bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stress response, behavior, and development are shaped by transposable element-induced mutations in Drosophila
Authors: Rech Gabriel E. , Bogaerts-Marquez Maria , Barrón Maite G. , Merenciano Miriam , Villanueva-Cañas José Luis , Horváth Vivien , Fiston-Lavier Anna-Sophie , Luyten Isabelle , Venkataram Sandeep , Quesneville Hadi , Petrov Dmitri A. , González Josefa 
Published: July 2018

AbstractMapping genotype to phenotype is challenging because of the difficulties in identifying both the traits under selection and the specific genetic variants underlying these traits. Most of the current knowledge of the genetic basis of adaptive evolution is based on the analysis of single nucleotide polymorphisms (SNPs). Despite increasing evidence for their causal role, the contribution of structural variants to adaptive evolution remains largely unexplored. In this work, we analyzed the population frequencies of 1,615 Transposable Element (TE) insertions in 91 samples from 60 worldwide natural populations ofDrosophila melanogaster. We identified a set of 300 TEs that are present at high population frequencies, and located in genomic regions with high recombination rate, where the efficiency of natural selection is high. The age and the length of these 300 TEs are consistent with relatively young and long insertions reaching high frequencies due to the action of positive selection. Indeed, we, and others, found evidence of selective sweeps and/or population differentiation for 65 of them. The analysis of the genes located nearby these 65 candidate adaptive insertions suggested that the functional response to selection is related with the GO categories of response to stimulus, behavior, and development. We further showed that a subset of the candidate adaptive TEs affect expression of nearby genes, and five of them have already been linked to an ecologically relevant phenotypic effect. Our results provide a more complete understanding of the genetic variation and the fitness-related traits relevant for adaptive evolution. Similar studies should help uncover the importance of TE-induced adaptive mutations in other species as well.
The structural extraction of Chinese medical narratives
Authors: Zhang Rongzhi , Zhang Haifei , Yao Zhiyu , Huang Zhengxing 
Published: July 2018

AbstractMedical narratives document a vast amount of clinical data. This data has a valuable secondary purpose, as it may be used to optimize health service delivery and improve the quality of medical care. However, medical narratives are typically recorded in an unstructured manner, which complicates the process of extracting the structured information required for optimization. In this paper, we address this problem by applying and comparing two models, a rule-based model and a model based on conditional random fields (CRFs), to a data set of Chinese medical narratives. Among 4626 manually annotated Chinese medical narratives, collected from Shanxi Dayi Hospital in China, the rule-based model achieved 95.87% precision, 69.82% recall, and an F-score of 80.80%, and the CRF-based model realized 95.99% precision, 65.11% recall, and a 77.59% F-score. These experimental results demonstrate the efficacy of both proposed models for structural extraction from Chinese medical narratives.
SREBP1 drives KRT80-dependent cytoskeletal changes and invasive behavior in endocrine resistant ERα breast cancer
Authors: Perone Ylenia , Farrugia Aaron J. , Meira Alba Rodriguez , Győrffy Balázs , Ion Charlotte , Uggetti Andrea , Patten Darren , Chronopoulos Antonios , Faronato Monica , Shousha Sami , Steel Jenny H , Davies Claire , Patel Naina , Rio Hernandez Armando del , Coombes Charles , Pruneri Giancarlo , Lim Adrian , Calvo Fernando , Magnani Luca 
Published: July 2018

AbstractApproximately 30% of women diagnosed with ERα breast cancer relapse with metastatic disease following adjuvant treatment with endocrine therapies1,2. The connection between acquisition of drug resistance and invasive potential is poorly understood. In this study, we demonstrate that the type II keratin topological associating domain (TAD)3 undergoes epigenetic reprogramming in cells that develop resistance to aromatase inhibitors (AI), leading to keratin 80 (KRT80) upregulation. In agreement, an increased number of KRT80-positive cells are observed at relapse in vivo while KRT80 expression associates with poor outcome using several clinical endpoints. KRT80 expression is driven by de novo enhancer activation by sterol regulatory element-binding protein 14 (SREBP1). KRT80 upregulation directly promotes cytoskeletal rearrangements at the leading edge, increased focal adhesion maturation and cellular stiffening, which collectively promote cancer cell invasion. Shear-wave elasticity imaging of prospective patients shows that KRT80 levels correlate with stiffer tumors in vivo. Collectively, our data uncover an unpredicted and potentially targetable direct link between epigenetic and cytoskeletal reprogramming promoting cell invasion in response to chronic AI treatment.
On the Depth of Deep Learning Models for Splice Site Identification
Authors: Elsousy Reem , Kathiresan Nagarajan , Boughorbel Sabri 
Published: July 2018

