cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.23946975
title: Supplementary Material for: Origin of residual tumor masses in BRCA1/2-driven ovarian carcinomas treated by neoadjuvant chemotherapy: selection of preexisting BRCA1/2-proficient tumor cells but not the gain of second ORF-restoring mutation

description: Introduction: Tubo-ovarian carcinomas (OCs) are highly sensitive to platinum-based neoadjuvant chemotherapy (NACT) but almost never demonstrate complete pathologic response. Methods: We analyzed paired primary and residual tumor tissues from 30 patients with hereditary BRCA1/2-driven OCs (BRCA1: 17; BRCA2: 13), who were treated by carboplatin/paclitaxel NACT (median number of cycles: 3, range 3-6). BRCA1/2 and TP53 genes were analyzed by the next-generation sequencing (NGS). The ratio between TP53 mutation-specific vs. wild-type reads was considered to monitor the proportion of tumor and non-tumor cells in the tissue sample, and the ratio between BRCA1/2 mutated and wild-type reads was used to estimate the presence of cells with the loss or retention of heterozygosity (LOH or ROH, respectively). Results: All 30 OCs had BRCA1/2 LOH in primary tumor and carried somatic TP53 mutation. Twenty-eight OCs had sufficient tumor cell cellularity in the post-NACT tissue to evaluate the ratio between mutated and wild-type BRCA1/2 alleles. Five (18%) out of 28 informative tumor pairs showed transition from LOH to ROH during NACT presumably affecting all or the vast majority of residual tumor cells. There were no signals of the emergence of a second open reading frame (ORF) restoring BRCA1/2 mutation. Conclusion: Chemonaive BRCA1/2-driven carcinomas may contain a fraction of tumor cells with preserved BRCA1/2 heterozygosity. NACT can cause a selection of pre-existing BRCA1/2-proficient tumor cells, without gaining secondary reversal BRCA1/2 mutations.
DOI: 10.1285/i20356609v14i1p57
title: Regionalism on the Run: ASEAN, EU, AU and MERCOSUR Responses Amid the COVID-19 Crisis

description: The transnational nature of COVID-19 created expectations of regionally-led initiatives to address this global challenge. The pandemic has transcended health issues accounting for several political and socioeconomic implications. This study seeks to investigate four regional organisations' responses during the 'first wave' to unravel regionalism's role in a time of crisis. To do so, the method of comparative analysis has been employed. ASEAN, EU, AU and MERCOSUR, four distinct organisations were selected to evaluate their responses in terms of crisis management efficacy, level of solidarity, promotion of multilateralism and international actorness. The findings highlight each organisation's successes and shortcomings while indicating the limits of regional cooperation in effectively responding to outbreaks of infectious diseases. This empirical analysis shows that regional responses were limited and mainly facilitated national policies. This further indicates regional organisations' inability to have a more proactive role in crisis management, boost their actorness and advance more inclusive and responsive global governance.
DOI: 10.18462/iir.icr.2019.0139
title: Design of a cold thermal energy storage unit for industrial applications using CO2 as refrigerant.
DOI: 10.13023/kgs.data.2020.01
title: Hydrology Data for Edge of Field Monitoring in a Sinkhole Dominated Karst Landscape, The Homeplace on the Green River

description: These data are a combination of precipitation quantity, spring flow, spring chemistry, spring and stream field measurement data, and dye trace results for a USDA funded research project at The Homeplace on the Green River in Taylor County, KY.
description: © 2020 University of Kentucky
DOI: 10.15121/1777170
title: Utah FORGE: Well 56-32 Drilling Data and Logs

description: This dataset consists of drilling data (Pason data spreadsheets, daily reports, days v. depth, mud logs), Schlumberger logs (FMI, shear anisotropy analysis, memory, sonic, array induction/spectral density/dual spaced neutron/gamma ray/caliper, spectral GR/temperature, and Gardner density correlation), and an end of well report (EOWR) for Utah FORGE well 56-32. This is a vertical well that will be used for seismic monitoring. It was drilled between February 7th and February 21st 2021 to a depth of 9,145 feet. More information about this well can be found at: https://utahforge.com/2021/02/09/drilling-progress-of-well-56-32/ (linked below)
DOI: 10.15121/1814488
title: Utah FORGE Well 78B-32 Daily Drilling Reports and Logs

