bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deglycosylation of Tropheryma whipplei biofilm and discrepancies between diagnostic results during Whipple’s disease progression
Authors: Audoly Gilles , Fenollar Florence , Lagier Jean-Christophe , Lepidi Hubert , Raoult Didier 
Published: March 2016

AbstractWhipple’s disease is a systemic infectious disease associated with the bacterium Tropheryma whipplei. Numerous reports have presented puzzling discrepancies between diagnosis methods. We addressed this confusion using fluorescent in situ hybridization and immunofluorescence assays to evaluate 34 duodenal biopsies and 1 lymph node biopsy from Whipple’s patients. We showed the presence of bacteria in both CK20+ epithelial cells and CD68+ macrophages. Bacteria are found embedded in a biofilm hindering the detection of T. whipplei. Only after treatment of biopsies by glycosidases, co-localization of T. whipplei RNA/DNA with bacterial proteins was restored. Moreover, using 13 bronchoalveolar lavages and 7 duodenal biopsies, we found that hydrolysis of the biofilm weakened the bacteria, facilitated bacterial DNA extraction and improved the sensitivity of qPCR detection by up to 1000x opening new perspectives for diagnostic and scientific approaches.
Three‐bridge buck inverter
Authors: Hong Feng , Liu Jun , Ji Baojian , Zhou Yufei , Wang Jianhua , Wang Chenghua 
Published: March 2016

On the basis of dual‐buck half‐bridge inverter, a three‐bridge buck inverter is proposed, which not only remains the advantages of dual‐buck half‐bridge inverter, but also improves the inverter's performance such as avoids shoot‐through problem, removes the reverse recovery losses of body diodes and so on. By adding a new bridge, the three‐level modulation and the single power supply are realised, which increase the DC voltage utilisation rate. In addition, smaller volume and weight of the system and higher system integration can be achieved using only one filter inductor compared with other dual‐buck‐type inverters. The unipolar sinusoidal pulse width modulation scheme is adopted in the inverter system, so the switching frequency is fixed, which is beneficial to the design of filter. The operating principle and characteristics of the proposed inverter are analysed in detail. A 1 kW prototype is established and tested, and the results of simulation and experiment verify the good performance of the proposed inverter.
Primary caregivers of young children are unaware of food neophobia and food preference development
Authors: Norton Julie , Raciti Maria M. 
Published: March 2016

Issues addressedThis research explored primary caregivers' awareness of food neophobia and how food preferences develop in young children aged between 1 and 2.5 years.MethodsThis qualitative study used case study methodology and comprised interviews with 24 primary caregivers of young children aged between 1 and 2.5 years. Results and conclusions: Primary caregivers of young children are unaware of food neophobia and food preference development in young children.So what?Raising primary caregivers' awareness of food neophobia and how food preferences develop in young children may encourage caregivers to decrease their children's exposure to non‐core foods.
Horizontally acquired genes in early-diverging pathogenic fungi enable the use of host nucleosides and nucleotides
Authors: Alexander William G. , Wisecaver Jennifer H. , Rokas Antonis , Hittinger Chris Todd 
Published: March 2016

Significance
Early-diverging fungi from the phylum Microsporidia are opportunistic pathogens of humans and other animals. A genome-wide search was conducted in four species of Microsporidia and one species of Cryptomycota for genes acquired by horizontal transfer from other organisms. Up to 2% of their genes had strong evidence for horizontal transfer. We showed that many transferred nucleic acid metabolism genes lie on the boundary of the host and pathogen metabolic networks. Finally, we functionally characterized the gene encoding thymidine kinase, whose multiple parallel transfers from three different sources strongly suggest an integral adaptive role in the lifestyles of these intracellular parasites. Microsporidian thymidine kinases activate a prodrug, suggesting a treatment route for microsporidian infections.
Modeling and analysis of collective cell migration in an in vivo three-dimensional environment
Authors: Cai Danfeng , Dai Wei , Prasad Mohit , Luo Junjie , Gov Nir S. , Montell Denise J. 
Published: March 2016

