bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predicting mortality in hemodialysis patients using machine learning analysis
Authors: Garcia-Montemayor Victoria , Martin-Malo Alejandro , Barbieri Carlo , Bellocchio Francesco , Soriano Sagrario , Pendon-Ruiz de Mier Victoria , Molina Ignacio R , Aljama Pedro , Rodriguez Mariano 
Published: June 2020

Abstract

Background
Besides the classic logistic regression analysis, non-parametric methods based on machine learning techniques such as random forest are presently used to generate predictive models. The aim of this study was to evaluate random forest mortality prediction models in haemodialysis patients.

Methods
Data were acquired from incident haemodialysis patients between 1995 and 2015. Prediction of mortality at 6 months, 1 year and 2 years of haemodialysis was calculated using random forest and the accuracy was compared with logistic regression. Baseline data were constructed with the information obtained during the initial period of regular haemodialysis. Aiming to increase accuracy concerning baseline information of each patient, the period of time used to collect data was set at 30, 60 and 90 days after the first haemodialysis session.

Results
There were 1571 incident haemodialysis patients included. The mean age was 62.3 years and the average Charlson comorbidity index was 5.99. The mortality prediction models obtained by random forest appear to be adequate in terms of accuracy [area under the curve (AUC) 0.68–0.73] and superior to logistic regression models (ΔAUC 0.007–0.046). Results indicate that both random forest and logistic regression develop mortality prediction models using different variables.

Conclusions
Random forest is an adequate method, and superior to logistic regression, to generate mortality prediction models in haemodialysis patients.
Genome-wide study on the polysomic genetic factors conferring plasticity of flower sexuality in hexaploid persimmon
Authors: Masuda Kanae , Yamamoto Eiji , Shirasawa Kenta , Onoue Noriyuki , Kono Atsushi , Ushijima Koichiro , Kubo Yasutaka , Tao Ryutaro , Henry Isabelle M , Akagi Takashi 
Published: June 2020

AbstractSexuality is one of the fundamental mechanisms that work towards maintaining genetic diversity within a species. In diploid persimmons (Diospyros spp.), separated sexuality, the presence of separate male and female individuals (dioecy), is controlled by the Y chromosome-encoded small-RNA gene, OGI. On the other hand, sexuality in hexaploid Oriental persimmon (Diospyros kaki) is more plastic, with OGI-bearing genetically male individuals, able to produce both male and female flowers (monoecy). This is thought to be linked to the partial inactivation of OGI by a retrotransposon insertion, resulting in DNA methylation of the OGI promoter region. To identify the genetic factors regulating branch sexual conversion, genome-wide correlation/association analyses were conducted using ddRAD-Seq data from an F1 segregating population, and using both quantitative and diploidized genotypes, respectively. We found that allelic ratio at the Y-chromosomal region, including OGI, was correlated with male conversion based on quantitative genotypes, suggesting that OGI can be activated in cis in a dosage-dependent manner. Genome-wide association analysis based on diploidized genotypes, normalized for the effect of OGI allele dosage, detected three fundamental loci associated with male conversion. These loci underlie candidate genes, which could potentially act epigenetically for the activation of OGI expression.
Comparative Analysis of Genomic Repeat Content in Gomphocerine Grasshoppers Reveals Expansion of Satellite DNA and Helitrons in Species with Unusually Large Genomes
Authors: Shah Abhijeet , Hoffman Joseph I , Schielzeth Holger 
Published: June 2020

