bluuebunny/crossref_metadata_2025_split huggingface dataset:
A mechanistic model for the negative binomial distribution of single-cell mRNA counts
Authors: Amrhein Lisa , Harsha Kumar , Fuchs Christiane 
Published: June 2019

SummarySeveral tools analyze the outcome of single-cell RNA-seq experiments, and they often assume a probability distribution for the observed sequencing counts. It is an open question of which is the most appropriate discrete distribution, not only in terms of model estimation, but also regarding interpretability, complexity and biological plausibility of inherent assumptions. To address the question of interpretability, we investigate mechanistic transcription and degradation models underlying commonly used discrete probability distributions. Known bottom-up approaches infer steady-state probability distributions such as Poisson or Poisson-beta distributions from different underlying transcription-degradation models. By turning this procedure upside down, we show how to infer a corresponding biological model from a given probability distribution, here the negative binomial distribution. Realistic mechanistic models underlying this distributional assumption are unknown so far. Our results indicate that the negative binomial distribution arises as steady-state distribution from a mechanistic model that produces mRNA molecules in bursts. We empirically show that it provides a convenient trade-off between computational complexity and biological simplicity.Graphical Abstract
Exogenous application of KNO3 elevates the salinity tolerance of Stevia rebaudiana through ion homeostasis mechanism
Authors: Mahajan Mitali , Sharma Surbhi , Kumar Pawan , Pal Probir Kumar 
Published: June 2019

AbstractThough relatively little is understood of adaptation, physiological and metabolic changes of Stevia rebaudiana under exposure to salinity stress, it is hypothesized that exogenous application of potassium (K+) could elevates the salinity tolerance through ions homeostasis. Thus, an experiment was conducted with twenty treatment combinations comprising four salinity levels (irrigation with normal water as control and three level of NaCl at 40, 80 and 120 mM) and five different concentrations of KNO3 (0.0, 2.5, 5.0, 7.5, and 10.0 g L−1). Dry leaf yield was not negatively affected with mild salinity (40 mM). However, the detrimental effects were observed at moderate and higher salinity levels (80 and 120 mM). The uptakes of K+, Ca2+, and N were significantly reduced at higher salinity level, whereas accumulations of Na+ and Cl− ions in plant tissues were substantially increased. Proline content in leaf was also increased significantly (P≤0.05) in response to salt stress. Among the foliar application, KNO3 at 5.0 gL−1 registered significantly (P≤0.05) higher dry leaf yield compared with control. Exogenous application of K+ under moderate salinity stress maintained ion balance in cytosol, particularly K: Na. Thus, the salinity tolerance of stevia can be elevated to some extent through exogenous application of K+.HighlightThe detrimental effects of moderate and higher salinity levels on growth and dry leaf yield of stevia were observed. However, tolerance level can be elevated through exogenous application of KNO3.
Alignment and mapping methodology influence transcript abundance estimation
Authors: Srivastava Avi , Malik Laraib , Sarkar Hirak , Zakeri Mohsen , Almodaresi Fatemeh , Soneson Charlotte , Love Michael I. , Kingsford Carl , Patro Rob 
Published: June 2019

AbstractBackgroundThe accuracy of transcript quantification using RNA-seq data depends on many factors, such as the choice of alignment or mapping method and the quantification model being adopted. While the choice of quantification model has been shown to be important, considerably less attention has been given to comparing the effect of various read alignment approaches on quantification accuracy.ResultsWe investigate the influence of mapping and alignment on the accuracy of transcript quantification in both simulated and experimental data, as well as the effect on subsequent differential expression analysis. We observe that, even when the quantification model itself is held fixed, the effect of choosing a different alignment methodology, or aligning reads using different parameters, on quantification estimates can sometimes be large, and can affect downstream differential expression analyses as well. These effects can go unnoticed when assessment is focused too heavily on simulated data, where the alignment task is often simpler than in experimentally-acquired samples. We also introduce a new alignment methodology, called selective alignment, to overcome the shortcomings of lightweight approaches without incurring the computational cost of traditional alignment.ConclusionWe observe that, on experimental datasets, the performance of lightweight mapping and alignment-based approaches varies significantly and highlight some of the underlying factors. We show this variation both in terms of quantification and downstream differential expression analysis. In all comparisons, we also show the improved performance of our proposed selective alignment method and suggest best practices for performing RNA-seq quantification.
Benchmarking Transposable Element Annotation Methods for Creation of a Streamlined, Comprehensive Pipeline
Authors: Ou Shujun , Su Weija , Liao Yi , Chougule Kapeel , Ware Doreen , Peterson Thomas , Jiang Ning , Hirsch Candice N. , Hufford Matthew B. 
Published: June 2019

