cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8067512
title: Supplementary Material for: Spontaneous Extracellular Matrix Accumulation in a Human in vitro Model of Renal Fibrosis Is Mediated by αV Integrins

description: <b><i>Background:</i></b> Tubulointerstitial fibrosis is a key feature of chronic kidney diseases leading to renal failure. It is characterised by the infiltration of fibroblasts and aberrant accumulation of extracellular matrix (ECM) proteins, which are associated with progressive loss of renal function. Integrins play a major role in fibrosis, but the mechanisms through which they do this are not fully understood. <b><i>Objective:</i></b> Using a complex cell system, we test the hypothesis that integrins are pro-fibrotic via regulation of functional interactions between tubular epithelial cells and renal fibroblasts. <b><i>Method:</i></b> Contact co-culture of human primary renal proximal tubular epithelial cells and renal fibroblasts promoted the spontaneous accumulation of a mature ECM rich in interstitial collagens, which was considerably in excess of that seen in the individual mono-cultures. Both cell types persisted throughout the culture and were capable of expressing multiple ECM components. <b><i>Results:</i></b> While ECM accumulation was inhibited by the clinically proven anti-fibrotic, nintedanib, and was partially abrogated by transforming growth factor β neutralisation, its levels did not return to basal, indicating additional pathways were implicated in the pro-ECM response. Application of anti-integrin blocking antibodies and small molecules demonstrated a major role of the αV integrins in the ECM accumulation during fibroblast: epithelial cell interactions. <b><i>Conclusion:</i></b> Integrin-mediated pathways can facilitate the spontaneous accumulation of ECM during fibroblast: epithelial cell interactions, and this direct renal co-culture assay system could provide a translational in vitro assay for investigating novel pathways involved in the pro-ECM response and the screening of renal anti-fibrotic agents.
DOI: 10.6084/m9.figshare.8067515.v1
title: Stay awhile in my burrow! Interspecific associations of vertebrates to Indian crested porcupine burrows

description: The Indian crested porcupine, <i>Hystrix indica</i>, is a significant ecosystem engineer that builds extensive burrows in the semi-arid regions of north-west India. Many different animals use these burrows as temporary retreats or permanent shelters. Camera-traps were used to record 22 species using porcupine burrows, including 10 mammals, 8 birds, 3 reptiles, and 1 amphibian. In addition to birds foraging inside and around the entrance, the most common and persistent visitors were mongooses, rats, squirrels, hares, jungle cats, and small Indian civets. A bat species, <i>Hipposideros</i> sp. was found to be permanent occupants of porcupine burrows, while Indian rock pythons and jackals exhibited seasonal use. During winter, pythons basked outside the burrows and constricted their activities to the daytime. Conversely, porcupines are nocturnal and use deeper parts of their burrows than the pythons. Temporal usage patterns and spatial segregation allows for mutualistic behaviour between pythons and porcupines. Jackals were also found to use porcupine burrows during their summer breeding season, employing aggression to evict both porcupines and pythons. The study demonstrates a functional role for porcupines, which are capable of constructing “landmark” structures in the semi-arid regions of north-west India that support a range of micro-communities.
DOI: 10.6084/m9.figshare.8067569.v1
title: A simple root-soil coupling system

description: Using a simple novel dual porosity system, we try to understand redistribution of water and changes in the evaporation patterns in the presence of a root-mimic (consisting of smaller particles) surrounded by a soil-mimic consisting of larger particles.<br>
DOI: 10.6084/m9.figshare.8067479
title: Supplementary Material for: Blood Pressure and Cognitive Decline in Prevalent Hemodialysis Patients