Significance
Many cells travel within an organism to perform important duties in development, homeostasis, and disease. Questions remain as to why cells migrate in diverse forms: some travel as single cells, whereas others move collectively in groups of different sizes. What is also unclear is how extracellular conditions influence migration. In our study, which combines live imaging with theoretical modeling, we address these questions and reveal how both physical and chemical features of the microenvironment influence the optimum size of a migrating cell group.
Turbulent dynamo in a collisionless plasma
Authors: Rincon François , Califano Francesco , Schekochihin Alexander A. , Valentini Francesco 
Published: March 2016

Significance
Although magnetic field amplification by a dynamo effect converting kinetic flow energy into magnetic energy has long been shown in conventional magnetohydrodynamic fluids, whether a similar effect is possible in more dynamically complex weakly collisional plasmas, such as those encountered in astrophysical objects on extragalactic scales, is not known. We present the first, to our knowledge, conclusive numerical evidence and dynamical picture of magnetic field amplification by chaotic motions in a collisionless plasma. The results suggest that such a plasma dynamo may be a realizable physical effect in “laboratory astrophysics” experiments and support the idea that turbulent dynamos may significantly contribute to the magnetization of weakly collisional high-energy density astrophysical plasmas, such as the intracluster medium of galaxy clusters.
PheKB: a catalog and workflow for creating electronic phenotype algorithms for transportability
Authors: Kirby Jacqueline C , Speltz Peter , Rasmussen Luke V , Basford Melissa , Gottesman Omri , Peissig Peggy L , Pacheco Jennifer A , Tromp Gerard , Pathak Jyotishman , Carrell David S , Ellis Stephen B , Lingren Todd , Thompson Will K , Savova Guergana , Haines Jonathan , Roden Dan M , Harris Paul A , Denny Joshua C 
Published: March 2016

Abstract
Objective Health care generated data have become an important source for clinical and genomic research. Often, investigators create and iteratively refine phenotype algorithms to achieve high positive predictive values (PPVs) or sensitivity, thereby identifying valid cases and controls. These algorithms achieve the greatest utility when validated and shared by multiple health care systems.
Materials and Methods We report the current status and impact of the Phenotype KnowledgeBase (PheKB, http://phekb.org ), an online environment supporting the workflow of building, sharing, and validating electronic phenotype algorithms. We analyze the most frequent components used in algorithms and their performance at authoring institutions and secondary implementation sites.
Results As of June 2015, PheKB contained 30 finalized phenotype algorithms and 62 algorithms in development spanning a range of traits and diseases. Phenotypes have had over 3500 unique views in a 6-month period and have been reused by other institutions. International Classification of Disease codes were the most frequently used component, followed by medications and natural language processing. Among algorithms with published performance data, the median PPV was nearly identical when evaluated at the authoring institutions (n = 44; case 96.0%, control 100%) compared to implementation sites (n = 40; case 97.5%, control 100%).
Discussion These results demonstrate that a broad range of algorithms to mine electronic health record data from different health systems can be developed with high PPV, and algorithms developed at one site are generally transportable to others.
Conclusion By providing a central repository, PheKB enables improved development, transportability, and validity of algorithms for research-grade phenotypes using health care generated data.
Efficient identification of nationally mandated reportable cancer cases using natural language processing and machine learning
Authors: Osborne John D , Wyatt Matthew , Westfall Andrew O , Willig James , Bethard Steven , Gordon Geoff 
Published: March 2016