AbstractSequencing technology and assembly algorithms have matured to the point that high-qualityde novoassembly is possible for large, repetitive genomes. Current assemblies traverse transposable elements (TEs) and allow for annotation of TEs. There are numerous methods for each class of elements with unknown relative performance metrics. We benchmarked existing programs based on a curated library of rice TEs. Using the most robust programs, we created a comprehensive pipeline called Extensivede-novoTE Annotator (EDTA) that produces a condensed TE library for annotations of structurally intact and fragmented elements. EDTA is open-source and freely available:https://github.com/oushujun/EDTA.
3D-printed moulds for image-guided surgical biopsies: an open source computational platform
Authors: Crispin-Ortuzar Mireia , Gehrung Marcel , Ursprung Stephan , Gill Andrew B , Warren Anne Y , Beer Lucian , Gallagher Ferdia A , Mitchell Thomas J , Mendichovszky Iosif A , Priest Andrew N , Stewart Grant D , Sala Evis , Markowetz Florian 
Published: June 2019

ABSTRACTPURPOSESpatial heterogeneity of tumours is a major challenge in precision oncology. The relationship between molecular and imaging heterogeneity is still poorly understood, as it relies on the accurate co-registration of medical images and tissue biopsies. tumour moulds can guide the localization of biopsies, but their creation is time consuming, technologically challenging, and difficult to interface with routine clinical practice. These hurdles have so far hindered the progress in the area of multiscale integration of tumour heterogeneity data.METHODSWe have developed an open source computational framework to automatically produce patient-specific 3D-printed moulds that can be used in the clinical setting. Our approach achieves accurate co-registration of sampling location between tissue and imaging, and integrates seamlessly with clinical, imaging and pathology workflows.RESULTSWe applied our framework to patients with renal cancer undergoing radical nephrectomy. We created personalised moulds for five patients, obtaining Dice similarity coefficients between imaging and tissue sections ranging from 0.86 to 0.93 for tumour regions, and between 0.70 and 0.76 for healthy kidney. The framework required minimal manual intervention, producing the final mould design in just minutes, while automatically taking into account clinical considerations such as a preference for specific cutting planes.CONCLUSIONOur work provides a robust and automated interface between imaging and tissue samples, enabling the development of clinical studies to probe tumour heterogeneity on multiple spatial scales.
A systematic review of fidelity measurements in complex interventions for people with intellectual disabilities and behaviours that challenge
Authors: Paulauskaite Laura , Hassiotis Angela , Ali Afia 
Published: June 2019

Purpose
Fidelity data in clinical trials are not only necessary for appraising the internal and external validity, but also could provide useful insights how to improve the application of an intervention in everyday settings. The purpose of this paper is to understand the current literature of fidelity measurements in complex interventions for people with intellectual disabilities (ID) and behaviours that challenge.

Design/methodology/approach
The electronic databases MEDLINE, Embase, PsycINFO, Web of Science and CINAHL Plus were searched for studies published between 1990 to 2017 that have mentioned fidelity in randomised controlled trials of complex interventions for people with ID and behaviours that challenge based on positive behaviour support or applied behaviour analysis principles. The authors also searched the grey literature and reference lists.

Findings
Five randomised controlled trials were included in the review. The authors found variable and inconsistent fidelity measurements reported in the studies. The most frequently provided fidelity elements found in four out of five studies were adherence of implementation, dose and some aspects of quality of delivery.

Research limitations/implications
Research recommendations for a standardised approach of measuring fidelity in such studies are suggested.

Originality/value
The first review of such type that confirms the paucity of research measuring fidelity in complex interventions in this population.
Effects of two fibers used separately and in combination on physico-chemical, textural, nutritional and sensory properties of beef fresh sausage
Authors: Ben Slima Sirine , Ktari Naourez , Triki Mehdi , Trabelsi Imen , Moussa Hafedh , Makni Skandar , Abdeslam Asehraou , Herrero Ana Maria , Jiménez-Colmenero Francisco , Ruiz-Capillas Claudia , Ben Salah Riadh 
Published: June 2019

Purpose
The purpose of this paper is to investigate the influence of different dietary fibers on color, nutritional, physico-chemical, sensory and textural properties of fresh sausage.

Design/methodology/approach
This study was undertaken to determine the effects of partial beef meat substitution (15, 10.5 and 6 percent) at different combinations: barley beta-glucan concentrate (BBC at 1 percent) alone, carrot fiber (ID809 at 1 percent) alone and a mixture of both fibers (BBC and ID809 at 0.5 percent of each), on the quality of fresh sausage.

