bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diabetes: A review of awareness, comorbidities, and quality of life in India
Authors: Bansode Balasaheb , Nagarajan Rangasamy 
Published: November 2018

AbstractDiabetes is one of the major contributors for the noncommunicable diseases. The disease burden due to diabetes is huge, and it not only puts pressure on the diabetes patients but also it adds pressure on the economy of the developing and underdeveloped nations. In India, the burden due to diabetes is more important as every fifth person is a diabetic. This paper reviews awareness and source of knowledge of diabetes, awareness about risk factors, and complications of diabetes in India. The review reveals that (a) awareness about diabetes is less in India; (b) awareness regarding specific risk factors associated with diabetes (obesity, tobacco use, alcohol consumption, and high blood pressure) is found to be less; (c) there is a negative association between duration of diabetes and health-related quality of life; and (d) microvascular complications (retinopathy, nephropathy, neuropathy, and coronary diseases) are major comorbidities affecting the diabetes patients. The review reveals that it is imperative to work effectively toward implementing a holistic program for diabetes prevention by ensuring proper awareness in the community.
‘The fourth commandment effect’: church attendance and intergenerational support in late parent–child relationships
Authors: Tosi Marco , Oncini Filippo 
Published: November 2018

ABSTRACT
We examine whether church attendance is related to intergenerational support from children to older parents in Italy. First, we focus on the role of church attendance on different forms of assistance, by distinguishing between practical support and personal assistance. Second, we attempt to disentangle the role of church attendance from that of traditionalism. We analyse data from the ISTAT survey ‘Family and Social Subject’ 2003 using multinomial logistic regression models and the KHB method for the decomposition of direct and indirect effects. Results show the existence of an association between church attendance and the probability of providing practical support to older parents, whereas there is no association with personal assistance. Regular churchgoers are more likely to provide practical support to their parents than the non-catholic, with occasional churchgoers falling somewhere in between. We find little support to the hypothesis that the association between religious practices and intergenerational support is explained by traditional family attitudes, although more traditional children are more likely to live with their parents. In the discussion, we argue that church attendance offers the opportunity for adult children to learn pro-family teachings that are positively related to supportive behaviors in later life.
Examiner accuracy in cognitive testing in multisite brain-tumor clinical trials: an analysis from the Alliance for Clinical Trials in Oncology
Authors: Cerhan Jane H , Anderson S Keith , Butts Alissa M , Porter Alyx B , Jaeckle Kurt , Galanis Evanthia , Brown Paul D 
Published: November 2018

Abstract

Background
Cognitive function is an important outcome in brain-tumor clinical trials. Cognitive examiners are often needed across multiple sites, many of whom have no prior testing experience. To ensure quality, we looked at examiner errors in administering a commonly used cognitive test battery, determined whether the errors were correctable upon central review, and considered whether the same errors would be detected using onsite electronic data entry.

Methods
We looked at 500 cognitive exams administered for brain-tumor trials led by the Alliance for Clinical Trials in Oncology (Alliance). Of 2277 tests examined, 32 noncorrectable errors were detected with routine central review (1.4% of tests administered), and thus removed from the database of the respective trial. The invalidation rate for each test was 0.8% for each part of the Hopkins Verbal Learning Test-Revised, 0.8% for Controlled Oral Word Association, 1.8% for Trail Making Test-A and 2.6% for Trail Making Test-B. It was estimated that, with onsite data entry and no central review, 4.9% of the tests entered would have uncorrected errors and 1.3% of entered tests would be frankly invalid but not removed.

Conclusions
Cognitive test results are useful and robust outcome measures for brain-tumor clinical trials. Error rates are extremely low, and almost all are correctable with central review of scoring, which is easy to accomplish. We caution that many errors could be missed if onsite electronic entry is utilized instead of central review, and it would be important to mitigate the risk of invalid scores being entered.