AbstractThe success of deep learning has been shown in various fields including computer vision, speech recognition, natural language processing and bioinformatics. The advance of Deep Learning in Computer Vision has been an important source of inspiration for other research fields. The objective of this work is to adapt known deep learning models borrowed from computer vision such as VGGNet, Resnet and AlexNet for the classification of biological sequences. In particular, we are interested by the task of splice site identification based on raw DNA sequences. We focus on the role of model architecture depth on model training and classification performance.We show that deep learning models outperform traditional classification methods (SVM, Random Forests, and Logistic Regression) for large training sets of raw DNA sequences. Three model families are analyzed in this work namely VGGNet, AlexNet and ResNet. Three depth levels are defined for each model family. The models are benchmarked using the following metrics: Area Under ROC curve (AUC), Number of model parameters, number of floating operations. Our extensive experimental evaluation show that shallow architectures have an overall better performance than deep models. We introduced a shallow version of ResNet, named S-ResNet. We show that it gives a good trade-off between model complexity and classification performance.Author summaryDeep Learning has been widely applied to various fields in research and industry. It has been also succesfully applied to genomics and in particular to splice site identification. We are interested in the use of advanced neural networks borrowed from computer vision. We explored well-known models and their usability for the problem of splice site identification from raw sequences. Our extensive experimental analysis shows that shallow models outperform deep models. We introduce a new model called S-ResNet, which gives a good trade-off between computational complexity and classification accuracy.
Characterizing peer-judged answer quality on academic Q&A sites
Authors: Li Lei , He Daqing , Zhang Chengzhi , Geng Li , Zhang Ke 
Published: July 2018

Purpose
Academic social (question and answer) Q&A sites are now utilised by millions of scholars and researchers for seeking and sharing discipline-specific information. However, little is known about the factors that can affect their votes on the quality of an answer, nor how the discipline might influence these factors. The paper aims to discuss this issue.

Design/methodology/approach
Using 1,021 answers collected over three disciplines (library and information services, history of art, and astrophysics) in ResearchGate, statistical analysis is performed to identify the characteristics of high-quality academic answers, and comparisons were made across the three disciplines. In particular, two major categories of characteristics of the answer provider and answer content were extracted and examined.

Findings
The results reveal that high-quality answers on academic social Q&A sites tend to possess two characteristics: first, they are provided by scholars with higher academic reputations (e.g. more followers, etc.); and second, they provide objective information (e.g. longer answer with fewer subjective opinions). However, the impact of these factors varies across disciplines, e.g., objectivity is more favourable in physics than in other disciplines.

Originality/value
The study is envisioned to help academic Q&A sites to select and recommend high-quality answers across different disciplines, especially in a cold-start scenario where the answer has not received enough judgements from peers.
Does the New Rural Pension Scheme crowd out private transfers from children to parents? Empirical evidence from China
Authors: Ning Manxiu , Liu Weiping , Gong Jinquan , Liu Xudong 
Published: July 2018

Purpose
The purpose of this paper is to examine the effect of New Rural Pension Scheme (NRPS) on the private transfer behavior of the non-co-resident adult children to their elderly parents in rural China, and hence address the income redistribution effectiveness of public program for the elderly in rural China.

Design/methodology/approach
Pooled data from two waves of the China Health and Retirement Longitudinal Study and the combination of regression discontinuity design and difference in difference method are used to perform the analysis.

Findings
No evidence is found that pension payment from NRPS program does significantly crowd out the economic support from the adult children to their elder parents. The heterogeneous effects at different income percentile indicate that pension payment significantly increases the probability of receiving gross transfers and likelihood of the net transfer being positive for those elderly individuals with low income; in particular, the distinctive “family binding” arrangement may dramatically contribute to increasing the probability of receiving private transfers for the pension recipients.

