bluuebunny/crossref_metadata_2025_split huggingface dataset:
LinkedSV for detection of mosaic structural variants from linked-read exome and genome sequencing data
Authors: Fang Li , Kao Charlly , Gonzalez Michael V , Mafra Fernanda A , Pellegrino da Silva Renata , Li Mingyao , Wenzel Sören , Wimmer Katharina , Hakonarson Hakon , Wang Kai 
Published: September 2018

AbstractLinked-read sequencing provides long-range information on short-read sequencing data by barcoding reads originating from the same DNA molecule, and can improve the detection and breakpoint identification for structural variants (SVs). We present LinkedSV for SV detection on linked-read sequencing data. LinkedSV considers barcode overlapping and enriched fragment endpoints as signals to detect large SVs, while it leverages read depth, paired-end signals and local assembly to detect small SVs. Benchmarking studies demonstrates that LinkedSV outperforms existing tools, especially on exome data and on somatic SVs with low variant allele frequencies. We demonstrate clinical cases where LinkedSV identifies disease causal SVs from linked-read exome sequencing data missed by conventional exome sequencing, and show examples where LinkedSV identifies SVs missed by high-coverage long-read sequencing. In summary, LinkedSV can detect SVs missed by conventional short-read and long-read sequencing approaches, and may resolve negative cases from clinical genome/exome sequencing studies.
CluSim: a Python package for the comparison of clusterings and dendrograms
Authors: Gates Alexander J. , Ahn Yong-Yeol 
Published: September 2018

SummaryQuantifying the similarity of clusterings is a fundamental step in data analysis. Clustering similarity is the basis for method evaluation, consensus clustering, and tracking the temporal evolution of clusters, among many other tasks. Here we provide CluSim, a comprehensive Python package for the comparison of partitions, overlapping clusterings, and hierarchical clusterings (dendrograms) with more than 20 similarity measures. The CluSim package provides both analytic and empirical methods for assessing the similarity of clusterings in the context of a random model, and provides the novel element-centric approaches for clustering similarity measure that we introduced recently. We illustrate the use of the package through two examples: an evaluation of the clustering of Gene Expression data in the context of different random models, and detailed analysis of model incongruence using element-centric comparisons between a set of phylogentic trees (dendrograms).Availability and implementationThe CluSim Python package and accompanying jupyter notebook is available at https://github.com/Hoosier-Clusters/clusim with the MIT open source licence.Contactajgates42@gmail.comor yyahn@iu.edu
Implicit temporal predictability biases slow oscillatory phase in auditory cortex and enhances pitch discrimination sensitivity
Authors: Herbst Sophie K. , Obleser Jonas 
Published: September 2018

AbstractCan human listeners use strictly implicit temporal contingencies in auditory input to form temporal predictions, and if so, how are these predictions represented endogenously? To assess this question, we implicitly manipulated foreperiods in an auditory pitch discrimination task. Unbeknownst to participants, the pitch of the standard tone could either be deterministically predictive of the onset of the target tone, or convey no predictive information. Both conditions were presented interleaved in one stream, and separated by variable inter-stimulus intervals such that there was no dominant stimulus rhythm throughout. Even though participants were unaware of the implicit temporal contingencies, pitch discrimination sensitivity (i.e. the slope of the psychometric function) increased when the onset of the target tone was predictable in time (N = 49). Concurrently recorded EEG data (N = 24) revealed that standard tones which initiated temporal predictions evoked a more negative N1 component than non-predictive standards, and were followed by an increase in delta power during the foreperiod. Furthermore, the phase angle of delta oscillations (1–3Hz) evoked by the standard tone predicted pitch discrimination sensitivity at the target tone (1.75 s later on average), which suggests that temporal predictions can be initiated by an optimized delta phase reset. In sum, we show that auditory perception benefits from implicit temporal contingencies, and provide evidence for a role of slow neural oscillations in the endogenous representation of temporal predictions, in absence of exogenously driven entrainment to rhythmic input.Significance StatementTemporal contingencies are ubiquitous in sensory environments, especially in the auditory domain, and have been shown to facilitate perception and action. Yet, how these contingencies in exogenous inputs are transformed into an endogenous representation of temporal predictions is not known. Here, we implicitly induced temporal predictability in the absence of a rhythmic input structure, that is without exogenously driven entrainment of neural oscillations. Our results show that even implicit and non-rhythmic temporal predictions are extracted and used by human observers, underlining the role of timing in sensory processing. Furthermore, our EEG results point towards an instrumental role of delta oscillations in initiating temporal predictions by an optimized phase reset in response to a temporally predictive cue.
The controlled direct effect of temperament at 2-3 years on cognitive and academic outcomes at 6-7 years
Authors: Chong Shiau Y. , Chittleborough Catherine R. , Gregory Tess , Lynch John , Mittinty Murthy N. , Smithers Lisa G. 
Published: September 2018