description: <b><i>Background:</i></b> Hypertension is associated with cognitive decline in the general population. It is unclear what impact blood pressure (BP) has on cognitive decline in patients receiving maintenance hemodialysis (HD). <b><i>Methods:</i></b> Using a longitudinal cohort of 314 prevalent HD patients without dementia at baseline, we examined the association of predialysis systolic BP (SBP) and diastolic BP (DBP), pulse pressure, and intradialytic SBP change (pre minus post), averaged for a month, with cognitive decline. Cognitive function was determined by a neurocognitive battery, administered yearly. Individual cognitive test results were reduced into 2 domain scores using principal components analysis (by definition mean of 0 and SD of 1), representing memory and executive function. Joint models, allowing for characterization of cognitive score slopes and including adjustment for potential confounders, were utilized to account for competing risks from death, dropout, or kidney transplantation. <b><i>Results:</i></b> Mean age was 62 years; 54% were men, 23% were black, and 90% had at least a high school education. During median follow-up of 2.1 years (25th–75th: 1.0–4.5), 191 had at least one follow-up test, 148 died, and 43 received kidney transplants. Low predialysis DBP and high pulse pressure were both associated with steeper executive function decline (each 10 mm Hg lower DBP = –0.03 SD [–0.01 to –0.05] per year steeper decline) in executive function (each 10 mm Hg higher pulse pressure = –0.03 SD [–0.06 to –0.01] steeper decline) but not for memory function. SBP and intradialytic change were not associated with steeper decline for either memory or executive function. <b><i>Conclusions:</i></b> No relationship was seen between SBP or intradialytic change in BP with cognitive decline. In prevalent HD patients, lower predialysis DBP and wider predialysis pulse pressure are associated with steeper cognitive decline in executive function but not memory.
DOI: 10.6084/m9.figshare.8067512.v1
title: Supplementary Material for: Spontaneous Extracellular Matrix Accumulation in a Human in vitro Model of Renal Fibrosis Is Mediated by αV Integrins

description: <b><i>Background:</i></b> Tubulointerstitial fibrosis is a key feature of chronic kidney diseases leading to renal failure. It is characterised by the infiltration of fibroblasts and aberrant accumulation of extracellular matrix (ECM) proteins, which are associated with progressive loss of renal function. Integrins play a major role in fibrosis, but the mechanisms through which they do this are not fully understood. <b><i>Objective:</i></b> Using a complex cell system, we test the hypothesis that integrins are pro-fibrotic via regulation of functional interactions between tubular epithelial cells and renal fibroblasts. <b><i>Method:</i></b> Contact co-culture of human primary renal proximal tubular epithelial cells and renal fibroblasts promoted the spontaneous accumulation of a mature ECM rich in interstitial collagens, which was considerably in excess of that seen in the individual mono-cultures. Both cell types persisted throughout the culture and were capable of expressing multiple ECM components. <b><i>Results:</i></b> While ECM accumulation was inhibited by the clinically proven anti-fibrotic, nintedanib, and was partially abrogated by transforming growth factor β neutralisation, its levels did not return to basal, indicating additional pathways were implicated in the pro-ECM response. Application of anti-integrin blocking antibodies and small molecules demonstrated a major role of the αV integrins in the ECM accumulation during fibroblast: epithelial cell interactions. <b><i>Conclusion:</i></b> Integrin-mediated pathways can facilitate the spontaneous accumulation of ECM during fibroblast: epithelial cell interactions, and this direct renal co-culture assay system could provide a translational in vitro assay for investigating novel pathways involved in the pro-ECM response and the screening of renal anti-fibrotic agents.
DOI: 10.6084/m9.figshare.8067584.v3
title: Data From : Role of sociality in the response of killer whales to an additive mortality event

description: The fileset contains supporting data for the paper: <br>Role of sociality in the response of killer whales to an additive mortality event <br><br>The fileset contains data used to analyse the social structure and survival of the killer whales Crozet populations.
DOI: 10.17608/k6.auckland.8067449
title: Data: H and O isotope signatures of soil and xylem samples, cacao agroforest, Indonesia.

description: This data set contains soil and xylem water delta<sup>18</sup>O and delta<sup>2</sup>H values of soil and xylem samples collected from cacao and shade trees (gliricidia) in a cacao agroforest, Marena, Indonesia, from Jan 2007 to April 2008.
DOI: 10.6084/m9.figshare.8067584.v2
title: Data-Busson et al. PNAS.xlsx

description: Dataset of the paper Busson et al., 2019 published in PNAS
DOI: 10.6084/m9.figshare.8067407
title: Data comparing substitution with albumin and partial substitution with fresh frozen plasma during selective plasma exchange in ABO-incompatible kidney transplantation

