bluuebunny/crossref_metadata_2025_split huggingface dataset:
DTMiner: identification of potential disease targets through biomedical literature mining
Authors: Xu Dong , Zhang Meizhuo , Xie Yanping , Wang Fan , Chen Ming , Zhu Kenny Q. , Wei Jia 
Published: August 2016

Motivation: Biomedical researchers often search through massive catalogues of literature to look for potential relationships between genes and diseases. Given the rapid growth of biomedical literature, automatic relation extraction, a crucial technology in biomedical literature mining, has shown great potential to support research of gene-related diseases. Existing work in this field has produced datasets that are limited both in scale and accuracy.
Results: In this study, we propose a reliable and efficient framework that takes large biomedical literature repositories as inputs, identifies credible relationships between diseases and genes, and presents possible genes related to a given disease and possible diseases related to a given gene. The framework incorporates name entity recognition (NER), which identifies occurrences of genes and diseases in texts, association detection whereby we extract and evaluate features from gene–disease pairs, and ranking algorithms that estimate how closely the pairs are related. The F1-score of the NER phase is 0.87, which is higher than existing studies. The association detection phase takes drastically less time than previous work while maintaining a comparable F1-score of 0.86. The end-to-end result achieves a 0.259 F1-score for the top 50 genes associated with a disease, which performs better than previous work. In addition, we released a web service for public use of the dataset.
Availability and Implementation: The implementation of the proposed algorithms is publicly available at http://gdr-web.rwebox.com/public_html/index.php?page=download.php. The web service is available at http://gdr-web.rwebox.com/public_html/index.php.
Contact: jenny.wei@astrazeneca.com or kzhu@cs.sjtu.edu.cn
Supplementary information: Supplementary data are available at Bioinformatics online.
VLBI observations of flared optical quasar CGRaBS J0809+5341
Authors: An Tao , Cui Yu-Zhu , Paragi Zsolt , Frey Sándor , Gurvits Leonid I. , Gabányi Krisztina É. 
Published: August 2016

Abstract
A bright optical flare was detected in the high-redshift (z = 2.133) quasar CGRaBS J0809+5341 on 2014 April 13. The absolute magnitude of the object reached −30.0 during the flare, making it the brightest one (in flaring stage) among all known quasars so far. The 15-GHz flux density of CGRaBS J0809+5341 monitored in the period from 2008 to 2016 also reached its peak at the same time. To reveal any structural change possibly associated with the flare in the innermost radio structure of the quasar, we conducted a pilot very long baseline interferometry (VLBI) observation of CGRaBS J0809+5341 using the European VLBI Network (EVN) at 5 GHz on 2014 November 18, about seven months after the prominent optical flare. Three epochs of follow-up KaVA (Korean VLBI Network and VLBI Exploration of Radio Astrometry Array) observations were carried out at 22- and 43-GHz frequencies from 2015 February 25 to June 4, with the intention of exploring a possibly emerging new radio jet component associated with the optical flare. However, these high-resolution VLBI observations revealed only the milliarcsecond-scale compact “core” that was known in the quasar from earlier VLBI images, and showed no sign of any extended jet structure. Neither the size nor the flux density of the “core” changed considerably after the flare, according to our VLBI monitoring. The results suggest that any putative radio ejecta associated with the major optical and radio flare could not yet be separated from the “core” component, or the newly-born jet was short-lived.
Trends in the Nonmedical Use of OxyContin, United States, 2006 to 2013
Authors: Jones Christopher M. , Muhuri Pradip K. , Lurie Peter G. 
Published: August 2016

Objectives:
The role of the opioid OxyContin in the opioid abuse epidemic has been well documented. In 2010, OxyContin was reformulated to make it more difficult to abuse. We assessed past-year OxyContin nonmedical use among a nationally representative population and among nonmedical users of opioid pain relievers in the United States between 2006 and 2013.

