bluuebunny/crossref_metadata_2025_split huggingface dataset:
GenEpi: Gene-based Epistasis Discovery Using Machine Learning
Authors: Chang Yu-Chuan , Wu June-Tai , Hong Ming-Yi , Tung Yi-An , Hsieh Ping-Han , Yee Sook Wah , Giacomini Kathleen M. , Oyang Yen-Jen , Chen Chien-Yu ,   for the Alzheimer’s Disease Neuroimaging Initiative
Published: September 2018

AbstractGenome-wide association studies (GWAS) provide a powerful means to identify associations between genetic variants and phenotypes. However, GWAS techniques for detecting epistasis, the interactions between genetic variants associated with phenotypes, are still limited. We believe that developing an efficient and effective GWAS method to detect epistasis will be a key for discovering sophisticated pathogenesis, which is especially important for complex diseases such as Alzheimer’s disease (AD). In this regard, this study presents GenEpi, a computational package to uncover epistasis associated with phenotypes by the proposed machine learning approach. GenEpi identifies both within-gene and cross-gene epistasis through a two-stage modeling workflow. In both stages, GenEpi adopts two-element combinatorial encoding when producing features and constructs the prediction models by L1-regularized regression with stability selection. The simulated data showed that GenEpi outperforms other widely-used methods on detecting ground-truth epistasis. As real data is concerned, this study uses AD as an example to reveal the capability of GenEpi in finding disease-related variants and variant interactions that show both biological meanings and predictive power.Availability:GenEpi is an open-source python package and available free of charge only for non-commercial users. The package can be downloaded fromhttps://github.com/Chester75321/GenEpi, and has also been published on The Python Package Index.
Proximity sensors reveal social information transfer in maternity colonies of Common noctule bats
Authors: Ripperger Simon , Günther Linus , Wieser Hanna , Duda Niklas , Hierold Martin , Cassens Björn , Kapitza Rüdiger , Kölpin Alexander , Mayer Frieder 
Published: September 2018

SummaryBats are a highly gregarious taxon suggesting that social information should be readily available for making decision. Social information transfer in maternity colonies might be a particularly efficient mechanism for naïve pups to acquire information on resources from informed adults. However, such behaviour is difficult to study in the wild, in particular in elusive and small-bodied animals such as bats.The goal of this study was to investigate the role of social information in acquiring access to two types of resources, which are crucial in the life of a juvenile bat: suitable roosting sites and fruitful feeding grounds. We hypothesized that fledging offspring will make use of social information by following informed members of the social groups to unknown roosts or foraging sites.In the present study we applied for the first time the newly developed miniaturized proximity sensor system ‘BATS’, a fully automated system for documenting associations among individual bats both while roosting and while on the wing. We quantified associations among juveniles and other group member while switching roosts and during foraging.We found clear evidence for information transfer while switching roosts, mainly among juveniles and their genetically identified mothers. Anecdotal observations suggest intentional guidance behaviour by mothers, indicated by repeated commuting flights among the pup and the target roost. Infrequent, short meetings with colony members other than the mother indicate local enhancement at foraging sites, but no intentional information transfer.Our study illustrates how advances in technology enable researchers to solve long-standing puzzles. Miniaturized proximity sensors facilitate the automated collection of continuous data sets and represent an ideal tool to gain novel insights into the sociobiology of elusive and small-bodied species.
Beta and theta oscillations differentially support free versus forced control over multiple-target search
Authors: van Driel Joram , Ort Eduard , Fahrenfort Johannes J. , Olivers Christian N. L. 
Published: September 2018

AbstractMany important situations require human observers to simultaneously search for more than one object. Despite a long history of research into visual search, the behavioral and neural mechanisms associated with multiple-target search are poorly understood. Here we test the novel theory that the efficiency of looking for multiple targets critically depends on the mode of cognitive control the environment affords to the observer. We used an innovative combination of EEG and eye tracking while participants searched for two targets, within two different contexts: Either both targets were present in the search display and observers were free to prioritize either one of them, thus enabling proactive control over selection; or only one of the two targets would be present in each search display, which requires reactive control to reconfigure selection when the wrong target is prioritized. During proactive control, both univariate and multivariate signals of beta-band (15–35 Hz) power suppression prior to display onset predicted switches between target selections. This signal originated over midfrontal and sensorimotor regions and has previously been associated with endogenous state changes. In contrast, imposed target selections requiring reactive control elicited prefrontal power enhancements in the delta/theta-band (2–8 Hz), but only after display onset. This signal predicted individual differences in associated oculomotor switch costs, reflecting reactive reconfiguration of target selection. The results provide compelling evidence that multiple target representations are differentially prioritized during visual search, and for the first time reveal distinct neural mechanisms underlying proactive and reactive control over multiple-target search.Significance StatementSearching for more than one object in complex visual scenes can be detrimental for search performance. While perhaps annoying in daily life, this can have severe consequences in professional settings such as medical and security screening. Previous research has not yet resolved whether multiple-target search involves changing priorities in what people attend to, and how such changes are controlled. We approached these questions by concurrently measuring cortical activity and eye movements using EEG and eye tracking, while observers searched for multiple possible targets. Our findings provide the first unequivocal support for the existence of two modes of control during multiple-target search, which are expressed in qualitatively distinct time-frequency signatures of the EEG both before and after visual selection.
Molecular basis for activation of lecithin:cholesterol acyltransferase by a compound that increases HDL cholesterol
Authors: Manthei Kelly A. , Yang Shyh-Ming , Baljinnyam Bolormaa , Chang Louise , Glukhova Alisa , Yuan Wenmin , Freeman Lita A. , Maloney David J. , Schwendeman Anna , Remaley Alan T. , Jadhav Ajit , Tesmer John J.G. 
Published: September 2018