description: Selective Plasma Exchange (SePE) is a type of plasma exchange in which the plasma separation membrane has a smaller pore size than conventional plasma separation membranes, so that small and medium molecular weight<br>substances can be removed, while larger molecular weight substances are not.<br>This dataset provides Clinical data from 30 ABO-incompatible kidney transplantation recipients before and after receiving SePE, and for patients receiving SePE using albumin alone versus partially using fresh frozen plasma (FFP).<br>The data are presented in a single <b>.csv</b> file with 16 columns. Columns headings are as follows:- <b>case_id</b>: numerical identifier for 30 recipients of ABOi kidney transplantation - <b>session_id</b>: SePE session. Group A (using albumin alone): n=41; Group F (partially using FFP): n=17- <b>TIME_pre1_post2</b>: pre-transplant = 1; post-transplant = 2- <b>Alb_0orFFP_1</b>: albumin alone = 0; fresh frozen plasma = 1- <b>Anticoa_NM_1</b>: anticoagulant nafamostat mesilate (NM) used- <b>SePE_0orSePE+HD_1</b>: SePE alone = 0; SePE plus hemodialysis (HD) = 1- <b>IgM_Titers</b>: Concentration of serum IgM, determined by titer testing- <b>IgG_Titers</b>: Concentration of serum IgG, determined by titer testing- <b>Fib</b>: coagulation factor fibrinogen- <b>F13</b>: coagulation factor XIII- <b>IgM</b>: immunoglobulin M- <b>IgG</b>: immunoglobulin G- <b>SBP</b>: systolic blood pressure- <b>DBP</b>: diastolic blood pressure- <b>PR</b>: pulse rate- <b>Side-effects</b>: had side-effects, such as rashes, nausea, abdominal pain, etc<br>The related manuscript describes a retrospective case-series study conducted on patients who underwent ABOi kidney transplantation at the Department of Urology, Osaka City University Hospital between January 2015 and December 2018. The aim of the study was to compare the clinical effects of SePE using albumin alone to SePE partially using FFP.
DOI: 10.6084/m9.figshare.8067419
title: Data and Code supporting manuscript from Quantifying the consequences of measles-induced immune modulation for whooping cough epidemiology

description: Measles, an acute viral disease, continues to be an important cause of childhood mortality worldwide. Infection with the measles virus is thought to be associated with a transient but profound period of immune suppression. Recently, it has been claimed that measles-induced immune manipulation lasts for about 30 months and results in increased susceptibility to other co-circulating infectious diseases and more severe disease outcomes upon infection. We tested this hypothesis using model-based inference applied to parallel historical records of measles and whooping cough mortality and morbidity. Specifically, we used maximum likelihood to fit a mechanistic transmission model to incidence data from three different eras, spanning mortality records from 1904 to 1912 and 1922 to 1932 and morbidity records from 1946 to 1956. Our aim was to quantify the timing, severity and pathogenesis impacts of measles-induced immune modulation and their consequences for whooping cough epidemiology across a temporal gradient of measles transmission. We identified an increase in susceptibility to whooping cough following recent measles infection by approximately 85-, 10- and 36-fold for the three eras, respectively, although the duration of this effect was variable. Overall, while the immune impacts of measles may be strong and clearly evident at the individual level, their epidemiological signature in these data appears both modest and inconsistent.This article is part of the theme issue ‘Detection, forecasting and control of infectious disease epidemics: modelling outbreaks in humans, animals and plants Part 1’.
DOI: 10.6084/m9.figshare.8067407.v1
title: Data comparing substitution with albumin and partial substitution with fresh frozen plasma during selective plasma exchange in ABO-incompatible kidney transplantation

