cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3822249
title: Supplementary Material for: Hypoxia-Inducible Factor-1α Activates the Transforming Growth Factor-β/SMAD3 Pathway in Kidney Tubular Epithelial Cells

description: <i>Background:</i> Kidney injury, including chronic kidney disease and acute kidney injury, is a worldwide health problem. Hypoxia and transforming growth factor-β (TGF-β) are well-known factors that promote kidney injury. Hypoxia-inducible factor (HIF) and SMAD3 are their main downstream transcriptional factors. Hypoxia-HIF pathway and TGF-β/SMAD3 pathway play a crucial role in the progression of kidney injury. However, reports on their interactions are limited, and the global transcriptional regulation under their control is almost unknown. <i>Methods:</i> Kidney tubular epithelial cells were cultured and stimulated by hypoxia and TGF-β. We detected global binding sites of HIF-1α and SMAD3 in cells using chromatin immunoprecipitation-sequencing (ChIP-Seq), and measured the gene expression using RNA-sequencing (RNA-Seq). ChIP-quantitative PCR (qPCR) was used to quantitatively evaluate bindings of SMAD3.<i>Results:</i> ChIP-Seq revealed that 2,065 and 5,003 sites were bound by HIF-1α and SMAD3, respectively, with 614 sites co-occupied by both factors. RNA-Seq showed that hypoxia and TGF-β stimulation causes synergistic upregulation of 249 genes, including collagen type I alpha 1 (COL1A1) and serpin peptidase inhibitor, clade E, member 1, which are well-known to be involved in fibrosis. Ontology of the 249 genes implied that the interaction of HIF-1α and SMAD3 is related to biological processes such as fibrosis. ChIP-qPCR of SMAD3 at HIF-1α binding sites near COL1A1 and SERPINE1 indicated that HIF-1α promotes the bindings of SMAD3, which is induced by TGF-β. <i>Conclusions:</i> These findings suggest that HIF-1α induced by hypoxia activates the TGF-β/SMAD3 pathway. This mechanism may promote kidney injury, especially by upregulating genes related to fibrosis.
DOI: 10.6084/m9.figshare.3822222
title: Supplementary Material for: Patients' Characteristics Affect the Survival Benefit of Warfarin Treatment for Hemodialysis Patients with Atrial Fibrillation. A Historical Cohort Study

description: <i>Background:</i> Stroke prevention in dialysis-dependent patients with atrial fibrillation (AF) is an unresolved clinical dilemma. Indeed, no randomized controlled trial evaluating the efficacy and safety of oral anticoagulants in this population, has been conducted so far. Observational research on the use of warfarin in patients on dialysis has shown conflicting results. This uncertainty is mirrored by the wide variations in warfarin prescription patterns across centers. We sought to evaluate the association between the use of vitamin K antagonists (VKAs) and mortality among hemodialysis patient with AF and to assess potential factors affecting the risk-benefit profile of warfarin in this population. <i>Methods:</i> A total of 91,987 patients registered in the European Clinical Dialysis Database® system from January 2004 to January 2015. Of which, 9,238 patients were identified with a diagnosis of AF. After excluding ineligible patients, a 1:1 propensity score matched cohort of 1,324 warfarin users and non-users were assembled. <i>Results:</i> VKA use was associated with both increased 90-day survival (hazard ratio, HR 0.47, p &lt; 0.01) and 6-year survival (HR 0.76, p &lt; 0.01); however, a trend indicated a stronger early benefit (p for time-interaction &lt;0.01). Moderation analysis showed that patients' age and clinical history of stroke strongly influenced warfarin-related benefits on survival. <i>Conclusion:</i> VKA may provide an early survival benefit; however, this is partially offset later during the follow-up. In addition, heterogeneous risk-benefit profiles were observed among subgroups of dialysis-dependent patients with AF, further emphasizing the complexities of tailoring stroke prevention strategies in this population.
DOI: 10.6084/m9.figshare.3822216
title: Supplementary Material for: Parathyroidectomy Increases Heart Rate Variability and Leptin Levels in Patients with Stage 5 Chronic Kidney Disease

