bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nurse provision of support to help inpatients quit smoking
Authors: Malone V. , Ezard N. , Hodge S. , Ferguson L. , Schembri A. , Bonevski B. 
Published: December 2016

Issue addressedIdentification of the factors that facilitate nurses to provide smoking cessation advice to hospitalised patients.MethodSix semistructured focus groups with 26 nurses were conducted in June 2015. Participants completed a structured survey to collect patient demographic data and assess attitudes towards their role in addressing smoking cessation among inpatients.ResultsImportant themes that emerged from the qualitative data were: nurses’ negative perceptions of smokers, nurses’ confidence in their knowledge of smoking cessation care and nurses’ uncertainty around whose role it is to provide smoking cessation care.ConclusionNurses require training in order to confidently and competently address smoking among inpatients as part of routine care. Formal ways to document the smoking status of inpatients and the offer of smoking cessation support from a nurse to an inpatient would enhance the communication between nurses around which inpatients had been asked about their smoking status and which had not. For patients who are resistant to conventional cessation strategies, innovative ways are needed to reduce the harm caused to them by tobacco use.So what?Nurses need to be provided with education and training around smoking cessation to increase their confidence and skills to provide smoking cessation care to inpatients.
Congenital myopathy results from misregulation of a muscle Ca2+channel by mutant Stac3
Authors: Linsley Jeremy W. , Hsu I-Uen , Groom Linda , Yarotskyy Viktor , Lavorato Manuela , Horstick Eric J. , Linsley Drew , Wang Wenjia , Franzini-Armstrong Clara , Dirksen Robert T. , Kuwada John Y. 
Published: December 2016

SignificanceSkeletal muscle contractions are regulated by a process called excitation–contraction (EC) coupling, and defects in it are associated with numerous human myopathies. Recently,stac3(SH3 and cysteine-rich domain 3) was identified as a key regulator of EC coupling and aSTAC3mutation as causal for the debilitating Native American myopathy (NAM). We now show that Stac3 controls EC coupling by regulating Ca2+channels in muscles. Both the NAM mutation and a mutation that leads to the loss of Stac3 decrease the amount, organization, stability, and voltage sensitivity of Ca2+channels. Furthermore, we find evidence that the NAM allele ofSTAC3is linked to malignant hyperthermia, a common pharmacogenic disorder. These findings define critical roles for Stac3 in muscle contraction and human disease.
A note on the Erdős-Hajnal property for stable graphs
Authors: Chernikov Artem , Starchenko Sergei 
Published: December 2016

In this note we give a proof of the Erdős–Hajnal conjecture for families of finite (hyper-)graphs without the

m
m

-order property. This theorem is in fact implicitly proved by M. Malliaris and S. Shelah (2014), however we use a new technique of independent interest combining local stability and pseudo-finite model theory.
Planning bioinformatics workflows using an expert system
Authors: Chen Xiaoling , Chang Jeffrey T 
Published: December 2016

Abstract

Motivation
Bioinformatic analyses are becoming formidably more complex due to the increasing number of steps required to process the data, as well as the proliferation of methods that can be used in each step. To alleviate this difficulty, pipelines are commonly employed. However, pipelines are typically implemented to automate a specific analysis, and thus are difficult to use for exploratory analyses requiring systematic changes to the software or parameters used.

Results
To automate the development of pipelines, we have investigated expert systems. We created the Bioinformatics ExperT SYstem (BETSY) that includes a knowledge base where the capabilities of bioinformatics software is explicitly and formally encoded. BETSY is a backwards-chaining rule-based expert system comprised of a data model that can capture the richness of biological data, and an inference engine that reasons on the knowledge base to produce workflows. Currently, the knowledge base is populated with rules to analyze microarray and next generation sequencing data. We evaluated BETSY and found that it could generate workflows that reproduce and go beyond previously published bioinformatics results. Finally, a meta-investigation of the workflows generated from the knowledge base produced a quantitative measure of the technical burden imposed by each step of bioinformatics analyses, revealing the large number of steps devoted to the pre-processing of data. In sum, an expert system approach can facilitate exploratory bioinformatic analysis by automating the development of workflows, a task that requires significant domain expertise.

