cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7974614
title: Raw data from: "Thermal mismatches explain consumer-resource dynamics in response to environmental warming".

description: Data from: Álvarez-Codesal, S, Faillace CA, Garreau, A, Bestion, E, Synodinos, AD, & Montoya, JM. 2023. Thermal mismatches explain consumer-resource dynamics in response to environmental warming. Ecology and Evolution.<br> Composed of seven associated datasets: - Algae_Net_Photosynthesis.csv - Daphnia_Ingestion.csv - Algae_Respiration.csv - Daphnia_Ingestion.csv - Daphnia_respiration.csv - Interaction_Strength.csv - Energy_Balance_Ratios_dataset.csv A detailed explanation of the methods is provided in the related Alvarez-Codesal et al. 2023 article, please refer to it for a full understanding of the methods and results. Briefly: our aim was to quantify the impact of warming on consumer-resource interactions, using as consumer <em>Daphnia pulex</em>, and as resources two algae species, <em>Chlamydomonas reinhardtii</em> and <em>Desmodesmus</em> sp. First, we measured thermal dependencies of physiological rates related to energy gain (i.e., ingestion, net photosynthesis) and loss (i.e., respiration) for <em>Daphnia</em> and the algae in basal conditions at eight temperatures. From these, we calculated species energetic balances as net photosynthesis-to-respiration ratio (P/R<sub>r</sub>) for resources, or as ingestion-to-respiration ratio (I/R<sub>c</sub>) for consumers, using predicted values of each (per capita) rate from the models. We used energetic balances as an indicator of how species respond to increasing temperatures, defining intraspecific energetic mismatches when the energetic balance decreases. Second, we inferred interspecific thermal mismatches (inter-TM) by comparing individual energetic balances for both consumer-resource pairs, and identified the thermal mismatch regions, where: 1) trends of energetic balances contrast between the interacting species; and 2) both species reduce their energetic balance with increasing temperature. The inter-TMs were used to increase our qualitative understanding on the outcomes of thermal dependencies of interaction strength. Third, we calculated the natural logarithm of the consumer-resource energetic balance for each interacting pair as the ratio between consumer energetic balance and the resource energetic balance to get qualitative predictions on the trends of interaction strength with temperature. Finally, we measured experimentally thermal dependencies of interaction strength for each consumer-resource pair and verified if our predictions using the thermal mismatches fitted the trends of interaction strengths across temperatures.
DOI: 10.5281/zenodo.7974613
title: Raw data from: "Thermal mismatches explain consumer-resource dynamics in response to environmental warming".

description: Data from: Álvarez-Codesal, S, Faillace CA, Garreau, A, Bestion, E, Synodinos, AD, & Montoya, JM. 2023. Thermal mismatches explain consumer-resource dynamics in response to environmental warming. Ecology and Evolution.<br> Composed of seven associated datasets: - Algae_Net_Photosynthesis.csv - Daphnia_Ingestion.csv - Algae_Respiration.csv - Daphnia_Ingestion.csv - Daphnia_respiration.csv - Interaction_Strength.csv - Energy_Balance_Ratios_dataset.csv A detailed explanation of the methods is provided in the related Alvarez-Codesal et al. 2023 article, please refer to it for a full understanding of the methods and results. Briefly: our aim was to quantify the impact of warming on consumer-resource interactions, using as consumer <em>Daphnia pulex</em>, and as resources two algae species, <em>Chlamydomonas reinhardtii</em> and <em>Desmodesmus</em> sp. First, we measured thermal dependencies of physiological rates related to energy gain (i.e., ingestion, net photosynthesis) and loss (i.e., respiration) for <em>Daphnia</em> and the algae in basal conditions at eight temperatures. From these, we calculated species energetic balances as net photosynthesis-to-respiration ratio (P/R<sub>r</sub>) for resources, or as ingestion-to-respiration ratio (I/R<sub>c</sub>) for consumers, using predicted values of each (per capita) rate from the models. We used energetic balances as an indicator of how species respond to increasing temperatures, defining intraspecific energetic mismatches when the energetic balance decreases. Second, we inferred interspecific thermal mismatches (inter-TM) by comparing individual energetic balances for both consumer-resource pairs, and identified the thermal mismatch regions, where: 1) trends of energetic balances contrast between the interacting species; and 2) both species reduce their energetic balance with increasing temperature. The inter-TMs were used to increase our qualitative understanding on the outcomes of thermal dependencies of interaction strength. Third, we calculated the natural logarithm of the consumer-resource energetic balance for each interacting pair as the ratio between consumer energetic balance and the resource energetic balance to get qualitative predictions on the trends of interaction strength with temperature. Finally, we measured experimentally thermal dependencies of interaction strength for each consumer-resource pair and verified if our predictions using the thermal mismatches fitted the trends of interaction strengths across temperatures.
DOI: 10.6084/m9.figshare.22593121
title: Inference in High-Dimensional Online Changepoint Detection

