bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hemostatic Genes Exhibit a High Degree of Allele-Specific Regulation in Liver
Authors: Olsson Lindvall Martina , Hansson Lena , Klasson Sofia , Davila Lopez Marcela , Jern Christina , Stanne Tara M. 
Published: April 2019

Objective Elucidating the genetic basis underlying hepatic hemostatic gene expression variability may contribute to unraveling genetic factors contributing to thrombotic or bleeding disorders. We aimed to identify novel cis-regulatory variants involved in regulating hemostatic genes by analyzing allele-specific expression (ASE) in human liver samples.
Study Design Biopsies of human liver tissue and blood were collected from adults undergoing liver surgery at the Sahlgrenska University Hospital (n = 20). Genomic deoxyribonucleic acid (gDNA) and total ribonucleic acid (RNA) were isolated. A targeted approach was used to enrich and sequence 35 hemostatic genes for single nucleotide polymorphism (SNP) analysis (gDNAseq) and construct individualized genomes for transcript alignment. The allelic ratio of transcripts from targeted RNAseq was determined via ASE analysis. Public expression quantitative trait loci (eQTL) and genome-wide association study (GWAS) data were used to assess novelty and importance of the ASE SNPs (and proxies, r
2 ≥ 0.8) for relevant traits/diseases.
Results Sixty percent of the genes studied showed allelic imbalance across 53 SNPs. Of these, 7 SNPs were previously validated in liver eQTL studies. For 32 with eQTLs in other cell/tissue types, this is the first time genotype-specific expression is demonstrated in liver, and for 14 ASE SNPs, this is the first ever reported genotype–expression association. A total of 29 ASE SNPs were previously associated with the respective plasma protein levels and 17 ASE SNPs to other relevant GWAS traits including venous thromboembolism, coronary artery disease, and stroke.
Conclusion Our study provides a comprehensive ASE analysis of hemostatic genes and insights into the regulation of hemostatic genes in human liver.
Integrating concentrated solar power with seawater desalination technologies: a multi-regional environmental assessment
Authors: Alhaj Mohamed , Al-Ghamdi Sami G 
Published: April 2019

Abstract
Using renewable energy to power seawater desalination technologies can reduce the environmental impacts of a process which is essential for global water security. However, the uneven geospatial distribution of renewable energy resources and regions of water scarcity results in unequal environmental benefits which creates uncertainty for global policy making. Hence, this study explores the relation between renewable energy resources, freshwater demand, and associated environmental impacts of desalination plants driven by renewable energy at a global scale using a comparative life-cycle assessment approach. We focus on an optimized solar-driven thermal desalination plant that we developed which can be used in seawater and brackish water treatment. By examining the life-cycle impact of the proposed plant in seven water-stressed cities, we found that the mean value for CO2 emissions is 4.32 kg CO2 eq./m3 of desalted water which is 47% lower than conventional thermal desalination. There is a variation by as much as 80% and 95% in the climate change and water depletion, categories respectively across the selected cities. The multi-city analysis provides energy and water utilities, CSP project developers, and environmental authorities a global assessment of the environmental impact of solar desalination and sheds light on the correlation between solar intensity and seawater conditions on the overall environmental impact of this technology.
Comparison of resource assessment methods with numerical reservoir model between heat stored and experimental design: case study Ciwidey-Patuha geothermal field
Authors: Ashat Ali , Pratama Heru Berian , Itoi Ryuichi 
Published: April 2019

Abstract
A successful geothermal field size assessment requires integrative data analysis of all aspects to determine the optimum capacity to be installed. Nowadays, numerical simulation becomes a powerful tool in a geothermal resource assessment process. However, this method involves significant uncertainty of subsurface information as an input. Then a study of resource assessment methods, such as heat stored and experimental design, needs inputs coming from the result/output of reservoir numerical. The calculation of both methods based on a range of reservoir parameter values can be carried out using stochastic methods (Monte Carlo Simulation). It applies a probabilistic method of resource assessment to capture uncertainties. A sophisticated numerical reservoir model of Ciwidey-Patuha Geothermal Field, West Java-Indonesia in the natural state condition was used as a case study to determine the generating potential of the reservoir.
Histiocytic Sarcoma Following B-Lymphoblastic Leukemia/Lymphoma
Authors: Geyer Julia T , Yigit Nuri , Miyaguchi Ayako , Cheng Shuhua , Casano Joseph , Mathew Susan , Desai Pinkal , Gergis Usama , Tam Wayne 
Published: April 2019

