bluuebunny/crossref_metadata_2025_split huggingface dataset:
Movement of feeder-using songbirds: the influence of urban features
Authors: Cox Daniel T. C. , Inger Richard , Hancock Steven , Anderson Karen , Gaston Kevin J. 
Published: November 2016

AbstractPrivate gardens provide vital opportunities for people to interact with nature. The most popular form of interaction is through garden bird feeding. Understanding how landscape features and seasons determine patterns of movement of feeder-using songbirds is key to maximising the well-being benefits they provide. To determine these patterns we established three networks of automated data loggers along a gradient of greenspace fragmentation. Over a 12-month period we tracked 452 tagged blue titsCyantistes caeruleusand great titsParus majormoving between feeder pairs 9,848 times, to address two questions: (i) Do urban features within different forms, and season, influence structural (presence-absence of connections between feeders by birds) and functional (frequency of these connections) connectivity? (ii) Are there general patterns of structural and functional connectivity across forms? Vegetation cover increased connectivity in all three networks, whereas the presence of road gaps negatively affected functional but not structural connectivity. Across networks structural connectivity was lowest in the summer when birds maintain breeding territories, however patterns of functional connectivity appeared to vary with habitat fragmentation. Using empirical data this study shows how key urban features and season influence movement of feeder-using songbirds, and we provide evidence that this is related to greenspace fragmentation.
Room temperature electrically tunable rectification magnetoresistance in Ge-based Schottky devices
Authors: Huang Qi-kun , Yan Yi , Zhang Kun , Li Huan-huan , Kang Shishou , Tian Yu-feng 
Published: November 2016

AbstractElectrical control of magnetotransport properties is crucial for device applications in the field of spintronics. In this work, as an extension of our previous observation of rectification magnetoresistance, an innovative technique for electrical control of rectification magnetoresistance has been developed by applying direct current and alternating current simultaneously to the Ge-based Schottky devices, where the rectification magnetoresistance could be remarkably tuned in a wide range. Moreover, the interface and bulk contribution to the magnetotransport properties has been effectively separated based on the rectification magnetoresistance effect. The state-of-the-art electrical manipulation technique could be adapt to other similar heterojunctions, where fascinating rectification magnetoresistance is worthy of expectation.
The Effect of Silica Nanoparticles on Human Corneal Epithelial Cells
Authors: Park Joo-Hee , Jeong Hyejoong , Hong Jinkee , Chang Minwook , Kim Martha , Chuck Roy S. , Lee Jimmy K. , Park Choul-Yong 
Published: November 2016

AbstractOcular drug delivery is an interesting field in current research. Silica nanoparticles (SiNPs) are promising drug carriers for ophthalmic drug delivery. However, little is known about the toxicity of SiNPs on ocular surface cells such as human corneal epithelial cells (HCECs). In this study, we evaluated the cytotoxicity induced by 50, 100 and 150 nm sizes of SiNPs on cultured HCECs for up to 48 hours. SiNPs were up-taken by HCECs inside cytoplasmic vacuoles. Cellular reactive oxygen species generation was mildly elevated, dose dependently, with SiNPs, but no significant decrease of cellular viability was observed up to concentrations of 100 μg/ml for three different sized SiNPs. Western blot assays revealed that both cellular autophagy and mammalian target of rapamycin (mTOR) pathways were activated with the addition of SiNPs. Our findings suggested that 50, 100 and 150 nm sized SiNPs did not induce significant cytotoxicity in cultured HCECs.
The Composition of Early Vocabulary in Spanish Children With Down Syndrome and Their Peers With Typical Development
Authors: Checa Elena , Galeote Miguel , Soto Pilar 
Published: November 2016