description: We introduce and study two new inferential challenges associated with the sequential detection of change in a high-dimensional mean vector. First, we seek a confidence interval for the changepoint, and second, we estimate the set of indices of coordinates in which the mean changes. We propose an online algorithm that produces an interval with guaranteed nominal coverage, and whose length is, with high probability, of the same order as the average detection delay, up to a logarithmic factor. The corresponding support estimate enjoys control of both false negatives and false positives. Simulations confirm the effectiveness of our methodology, and we also illustrate its applicability on the U.S. excess deaths data from 2017 to 2020. The supplementary material, which contains the proofs of our theoretical results, is available online.
DOI: 10.6084/m9.figshare.22593121.v2
title: Inference in High-Dimensional Online Changepoint Detection

description: We introduce and study two new inferential challenges associated with the sequential detection of change in a high-dimensional mean vector. First, we seek a confidence interval for the changepoint, and second, we estimate the set of indices of coordinates in which the mean changes. We propose an online algorithm that produces an interval with guaranteed nominal coverage, and whose length is, with high probability, of the same order as the average detection delay, up to a logarithmic factor. The corresponding support estimate enjoys control of both false negatives and false positives. Simulations confirm the effectiveness of our methodology, and we also illustrate its applicability on the U.S. excess deaths data from 2017 to 2020. The supplementary material, which contains the proofs of our theoretical results, is available online.
DOI: 10.6084/m9.figshare.22593121.v1
title: Inference in High-dimensional Online Changepoint Detection

description: We introduce and study two new inferential challenges associated with the sequential detection of change in a high-dimensional mean vector. First, we seek a confidence interval for the changepoint, and second, we estimate the set of indices of coordinates in which the mean changes. We propose an online algorithm that produces an interval with guaranteed nominal coverage, and whose length is, with high probability, of the same order as the average detection delay, up to a logarithmic factor. The corresponding support estimate enjoys control of both false negatives and false positives. Simulations confirm the effectiveness of our methodology, and we also illustrate its applicability on the US excess deaths data from 2017–2020. The supplementary material, which contains the proofs of our theoretical results, is available online.
DOI: 10.5281/zenodo.7974586
title: Porte drug repurposing dataset for epilepsy