description: This data set includes the daily drilling reports and Pason data for well 78B-32 and Schlumberger logs acquired after drilling completion. This well was drilled between June 27th and July 31st of 2021. Also included is raw and processed data for a variety of well data metrics including temperature, porosity, density, and sonic data. This data was taken at the Utah FORGE site as part of the Utah FORGE project.
DOI: 10.17608/k6.auckland.22144289
title: Succinate-mediated ROS production in the anoxia-tolerant epaulette (Hemiscyllium ocellatum) and grey carpet (Chiloscyllium punctatum) sharks.

description: Supporting data for the manuscript entitled: Succinate-mediated ROS production in the anoxia-tolerant epaulette (Hemiscyllium ocellatum) and grey carpet (Chiloscyllium punctatum) sharks.
DOI: 10.5281/zenodo.6618379
title: Verkko beta2 source and assemblies evaluated in manuscript

description: This is the Verkko source code used for all results in the verkko manuscript. The package includes verkko, graphaligner, mbg, and rukki code. Code is licensed as described in the included license files. All assemblies are in the paper are also included. The versions of other tools used were Flye v2.9-b1774, Hifiasm v0.16-r375, and LJA v0.2. All assemblies are CC0 as government work.
DOI: 10.5281/zenodo.7689032
title: Measurements of savanna landscap fire emission factors for CO2, CO, CH4 and N2O using a UAV-based sampling methodology

description: This dataset contains direct measurements of biomass burning emission factors for CO<sub>2</sub>, CO, CH<sub>4</sub> and N<sub>2</sub>O. It includes over 4500 EF bag measurements sampled using an unmanned aerial system (UAS), and measured fuel parameters and fire severity proxies during 129 individual fires. The measurements cover a variety of savanna ecosystems in Brazil, Australia, Botswana, Zambia, South-Africa and Mozambique under different seasonal conditions, sampled over the course of six fire seasons between 2017 and 2022. The table in the included word file explains the individual columns in the excell file.
description: {"references": ["Vernooij, R., Winiger, P., Wooster, M., Strydom, T., Poulain, L., Dusek, U., Grosvenor, M., Roberts, G. J., Schutgens, N. and Werf, G. R. Van Der: A quadcopter unmanned aerial system (UAS)-based methodology for measuring biomass burning emission factors, Atmos. Meas. Tech., 15(July), 4271\u20134294, doi:10.5194/amt-15-4271-2022, 2022.", "ernooij, R., Giongo, M., Assis Borges, M., Costa, M. ximo M., Carolina Sena Barradas, A. and Van Der Werf, G. R.: Intraseasonal variability of greenhouse gas emission factors from biomass burning in the Brazilian Cerrado, Biogeosciences, 18(4), 1375\u20131393, doi:10.5194/bg-18-1375-2021, 2021."]}
DOI: 10.5284/1035238
title: Analysis of Roman Silver coins, Augustus to the reform of Trajan (27 BC - AD 100)

description: In 2001 funding was obtained from the Leverhulme Trust (Grant No. RF&G/6/2002/0336) and the Faculty of Arts and Sciences Research Committee and the University Research Board of the American University of Beirut, Lebanon to undertake a one year project to apply this methodology to the coinage of the first Imperial dynasty, that of the Julio-Claudians. A more sensitive analytical technique was employed, inductively-coupled plasma atomic emission spectrometry (ICP-AES), that enabled much better quality data for important trace elements, such as arsenic, tin and bismuth, to be obtained. These data, together with scanning electron microscopy (SEM), micro-analysis (SEM-EDS), optical microscopy (metallography) and some limited lead isotope analysis by laser ablation multi-collector inductively-coupled plasma mass spectrometry (LA-MC-ICP-MS) form the basis of a series of publications in print (Butcher and Ponting 2005a), in press (Butcher and Ponting 2005b) and in preparation.

