bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Long-Term Study of Application of Joshi's External Stabilizing System in Displaced Intra-articular Distal End Radius Fractures
Authors: Shukla Rajeev , Champawat Vishal , Jain Ravi 
Published: August 2018

Background Fractures of the distal end radius are a common upper extremity fracture. Intra-articular distal end radius fractures are recognized as very complex injuries with a variable prognosis. The aim of the study was to assess the long-term functional outcome of patients treated with Joshi's external stabilizing system (JESS) for displaced intra-articular distal end radius fractures.
Materials and Methods A total of 170 patients with intra-articular distal end radius fracture were treated with JESS from 2014 to 2017. The patients were followed up at 2, 6 weeks, 6 months, 1, and 2 years (final) after the surgery. The assessment of pain, range of motion, grip strength, and satisfaction were assessed at 6 months, 1, and 2 years (final) follow-up and scored according to modified Mayo wrist scoring system.
Results The good and/or excellent results were found in 82.2% of cases. We observed that patients with age less than 50 years had greater prognosis as compared with patients with more than 50 years of age. Final outcome was also found better in males as compared with females at 6 months, 1, and 2 years postoperatively.
Conclusion JESS is an effective treatment technique for intra-articular distal end radius fractures in our community. On long-term follow-up of the patients treated with JESS for intra-articular distal end radius fractures, the functional and radiological outcomes were good with low complication rate.
The conceptual structure of face impressions
Authors: Stolier Ryan M. , Hehman Eric , Keller Matthias D. , Walker Mirella , Freeman Jonathan B. 
Published: August 2018

Significance
Current theory of face-based trait impressions focuses on their foundation in facial morphology, from which emerges a correlation structure of face impressions due to shared feature dependence, “face trait space.” Here, we proposed that perceivers’ lay conceptual beliefs about how personality traits correlate structure their face impressions. We demonstrate that “conceptual trait space” explains a substantial portion of variance in face trait space. Further, we find that perceivers who believe any set of personality traits (e.g., trustworthiness, intelligence) is more correlated in others use more similar facial features when making impressions of those traits. These findings suggest lay conceptual beliefs about personality play a crucial role in face-based trait impressions and may underlie both their similarities and differences across perceivers.
Simultaneous improvements of strength and toughness in topologically interlocked ceramics
Authors: Mirkhalaf Mohammad , Zhou Tao , Barthelat Francois 
Published: August 2018

Significance
Topologically interlocked materials (TIMs) use frictional sliding to generate large deformations and build toughness in otherwise all brittle components. TIMs can be up to 10 times more impact resistant than their monolithic form, but this improvement usually comes at the expense of static strength. Here we report a TIM design based on octahedral blocks which is not only much tougher (50×) than monolithic plates of the same material, but also stronger (1.2×). With no evidence of upper bounds for strength and toughness, TIMs have a tremendous potential as high-performance structural materials. Based on our experiments we propose a nondimensional “interlocking parameter” which could guide the exploration of new TIM designs and other new architectured systems.
EstimatingEx AnteCost Functions for Stochastic Technologies
Authors: Chambers Robert G. , Serra Teresa 
Published: August 2018

AbstractThis paper revisits the problem of estimatingex antecost functions previously studied by Pope and Just in 1996, as well as Moschini in 2001. Anex antecost function that generalizes theirex antecost functions is introduced, and an econometric procedure for estimating a flexible approximation to it is developed. That generalized cost function is economically relevant not only for the Pope and Just 1996 choice setting, but for general producer risk preferences, general stochastic technologies, and general forms of price uncertainty. An econometric strategy for estimating the resulting cost structure that adapts Moschini's 2001 “full‐information” approach is developed, followed by an econometric application to U.S. agriculture.
Phylo-PFP: improved automated protein function prediction using phylogenetic distance of distantly related sequences
Authors: Jain Aashish , Kihara Daisuke 
Published: August 2018

Abstract

Motivation
Function annotation of proteins is fundamental in contemporary biology across fields including genomics, molecular biology, biochemistry, systems biology and bioinformatics. Function prediction is indispensable in providing clues for interpreting omics-scale data as well as in assisting biologists to build hypotheses for designing experiments. As sequencing genomes is now routine due to the rapid advancement of sequencing technologies, computational protein function prediction methods have become increasingly important. A conventional method of annotating a protein sequence is to transfer functions from top hits of a homology search; however, this approach has substantial short comings including a low coverage in genome annotation.

