cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9963071.v1
title: Supplementary Material for: Long-Term Follow-Up of Advanced Liver Disease after Sustained Virological Response to Treatment of Hepatitis C with Direct-Acting Antivirals: Outcomes from a Real-World Portuguese Cohort

description: <b><i>Background:</i></b> Direct-acting antivirals (DAA) have revolutionized hepatitis C treatment, with high sustained virological response (SVR) rates reported, even in historically difficult-to-treat groups. SVR is associated with a decreased risk of hepatocellular carcinoma (HCC), need for transplantation, and overall and liver-related mortality. Data from real-life cohorts on the medium- to long-term outcomes of patients with advanced liver disease and DAA-induced SVR are still missing. <b><i>Objectives:</i></b> To report and analyze the long-term outcomes of DAA-induced SVR in a real-life cohort of patients with advanced liver disease. <b><i>Method:</i></b> In this retrospective, longitudinal, single-center study, we collected data from patients with chronic hepatitis C infection and advanced liver disease (cirrhosis or advanced fibrosis) that had initiated DAA treatment between February 2015 and January 2017. <b><i>Results:</i></b> A total of 237 patients were included. A treatment completion rate of 98.7% and an SVR rate of 97.8% (intention to treat: 96.6%) were found. Of the 229 patients with SVR, 67.2% were cirrhotic (64.2% Child-Pugh class A; 3.1% Child-Pugh class B) and 32.8% had stage F3 fibrosis, with an average follow-up of 28 months. The overall mortality rate was 19/1,000 person-years and the liver-related mortality rate was 9.5/1,000 person-years. The hepatic decompensation incidence rate was 25/1,000 person-years and the HCC incidence rate was 11.6/1,000 person-years. There was a sustained increase in serum platelet values during up to 2 years of follow-up. A history of pretreatment decompensation and baseline platelet and albumin values were significantly associated with the occurrence of adverse liver events after the end of treatment. <b><i>Conclusions:</i></b> A DAA-induced SVR remains durable and is associated with an excellent clinical prognosis in patients with compensated advanced liver disease and with improvement or disease stabilization in decompensated patients. SVR is associated with a low risk of – yet does not prevent – HCC occurrence or disease progression, especially in the presence of other causes of liver injury. It is recommended that these patients be kept under surveillance.
DOI: 10.6084/m9.figshare.9963020
title: Salinity Variation in Neap Tide in Humen Estuary

description: The data were measured in Humen estuary in 2005. It was used to calibrate and validate an analytical model of salinity variation. The information of the data collection can be found in the paper "Analytical model captures intratidal variation in salinity in a convergent, well-mixed estuary" published in Hydrol. Earth Syst. Sci.
DOI: 10.6084/m9.figshare.9963020.v1
title: Salinity Variation in Neap Tide in Humen Estuary

description: The data were measured in Humen estuary in 2005. It was used to calibrate and validate an analytical model of salinity variation. The information of the data collection can be found in the paper "Analytical model captures intratidal variation in salinity in a convergent, well-mixed estuary" published in Hydrol. Earth Syst. Sci.
DOI: 10.6084/m9.figshare.9962981
title: MOESM1 of Recovering the capability to work among patients with chronic low Back pain after a four-week, multidisciplinary biopsychosocial rehabilitation program: 18-month follow-up study

description: Additional file 1: Program Design.
DOI: 10.6084/m9.figshare.9962969
title: MOESM1 of Relating the gut metagenome and metatranscriptome to immunotherapy responses in melanoma patients

description: Additional file 1. Supplementary Tables S1-S6.
DOI: 10.6084/m9.figshare.9962981.v1
title: MOESM1 of Recovering the capability to work among patients with chronic low Back pain after a four-week, multidisciplinary biopsychosocial rehabilitation program: 18-month follow-up study

description: Additional file 1: Program Design.
DOI: 10.6084/m9.figshare.9962969.v1
title: MOESM1 of Relating the gut metagenome and metatranscriptome to immunotherapy responses in melanoma patients

