bluuebunny/crossref_metadata_2025_split huggingface dataset:
The blossoming of negation in gesture, sign and oral productions
Authors: Morgenstern Aliyah , Blondel Marion , Beaupoil-Hourdel Pauline , Benazzo Sandra , Boutet Dominique , Kochan Angelika , Limousin Fanny 
Published: February 2018

Abstract
Negation constructions in longitudinal adult-child data are an excellent source for the study of multimodality in language acquisition. First negative constructions seem to take over from early forms of rejection and avoidance, but tracing the transitions between actions and gestures, and between gestures and signed or spoken expressions in young children is quite complex. We focus on multimodal analysis of negation in the productions of five children between the ages of 0;10 and 3;6 interacting with their parents in various linguistic environments (monolingual French, monolingual English, monolingual LSF, bilingual French/LSF, bilingual French/Italian). We present the individual multimodal path of each child, illustrate the continuum between actions, gestures and signed/spoken constructions and analyze the common trend that leads children into symbolic communication through multi-semiotic means of expression.
Early predictors of language development in Autism Spectrum Disorder
Authors: Tager-Flusberg Helen 
Published: February 2018

Abstract
Although deficits in language are no longer considered diagnostic of Autism Spectrum Disorder (ASD), delays in language are among the earliest concerns noted by parents. By the time children with ASD enter school, their language skills vary widely from intact linguistic ability to no spoken language, though in all cases, communication is impaired and atypical. This chapter first reviews the research on the earliest behavioral and neural predictors of language in ASD based on studies that have prospectively followed infants who are at familial risk for ASD because they have an older sibling with the disorders. In the second part of the chapter research on behavioral predictors of language development in toddlers and preschoolers with ASD is presented. The gaps in the current literature and the clinical implications are discussed in the final sections.
Integrative pipeline for profiling DNA copy number and inferring tumor phylogeny
Authors: Urrutia Eugene , Chen Hao , Zhou Zilu , Zhang Nancy R , Jiang Yuchao 
Published: February 2018

Abstract

Summary
Copy number variation is an important and abundant source of variation in the human genome, which has been associated with a number of diseases, especially cancer. Massively parallel next-generation sequencing allows copy number profiling with fine resolution. Such efforts, however, have met with mixed successes, with setbacks arising partly from the lack of reliable analytical methods to meet the diverse and unique challenges arising from the myriad experimental designs and study goals in genetic studies. In cancer genomics, detection of somatic copy number changes and profiling of allele-specific copy number (ASCN) are complicated by experimental biases and artifacts as well as normal cell contamination and cancer subclone admixture. Furthermore, careful statistical modeling is warranted to reconstruct tumor phylogeny by both somatic ASCN changes and single nucleotide variants. Here we describe a flexible computational pipeline, MARATHON, which integrates multiple related statistical software for copy number profiling and downstream analyses in disease genetic studies.

Availability and implementation
MARATHON is publicly available at https://github.com/yuchaojiang/MARATHON.

Supplementary information
Supplementary data are available at Bioinformatics online.
Health and Housework in Later Life: A Longitudinal Study of Retired Couples
Authors: Leopold Thomas , Schulz Florian 
Published: February 2018

AbstractObjectivesTo examine how changes in wives’ and husbands’ health influenced housework time and domestic outsourcing in retired couples.MethodWe estimated fixed-effects models to test hypotheses about the gendered influence of health declines on absolute and relative measures of time spent on routine and nonroutine housework as well as the probability of outsourcing housework. The data were obtained from 23 waves of the German Socio-Economic Panel Study, comprising N = 25,119 annual observations of N = 3,889 retired couples aged 60–85 years.ResultsWives’ and husbands’ housework time declined with health status, but these effects were large only for serious health problems. We found evidence for within-couple compensation of spouses’ health declines, a mechanism that was limited to indispensable tasks of routine housework. The probability of getting paid help from outside the household increased with declining health, and this increase was more strongly tied to wives’ health declines than to husbands’ health declines.DiscussionThe results demonstrate the relevance of health status for the performance of housework in retired couples. The evidence attests to the resilience of couples during later-life stages in which health issues may severely inhibit domestic productivity.
Age of Migration and the Incidence of Cognitive Impairment: A Cohort Study of Elder Mexican-Americans
Authors: Garcia Marc A , Reyes Adriana M , Downer Brian , Saenz Joseph L , Samper-Ternent Rafael A , Raji Mukaila 
Published: February 2018

