bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of a bioassay to detect T-cell-activating impurities for T-cell-dependent bispecific antibodies
Authors: Lee Ho Young , Contreras Edward , Register Ames C. , Wu Qiang , Abadie Kathleen , Garcia Khristofer , Wong Pin Yee , Jiang Guoying 
Published: March 2019

AbstractT-cell-dependent bispecific antibodies (TDBs) are promising cancer immunotherapies that recruit a patient’s T cells to kill cancer cells. There are increasing numbers of TBDs in clinical trials, demonstrating their widely recognized therapeutic potential. Due to the fact that TDBs engage and activate T cells via an anti-CD3 (aCD3) arm, aCD3 homodimer (aCD3 HD) and high-molecular-weight species (HMWS) are product-related impurities that pose a potential safety risk by triggering off-target T-cell activation through bivalent engagement and dimerization of T-cell receptors (TCRs). To monitor and control the level of unspecific T-cell activation, we developed a sensitive and quantitative T-cell-activation assay, which can detect aCD3 HD in TDB drug product by exploiting its ability to activate T cells in the absence of target cells. This assay providesin-vivo-relevant off-target T-cell-activation readout. Furthermore, we have demonstrated that this assay can serve as a platform assay for detecting T-cell-activating impurities across a broad spectrum of aCD3 bispecific molecules. It therefore has the potential to significantly benefit many T-cell-recruiting bispecific programs.
Comparison of the bioavailability of benzo[a]pyrene (B[a]P) in a B[a]P-contaminated soil using the different addition approaches
Authors: Ye Xinxin , Ma Jingjing , Wei Junling , Sun Kai , Xiong Qizhong 
Published: March 2019

AbstractDetermination of the bioavailability of the hydrophobic organic contaminant benzo[a]pyrene (B[a]P) is extremely important for assessing its environmental risk. The effect of addition manner of B[a]P on the bioavailability and toxicity of B[a]P in soil remains unclear. In this study, soil samples, spiked with B[a]P by one-time or multiple-time additions, were tested to investigate the available fraction of B[a]P in soils, the uptake of B[a]P by red wiggler worms (Eisenia fetida), as well as superoxide dismutase (SOD) and peroxidase (POD) activities in earthworm coelomocytes at different periods. Results showed that the available fraction of B[a]P in soils and the amount of B[a]P assimilated by earthworms declined sharply from 1 d to 28 d during the incubation period and then decreased slowly from 28 to 56 d in both the one-time and the multiple-time addition tests. The available fraction of B[a]P in soils and its uptake by earthworms were significantly lower in multiple-time addition samples than those in one-time addition samples, a finding which was consistent with the SOD and POD activities in earthworms during the whole 56-d incubation period. These variations in the characteristics of the two addition treatments may be due to the differences in the way the B[a]P aged in the soil. These results indicated that the addition method was an important factor influencing the bioavailability of organic contaminants in soils.
Towards a gamete matching platform: using immunogenetics and artificial intelligence to predict recurrent miscarriage
Authors: Mora-Sánchez Aldo , Aguilar-Salvador Daniel-Isui , Nowak Izabela 
Published: March 2019

AbstractThe degree of Allele sharing of the Human Leukocyte Antigen (HLA) genes has been linked with recurrent miscarriage (RM). However, no clear genetic markers of RM have yet been identified, possibly because of the complexity of interactions between paternal and maternal genes during embryo development. We propose a methodology to analyse HLA haplotypes from couples either with histories of successful pregnancies or RM. This article describes a method of RM genetic-risk calculation. The proposed HLA representation techniques allowed us to create an algorithm (IMMATCH) to retrospectively predict RM with an AUC = 0.71 (p = 0.0035) thanks to high-resolution typing and the use of linear algebra on peptide binding affinity data. The algorithm features an adjustable threshold to increase either sensitivity or specificity, allowing a sensitivity of 86%. Combining immunogenetics with artificial intelligence could create personalised tools to better understand the genetic causes of unexplained infertility and a gamete matching platform that could increase pregnancy success rates.
LncRNA SNHG20 predicts a poor prognosis and promotes cell progression in epithelial ovarian cancer
Authors: Wang Dandan , Dai Jianrong , Hou Shunyu , Qian Yonghong 
Published: March 2019

