cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7285430
title: Additional file 1: of Discovery of a diagnostic biomarker for colon cancer through proteomic profiling of small extracellular vesicles

description: Table S1. Protein list of small-EVs from HCT-116 and HT-29 CC cell lines. (XLSX 45 kb)
DOI: 10.6084/m9.figshare.7285433.v1
title: Additional file 2: of Discovery of a diagnostic biomarker for colon cancer through proteomic profiling of small extracellular vesicles

description: Table S2. Protein list of small-EVs from CRL1541 normal colon cell line. (XLSX 14 kb)
DOI: 10.7284/120342
title: GNSS (Global Navigation Satellite System) data collected during research cruise SAV-13-25 using a Furuno GP-90 instrument system onboard the platform RV Savannah

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7285430.v1
title: Additional file 1: of Discovery of a diagnostic biomarker for colon cancer through proteomic profiling of small extracellular vesicles

description: Table S1. Protein list of small-EVs from HCT-116 and HT-29 CC cell lines. (XLSX 45 kb)
DOI: 10.7284/120343
title: Gyrocompass data collected during research cruise SAV-13-25 using a Yokogawa CMZ700B instrument system onboard the platform RV Savannah

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/120340
title: Meteorological Station data collected during research cruise SAV-13-25 using a RM Young 26800 instrument system onboard the platform RV Savannah

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7285415
title: Supplementary Material for: The Landscape of Non-Coding RNA in an Adult Pig Model of Intrauterine Growth Restriction

description: <b><i>Background/Aims:</i></b> Intrauterine growth restriction (IUGR) is a risk factor for adult metabolic syndrome, but how this disease is regulated by lncRNAs and circRNAs remains elusive. <b><i>Methods:</i></b> Here, we employed adult IUGR and normal pigs as models to evaluate the expression of various global lncRNAs and circRNAs in pig livers using RNA-seq. <b><i>Results:</i></b> In total, we obtained 1,162 million raw reads of approximately 104.54 Gb high quality data. After a strict five-step filtering process, 3,368 lncRNAs were identified, including 300 differentially expressed lncRNAs (<i>p</i> &lt; 0.05) in the IUGR group relative to the control group. The cis-regulatory analysis identified target genes that were enriched in specific GO terms and pathways (<i>p</i> &lt; 0.05), including amino acid metabolism, oxidoreductase activity, PPAR signaling pathway, and insulin signaling pathway. These are closely related to the observed phenotypes of increased gluconeogenesis and impaired mitochondrial oxidative phosphorylation in adulthood of the IUGR group. Additionally, we also identified 403 circRNAs, of which 44 were differentially expressed (<i>p</i> &lt; 0.05). Interestingly, our results identified ATF4-miR214-circRNA7964 and TCF7-miR22-3p-circRNA16347 as two competing endogenous networks, which were closely associated with the observed increase in hepatic gluconeogenesis in the IUGR group. <b><i>Conclusion:</i></b> Together, this study reveals a multitude of candidate lncRNAs and circRNAs involved in the development of IUGR pigs, which could facilitate further researches on the molecular mechanisms of metabolic syndrome.
DOI: 10.7284/120339
title: Singlebeam Echosounder data collected during research cruise SAV-13-25 using a Furuno FCV-582 instrument system onboard the platform RV Savannah

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/120344
title: TSG (Thermosalinograph) data collected during research cruise SAV-13-25 using a Sea-Bird SBE-21 instrument system onboard the platform RV Savannah

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/120345
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise SAV-13-26 using a RDI WM-300 instrument system onboard the platform RV Savannah

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/120349
title: GNSS (Global Navigation Satellite System) data collected during research cruise SAV-13-26 using a Furuno GP-90 instrument system onboard the platform RV Savannah

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7285346
title: Dataset Time to persistent and newly stunted.xlsx

description: Longitudinal Cohort study on time to persistent and newly stunting among children with HIV who use HAART
DOI: 10.7284/120350
title: Gyrocompass data collected during research cruise SAV-13-26 using a Yokogawa CMZ700B instrument system onboard the platform RV Savannah