description: <i>Background:</i> In chronic kidney disease (CKD) patients, decreased heart rate variability (HRV) reflects impaired cardiac automatic nervous function and high risk of cardiovascular disease (CVD). Lower HRV in patients with severe secondary hyperparathyroidism (SHPT), a clinical manifestation of CKD-mineral and bone disorder (CKD-MBD), could be reversed by parathyroidectomy (PTX). It has been proved that leptin interacts with the autonomic nervous function. However, the associations between leptin and HRV in CKD patients and their longitudinal changes in SHPT patients after PTX are still unknown. <i>Methods:</i> This was a cross-sectional study including 141 stage 5 CKD patients, and a prospective study in 36 severe SHPT patients with PTX. HRV was measured by Holter and serum leptin was measured by ELISA. Serum leptin levels were adjusted for body mass index (BMI) and transformed using natural logarithm (lnleptin/BMI). <i>Results:</i> With a gradient of lnleptin/BMI across quartiles from Q1 to Q4 in CKD patients, HRV indices showed no differences among quartiles. Patients in Q1 group had higher mean 24 h heart rates, and lower ln(very low frequency) (lnVLF) than other quartiles, although there were no statistically significant difference. In multivariate stepwise regression, serum leptin/BMI was an independent predictor for low frequency/high frequency. HRV indices and lnleptin/BMI levels were increased in severe SHPT patients after PTX. Compared to other quartiles, SHPT patients in Q1 group had larger improvement of lnVLF after PTX. <i>Conclusion:</i> Circulating leptin levels may be a novel treatment target to reduce CVD risk in advanced CKD-MBD patients.
DOI: 10.6084/m9.figshare.3822216.v1
title: Supplementary Material for: Parathyroidectomy Increases Heart Rate Variability and Leptin Levels in Patients with Stage 5 Chronic Kidney Disease

description: <i>Background:</i> In chronic kidney disease (CKD) patients, decreased heart rate variability (HRV) reflects impaired cardiac automatic nervous function and high risk of cardiovascular disease (CVD). Lower HRV in patients with severe secondary hyperparathyroidism (SHPT), a clinical manifestation of CKD-mineral and bone disorder (CKD-MBD), could be reversed by parathyroidectomy (PTX). It has been proved that leptin interacts with the autonomic nervous function. However, the associations between leptin and HRV in CKD patients and their longitudinal changes in SHPT patients after PTX are still unknown. <i>Methods:</i> This was a cross-sectional study including 141 stage 5 CKD patients, and a prospective study in 36 severe SHPT patients with PTX. HRV was measured by Holter and serum leptin was measured by ELISA. Serum leptin levels were adjusted for body mass index (BMI) and transformed using natural logarithm (lnleptin/BMI). <i>Results:</i> With a gradient of lnleptin/BMI across quartiles from Q1 to Q4 in CKD patients, HRV indices showed no differences among quartiles. Patients in Q1 group had higher mean 24 h heart rates, and lower ln(very low frequency) (lnVLF) than other quartiles, although there were no statistically significant difference. In multivariate stepwise regression, serum leptin/BMI was an independent predictor for low frequency/high frequency. HRV indices and lnleptin/BMI levels were increased in severe SHPT patients after PTX. Compared to other quartiles, SHPT patients in Q1 group had larger improvement of lnVLF after PTX. <i>Conclusion:</i> Circulating leptin levels may be a novel treatment target to reduce CVD risk in advanced CKD-MBD patients.
DOI: 10.6084/m9.figshare.3822168
title: The effect of downhill and uphill running training on antioxidant enzymes, autophagy and BMP molecules, and muscle growth factors in the rectus femoris (RF) and vastus lateralis (VL) muscles.

description: The running training has an effect to age-related muscle and bone wasting which result in physical activity and quality of life in the elderly. However, whether downhill running effect on age-related muscle and bone wasting, and its mechanisms are still unclear. In this study, gradual downhill running can be improve skeletal muscle growth and bone formation by enhancing autophagy and bone morphogenetic protein signaling in aged rats. Therefore, downhill running training might be a practical intervention to improve skeletal muscle and bone protection for the elderly.
DOI: 10.6084/m9.figshare.3822168.v1
title: The effect of downhill and uphill running training on antioxidant enzymes, autophagy and BMP molecules, and muscle growth factors in the rectus femoris (RF) and vastus lateralis (VL) muscles.