Availability and Implementation
https://github.com/jefftc/changlab
Introducing COCOS: codon consequence scanner for annotating reading frame changes induced by stop-lost and frame shift variants
Authors: Butkiewicz Mariusz , Haines Jonathan L , Bush William S 
Published: December 2016

Abstract

Summary
Reading frame altering genomic variants can impact gene expression levels and the structure of protein products, thus potentially inducing disease phenotypes. Current annotation approaches report the impact of such variants in the context of altered DNA sequence only; attributes of the resulting transcript, reading frame and translated protein product are not reported. To remedy this shortcoming, we present a new genetic annotation approach termed Codon Consequence Scanner (COCOS). Implemented as an Ensembl variant effect predictor (VEP) plugin, COCOS captures amino acid sequence alterations stemming from variants that produce an altered reading frame, such as stop-lost variants and small insertions and deletions (InDels). To highlight its significance, COCOS was applied to data from the 1000 Genomes Project. Transcripts affected by stop-lost variants introduce a median of 15 amino acids, while InDels have a more extensive impact with a median of 66 amino acids being incorporated. Captured sequence alterations are written out in FASTA format and can be further analyzed for impact on the underlying protein structure.

Availability and Implementation
COCOS is available to all users on github: https://github.com/butkiem/COCOS
An Evidence-Based Algorithm for Early Prognosis of Severe Dengue in the Outpatient Setting
Authors: Nguyen Minh Tuan , Ho Thi Nhan , Nguyen Van Vinh Chau , Nguyen Thanh Hung , Ha Manh Tuan , Ta Van Tram , Nguyen Le Da Ha , Phan Loi , Han Khoi Quang , Duong Thi Hue Kien , Tran Nguyen Bich Chau , Wills Bridget , Wolbers Marcel , Simmons Cameron P. 
Published: December 2016

Abstract

Background.
Early prediction of severe dengue could significantly assist patient triage and case management.

Methods.
We prospectively investigated 7563 children with ≤3 days of fever recruited in the outpatient departments of 6 hospitals in southern Vietnam between 2010 and 2013. The primary endpoint of interest was severe dengue (2009 World Health Organization Guidelines), and predefined risk variables were collected at the time of enrollment to enable prognostic model development.

Results.
The analysis population comprised 7544 patients, of whom 2060 (27.3%) had laboratory-confirmed dengue; nested among these were 117 (1.5%) severe cases. In the multivariate logistic model, a history of vomiting, lower platelet count, elevated aspartate aminotransferase (AST) level, positivity in the nonstructural protein 1 (NS1) rapid test, and viremia magnitude were all independently associated with severe dengue. The final prognostic model (Early Severe Dengue Identifier [ESDI]) included history of vomiting, platelet count, AST level. and NS1 rapid test status.

Conclusions.
The ESDI had acceptable performance features (area under the curve = 0.95, sensitivity 87% (95% confidence interval [CI], 80%–92%), specificity 88% (95% CI, 87%–89%), positive predictive value 10% (95% CI, 9%–12%), and negative predictive value of 99% (95% CI, 98%–100%) in the population of all 7563 enrolled children. A score chart, for routine clinical use, was derived from the prognostic model and could improve triage and management of children presenting with fever in dengue-endemic areas.
Deep learning for pharmacovigilance: recurrent neural network architectures for labeling adverse drug reactions in Twitter posts
Authors: Cocos Anne , Fiks Alexander G , Masino Aaron J 
Published: December 2016

