bluuebunny/crossref_metadata_2025_split huggingface dataset:
Performance of various gridded temperature and precipitation datasets over Northwest Himalayan Region
Authors: Kanda Neha , Negi H S , Rishi Madhuri S , Kumar Anant 
Published: June 2020

Abstract
This study evaluated the performance of 07 gridded datasets viz. Asian Precipitation Highly-resolved Observational Data Integration towards Evaluation of Water Resources (APHRODITE), Climate Research Unit Time-Series (CRU-TS), University of Delaware (UDEL), Tropical rainfall Measurement Mission (TRMM)/ TMPA (TRMM Multi-Satellite Precipitation Analysis), Global Precipitation Climatology Centre (GPCC), Princeton Global Forcings Dataset (PGF), and European Reanalysis Interim (ERA-I) in capturing the amount, seasonality and trend of precipitation over different climatic zones of Northwestern Himalaya (NWH) i.e. Lower Himalaya (LH), Greater Himalaya (GH) and Karakoram Himalaya (KH). A similar comparison was also done for the temperature data but only with 05 datasets, viz. APHRODITE, CRU-TS, PGF, UDEL and ERA-I since TMPA and GPCC are precipitation datasets only. This study is a maiden attempt where in situ observation includes the data from elevations above 5000 m amsl (07 observatories) in NWH (Indian sub-region). Results reveal that for precipitation over NWH; ERA-I, GPCC, and TMPA/TRMM were found to be quite reliable datasets. For temperature, all datasets performed quite well but CRU-TS and ERA-I provided more reliable estimates. The mean absolute error ranged from 13.5 mm/month to 150.7 mm/month for precipitation and 0.75°C/month to 9.9°C/month for temperature. High values of the errors underpin the need for bias correction. On the basis of this analysis, monthly correction factors for wintertime temperature and precipitation have also been suggested for each dataset which when multiplied with corresponding datasets would result in closely approximated values for the area of interest. These results can serve as a guide for bias correction and selection of appropriate gridded datasets for use in studies pertaining to hydrological modeling over NWH.
Optimal modeling pattern of variables selection on analog complex using UVE-PLS regression
Authors: Li Qianqian , Huang Yue , Tian Kuangda 
Published: June 2020

Abstract
This study aimed to determine the composition of chemical complex by partial least square (PLS) regression models combined with uninformative variable elimination (UVE). The near-infrared (NIR) spectra of the forty samples were determined and then UVE was used to compress full NIR spectra from 12011 redundant variables to dozens of variables. Finally, 54, 16, 27, 31 and 42 variables were selected by UVE for 2,2,4-Trimethylpentane, Heptane, Cyclohexane, Ethyl formate and Butyl acetate respectively. Selected variables were used as the inputs of PLS model for quantitative analysis which made the prediction of the model more robust and accurate compared with the conventional PLS.
Evaluation of water repellency in bentonite filled polypropylene composites via physical and mechanical methods
Authors: Yildirimkaraman Oyku , Yildiz Umit Hakan , Akar Alinda Oyku , Tayfun Umit 
Published: June 2020

Abstract
With the advent of polymeric materials having dimensional stability, outdoor applications for polymer composites are increasing expeditiously. The employment of durable material in wet environments is the most effective means of water repellency. Silane modification was applied to bentonite clay for the donation of hydrophobicity on its surface. Surface functionalities of powder surfaces were confirmed by FTIR-ATR spectroscopy and SEM techniques. Polypropylene composities involving pristine and modified bentonite powders were produced in bulk and film forms at three different loading ratios. Water permeability of bulk and film samples was evaluated via water absorption test. In addition to water uptake values, optical microscopy was utilized in order to visualize the structural deterioration of composite samples after water immersion. Mechanical behaviours of composite materials before and after water absorption test were reported in order to analyze the effect of water aging. Based on the findings, in-depth discussions were performed by comparison with basic models postulated regarding migration of water molecules into polymer structure.
Compliance With Standards for STARD 2015 Reporting Recommendations in Pathology
Authors: Hogan Keenan O , Fraga Garth R 
Published: June 2020

Abstract

Objectives
Lack of experimental reproducibility has led to growing interest in guidelines to enhance completeness and transparency in research reporting. This retrospective survey sought to determine compliance with Standards for Reporting of Diagnostic Accuracy Studies (STARD) 2015 statement in the recent pathology scientific literature.