description: The running training has an effect to age-related muscle and bone wasting which result in physical activity and quality of life in the elderly. However, whether downhill running effect on age-related muscle and bone wasting, and its mechanisms are still unclear. In this study, gradual downhill running can be improve skeletal muscle growth and bone formation by enhancing autophagy and bone morphogenetic protein signaling in aged rats. Therefore, downhill running training might be a practical intervention to improve skeletal muscle and bone protection for the elderly.
DOI: 10.6084/m9.figshare.3822156
title: A Matlab script to perform PCA on molecular dynamics trajectories

description: A Matlab script to perform principal component analysis on molecular dynamics trajectories and construct free energy surfaces using predominant principal components.
DOI: 10.6084/m9.figshare.3822135
title: response time for different contrasts

description: comparison of response time for normal contrast and low contrast<br>
DOI: 10.6084/m9.figshare.3822135.v1
title: response time for different contrasts

description: comparison of response time for normal contrast and low contrast<br>
DOI: 10.6084/m9.figshare.3822132
title: eye tracker data

description: comparison of fixation time under different conditions, recorded by eye tracker<br> <br>
DOI: 10.6084/m9.figshare.3822129
title: contrast, relative disparity comparison

description: impact factor comparison: contrast and relative disparity<br><br>
DOI: 10.6084/m9.figshare.3822126
title: Molecular adaptation in olfactory functions on the fire ant social chromosome - supplementary data

description: <br><b>sinvgnG-SocialChr-genes-cDNA.fna & sinvgnG-SocialChr-genes.gff:</b><br><br>For reference genome of <i>Solenopsis invicta</i> (version Si_gnG, http://www.ncbi.nlm.nih.gov/assembly/GCF_000188075.1/),<br>we have uploaded gene-annotations and cDNA sequences for the genes that reside in the non-recombining region of the social chromosome.<br><br><br><b>socialChrORclade.tree:</b><br><br>Subtree, in newick format, of the hymenopteran odorant -receptor (OR) gene tree. Showing the subfamily that includes a tandem cluster of 23 ORs located in the <i>Solenopsis invicta</i> social chromosome.<br><br><br><b>SiORs.cDNA.fna:</b><br><br>cDNA sequences of <i>Solenopsis invicta </i>odorant -receptor (OR) genes<br><br><br><br><br><br><br><br>
DOI: 10.6084/m9.figshare.3822129.v1
title: contrast, relative disparity comparison

description: impact factor comparison: contrast and relative disparity<br><br>
DOI: 10.6084/m9.figshare.3822126.v1
title: Molecular adaptation in olfactory functions on the fire ant social chromosome - supplementary data

description: <br><b>sinvgnG-SocialChr-genes-cDNA.fna & sinvgnG-SocialChr-genes.gff:</b><br><br>For reference genome of <i>Solenopsis invicta</i> (version Si_gnG, http://www.ncbi.nlm.nih.gov/assembly/GCF_000188075.1/),<br>we have uploaded gene-annotations and cDNA sequences for the genes that reside in the non-recombining region of the social chromosome.<br><br><br><b>socialChrORclade.tree:</b><br><br>Subtree, in newick format, of the hymenopteran odorant -receptor (OR) gene tree. Showing the subfamily that includes a tandem cluster of 23 ORs located in the <i>Solenopsis invicta</i> social chromosome.<br><br><br><b>SiORs.cDNA.fna:</b><br><br>cDNA sequences of <i>Solenopsis invicta </i>odorant -receptor (OR) genes<br><br><br><br><br><br><br><br>
DOI: 10.6084/m9.figshare.3822123
title: fixation and background texture comparison.xlsx

description: data for the comparison of impact parameter: background texture, fixation objects<br>
DOI: 10.6084/m9.figshare.3822120
title: Rio de Janeiro Botanical Garden Herbarium dataset - 2016-09-11