description: Selective Plasma Exchange (SePE) is a type of plasma exchange in which the plasma separation membrane has a smaller pore size than conventional plasma separation membranes, so that small and medium molecular weight<br>substances can be removed, while larger molecular weight substances are not.<br>This dataset provides Clinical data from 30 ABO-incompatible kidney transplantation recipients before and after receiving SePE, and for patients receiving SePE using albumin alone versus partially using fresh frozen plasma (FFP).<br>The data are presented in a single <b>.csv</b> file with 16 columns. Columns headings are as follows:- <b>case_id</b>: numerical identifier for 30 recipients of ABOi kidney transplantation - <b>session_id</b>: SePE session. Group A (using albumin alone): n=41; Group F (partially using FFP): n=17- <b>TIME_pre1_post2</b>: pre-transplant = 1; post-transplant = 2- <b>Alb_0orFFP_1</b>: albumin alone = 0; fresh frozen plasma = 1- <b>Anticoa_NM_1</b>: anticoagulant nafamostat mesilate (NM) used- <b>SePE_0orSePE+HD_1</b>: SePE alone = 0; SePE plus hemodialysis (HD) = 1- <b>IgM_Titers</b>: Concentration of serum IgM, determined by titer testing- <b>IgG_Titers</b>: Concentration of serum IgG, determined by titer testing- <b>Fib</b>: coagulation factor fibrinogen- <b>F13</b>: coagulation factor XIII- <b>IgM</b>: immunoglobulin M- <b>IgG</b>: immunoglobulin G- <b>SBP</b>: systolic blood pressure- <b>DBP</b>: diastolic blood pressure- <b>PR</b>: pulse rate- <b>Side-effects</b>: had side-effects, such as rashes, nausea, abdominal pain, etc<br>The related manuscript describes a retrospective case-series study conducted on patients who underwent ABOi kidney transplantation at the Department of Urology, Osaka City University Hospital between January 2015 and December 2018. The aim of the study was to compare the clinical effects of SePE using albumin alone to SePE partially using FFP.
DOI: 10.6084/m9.figshare.8067419.v1
title: Data and Code supporting manuscript from Quantifying the consequences of measles-induced immune modulation for whooping cough epidemiology

description: Measles, an acute viral disease, continues to be an important cause of childhood mortality worldwide. Infection with the measles virus is thought to be associated with a transient but profound period of immune suppression. Recently, it has been claimed that measles-induced immune manipulation lasts for about 30 months and results in increased susceptibility to other co-circulating infectious diseases and more severe disease outcomes upon infection. We tested this hypothesis using model-based inference applied to parallel historical records of measles and whooping cough mortality and morbidity. Specifically, we used maximum likelihood to fit a mechanistic transmission model to incidence data from three different eras, spanning mortality records from 1904 to 1912 and 1922 to 1932 and morbidity records from 1946 to 1956. Our aim was to quantify the timing, severity and pathogenesis impacts of measles-induced immune modulation and their consequences for whooping cough epidemiology across a temporal gradient of measles transmission. We identified an increase in susceptibility to whooping cough following recent measles infection by approximately 85-, 10- and 36-fold for the three eras, respectively, although the duration of this effect was variable. Overall, while the immune impacts of measles may be strong and clearly evident at the individual level, their epidemiological signature in these data appears both modest and inconsistent.This article is part of the theme issue ‘Detection, forecasting and control of infectious disease epidemics: modelling outbreaks in humans, animals and plants Part 1’.
DOI: 10.6084/m9.figshare.8067401
title: Discovery of hit molecules targeting allosteric site of hepatitis C virus NS5B polymerase

description: Nonstructural protein 5B (NS5B), the RNA-dependent RNA polymerase of Hepatitis C Virus (HCV), plays a key role in viral amplification and is an attractive and most explored target for discovery of new therapeutic agents for Hepatitis C. Though safe and effective, NS5B inhibitors were launched in 2013 (Sovaldi) and 2014 (Harvoni, Viekira Pak), the high price tags of these medications limit their use among poor people in developing countries. Hence, still there exists a need for cost-effective and short duration anti-HCV agents especially those targeting niche patient population who were non-respondent to earlier therapies or with comorbid conditions. The present study describes the discovery of novel non-nucleoside (NNI) inhibitors of NS5B using a series of rational drug design techniques such as virtual screening, scaffold matching and molecular docking. 2D and 3D structure based virtual screening technique identified 300 hit compounds. Top 20 hits were screened out from identified hits using molecular docking technique. Four molecules, that are representative of 20 hits were evaluated for binding affinity under <i>in vitro</i> conditions using surface plasmon resonance-based assay and the results emphasized that compound with CoCoCo ID: 412075 could exhibit good binding response toward NS5B and could be a potential candidate as NS5B inhibitor. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.8067401.v2
title: Discovery of hit molecules targeting allosteric site of hepatitis C virus NS5B polymerase

