cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4829233
title: Table S2. Unravelling an allochthonous, subaqueously deposited volcanic–epiclastic to subaerial andesitic lava assemblage in Hong Kong: age, stratigraphy and provenance studies of the Middle Jurassic Tuen Mun Formation

description: Table S2. Zircon Hf isotope data of detrital zircons from the Tuen Mun Formation.
DOI: 10.6084/m9.figshare.4829221
title: Table S1. Unravelling an allochthonous, subaqueously deposited volcanic–epiclastic to subaerial andesitic lava assemblage in Hong Kong: age, stratigraphy and provenance studies of the Middle Jurassic Tuen Mun Formation

description: Table S1. U–Pb data on zircon from sedimentary rocks in the Tuen Mun Valley area, Hong Kong
DOI: 10.6084/m9.figshare.4829221.v1
title: Table S1. Unravelling an allochthonous, subaqueously deposited volcanic–epiclastic to subaerial andesitic lava assemblage in Hong Kong: age, stratigraphy and provenance studies of the Middle Jurassic Tuen Mun Formation

description: Table S1. U–Pb data on zircon from sedimentary rocks in the Tuen Mun Valley area, Hong Kong
DOI: 10.6084/m9.figshare.4829176
title: mg_classifier databases

description: Databases for use with mg_classifier:16S rRNA SILVA 128 RDP 11.518S rRNA PR2
DOI: 10.6084/m9.figshare.4829215
title: Novel insights into systemic autoimmune rheumatic diseases using shared molecular signatures and an integrative analysis

description: We undertook this study to identify DNA methylation signatures of three systemic autoimmune rheumatic diseases (SARDs), namely rheumatoid arthritis, systemic lupus erythematosus, and systemic sclerosis, compared to healthy controls. Using a careful design to minimize confounding, we restricted our study to subjects with incident disease and performed our analyses on purified CD4<sup>+</sup> T cells, key effector cells in SARD. We identified differentially methylated (using the Illumina Infinium HumanMethylation450 BeadChip array) and expressed (using the Illumina TruSeq stranded RNA-seq protocol) sites between cases and controls, and investigated the biological significance of this SARD signature using gene annotation databases. We recruited 13 seropositive rheumatoid arthritis, 19 systemic sclerosis, 12 systemic lupus erythematosus subjects, and 8 healthy controls. We identified 33 genes that were both differentially methylated and expressed (26 over- and 7 under-expressed) in SARD cases versus controls. The most highly overexpressed gene was <i>CD1C</i> (log fold change in expression = 1.85, adjusted <i>P</i> value = 0.009). In functional analysis (Ingenuity Pathway Analysis), the top network identified was lipid metabolism, molecular transport, small molecule biochemistry. The top canonical pathways included the mitochondrial L-carnitine shuttle pathway (<i>P</i> = 5E-03) and PTEN signaling (<i>P</i> = 8E-03). The top upstream regulator was HNF4A (<i>P</i> = 3E-05). This novel SARD signature contributes to ongoing work to further our understanding of the molecular mechanisms underlying SARD and provides novel targets of interest.
DOI: 10.6084/m9.figshare.4829215.v1
title: Novel insights into systemic autoimmune rheumatic diseases using shared molecular signatures and an integrative analysis

description: We undertook this study to identify DNA methylation signatures of three systemic autoimmune rheumatic diseases (SARDs), namely rheumatoid arthritis, systemic lupus erythematosus, and systemic sclerosis, compared to healthy controls. Using a careful design to minimize confounding, we restricted our study to subjects with incident disease and performed our analyses on purified CD4<sup>+</sup> T cells, key effector cells in SARD. We identified differentially methylated (using the Illumina Infinium HumanMethylation450 BeadChip array) and expressed (using the Illumina TruSeq stranded RNA-seq protocol) sites between cases and controls, and investigated the biological significance of this SARD signature using gene annotation databases. We recruited 13 seropositive rheumatoid arthritis, 19 systemic sclerosis, 12 systemic lupus erythematosus subjects, and 8 healthy controls. We identified 33 genes that were both differentially methylated and expressed (26 over- and 7 under-expressed) in SARD cases versus controls. The most highly overexpressed gene was <i>CD1C</i> (log fold change in expression = 1.85, adjusted <i>P</i> value = 0.009). In functional analysis (Ingenuity Pathway Analysis), the top network identified was lipid metabolism, molecular transport, small molecule biochemistry. The top canonical pathways included the mitochondrial L-carnitine shuttle pathway (<i>P</i> = 5E-03) and PTEN signaling (<i>P</i> = 8E-03). The top upstream regulator was HNF4A (<i>P</i> = 3E-05). This novel SARD signature contributes to ongoing work to further our understanding of the molecular mechanisms underlying SARD and provides novel targets of interest.
DOI: 10.6084/m9.figshare.4829176.v1
title: mg_classifier databases

