cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5740266.v1
title: Effects of Precipitation Changes on Switchgrass Photosynthesis, Growth, and Biomass

description: Supplimental Data for Figures (Fig. 1 to Fig. 5) Dafeng Hui, Chih-Li Yu, Qi Deng, E. Kudjo Dzantor, Suping Zhou, Sam Dennis, Roger Sauve, Terrance L. Johnson, Philip A Fay, Weijun Shen, Yiqi Luo. Effects of Precipitation Changes on Switchgrass Photosynthesis, Growth, and Biomass: a Mesocosm Experiment. Data sheets for Fig 1: Monthly mean soil temperature and soil moisture in each precipitation treatment from February to October in 2014 and 2015 Data sheets for Fig 2: Monthly mean photosynthesis and transpiration in each precipitation treatment from February to October in 2014 and 2015 Data sheets for Fig 3: Multiple comparisons of leaf photosynthesis, stomatal conductance, transpiration, and water use efficiency among different precipitation treatments Data sheets for Fig 4: Multiple comparisons of number of tillers, maximum height, and biomass of leaf, stem and total plant, and leaf:stem ratio among different precipitation treatments Data sheets for Fig 5: Relationships among leaf photosynthesis, transpiration, water use efficiency (WUEi), number of tillers, plant height, biomass, leaf temperature, soil temperature, and soil moisture under all precipitation treatments. SAS_code: SAS code for ANOVA analyses
DOI: 10.6084/m9.figshare.5740080
title: Circadian PER2 protein oscillations do not persist in cycloheximide-treated mouse embryonic fibroblasts in culture

description: It is not known whether the endogenous mammalian core clock proteins sustain measurable oscillations in cells in culture where <i>de novo</i> translation is pharmacologically inhibited. We studied here the mammalian core clock protein PER2, which undergoes robust circadian oscillations in both abundance and phosphorylation. With a newly developed antibody that enables tracing the endogenous PER2 protein oscillations over circadian cycles with cultured mouse embryonic fibroblast cells, we provide evidence that PER2 does not persist noticeable circadian rhythms when translation is inhibited.
DOI: 10.6084/m9.figshare.5740080.v1
title: Circadian PER2 protein oscillations do not persist in cycloheximide-treated mouse embryonic fibroblasts in culture

description: It is not known whether the endogenous mammalian core clock proteins sustain measurable oscillations in cells in culture where <i>de novo</i> translation is pharmacologically inhibited. We studied here the mammalian core clock protein PER2, which undergoes robust circadian oscillations in both abundance and phosphorylation. With a newly developed antibody that enables tracing the endogenous PER2 protein oscillations over circadian cycles with cultured mouse embryonic fibroblast cells, we provide evidence that PER2 does not persist noticeable circadian rhythms when translation is inhibited.
DOI: 10.6084/m9.figshare.5740071
title: Supplemental Table 2

description: Complete list of proteins identified in adult female <i>Brugia malayi</i> extracellular vesicle (EV) proteome. Proteins extracted from EVs were subject to nano-scale LC-MS/MS. Spectral data were searched against the <i>B. malayi, Ascaris suum</i> and <i>Caenorhabditis elegans</i> UniProt databases using MASCOT to identify proteins. The complete list of proteins and the name of the gene encoding that protein (GN) is listed. UniProtKB (www.uniprot.org) identifiers are provided for each protein along with molecular weight (kDa). Proteins are ranked by their normalized spectral abundance factor (NSAF), a simple indicator of protein abundance in the sample reflecting the effect of protein length.<br>
DOI: 10.6084/m9.figshare.5740071.v1
title: Supplemental Table 2

description: Complete list of proteins identified in adult female <i>Brugia malayi</i> extracellular vesicle (EV) proteome. Proteins extracted from EVs were subject to nano-scale LC-MS/MS. Spectral data were searched against the <i>B. malayi, Ascaris suum</i> and <i>Caenorhabditis elegans</i> UniProt databases using MASCOT to identify proteins. The complete list of proteins and the name of the gene encoding that protein (GN) is listed. UniProtKB (www.uniprot.org) identifiers are provided for each protein along with molecular weight (kDa). Proteins are ranked by their normalized spectral abundance factor (NSAF), a simple indicator of protein abundance in the sample reflecting the effect of protein length.<br>
DOI: 10.6084/m9.figshare.5740044
title: Supplemental Table 1