In 2006 a second stage of the project was awarded funding from the Arts and Humanities Research Council (AHRC) over three years (Grant ID: 119434). This project used the same suite of analytical techniques to investigate a much larger number of coins, including an expanded programme of lead isotope analyses (by thermal ionisation mass spectrometry). The first stage of this project resulted in a number of journal publications and contributions to edited volumes (Butcher et al. 2009; Butcher and Ponting 2012; Ponting 2009 and 2012). In 2014 a substantial monograph will be published that brings together and discusses the results from all the above projects covering Roman Imperial silver coinage up until the Reform of Trajan. It is the raw data upon which this monograph is based that are archived here.
DOI: 10.5285/d023376c-08e3-451b-9d57-de13f14726bd
title: Biosphere Isotope Domain Map GB (V1): sulphur isotope data.

description: This file documents the Sulphur isotope data, and the manner in which it has been processed, to supply the reference data for isotope domains of the Isotope biosphere domains GB (V1) map.  It includes a summary of the analytical methods used to determine the isotope ratios though time.
DOI: 10.6084/m9.figshare.22567018
title: Supplementary Material for: Percutaneous trans-esophageal gastrostomy for oral intake in a case of anastomotic obstruction following total gastrectomy

description: Gastric cancer is one of the most common diseases globally. Total gastrectomy is often performed surgically. However, late-stage anastomotic passage obstruction after total gastrectomy is relatively rare. Here, we report a case involving a 73-year-old male patient who experienced repeated aspiration pneumonia due to anastomotic passage obstruction 22 years after a total gastrectomy for gastric cancer. He was eventually hospitalized in the Department of Gastroenterology at our hospital because of difficulty eating. Computed tomography revealed prominent dilation of the esophagus and the blind end of the elevated jejunum. Upper gastrointestinal endoscopy revealed a poorly extended site on the main side of the elevated jejunum; however, the passage through the scope was good. A percutaneous trans-esophageal gastrostomy was performed for oral intake. The patient experienced decreased nausea and vomiting. He gained weight and his general condition improved. He did not feel inconvenienced by percutaneous trans-esophageal gastrostomy and had no desire for surgery. Follow-up observations are currently being conducted, with tubes exchanged every 6 months. There are no reports of percutaneous trans-esophageal gastrostomy for oral intake for anastomotic passage obstruction following total gastrectomy; therefore, we report this as a reference when similar cases are encountered.
DOI: 10.6084/m9.figshare.23566995
title: Supplementary Material for: Availability of genetic tests in public health services in Brazil: data from the Brazilian Rare Diseases Network

description: Introduction: The Brazilian Policy for Comprehensive Care for People with Rare Diseases (BPCCPRD) was published in 2014, accrediting several reference centers and incorporating many genetic tests for the diagnosis of rare diseases (RDs). The Brazilian Network of Rare Diseases (RARAS) comprises more than 40 institutions that offer diagnosis and treatment for RDs in Brazil. This network includes Reference Services for Rare Diseases (RDRS), Reference Services for Newborn Screening (NSRS), and University Hospitals (UH) distributed in all Brazilian regions. Objective: To map the availability and distribution of the BPCCPRD diagnostic procedures in the Brazilian Unified Health System through RARAS. Method: Data were collected through a questionnaire on the REDCap platform, with 22 questions regarding the availability of procedures. Thirty-seven coordinators from RARAS participating centers received the questionnaire link for participation by email from August/2020 to March/2021. All participating institutions ethically approved this project. Results: Of the 37 institutions, 23 (62.16%) offered cytogenetic tests, 20 (54.05%) offered molecular procedures, and 22 (59.46%) offered inborn errors of metabolism (IEM) diagnostic tests. The identification of urinary glycosaminoglycans by thin-layer chromatography, electrophoresis, and/or quantitative measurement had the highest outsourcing rate. On the other hand, the procedure most frequently performed on-site was the peripheral blood karyotype with band technique. It was observed that 10 of the 37 centers (27%) did not provide access to investigated procedures (on-site or outsourced). The North and Midwest regions stood out in terms of the unavailability of such techniques in at least 40% of the evaluated institutions. Discussion and conclusion: This study reveals large discrepancies in the supply of diagnostic procedures in the Brazilian territory. Moreover, there is a broad collaboration between services through the outsourcing of multiple diagnostic techniques to address this issue. Finally, this work corroborates the importance of mapping services for the diagnosis and treatment of individuals with RDs to propose actions for the better supply and distribution of these procedures.
DOI: 10.6084/m9.figshare.23715972
title: Supplementary Material for: Rate-limiting enzymes in cardiometabolic health and aging in humans