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7285343
title: Genome analysis provides insights into the epidemiology of infection with Flavobacterium psychrophilum among farmed salmonid fish in Sweden

description: Illumina MiSeq whole genome sequencing data generated from 38 Swedish isolates and 3 Finnish isolates of <i>Flavobacterium psychrophilu,</i> available as 2 x 250 bp paired-end reads, as published in 'Genome analysis provides insights into the epidemiology of infection with <i>Flavobacterium psychrophilum</i> among farmed salmonid fish in Sweden' in <i>Microbial Genomi</i>cs.DOI: 10.1099/mgen.0.000241
DOI: 10.6084/m9.figshare.7285343.v1
title: Genome analysis provides insights into the epidemiology of infection with Flavobacterium psychrophilum among farmed salmonid fish in Sweden

description: Illumina MiSeq whole genome sequencing data generated from 38 Swedish isolates and 3 Finnish isolates of <i>Flavobacterium psychrophilu,</i> available as 2 x 250 bp paired-end reads, as published in 'Genome analysis provides insights into the epidemiology of infection with <i>Flavobacterium psychrophilum</i> among farmed salmonid fish in Sweden' in <i>Microbial Genomi</i>cs.DOI: 10.1099/mgen.0.000241
DOI: 10.7284/120347
title: Meteorological Station data collected during research cruise SAV-13-26 using a RM Young 26800 instrument system onboard the platform RV Savannah

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/120346
title: Singlebeam Echosounder data collected during research cruise SAV-13-26 using a Furuno FCV-582 instrument system onboard the platform RV Savannah

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/120351
title: TSG (Thermosalinograph) data collected during research cruise SAV-13-26 using a Sea-Bird SBE-21 instrument system onboard the platform RV Savannah

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7285289
title: Testing the Attentional Dwelling Hypothesis of Attentional Capture

description: Data sets for the two experiments published in "Testing the Attentional Dwelling Hypothesis of Attentional Capture" by Lamy D., Darnell. M., Levy A. and Bublil, C. in `journal Of Cognition (2018)
DOI: 10.6084/m9.figshare.7285289.v1
title: Testing the Attentional Dwelling Hypothesis of Attentional Capture

description: Data sets for the two experiments published in "Testing the Attentional Dwelling Hypothesis of Attentional Capture" by Lamy D., Darnell. M., Levy A. and Bublil, C. in `journal Of Cognition (2018)
DOI: 10.7284/120352
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise SAV-13-28 using a RDI WM-300 instrument system onboard the platform RV Savannah

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/120355
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise SAV-13-28 using a Sea-Bird SBE-25 instrument system onboard the platform RV Savannah

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7285151
title: Contrasting responses after fires of the source components of soil respiration and ecosystem respiration

description: Wildfire is an important ecological disturbance that can have cascading effects on ecosystem carbon (C) fluxes. Ecosystem respiration (ER) and soil respiration (SR) account for two of the largest terrestrial C fluxes to the atmosphere, and they play critical roles in regulating C–climate feedbacks. Here, the responses of ER, SR and their source components to experimental burning in a meadow grassland on the Tibetan Plateau were investigated. Fire treatment increased ER by 9% but decreased SR by 15%. The contrasting post-fire responses of SR and ER can be explained by the behaviour of their source components; that is, fire increased aboveground plant respiration (R<sub>agb</sub>) by 37%, but decreased heterotrophic respiration (HR) by 21%. Increases in ER and R<sub>agb</sub> were mainly related to enhanced plant productivity while smaller SR and HR were associated with reductions in microbial biomass and soil moisture. Accounting for the responses of ER, SR and their intrinsic components has advanced our understanding of how fire affects ecosystem C fluxes.
DOI: 10.6084/m9.figshare.7285151.v1
title: Contrasting responses after fires of the source components of soil respiration and ecosystem respiration

description: Wildfire is an important ecological disturbance that can have cascading effects on ecosystem carbon (C) fluxes. Ecosystem respiration (ER) and soil respiration (SR) account for two of the largest terrestrial C fluxes to the atmosphere, and they play critical roles in regulating C–climate feedbacks. Here, the responses of ER, SR and their source components to experimental burning in a meadow grassland on the Tibetan Plateau were investigated. Fire treatment increased ER by 9% but decreased SR by 15%. The contrasting post-fire responses of SR and ER can be explained by the behaviour of their source components; that is, fire increased aboveground plant respiration (R<sub>agb</sub>) by 37%, but decreased heterotrophic respiration (HR) by 21%. Increases in ER and R<sub>agb</sub> were mainly related to enhanced plant productivity while smaller SR and HR were associated with reductions in microbial biomass and soil moisture. Accounting for the responses of ER, SR and their intrinsic components has advanced our understanding of how fire affects ecosystem C fluxes.
DOI: 10.7284/120356
title: GNSS (Global Navigation Satellite System) data collected during research cruise SAV-13-28 using a Furuno GP-90 instrument system onboard the platform RV Savannah