Abstract
The long noncoding RNA small nucleolar RNA host gene 20 (SNHG20) has been demonstrated to play a crucial role in cancer progression. However, the functions of SNHG20 in epithelial ovarian cancer (EOC) are not well established. The aim of the present study was to investigate SNHG20 clinical significance and its underlying mechanism in proliferation and metastasis in EOC. The expression level of SNHG20 was identified via in situ hybridization (ISH) and quantitative RT-PCR (qRT-PCR). The proliferative and metastatic capacities by silencing SNHG20 expression in A2780 and CAOV-3 cells were measured by cell counting kit-8 (CCK-8) and transwell assays. The molecular mRNA and protein expressions were examined using qRT-PCR, Western blot, and double immunofluorescent staining. SNHG20 expression was markedly higher in serous EOC tissues than that in adjacent tissues and closely correlated with histological grade and lymph node (LN) status. Patients with high SNHG20 showed a shorter overall survival (OS) and SNHG20 was an independent risk factor for the prognosis of serous EOC. Knockdown of SNHG20 remarkably inhibited EOC cell proliferation, migration, and invasion, which was associated with dysregulation of P21, Cyclin D1, E-cadherin, and Vimentin. These results suggest that SNHG20 may serve as an independent prognostic predictor and function as a noncoding oncogene in EOC progression, which might be a possible novel diagnostic marker and treatment target.
Confidence of School-Based Speech-Language Pathologists and School Psychologists in Assessing Students With Hearing Loss and Other Co-Occurring Disabilities
Authors: Muncy Monica P. , Yoho Sarah E. , McClain Maryellen Brunson 
Published: March 2019

Purpose
This study assessed the confidence of speech-language pathologists (SLPs) and school psychologists (SPs) in working with children with hearing loss (HL) and other co-occurring disabilities. Professionals' opinions on barriers to and importance of interdisciplinary collaboration were also of interest.

Method
A 59-item online survey was distributed to SLPs and SPs in the United States through state professional organizations and social media posts. A total of 320 respondents completed the survey and met criteria. Perceptions of confidence across 5 different skill set types were assessed, along with experiences and attitudes concerning professional training and interdisciplinary collaboration.

Results
A 2-way analysis of variance revealed significant main effects of profession and skill set type on professionals' confidence in assessing a student with HL and other co-occurring disabilities, as well as their confidence in determining the etiology of a student's difficulties. Results from a multiple linear regression revealed the number of students worked with who have HL and the amount of training in graduate school as significant predictors of confidence in both aforementioned skill set types. Results indicate that respondents value interdisciplinary collaboration but that time and access to other professionals are barriers to collaboration.

Conclusions
Results of the current study indicate that many school-based SLPs and SPs have insufficient training or experience in working with students who have HL and other co-occurring disabilities. Limited training and experience with this unique population among practitioners have the potential to affect the quality of services provided to these students and thus need to be addressed within the school system and the fields of school psychology and speech-language pathology.

Supplemental Material

https://doi.org/10.23641/asha.7772867
Textile split ring resonator antenna integrated by embroidery
Authors: Hao J. , Leblanc A. , Burgnies L. , Djouadi A. , Cochrane C. , Rault F. , Koncar V. , Lheurette É. 
Published: March 2019

A split ring resonator (SRR) antenna integrated in textile by embroidery is reported. The antenna was designed and produced by targeting two goals. First, a size reduction of the antenna was achieved by means of an SRR. Secondly, the connection loss was reduced by using a copper wire dipole fixed by embroidery. On the basis of numerical simulations, three operating modes are evidenced depending on the individual resonance frequency either of the dipole or resonator‐related. Especially, a balanced mode is confirmed by experiments with two resonances measured at 1.8 and 2.2 GHz with a return loss greater than 31 dB. Finally, the textile antenna exhibits a radiation pattern similar to the radiation pattern of a dipole antenna.
Understanding Health Information Technology Induced Medication Safety Events by Two Conceptual Frameworks
Authors: Wang Ju , Liang Hongyuan , Kang Hong , Gong Yang 
Published: March 2019