AbstractObjectivesRare cases of clonally related histiocytic sarcoma (HS) following B-lymphoblastic leukemia/lymphoma (B-ALL/LBL) have been reported to date.MethodsWe present a patient with HS, which appeared as a breast mass 12 months after the initial diagnosis of B-ALL.ResultsBoth HS and the B-ALL shared IGH-MYC and IGK gene rearrangements. Next-generation sequencing and whole-exome sequencing (WES) studies detected 35 common mutations, as well as mutations unique to B-ALL (16) and HS (15), including BRAF D594G. The patient achieved complete remission of B-ALL, but HS failed to respond to many cycles of intensive chemotherapy regimens. A partial response was achieved with sorafenib, a BRAF-targeted therapy.ConclusionsTo our knowledge, this is the first study to demonstrate by WES that clonally related B-ALL and HS arise through divergent evolution from a common precursor. We present our findings together with a discussion of the previously reported cases of HS in patients with B-ALL.
The Impact of 3 Years of Targeted Indoor Residual Spraying With Pirimiphos-Methyl on Malaria Parasite Prevalence in a High-Transmission Area of Northern Zambia
Authors: Hast Marisa A , Chaponda Mike , Muleba Mbanga , Kabuya Jean-Bertin , Lupiya James , Kobayashi Tamaki , Shields Timothy , Lessler Justin , Mulenga Modest , Stevenson Jennifer C , Norris Douglas E , Moss William J 
Published: April 2019

Abstract
Malaria transmission in northern Zambia has increased in the past decade, despite malaria control activities. Evidence-based intervention strategies are needed to effectively reduce malaria transmission. Zambia’s National Malaria Control Centre conducted targeted indoor residual spraying (IRS) in Nchelenge District, Luapula Province, from 2014 to 2016 using the organophosphate insecticide pirimiphos-methyl. An evaluation of the IRS campaign was conducted by the Southern Africa International Centers of Excellence for Malaria Research using actively detected malaria cases in bimonthly household surveys carried out from April 2012 to July 2017. Changes in malaria parasite prevalence after IRS were assessed by season using Poisson regression models with robust standard errors, controlling for clustering of participants in households and demographic, geographical, and climatological covariates. In targeted areas, parasite prevalence declined approximately 25% during the rainy season following IRS with pirimiphos-methyl but did not decline during the dry season or in the overall study area. Within targeted areas, parasite prevalence declined in unsprayed households, suggesting both direct and indirect effects of IRS. The moderate decrease in parasite prevalence within sprayed areas indicates that IRS with pirimiphos-methyl is an effective malaria control measure, but a more comprehensive package of interventions is needed to effectively reduce the malaria burden in this setting.
Interpretation of the Individual Effect Under Treatment Spillover
Authors: Crawford Forrest W , Morozova Olga , Buchanan Ashley L , Spiegelman Donna 
Published: April 2019

Abstract
Some interventions are intended to benefit both individuals and the groups to which they belong. When a treatment given to one person exerts a causal effect on others, the treatment is said to exhibit spillover, dissemination, or interference. However, defining meaningful causal effects under spillover can be challenging. In this commentary, we discuss the meaning of the “individual effect,” a quantity proposed to summarize the effect of treatment on the person who receives it, when spillover may be present.
Predictive Value of Ov16 Antibody Prevalence in Different Subpopulations for Elimination of African Onchocerciasis
Authors: Coffeng Luc E , Stolk Wilma A , Golden Allison , de los Santos Tala , Domingo Gonzalo J , de Vlas Sake J 
Published: April 2019