description: Complete list of proteins identified in adult male <i>Brugia malayi </i>extracellular vesicle (EV) proteome. Proteins extracted from EVs were subject to nano-scale LC-MS/MS. Spectral data were searched against the <i>B. malayi</i>, <i>Ascaris suum</i> and <i>Caenorhabditis elegans</i> UniProt databases using MASCOT to identify proteins. The complete list of proteins and the name of the gene encoding that protein (GN) is listed. UniProtKB (www.uniprot.org) identifiers are provided for each protein along with molecular weight (kDa). Proteins are ranked by their normalized spectral abundance factor (NSAF), a simple indicator of protein abundance in the sample reflecting the effect of protein length. *proteins identified in separate proteomic runs such that NSAF can not be compared.
DOI: 10.6084/m9.figshare.5740044.v1
title: Supplemental Table 1

description: Complete list of proteins identified in adult male <i>Brugia malayi </i>extracellular vesicle (EV) proteome. Proteins extracted from EVs were subject to nano-scale LC-MS/MS. Spectral data were searched against the <i>B. malayi</i>, <i>Ascaris suum</i> and <i>Caenorhabditis elegans</i> UniProt databases using MASCOT to identify proteins. The complete list of proteins and the name of the gene encoding that protein (GN) is listed. UniProtKB (www.uniprot.org) identifiers are provided for each protein along with molecular weight (kDa). Proteins are ranked by their normalized spectral abundance factor (NSAF), a simple indicator of protein abundance in the sample reflecting the effect of protein length. *proteins identified in separate proteomic runs such that NSAF can not be compared.
DOI: 10.6084/m9.figshare.5739801
title: Extra-pair parentage and personality in a cooperatively breeding bird

description: True genetic monogamy is rare, even in socially monogamous systems, and multiple factors, such as behaviour, social structure, morphology and physiology, determined by the biological system can cause variation in EPP. Therefore, investigating the inherent differences in these factors amongst individuals could be informative. We investigated whether reproductive outcomes are associated with differences in the propensity to explore novel environments/objects in a promiscuous, island-dwelling cooperatively breeding bird, the Seychelles warbler. Our results showed that exploratory behaviour was not associated with the number of offspring produced by an individual, and thus the long-term fitness consequences of different exploratory tendencies did not differ. We also found that the propensity to engage in EPP in females was higher in dissimilar behavioural pairs, but due to the small effect size we hesitate to conclude that there are personality-dependent mating outcomes in the population.<br>
DOI: 10.6084/m9.figshare.5739801.v1
title: Extra-pair parentage and personality in a cooperatively breeding bird

description: True genetic monogamy is rare, even in socially monogamous systems, and multiple factors, such as behaviour, social structure, morphology and physiology, determined by the biological system can cause variation in EPP. Therefore, investigating the inherent differences in these factors amongst individuals could be informative. We investigated whether reproductive outcomes are associated with differences in the propensity to explore novel environments/objects in a promiscuous, island-dwelling cooperatively breeding bird, the Seychelles warbler. Our results showed that exploratory behaviour was not associated with the number of offspring produced by an individual, and thus the long-term fitness consequences of different exploratory tendencies did not differ. We also found that the propensity to engage in EPP in females was higher in dissimilar behavioural pairs, but due to the small effect size we hesitate to conclude that there are personality-dependent mating outcomes in the population.<br>
DOI: 10.6084/m9.figshare.5739711
title: Dataset for: Lumped-Parameter Models of the Pulmonary Vasculature during the Progression of Pulmonary Arterial Hypertension