Background While health information technology (health IT) is able to prevent medication errors in many ways, it may also potentially introduce new paths to errors. To understand the impact of health IT induced medication errors, this study aims to conduct a retrospective analysis of medication safety reports.
Methods From the U.S. Food and Drug Administration (FDA) Manufacturer and User Facility Device Experience database, we identified reports in which health IT is a contributing factor to medication errors. We applied two conceptual frameworks, Sittig and Singh's sociotechnical model and Coiera's information value chain, to examine the identified reports.
Results We identified 152 unique reports on health IT induced medication errors as the final report set for review. The majority (65.13%) of the reports involved multiple contributing factors according to the sociotechnical model. Three dimensions, that is, clinical content, human–computer interface, and people, were involved in more reports than the others. The transition of the effects of health IT on medication practice was summarized using information value chain. Health IT related contributing factors may lead to receiving wrong information, missing information, receiving partial information and delayed information, and receiving wrong information and missing information tend to cause the commission errors in decision-making.
Conclusion The two frameworks provide an opportunity to understand a comprehensive context of safety event and the impact of health IT induced errors on medication safety. The sociotechnical model helps identify the aspects causing medication safety issues. The information value chain helps uncover the effect of the health IT induced medication errors on health care process and patient outcomes.
Environment-dependent fitness gains can be driven by horizontal gene transfer of transporter-encoding genes
Authors: Milner David S. , Attah Victoria , Cook Emily , Maguire Finlay , Savory Fiona R. , Morrison Mark , Müller Carolin A. , Foster Peter G. , Talbot Nicholas J. , Leonard Guy , Richards Thomas A. 
Published: March 2019

SignificanceHorizontal gene transfer (HGT) is the transfer of genetic information between genomes by a route other than from parent to offspring. Of particular interest here are the transfers of transporter-encoding genes, which can allow an organism to utilize a new metabolite, often via the acquisition of a single foreign gene. Here we have identified a range of HGT events of transporter-encoding genes, characterized the substrate preferences for each HGT encoded protein, and demonstrated that the gain of one of these HGTs can provide yeast with a distinct competitive advantage in a given environment. This has wide implications for understanding how acquisition of single genes by HGT can drastically influence the environments fungi can colonize.
Chinese scholarship in Cognitive Translation Studies
Authors: Sun Sanjun , Xiao Kairong 
Published: March 2019

Abstract
In the last two decades, cognitive translation studies in China has been gaining momentum, which is spurred by
three lines or perspectives of inquiry: psychology (especially cognitive psychology and psycholinguistics), cognitive linguistics,
and translation process research (TPR). Despite the limited numbers of researchers in the first two lines, their increasing number
of monographs reflects their influence. Also, while the first two lines have distinctive Chinese characteristics, TPR has been
quite parallel to its Western counterpart. This paper offers a survey of Chinese researchers in the three lines, mainly including
those in the Chinese mainland, Hong Kong, Macau, and Taiwan. It briefly presents dissertations, publications and current lines of
work. As many of the researchers publish in Chinese only, this paper provides a window for looking at the Chinese research scene
in cognitive translation studies.
The Cultural Importance of Edible Insects in Oaxaca, Mexico
Authors: Hurd Kayla J , Shertukde Shruti , Toia Trevor , Trujillo Angelina , Pérez Ramona L , Larom David L , Love John J , Liu Changqi 
Published: March 2019