Abstract
The World Health Organization currently recommends assessing elimination of onchocerciasis by testing whether Ov16 antibody prevalence in children aged 0–9 years is below 0.1%. However, the certainty of evidence for this recommendation is considered to be low. We used the established ONCHOSIM model to investigate the predictive value of different Ov16-antibody prevalence thresholds in various age groups for elimination of onchocerciasis in a variety of endemic settings and for various mass drug administration scenarios. According to our simulations, the predictive value of Ov16 antibody prevalence for elimination depends highly on the precontrol epidemiologic situation, history of mass drug administration, the age group that is sampled, and the chosen Ov16-antibody prevalence threshold. The Ov16 antibody prevalence in children aged 5–14 years performs best in predicting elimination. Appropriate threshold values for this age group start at 2.0% for very highly endemic areas; for lower-endemic areas, even higher threshold values are safe to use. Guidelines can be improved by sampling school-aged children, which also is operationally more feasible than targeting children under age 10 years. The use of higher threshold values allows sampling of substantially fewer children. Further improvement can be achieved by taking a differentiated sampling approach based on precontrol endemicity.
Retired National Football League Players are Not at Greater Risk for Suicide
Authors: Iverson Grant L 
Published: April 2019

Abstract

Objective
Some researchers have claimed that former National Football League (NFL) players are at increased risk for suicide as a clinical feature of chronic traumatic encephalopathy (CTE). This review examines the literature on risk for suicide in former professional football players, and the association between suicide and CTE.

Method
A narrative review of the literature published between 1928 and 2018.

Results
Between 1928 and 2009, suicide was not considered to be a clinical feature of CTE in the literature. The best available evidence from epidemiological studies suggests that former NFL football players are at lesser risk for suicide, not greater risk, compared to men in the general population. However, surveys have revealed that a substantial minority of former NFL players have depression and other mental health problems, chronic pain and opioid use is relatively common, and those with depression and chronic pain also have greater life stress and financial difficulties. That minority would be at increased risk for suicidal thoughts and behaviors.

Conclusions
Researchers and clinicians are encouraged to be cautious and circumspect when considering the clinical presentation of former athletes, and to not assume that depression and suicidality are caused by specific types of neuropathology. This represents a reductionistic and Procrustean view. Some former football players have mental health problems, but it should not be assumed uncritically that the underlying cause is an inexorably progressive neurodegenerative disease. Providing evidence-informed and evidence-supported treatments for depression and suicidality might reduce suffering and improve their functioning.
Clustering and classification methods for single-cell RNA-sequencing data
Authors: Qi Ren , Ma Anjun , Ma Qin , Zou Quan 
Published: April 2019

AbstractAppropriate ways to measure the similarity between single-cell RNA-sequencing (scRNA-seq) data are ubiquitous in bioinformatics, but using single clustering or classification methods to process scRNA-seq data is generally difficult. This has led to the emergence of integrated methods and tools that aim to automatically process specific problems associated with scRNA-seq data. These approaches have attracted a lot of interest in bioinformatics and related fields. In this paper, we systematically review the integrated methods and tools, highlighting the pros and cons of each approach. We not only pay particular attention to clustering and classification methods but also discuss methods that have emerged recently as powerful alternatives, including nonlinear and linear methods and descending dimension methods. Finally, we focus on clustering and classification methods for scRNA-seq data, in particular, integrated methods, and provide a comprehensive description of scRNA-seq data and download URLs.
Prospective Clinical and Molecular Evaluation of Potential Plasmodium ovale curtisi and wallikeri Relapses in a High-transmission Setting
Authors: Groger Mirjam , Veletzky Luzia , Lalremruata Albert , Cattaneo Chiara , Mischlinger Johannes , Manego Zoleko Rella , Kim Johanna , Klicpera Anna , Meyer Elias L , Blessborn Daniel , Winterberg Markus , Adegnika Ayola A , Agnandji Selidji T , Kremsner Peter G , Mordmüller Benjamin , Mombo-Ngoma Ghyslain , Fuehrer Hans-Peter , Ramharter Michael 
Published: April 2019