description: Version 1.0.0 (05/26/2023) This is a drug repurposing dataset on epilepsy, compiled by Dr. Baptiste PORTE &lt;baptiste.porte@inserm.fr&gt; in January 2021 at Inserm UMR 1141 Neurodiderot, 48 boulevard Sérurier, F-75019 Paris, France. Its author has authorized the publication under the MIT licence of this dataset by Clémence Réda from the RECeSS project (Grant ID 101102016) on May 20th, 2023. It consists in two .CSV files: 1. Liste anticonvu.csv with 6 columns "Compound CID": Best match PubChem CID for the considered chemical compound<br> "drug_name": The common drug name<br> "score": preliminary drug class in {0: unknown effect on epileptic patients, 1: antiepileptic drug, that is, treatment for epileptic patients}<br> "verification": 1st bibliographic round for drug class in {0: unknown effect on epileptic patients, 1: antiepileptic drug, that is, treatment for epileptic patients}<br> "verif 2": final assigned drug class in {0: unknown effect on epileptic patients, 1: antiepileptic drug, that is, treatment for epileptic patients}<br> "details": justification -in French- for the final assigned drug class 2. Liste proconvu.csv "Compound CID": Best match PubChem CID for the considered chemical compound<br> "drug_name": The common drug name<br> "score": preliminary drug class in {0: unknown effect on epileptic patients, -1: proconvulsant drug, that is, seizure-inducing}<br> "verification": 1st bibliographic round for drug class in {0: unknown effect on epileptic patients, -1: proconvulsant drug, that is, seizure-inducing}<br> "verif 2": final assigned drug class in {0: unknown effect on epileptic patients, -1: proconvulsant drug, that is, seizure-inducing}<br> "effet convulsivant demontré": justification -in French- for the final assigned drug class For any questions, please contact the author at &lt;baptiste.porte@inserm.fr&gt; or the RECeSS project contributors at &lt;recess-project@proton.me&gt;.
DOI: 10.5281/zenodo.7974585
title: Porte drug repurposing dataset for epilepsy

description: Version 1.0.0 (05/26/2023) This is a drug repurposing dataset on epilepsy, compiled by Dr. Baptiste PORTE &lt;baptiste.porte@inserm.fr&gt; in January 2021 at Inserm UMR 1141 Neurodiderot, 48 boulevard Sérurier, F-75019 Paris, France. Its author has authorized the publication under the MIT licence of this dataset by Clémence Réda from the RECeSS project (Grant ID 101102016) on May 20th, 2023. It consists in two .CSV files: 1. Liste anticonvu.csv with 6 columns "Compound CID": Best match PubChem CID for the considered chemical compound<br> "drug_name": The common drug name<br> "score": preliminary drug class in {0: unknown effect on epileptic patients, 1: antiepileptic drug, that is, treatment for epileptic patients}<br> "verification": 1st bibliographic round for drug class in {0: unknown effect on epileptic patients, 1: antiepileptic drug, that is, treatment for epileptic patients}<br> "verif 2": final assigned drug class in {0: unknown effect on epileptic patients, 1: antiepileptic drug, that is, treatment for epileptic patients}<br> "details": justification -in French- for the final assigned drug class 2. Liste proconvu.csv "Compound CID": Best match PubChem CID for the considered chemical compound<br> "drug_name": The common drug name<br> "score": preliminary drug class in {0: unknown effect on epileptic patients, -1: proconvulsant drug, that is, seizure-inducing}<br> "verification": 1st bibliographic round for drug class in {0: unknown effect on epileptic patients, -1: proconvulsant drug, that is, seizure-inducing}<br> "verif 2": final assigned drug class in {0: unknown effect on epileptic patients, -1: proconvulsant drug, that is, seizure-inducing}<br> "effet convulsivant demontré": justification -in French- for the final assigned drug class For any questions, please contact the author at &lt;baptiste.porte@inserm.fr&gt; or the RECeSS project contributors at &lt;recess-project@proton.me&gt;.
DOI: 10.5281/zenodo.7974799
title: Raw data and analysis code for "Higher-order Process Matrix Tomography of a passively-stable Quantum SWITCH"

description: This folder contains the raw data and analysis coded need to reproduce all of the major results in the manuscript "Higher-order Process Matrix Tomography of a passively-stable Quantum SWITCH".
DOI: 10.5281/zenodo.7974798
title: Raw data and analysis code for "Higher-order Process Matrix Tomography of a passively-stable Quantum SWITCH"

description: This folder contains the raw data and analysis coded need to reproduce all of the major results in the manuscript "Higher-order Process Matrix Tomography of a passively-stable Quantum SWITCH".
DOI: 10.6084/m9.figshare.22679080.v4
title: Supplementary Tables for Veseli et al. 2023

description: Supplementary tables for the study by Veseli et al. titled "High metabolic independence is a determinant of microbial resilience in the face of gut stress".
DOI: 10.6084/m9.figshare.21731369
title: The_selfish_preen

description: The preening durations of several species of palaeognath birds and the common raven as well as the code used for analysis and data preparation for figures.
DOI: 10.6084/m9.figshare.21731369.v1
title: The_selfish_preen