ClinicalTrials.gov identifiers
NCT01781468 (Alliance A221101), NCT01372774 (NCCTG N107C), NCT00731731 (NCCTG N0874), and NCT00887146 (NCCTG N0577).
RADIATION SHIELDING STUDY FOR THE VERTICAL TEST SYSTEM FOR SUPERCONDUCTING RF CAVITIES
Authors: Zhou Dejun , Lin Lin , Feng Liwen , Quan Shengwen 
Published: November 2018

Abstract
A vertical test system (VTS) for superconducting radio frequency cavities had been designed and constructed at Peking University. During the test, field emission electrons in the cavity will be accelerated and some of them will hit the flange of cavity with high-energy. These high-energy electrons will have a significant impact on the radiation safety of the system and environment. In this paper, the Particle-in-Cell solver in CST software was used to analyze the behavior of electrons emitted from different field emission positions and found the worst field emission site which deposited the most energy on the cavity wall. The impact information of the electrons emitted from the worst field emission site was utilized to character the source term. Prompt dose equivalent rate distribution and residual radioactivity was predicted by using the Monte Carlo simulation program FLUKA. Further vertical test results are consistent with the simulation results.
BioKEEN: A library for learning and evaluating biological knowledge graph embeddings
Authors: Ali Mehdi , Hoyt Charles Tapley , Domingo-Fernández Daniel , Lehmann Jens , Jabeen Hajira 
Published: November 2018

AbstractKnowledge graph embeddings (KGEs) have received significant attention in other domains due to their ability to predict links and create dense representations for graphs’ nodes and edges. However, the software ecosystem for their application to bioinformatics remains limited and inaccessible for users without expertise in programming and machine learning. Therefore, we developed BioKEEN (Biological KnowlEdge EmbeddiNgs) and PyKEEN (Python KnowlEdge EmbeddiNgs) to facilitate their easy use through an interactive command line interface. Finally, we present a case study in which we used a novel biological pathway mapping resource to predict links that represent pathway crosstalks and hierarchies.AvailabilityBioKEEN and PyKEEN are open source Python packages publicly available under the MIT License at https://github.com/SmartDataAnalytics/BioKEEN and https://github.com/SmartDataAnalytics/PyKEEN as well as through PyPI.
Explorations with Conditioned Stimuli in Autoshaping Procedures
Authors: Nehrbas Jill F. , Smedley Elizabeth B. , Kyle S. Smith 
Published: November 2018

AbstractSign-tracking is a form of autoshaping where by animals reliably develop conditioned responses toward stimuli that predict an outcome. While the assignment of some value to a predictive cue may be adaptive (i.e., to be alerted to food and water sources), the attribution of value to predictive cues can be maladaptive as seen in behaviors elicited during addiction. Here we test if responding to the predictive cue changes in the context of other cues that are only partially predictive (Experiment 1). Previous work on sequential cues leading to reward have shown a bias in responding toward the first cue in the sequence over learning (Smedley and Smith 2018a, 2018b). Here we test if this effect is unique to discrete cues or if a bias in responding can be seen in a single, long cue (Experiment 2). Finally, we investigate if sign-tracking responses can reliably develop towards a cue that arrives after the delivery of reward (backwards conditioning, Experiment 3). Together, we aim to address various gaps in knowledge about the nature of the sign-tracking response.
APPLES: Scalable Distance-based Phylogenetic Placement with or without Alignments
Authors: Balaban Metin , Sarmashghi Shahab , Mirarab Siavash 
Published: November 2018