description: Additional file 1. Supplementary Tables S1-S6.
DOI: 10.6084/m9.figshare.9962882
title: MOESM2 of Quantitative proteomic analysis and functional characterization of Acanthamoeba castellanii exosome-like vesicles

description: Additional file 2: Table S2. Identification of proteins in EVs from A. castellanii by quantitative proteomic analysis.
DOI: 10.6084/m9.figshare.9962873
title: MOESM1 of Quantitative proteomic analysis and functional characterization of Acanthamoeba castellanii exosome-like vesicles

description: Additional file 1: Table S1. Primers used in this study.
DOI: 10.6084/m9.figshare.9962882.v1
title: MOESM2 of Quantitative proteomic analysis and functional characterization of Acanthamoeba castellanii exosome-like vesicles

description: Additional file 2: Table S2. Identification of proteins in EVs from A. castellanii by quantitative proteomic analysis.
DOI: 10.6084/m9.figshare.9962873.v1
title: MOESM1 of Quantitative proteomic analysis and functional characterization of Acanthamoeba castellanii exosome-like vesicles

description: Additional file 1: Table S1. Primers used in this study.
DOI: 10.6084/m9.figshare.9962777
title: Transcriptional profiling of the murine intervertebral disc and age-associated changes in the nucleus pulposus

description: <b>Purpose/Aim</b>: The intervertebral disc (IVD) is composed of cell types whose subtle phenotypic differences allow for the formation of distinct tissues. The role of the nucleus pulposus (NP) in the initiation and progression of IVD degeneration is well established; however, the genes and pathways associated with NP degeneration are poorly characterized. <b>Materials and Methods</b>: Using a genetic strategy for IVD lineage-specific fluorescent reporter expression to isolate cells, gene expression and bioinformatic analysis was conducted on the murine NP at 2.5, 6, and 21 months-of-age and the annulus fibrosus (AF) at 2.5 and 6 months-of-age. A subset of differentially regulated genes was validated by qRT-PCR. <b>Results</b>: Transcriptome analysis identified distinct profiles of NP and AF gene expression that were remarkably consistent at 2.5 and 6 months-of-age. <i>Prg4, Cilp, Ibsp</i> and <i>Comp</i> were increased &gt;50-fold in the AF relative to NP. The most highly enriched NP genes included <i>Dsc3</i> and <i>Cdh6</i>, members of the cadherin superfamily, and microRNAs <i>mir218-1</i> and <i>mir490</i>. Changes in the NP between 2.5 and 6 months-of-age were associated with up-regulation of molecular functions linked to laminin and Bmp receptor binding (including up-regulation of <i>Bmp5</i> & <i>7</i>), with the most up-regulated genes being <i>Mir703, Shh</i>, and <i>Sfrp5</i>. NP degeneration was associated with molecular functions linked to alpha-actinin binding (including up-regulation of <i>Ttn</i> & <i>Myot</i>) and cytoskeletal protein binding, with the overall most up-regulated genes being <i>Rnu3a, Snora2b</i> and <i>Mir669h</i>. <b>Conclusions</b>: This study provided insight into the phenotypes of NP and AF cells, and identified candidate pathways that may regulate degeneration.
DOI: 10.6084/m9.figshare.9962765
title: Harmonised LUCAS in-situ land cover and use database for field surveys from 2006 to 2018 in the European Union