description: A longitudinal study of monocrotaline-induced pulmonary arterial hypertension (PAH) was carried out in Sprague Dawley rats to investigate the changes in impedance (comprising resistance and compliance) produced by the elevated blood pressure. Using invasively measured blood flow as an input, blood pressure was predicted using 3- and 4-element Windkessel (3WK, 4WK) type lumped-parameter models. Resistance, compliance, and inductance model parameters were obtained for the five different treatment groups via least-squares errors. The treated animals reached levels of hypertension, where blood pressure increased 2 folds from control to chronic stage of PAH (mean pressure went from 24 ± 5 to 44 ± 6 mmHg, p&lt;0.0001) but blood flow remained overall unaffected. Like blood pressure, the wave-reflection coefficient significantly increased at the advanced stage of PAH (0.26±0.09 to 0.52±0.09, p&lt;0.0002). Our modeling efforts revealed that resistances and compliance changed during the disease progression, where changes in compliance occur before the changes in resistance. However, resistance and compliance are not directly inversely related. As PAH develops resistances increase nonlinearly (Rd exponentially and R at a slower rate) while compliance linearly decreases. And while 3WK and 4WK models capture the pressure-flow relation in the pulmonary vasculature during PAH, results from Akaike Information Criterion and sensitivity analysis allow us to conclude that the 3WK is the most robust and accurate model for this system. 95% confidence intervals of the predicted model parameters are included for the population studied. This work establishes insight into the complex remodeling process occurring in PAH.
DOI: 10.6084/m9.figshare.5739711.v1
title: Dataset for: Lumped-Parameter Models of the Pulmonary Vasculature during the Progression of Pulmonary Arterial Hypertension

description: A longitudinal study of monocrotaline-induced pulmonary arterial hypertension (PAH) was carried out in Sprague Dawley rats to investigate the changes in impedance (comprising resistance and compliance) produced by the elevated blood pressure. Using invasively measured blood flow as an input, blood pressure was predicted using 3- and 4-element Windkessel (3WK, 4WK) type lumped-parameter models. Resistance, compliance, and inductance model parameters were obtained for the five different treatment groups via least-squares errors. The treated animals reached levels of hypertension, where blood pressure increased 2 folds from control to chronic stage of PAH (mean pressure went from 24 ± 5 to 44 ± 6 mmHg, p&lt;0.0001) but blood flow remained overall unaffected. Like blood pressure, the wave-reflection coefficient significantly increased at the advanced stage of PAH (0.26±0.09 to 0.52±0.09, p&lt;0.0002). Our modeling efforts revealed that resistances and compliance changed during the disease progression, where changes in compliance occur before the changes in resistance. However, resistance and compliance are not directly inversely related. As PAH develops resistances increase nonlinearly (Rd exponentially and R at a slower rate) while compliance linearly decreases. And while 3WK and 4WK models capture the pressure-flow relation in the pulmonary vasculature during PAH, results from Akaike Information Criterion and sensitivity analysis allow us to conclude that the 3WK is the most robust and accurate model for this system. 95% confidence intervals of the predicted model parameters are included for the population studied. This work establishes insight into the complex remodeling process occurring in PAH.
DOI: 10.6084/m9.figshare.5739705
title: yeast-ups1-tal08

description: Shotgun proteomics using multidimensional liquid chromatography coupled with tandem mass spectrometrywere performed on all biological samples, including universalproteomics standard set (UPS1), the S. cerevisiae Gcn4 affinity-purified complex (Yeast), S. cerevisiaetranscription complexes using the Tal08 minichromosome(Tal08). The RAW files generated from thedifferent LC/MS/MS experiments were converted tomzXML format with the program ReadW. The MS/MSspectra were extracted from the mzXML file using theprogram MzXML2Search and all data was processedusing the SEQUEST software. <br>The UPS1 dataset, developed by Sigma-Aldrichcompany, contains 48 purified human proteins digestedwith trypsin. The SEQUEST search results include17,335 PSMs, among which 8974 PSMs match targetpeptides and 8361 PSMs match decoy peptides. TheYeast dataset contains 6652 proteins and SEQUESToutputs 14,892 PSMs, among which 6703 PSMs matchtarget peptides and 8189 PSMs match decoy peptides.
DOI: 10.6084/m9.figshare.5739693
title: Identification of fossil worm tubes from Phanerozoic hydrothermal vents and cold seeps