AbstractPlacing a new species on an existing phylogeny has increasing relevance to several applications. Placement can be used to update phylogenies in a scalable fashion and can help identify unknown query samples using (meta-)barcoding, skimming, or metagenomic data. Maximum likelihood (ML) methods of phylogenetic placement exist, but these methods are not scalable to reference trees with many thousands of leaves, limiting their ability to enjoy benefits of dense taxon sampling in modern reference libraries. They also rely onassembledsequences for the reference set and aligned sequences for the query. Thus, ML methods cannot analyze datasets where the reference consists of unassembled reads, a scenario relevant to emerging applications of genome-skimming for sample identification. We introduce APPLES, a distance-based method for phylogenetic placement. Compared to ML, APPLES is an order of magnitude faster and more memory efficient, and unlike ML, it is able to place on large backbone trees (tested for up to 200,000 leaves). We show that using dense references improves accuracy substantially so that APPLES on dense trees is more accurate than ML on sparser trees, where it can run. Finally, APPLES can accurately identify samples without assembled reference or aligned queries using kmer-based distances, a scenario that ML cannot handle. APPLES is available publically atgithub.com/balabanmetin/apples.
ExtendAlign: the post-analysis tool to correct and improve the alignment of dissimilar short sequences
Authors: Flores-Torres Mariana , Gómez-Romero Laura , Haase-Hernández Joshua I. , Aguilar-Ordóñez Israel , Tovar Hugo , Avendaño-Vázquez S. Eréndira , Flores-Jasso C. Fabián 
Published: November 2018

ABSTRACTIn this work, we evaluated several tools used for the alignment of short sequences and found that most aligners execute reasonably well for identical sequences, whereas a variety of alignment errors emerge for dissimilar ones. Since alignments are essential in computational biology, we developed ExtendAlign, a post-analysis tool that corrects these errors and improves the alignment of dissimilar short sequences. We used simulated and biological data to show that ExtendAlign outperforms the other aligners in most metrics tested. ExtendAlign is useful for pinpointing the identity percentage for alignments of short sequences in the range of ∼35–50% similarity.
Nuclei multiplexing with barcoded antibodies for single-nucleus genomics
Authors: Gaublomme Jellert T. , Li Bo , McCabe Cristin , Knecht Abigail , Drokhlyansky Eugene , Wittenberghe Nicholas Van , Waldman Julia , Dionne Danielle , Nguyen Lan , Jager Phil De , Yeung Bertrand , Zhao Xinfang , Habib Naomi , Rozenblatt-Rosen Orit , Regev Aviv 
Published: November 2018

AbstractSingle-nucleus RNA-Seq (snRNA-seq) enables the interrogation of cellular states in complex tissues that are challenging to dissociate, including frozen clinical samples. This opens the way, in principle, to large studies, such as those required for human genetics, clinical trials, or precise cell atlases of large organs. However, such applications are currently limited by batch effects, sequential processing, and costs. To address these challenges, we present an approach for multiplexing snRNA-seq, using sample-barcoded antibodies against the nuclear pore complex to uniquely label nuclei from distinct samples. Comparing human brain cortex samples profiled in multiplex with or without hashing antibodies, we demonstrate that nucleus hashing does not significantly alter the recovered transcriptome profiles. We further developed demuxEM, a novel computational tool that robustly detects inter-sample nucleus multiplets and assigns singlets to their samples of origin by antibody barcodes, and validated its accuracy using gender-specific gene expression, species-mixing and natural genetic variation. Nucleus hashing significantly reduces cost per nucleus, recovering up to about 5 times as many single nuclei per microfluidc channel. Our approach provides a robust technique for diverse studies including tissue atlases of isogenic model organisms or from a single larger human organ, multiple biopsies or longitudinal samples of one donor, and large-scale perturbation screens.
Riding the wave of genomics, to investigate aquatic coliphage diversity and activity
Authors: Michniewski Slawomir , Redgwell Tamsin , Grigonyte Aurelija , Rihtman Branko , Aguilo-Ferretjans Maria , Christie-Oleza Joseph , Jameson Eleanor , Scanlan David J. , Millard Andrew D. 
Published: November 2018

