cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.58020/y7xf-s477
title: Chronic Prostatitis Collaborative Research Network Cohort Study

description: Chronic prostatitis is a disabling condition of unknown origin affecting men of all ages and ethnic groups. Most have chronic pelvic pain associated with urinary frequency and urgency; however, they do not have demonstrable urinary or prostatic infections that can be detected by conventional microbiological techniques. In response to the growing concerns about the diagnosis and treatment of chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS), the Chronic Prostatitis Collaborative Research Network (CPCRN), which consists of six clinical centers and one data coordinating center, was established to study this syndrome in order to improve diagnosis and treatment. 

The CPCRN conducted a prospective observational cohort study designed to characterize CP/CPPS, examine symptoms and quality of life in affected men, and assess the economic impact of the condition. Men of any age with symptoms of discomfort or pain in the pelvic region for at least 3 of the 6 months prior were eligible for enrollment. The CPCRN cohort study consisted of a baseline screening phase and a longitudinal follow-up phase. During the baseline screening phase, eligibility criteria were assessed, and baseline data and biospecimens (including serum, prostatic fluid, and semen) were collected. Information on symptoms and quality of life, demographic and lifestyle factors, medical history, prior treatments and procedures, and health resource utilization was collected. 

The study found that CP/CPPS is a multifactorial problem affecting men of all ages and demographics. The condition is characterized by substantial variation in symptoms within and among subjects. There is no evidence that the disorder worsens significantly during 2 years of follow-up, and for about a third of men with long-standing symptoms there may be moderate to marked improvement during this period. Men with chronic prostatitis experience impairment in the mental and physical domains of general health related quality of life, and many have benefited only minimally from empirical, goal-directed therapy. The CPCRN has conducted numerous clinical trials to investigate the safety and efficacy of numerous treatments for CP/CPPS, for which more details are available on the NIDDK Repository website.
DOI: 10.58020/6dxf-ed78
title: Chronic Renal Insufficiency Cohort Study

description: The Chronic Renal Insufficiency Cohort (CRIC) Study is an observational study that examined risk factors for progression of chronic renal insufficiency (CRI) and cardiovascular disease (CVD) among CRI patients. The study enrolled adults aged 21 to 74 years with a broad spectrum of renal disease severity, half of whom were diagnosed with diabetes mellitus. Subjects underwent extensive clinical evaluation at baseline and at annual clinic visits and via telephone at 6 month intervals. Data on quality of life, dietary assessment, physical activity, health behaviors, depression, cognitive function, health care resource utilization, as well as blood and urine specimens were collected. Measures of kidney function and occurrence of new and worsening CVD  are the primary outcomes, among others.

Data from the recruitment and follow-up phases through Phase 3. Additionally, the data package includes variables related to APOL1, Echocardiogram, Electrocardiogram, and censored composite and individual outcomes. The data package includes data through 2021.
DOI: 10.58020/cezb-xp64
title: Complementary and Alternative Medicine for Urological Symptoms

description: The Complementary and Alternative Medicine for Urological Symptoms (CAMUS) study was a double-blind, placebo-controlled randomized clinical trial that investigated the efficacy of a widely available phytotherapy, saw palmetto extract, at up to 3 times the standard dose on lower urinary tract symptoms attributed to benign prostatic hyperplasia  (BPH) in men. Although saw palmetto fruit extract is widely used for treating lower urinary tract symptoms attributed to BPH, a well-design National Institutes of Health supported clinical trial (Avins A et al. JAMA) failed to a benefit of this treatment compared to placebo. The CAMUS study enrolled males with a peak urinary flow rate of at least 4 mL/s and an American Urological Associate Symptom Index (AUASI) score of between 8 and 24 at screening visits. Participants were randomly assigned equally to receive one, two, and then three 320 mg gelcaps daily containing a standardized saw palmetto fruit extract with dose escalations at 24 and 48 weeks; or an identical number of placebo gelcaps escalated similarly. The primary outcome was the change in AUASI score from baseline to 72 weeks. Participants were closely monitored for adverse events. The study concluded that saw palmetto extract used at up to 3 times the standard daily dose had no greater effect than placebo on improving lower urinary symptoms or other outcomes related to BPH.
DOI: 10.58020/956q-m463
title: Consortium for Radiologic Imaging Studies of Polycystic Kidney Disease