Materials and Methods:
Data are from the National Survey on Drug Use and Health. Prevalence estimates of past-year OxyContin nonmedical use overall and by sociodemographic, geographic, and substance use characteristics were calculated for each year, 2006 through 2013. Multivariable logistic regression was used to identify individual characteristics associated with past-year OxyContin nonmedical use before and after reformulation.

Results:
In 2013, the of past-year nonmedical use of OxyContin among people 12 years and older in the United States was 0.5%. This was significantly lower than the prevalence in 2010 (0.7%; P<0.05), but was similar to that in 2006 to 2009 and 2011 to 2012. Among past-year nonmedical users of pain relievers in 2013, the prevalence of OxyContin nonmedical use was 13.0%. This was significantly higher than the prevalence in 2006 (10.5%; P<0.05), and was similar to that in 2007 through 2012. Groups with increased odds of using OxyContin nonmedically in the past-year were similar before and after reformulation (2009-2010 and 2012-2013, respectively). For 2012-2013, odds for past-year OxyContin nonmedical use after reformulation were greatest for: people reporting ≥200 days of pain reliever nonmedical use, adjusted odds ratio (aOR)=3.61 (95% confidence interval [CI], 2.47-5.28); past-year heroin users, aOR=3.45 (95% CI, 2.22-5.37); and people with past-year pain reliever abuse or dependence, aOR=2.57 (95% CI, 1.88-3.51).

Discussion:
The prevalence of past-year OxyContin nonmedical use in 2013, 3 years after reformulation, was significantly lower than the prevalence in the reformulation year, but similar to other years before and after reformulation. The prevalence of OxyContin nonmedical use among nonmedical users of pain relievers was higher than or similar to historical prevalence rates before reformulation. Groups with increased odds of OxyContin nonmedical use were similar before and after reformulation.
Age, Sex, Health Insurance, and Race Associated With Increased Rate of Emergent Pediatric Gastrointestinal Procedures
Authors: Andrews Ashley , Franklin Linda , Rush Natasha , Witts Robin , Blanco David , Pall Harpreet 
Published: August 2016

ABSTRACTObjectives:Few studies have examined the role health disparities play in pediatric gastrointestinal (GI) procedures. We hypothesized that health disparity factors affect whether patients undergo an emergent versus nonemergent GI procedure. The aims were to characterize the existing pediatric population undergoing GI procedures at our institution and assess specific risk factors associated with emergent versus nonemergent care.Methods:We retrospectively reviewed the medical records of 2110 patients undergoing GI procedures from January 2012 to December 2014. Emergent procedures were performed on an urgent inpatient basis. All other procedures were considered nonemergent. Health disparity factors analyzed included age, sex, insurance type, race, and language. Logistic regression analysis identified the odds of undergoing emergent procedures for each factor.Results:Most study patients were boys (58.2%), primarily insured by Medicaid (63.8%), white (44.0%), and spoke English (91.7%). Ten percent of all patients had an emergent procedure. Logistic regression analysis showed significant odds ratios (P value) for ages 18 years older (2.16, 0.003), females (0.62, 0.001), commercial insurance users (0.49, <0.0001), African Americans (1.94, <0.0001), and other race (1.72, 0.039).Conclusions:Health disparities in age, sex, insurance, and race appear to exist in this pediatric population undergoing GI procedures. Patients older than 18 years, African Americans, and other races were significantly more likely to have an emergent procedure. Girls and commercial insurance users were significantly less likely to have an emergent procedure. More research is necessary to understand why these relations exist and how to establish appropriate interventions.
Palmitoylation of the oncogenic RhoGEF TGAT is dispensable for membrane localization and consequent activation of RhoA
Authors: van Unen Jakobus , Botman Dennis , Yin Taofei , Wu Yi I. , Hink Mark A. , Gadella Theodorus W.J. , Postma Marten , Goedhart Joachim 
Published: August 2016