Abstract
Insects have great potential to serve as a sustainable food source owing to their notable nutritional value, high feed conversion rate, and low environmental footprint. The sharing of well-established recipes in cultures where insect consumption is normalized can facilitate new product development among cultures where consumption is resisted. In the current investigation, we traveled to both rural and urban areas of Oaxaca, Mexico and studied the collection, processing, retailing, and eating practices of edible insects such as chapulines [Sphenarium purpurascens Charpentier (Pyrgomorphidae, Orthoptera) and Melanoplus mexicanus (Saussure) (Acrididae, Orthoptera)], chicatanas [Atta mexicana (F. Smith) (Formicidae, Hymenoptera)], maguey worms [Comadia redtenbacheri (Hammerschmidt) (Cossidae, Lepidoptera)], and cochineal [Dactylopius coccus Costa (Dactylopiidae, Hemiptera)]. In rural communities where access to other animal-based foods has been limited, insects provided important nutritional value that today also translates into important economic value. Community members know the habits of the insects and are skilled at collecting them using sophisticated techniques. After collection, the insects are often toasted with or without seasonings for flavor and preservation. The processed insects are readily available in urban markets, and their importance in Oaxacan cuisine cannot be overestimated. Chapulines, chicatanas, and maguey worms are key ingredients in many spice mixes, salsas, and mole sauces. Cochineal is used as a food colorant. These insects are also found in a variety of foods, both sweet and savory, including omelets, tamales, quesadillas, chocolate truffles, and sorbets. As evidenced by the culinary uses of insects in Oaxaca, there is substantial potential for edible insects to become a delicacy in Western cultures.
Long-Term Associations Between Disaster Experiences and Cardiometabolic Risk: A Natural Experiment From the 2011 Great East Japan Earthquake and Tsunami
Authors: Shiba Koichiro , Hikichi Hiroyuki , Aida Jun , Kondo Katsunori , Kawachi Ichiro 
Published: March 2019

AbstractWe investigated the association between disaster experience and the cardiometabolic risk of survivors 2.5 years after disaster onset, adjusting for health information predating the disaster, using natural experiment data stemming from the 2011 Great East Japan Earthquake and Tsunami. We used data from a cohort of adults aged 65 years or older in Iwanuma City, Japan, located 80 km (128 miles) west of the earthquake epicenter. The baseline survey was completed 7 months before the disaster, and the follow-up survey was performed among survivors approximately 2.5 years after the disaster. The survey data were linked to medical records with information on objectively measured cardiometabolic risk factors (n = 1,195). The exposure of interest was traumatic disaster experiences (i.e., housing damage and loss of loved ones). Fixed-effects regression showed that complete housing destruction was significantly associated with a 0.81-unit greater change in body mass index (weight (kg)/height (m)2; 95% confidence interval (CI): 0.24, 1.38), a 4.26-cm greater change in waist circumference (95% CI: 1.12, 7.41), and a 4.77-mg/dL lower change in high-density lipoprotein cholesterol level (95% CI: −7.96, −1.58) as compared with no housing damage. We also observed a significant association between major housing damage and decreased systolic blood pressure. Continued health checkups and supports for victims who lost homes should be considered to maintain their cardiometabolic health.
Experimentally induced antipredator responses are mediated by social and environmental factors
Authors: Groenewoud Frank , Kingma Sjouke A , Bebbington Kat , Richardson David S , Komdeur Jan 
Published: March 2019

AbstractNest predation is a common cause of reproductive failure for many bird species, and various antipredator defense behaviors have evolved to reduce the risk of nest predation. However, trade-offs between current reproductive duties and future reproduction often limit the parent’s ability to respond to nest predation risk. Individual responses to experimentally increased nest predation risk can give insights into these trade-offs. Here, we investigate whether social and ecological factors affect individual responses to predation risk by experimentally manipulating the risk of nest predation using taxidermic mounts in the cooperative breeding Seychelles warbler (Acrocephalus sechellensis). Our results show that dominant females, but not males, alarm called more often when they confront a nest predator model alone than when they do so with a partner, and that individuals that confront a predator together attacked more than those that did so alone. Dominant males increased their antipredator defense by spending more time nest guarding after a presentation with a nest predator, compared with a nonpredator control, but no such effect was found for females, who did not increase the time spent incubating. In contrast to incubation by females, nest guarding responses by dominant males depended on the presence of other group members and food availability. These results suggest that while female investment in incubation is always high and not dependent on social and ecological conditions, males have a lower initial investment, which allows them to respond to sudden changes in nest predation risk.
MeSHProbeNet: a self-attentive probe net for MeSH indexing
Authors: Xun Guangxu , Jha Kishlay , Yuan Ye , Wang Yaqing , Zhang Aidong 
Published: March 2019