description: The Consortium for Radiologic Imaging Studies of Polycystic Kidney Disease (CRISP) was established to develop and implement studies to test whether imaging techniques can provide accurate and reproducible markers of progression of renal disease in patients with polycystic kidney disease. Autosomal-dominant polycystic kidney disease (ADPKD) is characterized by gradual renal enlargement and cyst growth prior to loss of renal function; however, standard radiographic imaging has not provided the resolution and accuracy necessary to detect small changes in renal volume or to reliably measure renal cyst volumes. The CRISP cohort study longitudinally observed ADPKD individuals using high-resolution magnetic resonance (MR) imaging to determine if change in renal and cyst volumes can be detected over a short period of time, and if they correlate with decline in renal function early in disease.

Patients who were diagnosed with ADPKD and had a creatinine clearance of at least 70 mL/min were enrolled. Standardization studies were conducted at each participating clinical center. After, in the full-scale protocol, participants underwent standardized MR renal imaging, comprehensive clinical evaluation, evaluation of renal iothalamate clearance, and determination of 24-hour urinary albumin and electrolyte excretion. Stereology was used from T1-weighted images to quantify renal volume, and region-growing thresholding was used from T2-weighted images to determine cyst volume.

The CRISP cohort was also analyzed by molecular analysis. Given the high level of unclassified variants (UCV) in patients with ADPKD, the purpose of the molecular analysis was to systematically classify UCVs in the PKD1 and PKD2 genes. 

The current data package contains data through the CRISP 3 cycle as well as CRISP allele frequency data.
DOI: 10.58020/tt6f-yf90
title: Gut Microbiome and p-Inulin in CKD - TarGut CKD Study

description: Chronic Kidney Disease (CKD) is a condition in which the kidneys lose function over time.  Research has shown that individuals with kidney disease have an altered gut microbiome, the microorganisms that live in the human gastrointestinal tract.  This imbalance in the gut microbiome can aid in the progression of CKD.  Research also indicates that treatment with prebiotics, special plant fibers that promote the growth of healthy bacteria in the GI tract, can help restore balance in the gut microbiome.  However, more understanding is needed regarding variability in the performance and composition of the gut microbiome in individuals with CKD, and how this population can be impacted by interventions with prebiotic supplements.

The Gut Microbiome and p-Inulin in CKD (TarGut) Study was formed to determine if the gut microbiome of patients with CKD could be improved with treatment of p-inulin, a type of prebiotic.  After recruitment and enrollment, TarGut participants are evaluated for a period of 28 weeks.  This 28-week study period consists of three phases: an 8-week pre-treatment phase, 12-week active treatment phase, and 8-week post-treatment phase.  During the active treatment phase participants take the p-inulin supplement daily, but participants don’t receive any intervention during the pre- and post-treatment phases.  Biological samples are collected from study participants every week during the 28-week study period and assessed to determine microbial composition and function.
DOI: 10.58020/p1k3-eb54
title: Nonalcoholic Fatty Liver Disease (NAFLD) Pediatric Database

description: Nonalcoholic fatty liver disease (NAFLD) is the most common cause of liver disease in the preadolescent and adolescent age groups in the United States. Despite the prevalence of pediatric NAFLD, overweight, obesity, and related conditions remain underdiagnosed by health care providers. Because of the risk and expense of liver biopsies, it would be advantageous to identify clinical predictors of histologic severity so that children at greatest risk for progression could be identified. The Nonalcoholic Steatohepatitis Clinical Research Network (NASH CRN) was initiated by the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) in 2002 to conduct multicenter, collaborative studies on the etiology, contributing factors, natural history, complications, and treatment of NASH.