AbstractRho guanine exchange factors (RhoGEFs) control many aspects of the cellular cytoskeleton, and thereby regulate and control processes such as cell migration, cell adhesion and proliferation. TGAT is a splice variant of the RhoGEF Trio, with oncogenic potential. Whether the subcellular location of TGAT is critical for its activity is unknown. Confocal microscopy of fluorescent protein tagged TGAT revealed co-localization with a Golgi marker. Because plasma membrane localized RhoGEFs are particularly effective at activating RhoA, plasma membrane localization of TGAT was studied. In order to quantitatively measure plasma membrane association we developed a novel, highly sensitive image analysis method. The method requires a cytoplasmic marker and a plasma membrane marker, which are co-imaged with the tagged protein of interest. Linear unmixing is performed to determine the plasma membrane and cytoplasmic component in the fluorescence signal of protein of interest. The analysis revealed that wild-type TGAT is partially co-localized with the plasma membrane. Strikingly, cysteine TGAT-mutants lacking one or more palmitoylation sites in the C-tail, still showed membrane association. In contrast, a truncated variant, lacking the last 15 amino acids, TGATΔ15, lost membrane association. The functional role of membrane localization was determined by measuring TGAT activity in single cells with a RhoA FRET-sensor and F-actin levels. Mutants of TGAT that still maintained membrane association showed similar activity as wild-type TGAT. In contrast, the activity was abrogated for the cytoplasmic TGATΔ15variant. Synthetic recruitment of TGATΔ15to membranes confirmed that TGAT effectively activates RhoA at the plasma membrane. Together, these results show that membrane association of TGAT is critical for its activity, but that palmitoylation is dispensable.
Bacterial invasion of the pancreas revealed after analyses of the pancreatic cyst fluids
Authors: Narayanan Vilvapathy , Utomo Wesley K. , Bruno Marco J. , Peppelenbosch Maikel P. , Konstantinov Sergey R. 
Published: August 2016

AbstractThe involvement of bacterial translocation (BT) in the promotion of carcinogenesis has gained a considerable attention in the last years. At this point however BT has not been studied in the context of pancreatic cystic lesions and their development into pancreatic ductal adenocarcinoma. The aim of the study was to analyze if bacteria are present in pancreatic cyst fluid (PCF) collected from patients with suspected pancreatic cysts. Total DNA was isolated from sixty nine PCF. The occurrence of bacteria in PCF was analyzed using bacterial 16S rRNA gene-specific PCR-based method followed by sequence identification and quantitative PCR assay tuned up to different pathogenic and commensal human bacteria. Forty-seven out of sixty-nine samples (68%) were found positive for harboring bacterial 16S rRNA gene. Follow up sequencing analyses of the PCR products revealed that bacterial species related toFusobacterium spp., Bacteroides spp.,andBacillus spp.were predominating the PCF samples. The results suggest that specific bacteria can translocate to the pancreas and become detectable in the PCF.
Fitness costs of noise in biochemical reaction networks and the evolutionary limits of cellular robustness
Authors: David Van Dyken J. 
Published: August 2016