description: One of the main limitations to understanding the evolutionary history of hydrothermal vent and cold seep communities is the identification of tube fossils from ancient deposits. Tube-dwelling annelids are some of the most conspicuous inhabitants of modern vent and seep ecosystems, and ancient vent and seep tubular fossils are usually considered to have been made by annelids. However, the taxonomic affinities of many tube fossils from vents and seeps are contentious, or have remained largely undetermined due to difficulties in identification. In this study, we make a detailed chemical (Fourier-transform infrared spectroscopy and pyrolysis gas-chromatography mass-spectrometry) and morphological assessment of modern annelid tubes from six families, and fossil tubes (seven tube types from the Cenozoic, 12 Mesozoic and four Palaeozoic) from hydrothermal vent and cold seep environments. Characters identified from these investigations were used to explore for the first time the systematics of ancient vent and seep tubes within a cladistic framework. Results reveal details of the compositions and ultrastructures of modern tubes, and also suggest that two types of tubes from ancient vent localities were made by the annelid family Siboglinidae, which often dominates modern vents and seeps. Our results also highlight that several vent and seep tube fossils formerly thought to have been made by annelids cannot be assigned an annelid affiliation with any certainty. The findings overall improve the level of quality control with regard to interpretations of fossil tubes, and, most importantly, suggest that siboglinids likely occupied Mesozoic vents and seeps, greatly increasing the minimum age of the clade relative to earlier molecular estimates.
DOI: 10.6084/m9.figshare.5739693.v1
title: Identification of fossil worm tubes from Phanerozoic hydrothermal vents and cold seeps

description: One of the main limitations to understanding the evolutionary history of hydrothermal vent and cold seep communities is the identification of tube fossils from ancient deposits. Tube-dwelling annelids are some of the most conspicuous inhabitants of modern vent and seep ecosystems, and ancient vent and seep tubular fossils are usually considered to have been made by annelids. However, the taxonomic affinities of many tube fossils from vents and seeps are contentious, or have remained largely undetermined due to difficulties in identification. In this study, we make a detailed chemical (Fourier-transform infrared spectroscopy and pyrolysis gas-chromatography mass-spectrometry) and morphological assessment of modern annelid tubes from six families, and fossil tubes (seven tube types from the Cenozoic, 12 Mesozoic and four Palaeozoic) from hydrothermal vent and cold seep environments. Characters identified from these investigations were used to explore for the first time the systematics of ancient vent and seep tubes within a cladistic framework. Results reveal details of the compositions and ultrastructures of modern tubes, and also suggest that two types of tubes from ancient vent localities were made by the annelid family Siboglinidae, which often dominates modern vents and seeps. Our results also highlight that several vent and seep tube fossils formerly thought to have been made by annelids cannot be assigned an annelid affiliation with any certainty. The findings overall improve the level of quality control with regard to interpretations of fossil tubes, and, most importantly, suggest that siboglinids likely occupied Mesozoic vents and seeps, greatly increasing the minimum age of the clade relative to earlier molecular estimates.
DOI: 10.25442/hku.12839513
title: Proteogenomic analysis of gastrointestinal cancer

description: This dataset contains the scripts and files for reproducing the results of my thesis.<br>
DOI: 10.25442/hku.12839513.v1
title: Proteogenomic analysis of gastrointestinal cancer

description: This dataset contains the scripts and files for reproducing the results of my thesis.<br>
DOI: 10.6084/m9.figshare.5739627
title: Genes duplicated in Paedocypris genomes

description: This dataset contains the alignments and trees for all duplicated genes found in both <i>Paedocypris</i> genomes.
DOI: 10.6084/m9.figshare.5739621
title: Pharmacophore-based virtual screening of catechol-o-methyltransferase (COMT) inhibitors to combat Alzheimer’s disease

description: Alzheimer’s disease (AD) is one of the most significant neurodegenerative disorders and its symptoms mostly appear in aged people. Catechol-o-methyltransferase (COMT) is one of the known target enzymes responsible for AD. With the use of 23 known inhibitors of COMT, a query has been generated and validated by screening against the database of 1500 decoys to obtain the GH score and enrichment value. The crucial features of the known inhibitors were evaluated by the online ZINC Pharmer to identify new leads from a ZINC database. Five hundred hits were retrieved from ZINC Pharmer and by ADMET (absorption, distribution, metabolism, excretion, and toxicity) filtering by using FAF-Drug-3 and 36 molecules were considered for molecular docking. From the COMT inhibitors, opicapone, fenoldopam, and quercetin were selected, while ZINC63625100_413 ZINC39411941_412, ZINC63234426_254, ZINC63637968_451, and ZINC64019452_303 were chosen for the molecular dynamics simulation analysis having high binding affinity and structural recognition. This study identified the potential COMT inhibitors through pharmacophore-based inhibitor screening leading to a more complete understanding of molecular-level interactions.
DOI: 10.6084/m9.figshare.5739621.v1
title: Pharmacophore-based virtual screening of catechol-o-methyltransferase (COMT) inhibitors to combat Alzheimer’s disease