SummaryBacteriophages infectingEscherichia colihave been used as a proxy for faecal matter and water quality from a variety of environments. However, the diversity of coliphages that are present in seawater remains largely unknown, with previous studies largely focusing on morphological diversity. Here, we isolated and characterised coliphages from three coastal locations in the UK and Poland. This revealed a surprising genetic diversity, with comparative genomics and phylogenetic analysis of phage isolates facilitating the identification of putative new species within the generaRB69virusandT5virusand a putative new genus within the subfamilyTunavirinae. Furthermore, by combining this genomic data with proteomic and host range analyses a number of phage structural proteins were identified, one of which is likely to be responsible for the observed differences in host range.
ProtMiscuity: a database of promiscuous proteins
Authors: Rueda Ana Julia Velez , Palopoli Nicolas , Zacarías Matías , Parisi Gustavo 
Published: November 2018

AbstractSummaryProtMiscuity is a manually-curated database of promiscuous proteins. It is annotated with information about canonical and promiscuous activities comprising 88 different reactions in 57 proteins from 40 organisms. ProtMiscuity could assist in the study of the underlying mechanisms of promiscuous reactions by offering a collection of experimentally derived data, extensively linked with other databases providing biological, structural and functional information.Availability and ImplementationThe responsive web interface of ProtMiscuity provides support for easier navigation and visualization of the database contents on multiple devices. It is implemented in HTML, CSS, JavaScript, Angular4 and NodeJS. ProtMiscuity is hosted on our server and can be freely accessed at http://ufq.unq.edu.ar/protmiscuityContactGustavo Parisi (gustavo@unq.edu.ar)
Relating excitatory and inhibitory neurochemicals to visual perception: a magnetic resonance study of occipital cortex between migraine events
Authors: Chan Yu Man , Pitchaimuthu Kabilan , Wu Qi-Zhu , Carter Olivia L , Egan Gary F , Badcock David R , McKendrick *Allison M 
Published: November 2018

AbstractCertain perceptual measures have been proposed as indirect assays of brain neurochemical status in people with migraine. One such measure is binocular rivalry, however, previous studies have not measured rivalry characteristics and brain neurochemistry together in people with migraine. This study compared spectroscopy-measured levels of GABA and Glx (glutamine and glutamate complex) in visual cortex between 16 people with migraine and 16 non-headache controls, and assessed whether the concentration of these neurochemicals explains, at least partially, inter-individual variability in binocular rivalry perceptual measures. Mean Glx level was significantly reduced in migraineurs relative to controls, whereas mean occipital GABA levels were similar between groups. Neither GABA levels, nor Glx levels correlated with rivalry percept duration. Our results thus suggest that the previously suggested relationship between rivalry percept duration and GABAergic inhibitory neurotransmitter concentration in visual cortex is not strong enough to enable rivalry percept duration to be reliably assumed to be a surrogate for GABA concentration, at least in the context of healthy individuals and those that experience migraine.
Differential physiological role of BIN1 isoforms in skeletal muscle development, function and regeneration
Authors: Prokic Ivana , Cowling Belinda , Kutchukian Candice , Kretz Christine , Tasfaout Hichem , Hergueux Josiane , Wendling Olivia , Ferry Arnaud , Toussaint Anne , Gavriilidis Christos , Nattarayan Vasugi , Koch Catherine , Lainné Jeanne , Combe Roy , Tiret Laurent , Jacquemond Vincent , Pilot-Storck Fanny , Laporte Jocelyn 
Published: November 2018