Originality/value
The empirical findings would have far-reaching implications for the efficacy of public transfer or re-distributive programs such as NRPS; for the rural elderly, in particular, the unique “family binding” mechanism under the NRPS program may have positive welfare effects on the intended beneficiaries. Furthermore, an understanding of the inter-linkage between informal arrangements of elderly support and social re-distributive program provides further insight into the design of social security systems targeted to the vulnerable group in developing countries.
Constructing reading proficiency and struggle through tracked contexts
Authors: Learned Julie E. , Morgan Mary Jo 
Published: July 2018

PurposeThis paper aims to report on a study investigating how young people and teachers interpreted reading proficiency and difficulty across different tracks of English language arts in the sole high school serving a culturally diverse city.Design/methodology/approachFor six months, the researchers observed in three hierarchically tracked English classes. Participants were three teachers and 15 focal youths. The researchers also conducted semi-structured and open-ended interviews and collected classroom artifacts and students’ records.FindingsDespite adoption of the Common Core State Standards and a school-designed common English curriculum, both of which were to contribute to shared literacy objectives, students and teachers built highly contextualized understandings of reading proficiency, which diverged across tracks and mediated instruction. Across tracks, however, deficit discourses about reading struggle persisted, and students and teachers attributed difficulty to students’ attitudes and behaviors. Young people never described themselves in negative terms, which suggests they resisted the deficit labels tracking systems can generate.Originality/valueFindings extend research by showing how literacy-related tracking contributed to exclusionary contexts through which students were unproductively positioned at odds. Findings suggest a need for renewed rigor in the examination of tracking practices, particularly how notions of reading difficulty/proficiency position youths and mediate literacy instruction. Despite deficit conceptions of “struggling readers” across the school, youths never described themselves negatively and accepted reading difficulty as normal; how youths achieved such resourceful stances can be further investigated. These research directions will support the creation of English contexts that invite all youths into inquisitive, critical and agentive interactions with texts and each other.
Project risk management practices: the organizational maturity influence
Authors: Crispim José , Silva Luiz Henrique , Rego Nazaré 
Published: July 2018

Purpose
The purpose of this paper is to identify patterns of project risk management (PRM) practices’ adoption, and provides empirical evidence concerning the importance (and key attributes) of organizational PRM maturity to the use of risk-related practices and project performance.

Design/methodology/approach
The research involved two phases: interviews with five project managers, and a worldwide survey of project managers that resulted in the analysis of 865 valid questionnaire responses. Cluster analysis was used to classify PRM practices’ use, factor analysis to detect the structure of the relationship between the variables measuring PRM practices’ use and a multiple regression analysis (with canonical correlation) to further reveal the different degrees to which PRM practices and organizational maturity are associated.

Findings
The identified patterns of risk practices’ adoption indicate that different contexts of organization PRM maturity and project complexity influence practices selection. The PRM practices related with targets (e.g. time-phased budget plan) are the most used, and those related to tools and techniques (e.g. S-curve) are the least used. Additionally, the obtained results confirm that organizational PRM maturity influences risk practices’ usage, moderated by project complexity, and organizational PRM maturity influences project performance.

Originality/value
Empirical methods were used to investigate the relationship between organizational PRM maturity and a large set of PRM practices with project complexity as a moderator. Gaps in the use of PRM practices (i.e. areas where more PRM knowledge and training are needed) were identified. Finally, this work identifies the attributes of organizational maturity with implications in practices’ usage and project performance.
Does a more complex service offering increase uncertainty in operations?
Authors: Kreye Melanie E. 
Published: July 2018

PurposeThe purpose of this paper is to investigate how the complexity of the service offering (service complexity) affects the uncertainty during service operations in engineering services. Specifically, the authors compare the existence of organisational, relational, environmental and technological uncertainty in maintenance services and performance-based services.Design/methodology/approachThe authors present insights from four cases – two each for maintenance services and performance-based services. The in-depth data were based on 56 semi-structured interviews, multiple site visits, meeting notes, service contracts and other secondary data.FindingsThe case findings indicate that organisational and relational uncertainty were not linked to service complexity, while observations of environmental and technological uncertainty were higher and more varied for performance-based services. Based on these findings, the authors formulate four propositions regarding the relationship between service complexity and uncertainty in service operations.Originality/valueThis research contributes to the OM literature by suggesting that external sources of uncertainty increase with increasing service complexity, while internal sources of uncertainty remain unchanged.
Horizontal collaboration in response to modern slavery legislation
Authors: Benstead Amy V. , Hendry Linda C. , Stevenson Mark 
Published: July 2018