ABSTRACTLecithin:cholesterol acyltransferase (LCAT) and LCAT-activating small molecules are being investigated as treatments for coronary heart disease (CHD) and familial LCAT deficiency (FLD). Herein we report the crystal structure of LCAT bound to a potent activator and an acyl intermediate-like inhibitor, thereby revealing an active conformation of LCAT and that the activator is bound exclusively to its membrane-binding domain (MBD). Functional studies indicate that the compound does not modulate the affinity of LCAT for HDL, but instead stabilizes residues in the MBD and likely facilitates channeling of substrates into the active site. By demonstrating that these activators increase the activity of an FLD variant, we show that compounds targeting the MBD have therapeutic potential. In addition, our data better define the acyl binding site of LCAT and pave the way for rational design of LCAT agonists and improved biotherapeutics for augmenting or restoring reverse cholesterol transport in CHD and FLD patients.
Organoid culture media containing growth factors of defined cellular activity
Authors: Urbischek Manuela , Rannickmae Helena , Foets Thomas , Ravn Katharina , Hyvönen Marko , de la Roche Marc 
Published: September 2018

AbstractThe media components necessary for deriving and sustaining organoids from a number of epithelial tissues such as prostate, colon, gastric, liver, pancreas, and others have been established (1). Critical components of organoid media formulations are a set of growth factors that include EGF, R-spondins and BMP signalling antagonists such as Noggin or Gremlin. The practical limitation to organoid culture and the development of new applications for the technology is the use of defined cellular activities of growth factors in media formulations, in particular Noggin/Gremlin 1 and R-spondin 1. Here we report the production of highly pure recombinant Gremlin 1 and R-spondin 1 from bacterial expression and their use for culturing organoids. We detail the workflow for their purification, determination of cellular activity, quality control and their formulation in organoid media. The protocols we provide for generation of precisely formulated, cost-effective, organoid media of defined cellular activity will enable broader access to organoid technology and engender the development of novel applications.
The dormancy-specific regulator, SutA, is intrinsically disordered and modulates transcription initiation in Pseudomonas aeruginosa
Authors: Bergkessel Megan , Babin Brett M. , VanderVelde David G. , Sweredoski Michael J. , Moradian Annie , Eggleston-Rangel Roxana , Hess Sonja , Tirrell David A. , Artsimovitch Irina , Newman Dianne K. 
Published: September 2018

ABSTRACTThough bacteria in nature are often nutritionally limited and growing slowly, most of our understanding of core cellular processes such as transcription comes from studies in a handful of model organisms doubling rapidly under nutrient-replete conditions. We previously identified a small protein of unknown function, called SutA, in a global screen of proteins synthesized in Pseudomonas aeruginosa under growth arrest (Babin BM, et al. (2016) SutA is a bacterial transcription factor expressed during slow growth in Pseudomonas aeruginosa. PNAS 113(5):E597-605). SutA binds RNA polymerase (RNAP), causing widespread changes in gene expression, including upregulation of the ribosomal RNA (rRNA) genes. Here, using biochemical and structural methods, we examine how SutA interacts with RNAP and the functional consequences of these interactions. We show that SutA consists of a central α-helix with unstructured N- and C-terminal tails, and binds to the β1 domain of RNAP. It activates transcription from the P. aeruginosa rrn promoter by both the housekeeping sigma factor holoenzyme (Eσ70) and the general stress response sigma factor holoenzyme (EσS) in vitro, and its N-terminal tail is required for activation in both holoenzyme contexts. However, we find that the interaction between SutA and each holoenzyme is distinct, with the SutA C-terminal tail and an acidic loop unique to σ70 playing the determining roles in these differences. Our results add SutA to a growing list of transcription regulators that use their intrinsically disordered regions to remodel transcription complexes.SIGNIFICANCELittle is known about how bacteria regulate their activities during periods of dormancy, yet growth arrest dominates bacterial existence in most environments and is directly relevant to the problem of physiological antibiotic tolerance. Though much is known about transcription in the model organism, Escherichia coli, even there, our understanding of gene expression during dormancy is incomplete. Here we explore how transcription under growth arrest is modulated in Pseudomonas aeruginosa by the small acidic protein, SutA. We show that SutA binds to RNA polymerase and controls transcription by a mechanism that is distinct from other known regulators. Our work underscores the potential for fundamental, mechanistic discovery in this important and understudied realm of bacterial physiology.
Poly(2-chloroaniline) and poly(aniline-co-2-chloroaniline) films on ZnFe alloy plating
Authors: Akdag Abdurrahman , Ozyilmaz Gul , Ozyilmaz Ali Tuncay 
Published: September 2018