description: TEST VERSION - DO NOT USE IT - This archives follows the pattern of the Core Occurrence and Identification History Extension of the Darwin Core Archive data standard.
DOI: 10.6084/m9.figshare.3822117
title: Topography of Crater after nanosecond ablation pulses

description: Topography of the crater for several fluences for boron doped diamond.
DOI: 10.6084/m9.figshare.3822117.v1
title: Topography of Crater after nanosecond ablation pulses

description: Topography of the crater for several fluences for boron doped diamond.
DOI: 10.6084/m9.figshare.3822114
title: SEM picture of the ablation crater of boron doped diamond

description: SEM picture for several fluences of the ablation crater of a boron doped diamond using a nanosecond pulsed laser ablation.
DOI: 10.6084/m9.figshare.3822114.v1
title: SEM picture of the ablation crater of boron doped diamond

description: SEM picture for several fluences of the ablation crater of a boron doped diamond using a nanosecond pulsed laser ablation.
DOI: 10.6084/m9.figshare.3821928
title: Vak3 Blue sh Gal CV final Freq Sfift 1 col.pdf

description: <b>Blue and Red Shifted Galaxies are resulted due to frequency shifting in electromagnetic radiation near gravitating masses in Dynamic Universe Model<br></b><br> <b>Abstract: </b> According to General theory of relativity the frequency shift in electro-magnetic (EM) radiation close to a gravitating mass happens in one direction only, but in accordance with Dynamic Universe Model this frequency shift happens on both the sides of spectrum. Here we will derive the results using general Physics and Mathematics that changes the frequency of electromagnetic radiation passing near a moving gravitating mass. The frequency of the radiation will increase (Red shifted) when the relative movement of the gravitating body is in opposite direction to EM radiation and the frequency will reduce when in same direction (Blue shifted). <br><br> <b>1. Introduction: </b> <b> </b> General theory of relativity says that the frequency shift in electro-magnetic radiation near a gravitating mass happens in one direction only. Here in this paper we will see that Dynamic Universe Model says this frequency shift happens on both the sides of spectrum. That means towards the frequency of a mass like electron or positron also. In other words Dynamic Universe Model predicts conversion of energy into mass. Dynamic Universe model is a singularity free tensor based math model. The tensors used are linear without using any differential or integral equations. Only one calculated output set of values exists. Data means properties of each point mass like its three dimensional coordinates, velocities, accelerations and it’s mass. Newtonian two-body problem used differential equations. Einstein’s general relativity used tensors, which in turn unwrap into differential equations. Dynamic Universe Model uses tensors that give simple equations with interdependencies. Differential equations will not give unique solutions. Whereas Dynamic Universe Model gives a unique solution of positions, velocities and accelerations; for each point mass in the system for every instant of time. This new method of Mathematics in Dynamic Universe Model is different from all earlier methods of solving general N-body problem. <b><br> <br> </b>
DOI: 10.6084/m9.figshare.3817392
title: Data from "Reputation management promotes strategic adjustment of service quality in cleaner wrasse"

description: Adjusting one’s behaviour in response to eavesdropping bystanders is considered a sophisticated social strategy, yet the underlying mechanisms are not well studied. We provide evidence that cleaner wrasse, <i>Labroides dimidiatus</i> strategically adjust their levels of cooperation depending on the social environment of their habitat rather than as a physiological response to energetic needs. Cleaners can cooperate by eating ectoparasites off of “client” reef fishes, or can cheat and eat client mucus. Image scoring by bystander clients generally causes cleaners from socially complex habitats to increase levels of cooperation. However, stressed individuals may selectively provide tactile stimulation to small resident clients, which attracts bystanders close that are bitten, a form of tactical deception. We exogenously administered cortisol to mimic physiological stress and observed subsequent cleaning interactions of cleaners from socially complex and socially simple habitats. Crucially, the latter show no evidence of adjustment to bystanders when in normal state, and baseline cortisol levels were similar between habitats. Correspondingly, only energetically-stressed cleaners from socially-complex habitats increased service quality to small residents, the basis for tactical deception. It thus appears that strategic adjustments to cooperative behavior and tactical deception are context-dependent, forming part of general reputation management abilities in cleaner wrasse.<br> <br>
DOI: 10.6084/m9.figshare.3817392.v1
title: Data from "Reputation management promotes strategic adjustment of service quality in cleaner wrasse"