Methods
Two raters independently scored 171 pathology diagnostic accuracy studies for compliance with 34 STARD items and subcomponents. Overall adherence was calculated as a proportion after excluding nonapplicable items.

Results
After excluding nonapplicable items, there was 50% overall adherence to STARD reporting recommendations. In total, 15.44 ± 3.59 items were reported per article (range, 4-28 out of maximum possible of 34). There was substantial heterogeneity in individual item reporting, with greater than 75% reporting in eight of 34 items and less than 25% reporting in 11 of 34 items. Less than 10% of articles reported hypotheses, subgroup analyses for confounding, sample size calculations, subject flow diagrams, study registrations, and links to full study protocols. Significantly more items were reported in articles from journals that endorsed STARD (16.14 vs 14.84, P = .0175).

Conclusions
These findings demonstrate incomplete reporting of essential items in pathology diagnostic accuracy studies. More vigorous enforcement of reporting checklists might improve adherence to minimum reporting standards.
Regular Physical Activity Levels and Incidence of Restrictive Spirometry Pattern: A Longitudinal Analysis of 2 Population-Based Cohorts
Authors: Carsin Anne-Elie , Keidel Dirk , Fuertes Elaine , Imboden Medea , Weyler Joost , Nowak Dennis , Heinrich Joachim , Erquicia Silvia Pascual , Martinez-Moratalla Jesus , Huerta Ismael , Sanchez Jose-Luis , Schaffner Emmanuel , Caviezel Seraina , Beckmeyer-Borowko Anna , Raherison Chantal , Pin Isabelle , Demoly Pascal , Leynaert Bénédicte , Cerveri Isa , Squillacioti Giulia , Accordini Simone , Gislason Thorarinn , Svanes Cecilie , Toren Kjell , Forsberg Bertill , Janson Christer , Jogi Rain , Emtner Margareta , Real Francisco Gómez , Jarvis Debbie , Guerra Stefano , Dharmage Shyamali C , Probst-Hensch Nicole , Garcia-Aymerich Judith 
Published: June 2020

Abstract
We estimated the association between regular physical activity and the incidence of restrictive spirometry pattern. Forced expiratory volume in 1 second (FEV1), forced vital capacity (FVC), and physical activity were assessed in 2 population-based European cohorts (European Community Respiratory Health Survey: n = 2,757, aged 39–67 years; and Swiss Study on Air Pollution and Lung and Heart Diseases in Adults: n = 2,610, aged 36–82 years) first in 2000–2002 and again approximately 10 years later (2010–2013). Subjects with restrictive or obstructive spirometry pattern at baseline were excluded. We assessed the association of being active at baseline (defined as being physically active at least 2–3 times/week for ≥1 hour) with restrictive spirometry pattern at follow-up (defined as a postbronchodilation FEV1/FVC ratio of at least the lower limit of normal and FVC of &lt;80% predicted) using modified Poisson regression, adjusting for relevant confounders. After 10 years of follow-up, 3.3% of participants had developed restrictive spirometry pattern. Being physically active was associated with a lower risk of developing this phenotype (relative risk = 0.76, 95% confidence interval: 0.59, 0.98). This association was stronger among those who were overweight and obese than among those of normal weight (P for interaction = 0.06). In 2 large European studies, adults practicing regular physical activity were at lower risk of developing restrictive spirometry pattern over 10 years.
Improving transitions of care for critically ill adult patients on pulmonary arterial hypertension medications
Authors: Martirosov Amber Lanae , Smith Zachary Ryan , Hencken Laura , MacDonald Nancy C , Griebe Kristin , Fantuz Patricia , Grafton Gillian , Hegab Sara , Ismail Reem , Jackson Barb , Kelly Bryan , Miller Maxwell , Awdish Rana 
Published: June 2020

Abstract

Purpose
The purpose of this report is to describe the activities of critical care and ambulatory care pharmacists in a multidisciplinary transitions-of-care (TOC) service for critically ill patients with pulmonary arterial hypertension (PAH) receiving PAH medications.

