveillance

description: Supplemental figure and tables from the manuscript: Universal whole-sequence based plasmid typing and utility to prediction of host-range and epidemiological surveillance<br><b></b>
DOI: 10.6084/m9.figshare.11871999.v1
title: SupplementalTable - Closed Genomes

description: Supplemental table listing the closed genomes used in the benchmarking of the MOB-suite and derivation of the valid clustering threshold range.
DOI: 10.6084/m9.figshare.11871894
title: Discriminations of active from inactive HDAC8 inhibitors Part II: Bayesian classification study to find molecular fingerprints

description: In continuation of our earlier work (Doi: 10.1080/07391102.2019.1661876), a statistically validated and robust Bayesian model was developed on a large diverse set of HDAC8 inhibitors. The training set comprised of 676 small molecules and 293 compounds were considered as test set molecules. The findings of this analysis will help to explore some major directions regarding the HDAC8 inhibitor designing approach. Acrylamide (G1-G3, G9), <i>N</i>-substituted 2-phenylimidazole (G4-G8, G9, G12-G13, G16-G19), benzimidazole (G10-G11), piperidine substituted pyrrole (G13-G14) groups, alkyl/aryl amide (G15) and aryloxy carboxamide (G20) fingerprints were found to play a crucial role in HDAC8 inhibitory activity whereas -CH-N=CH- (B1, B4-B6, B14) motif, benzamide (B2-B3, B9-B13, B16-B17) groups and heptazepine (B7-B8, B15, B18-B20) group were found to influence negatively the HDAC8 inhibitory activity. The importance of such fingerprints was further validated by the HDAC8 enzyme and related inhibitor interactions at the receptor level. These results are in close agreement with those of our previous work that validate each other. Moreover, this comparative learning may enrich future endeavours regarding the designing strategy of HDAC8 inhibitors.
DOI: 10.6084/m9.figshare.11871888
title: Plants with genetically encoded autoluminescence

description: <b>Supplementary Data from the manuscript "Plants with genetically encoded autoluminescence".</b><br><b>Folder "01. Raw files from IVIS Spectrum CT": <br></b>source images for Supplementary Figure 6. <br><b>Folder "02. Raw files from Sony Alpha ILCE-7M3 camera":</b> <br>photos with ISO 3200 and shutter speed 30 sec (source for Supplementary Figure 4d), as well as with ISO 20000, with corresponding dark frames captured with the same settings but with objective lens closed. Also, a photo with 500 ms exposure and ISO 204800. Images were acquired with Samyang 35mm T1.5 ED AS UMC VDSLR lens, T = 1.5, the distance between the camera sensor and the samples was 40 cm. <br><b>Folder "03. Analysis of luminescence intensity":<br></b>contains analysis of luminescence intensity of plant tissues.<br><br><b>Folder "0</b><b>4. Plasmid sequences</b><b>":<br></b>contains maps of plasmids used in the study. <br><br>- - -<br>Please note that this Supplementary Data submission is related to the version of the paper published in Nature Biotechnology. It is different from the version submitted with the original Biorxiv publication of the paper (https://www.biorxiv.org/content/10.1101/809376v1). Specifically, Biorxiv-related submission lacks plasmid maps and only contains analysis of luminescence from flowers, not from other tissues.
DOI: 10.6084/m9.figshare.11871894.v1
title: Discriminations of active from inactive HDAC8 inhibitors Part II: Bayesian classification study to find molecular fingerprints

description: In continuation of our earlier work (Doi: 10.1080/07391102.2019.1661876), a statistically validated and robust Bayesian model was developed on a large diverse set of HDAC8 inhibitors. The training set comprised of 676 small molecules and 293 compounds were considered as test set molecules. The findings of this analysis will help to explore some major directions regarding the HDAC8 inhibitor designing approach. Acrylamide (G1-G3, G9), <i>N</i>-substituted 2-phenylimidazole (G4-G8, G9, G12-G13, G16-G19), benzimidazole (G10-G11), piperidine substituted pyrrole (G13-G14) groups, alkyl/aryl amide (G15) and aryloxy carboxamide (G20) fingerprints were found to play a crucial role in HDAC8 inhibitory activity whereas -CH-N=CH- (B1, B4-B6, B14) motif, benzamide (B2-B3, B9-B13, B16-B17) groups and heptazepine (B7-B8, B15, B18-B20) group were found to influence negatively the HDAC8 inhibitory activity. The importance of such fingerprints was further validated by the HDAC8 enzyme and related inhibitor interactions at the receptor level. These results are in close agreement with those of our previous work that validate each other. Moreover, this comparative learning may enrich future endeavours regarding the designing strategy of HDAC8 inhibitors.
DOI: 10.6084/m9.figshare.11871945.v1
title: Incorporating graphical structure of predictors in sparse quantile regression

description: Summary. Quantile regression in high dimensional settings is useful in analyzing high dimensional heterogeneous data. In this paper, different from existing methods in quantile regression which treat all the predictors equally with the same priori, we take advantage of the graphical structure among predictors to improve the performance of parameter estimation, model selection and prediction in sparse quantile regression. It is shown under mild conditions that the proposed method enjoys the model selection consistency and the oracle properties. An alternating direction method of multipliers (ADMM) algorithm with a linearization technique is proposed to implement the proposed method numerically, and its convergence is justified. Simulation studies are conducted, showing that the proposed method is superior to existing methods in terms of estimation accuracy and predictive power. The proposed method is also applied to a real dataset.
DOI: 10.6084/m9.figshare.11871864
title: P_troilus raw data from Thoracic scales of moths as a stealth coating against bat biosonar

description: Spreadsheet containing all raw data on the butterfly species <i>P. troilus</i>.
DOI: 10.6084/m9.figshare.11871864.v1
title: A_suraka raw data from Thoracic scales of moths as a stealth coating against bat biosonar