description: d'Andrimont, R., Yordanov, M., Martinez-Sanchez, L., Eiselt, B., Palmieri, A., Dominici, P., Gallego, J., Reuter, H.I., Joebges, C., Lemoine, G. and van der Velde, M., 2020. <b>Harmonised LUCAS in-situ land cover and use database for field surveys from 2006 to 2018 in the European Union</b>.<br><b><br></b>LUCAS_harmonised<b>├── 0_releaseNote.txt</b><b>├── 1_table</b><b>│ ├── lucas_harmo_exif.zip</b><b>│ ├── lucas_harmo_uf_2006.zip</b><b>│ ├── lucas_harmo_uf_2009.zip</b><b>│ ├── lucas_harmo_uf_2012.zip</b><b>│ ├── lucas_harmo_uf_2015.zip</b><b>│ ├── lucas_harmo_uf_2018.zip</b><b>│ └── lucas_harmo_uf.zip</b><b>├── 2_geometry</b><b>│ ├── LUCAS_gps_geom.zip</b><b>│ ├── LUCAS_th_geom.zip</b><b>│ └── LUCAS_trans_geom.zip</b><b>├── 3_supporting</b><b>│ ├── C3_legends.xls</b><b>│ ├── lucas_harmo_record_descriptor.xls</b><b>│ └── LUCAS-Variable_and_Classification_Changes.xlsx</b><b>└── 4_mappings</b><b> ├── 2006_lucas_harmo_allVars.csv</b><b> ├── 2009_lucas_harmo_allVars.csv</b><b> ├── 2012_lucas_harmo_allVars.csv</b><b> ├── 2015_lucas_harmo_allVars.csv</b><b> ├── 2018_lucas_harmo_allVars.csv</b><b> ├── columnRename.csv</b><b> ├── manChangedVars.csv</b><b> └── RecodeVars.csv</b><br>
DOI: 10.6084/m9.figshare.9962771
title: Supplementary Material for: Hypothalamic Structural and Functional Imbalances in Anorexia Nervosa

description: The hypothalamus contains integrative systems that support life, including physiological processes such as food intake, energy expenditure, and reproduction. Here, we show that anorexia nervosa (AN) patients, contrary to normal weight and constitutionally lean individuals, respond with a paradoxical reduction in hypothalamic levels of glutamate/glutamine (Glx) upon feeding. This reversal of the Glx response is associated with decreased wiring in the arcuate nucleus and increased connectivity in the lateral hypothalamic area, which are involved in the regulation on a variety of physiological and behavioral functions including the control of food intake and energy balance. The identification of distinct hypothalamic neurochemical dysfunctions and associated structural variations in AN paves the way for the development of new diagnostic and treatment strategies in conditions associated with abnormal body mass index and a maladaptive response to negative energy balance.
DOI: 10.6084/m9.figshare.9962777.v1
title: Transcriptional profiling of the murine intervertebral disc and age-associated changes in the nucleus pulposus

description: <b>Purpose/Aim</b>: The intervertebral disc (IVD) is composed of cell types whose subtle phenotypic differences allow for the formation of distinct tissues. The role of the nucleus pulposus (NP) in the initiation and progression of IVD degeneration is well established; however, the genes and pathways associated with NP degeneration are poorly characterized. <b>Materials and Methods</b>: Using a genetic strategy for IVD lineage-specific fluorescent reporter expression to isolate cells, gene expression and bioinformatic analysis was conducted on the murine NP at 2.5, 6, and 21 months-of-age and the annulus fibrosus (AF) at 2.5 and 6 months-of-age. A subset of differentially regulated genes was validated by qRT-PCR. <b>Results</b>: Transcriptome analysis identified distinct profiles of NP and AF gene expression that were remarkably consistent at 2.5 and 6 months-of-age. <i>Prg4, Cilp, Ibsp</i> and <i>Comp</i> were increased &gt;50-fold in the AF relative to NP. The most highly enriched NP genes included <i>Dsc3</i> and <i>Cdh6</i>, members of the cadherin superfamily, and microRNAs <i>mir218-1</i> and <i>mir490</i>. Changes in the NP between 2.5 and 6 months-of-age were associated with up-regulation of molecular functions linked to laminin and Bmp receptor binding (including up-regulation of <i>Bmp5</i> & <i>7</i>), with the most up-regulated genes being <i>Mir703, Shh</i>, and <i>Sfrp5</i>. NP degeneration was associated with molecular functions linked to alpha-actinin binding (including up-regulation of <i>Ttn</i> & <i>Myot</i>) and cytoskeletal protein binding, with the overall most up-regulated genes being <i>Rnu3a, Snora2b</i> and <i>Mir669h</i>. <b>Conclusions</b>: This study provided insight into the phenotypes of NP and AF cells, and identified candidate pathways that may regulate degeneration.
DOI: 10.6084/m9.figshare.9962762
title: Supplementary Material for: Rapid Progression of Autosomal Dominant Polycystic Kidney Disease: Urinary Biomarkers as Predictors