description: Databases for use with mg_classifier:16S rRNA SILVA 128 RDP 11.518S rRNA PR2
DOI: 10.6084/m9.figshare.4829095
title: Raw data of spindle length and migration in oocytes treated with different concentrations of FIPI.PDF

description: No changes in spindle length and migration were observed in oocytes treated with different concentrations of FIPI.
DOI: 10.6084/m9.figshare.4829104
title: Periglacial geomorphology of summit tors on Bodmin Moor, Cornwall, SW England

description: Three maps are presented that portray the periglacial geomorphology of the three summit areas of Bodmin Moor, Cornwall, SW England, including Brown Willy (scale 1:2630), Kilmar/Bearah/Sharp tors (scale 1:3335) and Rough/Little Rough/Showery tors (scale 1:2175). Landform elements include castellated tors with well-developed cantilevered or precariously balanced corestones, summit blockfields, rock-fronted lobes thought to record former permafrost creep, patterned ground (stripes) and lower slope accumulations of crudely stratified growan or weathered granite residue. The altitudinal arrangement of these periglacial landforms appears to be a signature of a well-established periglacial landsystem and hence the Bodmin Moor granite massif is a suitable exemplar for a mature upland periglacial landsystem unaffected by glacierization.
DOI: 10.6084/m9.figshare.4829104.v1
title: Periglacial geomorphology of summit tors on Bodmin Moor, Cornwall, SW England

description: Three maps are presented that portray the periglacial geomorphology of the three summit areas of Bodmin Moor, Cornwall, SW England, including Brown Willy (scale 1:2630), Kilmar/Bearah/Sharp tors (scale 1:3335) and Rough/Little Rough/Showery tors (scale 1:2175). Landform elements include castellated tors with well-developed cantilevered or precariously balanced corestones, summit blockfields, rock-fronted lobes thought to record former permafrost creep, patterned ground (stripes) and lower slope accumulations of crudely stratified growan or weathered granite residue. The altitudinal arrangement of these periglacial landforms appears to be a signature of a well-established periglacial landsystem and hence the Bodmin Moor granite massif is a suitable exemplar for a mature upland periglacial landsystem unaffected by glacierization.
DOI: 10.6084/m9.figshare.4829074
title: x

description: <br>
DOI: 10.6084/m9.figshare.4829095.v3
title: Raw data of spindle length and migration in oocytes treated with different concentrations of FIPI.PDF

description: No changes in spindle length and migration were observed in oocytes treated with different concentrations of FIPI.
DOI: 10.6084/m9.figshare.4829038
title: Supplementary Material for: New Concept of X-Ray Repair Cross-Complementing Groups 1 Polymorphisms and Gynecologic Cancer Risk

description: <b><i>Background:</i></b> Several meta-analyses have been conducted to examine the possible link between X-ray repair cross-complementing groups 1 (<i>XRCC1</i>) Arg399Gln polymorphism and cervical cancer risk. However, the results are controversial. Therefore, we carried out a more comprehensive meta-analysis to examine whether <i>XRCC1</i> polymorphisms are associated with general gynecologic cancer risk. <b><i>Methods:</i></b> Twenty studies, comprising 4,230 cases and 5,458 controls that included analyses of <i>XRCC1</i> polymorphisms (Arg194Trp, Arg280His, or Arg399Gln) were included in our study. <b><i>Results:</i></b> Overall, no significant association between any of the studied XRCC1 polymorphisms and gynecologic cancer risk was observed. However, in further stratified analyses, the Arg399Gln was definitely associated with increased gynecologic cancer risk in Asians (A vs. G: OR 1.24; 95% CI 1.02-1.53), which was also associated with increased cervical cancer risk (A vs. G: OR 1.20; 95% CI 1.00-1.44). Similarly, the Arg194Trp was significantly associated with increased gynecologic cancer risk in Asians (TT vs. CC: OR 1.87; 95% CI 1.02-3.42) and endometrial cancer (T vs. C: OR 1.45; 95% CI 1.05-2.02). <b><i>Conclusions:</i></b> These findings provided evidence that XRCC1 Arg399Gln and Arg194Trp variants may modify the susceptibility to gynecologic cancers based on ethnicity and type. Further studies with large sample size are warranted to extend our findings.
DOI: 10.6084/m9.figshare.4829074.v1
title: obesity_fMRI

