bluuebunny/crossref_metadata_2025_split huggingface dataset:
An Electronic Medical Record in Pediatric Medical Education: Survey of Medical Students' Expectations and Experiences
Authors: Cheng Daryl , Scodellaro Thomas , Uahwatanasakul Wonie , South Mike 
Published: November 2018

Objective This study sought to quantitatively characterize medical students' expectations and experiences of an electronic health record (EHR) system in a hospital setting, and to examine perceived and actual impacts on learning.
Methods Medical students from July to December 2016 at a tertiary pediatric institution completed pre- and postrotation surveys evaluating their expectations and experience of using an EHR during a pediatric medicine rotation. Survey data included past technology experience, EHR accessibility, use of learning resources, and effect on learning outcomes and patient–clinician communication.
Results Students generally reported high computer self-efficacy (4.16 ± 0.752, mean ± standard deviation), were comfortable with learning new software (4.08 ± 0.771), and expected the EHR to enhance their overall learning (4.074 ± 0.722). Students anticipated the EHR to be easy to learn, use, and operate, which was consistent with their experience (pre 3.86 vs. post 3.90, p = 0.56). Students did not expect nor experience that the EHR reduced their interaction, visual contact, or ability to build rapport with patients. The EHR did not meet expectations to facilitate learning around medication prescribing, placing orders, and utilizing online resources. Students found that the EHR marginally improved feedback surrounding clinical contributions to patient care from clinicians, although not to the expected levels (pre 3.50 vs. post 3.17, p < 0.01).
Conclusion Medical students readily engaged with the EHR, recognized several advantages in clinical practice, and did not consider their ability to interact with patients was impaired. There was widespread consensus that the EHR enhanced their learning and clinician's feedback, but not to the degree they had expected.
Key comparison BIPM.RI(I)-K1 of the air-kerma standards of VSL, The Netherlands, and the BIPM in 60Co gamma radiation
Authors: Kessler C , Burns D , Jansen B J , Pooter J A de , Prez L A de 
Published: November 2018

A key comparison of the standards for air kerma of VSL, Dutch Metrology Institute, The Netherlands (VSL) and of the Bureau International des Poids et Mesures (BIPM) was carried out in the 60Co radiation beam of the BIPM in December 2017. The comparison result, based on the calibration coefficients for two transfer chambers and expressed as a ratio of the VSL and the BIPM standards for air kerma, is 0.9963 with a combined standard uncertainty of 2.1 x 10-3. The results are analysed and presented in terms of degrees of equivalence, suitable for entry in the BIPM key comparison database.
KEY WORDS FOR SEARCH
Comparison, radiation dosimetry, air kerma, 60Co

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.
The final report has been peer-reviewed and approved for publication by the CCRI, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
Simulation Analysis of Influence of Boundary Parameters on the Performance of Gasoline Compression Ignition Engine
Authors: Lei peng , Zhang Guangde , Xie Kunpeng , Peng Chunmeng , Wang Huan 
Published: November 2018

Abstract
In order to solve the problems of combustion instability and excessive discharge of gasoline compression ignition (GCI) engine at low load, three-dimensional numerical simulation software CONVERGE is used to establish engine simulation model, and the main factors controlling combustion such as the oxygen content and the intake pressure are simulated and analyzed. The results show that when the volume fraction of the oxygen content of intake is 23%, higher thermal efficiency and lower emissions can be achieved. When the intake pressure is 0.12MPa, the peak of heat release rate is the highest and the combustion efficiency is high. The research results provide basic data and theoretical basis for achieving stable combustion at low load conditions.
RETRACTED: Construction of the Course System of Mechanical and Electronic Specialty for Applied Undergraduate Course -- Teaching Direction of Industrial Robot
Authors: Lu Yaping , Liu Hejian 
Published: November 2018