Abstract
Objective To help cancer registrars efficiently and accurately identify reportable cancer cases.
Material and Methods The Cancer Registry Control Panel (CRCP) was developed to detect mentions of reportable cancer cases using a pipeline built on the Unstructured Information Management Architecture – Asynchronous Scaleout (UIMA-AS) architecture containing the National Library of Medicine’s UIMA MetaMap annotator as well as a variety of rule-based UIMA annotators that primarily act to filter out concepts referring to nonreportable cancers. CRCP inspects pathology reports nightly to identify pathology records containing relevant cancer concepts and combines this with diagnosis codes from the Clinical Electronic Data Warehouse to identify candidate cancer patients using supervised machine learning. Cancer mentions are highlighted in all candidate clinical notes and then sorted in CRCP’s web interface for faster validation by cancer registrars.
Results CRCP achieved an accuracy of 0.872 and detected reportable cancer cases with a precision of 0.843 and a recall of 0.848. CRCP increases throughput by 22.6% over a baseline (manual review) pathology report inspection system while achieving a higher precision and recall. Depending on registrar time constraints, CRCP can increase recall to 0.939 at the expense of precision by incorporating a data source information feature.
Conclusion CRCP demonstrates accurate results when applying natural language processing features to the problem of detecting patients with cases of reportable cancer from clinical notes. We show that implementing only a portion of cancer reporting rules in the form of regular expressions is sufficient to increase the precision, recall, and speed of the detection of reportable cancer cases when combined with off-the-shelf information extraction software and machine learning.
Toward a better understanding of task demands, workload, and performance during physician-computer interactions
Authors: Mazur Lukasz M , Mosaly Prithima R , Moore Carlton , Comitz Elizabeth , Yu Fei , Falchook Aaron D , Eblan Michael J , Hoyle Lesley M , Tracton Gregg , Chera Bhishamjit S , Marks Lawrence B 
Published: March 2016

AbstractObjective To assess the relationship between (1) task demands and workload, (2) task demands and performance, and (3) workload and performance, all during physician-computer interactions in a simulated environment.Methods Two experiments were performed in 2 different electronic medical record (EMR) environments: WebCIS ( n = 12) and Epic ( n = 17). Each participant was instructed to complete a set of prespecified tasks on 3 routine clinical EMR-based scenarios: urinary tract infection (UTI), pneumonia (PN), and heart failure (HF). Task demands were quantified using behavioral responses (click and time analysis). At the end of each scenario, subjective workload was measured using the NASA-Task-Load Index (NASA-TLX). Physiological workload was measured using pupillary dilation and electroencephalography (EEG) data collected throughout the scenarios. Performance was quantified based on the maximum severity of omission errors.Results Data analysis indicated that the PN and HF scenarios were significantly more demanding than the UTI scenario for participants using WebCIS ( P &lt; .01), and that the PN scenario was significantly more demanding than the UTI and HF scenarios for participants using Epic ( P &lt; .01). In both experiments, the regression analysis indicated a significant relationship only between task demands and performance ( P &lt; .01).Discussion Results suggest that task demands as experienced by participants are related to participants' performance. Future work may support the notion that task demands could be used as a quality metric that is likely representative of performance, and perhaps patient outcomes.Conclusion The present study is a reasonable next step in a systematic assessment of how task demands and workload are related to performance in EMR-evolving environments.
Exfoliating Bark Does Not ProtectPlatanus occidentalisL. From Root-Climbing Lianas
Authors: Milks James R. , Hibbard J. , Rooney Thomas P. 
Published: March 2016