description: obesity fMRI data
DOI: 10.6084/m9.figshare.4829074.v3
title: obesity_fMRI

description: obesity fMRI data
DOI: 10.6084/m9.figshare.4829074.v2
title: SHR

description: SHR fMRI data
DOI: 10.6084/m9.figshare.4828963
title: Virologic outcomes in early antiretroviral treatment: HPTN 052

description: <b>Introduction:</b> The HIV Prevention Trials Network (HPTN) 052 trial demonstrated that early antiretroviral therapy (ART) prevented 93% of HIV transmission events in serodiscordant couples. Some linked infections were observed shortly after ART initiation or after virologic failure. <b>Objective:</b> To evaluate factors associated with time to viral suppression and virologic failure in participants who initiated ART in HPTN 052. <b>Methods:</b> 1566 participants who had a viral load (VL) &gt; 400 copies/mL at enrollment were included in the analyses. This included 832 in the early ART arm (CD4 350–550 cells/mm<sup>3</sup> at ART initiation) and 734 in the delayed ART arm (204 with a CD4 3 at ART initiation; 530 with any CD4 at ART initiation). Viral suppression was defined as two consecutive VLs ≤ 400 copies/mL after ART initiation; virologic failure was defined as two consecutive VLs &gt; 1000 copies/mL &gt; 24 weeks after ART initiation. <b>Results:</b> Overall, 93% of participants achieved viral suppression by 12 months. The annual incidence of virologic failure was 3.6%. Virologic outcomes were similar in the two study arms. Longer time to viral suppression was associated with younger age, higher VL at ART initiation, and region (Africa vs. Asia). Virologic failure was strongly associated with younger age, lower educational level, and lack of suppression by three months; lower VL and higher CD4 at ART initiation were also associated with virologic failure. <b>Conclusions:</b> Several clinical and demographic factors were identified that were associated with longer time to viral suppression and virologic failure. Recognition of these factors may help optimize ART for HIV treatment and prevention.
DOI: 10.6084/m9.figshare.4828948
title: Heliantus - CRootBox parameter file

description: CRootBox parameter file for Heliantus<br>from:<br>Potential and actual root growth variations in root systems: modeling them with a two-step stochastic approachPag̬s L, Xie J, Serra VPlant and Soil, 373, 723-735, 2013
DOI: 10.6084/m9.figshare.4828954
title: UrbanDictionary 1999-May2016 Definitions Corpus

description: This dataset is described here:<br>https://www.reddit.com/r/datasets/comments/63spoc/19gb_of_urban_dictionary_definitions_1999_may_2016/
DOI: 10.6084/m9.figshare.4828963.v1
title: Virologic outcomes in early antiretroviral treatment: HPTN 052

description: <b>Introduction:</b> The HIV Prevention Trials Network (HPTN) 052 trial demonstrated that early antiretroviral therapy (ART) prevented 93% of HIV transmission events in serodiscordant couples. Some linked infections were observed shortly after ART initiation or after virologic failure. <b>Objective:</b> To evaluate factors associated with time to viral suppression and virologic failure in participants who initiated ART in HPTN 052. <b>Methods:</b> 1566 participants who had a viral load (VL) &gt; 400 copies/mL at enrollment were included in the analyses. This included 832 in the early ART arm (CD4 350–550 cells/mm<sup>3</sup> at ART initiation) and 734 in the delayed ART arm (204 with a CD4 3 at ART initiation; 530 with any CD4 at ART initiation). Viral suppression was defined as two consecutive VLs ≤ 400 copies/mL after ART initiation; virologic failure was defined as two consecutive VLs &gt; 1000 copies/mL &gt; 24 weeks after ART initiation. <b>Results:</b> Overall, 93% of participants achieved viral suppression by 12 months. The annual incidence of virologic failure was 3.6%. Virologic outcomes were similar in the two study arms. Longer time to viral suppression was associated with younger age, higher VL at ART initiation, and region (Africa vs. Asia). Virologic failure was strongly associated with younger age, lower educational level, and lack of suppression by three months; lower VL and higher CD4 at ART initiation were also associated with virologic failure. <b>Conclusions:</b> Several clinical and demographic factors were identified that were associated with longer time to viral suppression and virologic failure. Recognition of these factors may help optimize ART for HIV treatment and prevention.
DOI: 10.6084/m9.figshare.4828942
title: Brassica oleracea - CRootBox parameter file