description: <b><i>Background:</i></b> Markers currently used to predict the likelihood of rapid disease progression in patients with autosomal dominant polycystic kidney disease (ADPKD) are expensive and time consuming to assess and often have limited sensitivity. New, easy-to-measure markers are therefore needed that alone or in combination with conventional risk markers can predict the rate of disease progression. In the present study, we investigated the ability of tubular damage and inflammation markers to predict kidney function decline. <b><i>Methods:</i></b> At baseline, albumin, immunoglobulin G, kidney injury molecule 1, β2 microglobulin (β2MG), heart-type fatty acid-binding protein, neutrophil gelatinase-associated lipocalin, and monocyte chemotactic protein-1 ­(MCP-1) were measured in 24-h urine samples of patients participating in a study investigating the therapeutic efficacy of lanreotide in ADPKD. Individual change in estimated glomerular filtration rate (eGFR) during follow-up was calculated using mixed-model analysis taking into account 13 ­eGFRs (chronic kidney disease EPIdemiology) per patient. Logistic regression analysis was used to select urinary biomarkers that had the best association with rapidly progressive disease. The predictive value of these selected urinary biomarkers was compared to other risk scores using C-statistics. <b><i>Results:</i></b> Included were 302 patients of whom 53.3% were female, with an average age of 48 ± 7 years, eGFR of 52 ± 12 mL/min/1.73 m<sup>2</sup>, and a height-adjusted total kidney volume (htTKV) of 1,082 (736–1,669) mL/m. At baseline, all urinary damage and inflammation markers were associated with baseline eGFR, also after adjustment for age, sex and baseline htTKV. For longitudinal analyses only patients randomized to standard care were considered (<i>n</i> = 152). A stepwise backward analysis revealed that β2MG and MCP-1 showed the strongest association with rapidly progressive disease. A urinary biomarker score was created by summing the ranking of tertiles of β2MG and MCP-1 excretion. The predictive value of this urinary biomarker score was higher compared to that of the Mayo htTKV classification (area under the curve [AUC] 0.73 [0.64–0.82] vs. 0.61 [0.51–0.71], <i>p</i> = 0.04) and comparable to that of the predicting renal outcomes in ­ADPKD score (AUC 0.73 [0.64–0.82] vs. 0.65 [0.55–0.75], <i>p</i> = 0.18). In a second independent cohort with better kidney function, similar results were found for the urinary biomarker score. <b><i>Conclusion:</i></b> Measurement of urinary β2MG and MCP-1 excretion allows selection of ADPKD patients with rapidly progressive disease, with a predictive value comparable to or even higher than that of TKV or <i>PKD</i> mutation. Easy and inexpensive to measure urinary markers therefore hold promise to help predict prognosis in ADPKD.
DOI: 10.6084/m9.figshare.9962759
title: Supplementary Material for: Predictors of Care Gaps in Home Dialysis: The Home Dialysis Virtual Ward Study