description: Alzheimer’s disease (AD) is one of the most significant neurodegenerative disorders and its symptoms mostly appear in aged people. Catechol-o-methyltransferase (COMT) is one of the known target enzymes responsible for AD. With the use of 23 known inhibitors of COMT, a query has been generated and validated by screening against the database of 1500 decoys to obtain the GH score and enrichment value. The crucial features of the known inhibitors were evaluated by the online ZINC Pharmer to identify new leads from a ZINC database. Five hundred hits were retrieved from ZINC Pharmer and by ADMET (absorption, distribution, metabolism, excretion, and toxicity) filtering by using FAF-Drug-3 and 36 molecules were considered for molecular docking. From the COMT inhibitors, opicapone, fenoldopam, and quercetin were selected, while ZINC63625100_413 ZINC39411941_412, ZINC63234426_254, ZINC63637968_451, and ZINC64019452_303 were chosen for the molecular dynamics simulation analysis having high binding affinity and structural recognition. This study identified the potential COMT inhibitors through pharmacophore-based inhibitor screening leading to a more complete understanding of molecular-level interactions.
DOI: 10.6084/m9.figshare.5739612
title: Sequence fingerprints distinguish erroneous from correct predictions of intrinsically disordered protein regions

description: More than 60 prediction methods for intrinsically disordered proteins (IDPs) have been developed over the years, many of which are accessible on the World Wide Web. Nearly, all of these predictors give balanced accuracies in the ~65%–~80% range. Since predictors are not perfect, further studies are required to uncover the role of amino acid residues in native IDP as compared to predicted IDP regions. In the present work, we make use of sequences of 100% predicted IDP regions, false positive disorder predictions, and experimentally determined IDP regions to distinguish the characteristics of native versus predicted IDP regions. A higher occurrence of asparagine is observed in sequences of native IDP regions but not in sequences of false positive predictions of IDP regions. The occurrences of certain combinations of amino acids at the pentapeptide level provide a distinguishing feature in the IDPs with respect to globular proteins. The distinguishing features presented in this paper provide insights into the sequence fingerprints of amino acid residues in experimentally determined as compared to predicted IDP regions. These observations and additional work along these lines should enable the development of improvements in the accuracy of disorder prediction algorithm.
DOI: 10.6084/m9.figshare.5739612.v1
title: Sequence fingerprints distinguish erroneous from correct predictions of intrinsically disordered protein regions

description: More than 60 prediction methods for intrinsically disordered proteins (IDPs) have been developed over the years, many of which are accessible on the World Wide Web. Nearly, all of these predictors give balanced accuracies in the ~65%–~80% range. Since predictors are not perfect, further studies are required to uncover the role of amino acid residues in native IDP as compared to predicted IDP regions. In the present work, we make use of sequences of 100% predicted IDP regions, false positive disorder predictions, and experimentally determined IDP regions to distinguish the characteristics of native versus predicted IDP regions. A higher occurrence of asparagine is observed in sequences of native IDP regions but not in sequences of false positive predictions of IDP regions. The occurrences of certain combinations of amino acids at the pentapeptide level provide a distinguishing feature in the IDPs with respect to globular proteins. The distinguishing features presented in this paper provide insights into the sequence fingerprints of amino acid residues in experimentally determined as compared to predicted IDP regions. These observations and additional work along these lines should enable the development of improvements in the accuracy of disorder prediction algorithm.
DOI: 10.5519/qd.6m00ciua
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (1 records)
DOI: 10.6084/m9.figshare.5739534
title: Additional file 3: of When honesty and cheating pay off: the evolution of honest and dishonest equilibria in a conventional signalling game

description: Dataset 2. Szalai and Számadó [25] parameter regions. (CSV 292 kb)
DOI: 10.6084/m9.figshare.5739534.v1
title: Additional file 3: of When honesty and cheating pay off: the evolution of honest and dishonest equilibria in a conventional signalling game

description: Dataset 2. Szalai and Számadó [25] parameter regions. (CSV 292 kb)
DOI: 10.6084/m9.figshare.5739531
title: Additional file 2: of When honesty and cheating pay off: the evolution of honest and dishonest equilibria in a conventional signalling game

description: Dataset 1. Szalai and Számadó [25] results. (CSV 1421 kb)