AbstractObjectiveSocial media is an important pharmacovigilance data source for adverse drug reaction (ADR) identification. Human review of social media data is infeasible due to data quantity, thus natural language processing techniques are necessary. Social media includes informal vocabulary and irregular grammar, which challenge natural language processing methods. Our objective is to develop a scalable, deep-learning approach that exceeds state-of-the-art ADR detection performance in social media.Materials and MethodsWe developed a recurrent neural network (RNN) model that labels words in an input sequence with ADR membership tags. The only input features are word-embedding vectors, which can be formed through task-independent pretraining or during ADR detection training.ResultsOur best-performing RNN model used pretrained word embeddings created from a large, non–domain-specific Twitter dataset. It achieved an approximate match F-measure of 0.755 for ADR identification on the dataset, compared to 0.631 for a baseline lexicon system and 0.65 for the state-of-the-art conditional random field model. Feature analysis indicated that semantic information in pretrained word embeddings boosted sensitivity and, combined with contextual awareness captured in the RNN, precision.DiscussionOur model required no task-specific feature engineering, suggesting generalizability to additional sequence-labeling tasks. Learning curve analysis showed that our model reached optimal performance with fewer training examples than the other models.ConclusionsADR detection performance in social media is significantly improved by using a contextually aware model and word embeddings formed from large, unlabeled datasets. The approach reduces manual data-labeling requirements and is scalable to large social media datasets.
Unraveling the conjunction paradox
Authors: Spottswood Emily 
Published: December 2016

The conjunction paradox arises when a claim requires proof of multiple elements and the likelihood of some elements are at least partially independent of the likelihood of others. In that situation, probability theory may dictate that the conjunction of the elements is less likely than their disjunction, implying that a defendant should not be found liable, even though each element is probably true when considered in isolation. Nonetheless, American jury instructions reject this implication, and many scholars of proof have sought to construct normative theories to justify that rejection.
This article collects and critiques two families of arguments about the conjunction paradox. First, I explain why an explanatory conception of proof cannot eliminate the paradox. Second, I show why various mathematical alternatives to standard probability theory are normatively deficient when applied to legal fact-finding. Instead, I suggest that the best way to resolve the paradox is through instructions that encourage juries to make appropriate adjustments for conjunctive and disjunctive likelihoods without having to frame their analyses in mathematical terms.
Can Solar Lanterns Improve Youth Academic Performance? Experimental Evidence from Bangladesh
Authors: Kudo Yuya , Shonchoy Abu S , Takahashi Kazushi 
Published: December 2016

Abstract
We conducted an experimental intervention in unelectrified areas of northern Bangladesh to investigate the effectiveness of solar products in improving children’s educational achievement. We found that treated households substituted solar lanterns for kerosene-based lighting products, helping to decrease total household expenditure. Solar lanterns increased the children’s home-study hours, particularly at night and before exams. The solar lanterns initially led to an increase in school attendance, but this effect diminished over time. However, the increased study hours and initial improvement in school attendance did not translate into improved academic performance. Varying the number of solar products within the treated households did not alter these results. Analyses that exploited the school grade treatment intensity also provided no evidence suggesting that spillover effects explained the “no academic performance effects.” These findings suggest that improving the home-study environment solely through the provision of solar products may have a limited impact on children’s educational achievement.
MACULAR MICROCYSTS IN SCHWARTZ–MATSUO SYNDROME
Authors: Chen Xuejing , Richter Grace M. , Caprioli Joseph , McCannel Tara A. 
Published: December 2016

Purpose:
To describe a case of macular microcysts associated with advanced secondary glaucoma from Schwartz–Matsuo syndrome.

Methods:
Clinical presentation, color fundus photography, optic disk photography, visual fields, and optical coherence tomography are presented.

Results:
A 32-year-old woman presented with advanced, unilateral secondary glaucoma associated with a macula-on rhegmatogenous retinal detachment. She was diagnosed with Schwartz–Matsuo syndrome. Spectral domain optical coherence tomography showed macular microcystic changes in the paracentral retina at the level of the inner nuclear layer.

Conclusion:
Macular microcystic changes in the paracentral inner nuclear layer on spectral domain optical coherence tomography have been described in eyes with optic atrophy associated with a variety of diseases. This is the first described case of macular microcysts associated with advanced secondary glaucoma from Schwartz–Matsuo syndrome and may offer insights into the pathogenesis of these microcysts.
Validating Facial Aesthetic Surgery Results with the FACE-Q
Authors: Kappos Elisabeth A. , Temp Mathias , Schaefer Dirk J. , Haug Martin , Kalbermatten Daniel F. , Toth Bryant A. 
Published: December 2016

Background:
In aesthetic clinical practice, surgical outcome is best measured by patient satisfaction and quality of life. For many years, there has been a lack of validated questionnaires. Recently, the FACE-Q was introduced, and the authors present the largest series of face-lift patients evaluated by the FACE-Q with the longest follow-up to date.