description: Nonstructural protein 5B (NS5B), the RNA-dependent RNA polymerase of Hepatitis C Virus (HCV), plays a key role in viral amplification and is an attractive and most explored target for discovery of new therapeutic agents for Hepatitis C. Though safe and effective, NS5B inhibitors were launched in 2013 (Sovaldi) and 2014 (Harvoni, Viekira Pak), the high price tags of these medications limit their use among poor people in developing countries. Hence, still there exists a need for cost-effective and short duration anti-HCV agents especially those targeting niche patient population who were non-respondent to earlier therapies or with comorbid conditions. The present study describes the discovery of novel non-nucleoside (NNI) inhibitors of NS5B using a series of rational drug design techniques such as virtual screening, scaffold matching and molecular docking. 2D and 3D structure based virtual screening technique identified 300 hit compounds. Top 20 hits were screened out from identified hits using molecular docking technique. Four molecules, that are representative of 20 hits were evaluated for binding affinity under <i>in vitro</i> conditions using surface plasmon resonance-based assay and the results emphasized that compound with CoCoCo ID: 412075 could exhibit good binding response toward NS5B and could be a potential candidate as NS5B inhibitor. Communicated by Ramaswamy H. Sarma
DOI: 10.6084/m9.figshare.8067401.v1
title: Discovery of hit molecules targeting allosteric site of hepatitis C virus NS5B polymerase

description: Nonstructural protein 5B (NS5B), the RNA-dependent RNA polymerase of Hepatitis C Virus (HCV), plays a key role in viral amplification and is an attractive and most explored target for discovery of new therapeutic agents for Hepatitis C. Though safe and effective, NS5B inhibitors were launched in 2013 (Sovaldi) and 2014 (Harvoni, Viekira Pak), the high price tags of these medications limit their use among poor people in developing countries. Hence, still there exists a need for cost-effective and short duration anti-HCV agents especially those targeting niche patient population who were non-respondent to earlier therapies or with comorbid conditions. The present study describes the discovery of novel non-nucleoside (NNI) inhibitors of NS5B using a series of rational drug design techniques such as virtual screening, scaffold matching and molecular docking. 2D and 3D structure based virtual screening technique identified 300 hit compounds. Top 20 hits were screened out from identified hits using molecular docking technique. Four molecules, that are representative of 20 hits were evaluated for binding affinity under <i>in vitro</i> conditions using surface plasmon resonance-based assay and the results emphasized that compound with CoCoCo ID: 412075 could exhibit good binding response toward NS5B and could be a potential candidate as NS5B inhibitor. Communicated by Ramaswamy H. Sarma
DOI: 10.17608/k6.auckland.8067338
title: Data: Water stable isotope signature of soil and xylem samples under different land use systems, Panama.

description: This data set contains soil and xylem water delta<sup>18</sup>O and delta<sup>2</sup>H values of soil and plant tissue samples collected in different land use systems around Santa Fe, Central Panama in 2008. The samples were collected and analysed by Francois Jost for his Masterthesis entitled "Using Stable Isotopes (D, <sup>18</sup>O) to Estimate Plant Water Uptake in Different Vegetation Types, Panama", University of Goettingen, 2009 under the supervision of Dr. Luitgard Schwendenmann.
DOI: 10.6084/m9.figshare.8067272
title: The impact of rural rotations on urban based postgraduate learners: A literature review

description: <b>Background/Objective:</b> The rural physician shortage remains an international crisis. Rural rotations are commonly used to address the issue. This review assesses the published evidence of the impact of rural rotations on urban-based postgraduate learners. <b>Methods:</b> The OVID Medline database was searched for eligible articles published in peer-reviewed academic journals between 1980 and 2017. Data were extracted and analyzed to draw inferences about the impact of rural rotations on urban-based postgraduate learners. The methodological quality of included articles was assessed with the Medical Education Research Study Quality Instrument (MERSQI). <b>Results:</b> The search identified 301 articles; 19 studies met inclusion criteria (mean MERSQI score 11.95). Of the various rural rotation characteristics reported, duration was most consistently associated with the eventual rural practice. No consensus of impact was found for other characteristics. Our review provided indications of the cumulative effect of the postgraduate rural rotation, rural origin, and rural intent on rural practice decisions. <b>Conclusions:</b> The importance of rural rotations during urban postgraduate training for the outcome of rural practice is apparent. However, the reliance of medical educational systems on the rural rotation, specifically duration, does not accurately reflect the complexity of the choice to practice in a rural community.