PurposeThere are very few studies, and at present none in Spanish, on vocabulary composition in children with Down syndrome (DS). Nor has the topic been widely assessed in Spanish-speaking children with typical development (TD). This study analyzed the composition of early vocabularies in a large sample of Spanish-speaking children with DS and compared it with that of children with TD.MethodWe studied 108 children with DS and 108 children with TD with mental ages between 8 and 29 months, matched for size of productive vocabulary and gender. The MacArthur-Bates Communicative Development Inventories (Fenson et al., 1993, 2007), adapted to the language development profile of children with DS, were used. The categories examined were nouns, predicates, closed-class words, and social words.ResultsThe performance of children with DS was similar to that of children with TD with the same vocabulary size. The only significant difference was the larger production of nouns by children with DS. The trends of development in the different classes of words were also similar.ConclusionsThe strategies used by children with DS to learn vocabulary may be similar to those used by children with TD in the first stages of language learning.
Cohesive Referencing Errors During Narrative Production as Clinical Evidence of Central Nervous System Abnormality in School-Aged Children With Fetal Alcohol Spectrum Disorders
Authors: Thorne John C. , Coggins Truman E. 
Published: November 2016

Purpose
Previous evidence suggests that cohesive referencing errors made during narratives may be a behavior that is revealing of underlying central nervous system abnormality in children with fetal alcohol spectrum disorders (FASD). The current research extends this evidence.

Method
Retrospective analysis of narrative and clinical data from 152 children (ages 6 to 14), 72 of whom had confirmed FASD, was used. Narrative analysis was conducted blind to diagnostic status, age, or gender. Group performance was compared. The associations between measures of cohesive referencing and clinically gathered indices of the degree of central nervous system abnormality were examined.

Results
Results show clear associations between elevated rates of cohesive referencing errors and central nervous system abnormality. Elevated error rates were more common in children with FASD than those without, and prevalence increased predictably across groups with more severe central nervous system abnormality. Risk is particularly elevated for those with microcephaly or a diagnosis of fetal alcohol syndrome.

Conclusion
Cohesive referencing errors during narrative are a viable behavioral marker of the kinds of central nervous system abnormality associated with prenatal alcohol exposure, having significant potential to become a valuable diagnostic and research tool.
The Prevalence of Cruciate Ligament and Meniscus Knee Injury in Young Adults and Associations with Gender, Body Mass Index, and Height a Large Cross-Sectional Study
Authors: Thein Ran , Gordon Barak , Burstein Gideon , Tenenbaum Shay , Derazne Estela , Tzur Dorit , Shamis Ari , Afek Arnon , Kreiss Yitshak , Hershkovich Oded 
Published: November 2016

AbstractAnterior cruciate ligament and meniscal injuries are associated with secondary osteoarthrosis which may lead to functional impairment and economic burden. The prevalence of knee injury has not been studied in depth. Our purpose was to report the prevalence of knee ligament and meniscal injuries and their associations with gender, body mass index (BMI), and height in young adults and to characterize individuals with meniscal injuries who gained full recovery. A cross-sectional, population-based study was conducted. Information on the disability codes of knee ligament and meniscal injury according to the Regulations of Medical Fitness Determination was retrieved from a medical database containing records of young prerecruits into mandatory service. Logistic regression assessed the association between genders, BMI, and body height to knee injuries. A total of 825,187 subjects were included. Prevalence of knee injuries was 0.35%. Males had 2.2-fold more knee injuries than females. Increased BMI was associated with increased prevalence of knee injury in both genders, more significantly in females (overweight and obese females had an odds ratio of 1.406 and 1.519, respectively, to suffer from concomitant meniscal and ligamentous knee injury). Being underweight was associated with a lower prevalence of knee injury. An above normal BMI was more significantly associated with meniscal and/or ligament injuries that did not fully recover (females > males). Body height was associated with isolated meniscal injury in both genders. We found an association between BMI, body height, and knee injury in both males and females. Higher body height and higher BMI might be risk factors for knee injuries. Higher BMI was associated with greater probability of disability coding. Meniscal and ligament injuries are more common among males.
Optically transparent semiconducting polymer nanonetwork for flexible and transparent electronics
Authors: Yu Kilho , Park Byoungwook , Kim Geunjin , Kim Chang-Hyun , Park Sungjun , Kim Jehan , Jung Suhyun , Jeong Soyeong , Kwon Sooncheol , Kang Hongkyu , Kim Junghwan , Yoon Myung-Han , Lee Kwanghee 
Published: November 2016