AbstractEukaryotic organisms vary widely in genome size and much of this variation can be explained by differences in the abundance of repetitive elements. However, the phylogenetic distributions and turnover rates of repetitive elements are largely unknown, particularly for species with large genomes. We therefore used de novo repeat identification based on low coverage whole-genome sequencing to characterize the repeatomes of six species of gomphocerine grasshoppers, an insect clade characterized by unusually large and variable genome sizes. Genome sizes of the six species ranged from 8.4 to 14.0 pg DNA per haploid genome and thus include the second largest insect genome documented so far (with the largest being another acridid grasshopper). Estimated repeat content ranged from 79% to 96% and was strongly correlated with genome size. Averaged over species, these grasshopper repeatomes comprised significant amounts of DNA transposons (24%), LINE elements (21%), helitrons (13%), LTR retrotransposons (12%), and satellite DNA (8.5%). The contribution of satellite DNA was particularly variable (ranging from &lt;1% to 33%) as was the contribution of helitrons (ranging from 7% to 20%). The age distribution of divergence within clusters was unimodal with peaks ∼4–6%. The phylogenetic distribution of repetitive elements was suggestive of an expansion of satellite DNA in the lineages leading to the two species with the largest genomes. Although speculative at this stage, we suggest that the expansion of satellite DNA could be secondary and might possibly have been favored by selection as a means of stabilizing greatly expanded genomes.
Genomic Signatures of Local Adaptation in Clam Shrimp (Eulimnadia texana) from Natural Vernal Pools
Authors: Baldwin-Brown James G , Long Anthony D 
Published: June 2020

AbstractVernal pools are unique in their isolation and the strong selection acting on their resident species. Vernal pool clam shrimp (Eulimnadia texana) are a promising model due to ease of culturing, short generation time, small genomes, and obligate desiccated diapaused eggs. Clam shrimp are also androdioecious (sexes include males and hermaphrodites), and here we use population-scaled recombination rates to support the hypothesis that the heterogametic sex is recombination free in these shrimp. We collected short-read sequence data from pooled samples from different vernal pools to gain insights into local adaptation. We identify genomic regions in which some populations have allele frequencies that differ significantly from the metapopulation. BayPass (Gautier M. 2015. Genome-wide scan for adaptive divergence and association with population-specific covariates. Genetics 201(4):1555–1579.) detected 19 such genomic regions showing an excess of population subdivision. These regions on average are 550 bp in size and had 2.5 genes within 5 kb of them. Genes located near these regions are involved in Malpighian tubule function and osmoregulation, an essential function in vernal pools. It is likely that salinity profiles vary between pools and over time, and variants at these genes are adapted to local salinity conditions.
Rampant Nuclear Transfer and Substitutions of Plastid Genes in Passiflora
Authors: Shrestha Bikash , Gilbert Lawrence E , Ruhlman Tracey A , Jansen Robert K 
Published: June 2020

Abstract
Gene losses in plastid genomes (plastomes) are often accompanied by functional transfer to the nucleus or substitution of an alternative nuclear-encoded gene. Despite the highly conserved gene content in plastomes of photosynthetic land plants, recent gene loss events have been documented in several disparate angiosperm clades. Among these lineages, Passiflora lacks several essential ribosomal genes, rps7, rps16, rpl20, rpl22, and rpl32, the two largest plastid genes, ycf1 and ycf2, and has a highly divergent rpoA. Comparative transcriptome analyses were performed to determine the fate of the missing genes in Passiflora. Putative functional transfers of rps7, rpl22, and rpl32 to nucleus were detected, with the nuclear transfer of rps7, representing a novel event in angiosperms. Plastid-encoded rps7 was transferred into the intron of a nuclear-encoded plastid-targeted thioredoxin m-type gene, acquiring its plastid transit peptide (TP). Plastid rpl20 likely experienced a novel substitution by a duplicated, nuclear-encoded mitochondrial-targeted rpl20 that has a similar gene structure. Additionally, among rosids, evidence for a third independent transfer of rpl22 in Passiflora was detected that gained a TP from a nuclear gene containing an organelle RNA recognition motif. Nuclear transcripts representing rpoA, ycf1, and ycf2 were not detected. Further analyses suggest that the divergent rpoA remains functional and that the gene is under positive or purifying selection in different clades. Comparative analyses indicate that alternative translocon and motor protein complexes may have substituted for the loss of ycf1 and ycf2 in Passiflora.
Metagenomic analysis of planktonic riverine microbial consortia using nanopore sequencing reveals insight into river microbe taxonomy and function
Authors: Reddington Kate , Eccles David , O'Grady Justin , Drown Devin M , Hansen Lars Hestbjerg , Nielsen Tue Kjærgaard , Ducluzeau Anne-Lise , Leggett Richard M , Heavens Darren , Peel Ned , Snutch Terrance P , Bayega Anthony , Oikonomopoulos Spyridon , Ragoussis Jiannis , Barry Thomas , van der Helm Eric , Jolic Dino , Richardson Hollian , Jansen Hans , Tyson John R , Jain Miten , Brown Bonnie L 
Published: June 2020