Results
Here we have developed Phylo-PFP, a new sequence-based protein function prediction method, which mines functional information from a broad range of similar sequences, including those with a low sequence similarity identified by a PSI-BLAST search. To evaluate functional similarity between identified sequences and the query protein more accurately, Phylo-PFP reranks retrieved sequences by considering their phylogenetic distance. Compared to the Phylo-PFP’s predecessor, PFP, which was among the top ranked methods in the second round of the Critical Assessment of Functional Annotation (CAFA2), Phylo-PFP demonstrated substantial improvement in prediction accuracy. Phylo-PFP was further shown to outperform prediction programs to date that were ranked top in CAFA2.

Availability and implementation
Phylo-PFP web server is available for at http://kiharalab.org/phylo_pfp.php.

Supplementary information
Supplementary data are available at Bioinformatics online.
Efficient computation of the kinship coefficients
Authors: Kirkpatrick Brent , Ge Shufei , Wang Liangliang 
Published: August 2018

Abstract

Motivation
For families, kinship coefficients are quantifications of the amount of genetic sharing between a pair of individuals. These coefficients are critical for understanding the breeding habits and genetic diversity of diploid populations. Historically, computations of the inbreeding coefficient were used to prohibit inbred marriages and prohibit breeding of some pairs of pedigree animals. Such prohibitions foster genetic diversity and help prevent recessive Mendelian disease at a population level.

Results
This paper gives the fastest known algorithms for computing the kinship coefficient of a set of individuals with a known pedigree, especially for large pedigrees. These algorithms outperform existing methods. In addition, the algorithms given here consider the possibility that the founders of the known pedigree may themselves be inbred and compute the appropriate inbreeding-adjusted kinship coefficients, which has not been addressed in literature. The exact kinship algorithm has running-time O(n2) for an n-individual pedigree. The recursive-cut exact kinship algorithm has running time O(s2m) where s is the number of individuals in the largest segment of the pedigree and m is the number of cuts. The approximate algorithm has running-time O(nd) for an n-individual pedigree on which to estimate the kinship coefficients of n individuals of interest from n founder kinship coefficients and d is the number of samples.

Availability and implementation
The above polynomial-time exact algorithm and the linear-time approximation algorithms are implemented as PedKin in C++ and are available under the GNU GPL v2.0 open source license. The PedKin source code is available at: http://www.intrepidnetcomputing.com/research/code/.
Haplotype matching in large cohorts using the Li and Stephens model
Authors: Lunter Gerton 
Published: August 2018

Abstract

Motivation
The Li and Stephens model, which approximates the coalescent describing the pattern of variation in a population, underpins a range of key tools and results in genetics. Although highly efficient compared to the coalescent, standard implementations of this model still cannot deal with the very large reference cohorts that are starting to become available, and practical implementations use heuristics to achieve reasonable runtimes.

Results
Here I describe a new, exact algorithm (‘fastLS’) that implements the Li and Stephens model and achieves runtimes independent of the size of the reference cohort. Key to achieving this runtime is the use of the Burrows-Wheeler transform, allowing the algorithm to efficiently identify partial haplotype matches across a cohort. I show that the proposed data structure is very similar to, and generalizes, Durbin’s positional Burrows-Wheeler transform.
miES: predicting the essentiality of miRNAs with machine learning and sequence features
Authors: Song Fei , Cui Chunmei , Gao Lin , Cui Qinghua 
Published: August 2018

Abstract

Motivation
MicroRNAs (miRNAs) are one class of small noncoding RNA molecules, which regulate gene expression at the post-transcriptional level and play important roles in health and disease. To dissect the critical miRNAs in miRNAome, it is needed to predict the essentiality of miRNAs, however, bioinformatics methods for this purpose are limited.

Results
Here we propose miES, a novel algorithm, for the prioritization of miRNA essentiality. miES implements a machine learning strategy based on learning from positive and unlabeled samples. miES uses sequence features of known essential miRNAs and performs miRNAome-wide searching for new essential miRNAs. miES achieves an AUC of 0.9 for 5-fold cross validation. Moreover, experiments further show that the miES score is significantly correlated with some established biological metrics for miRNA importance, such as miRNA conservation, miRNA disease spectrum width (DSW) and expression level.