Methods:
Two hundred consecutive patients were identified who underwent high–superficial musculoaponeurotic system face lifts, with or without additional facial rejuvenation procedures, between January of 2005 and January of 2015. Patients were sent eight FACE-Q scales and were asked to answer questions with regard to their satisfaction. Rank analysis of covariance was used to compare different subgroups.

Results:
The response rate was 38 percent. Combination of face lift with other procedures resulted in higher satisfaction than face lift alone (p < 0.05). Patients who underwent lipofilling as part of their face lift showed higher satisfaction than patients without lipofilling in three subscales (p < 0.05).

Conclusions:
Facial rejuvenation surgery, combining a high–superficial musculoaponeurotic system face lift with lipofilling and/or other facial rejuvenation procedures, resulted in a high level of patient satisfaction. The authors recommend the implementation of the FACE-Q by physicians involved in aesthetic facial surgery, to validate their clinical outcomes from a patient’s perspective.
A Temporoparietal Fascia Pocket Method in Elevation of Reconstructed Auricle for Microtia
Authors: Kurabayashi Takashi , Asato Hirotaka , Suzuki Yasutoshi , Kaji Nobuyuki , Mitoma Yoko 
Published: December 2016

Background:
In two-stage procedures for reconstruction of microtia, an axial flap of temporoparietal fascia is widely used to cover the costal cartilage blocks placed behind the framework. Although a temporoparietal fascia flap is undoubtedly reliable, use of the flap is associated with some morbidity and comes at the expense of the option for salvage surgery.

Methods:
The authors devised a simplified procedure for covering the cartilage blocks by creating a pocket in the postauricular temporoparietal fascia. In this procedure, the constructed auricle is elevated from the head superficially to the temporoparietal fascia, and a pocket is created under the temporoparietal fascia and the capsule of the auricle framework. Then, cartilage blocks are inserted into the pocket and fixed. A total of 38 reconstructed ears in 38 patients with microtia ranging in age from 9 to 19 years were elevated using the authors’ method from 2002 to 2014 and followed for at least 5 months. To evaluate the long-term stability of the method, two-way analysis of variance (p < 0.05) was carried out to analyze the effect on the projection angles of the method (an axial temporoparietal fascia flap method versus a temporoparietal fascia pocket method) over long-term follow-up.

Results:
Good projection of the auricles and creation of well-defined temporoauricular sulci were achieved. Furthermore, the sulci had a tendency to hold their steep profile over a long period.

Conclusions:
The temporoparietal fascia pocket method is simple but produces superior results. Moreover, pocket creation is less invasive and has the benefit of sparing temporoparietal fascia flap elevation.

CLINICAL QUESTION/LEVEL OF EVIDENCE:
Therapeutic, IV.
Transcranial stimulation enhances memory-relevant sleep oscillations and their functional coupling in mild cognitive impairment
Authors: Ladenbauer Julia , Ladenbauer Josef , Külzow Nadine , de Boor Rebecca , Avramova Elena , Grittner Ulrike , Flöel Agnes 
Published: December 2016

AbstractAlzheimer’s disease (AD) not only involves loss of memory functions but also prominent deterioration of sleep physiology, already evident in the stage ofmild cognitive impairment(MCI). Cortical slow oscillations (SO, 0.5-1 Hz) and thalamo-cortical spindle activity (12-15 Hz) during sleep, and their temporal coordination, are considered critical for memory formation. We investigated the potential of slow oscillatory transcranial direct current stimulation (so-tDCS), applied during a daytime nap in a sleep state-dependent manner, to modulate these activity patterns and sleep-related memory consolidation in 16 patients with MCI.Stimulation significantly increased overall SO and spindle power, amplified spindle power during SO up-phases, and led to stronger synchronization between SO and spindle power fluctuations in electroencephalographic recordings. Moreover, visual declarative memory was improved by so-tDCS compared to sham stimulation, associated with stronger synchronization. These findings indicate a well-tolerated therapeutic approach for disordered sleep physiology and deficits in memory consolidation in MCI patients.
A SUMO-Ubiquitin Relay Recruits Proteasomes to Chromosome Axes to Regulate Meiotic Recombination
Authors: Rao H.B.D. Prasada , Qiao Huanyu , Bhatt Shubhang K. , Bailey Logan R.J. , Tran Hung D. , Bourne Sarah L. , Qiu Wendy , Deshpande Anusha , Sharma Ajay N. , Beebout Connor J. , Pezza Roberto J. , Hunter Neil 
Published: December 2016