Summary
Initiation of medications for treatment of PAH involves complex medication access steps. In the ambulatory care setting, multidisciplinary teams often have a process for completing these steps to ensure access to PAH medications. Patients with PAH are frequently admitted to an intensive care unit (ICU), and their home PAH medications are continued and/or new medications are initiated in the ICU setting. Inpatient multidisciplinary teams are often unfamiliar with the medication access steps unique to PAH medications. The coordination and completion of medication access steps in the inpatient setting is critical to ensure access to medications at discharge and prevent delays in care. A PAH-specific TOC bundle for patients prescribed a PAH medication who are admitted to the ICU was developed by a multidisciplinary team at an academic teaching hospital. The service involves a critical care pharmacist completing a PAH medication history, assessing for PAH medication access barriers, and referring patients to an ambulatory care pharmacist for postdischarge telephone follow-up. In collaboration with the PAH multidisciplinary team, a standardized workflow to be initiated by the critical care pharmacist was developed to streamline completion of PAH medication access steps. Within 3 days of hospital discharge, the ambulatory care pharmacist calls referred patients to ensure access to PAH medications, provide disease state and medication education, and request that the patient schedule a follow-up office visit to take place within 14 days of discharge.

Conclusion
Collaboration by a PAH multidisciplinary team, critical care pharmacist, and ambulatory care pharmacist can improve TOC related to PAH medication access for patients with PAH. The PAH TOC bundle serves as a model that may be transferable to other health centers.
FastMulRFS: fast and accurate species tree estimation under generic gene duplication and loss models
Authors: Molloy Erin K , Warnow Tandy 
Published: June 2020

Abstract

Motivation
Species tree estimation is a basic part of biological research but can be challenging because of gene duplication and loss (GDL), which results in genes that can appear more than once in a given genome. All common approaches in phylogenomic studies either reduce available data or are error-prone, and thus, scalable methods that do not discard data and have high accuracy on large heterogeneous datasets are needed.

Results
We present FastMulRFS, a polynomial-time method for estimating species trees without knowledge of orthology. We prove that FastMulRFS is statistically consistent under a generic model of GDL when adversarial GDL does not occur. Our extensive simulation study shows that FastMulRFS matches the accuracy of MulRF (which tries to solve the same optimization problem) and has better accuracy than prior methods, including ASTRAL-multi (the only method to date that has been proven statistically consistent under GDL), while being much faster than both methods.

Availability and impementation
FastMulRFS is available on Github (https://github.com/ekmolloy/fastmulrfs).

Supplementary information
Supplementary data are available at Bioinformatics online.
Distance indexing and seed clustering in sequence graphs
Authors: Chang Xian , Eizenga Jordan , Novak Adam M , Sirén Jouni , Paten Benedict 
Published: June 2020

Abstract

Motivation
Graph representations of genomes are capable of expressing more genetic variation and can therefore better represent a population than standard linear genomes. However, due to the greater complexity of genome graphs relative to linear genomes, some functions that are trivial on linear genomes become much more difficult in genome graphs. Calculating distance is one such function that is simple in a linear genome but complicated in a graph context. In read mapping algorithms such distance calculations are fundamental to determining if seed alignments could belong to the same mapping.

Results
We have developed an algorithm for quickly calculating the minimum distance between positions on a sequence graph using a minimum distance index. We have also developed an algorithm that uses the distance index to cluster seeds on a graph. We demonstrate that our implementations of these algorithms are efficient and practical to use for a new generation of mapping algorithms based upon genome graphs.

Availability and implementation
Our algorithms have been implemented as part of the vg toolkit and are available at https://github.com/vgteam/vg.
Identifying tumor clones in sparse single-cell mutation data
Authors: Myers Matthew A , Zaccaria Simone , Raphael Benjamin J 
Published: June 2020

Abstract

Motivation
Recent single-cell DNA sequencing technologies enable whole-genome sequencing of hundreds to thousands of individual cells. However, these technologies have ultra-low sequencing coverage (&lt;0.5× per cell) which has limited their use to the analysis of large copy-number aberrations (CNAs) in individual cells. While CNAs are useful markers in cancer studies, single-nucleotide mutations are equally important, both in cancer studies and in other applications. However, ultra-low coverage sequencing yields single-nucleotide mutation data that are too sparse for current single-cell analysis methods.