description: Spreadsheet containing all raw data on the moth species <i>A. suraka</i>.
DOI: 10.6084/m9.figshare.11871756
title: CuPCP_XES.zip

description: Pump-probe XES data collected at Alvra instrument of SwissFEL . P K-alpha XES spectra of [Cu4(PCP)3]+<br>
DOI: 10.6084/m9.figshare.11871756.v1
title: CuPCP_XES.zip

description: Pump-probe XES data collected at Alvra instrument of SwissFEL . P K-alpha XES spectra of [Cu4(PCP)3]+<br>
DOI: 10.6084/m9.figshare.11871753
title: Grayscale images full resolution

description: Grayscale images full resolution
DOI: 10.6084/m9.figshare.11871864.v3
title: G_agamemnon raw data from Thoracic scales of moths as a stealth coating against bat biosonar

description: Spreadsheet containing all raw data on the butterfly species <i>G. agamemnon</i>
DOI: 10.6084/m9.figshare.11871699
title: JRC2018F_JRCFIB2018F_h5

description: Transformation between JRC 2018 Female template and the Janelia FlyEM Hemibrain FIB-SEM dataset. https://www.janelia.org/project-team/flyem/hemibrain<br><br>This transformation operates in units of microns. Therefore, any point coordinates must be converted to micron units before applying this transformation.
DOI: 10.6084/m9.figshare.11871699.v1
title: JRC2018F_JRCFIB2018F_h5

description: Transformation between JRC 2018 Female template and the Janelia FlyEM Hemibrain FIB-SEM dataset. https://www.janelia.org/project-team/flyem/hemibrain<br><br>This transformation operates in units of microns. Therefore, any point coordinates must be converted to micron units before applying this transformation.
DOI: 10.6084/m9.figshare.11871864.v8
title: C_promethea raw data from Thoracic scales of moths as a stealth coating against bat biosonar

description: Spreadsheet containing all raw data on the moth species <i>C. promethea</i>
DOI: 10.6084/m9.figshare.11871864.v10
title: P_troilus raw data from Thoracic scales of moths as a stealth coating against bat biosonar

description: Spreadsheet containing all raw data on the butterfly species <i>P. troilus</i>.
DOI: 10.6084/m9.figshare.11871570
title: RbClO4 data

description: The raw data for the RbClO4 solid-state NMR dataset
DOI: 10.6084/m9.figshare.11871570.v1
title: RbClO4 data

description: The raw data for the RbClO4 solid-state NMR dataset
DOI: 10.6084/m9.figshare.11871546
title: kidney cancer and HIF

description: The data can be imported into VoSViewer software and make the result you need.
DOI: 10.6084/m9.figshare.11871537
title: Metadata record for: Physical activity, time use, and food intakes of rural households in Ghana, India, and Nepal

description: This dataset contains key characteristics about the data described in the Data Descriptor Physical activity, time use, and food intakes of rural households in Ghana, India, and Nepal. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format <br><br> Versioning Note:Version 2 was generated when the metadata format was updated from JSON to JSON-LD. This was an automatic process that changed only the format, not the contents, of the metadata.<br> <br>
DOI: 10.6084/m9.figshare.11871546.v1
title: kidney cancer and HIF

description: The data can be imported into VoSViewer software and make the result you need.
DOI: 10.6084/m9.figshare.11871534
title: Supplementary Material for: Exploratory Analysis to Identify Candidates Benefitting from Combination Therapy of Transarterial Chemoembolization and Sorafenib for First-Line Treatment of Unresectable Hepatocellular Carcinoma: A Multicenter Retrospective Observational Study

description: <b><i>Introduction:</i></b> The benefits of combining transarterial chemoembolization (TACE) and sorafenib (TACE-S) over TACE alone for treatment of unresectable hepatocellular carcinoma (HCC) remain controversial. Yet, such populations are heterogeneous in terms of baseline characteristics. <b><i>Objective:</i></b> To investigate the predictors of survival benefits from added sorafenib and identify the potential candidates for TACE-S. <b><i>Methods:</i></b> This multicenter observational study was conducted in 17 Chinese tertiary hospitals for patients with unresectable, liver-confined HCC. Eligible patients with performance status score of ≤1 and Child-Pugh score of ≤7 were treated with TACE or TACE-S. Interactions between treatment and baseline variables were evaluated to find indicators for survival benefits, based on which the patients were stratified. Multivariate models adjusted for baseline characteristics or propensity score were used to compare overall survival (OS) and time to tumor progression (TTP). <b><i>Results:</i></b> From January 2009 to December 2015, 1,719 consecutive patients received TACE (<i>n</i> = 1,406) or TACE-S (<i>n</i> = 313). Although TACE-S compared with TACE improved TTP (adjusted hazard ratio [HR] 0.75, <i>p</i> = 0.008), no difference in OS was observed (adjusted HR 0.87, <i>p</i> = 0.090). Nevertheless, the tumor burden (sum of maximum diameter of largest tumor [cm] and tumor number) and albumin-bilirubin (ALBI) score independently predicted the survival benefits from added sorafenib (interaction <i>p</i>&lt; 0.001). For patients with either moderate tumor burden (7–13) or low ALBI score (no more than –2.8) defined as candidates, TACE-S prolonged OS (adjusted HR 0.73, <i>p</i> = 0.003) and TTP (adjusted HR 0.72, <i>p</i> = 0.014) compared to TACE alone, whereas its superiority disappeared in non-candidates. <b><i>Conclusions:</i></b> Not all unresectable HCC patients but those with moderate tumor burden or low ALBI score achieve survival benefits from TACE-S compared with TACE alone. Future randomized controlled trials focusing on the subset are warranted.