AbstractBackground and ObjectivesTo explore nativity and age of migration differentials in the incidence of cognitive impairment among older Mexican-Americans.Research Design and MethodsWe employ maximum-likelihood discrete time hazard models to estimate risk ratios of cognitive impairment in a sample of 2,708 Mexican-Americans 65 and older who were cognitively healthy at baseline over a follow-up period of up to 20 years.ResultsLate-life immigrant women have a 46% higher risk of cognitive impairment compared to U.S.-born Mexican-American women. Conversely, midlife immigrant men have a 29% lower risk of cognitive impairment compared to U.S.-born Mexican-American men. The incidence of cognitive impairment did not differ for early-life and midlife immigrant women relative to U.S.-born women or for early- and late-life immigrant men compared to U.S.-born men.Discussion and ImplicationsDifferences in cognitive impairment risk between U.S.-born and foreign-born Mexican-American subgroups may be partly due to health selectivity. Cognitive impairment is more prevalent among immigrant groups which may result in a higher burden on family members and/or high dependency on public resources. Programs are needed that can detect decline at earlier stages and reduce the risk for cognitive impairment among older immigrants entering their last decades of life.
Provider-performed microscopy empowers PAs at the point of care
Authors: Brown Gina R. , Wigdahl Joshua B. , Stebens Tiana M. 
Published: February 2018

ABSTRACT
Provider-performed microscopy (PPM) is a diagnostic tool recommended when patients present with several types of gynecologic infections or fungal infections of skin or nails. PPM allows for immediate and accurate treatment, and can strengthen the relationship between clinician and patient. This article reviews two microscopy techniques, the saline wet mount and the potassium hydroxide (KOH) preparation, and discusses their indications for use.
Safe Zone Quantification of the Third Sacral Segment in Normal and Dysmorphic Sacra
Authors: Hwang John S. , Reilly Mark C. , Shaath Mohammad K. , Changoor Stuart , Eastman Jonathan , Routt Milton Lee (Chip) , Sirkin Michael S. , Adams Mark R. 
Published: February 2018

Objective:
To quantify the osseous anatomy of the dysmorphic third sacral segment and assess its ability to accommodate internal fixation.

Design:
Retrospective chart review of a trauma database.

Setting:
University Level 1 Trauma Center.

Patients:
Fifty-nine patients over the age of 18 with computed tomography scans of the pelvis separated into 2 groups: a group with normal pelvic anatomy and a group with sacral dysmorphism.

Main Outcome Measurements:
The sacral osseous area was measured on computed tomography scans in the axial, coronal, and sagittal planes in normal and dysmorphic pelves. These measurements were used to determine the possibility of accommodating a transiliac transsacral screw in the third sacral segment.

Results:
In the normal group, the S3 coronal transverse width averaged 7.71 mm and the S3 axial transverse width averaged 7.12 mm. The mean S3 cross-sectional area of the normal group was 55.8 mm. The dysmorphic group was found to have a mean S3 coronal transverse width of 9.49 mm, an average S3 axial transverse width of 9.14 mm, and an S3 cross-sectional area of 77.9 mm.

Conclusions:
The third sacral segment of dysmorphic sacra has a larger osseous pathway available to safely accommodate a transiliac transsacral screw when compared with normal sacra. The S3 segment of dysmorphic sacra can serve as an additional site for screw placement when treating unstable posterior pelvic ring fractures.
The Utility of ICU Readmission as a Quality Indicator and the Effect of Selection*
Authors: Maharaj Ritesh , Terblanche Marius , Vlachos Savvas 
Published: February 2018

Objectives:
Intensive care readmission rates are used to signal quality, yet it is unclear whether they represent poor quality in the transition of care from the ICU to the ward, patient factors, or differences in survival of the initial admission. This study aims to measure the selection effect of surviving the initial ICU admission on readmission rates.

Design:
Retrospective cohort study of adult patients admitted to ICUs participating in the Case Mix Program database from the Intensive Care National Audit Research Centre.

Settings:
The study includes 262 ICUs in the United Kingdom.