Abstract

Background
Riverine ecosystems are biogeochemical powerhouses driven largely by microbial communities that inhabit water columns and sediments. Because rivers are used extensively for anthropogenic purposes (drinking water, recreation, agriculture, and industry), it is essential to understand how these activities affect the composition of river microbial consortia. Recent studies have shown that river metagenomes vary considerably, suggesting that microbial community data should be included in broad-scale river ecosystem models. But such ecogenomic studies have not been applied on a broad “aquascape” scale, and few if any have applied the newest nanopore technology.

Results
We investigated the metagenomes of 11 rivers across 3 continents using MinION nanopore sequencing, a portable platform that could be useful for future global river monitoring. Up to 10 Gb of data per run were generated with average read lengths of 3.4 kb. Diversity and diagnosis of river function potential was accomplished with 0.5–1.0 ⋅ 106 long reads. Our observations for 7 of the 11 rivers conformed to other river-omic findings, and we exposed previously unrecognized microbial biodiversity in the other 4 rivers.

Conclusions
Deeper understanding that emerged is that river microbial consortia and the ecological functions they fulfil did not align with geographic location but instead implicated ecological responses of microbes to urban and other anthropogenic effects, and that changes in taxa manifested over a very short geographic space.
Trans-NanoSim characterizes and simulates nanopore RNA-sequencing data
Authors: Hafezqorani Saber , Yang Chen , Lo Theodora , Nip Ka Ming , Warren René L , Birol Inanc 
Published: June 2020

Abstract

Background
Compared with second-generation sequencing technologies, third-generation single-molecule RNA sequencing has unprecedented advantages; the long reads it generates facilitate isoform-level transcript characterization. In particular, the Oxford Nanopore Technology sequencing platforms have become more popular in recent years owing to their relatively high affordability and portability compared with other third-generation sequencing technologies. To aid the development of analytical tools that leverage the power of this technology, simulated data provide a cost-effective solution with ground truth. However, a nanopore sequence simulator targeting transcriptomic data is not available yet.

Findings
We introduce Trans-NanoSim, a tool that simulates reads with technical and transcriptome-specific features learnt from nanopore RNA-sequncing data. We comprehensively benchmarked Trans-NanoSim on direct RNA and complementary DNA datasets describing human and mouse transcriptomes. Through comparison against other nanopore read simulators, we show the unique advantage and robustness of Trans-NanoSim in capturing the characteristics of nanopore complementary DNA and direct RNA reads.

Conclusions
As a cost-effective alternative to sequencing real transcriptomes, Trans-NanoSim will facilitate the rapid development of analytical tools for nanopore RNA-sequencing data. Trans-NanoSim and its pre-trained models are freely accessible at https://github.com/bcgsc/NanoSim.
Measurement error as an explanation for the alcohol harm paradox: analysis of eight cohort studies
Authors: Peña Sebastián , Mäkelä Pia , Härkänen Tommi , Heliövaara Markku , Gunnar Teemu , Männistö Satu , Laatikainen Tiina , Vartiainen Erkki , Koskinen Seppo 
Published: June 2020

Abstract

Background
Despite reporting lower levels of alcohol consumption, people with lower socio-economic status (SES) experience greater alcohol-related harm. Whether differential biases in the measurement of alcohol use could explain this apparent paradox is unknown. Using alcohol biomarkers to account for measurement error, we examined whether differential exposure to alcohol could explain the socio-economic differences in alcohol mortality.

