cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.7618817
title: Metabolite analysis and nucleoside determination using reproducible UHPLC-Q-ToF-IMS in <i>Ophiocordyceps sinensis</i>

description: A fast, reliable and reproducible UHPLC-IMS method was developed and validated for simultaneous determination of eight nucleosides (adenine, adenosine, cordycepin, guanosine, inosine, thymidine, thymine and uracil) in natural <i>Ophiocordyceps sinensis.</i> Present study was conducted to determine the marker nucleoside contents in low quantities using the developed method. Methanol and water in combination were used as extraction solvents due to hydrophilic nature of nucleosides. These nucleosides showed good linearity (<i>r</i><sup>2</sup><i>&gt;</i>0.99), LOD (0.28–0.97ng/mL), LOQ (0.79–3.20 ng/mL), recoveries (88.3 and 103.2%), reproducibility, stability and intra- and inter-day precision (&lt;2.87%). Method was validated using three samples of natural <i>Ophiocordyceps</i> collected from different geographical region. PCA analysis depicted that adenine, adenosine, guanine, guanosine, uracil and uridine were major components contributing to total variance. Highest nucleosides content (5124 µg/g) was detected in STD-1. The presence of cordycepin, an important marker compound was identified for first time using ion mobility mass spectrometry (IMMS) technique. Metabolomics approach resulted 18, 12 and 9 metabolites in three samples (STD-1, STD-II and STD-III, respectively) using METLIN database which opened the new avenues to identify and explore more novel biomarkers in <i>Ophiocordyceps.</i> We anticipate that these methods may be applied to verify/certification of <i>Ophiocordyceps</i> containing marker nucleosides for their dietary intake.
DOI: 10.6084/m9.figshare.7618880.v1
title: README.txt

description: The README.txt provides an overview of the supplementary data accompanying our article in Nature Microbiology entitled: "Proposal of the reverse flow model for the origin of the eukaryotic cell based on comparative analysis of Asgard archaeal metabolism"<br><br><br> <br>
DOI: 10.7284/115394
title: Speedlog data collected during research cruise EN549 using a EDO MRQ-4015D instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7618817.v1
title: Metabolite analysis and nucleoside determination using reproducible UHPLC-Q-ToF-IMS in <i>Ophiocordyceps sinensis</i>

description: A fast, reliable and reproducible UHPLC-IMS method was developed and validated for simultaneous determination of eight nucleosides (adenine, adenosine, cordycepin, guanosine, inosine, thymidine, thymine and uracil) in natural <i>Ophiocordyceps sinensis.</i> Present study was conducted to determine the marker nucleoside contents in low quantities using the developed method. Methanol and water in combination were used as extraction solvents due to hydrophilic nature of nucleosides. These nucleosides showed good linearity (<i>r</i><sup>2</sup><i>&gt;</i>0.99), LOD (0.28–0.97ng/mL), LOQ (0.79–3.20 ng/mL), recoveries (88.3 and 103.2%), reproducibility, stability and intra- and inter-day precision (&lt;2.87%). Method was validated using three samples of natural <i>Ophiocordyceps</i> collected from different geographical region. PCA analysis depicted that adenine, adenosine, guanine, guanosine, uracil and uridine were major components contributing to total variance. Highest nucleosides content (5124 µg/g) was detected in STD-1. The presence of cordycepin, an important marker compound was identified for first time using ion mobility mass spectrometry (IMMS) technique. Metabolomics approach resulted 18, 12 and 9 metabolites in three samples (STD-1, STD-II and STD-III, respectively) using METLIN database which opened the new avenues to identify and explore more novel biomarkers in <i>Ophiocordyceps.</i> We anticipate that these methods may be applied to verify/certification of <i>Ophiocordyceps</i> containing marker nucleosides for their dietary intake.
DOI: 10.6084/m9.figshare.7618790
title: sup. Table S3

description: Integrated DNA methylation and DNA hydroxymethylation define epigenetic of etiology dilated cardiomyopathy
DOI: 10.7284/115396
title: TSG (Thermosalinograph) data collected during research cruise EN549 using a Sea-Bird SBE-21 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7618787
title: sup. Table S2

description: Integrated DNA methylation and DNA hydroxymethylation define epigenetic of etiology dilated cardiomyopathy
DOI: 10.6084/m9.figshare.7618790.v2
title: sup. Table S3

description: Integrated DNA methylation and DNA hydroxymethylation define epigenetic of etiology dilated cardiomyopathy
DOI: 10.6084/m9.figshare.7618769
title: sup. Table S1