description: Adjusting one’s behaviour in response to eavesdropping bystanders is considered a sophisticated social strategy, yet the underlying mechanisms are not well studied. We provide evidence that cleaner wrasse, <i>Labroides dimidiatus</i> strategically adjust their levels of cooperation depending on the social environment of their habitat rather than as a physiological response to energetic needs. Cleaners can cooperate by eating ectoparasites off of “client” reef fishes, or can cheat and eat client mucus. Image scoring by bystander clients generally causes cleaners from socially complex habitats to increase levels of cooperation. However, stressed individuals may selectively provide tactile stimulation to small resident clients, which attracts bystanders close that are bitten, a form of tactical deception. We exogenously administered cortisol to mimic physiological stress and observed subsequent cleaning interactions of cleaners from socially complex and socially simple habitats. Crucially, the latter show no evidence of adjustment to bystanders when in normal state, and baseline cortisol levels were similar between habitats. Correspondingly, only energetically-stressed cleaners from socially-complex habitats increased service quality to small residents, the basis for tactical deception. It thus appears that strategic adjustments to cooperative behavior and tactical deception are context-dependent, forming part of general reputation management abilities in cleaner wrasse.<br> <br>
DOI: 10.6084/m9.figshare.3817386
title: Metabolite BridgeDb ID Mapping Database (20160910)

description: BridgeDb ID mapping database for metabolites, using HMDB 3.6, ChEBI 142, and Wikidata (7 September 2016) as data sources. This release includes names of compounds in ChEBI, useful for drawing new metabolic pathways in PathVisio.<br>See the attached QC for more details on the changes.
DOI: 10.6084/m9.figshare.3817386.v1
title: Metabolite BridgeDb ID Mapping Database (20160910)

description: BridgeDb ID mapping database for metabolites, using HMDB 3.6, ChEBI 142, and Wikidata (7 September 2016) as data sources. This release includes names of compounds in ChEBI, useful for drawing new metabolic pathways in PathVisio.<br>See the attached QC for more details on the changes.
DOI: 10.6084/m9.figshare.3817383
title: Exploring lithic variability during the Gravettian in Iberia: Lithic technology, use-wear analysis and raw material sourcing from the Gravettian occupation of Arbreda Cave (Catalunya, Spain)

description: The Paleolithic sites from the region of Serinyà, (Catalonia, Spain), provide a complete and important chronostratigraphic record for the Middle and Upper Paleolithic sequence of Northeast Iberian Peninsula. From this territory, the site of l’Arbreda Cave shows the most important evidence for the initial phase of the Upper Paleolithic, illustrated by Aurignacian and Gravettian occupations. Recently the origins and expansion of the Gravettian in Iberia has been one of the most debate topics, particularly regarding the meaning of the variability of the Gravettian lithic industries in this region. In this work we focus on the study of the Gravettian lithic assemblage from level E of Arbreda Cave dated from c.26 kaBP, combining techno-typological, use-wear analysis and raw material characterization and sourcing. Technological analysis shows that Gravettian lithic assemblage from Arbreda is characterized by prismatic reduction strategies focuses on laminar debitage, reflected in the high frequency of backed technology among retouched tools, including well-preserved La Gravette and Microgravette points. Preliminary use-wear analysis focused on macro analysis of the projectile points and preservation conditions of micro wear traces. Local flint, in NE Iberia, is characterized by small nodules with low quality, and during the Gravettian laminar debitage was preformed on imported raw materials from sources that are located north of the Pyrenees Basin Narbonne-Sigean (approx. 100 km away to the north of Arbreda) and Costières du Gard (about 240 km) in the Rhone river mouth. Combining all lithic analyses, our data shows that, during the Gravettian, the site occupation was likely characterized by the exploitation of local resources, during which, hunting might have been one of the most important human activities at the site. Data presented here contributes to our investigation on the lithic variability, in order to understand how humans adapt during the origins of the Gravettian in Iberia.