jimnoneill/paper-to-field-training huggingface dataset:
Replication Data for: The Unequal Burden of War: The Effect of Armed Conflict on the Gender Gap in Life Expectancy (with Thomas Plümper), International Organization, 60 (3), 2006, 723-754

Field: Social Sciences (Social Sciences)

Most combatants in armed conflict are men, so naturally men are the major direct victims of military operations. Yet armed conflicts have important indirect negative consequences on agriculture, infrastructure, public health provision, and social order. These indirect consequences are often overlooked and underappreciated. They also affect women—arguably more so than men. This article provides the first rigorous analysis of the impact of armed conflict on female life expectancy relative to male+ We find that over the entire conflict period, interstate and civil wars on average affect women more adversely than men. In peacetime, women typically live longer than men. Hence, armed conflict tends to decrease the gap between female and male life expectancy. For civil wars, we also find that ethnic wars and wars in “failed” states are much more damaging to women than other civil wars. Our findings challenge policymakers as well as international and humanitarian organizations to develop policies that tackle the large indirect and long-term negative health impacts of armed conflicts.
PTU-069 Detection of cystic duct stones during laparoscopic cholecystectomy

Field: Medicine (Health Sciences)

Introduction With the advent of the Laparoscopic Cholecystectomy (LC) era, the loss of tactile element hindered the detection of cystic duct stones (CDS) during surgery. These stones are implicated in the post cholecystectomy pain syndrome, failure of the insertion of intra-operative cholangiogram (IOC) catheter and the subsequent development of common bile duct (CBD) stones. The aim of this analysis is to quantify the frequency of the incidental finding of CDS during LC. Methods A cohort of consecutive patients undergoing LC during the period from November 2006 to May 2010 were included. Data were prospectively collected. Their liver function tests were documented in the preoperative period. The procedure entailed careful dissection of the cystic duct (CD) to the proximity of common bile duct. A clip was then placed at the gall bladder to CD junction. If an IOC was required, the CD was opened in the routine fashion. A partially closed endoclip was then used to milk the CD towards the gallbladder; any CDS encountered were retrieved and documented. If IOC was not indicated, the CD was milked prior to the application of gallbladder/CD clip. Results The study included 330 patients; 80 male and 250 females. Age ranged between 16 and 88 years (Median 50, IQR: 36–62). In 266 patients no CDS were detected. However, in 64 (19%) patients CDS were identified using the above technique; with 28 (45%) having a single stone. The remaining 36 (55%) patients had more than one stone with a maximum detected number of seven stones. Preoperative imaging failed to detect any CDS. Of those 64 patients with CDS, 47 (75%) showed deranged liver function tests at some stage of their disease prior to surgery. In comparison, of the 266 patients with no CDS, 152 (57%) also demonstrated abnormal liver function tests. Conclusion The results demonstrate the fact pre-operative investigations are not helpful in diagnosing CDS. Their occurrence is common. In order to detect CDS, specific intra-operative awareness and vigilance are needed. Careful upward milking of the cystic duct before applying clips is a simple, safe and effective way of detecting and extracting these stones. This study changed our practice as this procedure is now included in all our Laparoscopic chlecystectomies. Competing interests None declared.
Designing and Implementing a Portable Near-Infrared Imaging System for Monitoring of Human’s Functional Brain Activity

Field: Engineering (Physical Sciences)

Functional near-infrared spectroscopy (fNIRS) is a non-invasive technique for monitoring of brain functional activity. It uses near-infrared (NIR) light to get the information related to brain hemodynamic response as most of the tissues in the brain are transparent to NIR light. The main goal of this study was to design, implement and evaluate a continuous-wave near-infrared spectroscopy (CW-NIRS) system for human’s brain cognitive functions. This system is portable, and works with a small rechargeable battery; thus, it may be used for bedside monitoring. In our CW-NIRS system, we used 3 multi-wavelength LEDs and 8 photodiodes (with built-in amplifiers) resulting in 12 channels (voxels). The collected signals of these 12 channels, at a sampling rate of 15 Hz, can be used for 2D image reconstruction to monitor functional brain activity. All LEDs and photodiodes are placed on a flexible printed circuit board (PCB), which covers the forehead to measure hemodynamic response of the prefrontal cortex. We also developed a software in MATLAB for analysis of optical signals recorded by our CW-NIRS system. This software provides 2D image reconstruction and monitoring of changes in concentration of oxygenated ([HbO2]) and deoxygenated ([HbR]) hemoglobin as well as the total hemoglobin ([HbT]) for the 12 channels over the prefrontal cortex (forehead). The software has also an embedded statistical analysis option for analyzing the collected signals and displaying the results. The developed CW-NIRS system was evaluated on 14 individuals (24±3 years old) on two common cognitive tasks: verbal fluency task (VFT) and color distinction task (CDT). In both tests, we observed that as the cognitive task begins [HbO2] and [HbT] increase and [HbR] decreases, after a few seconds delay. Furthermore, at the end of the tasks as subjects close their eyes in the second rest state, all three hemodynamic signals converge toward baseline ([HbO2] and [HbT] decrease and [HbR] increases). Also, the difference between hemodynamic signals at the rest state and task state was highly significant (p < 9.95e-11) in all 12 channels and in both cognitive tasks. The results confirm the ability of the designed CW-NIRS system to detect functional brain activities.
Nursing Staff Needs in Providing Palliative Care for Persons With Dementia at Home or in Nursing Homes: A Survey