description: 5mC and 5hmC genes in the aetiology of dilated cardiomyopathy
DOI: 10.6084/m9.figshare.7618787.v2
title: sup. Table S2

description: Integrated DNA methylation and DNA hydroxymethylation define epigenetic of etiology dilated cardiomyopathy
DOI: 10.6084/m9.figshare.7618790.v1
title: sup. Table T3

description: Integrated DNA methylation and DNA hydroxymethylation define epigenetic of etiology dilated cardiomyopathy
DOI: 10.7284/115397
title: TSG (Thermosalinograph) data collected during research cruise EN549 using a Sea-Bird SBE-45 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7618754
title: Dihaloplatinum(II) complexes having diimine ligands: crystal structure, thermal properties, cytotoxicity effects against breast cancer cells and application as a precursor towards nanoparticles

description: The reaction of potassium tetrachloroplatinate(II) with dimethylsulfide and a mixture of HBr/KBr affords <i>trans</i>-[PtBr<sub>2</sub>(SMe<sub>2</sub>)<sub>2</sub>]; [PtBr<sub>2</sub>(Me<sub>2</sub>bpy)] (Me<sub>2</sub>bpy = 4,4'-dimethyl-2,2'-bipyridine) was prepared from the reaction of <i>trans</i>-[PtBr<sub>2</sub>(SMe<sub>2</sub>)<sub>2</sub>] with Me<sub>2</sub>bpy. The crystal structure of the yellow form of [PtBr<sub>2</sub>(bu<sub>2</sub>bpy)] (bu<sub>2</sub>bpy = 4,4'-di-<i>tert</i>-butyl-2,2'-bipyridine) was determined by X-ray crystallography. The X-ray single-crystal structure determination of complex [PtBr<sub>2</sub>(bu<sub>2</sub>bpy)] reveals that the platinum adopts a square planar geometry with a twofold axis through the platinum atoms. Thermal properties of the related series of diimine platinum(II) complexes [PtX<sub>2</sub>(bu<sub>2</sub>bpy)] (X = Cl, Br, I) reveal that the thermal stabilities increase [PtI<sub>2</sub>(bu<sub>2</sub>bpy)] 2(bu<sub>2</sub>bpy)] 2(bu<sub>2</sub>bpy)]. [PtBr<sub>2</sub>(bpy)] (bpy = 2,2'-bipyridine), [PtBr<sub>2</sub>(Me<sub>2</sub>bpy)] and [PtX<sub>2</sub>(bu<sub>2</sub>bpy)] (X = Cl, Br, I) were studied by MTT assay against two human breast cancer cell lines of MCF-7 and MDA-MB-468 with [PtCl<sub>2</sub>(bu<sub>2</sub>bpy)] having a higher cytotoxic effect towards both cancer cell lines, which shows the significant role of the halide and diimine ligand. Semi-spherical Pt(0) nanoparticles (NPCs) were prepared by the simple calcination of [PtX<sub>2</sub>(bu<sub>2</sub>bpy)] (X = Cl, Br, I) at 800 °C in air.
DOI: 10.6084/m9.figshare.7618769.v2
title: sup. Table S1

description: 5mC and 5hmC genes in the aetiology of dilated cardiomyopathy
DOI: 10.6084/m9.figshare.7618787.v1
title: sup. Table T2

description: Integrated DNA methylation and DNA hydroxymethylation define epigenetic of etiology dilated cardiomyopathy
DOI: 10.6084/m9.figshare.7618769.v1
title: sup. Table T1

description: 5mC and 5hmC genes in the aetiology of dilated cardiomyopathy
DOI: 10.7284/121948
title: ADCP (Acoustic Doppler Current Profiler) data collected during research cruise EN550 using a Hawaii UHDAS instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7618739
title: Genomic structure of a crossbred Landrace pig population

description: S1 Output files: Shared ROHs Analysis. Information of: Chromosome; Begin and end of Segment; Number of animals and Percent of animals.<br><br>S2 Output files: Plink Output: Linkage disequilibrium analysis.<br><br><br>
DOI: 10.6084/m9.figshare.7618739.v1
title: Genomic structure of a crossbred Landrace pig population

description: S1 Output files: Shared ROHs Analysis. Information of: Chromosome; Begin and end of Segment; Number of animals and Percent of animals.<br><br>S2 Output files: Plink Output: Linkage disequilibrium analysis.<br><br><br>
DOI: 10.6084/m9.figshare.7618754.v2
title: Dihaloplatinum(II) complexes having diimine ligands: crystal structure, thermal properties, cytotoxicity effects against breast cancer cells and application as a precursor towards nanoparticles