Purpose
The purpose of this paper is to evaluate and compare the protective, anticorrosion behaviors and electrochemically synthesis of poly(2-chloroaniline) (PCANI) and poly(2-chloroaniline-co-aniline) P(CANI-co-ANI) films on thin zinc–iron plated carbon steel (CS).

Design/methodology/approach
Zinc–iron (ZnFe) alloy plating was successfully achieved on CS applying 3 mA constant current value. The PCANI and P(CANI-co-ANI) films on ZnFe-plated CS electrode were synthesized by cyclic voltammetry technique using monomer(s) containing 0.20 M sodium oxalate solution. The CS/ZnFe electrodes with and without PCANI or P(CANI-co-ANI) films were characterized using SEM and anodic linear sweep voltammograms. The anticorrosive behaviors of uncoated and coated electrodes were studied in 3.5 per cent NaCl solution by corrosion techniques which include open circuit potential measurements, the anodic polarization curves and alternative current electrochemical impedance spectroscopy (EIS) technique.

Findings
The protection efficiency values (E per cent) for CS/ZnFe, ZnCS/ZnFe/PCANI and CS/ZnFe/P(CANI-co-ANI) electrodes were calculated as 71.05, 84.53 and 92.79, respectively, after 168 h of immersion time. The results showed that P(CANI-co-ANI) coating on ZnFe-plated CS electrode exhibited higher corrosion resistance and provided better barrier property in comparison with PCANI coating and ZnFe alloy plating, in longer exposure time.

Originality/value
A number of reports on the synthesis and characterization of PANI have appeared in the literature during the past decade, but there is no such publication of PCANI. At the same time, the synthesis of PCANI onto the surface of metal alloy coating being the first of this kind, no such proceedings have been reported in the literature so far.
Entry of Reliance Jio in the telecom industry: a ripple in the ocean
Authors: Rishi Bikramjit , Kacker Archit , Gupta Shreya 
Published: September 2018

Subject area
Marketing Management, Marketing Strategy and Marketing Communication.

Study level/applicability
The case is targeted at students of post-graduation and under-graduation programs in Business Administration, specializing in Marketing Management or Marketing Strategy.

Case overview
Mukesh Ambani’s announcement about the launching of Reliance Jio at the 41st Annual General Meeting (AGM) of Reliance Industries Limited (RIL) in June 2015 sent shock waves in the telecom industry. Everyone, including the customers, competitors and the entire telecom industry, was excited to know whether Reliance Jio would be able to make a dent or fizzle out like a weak firecracker. Was it time for the top players to be worried and pull their socks up or will it be an inconsequential ripple in the ocean? Mukesh Ambani saw the telecom sector from a new viewpoint and proposed a complete set of solution in the form of Reliance Jio SIM card that addressed the different needs of customers through various applications. This has spread rumors of a merger between Idea and Vodafone in India, which can have a huge impact on Reliance Jio and the telecom sector in general. The profitability indicator that was earlier determined as the average revenue per user (ARPU) will continue to dominate. The companies will be scrambling to find different ways to increase the ARPU to maximize the returns. This would also lead to a downsize in the cost in such a way that their operations do not suffer and profitability is also not negatively affected.

Expected learning outcomes
To better understand the entry strategy of firms in highly volatile business situations. To know about the competitors and their contribution to the operational and strategic changes of a new entrant. To understand the proceedings associated with marketing communication for establishing a product in a highly competitive market. To know about the impact of joining hands with the competitors on a new entrant.

Supplementary materials
Teaching notes are available for educators only. Please contact your library to gain login details or email support@emeraldinsight.com to request teaching notes.

Subject code
CSS 8: Marketing.
Digital library keyword analysis for visualization education research
Authors: Bratt Sharon 
Published: September 2018

Purpose
The purpose of this paper is to assess the efficacy of the Institute of Electrical and Electronics Engineers (IEEE) Xplore digital library search engine to return relevant materials on information visualization pedagogy literature and to recommend search strategies to assist the digital library academic readership improve the efficacy of their search tasks. Furthermore, the results are of interest to general readers using similar digital repositories.