Methods
Participants from eight representative health surveys (n = 52 164, mean age 47.7 years) were linked to mortality data and followed up until December 2016. The primary outcome was alcohol-attributable mortality. We used income and education as proxies for SES. Exposures include self-reported alcohol use and four alcohol biomarkers [serum gamma-glutamyl transferase (available in all surveys), carbohydrate-deficient transferrin, alanine aminotransferase and aspartate aminotransferase (available in subsamples)]. We used shared frailty Cox proportional hazards to account for survey heterogeneity.

Results
During a mean follow-up of 20.3 years, totalling 1 056 844 person-years, there were 828 alcohol-attributable deaths. Lower SES was associated with higher alcohol mortality despite reporting lower alcohol use. Alcohol biomarkers were associated with alcohol mortality and improved the predictive ability when used in conjunction with self-reported alcohol use. Alcohol biomarkers explained a very small fraction of the socio-economic differences in alcohol mortality, since hazard ratios either slightly attenuated (percent attenuation range 1.0–12.1%) or increased.

Conclusions
Using alcohol biomarkers in addition to self-reported alcohol use did not explain the socio-economic differences in alcohol mortality. Differential bias in the measurement of alcohol use is not a likely explanation for the alcohol-harm paradox.
Combining the Runge Approximation and the Whitney Embedding Theorem in Hybrid Imaging
Authors: Alberti Giovanni S , Capdeboscq Yves 
Published: June 2020

Abstract
This paper addresses enforcing non-vanishing constraints for solutions to a 2nd-order elliptic partial differential equation by appropriate choices of boundary conditions. We show that, in dimension $d\geq 2$, under suitable regularity assumptions, the family of $2d$ solutions such that their Jacobian has maximal rank in the domain is both open and dense. The case of less regular coefficients is also addressed, together with other constraints, which are relevant for applications to recent hybrid imaging modalities. Our approach is based on the combination of the Runge approximation property and the Whitney projection argument [ 44]. The method is very general and can be used in other settings.
Envisioning an artificial intelligence documentation assistant for future primary care consultations: A co-design study with general practitioners
Authors: Kocaballi A Baki , Ijaz Kiran , Laranjo Liliana , Quiroz Juan C , Rezazadegan Dana , Tong Huong Ly , Willcock Simon , Berkovsky Shlomo , Coiera Enrico 
Published: June 2020

Abstract

Objective
The study sought to understand the potential roles of a future artificial intelligence (AI) documentation assistant in primary care consultations and to identify implications for doctors, patients, healthcare system, and technology design from the perspective of general practitioners.

Materials and Methods
Co-design workshops with general practitioners were conducted. The workshops focused on (1) understanding the current consultation context and identifying existing problems, (2) ideating future solutions to these problems, and (3) discussing future roles for AI in primary care. The workshop activities included affinity diagramming, brainwriting, and video prototyping methods. The workshops were audio-recorded and transcribed verbatim. Inductive thematic analysis of the transcripts of conversations was performed.

Results
Two researchers facilitated 3 co-design workshops with 16 general practitioners. Three main themes emerged: professional autonomy, human-AI collaboration, and new models of care. Major implications identified within these themes included (1) concerns with medico-legal aspects arising from constant recording and accessibility of full consultation records, (2) future consultations taking place out of the exam rooms in a distributed system involving empowered patients, (3) human conversation and empathy remaining the core tasks of doctors in any future AI-enabled consultations, and (4) questioning the current focus of AI initiatives on improved efficiency as opposed to patient care.

Conclusions
AI documentation assistants will likely to be integral to the future primary care consultations. However, these technologies will still need to be supervised by a human until strong evidence for reliable autonomous performance is available. Therefore, different human-AI collaboration models will need to be designed and evaluated to ensure patient safety, quality of care, doctor safety, and doctor autonomy.
Estimation of lifetime cumulative mortality risk of lung cancer by smoking status in Japan
Authors: Hori Megumi , Saito Eiko , Katanoda Kota , Tsugane Shoichiro 
Published: June 2020