Demographic data was obtained via structured interview and questionnaires. Height, weight, waist, and hip measurements, Tanner staging, and the presence and severity of acanthosis nigricans were assessed. Biopsy specimens were evaluated for the following according to the validated histologic NASH CRN scoring system: steatosis, portal inflammation, lobular inflammation, ballooning degeneration, and fibrosis. A NAFLD activity score (NAS) was tabulated by summing scores for steatosis, lobular inflammation, and ballooning degeneration.
DOI: 10.58020/nm6n-qe65
title: The HALT Progression of Polycystic Kidney Disease

description: Autosomal dominant polycystic kidney disease (ADPKD) impacts 1 in 400 to 1 in 1000 live births and accounts for about 4.6% of the kidney replacement population in the US. Hypertension is the most common manifestation and an important risk factor for its progression to end stage renal disease (ESRD) and cardiovascular morbidity and mortality.

The HALT Progression of Polycystic Kidney Disease (HALT PKD) studies were two simultaneous multicenter clinical trials designed to test the efficacy of interruption of the renin-angiotensin-aldosterone system (RAAS) on the progression of cystic disease and the decline in renal function in ADPKD. Specifically, the studies assessed the effects of ACE-I/ARB combination therapy as compared to ACE-I monotherapy in hypertensive ADPKD subjects.

The two studies varied on eligibility criteria (particularly kidney function), blood pressure treatment, and primary outcome measure. Study A investigates treatment effects on individuals with early ADPKD and implements a standard (120-130/70-80 mm Hg) vs. low (95-110/60-75 mmHg) blood pressure control target for both treatment arms in a 2x2 design. Study B investigates treatment effects on individuals with moderately advanced ADPKD in the setting of standard blood pressure control (110-130/80 mm Hg). Participants enrolled in study A were followed for at least five years, while those enrolled in study B were followed for five to eight years, with the average length of follow-up being six and a half years.

The complete HALT PKD data package is available for request.
DOI: 10.58020/bhat-mx96
title: The Nonalcoholic Steatohepatitis Research Network (NASH CRN) Pioglitazone vs Vitamin E vs Placebo for Treatment of Non-Diabetic Patients With Nonalcoholic Steatohepatitis

description: Nonalcoholic steatohepatitis (NASH) is a common liver disease associated with obesity and diabetes. NASH is a progressive disorder that can lead to cirrhosis and liver failure, and there is no definitive treatment. Insulin resistance and oxidative stress (resulting in lipid peroxidation) are considered to be the two most important mechanisms in the pathogenesis of NASH.<br><br>PIVENS hypothesized that pioglitazone and vitamin E will lead to improvement in hepatic histology in nondiabetic adults with biopsy proven NASH through changes in insulin resistance or oxidative stress. Before and post-treatment liver biopsies were read centrally in a masked fashion for an assessment of steatohepatitis and a NAFLD Activity Score (NAS) consisting of steatosis, lobular inflammation, and hepatocyte ballooning.<br><br>PIVENS enrollment started in January 2005 and ended in January 2007 with 247 patients randomized to receive either pioglitazone (30 mg q.d.), vitamin E (800 IU q.d.), or placebo for 96 weeks. Participants were followed for an additional 24 weeks after stopping the treatment. Both at the initial evaluation and at the completion of treatment 96 weeks later, subjects underwent an assessment of body weight, height, and waist and hip circumferences, and blood samples were obtained for routine biochemical tests and assessment of fasting levels of lipids, glucose, and insulin. Body composition was assessed with the use of dual-energy x-ray absorptiometry. The Medical Outcomes Study 36-Item Short-Form Health Survey (SF-36) was administered for the assessment of quality of life. 

The complete PIVENS data is now available.
DOI: 10.5281/zenodo.4734615
title: An ice sheet model ensemble of the last deglaciation in the Ross Sea, Antarctica