Abstract
Under the background of “Internet + Made in China 2025” production and education integration innovation promotion plan. According to the professional uniqueness and social needs of applied undergraduate education. Take the teaching direction of industrial robots in the field of mechanical electronics as an example. The paper proposed the teaching of professional basic courses as the basis, the professional direction of curriculum teaching as the focus, professional quality and innovative entrepreneurship education curriculum as a fundamental, three training courses for the innovation of the curriculum system. All kinds of courses include in-class courses (the first class) and extra-curricular courses (the second class), the two classes with other courses, enrich the entire teaching system. And through the series of industrial robotic laboratory construction and management model innovations, it can achieve the true experience of students’ corporate life and the wide range of students’ second classroom activities; it can cultivate excellent applied talents.
Construction and next-generation sequencing analysis of a large phage-displayed VNAR single-domain antibody library from six naïve nurse sharks
Authors: Feng Mingqian , Bian Hejiao , Wu Xiaolin , Fu Tianyun , Fu Ying , Hong Jessica , Fleming Bryan D , Flajnik Martin F , Ho Mitchell 
Published: November 2018

ABSTRACT

Background
Shark new antigen receptor variable domain (VNAR) antibodies can bind restricted epitopes that may be inaccessible to conventional antibodies.

Methods
Here, we developed a library construction method based on polymerase chain reaction (PCR)-Extension Assembly and Self-Ligation (named “EASeL”) to construct a large VNAR antibody library with a size of 1.2 × 1010 from six naïve adult nurse sharks (Ginglymostoma cirratum).

Results
The next-generation sequencing analysis of 1.19 million full-length VNARs revealed that this library is highly diversified because it covers all four classical VNAR types (Types I–IV) including 11% of classical Type I and 57% of classical Type II. About 30% of the total VNARs could not be categorized as any of the classical types. The high variability of complementarity determining region (CDR) 3 length and cysteine numbers are important for the diversity of VNARs. To validate the use of the shark VNAR library for antibody discovery, we isolated a panel of VNAR phage binders to cancer therapy-related antigens, including glypican-3, human epidermal growth factor receptor 2 (HER2), and programmed cell death-1 (PD1). Additionally, we identified binders to viral antigens that included the Middle East respiratory syndrome (MERS) and severe acute respiratory syndrome (SARS) spike proteins. The isolated shark single-domain antibodies including Type I and Type II VNARs were produced in Escherichia coli and validated for their antigen binding. A Type II VNAR (PE38-B6) has a high affinity (Kd = 10.1 nM) for its antigen.

Conclusions
The naïve nurse shark VNAR library is a useful source for isolating single-domain antibodies to a wide range of antigens. The EASeL method may be applicable to the construction of other large diversity gene expression libraries.
Trap Crops: How Far We Are From Using Them in Cereal Crops?
Authors: Sharma Anamika , Shrestha Govinda , Reddy Gadi V P 
Published: November 2018

AbstractTrap crops are plants grown along with the main crop in order to manipulate insect behavior to manage the insect pests and are used as a cultural management strategy in several crops. Trap crops also provide habitat to natural enemies and can reduce the need for insecticides and hence reduce the development of insecticide resistance. The attractiveness of the trap crop, the timing of planting, and the space it occupies are major factors to consider before selecting and using a trap crop. The addition of semiochemicals and incorporation of ‘stimulo-deterrent diversion’ can increase the efficiency of trap crops. The important insect pests of cereal crops reported to managed by using trap crops include the wheat stem sawfly, Cephus cinctus Norton (Hymenoptera: Cephidae), on wheat and the stem borers Chilo partellus (Swinhoe) and Busseola fusca (Fuller) on maize and sorghum. Other insect pests such as soil-dwelling wireworms [Agriotes obscurus L., Limonius californicus (Mannerheim) (Coleoptera: Elateridae)] on potatoes and the aphids Schizaphis graminum (Rondani) (Hemiptera: Aphididae), and Rhopalosiphum padi L. on wheat and the brown planthopper Nilaparvata lugens (Stål) on rice are also possible to manage by using trap crops. Cereal crops such as maize and wheat are sometimes themselves used as trap crops, yet there have been only a handful of attempts made to use trap crops in cereal crops. The major limiting factors in using trap crops in cereal crops are environmental conditions, variation in landscape and cultivation practices. Nonetheless, trap crops remain an important tool of integrated pest management, and future studies should work to improve the efficacy, cost efficiency, and availability of alternative trap crops for use in cereal cultivation.
Evaluation of Exposure Assessment Tools under REACH: Part II—Higher Tier Tools
Authors: Lee Eun Gyung , Lamb Judith , Savic Nenad , Basinas Ioannis , Gasic Bojan , Jung Christian , Kashon Michael L , Kim Jongwoon , Tischer Martin , van Tongeren Martie , Vernez David , Harper Martin 
Published: November 2018