AbstractThere is widespread interest in temperament and its impact upon cognitive and academic outcomes. Parents adjust their parenting according to their child’s temperament, however, previous studies have not accounted for parenting while estimating the association between temperament and academic outcomes. We examined the controlled direct effect of temperament (2-3 years) on cognitive and academic outcomes (6-7 years) when mediation by parenting practices (4-5 years) was held constant. Participants were from the Longitudinal Study of Australian Children (n=5107). Cognitive abilities were measured by the Peabody Picture Vocabulary Test (verbal) and the Matrix Reasoning test (non-verbal). Literacy and numeracy were reported by teachers using the Academic Rating Scale. Mothers reported children’s temperament using the Short Temperament Scale for Toddlers (subscales: reactivity, approach, and persistence). Parenting practices included items about engagement in activities with children. Marginal structural models with inverse probability of treatment weights were used to estimate the controlled direct effect of temperament, when setting parenting to the mean. All temperament subscales were associated with cognitive abilities, with persistence showing the largest controlled direct effect on verbal (β=0.58; 95%CI 0.27, 0.89) and non-verbal (β=0.19; 0.02, 0.34) abilities. Higher persistence was associated with better literacy (β=0.08; 0.03, 0.13) and numeracy (β=0.08; 0.03, 0.13), and higher reactivity with lower literacy (β=−0.08; −0.11, −0.05) and numeracy (β=−0.07; −0.10, −0.04). There was little evidence that temperamental approach influenced literacy or numeracy. Overall, there was a small controlled direct effect of temperament on cognitive and academic outcomes after accounting for parenting and confounders.
Optimal diameter reduction ratio of acinar airways in human lungs
Authors: Park Keunhwan , Son Taeho , Cho Young-Jae , Jeon Noo Li , Kim Wonjung , Kim Ho- Young 
Published: September 2018

AbstractIn the airway network of a human lung, the airway diameter gradually decreases through multiple branching. The diameter reduction ratio of the conducting airways that transport gases without gas exchange is 0.79, but this reduction ratio changes to 0.94 in acinar airways beyond transitional bronchioles. While the reduction in the conducting airways was previously rationalized on the basis of Murray’s law, our understanding of the design principle behind the acinar airways has been far from clear. Here we elucidate that the change in gas transfer mode is responsible for the transition in the diameter reduction ratio. The oxygen transfer rate per unit surface area is maximized at the observed geometry of acinar airways, which suggests the minimum cost for the construction and maintenance of the acinar airways. The results revitalize and extend the framework of Murray’s law over an entire human lung.
Gαq sensitizes TRPM8 to inhibition by PI(4,5)P2 depletion upon receptor activation
Authors: Liu Luyu , Yudin Yevgen , Kang Chifei , Shirokova Natalia , Rohacs Tibor 
Published: September 2018