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/120357
title: Gyrocompass data collected during research cruise SAV-13-28 using a Yokogawa CMZ700B instrument system onboard the platform RV Savannah

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/120354
title: Meteorological Station data collected during research cruise SAV-13-28 using a RM Young 26800 instrument system onboard the platform RV Savannah

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/120353
title: Singlebeam Echosounder data collected during research cruise SAV-13-28 using a Furuno FCV-582 instrument system onboard the platform RV Savannah

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7285127
title: Supplementary Material for: Transcriptome Profile Analysis Reveals an Estrogen Induced LncRNA Associated with Lipid Metabolism and Carcass Traits in Chickens (Gallus Gallus)

description: <b><i>Background/Aims:</i></b> Accumulating evidences have demonstrated that long noncoding RNAs (lncRNA) play important roles in hepatic lipid metabolism in mammals. However, no systematic screening of the potential lncRNAs in the livers of laying hens has been performed, and few studies have been reported concerning the effects of the lncRNAs on lipid metabolism in the livers of chickens during egg-laying period. The purpose of this study was to compare the difference in lncRNA expression in the livers of pre-laying and peak-laying hens at the age of 20 and 30 weeks old by transcriptome sequencing and to investigate the interaction networks among lncRNAs, mRNAs and miRNAs. Moreover, the regulatory mechanism and biological function of lncLTR, a significantly differentially expressed lncRNA in the liver between pre- and peak-laying hens, was explored <i>in vitro</i> and <i>in vivo</i>. <b><i>Methods:</i></b> Bioinformatics analyses were conducted to identify the differentially expressed (DE) lncRNAs between the two groups of hens. The target genes of the DE lncRNA were predicated for further functional enrichment. An integrated analysis was performed among the DE lncRNA datasets, DE mRNAs and DE miRNA datasets obtained from the same samples to predict the interaction relationship. In addition, <i>in vivo</i> and <i>in vitro</i> trials were carried out to determine the expression regulation of lncLTR, and polymorphism association analysis was conducted to detect the biological role of ncLTR. <b><i>Results:</i></b> A total of 124 DE lncRNAs with a <i>P</i>-value ≤ 0.05 were identified. Among them, 44 lncRNAs including 30 known and 14 novel lncRNAs were significant differentially expressed (SDE) with FDR ≤ 0.05. Thirty-two lncRNAs were upregulated and 12 were downregulated in peak-laying group compared with pre-laying group. The functional enrichment results revealed that target genes of some lncRNAs are involved in the lipid metabolism process. Integrated analysis suggested that some of the genes involved in lipid metabolism might be regulated by both the lncRNA and the miRNA. In addition, an upregulated lncRNA, designated lncLTR, was demonstrated to be induced by estrogen via ERβ signaling. The c242. G&gt;A SNP in lncLTR was significantly associated with chicken carcass weight, evisceration weight, semi-evisceration weight, head weight, double-wing weight, claw weight traits, and blood biochemical index, especially for the blood triglyceride content. <b><i>Conclusion:</i></b> A series of lncRNAs associated with lipid metabolism in the livers of chickens were identified by transcriptome sequencing and functional analysis, providing a valuable data resource for further studies on chicken hepatic metabolism activities. LncLTR was regulated by estrogen via ERβ signaling and associated with chicken carcass trait and blood triglyceride content.
DOI: 10.7284/120358
title: TSG (Thermosalinograph) data collected during research cruise SAV-13-28 using a Sea-Bird SBE-21 instrument system onboard the platform RV Savannah