description: This dataset contains netCDF output files and make files for 52 simulations of past behavior of the Antarctic Ice Sheet, using the Pennsylvania State University ice sheet model (e.g., Pollard and DeConto, 2012). There are two full-continent simulations at 40 km resolution from 125 kyr BP to present, two full-continent simulations at 20 km resolution from 25 kyr BP to present, and 48 nested simulations over the Ross Sea sector at 10 km resolution from 20 kyr BP to present. The 40 km resolution runs provide the initial conditions for the 20 km resolution runs, and the 20 km resolution runs provide initial and boundary conditions for the 10 km resolution runs. These simulations are presented and discussed by Hillebrand et al. (2021). The model output in the netCDF files can be easily viewed using the ncview tool. References: Pollard, D. and DeConto, R. M.: Description of a hybrid ice sheet-shelf model, and application to Antarctica, Geosci. Model Dev., 5, 1273–1295, https://doi.org/10.5194/gmd-5-1273-2012, 2012. Hillebrand, T. R., Stone, J. O., Koutnik, M., King, C., Conway, H., Hall, B., Nichols, K., Goehring, B., and Gillespie, M. K.: Holocene thinning of Darwin and Hatherton glaciers, Antarctica, and implications for grounding-line retreat in the Ross Sea, The Cryosphere, 15, 3329–3354, https://doi.org/10.5194/tc-15-3329-2021, 2021.
description: {"references": ["Hillebrand, T. R., Stone, J. O., Koutnik, M., King, C., Conway, H., Hall, B., Nichols, K., Goehring, B., and Gillespie, M. K.: Holocene thinning and grounding-line retreat of Darwin and Hatherton Glaciers, Antarctica, The Cryosphere Discussions, 1\u201342, https://doi.org/10.5194/tc-2020-356, 2020.", "Pollard, D. and DeConto, R. M.: Description of a hybrid ice sheet-shelf model, and application to Antarctica, Geosci. Model Dev., 5, 1273\u20131295, https://doi.org/10.5194/gmd-5-1273-2012, 2012."]}
DOI: 10.5281/zenodo.4734614
title: An ice sheet model ensemble of the last deglaciation in the Ross Sea, Antarctica

description: This dataset contains netCDF output files and make files for 52 simulations of past behavior of the Antarctic Ice Sheet, using the Pennsylvania State University ice sheet model (e.g., Pollard and DeConto, 2012). There are two full-continent simulations at 40 km resolution from 125 kyr BP to present, two full-continent simulations at 20 km resolution from 25 kyr BP to present, and 48 nested simulations over the Ross Sea sector at 10 km resolution from 20 kyr BP to present. The 40 km resolution runs provide the initial conditions for the 20 km resolution runs, and the 20 km resolution runs provide initial and boundary conditions for the 10 km resolution runs. These simulations are presented and discussed by Hillebrand et al. (2021). The model output in the netCDF files can be easily viewed using the ncview tool. References: Pollard, D. and DeConto, R. M.: Description of a hybrid ice sheet-shelf model, and application to Antarctica, Geosci. Model Dev., 5, 1273–1295, https://doi.org/10.5194/gmd-5-1273-2012, 2012. Hillebrand, T. R., Stone, J. O., Koutnik, M., King, C., Conway, H., Hall, B., Nichols, K., Goehring, B., and Gillespie, M. K.: Holocene thinning of Darwin and Hatherton glaciers, Antarctica, and implications for grounding-line retreat in the Ross Sea, The Cryosphere, 15, 3329–3354, https://doi.org/10.5194/tc-15-3329-2021, 2021.
description: {"references": ["Hillebrand, T. R., Stone, J. O., Koutnik, M., King, C., Conway, H., Hall, B., Nichols, K., Goehring, B., and Gillespie, M. K.: Holocene thinning and grounding-line retreat of Darwin and Hatherton Glaciers, Antarctica, The Cryosphere Discussions, 1\u201342, https://doi.org/10.5194/tc-2020-356, 2020.", "Pollard, D. and DeConto, R. M.: Description of a hybrid ice sheet-shelf model, and application to Antarctica, Geosci. Model Dev., 5, 1273\u20131295, https://doi.org/10.5194/gmd-5-1273-2012, 2012."]}
DOI: 10.5281/zenodo.4735624
title: Flow-band model simulations of the Darwin-Hatherton Glacier System, Antarctica since the Last Glacial Maximum