Findings
Results revealed that the supplementation of dietary fibers generally decreased protein contents and increased moisture. Color parameters were significantly affected by the addition of dietary fibers. Meat substitution with dietary fibers tended toward red coloration, which enhanced sensory properties of fresh sausages, especially general acceptability. Fresh sausages formulated with a mixture of dietary fibers recorded good firmness. Indeed, it increased extrusion force values and provided a greater hardness at sensory level. This manuscript reports that beef sausage formulated with a mixture of BBC and ID809 and reduced beef meat rate improved acceptability to consumer.

Originality/value
The paper approaches a new subject that may be relevant to functional food. There are few research works to evaluate consumer preferences of new product developments and to achieve healthier and more economic fresh sausages formulated with a mixture of two fibers after reducing beef meat content.
Underage drinking as a natural part of growing up: a UK study of parental beliefs
Authors: Fulton Emily , Baines Darrin , Bartle Naomi 
Published: June 2019

Purpose
Parental beliefs about underage drinking are known to influence the drinking behaviours of their children. The purpose of this paper is to explore parental beliefs about their own child drinking alcohol and young people in general, in order to ascertain whether there is a need to target such beliefs in the design of public health interventions.

Design/methodology/approach
Parents of 11–18 year olds attending one of nine schools in the Midlands of England, UK were invited to take part. Participants completed a newly designed 40-item questionnaire measuring parental beliefs about the impact and causes of underage drinking; talking to their child about alcohol; and how much and how often they thought their child consumed alcohol.

Findings
In total, 185 parents took part in the study, reporting on their eldest child aged 18 or under. The majority of parents agreed that underage drinking is detrimental to child health and wellbeing. However, over 60 per cent believed that alcohol consumption is a “natural part of growing up”, and stronger agreement with this belief was associated with higher parental reports of alcohol consumption in their children.

Social implications
The majority of parents recognised the risks and negative effects of alcohol; however, many also believe it is a natural part of growing up. Parents may hold conflicting beliefs about underage drinking, which could impact on the drinking beliefs and behaviours of their children.

Originality/value
Public health interventions may need to counter the common parental belief that underage drinking is a normal part of growing up and therefore to be expected. Clear messages about the impact parent beliefs and behaviour have on young people drinking, to ensure parents recognise that messages are aimed at themselves, and not just “other parents” are imperative.
How much of library digital content is checked out but never used?
Authors: Lieu Angela , Zhao Dangzhi 
Published: June 2019

Purpose
This paper aims to identify patterns, trends and potential implications related to post-checkout non-usage (material that is checked out by a user, but subsequently never opened and/or downloaded) of library digital content.

Design/methodology/approach
A large urban Canadian public library’s data (2013-2017) from Rakuten OverDrive was analyzed. Pending items (items that are checked out, but neither opened nor downloaded) were compared with total checkouts to determine post-checkout non-usage rates.

Findings
Checkouts and overall rates of post-checkout non-usage of e-books and e-audiobooks have risen significantly and consistently. Juvenile and non-fiction e-books demonstrate higher post-checkout non-usage rates than adult and fiction e-books, respectively. The library spends up to US$10,700 per year on metered access e-books that are never opened by users. This number has grown significantly over the years.

Originality/value
E-materials in libraries have been growing rapidly, but their current lending models are still largely a direct application of concepts in traditional library services that have developed based on physical materials, such as checkouts, due dates, renewals, holds and wait times. However, e-materials do not have the limitation of physical materials that prevents other users from accessing a checked-out item, which makes many of the traditional concepts no longer applicable. New concepts and lending models should be developed that allow users to access any library e-materials at any time, and are financially functional and sustainable for both libraries and e-content providers.
Information protection behaviors: morality and organizational criticality
Authors: Lankton Nancy K. , Stivason Charles , Gurung Anil 
Published: June 2019

Purpose
Organizational insiders play a critical role in protecting sensitive information. Prior research finds that moral beliefs influence compliance decisions. Yet, it is less clear what factors influence moral beliefs and the conditions under which those factors have stronger/weaker effects. Using an ethical decision-making model and value congruence theory, this study aims to investigate how moral intensity and organizational criticality influence moral beliefs and intentions to perform information protection behaviors.

Design/methodology/approach
The hypotheses were tested using a scenario-based survey of 216 organizational insiders. Two of the scenarios depict low criticality information security protection behaviors and two depict high criticality behaviors.

Findings
A major finding is that users rely more on perceived social consensus and magnitude of consequences when organizational criticality is low and on temporal immediacy and proximity when criticality is high. In addition, the moral intensity dimensions explain more variance in moral beliefs when organizational criticality is low.

Research limitations/implications
The study is limited by its sample, which is organizational insiders at a mid-size university. It is also limited in that it only examined four of the six moral intensity dimensions.

Practical implications
The findings can guide management about which moral intensity dimensions are more important to focus on when remediating tone at the top and other leadership weaknesses relating to information security.