Patients:
The study includes 682,975 patients admitted to ICUs between 2010 and 2014.

Interventions:
None.

Measurements and Main Results:
The study includes 682,975 patients admitted to ICUs in the United Kingdom. There were 591,710 patients discharged alive, of which 9,093 (1.53%) were readmitted within the first 2 days of ICU discharge. Post-ICU admission hospital mortality and ICU readmission were poorly correlated (r = 0.130). The addition of a selection model resulted in a weaker correlation (r = 0.082).

Conclusions:
ICU readmission performed poorly as a performance metric. The selection process by which only patients who survive their index admission are eligible for readmission has a significant effect on ICU readmission rankings, particularly the higher ranked ICUs. Failure to consider this selection bias gives misleading signals about ICU performance and leads to faulty design of incentive schemes.
Differences in Optic Nerve Head, Retinal Nerve Fiber Layer, and Ganglion Cell Complex Parameters Between Caucasian and Chinese Subjects
Authors: Chansangpetch Sunee , Huang Guofu , Coh Paul , Oldenburg Catherine , Amoozgar Behzad , He Mingguang , Lin Shan C. 
Published: February 2018

Purpose:
To compare optic nerve head, peripapillary retinal nerve fiber layer (pRNFL), and ganglion cell complex (GCC) parameters between Caucasian and ethnic Chinese.

Materials and Methods:
Normal subjects above 40 years old and self-identified as being Caucasian and Chinese were recruited. They were evaluated with spectral-domain optical coherence tomography (RTVue-100). Parameters related to the optic nerve head, pRNFL, and GCC analysis protocols were acquired. Multivariable linear regression was performed adjusting for potential confounders.

Results:
Data from 116 Caucasian and 130 Chinese subjects were available for analysis. Mean age of all participants was 66.72 (SD 10.82) years. There were statistically significant differences for disc area (DA), area cup-to-disc, vertical cup-to-disc, and cup volume (P=0.02, 0.004, 0.02, and 0.03, respectively), greater in Chinese. After adjusting for age, sex, axial length (AL), intraocular pressure (IOP), DA, and GCC thickness, Chinese subjects had significantly greater thickness in all pRNFL parameters (mean differences ranged between 4.29 and 9.93 μm; all P<0.001) except the nasal quadrant. GCC outcomes were also adjusted for DA and pRNFL; Caucasians had significantly higher average GCC and inferior GCC (mean difference 2.97 and 3.45 μm, respectively; P<0.01), whereas the Chinese group had significantly higher ganglion cell global loss volume (mean difference 2.47 %, P<0.001).

Conclusions:
This study suggests there is significantly greater pRNFL thickness in Chinese, which were independent of age, AL, IOP, and DA, and possibly greater GCC in Caucasians after adjustment for age, AL, IOP, DA, and pRNFL thickness.
Sexually Transmitted Infection Positivity Rate and Treatment Uptake Among Female and Male Sexual Assault Victims Attending The Amsterdam STI Clinic Between 2005 and 2016
Authors: van Rooijen Martijn S. , Schim van der Loeff Maarten F. , van Kempen Loes , de Vries Henry J.C. 
Published: February 2018

Background
Victims could become infected with sexually transmitted infections (STIs) during a sexual assault. Several guidelines recommend presumptive antimicrobial therapy for sexual assault victims (SAVs). We assessed the STI positivity rate and treatment uptake of female and male SAVs at the Amsterdam STI clinic.

Methods
Sexual assault victims answered assault-related questions and were tested for bacterial STI (chlamydia, gonorrhea, and syphilis), hepatitis B, and HIV during their initial visits. Sexual assault victim characteristics were compared with non-SAV clients. Backward multivariable logistic regression analysis was conducted to assess whether being an SAV was associated with a bacterial STI. The proportion of those returning for treatment was calculated.

Results
From January 2005 to September 2016, 1066 (0.6%) of 168,915 and 135 (0.07%) of 196,184 consultations involved female and male SAVs, respectively. Among female SAVs, the STI positivity rate was 11.2% versus 11.6% among non-SAVs (P = 0.65). Among male SAVs, the STI positivity rate was 12.6% versus 17.7% among non-SAVs (P = 0.12). In multivariable analysis, female SAVs did not have increased odds for an STI (odds ratio 0.94; 95% confidence interval, 0.77–1.13), and male SAVs had significantly lower odds for an STI (odds ratio, 0.60; 95% confidence interval, 0.36–0.98). Of SAVs requiring treatment, 89.0% (female) and 92.0% (male) returned.