description: CRootBox parameter file for Brassica oleracea<br>from:<br>Estimating the parameters of a 3-D root distribution function from root observations with the trench profile method: case study with simulated and field-observed root dataVansteenkiste J, Van Loon J, Garr̩ S, Pag̬s L, Schrevens E, Diels JPlant and Soil, 375, 75-88, 2014
DOI: 10.6084/m9.figshare.4828945
title: Crypsis aculeata - CRootBox parameter file

description: CRootbox parameter file for Crypsis aculeata. <br>from:<br>Simultaneous modeling of transient three-dimensional root growth and soil water flowClausnitzer V, Hopmans J WPlant and Soil, 164, 299-314, 1994
DOI: 10.6084/m9.figshare.4828948.v1
title: Heliantus - CRootBox parameter file

description: CRootBox parameter file for Heliantus<br>from:<br>Potential and actual root growth variations in root systems: modeling them with a two-step stochastic approachPag̬s L, Xie J, Serra VPlant and Soil, 373, 723-735, 2013
DOI: 10.6084/m9.figshare.4828939
title: Brassica napus - CRootBox parameter file

description: CRootBox parameter file for Brassica napus. <br>from:<br>The algorithmic beauty of plant roots: an L-System model for dynamic root growth simulationLeitner D, Klepsch S, Knie A, Schnepf AMathematical and Computer Modelling of Dynamical Systems, 16, 575-587, 2010
DOI: 10.6084/m9.figshare.4828936
title: Anagallis femina - CRootBox parameter file

description: CRootBox parameter files for Anagalis femina. <br>From:<br>The algorithmic beauty of plant roots: an L-System model for dynamic root growth simulationLeitner D, Klepsch S, Knie A, Schnepf AMathematical and Computer Modelling of Dynamical Systems, 16, 575-587, 2010
DOI: 10.6084/m9.figshare.4828936.v2
title: Anagallis femina - CRootBox parameter file

description: CRootBox parameter files for Anagalis femina. <br>From:<br>The algorithmic beauty of plant roots: an L-System model for dynamic root growth simulationLeitner D, Klepsch S, Knie A, Schnepf AMathematical and Computer Modelling of Dynamical Systems, 16, 575-587, 2010
DOI: 10.6084/m9.figshare.4828942.v1
title: Brassica oleracea - CRootBox parameter file

description: CRootBox parameter file for Brassica oleracea<br>from:<br>Estimating the parameters of a 3-D root distribution function from root observations with the trench profile method: case study with simulated and field-observed root dataVansteenkiste J, Van Loon J, Garr̩ S, Pag̬s L, Schrevens E, Diels JPlant and Soil, 375, 75-88, 2014
DOI: 10.6084/m9.figshare.4828945.v1
title: Crypsis aculeata - CRootBox parameter file

description: CRootbox parameter file for Crypsis aculeata. <br>from:<br>Simultaneous modeling of transient three-dimensional root growth and soil water flowClausnitzer V, Hopmans J WPlant and Soil, 164, 299-314, 1994
DOI: 10.6084/m9.figshare.4828921
title: Dataset for: ACUTE AND CHRONIC CHANGES IN RAT SOLEUS MUSCLE AFTER HIGH-FAT HIGH-SUCROSE DIET

description: The effects of obesity on different musculoskeletal tissues are not well understood. The glycolytic quadriceps muscles are compromised with obesity, but due to its high oxidative capacity, the soleus muscle may be protected against obesity-induced muscle damage. Purpose: To determine the time-course relationship between a high-fat high-sucrose (HFS) metabolic challenge and soleus muscle integrity, defined as intramuscular fat invasion, fibrosis and molecular alterations over six time-points. Methods: Male Sprague-Dawley rats were fed a HFS diet (n=64) and sacrificed at serial short-term (3-days, 1-week, 2-weeks, 4-weeks) and long-term (12-weeks, 28-weeks) time points. Chow-fed controls (n=21) were sacrificed at 4, 12 and 28 weeks. At sacrifice, animals were weighed, body composition was calculated (DXA), and soleus muscles were harvested and flash-frozen. Cytokine and adipokine mRNA levels for soleus muscles were assessed using RT-qPCR. Histological assessment of muscle fibrosis and intramuscular fat was conducted, and CD68+ cell number was determined using immunohistochemistry. Results: HFS animals demonstrated significant increases in body fat by 1-week, and this increase in body fat was sustained through 28-weeks on the HFS diet. Short-term time-point soleus muscles demonstrated upregulated mRNA levels for inflammation, atrophy, and oxidative stress molecules. However, intramuscular fat, fibrosis, and CD68+ cell number were similar to their respective control group at all time-points evaluated. Conclusions: The oxidative capacity of the soleus may be protective against diet-induced alterations to muscle integrity. Increasing oxidative capacity of muscles using aerobic exercise may be a beneficial strategy for mitigating obesity-induced muscle damage, and its consequences.
DOI: 10.6084/m9.figshare.4828936.v1
title: Anagallis femina - CRootBox parameter file