Originality/value
This study adds value by investigating the separate dimensions of moral intensity on information protection behaviors. It also is the first to examine moral intensity under conditions of low and high organizational criticality.
Service-delivery success and failure under the sharing economy
Authors: Furunes Trude , Mkono Muchazondida 
Published: June 2019

PurposeInformed by the role and script theory, this paper aims to explore workforce and customer experiences related to service delivery under the sharing economy. The study is expedient as the sharing economy spreads its disruptive innovation across the hospitality industry.Design/methodology/approachThis paper applies a qualitative approach, sourcing online data from virtual platforms.FindingsThe results indicate both positive and negative experiences for customers and the workforce, and the paper highlights the challenges of fragmented service delivery as a result of service delivery mediated through mobile applications.Practical implicationsFood delivery mediated through mobile applications is likely to expand as more households are lured by its convenience. This change has implications for both restaurants and the workforce.Originality/valueAlthough a growing number of studies analyse the impact of the sharing economy on the hospitality industry, much of the focus has been on accommodation, and the impact and implications for the food-service segment has not been thoroughly investigated yet.
Self-verification striving and employee outcomes
Authors: Kim Tae-Yeol , Gilbreath Brad , David Emily M. , Kim Sang-Pyo 
Published: June 2019

PurposeThe purpose of this paper is to test whether self-verification striving serves as an individual difference antecedent of emotional labor and explore whether various emotional labor tactics acted as mediating mechanisms through which self-verification striving relates to employee outcomes.Design/methodology/approachThe sample used in this paper consisted of supervisor–subordinate dyads working in six hotels in South Korea and used multi-level analyses and the Monte Carlo method to test the research hypotheses presented in this paper.FindingsSelf-verification striving was positively and directly related to job performance as well as two out of three forms of emotional labor (i.e. the expression of naturally felt emotions and deep acting). Self-verification striving also indirectly related to job satisfaction through the expression of naturally felt emotions and indirectly related to job performance through deep acting.Practical implicationsThe findings of this paper suggest that organizations should consider self-verification striving as an employment selection criterion and provide training programs to help their customer service employees engage in appropriate types of emotional labor.Originality/valueThis paper is the first to explore the underlying mechanisms through which self-verification striving relates to employee outcomes. It also empirically bolsters the notion that expressing naturally felt emotions is an important means of authentic self-expression that positively contributes to job satisfaction. Further, the authors found that self-verification striving positively relates to job performance partially through deep acting. Moreover, they have shown that self-verification striving, as an individual differences variable, is an antecedent of different types of emotional labor.
Management of traditional retail markets in the UK: comparative case studies
Authors: Hoang Dong , Barnes Cathy , Munroe Olga 
Published: June 2019

Purpose
The purpose of this paper is to examine the current state of the management of traditional retail markets (TRM) in the UK. TRM are indoor and outdoor markets located in town and city centres across the UK, selling food, household goods, clothing and the like.

Design/methodology/approach
The paper employs a comparative analysis approach of multiple cases using an analytical framework drawn from place management and retail business management literature. The study investigates 11 retail markets in the UK, including 7 run by Local Councils, 2 privately run and 2 operated by Charity Trusts.

Findings
The paper identifies the management challenges of TRM lying at the intersect between its private-like business entity and the management overseen by local authorities, whose roles and functions are mainly on delivering public services. Although some council markets struggle, it remains a popular model for TRM because it offers social space and inclusion which other types of markets lack. The study also highlights that the environment within which TRM operate, such as policy, infrastructure, business and entrepreneurial aspects play an important role in influencing the performance of the markets.

Originality/value
The paper contributes to the retail literature’s conceptual and empirical understanding of TRM management – the area which has been mostly neglected and under-researched. It offers an integrated analytical framework, including four dimensions of policy, infrastructure, business and entrepreneurial environment to advance the current limited understanding of this traditional form of retailing and sheds light on future research in this area.
Foreign market learning: an integrative model of its antecedents, processes and outcomes
Authors: Nordin Fredrik , Lindbergh Jessica 
Published: June 2019

PurposeThe purpose of this paper is to offer an integrative model of foreign market learning, including different learning processes, antecedents and outcomes.Design/methodology/approachThe paper makes a critical review of the relevant literature, drawing on a keywords-based search of three major databases and a range of other published work for a broader perspective on the subject.FindingsThe resulting integrative model shows in a number of ways how companies can learn and benefit from differences in foreign markets and what results this can lead to.Research limitations/implicationsThe sample of subject-specific contributions to the literature may have been insufficient, and a wider selection of keywords to identify them might have captured a richer variety of concepts and opinions.Originality/valueThe integrative model contributes to the literature on foreign market learning and innovation and serves as a basis for future studies and current management strategy.