Conclusions
The STI positivity rate among female SAVs was comparable with female non-SAVs, but male SAVs had lower odds for having a bacterial STI than did male non-SAVs, when adjusting for confounders. The return rate of SAV for treatment was high and therefore does not support the recommendations for presumptive therapy.
Psychological Stress and Mitochondria: A Systematic Review
Authors: Picard Martin , McEwen Bruce S. 
Published: February 2018

ABSTRACT

Objective
Mitochondria are multifunctional life-sustaining organelles that represent a potential intersection point between psychosocial experiences and biological stress responses. This article provides a systematic review of the effects of psychological stress on mitochondrial structure and function.

Methods
A systematic review of the literature investigating the effects of psychological stress on mitochondrial function was conducted. The review focused on experimentally controlled studies allowing us to draw causal inference about the effect of induced psychological stress on mitochondria.

Results
A total of 23 studies met the inclusion criteria. All studies involved male laboratory animals, and most demonstrated that acute and chronic stressors influenced specific facets of mitochondrial function, particularly within the brain. Nineteen studies showed significant adverse effects of psychological stress on mitochondria and four found increases in function or size after stress. In humans, only six observational studies were available, none with experimental designs, and most only measured biological markers that do not directly reflect mitochondrial function, such as mitochondrial DNA copy number.

Conclusons
Overall, evidence supports the notion that acute and chronic stressors influence various aspects of mitochondrial biology, and that chronic stress exposure can lead to molecular and functional recalibrations among mitochondria. Limitations of current animal and human studies are discussed. Maladaptive mitochondrial changes that characterize this subcellular state of stress are termed mitochondrial allostatic load. Prospective studies with sensitive measures of specific mitochondrial outcomes will be needed to establish the link between psychosocial stressors, emotional states, the resulting neuroendocrine and immune processes, and mitochondrial energetics relevant to mind-body research in humans.
Urinary Management With an External Female Collection Device
Authors: Beeson Terrie , Davis Carmen 
Published: February 2018

BACKGROUND:
Strategies to decrease use of female indwelling urinary catheters and catheter-associated urinary tract infections are challenging due to the limited availability of proper fitting external collection devices. Female urinary incontinence predisposes the skin to potential pain, itching, burning, infection, or pressure injuries.

CASE STUDIES:
This article discusses 3 patients' trajectory of care with use of an external female urinary collection device. All of these females were incontinent of urine after the indwelling urinary catheter was removed and managed with an external female urinary collection device.

CONCLUSIONS:
The use of an external female urinary collection device is a feasible alternative to an indwelling urinary catheter as well as managing urinary incontinence.
Machine learning algorithms for systematic review: reducing workload in a preclinical review of animal studies and reducing human screening error
Authors: Bannach-Brown Alexandra , Przybyła Piotr , Thomas James , Rice Andrew S.C. , Ananiadou Sophia , Liao Jing , Macleod Malcolm Robert 
Published: February 2018

AbstractBackgroundHere we outline a method of applying existing machine learning (ML) approaches to aid citation screening in an on-going broad and shallow systematic review of preclinical animal studies, with the aim of achieving a high performing algorithm comparable to human screening.MethodsWe applied ML approaches to a broad systematic review of animal models of depression at the citation screening stage. We tested two independently developed ML approaches which used different classification models and feature sets. We recorded the performance of the ML approaches on an unseen validation set of papers using sensitivity, specificity and accuracy. We aimed to achieve 95% sensitivity and to maximise specificity. The classification model providing the most accurate predictions was applied to the remaining unseen records in the dataset and will be used in the next stage of the preclinical biomedical sciences systematic review. We used a cross validation technique to assign ML inclusion likelihood scores to the human screened records, to identify potential errors made during the human screening process (error analysis).ResultsML approaches reached 98.7% sensitivity based on learning from a training set of 5749 records, with an inclusion prevalence of 13.2%. The highest level of specificity reached was 86%. Performance was assessed on an independent validation dataset. Human errors in the training and validation sets were successfully identified using assigned the inclusion likelihood from the ML model to highlight discrepancies. Training the ML algorithm on the corrected dataset improved the specificity of the algorithm without compromising sensitivity. Error analysis correction leads to a 3% improvement in sensitivity and specificity, which increases precision and accuracy of the ML algorithm.ConclusionsThis work has confirmed the performance and application of ML algorithms for screening in systematic reviews of preclinical animal studies. It has highlighted the novel use of ML algorithms to identify human error. This needs to be confirmed in other reviews, , but represents a promising approach to integrating human decisions and automation in systematic review methodology.
Pleiotropic Mapping and Annotation Selection in Genome-wide Association Studies with Penalized Gaussian Mixture Models
Authors: Zeng Ping , Hao Xinjie , Zhou Xiang 
Published: February 2018