description: The reaction of potassium tetrachloroplatinate(II) with dimethylsulfide and a mixture of HBr/KBr affords <i>trans</i>-[PtBr<sub>2</sub>(SMe<sub>2</sub>)<sub>2</sub>]; [PtBr<sub>2</sub>(Me<sub>2</sub>bpy)] (Me<sub>2</sub>bpy = 4,4'-dimethyl-2,2'-bipyridine) was prepared from the reaction of <i>trans</i>-[PtBr<sub>2</sub>(SMe<sub>2</sub>)<sub>2</sub>] with Me<sub>2</sub>bpy. The crystal structure of the yellow form of [PtBr<sub>2</sub>(bu<sub>2</sub>bpy)] (bu<sub>2</sub>bpy = 4,4'-di-<i>tert</i>-butyl-2,2'-bipyridine) was determined by X-ray crystallography. The X-ray single-crystal structure determination of complex [PtBr<sub>2</sub>(bu<sub>2</sub>bpy)] reveals that the platinum adopts a square planar geometry with a twofold axis through the platinum atoms. Thermal properties of the related series of diimine platinum(II) complexes [PtX<sub>2</sub>(bu<sub>2</sub>bpy)] (X = Cl, Br, I) reveal that the thermal stabilities increase [PtI<sub>2</sub>(bu<sub>2</sub>bpy)] 2(bu<sub>2</sub>bpy)] 2(bu<sub>2</sub>bpy)]. [PtBr<sub>2</sub>(bpy)] (bpy = 2,2'-bipyridine), [PtBr<sub>2</sub>(Me<sub>2</sub>bpy)] and [PtX<sub>2</sub>(bu<sub>2</sub>bpy)] (X = Cl, Br, I) were studied by MTT assay against two human breast cancer cell lines of MCF-7 and MDA-MB-468 with [PtCl<sub>2</sub>(bu<sub>2</sub>bpy)] having a higher cytotoxic effect towards both cancer cell lines, which shows the significant role of the halide and diimine ligand. Semi-spherical Pt(0) nanoparticles (NPCs) were prepared by the simple calcination of [PtX<sub>2</sub>(bu<sub>2</sub>bpy)] (X = Cl, Br, I) at 800 °C in air.
DOI: 10.7284/121947
title: CTD (Conductivity, Temperature, Depth) data collected during research cruise EN550 using a Sea-Bird SBE-911+ instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7618727
title: Expression profile and TCR typing information of single T cells derived from 12 colorectal cancer patients

description: The expression profile contains 10,805 cells and 12,547 genes, of which the expression values were quantified by log2 (TPM+ 1).The table of sample characteristics includes the information of patient origins, cell types, clusters and TCR sequences of single T cells.The table of marker genes contains signatures for each T cell clusters identified by ANOVA analysis.
DOI: 10.6084/m9.figshare.7618727.v1
title: Expression profile and TCR typing information of single T cells derived from 12 colorectal cancer patients

description: The expression profile contains 10,805 cells and 12,547 genes, of which the expression values were quantified by log2 (TPM+ 1).The table of sample characteristics includes the information of patient origins, cell types, clusters and TCR sequences of single T cells.The table of marker genes contains signatures for each T cell clusters identified by ANOVA analysis.
DOI: 10.7284/121945
title: GNSS (Global Navigation Satellite System) data collected during research cruise EN550 using a Furuno GP-90D instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7618712
title: eQTL result files

description: This is the workspace image of R after running the eQTL analysis from the example section.<br>
DOI: 10.6084/m9.figshare.7618715
title: Energetic correlates and the physiological basis for seaward migration in sea trout kelts

description: This is the dataset for our manuscript entitled "Energetic correlates and the physiological basis for seaward migration in sea trout kelts"
DOI: 10.6084/m9.figshare.7618712.v1
title: eQTL result files

description: This is the workspace image of R after running the eQTL analysis from the example section.<br>
DOI: 10.6084/m9.figshare.7618715.v1
title: Energetic correlates and the physiological basis for seaward migration in sea trout kelts

description: This is the dataset for our manuscript entitled "Energetic correlates and the physiological basis for seaward migration in sea trout kelts"
DOI: 10.7284/121946
title: GNSS (Global Navigation Satellite System) data collected during research cruise EN550 using a Northstar 952 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.7284/121949
title: Gyrocompass data collected during research cruise EN550 using a Sperry MK-37 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7618676
title: Matlab Code from A model of the oscillatory mechanical forces in the conventional outflow pathway