Field: Nursing (Health Sciences)

Abstract Purpose This study aimed to evaluate what types and forms of support nursing staff need in providing palliative care for persons with dementia. Another aim was to compare the needs of nursing staff with different educational levels and working in home care or in nursing homes. Design A cross‐sectional, descriptive survey design was used. Methods A questionnaire was administered to a convenience sample of Dutch nursing staff working in the home care or nursing home setting. Data were collected from July through October 2018. Quantitative survey data were analyzed using descriptive statistics. Data from two open‐ended survey questions were investigated using content analysis. Findings The sample comprised 416 respondents. Nursing staff with different educational levels and working in different settings indicated largely similar needs. The highest‐ranking needs for support were in dealing with family disagreement in end‐of‐life decision making (58%), dealing with challenging behaviors (41%), and recognizing and managing pain (38%). The highest‐ranking form of support was peer‐to‐peer learning (51%). If respondents would have more time to do their work, devoting personal attention would be a priority. Conclusions Nursing staff with different educational levels and working in home care or in nursing homes endorsed similar needs in providing palliative care for persons with dementia and their loved ones. Clinical Relevance It is critical to understand the specific needs of nursing staff in order to develop tailored strategies. Interventions aimed at increasing the competence of nursing staff in providing palliative care for persons with dementia may target similar areas to support a heterogeneous group of nurses and nurse assistants, working in home care or in a nursing home.
Oral microbiome gene catalog, 95% nucleotide identity

Field: Immunology and Microbiology (Life Sciences)

Non-redundant microbial gene catalog (clustered at 95% sequence identity) from 1,473 oral microbiome shotgun metagenomic samples.
This is one of two raw output files from CD-HIT. It is a fasta file containing the sequences of the consensus genes – the longest genes in each cluster – as well as their ID's. These ID's map back to the second CD-HIT output file, the cluster (extension: .clstr) file.
Modeling rock destruction under blasting of closely spaced borehole charges

Field: Engineering (Physical Sciences)

The design scheme is developed, and simulation of radial cracks growth under blasting of closely spaced borehole charges is carried out. The case studies of confined explosion of two charges located in neighboring boreholes are considered. Blasting of decoupled charges in neighboring boreholes is investigated. The free surface effect on a shape and size of radial cracks under explosion of two closely spaced boreholes rising to the surface is simulated. The blast pattern to gain the maximum size of the destruction zone is determined.
Data from Cancer-Associated SF3B1 Mutations Confer a BRCA-Like Cellular Phenotype and Synthetic Lethality to PARP Inhibitors

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

<div>Abstract<p>Mutations in <i>SF3B1</i> have been identified across several cancer types. This key spliceosome component promotes the efficient mRNA splicing of thousands of genes including those with crucial roles in the cellular response to DNA damage. Here, we demonstrate that depletion of SF3B1 specifically compromises homologous recombination (HR) and is epistatic with loss of BRCA1. More importantly, the most prevalent cancer-associated mutation in SF3B1, K700E, also affects HR efficiency and as a consequence, increases the cellular sensitivity to ionizing radiation and a variety of chemotherapeutic agents, including PARP inhibitors. In addition, the SF3B1 K700E mutation induced unscheduled R-loop formation, replication fork stalling, increased fork degradation, and defective replication fork restart. Taken together, these data suggest that tumor-associated mutations in SF3B1 induce a BRCA-like cellular phenotype that confers synthetic lethality to DNA-damaging agents and PARP inhibitors, which can be exploited therapeutically.</p>Significance:<p>The cancer-associated SF3B1<sup>K700E</sup> mutation induces DNA damage via generation of genotoxic R-loops and stalled replication forks, defective homologous recombination, and increased replication fork degradation, which can be targeted with PARP inhibitors.</p></div>
Analysis of Huntingtin Protein Aggregation Mechanisms and the Development of a Clinically-Derived Human Cell Model of Huntington's Disease

Field: Neuroscience (Life Sciences)