description: Introduction. Rate-limiting enzymes (RLEs) are innate slow points in metabolic pathways, and many function in bioprocesses related to nutrient sensing. Many RLEs carry causal mutations relevant to inherited metabolic disorders. Because the activity of RLEs in cardiovascular health is poorly characterized, our objective was to assess their involvement in cardiometabolic health and disease, and where altered biophysical and biochemical functions can promote disease. Methods. A dataset of 380 human RLEs was compared to protein and gene datasets for factors likely to contribute to cardiometabolic disease, including proteins showing significant age-related altered expression in blood, and genetic loci with variants that associate with common cardiometabolic phenotypes. The biochemical reactions catalyzed by RLEs were evaluated for metabolites enriched in RLE subsets associating with various cardiometabolic phenotypes. Most significance tests were based on Z-score enrichment converted to P values with a normal distribution function. Results. Of 380 RLEs analyzed, 112 function in mitochondria, and 53 are assigned to inherited metabolic disorders. There was a depletion of RLE proteins known as aging biomarkers. At the gene level, RLEs were assessed for common genetic variants that associated with important cardiometabolic traits of LDL-cholesterol or any of the five outcomes pertinent to metabolic syndrome. This revealed several RLEs with links to cardiometabolic traits, from a minimum of 26 for HDL-cholesterol to a maximum of 45 for plasma glucose. Analysis of these GWAS-linked RLEs for enrichment of the molecular constituents of the catalyzed reactions disclosed a number of significant phenotype-metabolite links. These included blood pressure with acetate (P = 2.2x10-4) and NADP+ (P = 0.0091), plasma HDL-cholesterol and triglyceride with diacylglycerol (P = 2.6x10-5, 6.4x10-5, respectively) and diolein (P = 2.2x10-6, 5.9x10-6), and waist circumference with D-glucosamine 6-phosphate (P = 1.8x10-4). Conclusion. In the context of cardiometabolic health, aging and disease, these results highlight key diet-derived metabolites that are central to specific rate-limited processes that are linked to cardiometabolic health. These metabolites include acetate and diacylglycerol, pertinent to blood pressure and triglycerides, respectively, as well as diacylglycerol and HDL-cholesterol.
DOI: 10.6084/m9.figshare.23736039
title: Supplementary Material for: Your Family Connects: A Theory-Based Intervention to Encourage Communication About Possible Inherited Cancer Risk among Ovarian Cancer Survivors and Close Relatives

description: Introduction: Encouraging family communication about possible genetic risk has become among the most important avenues for achieving the full potential of genomic discovery for primary and secondary prevention. Yet, effective family-wide risk communication (i.e., conveying genetic risk status and its meaning for other family members) remains a critical gap in the field. We aim to describe the iterative process of developing a scalable population-based communication outreach intervention, Your Family Connects, to reach ovarian cancer survivors and close relatives to communicate the potential for inherited risk and to consider genetic counseling. Methods: Relational-level theories (e.g., interdependence theory) suggest that interventions to promote family cancer risk communication will be most effective if they consider the qualities of specific relationships and activate motives to preserve the relationship. Informed by these theories, we collaborated with 14 citizen scientists (survivors of ovarian cancer or relatives) and collected 261 surveys and 39 structured interviews over 12 weeks of citizen science activities in 2020. Results: The citizen science findings and consideration of relational-level theories informed the content and implementation of Your Family Connects (www.yourfamilyconnects.org). CS results showed survivors favor personal contact with close relatives, but relatives were open to alternative contact methods, such as through health professionals. Recognizing the need for varied approaches based on relationship dynamics, we implemented a relative contact menu to enable survivors identify at-risk relatives and provide multiple contact options (i.e., survivor contact, health professional contact, and delayed contact). In line with relational autonomy principles, we included pros and cons for each option, assisting survivors in choosing suitable contact methods for each relative. Discussion: Our developed intervention represents a novel application of relational-level theories and partnership with citizen scientists to expand genetic services reach to increase the likelihood for fair distribution of cancer genomic advances. The Your Family Connects intervention as part of a randomized trial in collaboration with the Georgia Cancer Registry compared with standard outreach.
DOI: 10.6084/m9.figshare.24031971
title: Supplementary Material for: Rapid Malignant Transformation of Tubulovillous Adenoma, Initially Presenting as McKittrick–Wheelock Syndrome: a Case-Report