Design/methodology/approach
An initial scoping review using EBSCO Discovery services returned the number and accessibility of sources and publications-based various Boolean searches. A revised search strategy focused the search to IEEE publications as the primary source of visualization research. A corpus of keywords were extracted from the 44 relevant articles and analyzed for relevance, keyword trends and contexts of use.

Findings
Keyword analysis results show visualization education research is confounded by several information retrieval issues: relevancy, incomplete taxonomy, non-standard lexicon, diverse disciplines and under-representation. Recommendations include: search strategies, alternative digital collections, a potential opportunity for research in information visualization pedagogy to address this gap in an emerging field and the need for more effective interactive tools to assist with keyword selection.

Research limitations/implications
The study focused on the IEEE publications as the primary source of visualization research.

Practical implications
A repository of visualization education research that is easily findable and relevant benefits both faculty using information visualization in their teaching and academics whose work must be disseminated to the broadest audience. Strategic keyword selection, interactive keyword tools or more robust thesaurus will enable IEEE Xplore digital library users to optimize their interaction with the system. Furthermore, results suggest a need for more research in information visualization pedagogy.

Originality/value
This is the only study to uniquely assess the efficacy of the IEEE Xplore digital library database system to retrieve relevant visualization education literature based on keyword search.
Effect of funding source on reporting bias in studies of intravitreal anti‐vascular endothelial growth factor therapy for retinal vein occlusion
Authors: Venincasa Michael J. , Kuriyan Ajay E. , Sridhar Jayanth 
Published: September 2018

AbstractPurposeTo examine the relationship between industry funding and outcome reporting bias in high‐quality studies investigating the use of intravitreal anti‐vascular endothelial growth factor (VEGF) agents for patients with macular oedema secondary to branch or central retinal vein occlusion (RVO).MethodsThis systematic review in PubMed and Ovid MEDLINE examined all randomized clinical trials and meta‐analyses published in journals with impact factor of ≥2 that investigated effectiveness of intravitreal anti‐VEGF therapy in patients with RVO. The main outcome measure was correspondence between statistical outcome and abstract conclusion wording.ResultsForty‐five studies met inclusion criteria; 38 (84%) showed correspondence between outcome and abstract conclusion without difference between industry‐funded and nonindustry‐funded publications (p = 0.39) or between publications in journals with impact factor ≥3 versus <3 (p = 0.96).ConclusionIn high‐quality studies of intravitreal anti‐VEGF therapy for RVO, neither industry funding nor journal impact factor affected the rate of outcome reporting bias.
Enhanced luminescence in Tb3+‐doped germanate glass ceramic scintillators containing CaF2 nanocrystals
Authors: Zhao Jingtao , Huang Lihui , Zhao Shilong , Xu Shiqing 
Published: September 2018

AbstractTb3+‐doped germanate glass ceramics containing CaF2 nanocrystals were prepared by melt quenching method with subsequent heat treatment. Their microstructures were investigated by XRD and TEM techniques. Their optical properties were studied by the transmittance, the photoluminescence, and the X‐ray excited luminescence (XEL). The luminescence intensity in the glass ceramics under 377 nm light and X‐ray excitations is significantly enhanced. The maximum integrated XEL intensity of the glass ceramics is about 50% of that of the commercial Bi4Ge3O12 (BGO) scintillating crystal. The results indicate that Tb3+‐doped germanate glass ceramic could be a promising scintillating material used in X‐ray detection for slow event.
Damping Low Frequency Oscillations via FACTS-POD Controllers Tuned by Bees Algorithm
Authors: Arzeha Nurul Aziah , Mustafa Mohd Wazir , Mohamad Idris Rasyidah 
Published: September 2018

Power systems are often subject to low frequency electro-mechanical oscillations resulting from electrical disturbances and consequence of the development of interconnection of large power system. Flexible Alternating Current Transmission System (FACTS) devices with Power Oscillation Damping (POD) as the supplemet controller has been recent research interest in damping the oscillation. Bees Algorithm (BA) is applied to optimized the parameters of the FACTS-POD controller. The main objective of optimization is to improve the system stability by moving the electro-mechanical eigenvalues on the s-plane to the left as far as possible. The controller is tested on a 3-machine 9-bus system and simulated in PSAT in MATLAB environment. The system is disturbed by increasing 10% mechanical input to Generator 2 and second disturbance is the system experiencing a three-phase fault. The performance of the system with the FACTS-POD controller is observed in terms of position of electromechanical eigenvalues on s-plane and damping responses of power oscillations where both terms shows significant improvement as compared to the system without FACTS-POD controller.