AbstractLianas are structural parasites that depress growth, fertility and survival rates of their hosts, but the magnitude to which they alter these rates differ among host species. We tested the hypothesis that sycamore (Platanus occidentalisL.) would have fewer adventitious root-climbing lianas. We reasoned that becauseP. occidentalispossesses exfoliating bark, it would periodically shed newly-established lianas from the trunk. We investigated the distribution of lianas on the trunks of trees ≥10 cm DBH in floodplains in southwestern Ohio. Contrary to predictions,P. occidentalistrees had significantly more root-climbing lianas than expected at three of five sites, and significantly fewer than expected at one site. In contrast, members of theAcergenus (boxelder (A. negundoL.), sugar maple (A. saccharumL.) and silver maple (A. saccharinumL.) had less than half of the root-climbing lianas as expected. We find no support for our hypothesis that bark exfoliation protectsP. occidentalistrees from root-climbing lianas in our study, and suggest possible mechanisms that might protectAcerspecies from adventitious root-climbing lianas.
SCPattern: A statistical approach to identify and classify expression changes in single cell RNA-seq experiments with ordered conditions
Authors: Leng Ning , Chu Li-Fang , Choi Jeea , Kendziorski Christina , Thomson James A. , Stewart Ron 
Published: March 2016

AbstractMotivationWith the development of single cell RNA-seq (scRNA-seq) technology, scRNA-seq experiments with ordered conditions (e.g. time-course) are becoming common. Methods developed for analyzing ordered bulk RNA-seq experiments are not applicable to scRNA-seq, since their distributional assumptions are often violated by additional heterogeneities prevalent in scRNA-seq. Here we present SC-Pattern - an empirical Bayes model to characterize genes with expression changes in ordered scRNA-seq experiments. SCPattern utilizes the non-parametrical Kolmogorov-Smirnov statistic, thus it has the flexibility to identify genes with a wide variety of types of changes. Additionally, the Bayes framework allows SCPattern to classify genes into expression patterns with probability estimates.ResultsSimulation results show that SCPattern is well powered for identifying genes with expression changes while the false discovery rate is well controlled. SCPattern is also able to accurately classify these dynamic genes into directional expression patterns. Applied to a scRNA-seq time course dataset studying human embryonic cell differentiation, SCPattern detected a group of important genes that are involved in mesendoderm and definitive endoderm cell fate decisions, positional patterning, and cell cycle.Availability and ImplementationThe SCPattern is implemented as an R package along with a user-friendly graphical interface, which are available at:https://github.com/lengning/SCPatternContact:rstewart@morgridge.org
Locally Epistatic Models for Genome-wide Prediction and Association by Importance Sampling
Authors: Akdemir Deniz , Jannink Jean-Luc 
Published: March 2016

AbstractIn statistical genetics an important task involves building predictive models for the genotype-phenotype relationships and thus attribute a proportion of the total phenotypic variance to the variation in genotypes. Numerous models have been proposed to incorporate additive genetic effects into models for prediction or association. However, there is a scarcity of models that can adequately account for gene by gene or other forms of genetical interactions. In addition, there is an increased interest in using marker annotations in genome-wide prediction and association. In this paper, we discuss an hybrid modeling methodology which combines the parametric mixed modeling approach and the non-parametric rule ensembles. This approach gives us a flexible class of models that can be used to capture additive, locally epistatic genetic effects, gene x background interactions and allows us to incorporate one or more annotations into the genomic selection or association models. We use benchmark data sets covering a range of organisms and traits in addition to simulated data sets to illustrate the strengths of this approach. The improvement of model accuracies and association results suggest that a part of the ’’missing heritability” in complex traits can be captured by modeling local epistasis.
The Mechanistic Underpinnings of anago1-Mediated, Environmentally Dependent, and Stochastic Phenotype
Authors: Mason G. Alex , Lemus Tzitziki , Queitsch Christine 
Published: March 2016