Abstract
Stoffenmanager®v4.5 and Advanced REACH Tool (ART) v1.5, two higher tier exposure assessment tools for use under REACH, were evaluated by determining accuracy and robustness. A total of 282 exposure measurements from 51 exposure situations (ESs) were collected and categorized by exposure category. In this study, only the results of liquids with vapor pressure (VP) &gt; 10 Pa category having a sufficient number of exposure measurements (n = 251 with 42 ESs) were utilized. In addition, the results were presented by handling/activity description and input parameters for the same exposure category. It should be noted that the performance results of Stoffenmanager and ART in this study cannot be directly compared for some ESs because ART allows a combination of up to four subtasks (and nonexposed periods) to be included, whereas the database for Stoffenmanager, separately developed under the permission of the legal owner of Stoffenmanager, permits the use of only one task to predict exposure estimates. Thus, it would be most appropriate to compare full-shift measurements against ART predictions (full shift including nonexposed periods) and task-based measurements against task-based Stoffenmanager predictions. For liquids with VP &gt; 10 Pa category, Stoffenmanager®v4.5 appeared to be reasonably accurate and robust when predicting exposures [percentage of measurements exceeding the tool’s 90th percentile estimate (%M &gt; T) was 15%]. Areas that could potentially be improved include ESs involving the task of handling of liquids on large surfaces or large work pieces, allocation of high and medium VP inputs, and absence of local exhaust ventilation input. Although the ART’s median predictions appeared to be reasonably accurate for liquids with VP &gt; 10 Pa, the %M &gt; T for the 90th percentile estimates was 41%, indicating that variance in exposure levels is underestimated by ART. The %M &gt; T using the estimates of the upper value of 90% confidence interval (CI) of the 90th percentile estimate (UCI90) was considerably reduced to 18% for liquids with VP &gt; 10 Pa. On the basis of this observation, users might be to consider using the upper limit value of 90% CI of the 90th percentile estimate for predicting reasonable worst case situations. Nevertheless, for some activities and input parameters, ART still shows areas to be improved. Hence, it is suggested that ART developers review the assumptions in relation to exposure variability within the tool, toward improving the tool performance in estimating percentile exposure levels. In addition, for both tools, only some handling/activity descriptions and input parameters were considered. Thus, further validation studies are still necessary.
BacPaCS—Bacterial Pathogenicity Classification via Sparse-SVM
Authors: Barash Eran , Sal-Man Neta , Sabato Sivan , Ziv-Ukelson Michal 
Published: November 2018

Abstract

Motivation
Bacterial infections are a major cause of illness worldwide. However, most bacterial strains pose no threat to human health and may even be beneficial. Thus, developing powerful diagnostic bioinformatic tools that differentiate pathogenic from commensal bacteria are critical for effective treatment of bacterial infections.

Results
We propose a machine-learning approach for classifying human-hosted bacteria as pathogenic or non-pathogenic based on their genome-derived proteomes. Our approach is based on sparse Support Vector Machines (SVM), which autonomously selects a small set of genes that are related to bacterial pathogenicity. We implement our approach as a tool—‘Bacterial Pathogenicity Classification via sparse-SVM’ (BacPaCS)—which is fully automated and handles datasets significantly larger than those previously used. BacPaCS shows high accuracy in distinguishing pathogenic from non-pathogenic bacteria, in a clinically relevant dataset, comprising only human-hosted bacteria. Among the genes that received the highest positive weight in the resulting classifier, we found genes that are known to be related to bacterial pathogenicity, in addition to novel candidates, whose involvement in bacterial virulence was never reported.

Availability and implementation
The code and the resulting model are available at: https://github.com/barashe/bacpacs.