AbstractMotivationGenome-wide association studies (GWASs) have identified many genetic loci associated with complex traits. A substantial fraction of these identified loci are associated with multiple traits – a phenomena known as pleiotropy. Identification of pleiotropic associations can help characterize the genetic relationship among complex traits and can facilitate our understanding of disease etiology. Effective pleiotropic association mapping requires the development of statistical methods that can jointly model multiple traits with genome-wide SNPs together.ResultsWe develop a joint modeling method, which we refer to as the integrative MApping of Pleiotropic association (iMAP). iMAP models summary statistics from GWASs, uses a multivariate Gaussian distribution to account for phenotypic correlation, simultaneously infers genome-wide SNP association pattern using mixture modeling, and has the potential to reveal causal relationship between traits. Importantly, iMAP integrates a large number of SNP functional annotations to substantially improve association mapping power, and, with a sparsity-inducing penalty, is capable of selecting informative annotations from a large, potentially noninformative set. To enable scalable inference of iMAP to association studies with hundreds of thousands of individuals and millions of SNPs, we develop an efficient expectation maximization algorithm based on an approximate penalized regression algorithm. With simulations and comparisons to existing methods, we illustrate the benefits of iMAP both in terms of high association mapping power and in terms of accurate estimation of genome-wide SNP association patterns. Finally, we apply iMAP to perform a joint analysis of 48 traits from 31 GWAS consortia together with 40 tissue-specific SNP annotations generated from the Roadmap Project. iMAP is freely available atwww.xzlab.org/software.html.
Multiple prebiotic metals mediate translation
Authors: Bray Marcus S. , Lenz Timothy K. , Haynes Jay William , Bowman Jessica C. , Petrov Anton S. , Reddi Amit R. , Hud Nicholas V. , Williams Loren Dean , Glass Jennifer B. 
Published: February 2018

ABSTRACTToday, Mg2+is an essential cofactor with diverse structural and functional roles in life’s oldest macromolecular machine, the translation system. We tested whether ancient Earth conditions (low O2, high Fe2+, high Mn2+) can revert the ribosome to a functional ancestral state. First, SHAPE (Selective 2’HydroxylAcylation analyzed byPrimerExtension) was used to compare the effect of Mg2+, Fe2+, and Mn2+on the tertiary structure of rRNA. Then, we usedin vitrotranslation reactions to test whether Fe2+or Mn2+could mediate protein production, and quantified ribosomal metal content. We found that: (i) Mg2+, Fe2+, and Mn2+had strikingly similar effects on rRNA folding; (ii) Fe2+and Mn2+can replace Mg2+as the dominant divalent cation during translation of mRNA to functional protein; (iii) Fe and Mn associate extensively with the ribosome. Given that the translation system originated and matured when Fe2+and Mn2+were abundant, these findings suggest that Fe2+and Mn2+played a role in early ribosomal evolution.SIGNIFICANCERibosomes are found in every living organism where they are responsible for the translation of messenger RNA into protein. The ribosome’s centrality to cell function is underscored by its evolutionary conservation; the core structure has changed little since its inception ~4 billion years ago when ecosystems were anoxic and metal-rich. The ribosome is a model system for the study of bioinorganic chemistry, owing to the many highly coordinated divalent metal cations that are essential to its function. We studied the structure, function, and cation content of the ribosome under early Earth conditions (low O2, high Fe2+, high Mn2+). Our results expand the roles of Fe2+and Mn2+in ancient and extant biochemistry as cofactors for ribosomal structure and function.