description: The preening durations of several species of palaeognath birds and the common raven as well as the code used for analysis and data preparation for figures.
DOI: 10.5281/zenodo.7974415
title: Pig——WENS

description: pig images from WENS
DOI: 10.5281/zenodo.7974414
title: Pig——WENS

description: pig images from WENS
DOI: 10.5281/zenodo.5795172
title: Input data for Atollgen pipeline

description: Input data for Atollgen pipeline Contains: Frozen island raw sources (atollgen database inputs) hmm database (integrase and mobility signatures coming from ConjScan and Pfam-A) categorisation metadata for each signature contained in the integrase and mobility database Frozen genomes sequences from the NCBI Frozen list of actinobacteria taxonomy ids Frozen defense-finder database Frozen cards Frozen data ensure reproducibility for the pipeline, but up-to-date data should give similar (yet not identical) results.
DOI: 10.5281/zenodo.5795173
title: Input data for Atollgen pipeline

description: Input data for Atollgen pipeline Contains: frozen island raw sources (atollgen database inputs) hmm database (integrase and mobility signatures coming from ConjScan and Pfam-A) categorisation metadata for each signature contained in the integrase and mobility database
DOI: 10.5281/zenodo.7866495
title: Input data for Atollgen pipeline

description: Input data for Atollgen pipeline Contains: Frozen island raw sources (atollgen database inputs) hmm database (integrase and mobility signatures coming from ConjScan and Pfam-A) categorisation metadata for each signature contained in the integrase and mobility database Frozen genomes sequences from the NCBI Frozen list of actinobacteria taxonomy ids Frozen defense-finder database Frozen cards Frozen data ensure reproducibility for the pipeline, but up-to-date data should give similar (yet not identical) results.
DOI: 10.25345/c5th8bx9r
title: MassIVE MSV000092039 - A phosphorylation-deficient isoform of the ribosomal protein eS6 is largely functional in laboratory-grown Arabidopsis thaliana
title: The eukaryote-specific ribosomal protein of the small subunit eS6 is a target of phosphorylation for the Target of rapamycin (TOR) kinase pathway. Although this phosphorylation event responds dynamically to environmental conditions and has been known and studied for about 50 years, its biochemical and physiological significance remains controversial and poorly understood. Here we report data from Arabidopsis thaliana, which indicate that plants expressing only a largely phospho-deficient isoform of eS6 grow essentially normally under laboratory conditions. The eS6A (RPS6A) paralog of eS6 can functionally rescue double mutations in both rps6a and rps6b when expressed at approximately twice the wild-type dosage. A mutant isoform of eS6A lacking the major six phosphorylatable serine and threonine residues in its carboxyl-terminal tail also rescued the lethality of the double mutant and complemented nearly all mutant phenotypes, including rosette growth, photosynthetic efficiency, polyribosome loading, and the vast majority of gene expression defects at the transcriptome and proteome level. When compared to plants that were rescued with a phospho-enabled version of eS6A, the phospho-deficient seedlings retained a mild pointed-leaf phenotype, and root growth was reduced, and certain cell cycle related mRNAs were misexpressed. The residual mRNA expression defects of the phospho-deficient seedlings could be understood as an incomplete rescue of the rps6 mutant defects, with little or no evidence for gain-of function defects. The proteomes of seedlings rescued with a phospho-enabled and a phospho-deficient isoform of eS6A also had subtle differences suggesting that the P-deficient isoform did not fully reverse the derepression of the ribosome biogenesis regulon that was observed in the single mutants. As expected, the phospho-deficient eS6A also rescued the rps6a and rps6b single mutants; however, phosphorylation of the eS6B paralog was lower than predicted, further underscoring that plants can tolerate phosphodeficiency of eS6 well. Our data also yield new insights into how plants cope with mutations in essential, duplicated ribosomal protein isoforms.
DOI: 10.34740/kaggle/dsv/5783915
title: Nigerian Presidential Election 2023 Tweets
DOI: 10.25345/c5pv6bh7v
title: MassIVE MSV000092040 - Combined transcriptomics and proteomics analysis unveiled the impact of vitamin C in modulating specific mitochondrial protein abundance in the mouse liver
title: : In the present study, we used the Gulo-/- female and male mice model which depends entirely on ascorbate derived from the diet. We tested different concentrations of ascorbate ranging from 0 to 0.4% (w/v) ascorbate, added into drinking water, until the age of four months. Importantly, the levels of ascorbate found in the liver of Gulo-/- mice reflect the amounts of ascorbate provided in drinking water. We performed label-free Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) global quantitative proteomic profiling to identify and quantify proteins in whole liver extracts from our different ascorbate treated cohorts of Gulo-/- females and males. We compared the proteomic profiles to the transcriptomic profiles of the same treated animals. Although several proteins of the mitochondrial complex III significantly correlated with vitamin C concentrations, their corresponding transcripts did not correlate with vitamin C in both females and males. Such observations were confirmed by western blot and quantitative RT-PCR analyses, respectively. Our findings suggest that transcriptome profiling alone provides an incomplete picture of molecular changes associated with vitamin C deficiency in the liver of mice and examination of changes in protein abundances is essential to unveil variations that are not transcriptionally regulated.
DOI: 10.5517/ccdc.csd.cc2bmwhc
title: CCDC 2164063: Experimental Crystal Structure Determination