AbstractThe crucial role of microRNAs in plant development is exceedingly well supported; their importance in environmental robustness is studied in less detail. Here, we describe a novel, environmentally dependent phenotype in hypomorphic argonaute1 (ago1) mutants and uncover its mechanistic underpinnings in Arabidopsis (Arabidopsis thaliana). AGO1 is a key player in microRNA-mediated gene regulation. We observed transparent lesions on embryonic leaves of ago1 mutant seedlings. These lesions increased in frequency in full-spectrum light. Notably, the lesion phenotype was most environmentally responsive in ago1-27 mutants. This allele is thought to primarily affect translational repression, which has been linked with the response to environmental perturbation. Using several lines of evidence, we found that these lesions represent dead and dying tissues due to an aberrant hypersensitive response. Although all three canonical defense hormone pathways (salicylic acid, jasmonate, and jasmonate/ethylene pathways) were up-regulated in ago1 mutants, we demonstrate that jasmonate perception drives the lesion phenotype. Double mutants of ago1 and coronatine insensitive1, the jasmonate receptor, showed greatly decreased frequency of affected seedlings. The chaperone HEAT SHOCK PROTEIN 90 (HSP90), which maintains phenotypic robustness in the face of environmental perturbations, is known to facilitate AGO1 function. HSP90 perturbation has been shown previously to up-regulate jasmonate signaling and to increase plant resistance to herbivory. Although single HSP90 mutants showed subtly elevated levels of lesions, double mutant analysis disagreed with a simple epistatic model for HSP90 and AGO1 interaction; rather, both appeared to act nonadditively in producing lesions. In summary, our study identifies AGO1 as a major, largely HSP90-independent, factor in providing environmental robustness to plants.
The subjective experience of adults with intellectual disabilities who have mental health problems within community settings
Authors: Robinson Laura , Escopri Nazima , Stenfert Kroese Biza , Rose John 
Published: March 2016

Purpose– Research into the views of people with dual intellectual and mental health difficulties is sparse. The purpose of this paper is to gain a greater understanding of how individuals with mild intellectual disabilities living in the community understand their psychotic symptoms and experiences.Design/methodology/approach– Five participants with intellectual disabilities and psychotic symptoms living in the community were interviewed. The interview schedule explored key areas: understanding and experiences of having an intellectual disability and a psychotic disorder, and of services provided. The data were analysed using Interpretative Phenomenological Analysis.Findings– The analysis elicited three main themes: self-concept: “How I understand and see myself”, incorporates what participants understood about their labels, their experiences, and how these labels fitted in with their self-concept; Impact: “How having mental health problems and learning difficulties affect my life”, encompasses communication barriers, lack of control, and stigma and vulnerability. The third main theme was coping: “How I cope with my mental health and learning difficulties”.Research limitations/implications– The findings suggest that the participants, rather than identifying with specific psychiatric labels perceive themselves as having individual and specific needs. The analysis highlights areas that can be developed to help with coping; ensuring people are respected and heard, empowerment through the development of positive social roles, and psycho-education. These results are a step towards developing understanding of this group of service users.Originality/value– There has been no previous research into the perspective of this service user group in the community. The study makes recommendations for future person-centred interventions.
Enhanced company performance through the development of network alliance management skills: a four-point framework
Authors: Thomas Mark 
Published: March 2016

Purpose
The prevalence of corporate alliances has increased significantly in the past 25 years. However, such coalitions do not always produce the required results – a problem that is exacerbated when several partners are involved in a network alliance. Part of the difficulty is that, often, firms do not recognize all of the key issues in the successful management of an alliance. This paper aims to outline a four-point model that can be used to help companies develop their employees and work more effectively within network alliances.

Design/methodology/approach
This paper is a conceptual paper that draws in examples from Apple and IBM as well as research from the automobile, oil and higher education industries. It then offers a practical ABCD framework to assist companies in developing their staff to work effectively within network alliances.

Findings
Many studies show that companies who habitually succeed at strategic alliances have developed superior management teams. Despite this, few companies actively encourage training or even set best practices for alliance management. Given the high cost of establishing alliances and the excessive failure rate, it would seem logical that companies would invest time in the development of skills for personnel, thereby facilitating alliance success. If organizations dedicated more time and funds to training staff in the efficient management of alliances, they would considerably increase the likelihood of their success.

Originality/value
This paper gives a practical framework that can be referred to when developing company employees to work more effectively within a network alliance. This framework is based on analysis from a broad range of industries.