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7285106
title: Supplementary Material for: Proteome and Transcriptome Reveal Involvement of Heat Shock Proteins and Indoleacetic Acid Metabolism Process in <b><i>Lentinula Edodes</i></b> Thermotolerance

description: <b><i>Background/Aims:</i></b> Heat stress could cause huge losses for <i>Lentinula edodes</i> in China and other Asian cultivation areas. Yet our understanding of mechanism how to defend to heat stress is incomplete. <b><i>Methods:</i></b> Using heat-tolerant and heat-sensitive strains of <i>L. edodes</i>, we reported a combined proteome and transcriptome analysis of <i>L. edodes</i> response to 40 °C heat stress for 24 h. Meanwhile, the effect of <i>LeDnaJ</i> on the thermotolerance and IAA (indoleacetic acid) biosynthesis in <i>L. edodes</i> was analyzed via the over-expression method. <b><i>Results:</i></b> The proteome results revealed that HSPs (heat shock proteins) such as Hsp40 (DnaJ), Hsp70, Hsp90 and key enzymes involved in tryptophan and IAA metabolism process LeTrpE, LeTrpD, LeTam-1, LeYUCCA were more highly expressed in S606 than in YS3357, demonstrating that HSPs and tryptophan as well as IAA metabolism pathway should play an important role in thermotolerance. Over-expression of <i>LeDnaJ</i> gene in S606 strains showed better tolerance to heat stress. It was also documented that intracellular IAA accumulation of S606 (8-fold up) was more than YS3357 (2-fold up), and exogenous IAA enhanced <i>L. edodes</i> tolerance to heat stress. <b><i>Conclusion:</i></b> Our data support the interest of LeTrpE, LeDnaJ, tryptophan and IAA could play a pivotal role in enhancing organism thermotolerance.
DOI: 10.7284/120359
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise SAV-13-29 using a RDI WM-300 instrument system onboard the platform RV Savannah

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7285088
title: Conformations of cysteine disulfides of peptide toxins: Advantage of differentiating forward and reverse asymmetric disulfide conformers

description: Conformations of cysteine disulfides were analyzed in X-ray, nuclear magnetic resonance (NMR), and co-crystal structures of peptide toxins retrieved from Protein Data Bank. The parameters side chain torsional angles, disulfide strain energy, interatomic Cα/Cβ distances, and Ramachandran angles were used as probes to derive conformational features of cysteine disulfides. Schmidt, Ho, and Hogg (2006) Allosteric disulfide bonds. <i>Biochemistry, 45</i>, 7429–7433 scheme was adapted to classify the disulfide conformations of peptide toxins. Anomalies were observed while treating “forward” and “reverse” asymmetric disulfide conformers as same disulfide conformation in peptide toxins. Thus, new scheme was proposed to classify “forward” and “reverse” asymmetric disulfide conformers separately. Total available conformers space for classification of toxins disulfides is 32. Interestingly, all 32 disulfide conformations are observed in peptide toxins. –LHSpiral is predominant disulfide conformation of peptide toxins. Significant variations were observed in population of occurrence of disulfide conformers, disulfide strain energy, and distribution of D<sub>Cα-Cα</sub> and D<sub>Cβ-Cβ</sub> values between X-ray, NMR, and co-crystal structures of peptide toxins. The observed differences in conformations of disulfides of same peptide toxins between different states were used as platform to demonstrate advantage of differentiating forward and reverse asymmetric disulfide conformers. Newly proposed scheme allows accurate representation of true conformational diversity of disulfides between X-ray and NMR structures of same peptide toxins. Newly proposed scheme also permits to derive additional structural information from nomenclature which was illustrated by comparing conformations of disulfides between unbound and bound form of toxin with channel/receptor. The results will be of interest for growing field of structural venomics and conformational analysis of peptide/protein disulfides. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.7285088.v1
title: Conformations of cysteine disulfides of peptide toxins: Advantage of differentiating forward and reverse asymmetric disulfide conformers