Significance
When various electronic appliances used in everyday life become deformable and transparent, they will provide tremendous versatility in the design and use of see-through, smart mobile applications, exceeding the limitations of the best developed conventional silicon technologies, which are available only in rigid, opaque forms. However, even recently discovered innovative semiconducting components have failed to simultaneously achieve such flexibility and transparency. Thus, the existing options still comprise only hard, planar, or opaque materials, and obtaining a “key” material for creating truly flexible and transparent electronics has presented a formidable challenge. We report an effective means of creating a “truly flexible, perfectly transparent” and high-mobility semiconducting material and demonstrate several high-end flexible and transparent applications based on a polymeric semiconductor system.
Transcriptomics and neuroanatomy of the clonal raider ant implicate an expanded clade of odorant receptors in chemical communication
Authors: McKenzie Sean K. , Fetter-Pruneda Ingrid , Ruta Vanessa , Kronauer Daniel J. C. 
Published: November 2016

Significance
Despite the importance of sociality in the evolutionary history of life, its molecular basis is still poorly understood. The role of novel genes vs. conserved genes is particularly hotly debated. Here we present evidence that a group of 180 odorant receptor genes in the clonal raider ant are expressed in neurons that have been shown to detect cuticular hydrocarbons, one of the most important classes of ant chemical signals. We show that these genes underwent a period of rapid gene duplication in the ancestors of ants and now comprise 0.5%–1.5% of all genes in ant genomes. This discovery provides a striking example of the importance of novel genes in social evolution.
Mechanical bounds to transcriptional noise
Authors: Sevier Stuart A. , Kessler David A. , Levine Herbert 
Published: November 2016

Significance
A complete understanding of transcription, which is the first process in the central dogma of biology, is of paramount importance for understand the living world. Many genes transcribe in a significantly noisy or bursty manner, and the understanding of this phenomenon has been the subject of much experimental and theoretical research. In this article, we present work that introduces mechanical feedback as the source of bursting through an intrinsically ordered stochastic process. The resulting statistical properties of gene expression contain a number of previously unexplained universal features of the central dogma.
Evaluating the evaluation of cancer driver genes
Authors: Tokheim Collin J. , Papadopoulos Nickolas , Kinzler Kenneth W. , Vogelstein Bert , Karchin Rachel 
Published: November 2016

SignificanceModern large-scale sequencing of human cancers seeks to comprehensively discover mutated genes that confer a selective advantage to cancer cells. Key to this effort has been development of computational algorithms to find genes that drive cancer based on their patterns of mutation in large patient cohorts. Because there is no generally accepted gold standard of driver genes, it has been difficult to quantitatively compare these methods. We present a machine-learning–based method for driver gene prediction and a protocol to evaluate and compare prediction methods. Our results suggest that most current methods do not adequately account for heterogeneity in the number of mutations expected by chance and consequently yield many false-positive calls, particularly in cancers with high mutation rate.
PRINCESS: Privacy-protecting Rare disease International Network Collaboration via Encryption through Software guard extensionS
Authors: Chen Feng , Wang Shuang , Jiang Xiaoqian , Ding Sijie , Lu Yao , Kim Jihoon , Sahinalp S Cenk , Shimizu Chisato , Burns Jane C , Wright Victoria J , Png Eileen , Hibberd Martin L , Lloyd David D , Yang Hai , Telenti Amalio , Bloss Cinnamon S , Fox Dov , Lauter Kristin , Ohno-Machado Lucila 
Published: November 2016

Abstract

Motivation
We introduce PRINCESS, a privacy-preserving international collaboration framework for analyzing rare disease genetic data that are distributed across different continents. PRINCESS leverages Software Guard Extensions (SGX) and hardware for trustworthy computation. Unlike a traditional international collaboration model, where individual-level patient DNA are physically centralized at a single site, PRINCESS performs a secure and distributed computation over encrypted data, fulfilling institutional policies and regulations for protected health information.