AbstractMeiosis produces haploid gametes through a succession of chromosomal events including pairing, synapsis and recombination. Mechanisms that orchestrate these events remain poorly understood. We found that the SUMO-modification and ubiquitin-proteasomes systems regulate the major events of meiotic prophase in mouse. Interdependent localization of SUMO, ubiquitin and proteasomes along chromosome axes was mediated largely by RNF212 and HEI10, two E3 ligases that are also essential for crossover recombination. RNF212-dependent SUMO conjugation effected a checkpoint-like process that stalls recombination by rendering the turnover of a subset of recombination factors dependent on HEI10-mediated ubiquitylation. We propose that SUMO conjugation establishes a precondition for designating crossover sites via selective protein stabilization. Thus, meiotic chromosome axes are hubs for regulated proteolysis via SUMO-dependent control of the ubiquitin-proteasome system.One Sentence SummaryChromosomal events of meiotic prophase in mouse are regulated by proteasome-dependent protein degradation.
Using Single Nucleotide Variations in Single-Cell RNA-Seq to Identify Subpopulations and Genotype-phenotype Linkage
Authors: Poirion Olivier , Zhu Xun , Ching Travers , Garmire Lana X. 
Published: December 2016

AbstractDespite its popularity, characterization of subpopulations with transcript abundance is subject to a significant amount of noise. We propose to use effective and expressed nucleotide variations (eeSNVs) from scRNA-seq as alternative features for tumor subpopulation identification. We developed a linear modeling framework, SSrGE, to link eeSNVs associated with gene expression. In all the datasets tested, eeSNVs achieve better accuracies than gene expression for identifying subpopulations. Previously validated cancer-relevant genes are also highly ranked, confirming the significance of the method. Moreover, SSrGE is capable of analyzing coupled DNA-seq and RNA-seq data from the same single cells, demonstrating its value in integrating multi-omics single cell techniques. In summary, SNV features from scRNA-seq data have merits for both subpopulation identification and linkage of genotype-phenotype relationship. The method SSrGE is available athttps://github.com/lanagarmire/SSrGE.
Dynamic compensation, parameter identifiability, and equivariances
Authors: Sontag Eduardo 
Published: December 2016

AbstractA recent paper by Karin, Swisa, Glaser, Dor, and Alon introduced the mathematical notion of dynamical compensation (DC) in biological circuits, arguing that DC helps explain important features of glucose homeostasis as well as other key physiological regulatory mechanisms. The present paper establishes a connection between DC and two well-known notions in systems biology: system equivalence and parameter (un)identifiability. This recasting leads to effective tests for verifying DC in mathematical models.
Bayesian non-central chi regression for neuroimaging
Authors: Wegmann Bertil , Eklund Anders , Villani Mattias 
Published: December 2016

AbstractWe propose a regression model for non-centralχ(NC-χ) distributed functional magnetic resonance imaging (fMRI) and diffusion weighted imaging (DWI) data, with the heteroscedastic Rician regression model as a prominent special case. The model allows both parameters in the NC-χdistribution to be linked to explanatory variables, with the relevant covariates automatically chosen by Bayesian variable selection. A highly efficient Markov chain Monte Carlo (MCMC) algorithm is proposed for simulating from the joint Bayesian posterior distribution of all model parameters and the binary covariate selection indicators. Simulated fMRI data is used to demonstrate that the Rician model is able to localize brain activity much more accurately than the traditionally used Gaussian model at low signal-to-noise ratios. Using a diffusion dataset from the Human Connectome Project, it is also shown that the commonly used approximate Gaussian noise model underestimates the mean diffusivity (MD) and the fractional anisotropy (FA) in the single-diffusion tensor model compared to the theoretically correct Rician model.