Results
We introduce SBMClone, a method to infer clusters of cells, or clones, that share groups of somatic single-nucleotide mutations. SBMClone uses a stochastic block model to overcome sparsity in ultra-low coverage single-cell sequencing data, and we show that SBMClone accurately infers the true clonal composition on simulated datasets with coverage at low as 0.2×. We applied SBMClone to single-cell whole-genome sequencing data from two breast cancer patients obtained using two different sequencing technologies. On the first patient, sequenced using the 10X Genomics CNV solution with sequencing coverage ≈0.03×, SBMClone recovers the major clonal composition when incorporating a small amount of additional information. On the second patient, where pre- and post-treatment tumor samples were sequenced using DOP-PCR with sequencing coverage ≈0.5×, SBMClone shows that tumor cells are present in the post-treatment sample, contrary to published analysis of this dataset.

Availability and implementation
SBMClone is available on the GitHub repository https://github.com/raphael-group/SBMClone.

Supplementary information
Supplementary data are available at Bioinformatics online.
Structural white matter connectometry of word production in aphasia: an observational study
Authors: Hula William D , Panesar Sandip , Gravier Michelle L , Yeh Fang-Cheng , Dresang Haley C , Dickey Michael Walsh , Fernandez-Miranda Juan C 
Published: June 2020

Abstract
While current dual-steam neurocognitive models of language function have coalesced around the view that distinct neuroanatomical networks subserve semantic and phonological processing, respectively, the specific white matter components of these networks remain a matter of debate. To inform this debate, we investigated relationships between structural white matter connectivity and word production in a cross-sectional study of 42 participants with aphasia due to unilateral left hemisphere stroke. Specifically, we reconstructed a local connectome matrix for each participant from diffusion spectrum imaging data and regressed these matrices on indices of semantic and phonological ability derived from their responses to a picture-naming test and a computational model of word production. These connectometry analyses indicated that both dorsally located (arcuate fasciculus) and ventrally located (inferior frontal-occipital, uncinate, and middle longitudinal fasciculi) tracts were associated with semantic ability, while associations with phonological ability were more dorsally situated, including the arcuate and middle longitudinal fasciculi. Associations with limbic pathways including the posterior cingulum bundle and the fornix were also found. All analyses controlled for total lesion volume and all results showing positive associations obtained false discovery rates &lt; 0.05. These results challenge dual-stream accounts that deny a role for the arcuate fasciculus in semantic processing, and for ventral-stream pathways in language production. They also illuminate limbic contributions to both semantic and phonological processing for word production.
Aberrant interaction between FUS and SFPQ in neurons in a wide range of FTLD spectrum diseases
Authors: Ishigaki Shinsuke , Riku Yuichi , Fujioka Yusuke , Endo Kuniyuki , Iwade Nobuyuki , Kawai Kaori , Ishibashi Minaka , Yokoi Satoshi , Katsuno Masahisa , Watanabe Hirohisa , Mori Keiko , Akagi Akio , Yokota Osamu , Terada Seishi , Kawakami Ito , Suzuki Naoki , Warita Hitoshi , Aoki Masashi , Yoshida Mari , Sobue Gen 
Published: June 2020

AbstractFused in sarcoma (FUS) is genetically and clinicopathologically linked to frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). We have previously reported that intranuclear interactions of FUS and splicing factor, proline- and glutamine-rich (SFPQ) contribute to neuronal homeostasis. Disruption of the FUS-SFPQ interaction leads to an increase in the ratio of 4-repeat tau (4R-tau)/3-repeat tau (3R-tau), which manifests in FTLD-like phenotypes in mice. Here, we examined FUS-SFPQ interactions in 142 autopsied individuals with FUS-related ALS/FTLD (ALS/FTLD-FUS), TDP-43-related ALS/FTLD (ALS/FTLD-TDP), progressive supranuclear palsy, corticobasal degeneration, Alzheimer’s disease, or Pick’s disease as well as controls. Immunofluorescent imaging showed impaired intranuclear co-localization of FUS and SFPQ in neurons of ALS/FTLD-FUS, ALS/FTLD-TDP, progressive supranuclear palsy and corticobasal degeneration cases, but not in Alzheimer’s disease or Pick’s disease cases. Immunoprecipitation analyses of FUS and SFPQ revealed reduced interactions between the two proteins in ALS/FTLD-TDP and progressive supranuclear palsy cases, but not in those with Alzheimer disease. Furthermore, the ratio of 4R/3R-tau was elevated in cases with ALS/FTLD-TDP and progressive supranuclear palsy, but was largely unaffected in cases with Alzheimer disease. We concluded that impaired interactions between intranuclear FUS and SFPQ and the subsequent increase in the ratio of 4R/3R-tau constitute a common pathogenesis pathway in FTLD spectrum diseases.
Increased Dendritic Orientation Dispersion in the Left Occipital Gyrus is Associated with Atypical Visual Processing in Adults with Autism Spectrum Disorder
Authors: Matsuoka Kiwamu , Makinodan Manabu , Kitamura Soichiro , Takahashi Masato , Yoshikawa Hiroaki , Yasuno Fumihiko , Ishida Rio , Kishimoto Naoko , Yasuda Yuka , Hashimoto Ryota , Taoka Toshiaki , Miyasaka Toshiteru , Kichikawa Kimihiko , Kishimoto Toshifumi 
Published: June 2020