ABSTRACTGene expression is inherently noisy, but little is known about whether noise affects cell function or, if so, how and by how much. Here I present a theoretical framework to quantify the fitness costs of gene expression noise and identify the evolutionary and synthetic targets of noise control. I find that gene expression noise reduces fitness by slowing the average rate of nutrient uptake and protein synthesis. This is a direct consequence of the hyperbolic (Michaelis-Menten) kinetics of most biological reactions, which I show cause “hyperbolic filtering”, a process that diminishes both the average rate and noise propagation of stochastic reactions. Interestingly, I find that transcriptional noise directly slows growth by slowing the average translation rate. Perhaps surprisingly, this is the largest fitness cost of transcriptional noise since translation strongly filters mRNA noise, making protein noise largely independent of transcriptional noise, consistent with empirical data. Translation, not transcription, then, is the primary target of protein noise control. Paradoxically, selection for protein-noise control favors increased ribosome-mRNA binding affinity, even though this increases translational bursting. However, I find that the efficacy of selection to suppress noise decays faster than linearly with increasing cell size. This predicts a stark, cell-size-mediated taxonomic divide in selection pressures for noise control: small unicellular species, including most prokaryotes, face fairly strong selection to suppress gene expression noise, whereas larger unicells, including most eukaryotes, experience extremely weak selection. I suggest that this taxonomic discrepancy in selection efficacy contributed to the evolution of greater gene-regulatory complexity in eukaryotes.ARTICLE SUMMARYGene expression is a probabilistic process, resulting in random variation in mRNA and protein abundance among cells called “noise”. Understanding how noise affects cell function is a major problem in biology. Here I present theory demonstrating that gene expression noise slows the average rate of cell division. Furthermore, by modeling stochastic gene expression with non-linearity, I identify novel mechanisms of cellular robustness. However, I find that the cost of noise, and therefore the strength of selection favoring robustness, decays faster than linearly with increasing cell size. This may help explain the vast differences in gene-regulatory complexity between prokaryotes and eukaryotes.
Development and Application of Equilibrium Thermodynamic Models Describing Coupled Protein Oligomerization and Ligand Binding
Authors: Rennie Martin L. , Kingston Richard L 
Published: August 2016

AbstractThe association and dissociation of protein oligomers is frequently coupled to the binding of ligands, facilitating the regulation of many biological processes. Equilibrium thermodynamic models are needed to describe the linkage between ligand binding and homo-oligomerization. These models must be parameterized in a way that makes physical interpretation straightforward, and allows elaborations or simplifications to be readily incorporated. We propose a systematic framework for the equilibrium analysis of ligand-linked oligomerization, treating in detail the case of a homo-oligomer with cyclic point group symmetry, where each subunit binds a ligand at a single site. Exploiting the symmetry of the oligomer, in combination with a nearest-neighbors approximation, we derive a class of site-specific ligand binding models involving only four parameters, irrespective of the size of the oligomer. The model parameters allow direct quantitative assessment of ligand binding cooperativity, and the influence of ligand binding on protein oligomerization, which are the key questions of biological interest. These models, which incorporate multiple types of linkage, are practically applicable, and we show how Markov Chain Monte Carlo (MCMC) methods can be used to characterize the agreement of the model with experimental data. Simplifications to the model emerge naturally, as its parameters take on extremal values. The nearest-neighbors approximation underpinning the model is transparent, and the model could be augmented in obvious fashion if the approximation were inadequate. The approach is generalizable, and could be used to treat more complex situations, involving more than a single kind of ligand, or a different protein symmetry.Author SummaryThe assembly and disassembly of protein complexes in response to the binding of ligands is a ubiquitous biological phenomenon. This is often linked, in turn, to the activation or deactivation of protein function. Methods are therefore needed to quantitate the linkage or coupling between protein assembly and effector binding, requiring the development of mathematical models describing the coupled binding processes. As proteins usually assemble in a symmetric fashion, the nature of any symmetry present has to be considered during model construction. We have developed a class of models than can effectively describe the coupling between effector binding and protein assembly into symmetric ring-like structures of any size. Despite the relatively complex mathematical form of the models, they are practically applicable. Markov Chain Monte Carlo methods, a form of Bayesian statistical analysis, can be used to analyze the fit of the models to experimental data, and recover the model parameters. This allows the direct assessment of the nature and magnitude of the coupling between effector binding and protein assembly, as well as other relevant characteristics of the system.
Tutors and Learners Without Borders: In a Relationship but it's Complicated
Authors: Gervacio Juvy Lizette 
Published: August 2016