ABSTRACTActivation of G-protein coupled receptors (GPCRs) was proposed to inhibit the cold and menthol sensitive Transient Receptor Potential Melastatin 8 (TRPM8) channels via direct binding of Gαq to the channel. It is well documented that TRPM8 requires the plasma membrane phospholipid phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2 or PIP2] for activity. It was claimed however that a decrease in cellular levels of this lipid does not contribute to channel inhibition upon receptor activation. Here we show that supplementing the whole cell patch pipette with PI(4,5)P2 reduced inhibition of TRPM8 by activation of Gαq-coupled receptors in mouse dorsal root ganglion (DRG) neurons. Activation of the same receptors induced Phospholipase C (PLC) activation and decreased plasma membrane PI(4,5)P2 levels in these neurons. PI(4,5)P2 also reduced inhibition of TRPM8 by activation of heterologously expressed Gαq-coupled muscarinic M1 receptors. Co-expression of a constitutively active Gαq protein that does not couple to PLC inhibited TRPM8 activity, and in cells expressing this protein decreasing PI(4,5)P2 levels using a voltage sensitive 5’-phosphatase induced a stronger inhibition of TRPM8 activity than in control cells. Our data indicate that PI(4,5)P2 depletion plays an important role in TRPM8 inhibition upon GPCR activation, and Gαq inhibits the channel by reducing its apparent affinity for PI(4,5)P2 and thus sensitizes the channel to inhibition by decreasing PI(4,5)P2 levels.
Tensorflow Based Deep Learning Model and Snakemake Workflow for Peptide-Protein Binding Predictions
Authors: Altay Gokmen 
Published: September 2018

AbstractIn this study, we first present a Tensorflow based Deep Learning (DL) model that provides high performances in predicting the binding of peptides to major histocompatibility complex (MHC) class I protein. Second, we provide the necessary Python codes to run the model and also easily input large train and test peptide binding benchmark dataset. Third, we provide Snakemake based workflow that allows to run all the model and performance analysis over all the different test alleles at once in parallel over computer and clusters. We also provide comparison analysis of the performances of various models. Finally, in order to help attaining to the best possible DL model by a community effort, this work is intended to be a ready to modify base model and workflow for the global Deep Learning community with no domain knowledge in MHC-peptide binding problem and thus provides all the necessary reference code templates and benchmarking data sets for further developments on the presented model architecture. All the reproducible Python codes, Snakemake workflow and benchmark data sets and a tutorial are available online at https://github.com/altayg/Deep-Learning-MHCI.
Heatlines visualization of convective heat flow during differential heating of porous enclosures with concave/convex side walls
Authors: Biswal Pratibha , Basak Tanmay 
Published: September 2018

Purpose
This paper is aimed to study natural convection in enclosures with curved (concave and convex) side walls for porous media via the heatline-based heat flow visualization approach.

Design/methodology/approach
The numerical scheme involving the Galerkin finite element method is used to solve the governing equations for several Prandtl numbers (Prm) and Darcy numbers (Dam) at Rayleigh number, Ram = 106, involving various wall curvatures. Finite element method is advantageous for curved domain, as the biquadratic basis functions can be used for adaptive automated mesh generation.

Findings
Smooth end-to-end heatlines are seen at the low Dam involving all the cases. At the high Dam, the intense heatline cells are seen for the Cases 1-2 (concave) and Cases 1-3 (convex). Overall, the Case 1 (concave) offers the largest average Nusselt number (

Nur¯) at the low Dam for all Prm. At the high Dam,

Nur¯ for the Case 1 (concave) is the largest involving the low Prm, whereas

Nur¯ is the largest for Case 1 (convex) involving the high Prm.

Practical implications
Thermal management for flow systems involving curved surfaces which are encountered in various practical applications may be complicated. The results of the current work may be useful for the material processing, thermal storage and solar heating applications

Originality/value
The heatline approach accompanied by energy flux vectors is used for the first time for the efficient heat flow visualization during natural convection involving porous media in the curved walled enclosures involving various wall curvatures.
Perceived value, relationship quality and positive WOM intention in banking
Authors: van Tonder Estelle , Petzer Daniël J. , van Vuuren Naomi , De Beer Leon T. 
Published: September 2018

Purpose
The purpose of this paper is to explore the proposed relationships between perceived usefulness (a dimension of perceived value), the relationship quality factors (competence trust and continuous commitment) and positive word-of-mouth intentions in an electronic banking setting.