Availability and implementation
The R source code is available at the download page of the web server, http://www.cuilab.cn/mies.

Supplementary information
Supplementary data are available at Bioinformatics online.
NCycDB: a curated integrative database for fast and accurate metagenomic profiling of nitrogen cycling genes
Authors: Tu Qichao , Lin Lu , Cheng Lei , Deng Ye , He Zhili 
Published: August 2018

AbstractMotivationThe nitrogen (N) cycle is a collection of important biogeochemical pathways in the Earth ecosystem and has gained extensive foci in ecology and environmental studies. Currently, shotgun metagenome sequencing has been widely applied to explore gene families responsible for N cycle processes. However, there are problems in applying publically available orthology databases to profile N cycle gene families in shotgun metagenomes, such as inefficient database searching, unspecific orthology groups and low coverage of N cycle genes and/or gene (sub)families.ResultsTo solve these issues, this study built a manually curated integrative database (NCycDB) for fast and accurate profiling of N cycle gene (sub)families from shotgun metagenome sequencing data. NCycDB contains a total of 68 gene (sub)families and covers eight N cycle processes with 84 759 and 219 146 representative sequences at 95 and 100% identity cutoffs, respectively. We also identified 1958 homologous orthology groups and included corresponding sequences in the database to avoid false positive assignments due to ‘small database’ issues. We applied NCycDB to characterize N cycle gene (sub)families in 52 shotgun metagenomes from the Global Ocean Sampling expedition. Further analysis showed that the structure and composition of N cycle gene families were most strongly correlated with latitude and temperature. NCycDB is expected to facilitate N cycle studies via shotgun metagenome sequencing approaches in various environments. The framework developed in this study can be served as a good reference to build similar knowledge-based functional gene databases in various processes and pathways.Availability and implementationNCycDB database files are available at https://github.com/qichao1984/NCyc.Supplementary informationSupplementary data are available at Bioinformatics online.
Traitpedia: a collaborative effort to gather species traits
Authors: Mier Pablo , Andrade-Navarro Miguel A 
Published: August 2018

Abstract

Summary
Traitpedia is a collaborative database aimed to collect binary traits in a tabular form for a growing number of species.

Availability and implementation
Traitpedia can be accessed from http://cbdm-01.zdv.uni-mainz.de/~munoz/traitpedia.

Supplementary information
Supplementary data are available at Bioinformatics online.
Early Developmental Trajectories of Functional Connectivity Along the Visual Pathways in Rhesus Monkeys
Authors: Kovacs-Balint Z , Feczko E , Pincus M , Earl E , Miranda-Dominguez O , Howell B , Morin E , Maltbie E , LI L , Steele J , Styner M , Bachevalier J , Fair D , Sanchez M 
Published: August 2018

Abstract
Early social interactions shape the development of social behavior, although the critical periods or the underlying neurodevelopmental processes are not completely understood. Here, we studied the developmental changes in neural pathways underlying visual social engagement in the translational rhesus monkey model. Changes in functional connectivity (FC) along the ventral object and motion pathways and the dorsal attention/visuo-spatial pathways were studied longitudinally using resting-state functional MRI in infant rhesus monkeys, from birth through early weaning (3 months), given the socioemotional changes experienced during this period. Our results revealed that (1) maturation along the visual pathways proceeds in a caudo-rostral progression with primary visual areas (V1–V3) showing strong FC as early as 2 weeks of age, whereas higher-order visual and attentional areas (e.g., MT–AST, LIP–FEF) show weak FC; (2) functional changes were pathway-specific (e.g., robust FC increases detected in the most anterior aspect of the object pathway (TE–AMY), but FC remained weak in the other pathways (e.g., AST–AMY)); (3) FC matures similarly in both right and left hemispheres. Our findings suggest that visual pathways in infant macaques undergo selective remodeling during the first 3 months of life, likely regulated by early social interactions and supporting the transition to independence from the mother.
Sustainability of clinical pathway guided care in cardiac surgery ICU patients; 9-years experience in over 7500 patients
Authors: van der Kolk B M , van den Boogaard M , van der Hoeven J G , Noyez L , Pickkers P 
Published: August 2018

Abstract

Objective
To determine trends over time regarding inclusion of post-operative cardiac surgery intensive care unit (ICU) patients in a clinical pathway (CP), and the association with clinical outcome.