Neurodegenerative diseases are characterized by selective neuronal vulnerability and subsequent degeneration in specific areas of the brain. Huntington’s Disease (HD) is inherited as an autosomal dominant mutation that primarily affects the cells of the striatum and the cerebral cortex, leading to a triad of symptoms that include the progressive loss of motor function, defects in cognitive ability and psychiatric manifestations. HD is caused by a CAG repeat expansion that exceeds 37 repeats in Exon1 of the ​HTT​ gene, manifesting as a pathogenic polyglutamine (polyQ) amino acid tract expansion in the huntingtin protein. HD is a late onset disorder, with disease onset around 40-50 years of age and symptoms that worsen over 10-20 years. Only a few symptomatic treatments are available and there is currently no cure for the disease. Therapeutics to target the huntingtin gene itself have only been in clinical trial in the past 2 years. The length of the expansion has an inverse relationship with the age of disease onset. Most patients that have repeats between 40-45 CAG, however, have varying age of disease onset. Recent genome-wide association studies (GWAS) have implicated DNA handling and repair pathways as modifiers of age of disease onset up to 6 years. Therapeutic approaches to modify and delay onset indefinitely through other genetic targets will require identification of pathological mechanisms that precede disease onset. Several hallmark phenotypes have been identified in cell and animal models, including pathogenic aggregate formation. These models are not reflective of human biology, using excessively large CAG repeats (>100) associated with the more aggressive, juvenile HD, overlooking the importance of GWAS results and the progression of disease with lower pathogenic CAG repeats (40-50 CAG). We have therefore generated novel, clinically-relevant human patient fibroblast cell lines and have characterized several disease phenotypes. My thesis presents a culmination of several projects that focus on disease modelling, primarily outlining phenotypic differences between wildtype and HD cells that will benefit our understanding of disease pathogenesis.
MIROC MIROC6 model output prepared for CMIP6 AerChemMIP histSST

Field: Environmental Science (Physical Sciences)

Coupled Model Intercomparison Project Phase 6 (CMIP6) datasets: These data include all datasets published for 'CMIP6.AerChemMIP.MIROC.MIROC6.histSST' with the full Data Reference Syntax following the template 'mip_era.activity_id.institution_id.source_id.experiment_id.member_id.table_id.variable_id.grid_label.version'. The MIROC6 climate model, released in 2017, includes the following components: aerosol: SPRINTARS6.0, atmos: CCSR AGCM (T85; 256 x 128 longitude/latitude; 81 levels; top level 0.004 hPa), land: MATSIRO6.0, ocean: COCO4.9 (tripolar primarily 1deg; 360 x 256 longitude/latitude; 63 levels; top grid cell 0-2 m), seaIce: COCO4.9. The model was run by the JAMSTEC (Japan Agency for Marine-Earth Science and Technology, Kanagawa 236-0001, Japan), AORI (Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba 277-8564, Japan), NIES (National Institute for Environmental Studies, Ibaraki 305-8506, Japan), and R-CCS (RIKEN Center for Computational Science, Hyogo 650-0047, Japan) (MIROC) in native nominal resolutions: aerosol: 250 km, atmos: 250 km, land: 250 km, ocean: 100 km, seaIce: 100 km. Project: These data have been generated as part of the internationally-coordinated Coupled Model Intercomparison Project Phase 6 (CMIP6; see also GMD Special Issue: http://www.geosci-model-dev.net/special_issue590.html). The simulation data provides a basis for climate research designed to answer fundamental science questions and serves as resource for authors of the Sixth Assessment Report of the Intergovernmental Panel on Climate Change (IPCC-AR6). CMIP6 is a project coordinated by the Working Group on Coupled Modelling (WGCM) as part of the World Climate Research Programme (WCRP). Phase 6 builds on previous phases executed under the leadership of the Program for Climate Model Diagnosis and Intercomparison (PCMDI) and relies on the Earth System Grid Federation (ESGF) and the Centre for Environmental Data Analysis (CEDA) along with numerous related activities for implementation. The original data is hosted and partially replicated on a federated collection of data nodes, and most of the data relied on by the IPCC is being archived for long-term preservation at the IPCC Data Distribution Centre (IPCC DDC) hosted by the German Climate Computing Center (DKRZ). The project includes simulations from about 120 global climate models and around 45 institutions and organizations worldwide. - Project website: https://pcmdi.llnl.gov/CMIP6.
Standardised Outcomes in Nephrology – Glomerular Disease (SONG-GD): developing a core outcome set for trials in glomerular disease

Field: Medicine (Health Sciences)