AbstractBackgroundPlasmodium ovale curtisi and wallikeri are perceived as relapsing malarial parasites. Contrary to Plasmodium vivax, direct evidence for this hypothesis is scarce. The aim of this prospective study was to characterize the reappearance patterns of ovale parasites.MethodsP. ovale spp. infected patients were treated with artemether-lumefantrine and followed biweekly for up to 1 year for the detection of reappearing parasitemia. Molecular analysis of reappearing isolates was performed to identify homologous isolates by genotyping and to define cases of relapse following predefined criteria.ResultsAt inclusion, 26 participants were positive for P. ovale curtisi and/or P. ovale wallikeri. The median duration of follow-up was 35 weeks. Reappearance of the same P. ovale species was observed in 46% of participants; 61% of P. ovale curtisi and 19% of P. ovale wallikeri infection-free intervals were estimated to end with reappearance by week 32. Based on the predefined criteria, 23% of participants were identified with 1 or 2 relapses, all induced by P. ovale curtisi.ConclusionThese findings are in line with the currently accepted relapse theory inasmuch as the reappearance of P. ovale curtisi strains following initial blood clearance was conclusively demonstrated. Interestingly, no relapse of P. ovale wallikeri was observed.
Synergistic effect of immunomodulatoryS100A8/A9and ciprofloxacin againstPseudomonas aeruginosabiofilm in a murine chronic wound model
Authors: Laulund Anne Sofie Boe , Trøstrup Hannah , Lerche Christian Johann , Thomsen Kim , Christophersen Lars , Calum Henrik , Høiby Niels , Moser Claus 
Published: April 2019

ABSTRACTThe majority of chronic wounds are associated with bacterial biofilms recalcitrant to antibiotics and host responses. Immunomodulatory S100A8/A9 is suppressed in Pseudomonas aeruginosa biofilm infected wounds. We aimed at investigating a possible additive effect between S100A8/A9 and ciprofloxacin against biofilms. Materials/methods: Thirty-two mice were injected with alginate-embedded P. aeruginosa following a third-degree burn. The mice were randomized into four groups receiving combination ciprofloxacin and S100A8/A9 or monotherapy ciprofloxacin, S100A8/A9 or a placebo and evaluated by host responses and quantitative bacteriology in wounds. In addition, in vitro checkerboard analysis was performed, with P. aeruginosa and ascending S100A8/A9 and ciprofloxacin concentrations. Results: S100A8/A9 augmented the effect of ciprofloxacin in vivo by lowering the bacterial quantity compared to the placebo arm and the two monointervention groups (P &lt; 0.0001). S100A8 and 100A9 were increased in the double-treated group as compared to the monointervention groups (P = 0.032, P = 0.0023). Tissue inhibitor of metalloproteinases-1 and keratinocyte\chemokine chemoattractant-1 were increased in the double-intervention group compared to the S100A8/A9 group (P = 0.050, P = 0.050). No in vitro synergism was detected. Conclusion: The observed ciprofloxacin-augmenting effect of S100A8/A9 in vivo was not confirmed by checkerboard analysis, indicating dependence on host cells for the S100A8/A9 effect. S100A8/A9 and ciprofloxacin is a promising therapy for optimizing chronic wound treatment.
Health-related Work Limitations Among Older Workers—the Role of Flexible Work Arrangements and Organizational Climate
Authors: Vanajan Anushiya , Bültmann Ute , Henkens Kène 
Published: April 2019