Results
To demonstrate PRINCESS’ performance and feasibility, we conducted a family-based allelic association study for Kawasaki Disease, with data hosted in three different continents. The experimental results show that PRINCESS provides secure and accurate analyses much faster than alternative solutions, such as homomorphic encryption and garbled circuits (over 40 000× faster).

Availability and Implementation
https://github.com/achenfengb/PRINCESS_opensource

Supplementary information
Supplementary data are available at Bioinformatics online.
Screening for medication errors using an outlier detection system
Authors: Schiff Gordon D , Volk Lynn A , Volodarskaya Mayya , Williams Deborah H , Walsh Lake , Myers Sara G , Bates David W , Rozenblum Ronen 
Published: November 2016

Objective: The study objective was to evaluate the accuracy, validity, and clinical usefulness of medication error alerts generated by an alerting system using outlier detection screening.
Materials and Methods: Five years of clinical data were extracted from an electronic health record system for 747 985 patients who had at least one visit during 2012–2013 at practices affiliated with 2 academic medical centers. Data were screened using the system to detect outliers suggestive of potential medication errors. A sample of 300 charts was selected for review from the 15 693 alerts generated. A coding system was developed and codes assigned based on chart review to reflect the accuracy, validity, and clinical value of the alerts.
Results: Three-quarters of the chart-reviewed alerts generated by the screening system were found to be valid in which potential medication errors were identified. Of these valid alerts, the majority (75.0%) were found to be clinically useful in flagging potential medication errors or issues.
Discussion: A clinical decision support (CDS) system that used a probabilistic, machine-learning approach based on statistically derived outliers to detect medication errors generated potentially useful alerts with a modest rate of false positives. The performance of such a surveillance and alerting system is critically dependent on the quality and completeness of the underlying data.
Conclusion: The screening system was able to generate alerts that might otherwise be missed with existing CDS systems and did so with a reasonably high degree of alert usefulness when subjected to review of patients’ clinical contexts and details.
The Impact of a National Faculty Development Program Embedded Within an Academic Professional Organization
Authors: Baldwin Constance D. , Gusic Maryellen E. , Chandran Latha 
Published: November 2016

A sizeable literature describes the effectiveness of institution-based faculty development programs in nurturing faculty educators as scholars, but national programs are less common and seldom evaluated. To fill this role, the Educational Scholars Program (ESP) was created within the Academic Pediatric Association (APA) in 2006. It is a national, three-year, cohort-based certification program focused on fostering educational scholarship. This article describes the development and outcomes of an innovative program embedded within the framework of a national professional organization, and offers a model for potential adaptation by similar organizations to enhance their support of educators.
After 10 years, 171 scholars have enrolled in the ESP, and 50 faculty have participated. Scholars are assigned a faculty advisor and participate in three full-day sessions at a national meeting; online, interactive learning modules; and a mentored, scholarly project. The program receives support from the APA in four organizational frames: structural, human resource, political, and symbolic. The self-perceived scholarly proficiency of the scholars in Cohort 1 increased significantly over time, and their productivity and collaborations increased during and after the program. Scholars wrote enthusiastically about their experience in yearly and postprogram evaluations. In interviews, eight past APA presidents explained that the ESP strengthened the APA’s mission, created new leaders, and provided a new model for other APA programs. Outcomes of the ESP suggest that a longitudinal faculty development program embedded within a national professional organization can create a social enterprise not only within the organization but also within the broader national community of educator–scholars.
B-Type Natriuretic Peptide Predicts Morbidity and Long-Term Mortality in Coronary Artery Bypass Grafting and Valve Surgery
Authors: Endicott Kendal M. , Amdur Richard L. , Greenberg Michael D. , Trachiotis Gregory D. 
Published: November 2016