description: Related Article: Vasile Lozovan, Victor Ch. Kravtsov, Yurii M. Chumakov, Natalia V. Costriucova, Nikita Siminel, Oleg Petuhov, Titus Vlase, Gabriela Vlase, Alic Barba, Marina S. Fonari|2023|Cryst.Growth Des.|23|3171|doi:10.1021/acs.cgd.2c01345
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2bmwjd
title: CCDC 2164064: Experimental Crystal Structure Determination

description: Related Article: Vasile Lozovan, Victor Ch. Kravtsov, Yurii M. Chumakov, Natalia V. Costriucova, Nikita Siminel, Oleg Petuhov, Titus Vlase, Gabriela Vlase, Alic Barba, Marina S. Fonari|2023|Cryst.Growth Des.|23|3171|doi:10.1021/acs.cgd.2c01345
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5281/zenodo.7974855
title: Dataset pro práci Algoritmus Brain storm optimization: aplikace a varianty

description: Veškerá data pro práci Algoritmus Brain storm optimization: aplikace a varianty
DOI: 10.5281/zenodo.7974854
title: Dataset pro práci Algoritmus Brain storm optimization: aplikace a varianty

description: Veškerá data pro práci Algoritmus Brain storm optimization: aplikace a varianty
DOI: 10.5517/ccdc.csd.cc2flgvc
title: CCDC 2252083: Experimental Crystal Structure Determination

description: Related Article: Zonghuan Lu, Wanqian Lv, Hongyi Liu, Yandie Liu, Shuhua Liao, Xijie Wang, Kelong Zhu|2023|Org.Lett.|25|3508|doi:10.1021/acs.orglett.3c01092
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2flgwd
title: CCDC 2252084: Experimental Crystal Structure Determination

description: Related Article: Zonghuan Lu, Wanqian Lv, Hongyi Liu, Yandie Liu, Shuhua Liao, Xijie Wang, Kelong Zhu|2023|Org.Lett.|25|3508|doi:10.1021/acs.orglett.3c01092
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2flgxf
title: CCDC 2252085: Experimental Crystal Structure Determination

description: Related Article: Zonghuan Lu, Wanqian Lv, Hongyi Liu, Yandie Liu, Shuhua Liao, Xijie Wang, Kelong Zhu|2023|Org.Lett.|25|3508|doi:10.1021/acs.orglett.3c01092
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2flgzh
title: CCDC 2252087: Experimental Crystal Structure Determination

description: Related Article: Zonghuan Lu, Wanqian Lv, Hongyi Liu, Yandie Liu, Shuhua Liao, Xijie Wang, Kelong Zhu|2023|Org.Lett.|25|3508|doi:10.1021/acs.orglett.3c01092
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.