Glomerular diseases are a major cause of kidney failure worldwide and are responsible for a large burden on patients and health systems. Patients may experience fatigue, reduced mobility, cognitive dysfunction, infertility, bone disease, cancer and impaired psychosocial wellbeing. Trials are the primary means of assessing interventions that may improve health outcomes, however outcomes reported in trials may lack relevance during treatment decision-making or be inconsistently reported which limits the effective comparison of treatments. The aim of the Standardised Outcomes in Nephrology – Glomerular Disease initiative (SONG-GD) was to establish a core outcome set for trials in adults with glomerular disease. The methods included this thesis are: a systematic review to analyse the scope and heterogeneity of reported outcomes for glomerular disease activity; focus groups with nominal group technique to identify and rank patient-important outcomes; an international two-round Delphi survey to develop consensus among diverse stakeholder groups; and two stakeholder workshops to discuss and endorse the proposed core outcomes. SONG-GD established the core outcomes of kidney function, disease activity, death, life participation and cardiovascular disease to be reported in all trials in adults with glomerular disease. Ultimately, this core outcome set will ensure the shared priorities of patients, care partners and health professionals are addressed by trial outcomes and improve the evidence base for shared treatment decision-making.
Access and Intensity of Mechanization: Empirical Evidence of Rice Farmers in Southern Ghana

Field: Agricultural and Biological Sciences (Life Sciences)

ABSTRACT The medium term development plan of Ghana proposed modernization of agriculture to lead the way in transforming the economy. Providing irrigation infrastructure and enhancing farmer access to farm machinery were major interventions proposed. In line with this, the government has been investing in irrigation infrastructure as well as importing farm machinery under various programmes in recent years. This study analyzed access and intensity of mechanization by rice farmers in southern Ghana. The Shai-Osudoku and Ketu North Districts were purposively selected and a total of 360 farmers were randomly sampled from 16 rice growing communities. In general, the results of the descriptive statistics revealed that about 74 % of farmers were still cultivating rice with considerably low level of mechanization. The double hurdle model was employed to estimate the determinants of access to mechanization and the intensity of mechanization. The empirical results of tier one of the double huddle model revealed that size of land, access to credit, availability of farm machinery, expenditure on labour, agrochemical expenditure, the square of age, and gender positively influenced access to mechanization. Seed expenditure, age and district locations negatively influenced access to mechanization. The empirical results of the tier two of the double hurdle model revealed that distance from farm to nearest mechanization centre, rice income, non-farm income and experience were significant variables that positively influenced intensity of mechanization. Land ownership and household size negatively influenced intensity of mechanization. These results have implications for capacity building and government support for rice farmers in southern Ghana.
Complement Factor I Deficiency With Recurrent Aseptic Meningitis

Field: Medicine (Health Sciences)

Patients with deficiency of the complement regulatory protein factor I typically present with systemic pyogenic bacterial infections, including meningitis. We report a novel case with total deficiency of factor I in serum and plasma; the patient experienced nine consecutive episodes of aseptic meningitis within a 2-year period. There was no history of previous bacterial sepsis. Aseptic meningitis recurred despite attempted penicillin prophylaxis. Each episode resolved rapidly without sequelae, with or without antibiotic treatment. Serum complement profiles showed persistently low levels of C3, factor B, and factor H and undetectable factor I protein. Family complement studies could not be performed. Except for a minimally increased titer of antinuclear antibody, no other immunologic abnormality was detected. Results of an oral ibuprofen challenge were negative. We conclude that deficiency of factor I may predispose to aseptic, as well as pyogenic bacterial, meningitis.
Application of Combined PBL Teaching Method in Postgraduate Oral Implantology Teaching

Field: Health Professions (Health Sciences)

Oral implantology is a discipline that combines theory and practice, and its research involves many fields such as ecology, psychology, and genetics. In view of the clinical application of this subject, this article will discuss the practice of combined PBL (problem-based learning) teaching method, introduce the background and significance of this topic in detail, and analyze the current status and development trends of related research at home and abroad. Next, this article combines PBL teaching method to design a model for oral implantology teaching at the postgraduate level, and discovers problems through experimental results and actual situations. The experimental results showed that the average score of the experimental class was 89.3 points, while the average score of the control class was 74.3 points; the participation rate of the experimental class ranged from 93% to 96%, while the participation rate of students in the control group ranged from 82% to 88%. The overall performance of students in the experimental group who have been trained by PBL teaching method is better than that of students who have not been trained, which shows that this method is feasible and can improve the effect of oral implantology teaching.
A Review of the Diagnosis and Management of Acute Flaccid Myelitis in the Emergency Department

Field: Medicine (Health Sciences)

Abstract Since 2014, biennial rises in acute flaccid myelitis (AFM) have brought attention to this rare but debilitating condition. Children with AFM typically present with acute onset, flaccid weakness accompanied by longitudinally extensive gray matter injury demonstrated on magnetic resonance imaging. A clearer understanding of the epidemiology and suspected pathogenesis of AFM may result in increased recognition. The purpose of this review article is to guide emergency physicians in recognizing key clinical features, initiating diagnostic evaluation and providing appropriate interventions for children with suspected AFM.