description: This dataset contains .mat files of model output from an isothermal, 1.5-dimensional, shallow-ice glacier flow-band model of Darwin and Hatherton glaciers, Antarctica, from the Last Glacial Maximum to present. These results are presented by Hillebrand et al. (2021). The model was used to determine the likelihood of three different deglaciation scenarios potentially allowable by geochronologic data collected near the modern grounding line of Darwin Glacier by evaluating the fit of the tributary Hatherton Glacier in the model to abundant geochronologic data. References: Hillebrand, T. R., Stone, J. O., Koutnik, M., King, C., Conway, H., Hall, B., Nichols, K., Goehring, B., and Gillespie, M. K.: Holocene thinning of Darwin and Hatherton glaciers, Antarctica, and implications for grounding-line retreat in the Ross Sea, The Cryosphere, 15, 3329–3354, https://doi.org/10.5194/tc-15-3329-2021, 2021.
description: {"references": ["Hillebrand, T. R., Stone, J. O., Koutnik, M., King, C., Conway, H., Hall, B., Nichols, K., Goehring, B., and Gillespie, M. K.: Holocene thinning and grounding-line retreat of Darwin and Hatherton Glaciers, Antarctica, The Cryosphere Discussions, 1\u201342, https://doi.org/10.5194/tc-2020-356, 2020."]}
DOI: 10.5281/zenodo.4735623
title: Flow-band model simulations of the Darwin-Hatherton Glacier System, Antarctica since the Last Glacial Maximum

description: This dataset contains .mat files of model output from an isothermal, 1.5-dimensional, shallow-ice glacier flow-band model of Darwin and Hatherton glaciers, Antarctica, from the Last Glacial Maximum to present. These results are presented by Hillebrand et al. (2021). The model was used to determine the likelihood of three different deglaciation scenarios potentially allowable by geochronologic data collected near the modern grounding line of Darwin Glacier by evaluating the fit of the tributary Hatherton Glacier in the model to abundant geochronologic data. References: Hillebrand, T. R., Stone, J. O., Koutnik, M., King, C., Conway, H., Hall, B., Nichols, K., Goehring, B., and Gillespie, M. K.: Holocene thinning of Darwin and Hatherton glaciers, Antarctica, and implications for grounding-line retreat in the Ross Sea, The Cryosphere, 15, 3329–3354, https://doi.org/10.5194/tc-15-3329-2021, 2021.
description: {"references": ["Hillebrand, T. R., Stone, J. O., Koutnik, M., King, C., Conway, H., Hall, B., Nichols, K., Goehring, B., and Gillespie, M. K.: Holocene thinning and grounding-line retreat of Darwin and Hatherton Glaciers, Antarctica, The Cryosphere Discussions, 1\u201342, https://doi.org/10.5194/tc-2020-356, 2020."]}
DOI: 10.5281/zenodo.7105680
title: Convergent genomics of longevity in rockfishes highlights the genetics of human lifespan variation

description: Longevity is a defining, heritable trait that varies dramatically between species. To resolve the genetic regulation of this trait, we have mined genomic variation in rockfishes, which range in longevity from 11 to over 205 years, along with the sea robin as an outgroup. We used the phylomapping methodology to target sequencing and assembly to conserved, functional loci, defined using available genomic resources from well-characterized species. These annotations are in the gtf. For analysis of coding elements, assembled contigs were trimmed to just the exons. Exons were concatenated and analyzed to generate gene trees with IQTree, fixed to match the species tree. Additional details of these assembly methods are available at DOI: 10.1038/s41559-019-0914-2 and DOI: 10.1126/sciadv.add2743
DOI: 10.5281/zenodo.7105679
title: Convergent genomics of longevity in rockfishes highlights the genetics of human lifespan variation

description: Longevity is a defining, heritable trait that varies dramatically between species. To resolve the genetic regulation of this trait, we have mined genomic variation in rockfishes, which range in longevity from 11 to over 205 years, along with the sea robin as an outgroup. We used the phylomapping methodology to target sequencing and assembly to conserved, functional loci, defined using available genomic resources from well-characterized species. These annotations are in the gtf. For analysis of coding elements, assembled contigs were trimmed to just the exons. Exons were concatenated and analyzed to generate gene trees with IQTree, fixed to match the species tree. Additional details of these assembly methods are available at DOI: 10.1038/s41559-019-0914-2 and DOI: 10.1126/sciadv.add2743