AbstractIn autism spectrum disorder (ASD), the complexity-specific hypothesis explains that atypical visual processing is attributable to selective functional changes in visual pathways. We investigated dendritic microstructures and their associations with functional connectivity (FC). Participants included 28 individuals with ASD and 29 typically developed persons. We explored changes in neurite orientation dispersion and density imaging (NODDI) and brain areas whose FC was significantly correlated with NODDI parameters in the explored regions of interests. Individuals with ASD showed significantly higher orientation dispersion index (ODI) values in the left occipital gyrus (OG) corresponding to the secondary visual cortex (V2). FC values between the left OG and the left middle temporal gyrus (MTG) were significantly negatively correlated with mean ODI values. The mean ODI values in the left OG were significantly positively associated with low registration of the visual quadrants of the Adolescent/Adult Sensory Profile (AASP), resulting in a significant positive correlation with passive behavioral responses of the AASP visual quadrants; additionally, the FC values between the left OG and the left MTG were significantly negatively associated with reciprocal social interaction. Our results suggest that abnormal V2 dendritic arborization is associated with atypical visual processing by altered intermediation in the ventral visual pathway.
Altered atrial cytosolic calcium handling contributes to the development of postoperative atrial fibrillation
Authors: Fakuade Funsho E , Steckmeister Vanessa , Seibertz Fitzwilliam , Gronwald Judith , Kestel Stefanie , Menzel Julia , Pronto Julius Ryan D , Taha Karim , Haghighi Fereshteh , Kensah George , Pearman Charles M , Wiedmann Felix , Teske Arco J , Schmidt Constanze , Dibb Katharine M , El-Essawi Aschraf , Danner Bernhard C , Baraki Hassina , Schwappach Blanche , Kutschka Ingo , Mason Fleur E , Voigt Niels 
Published: June 2020

Abstract

Aims
Atrial fibrillation (AF) is a commonly occurring arrhythmia after cardiac surgery (postoperative AF, poAF) and is associated with poorer outcomes. Considering that reduced atrial contractile function is a predictor of poAF and that Ca2+ plays an important role in both excitation–contraction coupling and atrial arrhythmogenesis, this study aims to test whether alterations of intracellular Ca2+ handling contribute to impaired atrial contractility and to the arrhythmogenic substrate predisposing patients to poAF.

Methods and results
Right atrial appendages were obtained from patients in sinus rhythm undergoing open-heart surgery. Cardiomyocytes were investigated by simultaneous measurement of [Ca2+]i and action potentials (APs, patch-clamp). Patients were followed-up for 6 days to identify those with and without poAF. Speckle-tracking analysis of preoperative echocardiography revealed reduced left atrial contraction strain in poAF patients. At the time of surgery, cellular Ca2+ transients (CaTs) and the sarcoplasmic reticulum (SR) Ca2+ content were smaller in the poAF group. CaT decay was slower in poAF, but the decay of caffeine-induced Ca2+ transients was unaltered, suggesting preserved sodium-calcium exchanger function. In agreement, western blots revealed reduced SERCA2a expression in poAF patients but unaltered phospholamban expression/phosphorylation. Computational modelling indicated that reduced SERCA activity promotes occurrence of CaT and AP alternans. Indeed, alternans of CaT and AP occurred more often and at lower stimulation frequencies in atrial myocytes from poAF patients. Resting membrane potential and AP duration were comparable between both groups at various pacing frequencies (0.25–8 Hz).

Conclusions
Biochemical, functional, and modelling data implicate reduced SERCA-mediated Ca2+ reuptake into the SR as a major contributor to impaired preoperative atrial contractile function and to the pre-existing arrhythmogenic substrate in patients developing poAF.