description: <b><i>Background:</i></b> Home dialysis patients may be at an increased risk of adverse events after transitional states. The home dialysis virtual ward (HDVW) trial was conducted in Canadian dialysis centers and aimed to evaluate potential care gaps and patient satisfaction during the HDVW. <b><i>Methods:</i></b> The HDVW was a multicenter single-arm trial including peritoneal dialysis and home hemodialysis patients after 4 different events (hospital discharge, medical procedure, antibiotics, completion of training). Telephone-led interviews using a standardized assessment tool were performed over a 2-week period to assess a patient’s care and adjust treatment as required. Upon completion, patients were surveyed to evaluate their perceived impact on domains of care using a rating scale; 1 not satisfied to 10 completely satisfied. <b><i>Results:</i></b> The HDVW trial included 193 patients with a median number of potential care gaps/interventions of 1 (0–2) per patient. Patients admitted to the HDVW after hospital discharge were at a higher risk of potential gaps in care (OR 2.16, 95% CI 1.29–3.62), while longer dialysis vintage was ­associated with a lower number of gaps/interventions (OR 0.97 per year, 95% CI 0.95–0.98). A total of 105/193 (54%) patients completed satisfaction surveys. Patients were highly satisfied with the HDVW (median rating scale score 8, IQR 2) and felt it had a positive impact (rating scale score ≥7) on their overall health, understanding of treatment and access to a nephrologist. <b><i>Conclusion:</i></b> The HDVW was effective at identifying several potential care gaps, and patients were satisfied across several domains of care. This intervention may be valuable in supporting home dialysis patients during care transitions.
DOI: 10.6084/m9.figshare.9962756
title: Chimpanzee Nut-Cracking PeerJ

description: The dataset and code that accompany the article submitted to PeerJ.<br>
DOI: 10.6084/m9.figshare.9962762.v1
title: Supplementary Material for: Rapid Progression of Autosomal Dominant Polycystic Kidney Disease: Urinary Biomarkers as Predictors

description: <b><i>Background:</i></b> Markers currently used to predict the likelihood of rapid disease progression in patients with autosomal dominant polycystic kidney disease (ADPKD) are expensive and time consuming to assess and often have limited sensitivity. New, easy-to-measure markers are therefore needed that alone or in combination with conventional risk markers can predict the rate of disease progression. In the present study, we investigated the ability of tubular damage and inflammation markers to predict kidney function decline. <b><i>Methods:</i></b> At baseline, albumin, immunoglobulin G, kidney injury molecule 1, β2 microglobulin (β2MG), heart-type fatty acid-binding protein, neutrophil gelatinase-associated lipocalin, and monocyte chemotactic protein-1 ­(MCP-1) were measured in 24-h urine samples of patients participating in a study investigating the therapeutic efficacy of lanreotide in ADPKD. Individual change in estimated glomerular filtration rate (eGFR) during follow-up was calculated using mixed-model analysis taking into account 13 ­eGFRs (chronic kidney disease EPIdemiology) per patient. Logistic regression analysis was used to select urinary biomarkers that had the best association with rapidly progressive disease. The predictive value of these selected urinary biomarkers was compared to other risk scores using C-statistics. <b><i>Results:</i></b> Included were 302 patients of whom 53.3% were female, with an average age of 48 ± 7 years, eGFR of 52 ± 12 mL/min/1.73 m<sup>2</sup>, and a height-adjusted total kidney volume (htTKV) of 1,082 (736–1,669) mL/m. At baseline, all urinary damage and inflammation markers were associated with baseline eGFR, also after adjustment for age, sex and baseline htTKV. For longitudinal analyses only patients randomized to standard care were considered (<i>n</i> = 152). A stepwise backward analysis revealed that β2MG and MCP-1 showed the strongest association with rapidly progressive disease. A urinary biomarker score was created by summing the ranking of tertiles of β2MG and MCP-1 excretion. The predictive value of this urinary biomarker score was higher compared to that of the Mayo htTKV classification (area under the curve [AUC] 0.73 [0.64–0.82] vs. 0.61 [0.51–0.71], <i>p</i> = 0.04) and comparable to that of the predicting renal outcomes in ­ADPKD score (AUC 0.73 [0.64–0.82] vs. 0.65 [0.55–0.75], <i>p</i> = 0.18). In a second independent cohort with better kidney function, similar results were found for the urinary biomarker score. <b><i>Conclusion:</i></b> Measurement of urinary β2MG and MCP-1 excretion allows selection of ADPKD patients with rapidly progressive disease, with a predictive value comparable to or even higher than that of TKV or <i>PKD</i> mutation. Easy and inexpensive to measure urinary markers therefore hold promise to help predict prognosis in ADPKD.
DOI: 10.6084/m9.figshare.9962759.v1
title: Supplementary Material for: Predictors of Care Gaps in Home Dialysis: The Home Dialysis Virtual Ward Study