description: This folder contains all of the files required to run the simulations and generate the data used in the present study
DOI: 10.7284/121950
title: Gyrocompass data collected during research cruise EN550 using a Sperry MK-37 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7618646
title: Supplementary Material for: Cell Type-Specific Gene Expression of Alpha 5 Subunit-Containing Gamma-Aminobutyric Acid Subtype A Receptors in Human and Mouse Frontal Cortex

description: Converging evidence suggests that deficits in somatostatin (SST)-expressing neuron signaling contributes to major depressive disorder. Preclinical studies show that enhancing this signaling, specifically at α5 subunit-containing γ-ami­nobutyric acid subtype A receptors (α5-GABA<sub>A</sub>Rs), provides a potential means to overcome low SST neuron function. The cortical microcircuit comprises multiple subtypes of inhibitory γ-aminobutyric acid (GABA) neurons and excitatory pyramidal cells (PYCs). In this study, multilabel fluorescence in situ hybridization was used to characterize α5-GABA<sub>A</sub>R gene expression in PYCs and three GABAergic neuron subgroups – vasoactive intestinal peptide (VIP)-, SST-, and parvalbumin (PV)-expressing cells – in the human and mouse frontal cortex. Across species, we found the majority of gene expression in PYCs (human: 39.7%; mouse: 54.14%), less abundant expression in PV neurons (human: 20%; mouse: 16.33%), and no expression in VIP neurons (0%). Only human SST cells expressed GABRA5, albeit at low levels (human: 8.3%; mouse: 0%). Together, this localization suggests potential roles for α5-GABA<sub>A</sub>Rs within the cortical microcircuit: (1) regulators of PYCs, (2) regulators of PV cell activity across species, and (3) sparse regulators of SST cell inhibition in humans. These results will advance our ability to predict the effects of pharmacological agents targeting α5-GABA<sub>A</sub>Rs, which have shown therapeutic potential in preclinical animal models.
DOI: 10.6084/m9.figshare.7618676.v1
title: Matlab Code from A model of the oscillatory mechanical forces in the conventional outflow pathway

description: This folder contains all of the files required to run the simulations and generate the data used in the present study
DOI: 10.7284/121951
title: Speedlog data collected during research cruise EN550 using a EDO MRQ-4015D instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.7618646.v1
title: Supplementary Material for: Cell Type-Specific Gene Expression of Alpha 5 Subunit-Containing Gamma-Aminobutyric Acid Subtype A Receptors in Human and Mouse Frontal Cortex

description: Converging evidence suggests that deficits in somatostatin (SST)-expressing neuron signaling contributes to major depressive disorder. Preclinical studies show that enhancing this signaling, specifically at α5 subunit-containing γ-ami­nobutyric acid subtype A receptors (α5-GABA<sub>A</sub>Rs), provides a potential means to overcome low SST neuron function. The cortical microcircuit comprises multiple subtypes of inhibitory γ-aminobutyric acid (GABA) neurons and excitatory pyramidal cells (PYCs). In this study, multilabel fluorescence in situ hybridization was used to characterize α5-GABA<sub>A</sub>R gene expression in PYCs and three GABAergic neuron subgroups – vasoactive intestinal peptide (VIP)-, SST-, and parvalbumin (PV)-expressing cells – in the human and mouse frontal cortex. Across species, we found the majority of gene expression in PYCs (human: 39.7%; mouse: 54.14%), less abundant expression in PV neurons (human: 20%; mouse: 16.33%), and no expression in VIP neurons (0%). Only human SST cells expressed GABRA5, albeit at low levels (human: 8.3%; mouse: 0%). Together, this localization suggests potential roles for α5-GABA<sub>A</sub>Rs within the cortical microcircuit: (1) regulators of PYCs, (2) regulators of PV cell activity across species, and (3) sparse regulators of SST cell inhibition in humans. These results will advance our ability to predict the effects of pharmacological agents targeting α5-GABA<sub>A</sub>Rs, which have shown therapeutic potential in preclinical animal models.
DOI: 10.6084/m9.figshare.7618628
title: Facilitators and barriers to supporting individuals with spinal cord injury in the community: experiences of family caregivers and care recipients