Design
Retrospective cohort study.

Setting
ICU of an academic hospital.

Participants
All cardiac surgery patients operated between 2007 and 2015.

Measures and Results
A total of 7553 patients were operated. Three patient groups were identified: patients treated according to CP (n = 6567), patients excluded from the CP within the first 48 h (n = 633) and patients never included in CP (n = 353). Patients treated according to CP increased significantly over time from 74% to 95% and the median Log EuroSCORE (predicted mortality score) in this group increased significantly over time (P = 0.016). In-hospital length of stay (LOS) decreased in all groups, but significantly in CP group (P < 0.001). Overall, the in-hospital, and 1-year mortality decreased from 1.5 to 1.1% and 3.7 to 2.9%, respectively (both P < 0.05). Patients with a Log EuroSCORE >10 were more likely excluded from CP (P < 0.001), but, if included in CP, these patients had a significantly shorter Intensive Care stay and in-hospital stay compared to excluded patients with a Log EuroSCORE >10 (both P < 0.001).

Conclusions
The use of a CP for all post-operative cardiac surgery patients in the ICU is sustainable. While more complex patients were treated according to the CP, clinical outcome improved in the CP group.
Beyond smartphones and sensors: choosing appropriate statistical methods for the analysis of longitudinal data
Authors: Barnett Ian , Torous John , Staples Patrick , Keshavan Matcheri , Onnela Jukka-Pekka 
Published: August 2018

AbstractObjectivesAs smartphones and sensors become more prominently used in mobile health, the methods used to analyze the resulting data must also be carefully considered. The advantages of smartphone-based studies, including large quantities of temporally dense longitudinally captured data, must be matched with the appropriate statistical methods in order draw valid conclusions. In this paper, we review and provide recommendations in 3 critical domains of analysis for these types of temporally dense longitudinal data and highlight how misleading results can arise from improper use of these methods.Target AudienceClinicians, biostatisticians, and data analysts who have digital phenotyping data or are interested in performing a digital phenotyping study or any other type of longitudinal study with frequent measurements taken over an extended period of time.ScopeWe cover the following topics: 1) statistical models using longitudinal repeated measures, 2) multiple comparisons of correlated tests, and 3) dimension reduction for correlated behavioral covariates. While these 3 classes of methods are frequently used in digital phenotyping data analysis, we demonstrate via actual clinical studies data that they may sometimes not perform as expected when applied to novel digital data.
Wealth in Ex-Combatants: Examining the Resilience of Ex-Command Structures in Postwar Liberia
Authors: Themnér Anders 
Published: August 2018

AbstractRecent research has shown that disarmament, demobilization, and reintegration (DDR) programs often fail to uproot wartime command structures. A key question is why some ex-commanders succeed in retaining control over their ex-fighters, while others are less successful. This study seeks to address this question by comparing four former midlevel commanders (ex-MiLCs) in Liberia and the ex-combatant networks that they head. Contrary to previous assumptions, which have stressed the tendency of ex-fighters to flock around ex-commanders operating in spaces of marginality, I argue that ex-MiLCs employed as government brokers and who funnel patronage from ruling elites to ex-combatants are likely to possess the most durable networks. These findings highlight how ex-military bonds thrive where previous research expects them to be weakest: close to government elites who are often designated as “agents of change” by international peacemakers.
Effects of Menthol Flavor Cigarettes or Total Urinary Menthol on Biomarkers of Nicotine and Carcinogenic Exposure and Behavioral Measures
Authors: Ahijevych Karen , Szalacha Laura A , Tan Alai 
Published: August 2018