Global tutoring and learning communities are composed of different people who share a common interest or a common goal. Learners aim to acquire knowledge and skills; while tutors aim to provide content support, coaching and motivation to learners. The interaction is done through the use of technology, specifically the Internet. Management of these communities can be a challenge because members are not only separated by space and time but they come from different cultures, contextual backgrounds and institutions. If managed well, global tutoring and learning communities can transcend barriers and be very effective, efficient and also inexpensive.
The paper looks into how online tutors and learners are effectively and efficiently managed and sustained. Specifically, it aims to: a) define global tutoring and learning communities and their rationale; b) describe the strategies and good practices employed in the planning, implementation, monitoring and evaluation; c)determine the effective communication tools used to manage and sustain global teams; and d) identify the challenges and lessons to maintain and sustain global tutoring and learning communities.
The paper is based on studies as well as actual experiences and written reports on managing global learning and tutoring communities. It will look into how teams are managed from planning, implementation to monitoring and evaluation. Specifically, it will provide a glimpse on how learners and tutors from different countries and nationalities are managed in the elearning Development and Implementation (eLDI) program and e-skills program. These courses are jointly offered by the University of the Philippines Open University (UPOU) and InWEnt, Capacity Building International, Germany and have learners and tutors from various countries not only from Asia, but from Africa and the Middle East. The paper also draws lessons on how to maintain tutors and learners without borders.
How flexible do students prefer their learning to be?
Authors: LI Kam Cheong 
Published: August 2016

The term 'flexible learning' has been used in the literature for decades in a rather general sense and has been closely associated with open and distance education. The notion of flexibility has been examined on various dimensions, such as admission criteria, students' control of learning time, commitment, content and tasks. There has recently been a tendency to use the term in a more defined or technical sense.One research focus has revolved around course design for effective learning in relation to the learner and dimensions of flexibility.
This paper offers an updated review of the literature on the approaches to understanding flexible learning and the dimensions of flexibility involved. It also reports a preliminary study on distancelearners' preferences for flexibility in the courses in which they are engaged. In the study, a questionnaire was administered to 162 distance learners in Hong Kongto determine their preferred levels of flexibility on a range of dimensions. The results suggest that learners' preferences vary across dimensions. Based on the findings, it is argued that the diversity of learners' preferences and learning styles should be incorporated as an integral part of the mechanism for designing and reviewing study programmes.
Factors affecting stickiness and word of mouth in mobile applications
Authors: Kim Seeun , Baek Tae Hyun , Kim Youn-Kyung , Yoo Kyunga 
Published: August 2016

Purpose
The purpose of this study is to investigate user perceptions of mobile app characteristics and interrelationships among identified mobile app characteristics, perceived benefits and post-adoption behaviors.

Design/methodology/approach
Using a self-administered online survey (n = 503) drawn from a consumer panel of US smartphone users, this study tests the proposed model that explains why stickiness and word of mouth (WOM) are enhanced during the post-adoption stage.

Findings
The results indicate that user perceptions of mobile app characteristics, perceived ubiquity, perceived informativeness and perceived personalization are positively associated with mobile app usefulness, thereby leading to increased stickiness and positive WOM intentions. Furthermore, perceived personalization is found to become the strongest predictor of usefulness and playful engagement with the mobile app.

Research limitations/implications
The findings are derived from a one-shot correlational study. There is no guarantee that the proposed model establishes causal directions among the latent constructs. Therefore, future research should test the conceptual model in an experimental setting by manipulating the degree and types of ubiquity, informativeness and personalization.

Practical implications
The findings of this research provide managerial guidelines for developing effective mobile app strategies involving utilitarian and hedonic benefits, thereby enhancing user stickiness and WOM intentions.

Originality/value
This paper is the first attempt to develop a conceptual framework that integrates user perceptions of mobile app characteristics into the underlying process of post-adoption behaviors. It empirically demonstrates the importance of ubiquity, informativeness and personalization in building and sustaining loyal relationships with mobile app users.