Supplementary information
Supplementary data are available at Bioinformatics online.
DeepT3: deep convolutional neural networks accurately identify Gram-negative bacterial type III secreted effectors using the N-terminal sequence
Authors: Xue Li , Tang Bin , Chen Wei , Luo Jiesi 
Published: November 2018

Abstract

Motivation
Various bacterial pathogens can deliver their secreted substrates also called effectors through Type III secretion systems (T3SSs) into host cells and cause diseases. Since T3SS secreted effectors (T3SEs) play important roles in pathogen–host interactions, identifying them is crucial to our understanding of the pathogenic mechanisms of T3SSs. However, the effectors display high level of sequence diversity, therefore making the identification a difficult process. There is a need to develop a novel and effective method to screen and select putative novel effectors from bacterial genomes that can be validated by a smaller number of key experiments.

Results
We develop a deep convolution neural network to directly classify any protein sequence into T3SEs or non-T3SEs, which is useful for both effector prediction and the study of sequence-function relationship. Different from traditional machine learning-based methods, our method automatically extracts T3SE-related features from a protein N-terminal sequence of 100 residues and maps it to the T3SEs space. We train and test our method on the datasets curated from 16 species, yielding an average classification accuracy of 83.7% in the 5-fold cross-validation and an accuracy of 92.6% for the test set. Moreover, when comparing with known state-of-the-art prediction methods, the accuracy of our method is 6.31–20.73% higher than previous methods on a common independent dataset. Besides, we visualize the convolutional kernels and successfully identify the key features of T3SEs, which contain important signal information for secretion. Finally, some effectors reported in the literature are used to further demonstrate the application of DeepT3.

Availability and implementation
DeepT3 is freely available at: https://github.com/lje00006/DeepT3.

Supplementary information
Supplementary data are available at Bioinformatics online.
OPA2Vec: combining formal and informal content of biomedical ontologies to improve similarity-based prediction
Authors: Smaili Fatima Zohra , Gao Xin , Hoehndorf Robert 
Published: November 2018

AbstractMotivationOntologies are widely used in biology for data annotation, integration and analysis. In addition to formally structured axioms, ontologies contain meta-data in the form of annotation axioms which provide valuable pieces of information that characterize ontology classes. Annotation axioms commonly used in ontologies include class labels, descriptions or synonyms. Despite being a rich source of semantic information, the ontology meta-data are generally unexploited by ontology-based analysis methods such as semantic similarity measures.ResultsWe propose a novel method, OPA2Vec, to generate vector representations of biological entities in ontologies by combining formal ontology axioms and annotation axioms from the ontology meta-data. We apply a Word2Vec model that has been pre-trained on either a corpus or abstracts or full-text articles to produce feature vectors from our collected data. We validate our method in two different ways: first, we use the obtained vector representations of proteins in a similarity measure to predict protein–protein interaction on two different datasets. Second, we evaluate our method on predicting gene–disease associations based on phenotype similarity by generating vector representations of genes and diseases using a phenotype ontology, and applying the obtained vectors to predict gene–disease associations using mouse model phenotypes. We demonstrate that OPA2Vec significantly outperforms existing methods for predicting gene–disease associations. Using evidence from mouse models, we apply OPA2Vec to identify candidate genes for several thousand rare and orphan diseases. OPA2Vec can be used to produce vector representations of any biomedical entity given any type of biomedical ontology.Availability and implementationhttps://github.com/bio-ontology-research-group/opa2vecSupplementary informationSupplementary data are available at Bioinformatics online.
Age-Related Differences in Brain Morphology and the Modifiers in Middle-Aged and Older Adults
Authors: Zhao Lu , Matloff William , Ning Kaida , Kim Hosung , Dinov Ivo D , Toga Arthur W 
Published: November 2018