Design/methodology/approach
A survey was conducted among 511 electronic banking customers.

Findings
Continuous commitment was found to mediate the relationships between perceived usefulness and competence trust with positive word-of-mouth intention, respectively.

Research limitations/implications
The results indicate the role of perceived value and relationship quality in contributing to positive word-of-mouth intention.

Practical implications
The findings could also guide banking institutions in managing their existing electronic banking customers more appropriately and to encourage them to engage in word-of-mouth behaviour that will convince other potential users of the benefits of the service.

Originality/value
Little is known on a mediated model noting the connection between perceived value, the relationship quality factors competence trust and continuous commitment and positive word-of-mouth intention. The findings provide more insight into the matter and accordingly contribute to the developing body of knowledge on perceived value, relationship quality and behavioural intention and their importance to the stream of research on positive word of mouth.
An Uber ethical dilemma: examining the social issues at stake
Authors: Chee Florence M. 
Published: September 2018

Purpose
This paper aims to engage with the social issues emerging from the increasing reliance upon app-driven services, as they pertain to precarious labor and ethical standpoints in a digital era. Popular ride services such as Uber have been lauded for bringing much needed transportation services that are superior to expensive taxis or unpleasant or inaccessible public transit.

Design/methodology/approach
As a result of over three years of ongoing research and analysis, this paper is a comprehensive assessment of a number of social issues facing the integration of practices both signified and enacted in an economy driven by apps such as Uber. While these companies are indeed profitable, questions remain as to just how much of a panacea these practices actually herald.

Findings
Findings indicate that privatization and a lack of labor regulation may present a significant savings to the user, but full cost economics suggest that the social and environmental costs require consideration.

Research limitations/implications
The recommendations here refer to the ethical considerations forwarded in this paper and serve to open up dialog to further discuss the persistent issues facing a precarious future.

Practical implications
In terms of practical implications, there is a point of tension between governmental/regulatory bodies, disruptive innovators and users.

Social implications
Stakeholders of all stripes are scrambling to keep up with the pace and problematics of digital innovations and an inclusive critical dialog on app-driven services has yet to become a priority.

Originality/value
The original value of this analytical framework from a social justice perspective stands to catalyze action on a number of pervasive social issues surrounding digital ethics and policy.
Family firms, political connections and audit fees: evidence from Malaysian firms
Authors: Tee Chwee Ming 
Published: September 2018

Purpose
The purpose of this study is to examine the association between family firms and audit fees in an emerging economy setting. As family firms either face Type 1 or Type 2 agency problem, it seeks to gain a better understanding on family firms in an emerging economy such as Malaysia. Additionally, this study introduces political connections to investigate whether it can moderate the association between family firms and audit fees. Political connection is chosen as an important institutional feature because of its many and well-documented politically connected firms and pervasive political patronage system in Malaysia.

Design/methodology/approach
Based on a dataset of 750 firms or 7,848 firm-year observations from 2002 till 2015, panel regression analysis is used to investigate the research questions. As a robustness test, Heckman’s self-selection model is used to deal with the self-selection problem.

Findings
The results reveal that family firms are associated with higher audit fees, indicating that Type 2 dominates Type 1 agency problems in Malaysia. This positive relationship is stronger in family firms which are older and have higher family controlling shareholding. Further, the association is exacerbated if it is also connected to the ruling elite.

Originality/value
This study contributes to the literature by showing that institutional feature such as family firms and political connections can produce different firm outcomes between emerging and advanced economy, particularly in auditing. This study responds to calls for more research on auditing in family firms, particularly in emerging economy.
A consumer value approach to a holistic understanding of the winery experience
Authors: Massa Charlotte , Bédé Sébastien 
Published: September 2018

Purpose
The present study is part of a joint effort to gain a holistic understanding of the consumption experience. This paper aims to understand the essence of the winery experience through a better characterisation of the latter because of the consumer value approach and to define the main cultural differences between the Old World and the New World in this respect.