Abstract
The main objective of this study was to estimate the cumulative mortality risk for lung cancer according to smoking status and exposure to secondhand smoke (SHS) in Japan. We applied a life-table method to estimate the cumulative risk. Estimated lifetime cumulative risk for 20-year-old non-smokers, former, and current smokers was 3.2%, 7.6%, and 14.9% for men and 1.9%, 5.6%, and 7.2% for women, respectively. For males, the estimated risk was 3.2% for non-smokers not exposed to SHS and 4.1% for non-smokers exposed to SHS. For females, the estimated risk was 1.9% for non-smokers not exposed to SHS and 2.4% for non-smokers exposed to SHS. Lifetime cumulative mortality risk differed greatly according to smoking status. Moreover, SHS exposure resulted in observable differences in lifetime mortality risk. This study may be useful for the development of tailored prevention programs.
A Collaborative Way of Knowing: Bridging Computational Communication Research and Grounded Theory Ethnography
Authors: Ophir Yotam , Walter Dror , Marchant Eleanor R 
Published: June 2020

Abstract
One of the great strengths of the field of communication is its interdisciplinarity. Yet this strength brings challenges, including rifts between diverse subfields. In this study, we illustrate the rich potential of collaborations across subfields. Specifically, we argue that due to often-overlooked epistemological similarities, unsupervised machine learning and grounded theory ethnography subfields are well-suited for an especially enriching collaboration. To demonstrate, a team of computational and ethnographic researchers together applied the analysis of topic model networks approach to ethnographic field notes. We illustrate how the inclusion of the ethnographer in the modeling stages, and of the computational researchers in the analysis stages, led to mutual reflexivity affecting every stage of the study, enabling profound reflections on the technical, conceptual, and theoretical pillars of both subfields. We conclude by discussing the potential future of such collaborative ways of knowing to open doors for cutting-edge interdisciplinary research for the new information era.
A gastric duplication cyst incidentally discovered during an obesity surgery for a 55-year-old female: a rare case report from Syria
Authors: Mansour Marah , Souliman Ola , Ismail Sawsan , Alsuliman Tamim , Souleiman Fadi 
Published: June 2020

Abstract
A gastric duplication cyst (GDC) is an uncommon gastrointestinal (GI) tract anomaly in adults. Nonspecific symptoms make it difficult to diagnose, while radiological examination might be helpful. However, the final diagnosis is made after eradication and histopathological study. Herein we report a case of an asymptomatic, incidentally diagnosed gastric duplication cyst discovered during laparoscopic sleeve gastrectomy in a 55-year-old female.
Abiotic stress-mediated modulation of the chromatin landscape in Arabidopsis thaliana
Authors: Raxwal Vivek Kumar , Ghosh Sourav , Singh Somya , Katiyar-Agarwal Surekha , Goel Shailendra , Jagannath Arun , Kumar Amar , Scaria Vinod , Agarwal Manu 
Published: June 2020

AbstractLimited information is available on abiotic stress-mediated alterations of chromatin conformation influencing gene expression in plants. In order to characterize the effect of abiotic stresses on changes in chromatin conformation, we employed FAIRE-seq (formaldehyde-assisted isolation of regulatory element sequencing) and DNase-seq to isolate accessible regions of chromatin from Arabidopsis thaliana seedlings exposed to either heat, cold, salt, or drought stress. Approximately 25% of regions in the Arabidopsis genome were captured as open chromatin, the majority of which included promoters and exons. A large proportion of chromatin regions apparently did not change their conformation in response to any of the four stresses. Digital footprints present within these regions had differential enrichment of motifs for binding of 43 different transcription factors. Further, in contrast to drought and salt stress, both high and low temperature treatments resulted in increased accessibility of the chromatin. Also, pseudogenes attained increased chromatin accessibility in response to cold and drought stresses. The highly accessible and inaccessible chromatin regions of seedlings exposed to drought stress correlated with the Ser/Thr protein kinases (MLK1 and MLK2)-mediated reduction and increase in H3 phosphorylation (H3T3Ph), respectively. The presented results provide a deeper understanding of abiotic stress-mediated chromatin modulation in plants.