AbstractBrain structural morphology differs with age. This study examined age-differences in surface-based morphometric measures of cortical thickness, volume, and surface area in a well-defined sample of 8137 generally healthy UK Biobank participants aged 45–79 years. We illustrate that the complexity of age-related brain morphological differences may be related to the laminar organization and regional evolutionary history of the cortex, and age of about 60 is a break point for increasing negative associations between age and brain morphology in Alzheimer’s disease (AD)-prone areas. We also report novel relationships of age-related cortical differences with individual factors of sex, cognitive functions of fluid intelligence, reaction time and prospective memory, cigarette smoking, alcohol consumption, sleep disruption, genetic markers of apolipoprotein E, brain-derived neurotrophic factor, catechol-O-methyltransferase, and several genome-wide association study loci for AD and further reveal joint effects of cognitive functions, lifestyle behaviors, and education on age-related cortical differences. These findings provide one of the most extensive characterizations of age associations with major brain morphological measures and improve our understanding of normal structural brain aging and its potential modifiers.
Disseminated Gonococcal Infections in Patients Receiving Eculizumab: A Case Series
Authors: Crew Page E , Abara Winston E , McCulley Lynda , Waldron Peter E , Kirkcaldy Robert D , Weston Emily J , Bernstein Kyle T , Jones S Christopher , Bersoff-Matcha Susan J 
Published: November 2018

Abstract

Background
Gonorrhea is the second most commonly reported notifiable condition in the United States. Infrequently, Neisseria gonorrhoeae can cause disseminated gonococcal infection (DGI). Eculizumab, a monoclonal antibody, inhibits terminal complement activation, which impairs the ability of the immune system to respond effectively to Neisseria infections. This series describes cases of N. gonorrhoeae infection among patients receiving eculizumab.

Methods
Pre- and postmarketing safety reports of N. gonorrhoeae infection in patients receiving eculizumab worldwide were obtained from US Food and Drug Administration safety databases and the medical literature, including reports from the start of pivotal clinical trials in 2004 through 31 December 2017. Included patients had at least 1 eculizumab dose within the 3 months prior to N. gonorrhoeae infection.

Results
Nine cases of N. gonorrhoeae infection were identified; 8 were classified as disseminated (89%). Of the disseminated cases, 8 patients required hospitalization, 7 had positive blood cultures, and 2 required vasopressor support. One patient required mechanical ventilation. Neisseria gonorrhoeae may have contributed to complications prior to death in 1 patient; however, the fatality was attributed to underlying disease per the reporter.

Conclusions
Patients receiving eculizumab may be at higher risk for DGI than the general population. Prescribers are encouraged to educate patients receiving eculizumab on their risk for serious gonococcal infections and perform screening for sexually transmitted diseases (STDs) per the Centers for Disease Control and Prevention STD treatment guidelines or in suspected cases. If antimicrobial prophylaxis is used during eculizumab therapy, prescribers should consider trends in gonococcal antimicrobial susceptibility due to emerging resistance concerns.
Repigmentation in vitiligo universalis after starting dialysis—could they be related?
Authors: Farahbakhsh Navid , Nielson Colton , Gillihan Ryan 
Published: November 2018

AbstractVitiligo is an acquired disorder of pigmentation characterized by the development of white macules and patches on the skin. Although multiple theories have been proposed to understand the underlying pathophysiology behind the pigment loss, the exact etiology remains unknown. Vitiligo universalis is an extremely rare variant that causes nearly complete depigmentation of the entire body surface. Treatment is challenging, especially when pigment loss is generalized and diffuse. We present a unique case of a patient with vitiligo universalis that had remained untreated and stable for >20 years until she developed repigmentation shortly after initiation of dialysis.
Extracorporeal immunoadsorption in heparin- and protamine-induced thrombocytopaenia prior to cardiac surgery
Authors: Füreder Lisa , Böhmig Georg A , Schaefer Anne-Kristin , Steinlechner Barbara 
Published: November 2018

Abstract
Exposure to heparin and protamine during cardiac surgery on cardiopulmonary bypass (CPB) may trigger heparin-induced thrombocytopaenia and/or protamine-induced thrombocytopaenia. Further surgery on CPB with heparin and protamine in the presence of these antibodies implies increased thromboembolic risk. We present the successful application of extracorporeal immunoadsorption to deplete antibodies causing heparin-induced and protamine-induced thrombocytopaenia preoperatively.