AbstractBackground and ObjectivesGiven their increasing prevalence with age, chronic health conditions (CHCs) are substantially affecting older workers and organizations. An important question is whether and how flexible work arrangements and organizational climates may help to reduce the work limitations experienced by older workers. Grounded on the Job Demand–Resource model, we hypothesize that access to flexible work arrangements (working-time flexibility, workplace flexibility, phased retirement) and supportive organizational climates (healthy ageing climate, psychological safety climate) are vital job resources that are associated with fewer health-related work limitations among older workers experiencing CHCs.Research Design and MethodsMultilevel data were collected among 5,419 older workers (60–65 years) in 624 organizations in the Netherlands. Perceived health-related work limitations of older workers diagnosed with arthritis (N = 2,330), cardiovascular disease (N = 720), and sleep disorders (N = 816) were analyzed.ResultsMultilevel ordered logistic regression analyses revealed that perceived access to flexible working hours and a psychologically safe organizational climate was associated with fewer health-related work limitations among older workers with CHCs.Discussion and ImplicationsFacilitating longer working lives is a key policy challenge within organizations, in particular if older workers are constraint by CHCs. This study shows that offering flexible working hours and ensuring a psychologically safe climate, where older workers with health issues are inclined to share their work needs and preferences, are likely to contribute to healthy ageing in the workplace.
Exploring the determinants of distress health financing in Cambodia
Authors: Ir Por , Jacobs Bart , Asante Augustine D , Liverani Marco , Jan Stephen , Chhim Srean , Wiseman Virginia 
Published: April 2019

Abstract
Borrowing is a common coping strategy for households to meet healthcare costs in countries where social health protection is limited or non-existent. Borrowing with interest, hereinafter termed distress health financing or distress financing, can push households into heavy indebtedness and exacerbate the financial consequences of healthcare costs. We investigated distress health financing practices and associated factors among Cambodian households, using primary data from a nationally representative household survey of 5000 households. Multivariate logistic regression was used to determine factors associated with distress health financing. Results showed that 28.1% of households consuming healthcare borrowed to pay for that healthcare with 55% of these subjected to distress financing. The median loan was US$125 (US$200 for loans with interest and US$75 for loans without interest). Approximately 50.6% of healthcare-related loans were to pay for the costs of outpatient care in the past month, 45.8% for inpatient care and 3.6% for preventive care in the past 12 months. While the average period to pay off the loan was 8 months, 78% of households were still indebted from loans taken over 12 months before the survey. Distress financing is strongly associated with household poverty—the poorer the household the more likely it is to borrow, fall into debt and unable to pay off the debt—even for members of the health equity funds, a national scheme designed to improve financial access to health services for the poor. Other determinants of distress financing were household size, use of inpatient care and outpatient consultations with private providers or with both private and public providers. In order to ensure effective financial risk protection, Cambodia should establish a more comprehensive and effective social health protection scheme that provides maximum population coverage and prioritizes services for populations at risk of distress financing, especially poorer and larger households.
Toward a clinical text encoder: pretraining for clinical natural language processing with applications to substance misuse
Authors: Dligach Dmitriy , Afshar Majid , Miller Timothy 
Published: April 2019

Abstract

Objective
Our objective is to develop algorithms for encoding clinical text into representations that can be used for a variety of phenotyping tasks.

Materials and Methods
Obtaining large datasets to take advantage of highly expressive deep learning methods is difficult in clinical natural language processing (NLP). We address this difficulty by pretraining a clinical text encoder on billing code data, which is typically available in abundance. We explore several neural encoder architectures and deploy the text representations obtained from these encoders in the context of clinical text classification tasks. While our ultimate goal is learning a universal clinical text encoder, we also experiment with training a phenotype-specific encoder. A universal encoder would be more practical, but a phenotype-specific encoder could perform better for a specific task.

Results
We successfully train several clinical text encoders, establish a new state-of-the-art on comorbidity data, and observe good performance gains on substance misuse data.

Discussion
We find that pretraining using billing codes is a promising research direction. The representations generated by this type of pretraining have universal properties, as they are highly beneficial for many phenotyping tasks. Phenotype-specific pretraining is a viable route for trading the generality of the pretrained encoder for better performance on a specific phenotyping task.

Conclusions
We successfully applied our approach to many phenotyping tasks. We conclude by discussing potential limitations of our approach.