AbstractIntroductionThe effects of either menthol flavor cigarettes or total urinary menthol on nicotine dependence, biomarkers of addictive and carcinogenic exposure, and behavioral measures may inform differences and similarities of these two approaches.MethodsStratified recruitment by cigarette (menthol flavor or regular) and race (African American and white) yielded a balanced sample of 136 adult smokers in a 36-hour inpatient protocol. Exposure measures assessed during 24-hour data collection included urinary menthol, total NNAL [4-(methylnitrosamino)-1-(3-pyridyl)-1-butanol], 10 polycyclic aromatic hydrocarbon metabolites, baseline plasma cotinine, plasma nicotine pre- and post-smoking, exhaled carbon monoxide pre- and post-smoking, and cigarette puff volumes. The latter three were measured at four specified timepoints throughout the day.ResultsThere were no significant differences between menthol flavor and regular cigarette smokers in measures of nicotine dependence, biomarkers of addictive and carcinogenic exposures, or behavioral measures. Significant race × cigarette type interaction effects were found for two biomarkers: plasma nicotine and 3-hydroxyphenanthrene. Total urinary menthol was significantly associated with higher levels of nearly all dependent variables including puff volume, exhaled carbon monoxide, plasma nicotine and cotinine, NNAL, and polycyclic aromatic hydrocarbons. The significant effects of total urinary menthol were sustained after adjusting for menthol flavor and regular cigarette type and other covariates (eg, number of cigarettes per day, baseline cotinine, and baseline nicotine).ConclusionsUrinary menthol is an independent predictive biomarker for nicotine dependence, addictive and carcinogenic exposure, and behaviors.ImplicationsComparison of the effects of menthol flavor and total urinary menthol on nicotine dependence, biomarkers of addictive and carcinogenic exposure, and behavioral measures emphasizes the important significant contribution of total urinary menthol concentrations in contrast to no significant associations by dichotomous cigarette type with these biomarkers.
High Prevalence of Late-Stage Disease in Newly Diagnosed Human Immunodeficiency Virus Patients in Sierra Leone
Authors: Yendewa George A , Poveda Eva , Lakoh Sulaiman , Yendewa Sahr A , Jiba Darlinda F , Salgado-Barreira Angel , Sahr Foday , Salata Robert A 
Published: August 2018

Abstract
A high prevalence of late-stage disease (75.4%) and severe immunosuppression (23.3%) was observed in 155 newly diagnosed human immunodeficiency virus patients in Freetown, Sierra Leone during August to November 2017. Within the late-stage diagnosis group, a significantly high proportion of patients reported fever (84.2% vs 65.2%; P = .01), weight loss (82.2% vs 63.5%; P = .01), and malaise (89.7% vs 71.7%; P = .05). Fever was identified as the only independent predictor of late-stage disease in this study.
A Distraught Hero (Chariton 3.5.5–6)
Authors: Hutchinson G. O. 
Published: August 2018

AbstractThe book now sets the Plutarchan passages in a larger context by considering passages from novelists. The passage from Chariton portrays the young hero Chaereas preparing to set sail. The emotional speech and body language of his mother lead to a conflict of feelings, and a brief attempt at suicide. The passage shows rhythm serving Chariton’s version of the pointed style, and enabling small eruptions of ingenuity and extremity—not without some humour. Stylistically and imaginatively, the reader is in a quite different world from that of the Lives.
On Mandatory Criminal Sentences, Legislative Interpretation, and the Prospective Application of the Law: A View from Singapore
Authors: Lau Kwan Ho 
Published: August 2018

Abstract
Can a court find that a criminal sentence is mandatory under the penal legislation but choose, exceptionally, to apply that finding only to future cases? This raises an interesting question on the prospective application of a correct construction of legislation, requiring consideration of difficult issues surrounding not just the temporal application of the law but also the protection of the interests belonging to all citizenry, including convicted persons. Recent decisions in Singapore and elsewhere provide an opening for a more detailed inquiry to be undertaken.
Electromyographic Characterization of Abdominal Wall Trigger Points Developed After Caesarean Section and Response to Local Anaesthesia: An Observational Study
Authors: Poli-Neto O. B. , Campos Martins Chamochumbi C. , Toscano P. , Pitanguy Julio M. , Marques W. , Rosa-e-Silva J. C. , Candido-dos-Reis F. J. , Nogueira A. A. 
Published: August 2018

(Abstracted from BJOG 2018; doi: 10.1111/1471-0528.15204)
Chronic pain is a long-term complication of cesarean delivery. It occurs approximately in 1% to 18% of patients.