AbstractSkeletal muscle development and regeneration are tightly regulated processes. How the intracellular organization of muscle fibers is achieved during these steps is unclear. Here we focus on the cellular and physiological roles of amphiphysin 2 (BIN1), a membrane remodeling protein mutated in both congenital and adult centronuclear myopathies, that is ubiquitously expressed and has skeletal muscle-specific isoforms. We created and characterized constitutive, muscle-specific and inducible Bin1 homozygous and heterozygous knockout mice targeting either ubiquitous or muscle-specific isoforms. Constitutive Bin1-deficient mice died at birth from lack of feeding due to a skeletal muscle defect. T-tubules and other organelles were misplaced and altered, supporting a general early role of BIN1 on intracellular organization in addition to membrane remodeling. Whereas restricted deletion of Bin1 in unchallenged adult muscles had no impact, the forced switch from the muscle-specific isoforms to the ubiquitous isoforms through deletion of the in-frame muscle–specific exon delayed muscle regeneration. Thus, BIN1 ubiquitous function is necessary for muscle development and function while its muscle-specific isoforms fine-tune muscle regeneration in adulthood, supporting that BIN1 centronuclear myopathy with congenital onset are due to developmental defects while later onset may be due to regeneration defects.
Joint optimal decision of the shared distribution system through revenue-sharing and cooperative investment contracts
Authors: Wei Qiang , Li Sheng , Gou Xinyu , Huo Baofeng 
Published: November 2018

Purpose
The rapid development of e-commerce has caused not only explosive growth of the express delivery industry, but also ever-greater operational pressures. Models from the sharing economy may provide new ideas for operational improvement. The purpose of this paper is to consider an optimization method that reduces costs and increases efficiency. The proposed method enables a shared distribution system based on revenue-sharing and cooperative investment contracts.

Design/methodology/approach
The authors design a two-echelon supply chain (SC) of the shared distribution system with one shared distribution company and N express companies. In this SC, the express companies provide only inter-city transportation, and they outsource internal-city transportation to a shared distribution company. This distribution system differs from that of the traditional express delivery industry. The traditional system of delivery requires large numbers of empty trips (with no load to deliver), because the operating mode of urban distribution has been the franchise. To offer greater efficiency and performance, the authors introduce the sharing economy mode of express delivery. The authors examine the potential of a joint optimal decision-making strategy that involves revenue-sharing and cooperative investment contracts based on an order flow proportion (OFP) and a revenue-sharing factor (RSF). In this shared distribution system, the most important innovation is that all of the express companies jointly invest in and establish a shared distribution company based on OFP or RSF principles.

Findings
The profitability of an SC with revenue-sharing contracts based on an OFP system is much higher than that of a decentralized SC, and it is very close to the profitability of a centralized SC. In SCs with revenue-sharing contracts that are based on RSFs, there are many possible combinations of RSFs that can increase the overall profitability. The analyses indicate that the OFP system offers the best solution in designing revenue-sharing contracts based on RSFs.

Practical implications
This study indicates that revenue-sharing contracts based on both OFP and RSF principles can increase overall SC returns by 0.21 to 0.44 percent. In sum total, this improvement could mean a 0.84 to 1.76bn Yuan increase in revenues for the 400+ bn-Yuan express delivery industry.

Originality/value
The authors find that a combination of equity investment and SC coordination contracts makes the cooperation between SC members much more stable. Through this kind of shared distribution system, the scale of economy can further reduce the costs and increase the efficiency of the express delivery industry.
What geographical scope works best for rapidly internationalizing SMEs?
Authors: Melén Hånell Sara , Rovira Nordman Emilia 
Published: November 2018

PurposeThis paper aims to explore the benefits of a regional internationalization strategy and investigate how a rapidly internationalizing SME’s development of market knowledge relates to this strategy.Design/methodology/approachAfter a brief overview of the literature on international SMEs, the internalization approach and the IP-approach, a case study is introduced and analyzed.FindingsThe case findings illustrate that market knowledge steers the investigated firm to follow a regional approach of operations. The regional strategy lessens perceived risks, saves costs and generates sufficient knowledge about one market at a time.Practical implicationsIt is important for managers in rapidly internationalizing SMEs and for policymakers to recognize the benefits of supporting regional orientation initiatives for enhancing these firms’ internationalization.Originality/valueThis paper presents a longitudinal case study that contributes to further the understanding and insights into the operations of born regionals. By probing deeper into the ideas provided by the internalization approach, the IP-approach and research about international SMEs, the study contributes with a unified framework for understanding the benefits for rapidly internationalizing SMEs to operate on a regional scope.