description: <b>Purpose</b><b>:</b> Family members make an important contribution to informal and formal care, as well as the overall health and wellbeing of individuals with spinal cord injury. Caregiving often results in negative outcomes which, if not addressed, threaten the sustainability of these critical supports. We sought to explore the perceptions of individuals with spinal cord injury and their family caregivers regarding the facilitators and barriers to undertaking and sustaining the caregiving role in the community. <b>Methods:</b> A qualitative descriptive approach with semi-structured interviews. Thematic analysis was employed to determine key themes arising from individuals with spinal cord injury (<i>n</i> = 19) and their family members’ (<i>n</i> = 16) experiences. <b>Results:</b> The following four facilitators to caregiving were identified: access to community support services, positive coping in relationship, social support, and mastery of caregiving roles. Conversely, the following six barriers to caregiving were identified: lack of access to community resources, lack of knowledge about resources and formal training, fragmented continuity of care, negative coping in relationship, role strain, and caregiver injury or illness. <b>Conclusions:</b> The current study demonstrated that positive coping, social support, skills training, access to community services and continuity of care contribute significantly to the sustainability of the spinal cord injury family caregiving role. As such, the development of future caregiver interventions should consider these facilitators.Implications for RehabilitationFamily caregivers make an important contribution to the care processes and overall quality of life of individuals with spinal cord injury post-discharge into the community.The potential negative effects of caregiving could threaten the sustainability of these critical supports.Positive coping, social support, skills training, access to community services, and continuity of care contribute significantly to the sustainability of the spinal cord injury family caregiving role.This study shows the need for better integration of family members during the rehabilitation and discharge process to better prepare them for the caregiving role. Family caregivers make an important contribution to the care processes and overall quality of life of individuals with spinal cord injury post-discharge into the community. The potential negative effects of caregiving could threaten the sustainability of these critical supports. Positive coping, social support, skills training, access to community services, and continuity of care contribute significantly to the sustainability of the spinal cord injury family caregiving role. This study shows the need for better integration of family members during the rehabilitation and discharge process to better prepare them for the caregiving role.
DOI: 10.6084/m9.figshare.7618631
title: Supplementary Material for: Novel Benzodiazepine-Like Ligands with Various Anxiolytic, Antidepressant, or Pro-Cognitive Profiles

description: Altered gamma-aminobutyric acid (GABA) function is consistently reported in psychiatric disorders, normal aging, and neurodegenerative disorders and reduced function of GABA interneurons is associated with both mood and cognitive symptoms. Benzodiazepines (BZ) have broad anxiolytic, but also sedative, anticonvulsant and amnesic effects, due to nonspecific GABA-A receptor (GABAA-R) targeting. Varying the profile of activity of BZs at GABAA-Rs is predicted to uncover additional therapeutic potential. We synthesized four novel imidazobenzodiazepine (IBZD) amide ligands and tested them for positive allosteric modulation at multiple α-GABAA-R (α-positive allosteric modulators), pharmacokinetic properties, as well as anxiolytic and antidepressant activities in adult mice. Efficacy at reversing stress-induced or age-related working memory deficits was assessed using a spontaneous alternation task. Diazepam (DZP) was used as a control. Three ligands (GL-II-73, GL-II-74, and GL-II-75) demonstrated adequate brain penetration and showed predictive anxiolytic and antidepressant efficacies. GL-II-73 and GL-II-75 significantly reversed stress-induced and age-related working memory deficits. In contrast, DZP displayed anxiolytic but no antidepressant effects or effects on working memory. We demonstrate distinct profiles of anxiolytic, antidepressant, and/or pro-cognitive activities of newly designed IBZD amide ligands, suggesting novel therapeutic potential for IBZD derivatives in depression and aging.
DOI: 10.7284/121953
title: TSG (Thermosalinograph) data collected during research cruise EN550 using a Sea-Bird SBE-21 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.26180/5c484681591c0
title: Data to support TCRa and TCRb repertoire analysis of human thymocyte subsets (samples fk_167, fk_168 and fk_172)

description: The file contains human T cell receptor (TCR) sequences obtained by multiplex PCR amplification of cDNA molecules followed by Illumina sequencing. Sequences were aligned to the human genome using MIGEC software (see doi: 10.1038/nmeth.2960 for details). Except for the header row, each row contains information about a unique TCR nucleotide sequence. Column 1 stores the TCR chain (a, alpha; b, beta). Column 2 stores the T cell subset. Column 3 is an identifier for the thymus sample of origin. Columns 4 and 5 store the nucleotide sequence and amino acid sequence, respectively, of the complementarity-determining region 3 (CDR3). Columns 6 and 7 store the TCR variable (v) and joining (j) gene segment information.<br>
DOI: 10.7284/121954
title: TSG (Thermosalinograph) data collected during research cruise EN550 using a Sea-Bird SBE-45 instrument system onboard the platform RV Endeavor

description: Original (unprocessed) data collected during a Field_expedition