Design/methodology/approach
The authors felt that netnography offered the most suitable qualitative method to capture the meaning of a winery experience in an international context. To this end, we collected 3,065 original tourist reviews for 35 wineries, written from January 2015 to June 2016.

Findings
The findings suggest that a winery experience is made up of the following values: “hedonic”, “economic”, “social” and “legacy”. In addition, the results indicate that social and legacy values are more important for the Old World, while the New World tends to put more emphasis on economic and hedonic values.

Practical implications
Wineries need to deliver experiences that encourage tourists to explore what their enterprise has to offer. Given the importance of the customer experience to trigger wine purchases and positive word-of-mouth to promote brand loyalty, the findings can help winery managers to adapt their services in consequence.

Originality/value
Few studies have applied a consumer value approach or used netnography to examine tourists’ experiences from a cross-cultural perspective.
Reap exceptional value from M&A: manage it as a core competence
Authors: Galpin Timothy 
Published: September 2018

Purpose
Mergers and acquisitions (M&As) have become the preferred growth strategy for many executives. However, simply “doing deals” is not enough to create a competitive advantage for their companies. Only focusing on M&A as a financial transaction is too narrow of an approach, which is easily duplicated across firms. Using Woodward, Inc. as a case example, this article shows how using an actionable, end-to-end process model, and embedding integrated capabilities within the organization, across the entire process, managers can make M&A a core competence to provide a valuable, rare, and inimitable advantage for their firms.

Design/methodology/approach
A mixed-methods approach, combining action research with a narrative synthesis of empirical and practice literature was used to develop a comprehensive M&A process model - the Deal Flow Model - consisting of ten stages across three phases. The resource-based view, core competencies, and the VRIO framework provide a theoretical foundation for the model. An application of the Deal Flow Model using Woodward Inc. as a case example is also presented.

Findings
Only focusing on M&A as a financial transaction is too narrow of an approach, which is easily duplicated across firms. Instead, using an actionable, end-to-end process model, and embedding integrated capabilities within the organization across the entire M&A process provides a valuable, rare, and inimitable advantage for firms.

Research limitations/implications
Researchers will find the Deal Flow Model useful as a structure to examine the M&A process as a whole or to frame single-stage, single-discipline research in the broader context of the overall M&A process.

Practical implications
A practice-oriented Deal Flow Model, providing a cross-disciplinary, end-to-end view of the M&A process is presented. The model is designed to be actionable by managers, who can apply the process to build the M&A competence of their organization.

Originality/value
The Deal Flow Model is unique as it is designed to be actionable by managers, who can apply the process to build the M&A competence of their organization. Likewise, researchers will find the model useful as a structure to examine the M&A process as a whole or to frame single-stage, single-discipline research in the broader context of the overall M&A process.
TQM implementation in 3PL organisations vs organisations with in-house logistics department
Authors: Vouzas Fotis , Katsogianni Theano 
Published: September 2018

Purpose
The purpose of this paper is to present the results of an exploratory literature review investigating the similarities and differences in TQM implementation between 3PL organisations and organisations with an in-house logistics function.

Design/methodology/approach
The authors collected all relevant papers covering both types of organisations implementing TQM worldwide in a time period from 1991 until today. The aim was to identify key papers and analyse its contents based on the quality of services provided by these two types of organisations.

Findings
The survey contains information about the forces that encourage managers to implement quality practices in the logistics function, the reasons that impeded the implementation of such a quality programme, the quality methods being used and also the level of their satisfaction with the current quality management in logistics.

Research limitations/implications
This paper only mentioned the principal papers that have been published globally from 1991 – today.

Originality/value
The present study is one of the few that reviewed literature from the year 1991 – today in order to provide a comparison of quality management practices between 3PLs and in-house Logistics organisations.