description: CRootBox parameter files for Anagalis femina. <br>From:<br>The algorithmic beauty of plant roots: an L-System model for dynamic root growth simulationLeitner D, Klepsch S, Knie A, Schnepf AMathematical and Computer Modelling of Dynamical Systems, 16, 575-587, 2010
DOI: 10.6084/m9.figshare.4828915
title: Dataset for: Post-exercise essential amino acid supplementation amplifies skeletal muscle satellite cell proliferation in older men 24 hours post-exercise

description: Aged skeletal muscle has an attenuated and delayed ability to proliferate satellite cells in response to resistance exercise. The mechanistic target of rapamycin complex 1 (mTORC1) signaling pathway is a focal point for cell growth, however the effect of post-exercise mTORC1 activation on human skeletal muscle satellite cell (SC) proliferation is unknown. To test the proliferative capacity of skeletal muscle SC in aging muscle to a potent mTORC1 activator (i.e., EAA; essential amino acids) we recruited older (~72y) men to conduct leg resistance exercise (8sets x10reps) without (-EAA;n=8) and with (+EAA:n=11) ingestion of 10g of EAA 1h post exercise. Muscle biopsies were taken before exercise (Pre) and 24h post-exercise (Post) for assessment of expression and fiber type-specific Pax7+ SC, Ki67+Pax7+ SC and MyoD+ SC. -EAA did not show an increase in Pax7+ satellite cells at Post (p&gt;0.82). Although statistical significance for an increase in Pax7+ SC at 24 h post-RE was not observed in +EAA vs –EAA, we observed trends for a treatment difference (p&lt;0.1). When examining the change from Pre to Post trends were demonstrated (#/myofiber:p=0.076; and %/ myonuclei:p=0.065) for a greater increase in +EAA vs –EAA. Notably, we found an increases SC proliferation in +EAA, but not -EAA with increases in Ki67+ SC and MyoD+ cells (p&lt;0.05). Ki67+ SC also exhibited a significant group difference Post (p&lt;0.010). Pax7+ SC in fast twitch myofibers did not change and was not different between groups (p&gt;0.10). CDK2, MEF2C, RB1 mRNA only increased in +EAA (p&lt;0.05). Acute muscle satellite cell proliferative capacity may be partially rescued with post-exercise EAA ingestion in older men.
DOI: 10.6084/m9.figshare.4828921.v1
title: Dataset for: ACUTE AND CHRONIC CHANGES IN RAT SOLEUS MUSCLE AFTER HIGH-FAT HIGH-SUCROSE DIET

description: The effects of obesity on different musculoskeletal tissues are not well understood. The glycolytic quadriceps muscles are compromised with obesity, but due to its high oxidative capacity, the soleus muscle may be protected against obesity-induced muscle damage. Purpose: To determine the time-course relationship between a high-fat high-sucrose (HFS) metabolic challenge and soleus muscle integrity, defined as intramuscular fat invasion, fibrosis and molecular alterations over six time-points. Methods: Male Sprague-Dawley rats were fed a HFS diet (n=64) and sacrificed at serial short-term (3-days, 1-week, 2-weeks, 4-weeks) and long-term (12-weeks, 28-weeks) time points. Chow-fed controls (n=21) were sacrificed at 4, 12 and 28 weeks. At sacrifice, animals were weighed, body composition was calculated (DXA), and soleus muscles were harvested and flash-frozen. Cytokine and adipokine mRNA levels for soleus muscles were assessed using RT-qPCR. Histological assessment of muscle fibrosis and intramuscular fat was conducted, and CD68+ cell number was determined using immunohistochemistry. Results: HFS animals demonstrated significant increases in body fat by 1-week, and this increase in body fat was sustained through 28-weeks on the HFS diet. Short-term time-point soleus muscles demonstrated upregulated mRNA levels for inflammation, atrophy, and oxidative stress molecules. However, intramuscular fat, fibrosis, and CD68+ cell number were similar to their respective control group at all time-points evaluated. Conclusions: The oxidative capacity of the soleus may be protective against diet-induced alterations to muscle integrity. Increasing oxidative capacity of muscles using aerobic exercise may be a beneficial strategy for mitigating obesity-induced muscle damage, and its consequences.