description: <b><i>Background:</i></b> Home dialysis patients may be at an increased risk of adverse events after transitional states. The home dialysis virtual ward (HDVW) trial was conducted in Canadian dialysis centers and aimed to evaluate potential care gaps and patient satisfaction during the HDVW. <b><i>Methods:</i></b> The HDVW was a multicenter single-arm trial including peritoneal dialysis and home hemodialysis patients after 4 different events (hospital discharge, medical procedure, antibiotics, completion of training). Telephone-led interviews using a standardized assessment tool were performed over a 2-week period to assess a patient’s care and adjust treatment as required. Upon completion, patients were surveyed to evaluate their perceived impact on domains of care using a rating scale; 1 not satisfied to 10 completely satisfied. <b><i>Results:</i></b> The HDVW trial included 193 patients with a median number of potential care gaps/interventions of 1 (0–2) per patient. Patients admitted to the HDVW after hospital discharge were at a higher risk of potential gaps in care (OR 2.16, 95% CI 1.29–3.62), while longer dialysis vintage was ­associated with a lower number of gaps/interventions (OR 0.97 per year, 95% CI 0.95–0.98). A total of 105/193 (54%) patients completed satisfaction surveys. Patients were highly satisfied with the HDVW (median rating scale score 8, IQR 2) and felt it had a positive impact (rating scale score ≥7) on their overall health, understanding of treatment and access to a nephrologist. <b><i>Conclusion:</i></b> The HDVW was effective at identifying several potential care gaps, and patients were satisfied across several domains of care. This intervention may be valuable in supporting home dialysis patients during care transitions.
DOI: 10.6084/m9.figshare.9962765.v1
title: Harmonised LUCAS in-situ land cover and use database for field surveys from 2006 to 2018 in the European Union

description: --------------------------Release note of 14 08 2020--------------------------<br>The data are published with a publication describing how it was collected and organised along with some information about the data.<br>Please refer to "Harmonised LUCAS in-situ land cover and use database for field surveys from 2006 to 2018 in the European Union".<br><br>d'Andrimont, R., Yordanov, M., Martinez-Sanchez, L., Eiselt, B., Palmieri, A., Dominici, P., Gallego, J., Reuter, H.I., Joebges, C., Lemoine, G. and van der Velde, M., 2020. Harmonised LUCAS in-situ land cover and use database for field surveys from 2006 to 2018 in the European Union.<br>
DOI: 10.6084/m9.figshare.9962771.v1
title: Supplementary Material for: Hypothalamic Structural and Functional Imbalances in Anorexia Nervosa

description: The hypothalamus contains integrative systems that support life, including physiological processes such as food intake, energy expenditure, and reproduction. Here, we show that anorexia nervosa (AN) patients, contrary to normal weight and constitutionally lean individuals, respond with a paradoxical reduction in hypothalamic levels of glutamate/glutamine (Glx) upon feeding. This reversal of the Glx response is associated with decreased wiring in the arcuate nucleus and increased connectivity in the lateral hypothalamic area, which are involved in the regulation on a variety of physiological and behavioral functions including the control of food intake and energy balance. The identification of distinct hypothalamic neurochemical dysfunctions and associated structural variations in AN paves the way for the development of new diagnostic and treatment strategies in conditions associated with abnormal body mass index and a maladaptive response to negative energy balance.