description: Most cases of colorectal cancer develop from adenomatous polyps, slowly progressing within an average period of 8 – 10 years. McKittrick–Wheelock syndrome (MKWS) is a rare manifestation of tubulovillous adenoma. It generally presents as hypersecretory diarrhea with severe electrolyte and fluid depletion. Roughly 5% of the published cases have reported malignant histopathology associated with MKWS, with little to no data regarding the malignant transformation process of those patients. Our patient was a 53-year-old Asian woman suffering from chronic secretory diarrhea, resulting in severe volume, electrolyte depletion, and pre-renal azotemia, consistent for MKWS. Her symptoms initially improved with sulfasalazine but eventually worsened. She demonstrated signs of systemic (elevated leukocyte, CRP, and LDH) and local inflammation (dense lymphocyte infiltration in colorectal tissue) throughout the course of her disease. Serial pathological results showed rapid neoplastic progression of adenomatous polyp to adenocarcinoma within one year period. Surgical resection resulted in complete symptom resolution. Molecular examination showed a favorable profile of exon 4 KRAS mutation, normal NRAS, BRAF, CDX2, and CK20 expressions. Her molecular pattern did not reflect the profile of an aggressive disease, suggesting the possibility of oncogenic processes outside the major pathways of adenoma to carcinoma progression. Chronic inflammation is a well-established risk factor for colorectal cancer, and PGE2 has been observed as one of the key regulators of tumor initiation and growth. PGE2 is also responsible for hypersecretory diarrhea associated with MKWS.
DOI: 10.25386/genetics.10312070
title: Supplemental Material for Holdorf et al., 2020

description: Supplemental figures, tables, and legends for WormCat: an online tool for annotation and visualization of Caenorhabditis elegans genome-scale data
DOI: 10.6084/m9.figshare.23760057
title: Supplementary Material for: The Role of Biologic Mesh and Fundoplication in the Surgical Management of Hiatal Hernias: A Multicenter Evaluation

description: Introduction- Hiatal hernia repair is associated with substantial recurrence of both hiatal hernia and symptoms of gastroesophageal reflux (GER). While small randomized controlled trials demonstrate limited differences in outcomes with use of mesh or fundoplication type, uncertainty remains. Methods- A multicenter, retrospective review of patients undergoing surgical treatment of hiatal hernias between 2015-2020 was performed. Patients with mesh and with suture only repair were compared, and partial versus complete fundoplication was compared. Primary outcomes were hernia recurrence and occurrence of post-operative GER symptoms and dysphagia. Multivariable regression was performed to assess the effect of each intervention on clinical outcomes. Results- A total of 453 patients from four sites were followed for a median (IQR) of 17 (13) months. On multivariate analysis, mesh had no impact on hernia recurrence (odds ratio 0.993, 95% CI 0.53-1.87, p=0.982), and fundoplication type did not impact recurrence of post-operative GER symptoms (complete: odds ratio 0.607, 95% CI 0.33-1.12, p=0.112) or dysphagia (complete: odds ratio 1.17, 95% CI 0.56-2.43, p=0.677). Conclusion- During hiatal hernia repair, mesh and fundoplication type do not appear to have substantial impact on GER symptoms, dysphagia, or hernia recurrence. This multicenter study provides real-world evidence to support the findings of small RCTs.