description: Conformations of cysteine disulfides were analyzed in X-ray, nuclear magnetic resonance (NMR), and co-crystal structures of peptide toxins retrieved from Protein Data Bank. The parameters side chain torsional angles, disulfide strain energy, interatomic Cα/Cβ distances, and Ramachandran angles were used as probes to derive conformational features of cysteine disulfides. Schmidt, Ho, and Hogg (2006) Allosteric disulfide bonds. <i>Biochemistry, 45</i>, 7429–7433 scheme was adapted to classify the disulfide conformations of peptide toxins. Anomalies were observed while treating “forward” and “reverse” asymmetric disulfide conformers as same disulfide conformation in peptide toxins. Thus, new scheme was proposed to classify “forward” and “reverse” asymmetric disulfide conformers separately. Total available conformers space for classification of toxins disulfides is 32. Interestingly, all 32 disulfide conformations are observed in peptide toxins. –LHSpiral is predominant disulfide conformation of peptide toxins. Significant variations were observed in population of occurrence of disulfide conformers, disulfide strain energy, and distribution of D<sub>Cα-Cα</sub> and D<sub>Cβ-Cβ</sub> values between X-ray, NMR, and co-crystal structures of peptide toxins. The observed differences in conformations of disulfides of same peptide toxins between different states were used as platform to demonstrate advantage of differentiating forward and reverse asymmetric disulfide conformers. Newly proposed scheme allows accurate representation of true conformational diversity of disulfides between X-ray and NMR structures of same peptide toxins. Newly proposed scheme also permits to derive additional structural information from nomenclature which was illustrated by comparing conformations of disulfides between unbound and bound form of toxin with channel/receptor. The results will be of interest for growing field of structural venomics and conformational analysis of peptide/protein disulfides. Communicated by Ramaswamy H. Sarma
DOI: 10.7284/120362
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise SAV-13-29 using a Sea-Bird SBE-25 instrument system onboard the platform RV Savannah

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/120363
title: GNSS (Global Navigation Satellite System) data collected during research cruise SAV-13-29 using a Furuno GP-90 instrument system onboard the platform RV Savannah

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7285067
title: Multispectroscopic insight, morphological analysis and molecular docking studies of Cu<sup>II</sup>-based chemotherapeutic drug entity with human serum albumin (HSA) and bovine serum albumin (BSA)

description: The interaction studies of Cu<sup>II</sup> nalidixic acid–DACH chemotherapeutic drug entity, [C<sub>36</sub>H<sub>50</sub>N<sub>8</sub>O<sub>6</sub>Cu] with serum albumin proteins, <i>viz</i>., human serum albumin (HSA) and bovine serum albumin (BSA) employing UV–vis, fluorescence, CD, FTIR and molecular docking techniques have been carried out. Complex [C<sub>36</sub>H<sub>50</sub>N<sub>8</sub>O<sub>6</sub>Cu] demonstrated strong binding affinity towards serum albumin proteins <i>via</i> hydrophobic contacts with binding constants, <i>K</i> = 3.18 × 10<sup>5</sup> and 7.44 × 10<sup>4</sup> M<sup>–1</sup> for HSA and BSA, respectively implicating a higher binding affinity for HSA. The thermodynamic parameters ΔG, ΔH and ΔS at different temperatures were also calculated and the interaction of complex [C<sub>36</sub>H<sub>50</sub>N<sub>8</sub>O<sub>6</sub>Cu] with HSA and BSA was found to be enthalpy and entropy favoured, nevertheless, complex [C<sub>36</sub>H<sub>50</sub>N<sub>8</sub>O<sub>6</sub>Cu] demonstrated higher binding affinity towards HSA than BSA evidenced from its higher binding constant values. Time resolved fluorescence spectroscopy (TRFS) was carried out to validate the static quenching mechanism of HSA/BSA fluorescence. The collaborative results of spectroscopic studies indicated that the microenvironment and the conformation of HSA and BSA (α–helix) were significantly perturbed upon interaction with complex [C<sub>36</sub>H<sub>50</sub>N<sub>8</sub>O<sub>6</sub>Cu]. Hirshfeld surfaces analysis and fingerprint plots revealed various intermolecular interactions <i>viz</i>., N–H<b>····</b>O, O–H<b>····</b>O and C–H<b>····</b>O linkages in a 2–dimensional framework that provide crucial information about the supramolecular architectures in the complex. Molecular docking studies were carried out to ascertain the preferential binding mode and affinity of complex [C<sub>36</sub>H<sub>50</sub>N<sub>8</sub>O<sub>6</sub>Cu] at the target site of HSA and BSA. Furthermore, only for Transmission electroscopy microscopy micrographs of HSA and BSA in presence of complex [C<sub>36</sub>H<sub>50</sub>N<sub>8</sub>O<sub>6</sub>Cu] revealed major protein morphological transitions and aggregation which validates efficient delivery of complex by serum proteins to the target site. Communicated by Ramaswamy H. Sarma