Objective To assess whether B-type natriuretic peptide (BNP) levels are a useful predictor of morbidity and mortality as well as long-term survival in patients after coronary artery bypass grafting (CABG) and valve surgery. Methods A retrospective review of CABG and/or valve surgery patients from 2012 to 2015 at a single center was conducted. A total of 432 patients were identified (CABG, 295 patients; valve, 82 patients; and CABG + valve, 55 patients). B-type natriuretic peptide levels were divided into quartiles (Q1-Q4). Mortality data were available for up to 3.4 years after surgery. Results B-type natriuretic peptide quartile was independently associated with any complication on multivariate analysis. Patients in Q4 were at highest risk (adjusted odds ratio, 3.81; P = 0.047 vs Q1). There was a significant association between BNP quartile and time to death (logrank χ2, 8.30; P = 0.04) with greatest association 9 months postoperatively. B-type natriuretic peptide quartile was significantly associated with time to death in Cox regression in Q2 (hazard ratio [HR], 3.73 (1.04–13.44); P = 0.044) and Q4 (HR, 4.33 (1.14–16.44); P = 0.031). Q3 also had a higher risk of death (HR, 3.5 vs Q1); however, this was only significant at a trend level (P = 0.06). Using a risk model generated from logistic regression, we determined that the highest risk group had relative risk of complications 30 times higher than the lowest risk group. Conclusions B-type natriuretic peptide levels are an independent predictor of morbidity after CABG and/or valve surgery regardless of type of procedure or on/off bypass usage. B-type natriuretic peptide levels also correlate with time to death, highlighting the need for sustained follow-up and heart failure management to improve survival in patients with elevated BNP levels presenting for all cardiac surgery.
Agreement between arterial and venous lactate in emergency department patients: a prospective study of 157 consecutive patients
Authors: Paquet Anne-Laure , Valli Vanina , Philippon Anne-Laure , Devilliers Catherine , Bloom Ben , Hausfater Pierre , Riou Bruno , Freund Yonathan 
Published: November 2016

Introduction
In the emergency department (ED), lactate is routinely used for risk stratification. Whether venous or arterial lactate measured on blood gas is interchangeable is not known. We hypothesized that venous lactate can be used instead of arterial lactate for the evaluation of acute patients in the ED.

Patients and methods
This was a prospective single-center study. All patients requiring a lactate measurement were enrolled and we simultaneously drew arterial and venous blood. We followed up all patients to hospital discharge. Our primary aim was to evaluate agreements between the two measurements using Bland and Altman plots with the report of bias (mean difference) and limits of agreements. We also aimed to determine the rate of misclassification (defined as one measurement<1.8 mmol/l and the other>2.2). Our secondary aim was to evaluate their respective prognostic value to predict in-hospital death or admission in the ICU longer than 72 h.

Results
The mean age of the 132 analyzed patients was 62 years (SD: 18 years), and 59% were men. The mean difference (bias) between arterial and venous lactate was −0.6 mmol/l (limits of agreement: −1.7 to 0.6 mmol/l). The rate of misclassification was 8% (95% confidence interval: 3–2%). Both methods present similar performances for the prediction of poor outcomes, with an area under the receiving operator characteristic curves of 0.67 for both. Results were similar when focused only on septic patients.

Conclusion
Venous and arterial lactates do not agree well, and there is a high misclassification rate. Venous lactate does not appear to be interchangeable with arterial sampling.
Support Vector Machines Model of Computed Tomography for Assessing Lymph Node Metastasis in Esophageal Cancer with Neoadjuvant Chemotherapy
Authors: Wang Zhi-Long , Zhou Zhi-Guo , Chen Ying , Li Xiao-Ting , Sun Ying-Shi 
Published: November 2016

Objective
The aim of this study was to diagnose lymph node metastasis of esophageal cancer by support vector machines model based on computed tomography.

Materials and Methods
A total of 131 esophageal cancer patients with preoperative chemotherapy and radical surgery were included. Various indicators (tumor thickness, tumor length, tumor CT value, total number of lymph nodes, and long axis and short axis sizes of largest lymph node) on CT images before and after neoadjuvant chemotherapy were recorded. A support vector machines model based on these CT indicators was built to predict lymph node metastasis.

Results
Support vector machines model diagnosed lymph node metastasis better than preoperative short axis size of largest lymph node on CT. The area under the receiver operating characteristic curves were 0.887 and 0.705, respectively.

Conclusions
The support vector machine model of CT images can help diagnose lymph node metastasis in esophageal cancer with preoperative chemotherapy.