Abstract

Motivation
MEDLINE is the primary bibliographic database maintained by National Library of Medicine (NLM). MEDLINE citations are indexed with Medical Subject Headings (MeSH), which is a controlled vocabulary curated by the NLM experts. This greatly facilitates the applications of biomedical research and knowledge discovery. Currently, MeSH indexing is manually performed by human experts. To reduce the time and monetary cost associated with manual annotation, many automatic MeSH indexing systems have been proposed to assist manual annotation, including DeepMeSH and NLM’s official model Medical Text Indexer (MTI). However, the existing models usually rely on the intermediate results of other models and suffer from efficiency issues. We propose an end-to-end framework, MeSHProbeNet (formerly named as xgx), which utilizes deep learning and self-attentive MeSH probes to index MeSH terms. Each MeSH probe enables the model to extract one specific aspect of biomedical knowledge from an input article, thus comprehensive biomedical information can be extracted with different MeSH probes and interpretability can be achieved at word level. MeSH terms are finally recommended with a unified classifier, making MeSHProbeNet both time efficient and space efficient.

Results
MeSHProbeNet won the first place in the latest batch of Task A in the 2018 BioASQ challenge. The result on the last test set of the challenge is reported in this paper. Compared with other state-of-the-art models, such as MTI and DeepMeSH, MeSHProbeNet achieves the highest scores in all the F-measures, including Example Based F-Measure, Macro F-Measure, Micro F-Measure, Hierarchical F-Measure and Lowest Common Ancestor F-measure. We also intuitively show how MeSHProbeNet is able to extract comprehensive biomedical knowledge from an input article.
A Gaussian process model and Bayesian variable selection for mapping function-valued quantitative traits with incomplete phenotypic data
Authors: Vanhatalo Jarno , Li Zitong , Sillanpää Mikko J 
Published: March 2019

AbstractMotivationRecent advances in high dimensional phenotyping bring time as an extra dimension into the phenotypes. This promotes the quantitative trait locus (QTL) studies of function-valued traits such as those related to growth and development. Existing approaches for analyzing functional traits utilize either parametric methods or semi-parametric approaches based on splines and wavelets. However, very limited choices of software tools are currently available for practical implementation of functional QTL mapping and variable selection.ResultsWe propose a Bayesian Gaussian process (GP) approach for functional QTL mapping. We use GPs to model the continuously varying coefficients which describe how the effects of molecular markers on the quantitative trait are changing over time. We use an efficient gradient based algorithm to estimate the tuning parameters of GPs. Notably, the GP approach is directly applicable to the incomplete datasets having even larger than 50% missing data rate (among phenotypes). We further develop a stepwise algorithm to search through the model space in terms of genetic variants, and use a minimal increase of Bayesian posterior probability as a stopping rule to focus on only a small set of putative QTL. We also discuss the connection between GP and penalized B-splines and wavelets. On two simulated and three real datasets, our GP approach demonstrates great flexibility for modeling different types of phenotypic trajectories with low computational cost. The proposed model selection approach finds the most likely QTL reliably in tested datasets.Availability and implementationSoftware and simulated data are available as a MATLAB package ‘GPQTLmapping’, and they can be downloaded from GitHub (https://github.com/jpvanhat/GPQTLmapping). Real datasets used in case studies are publicly available at QTL Archive.Supplementary informationSupplementary data are available at Bioinformatics online.