PurposeThe purpose of this paper is to investigate how horizontal collaboration aids organisations in responding to modern slavery legislation and in gaining a socially sustainable competitive advantage.Design/methodology/approachAction research has been conducted in the textiles and fashion industry and a relational perspective adopted to interpret five collaborative initiatives taken to tackle modern slavery (e.g. joint training and supplier audits). The primary engagement has been with a multi-billion pound turnover company and its collaborations with 35 brands/retailers. A non-government organisation and a trade body have also participated.FindingsSuccessful horizontal collaboration is dependent on both relational capital and effective (formal and informal) governance mechanisms. In collaborating, firms have generated relational rents and reduced costs creating a socially sustainable competitive advantage, as suggested by the relational perspective. Yet, limits to horizontal collaboration also exist.Research limitations/implicationsThe focus is on one industry only, hence there is scope to extend the study to other industries or forms of collaboration taking place across industries.Practical implicationsSuccessful horizontal collaborative relationships rely on actors having a similar mindset and being able to decouple the commercial and sustainability agendas, especially when direct competitors are involved. Further, working with non-business actors can facilitate collaboration and provide knowledge and resources important for overcoming the uncertainty that is manifest when responding to new legislation.Social implicationsSocial sustainability improvements aim to enhance ethical trade and benefit vulnerable workers.Originality/valuePrior literature has focussed on vertical collaboration with few prior studies of horizontal collaboration, particularly in a socially sustainable supply chain context. Moreover, there has been limited research into modern slavery from a supply chain perspective. Both successful and unsuccessful initiatives are studied, providing insights into (in)effective collaboration.
Modeling brand market share change in emerging markets
Authors: Romaniuk Jenni , Dawes John , Nenycz-Thiel Magda 
Published: July 2018

Purpose
The purpose of this paper is to examine what happens to key brand performance metrics as brands change in market share, in the context of packaged goods. The metrics are: penetration—the number of buyers a brand has; and loyalty—measured as purchase frequency (PF) and share of category requirements (SCR).

Design/methodology/approach
The study utilizes 24 data sets in 17 packaged goods categories in three emerging markets: China, Malaysia and Indonesia. The authors examine changes in penetration, loyalty and SCR in the context of volume and value market share change. In addition, the authors examine whether initial price point and price movements influence the results.

Findings
The primary finding is that market share change is accompanied by a greater change in penetration than in any other metric. This finding is very consistent across categories and countries. The relative importance of the two loyalty metrics varies by country. SCR was a stronger factor in Indonesia, while PF was stronger in Malaysia. Analysis indicated that pricing strategy (initial price and promotional depth) did not alter the main pattern of results, suggesting the results hold for brands with different price levels and tactics.

Practical implications
Irrespective of circumstance, to grow in value or volume market share, brands should aim to grow in penetration, while the importance of changes in specific loyalty measures depends on market conditions.

Originality/value
This research extends past research on brand growth to the very different economic, geographic and cultural conditions of three crucially important emerging markets. Its main value lies in recommendations on how much to invest in building the size of the customer base vs consumer retention.
Is human capital the sixth factor?
Authors: Maiti Moinak , Balakrishnan A. 
Published: July 2018

Purpose
The purpose of this paper is to focus on one of the major emerging Asian economies – India – to examine the role of human capital in asset prices.

Design/methodology/approach
The analysis uses various statistical techniques (e.g. multifactor regression model, 3D graphs, GRS test and residual graphs) to test the role of human capital in asset prices.

Findings
A six-factor model designed for capturing the size, value, profitability, investment and human capital patterns in average portfolio returns performs better than both Fama–French’s (1993) three- and Fama–French’s (2015) five-factor model. The main problem of six-factor model is its failure in capturing the average returns on “microcap with low-value stocks that are highly profitable invests aggressively for asset growth but invests much lesser for human growth” and “microcap with unprofitable stocks whose returns behave like those of low-value firms with conservative investment”. The study finds the investment factor (CMA) of Fama–French’s (2015) five-factor model as the redundant factor for describing the portfolio average returns in the study sample.

Research limitations/implications
The paper argues that human capital also plays a role in predicting returns. This has significant public policy content.

Originality/value
The present study is novel for several reasons: first, it includes six-factor model descriptions; second, no comprehensive asset pricing study is done with human capital in Asian emerging markets, especially in India. Perhaps, this is the first study to examine whether portfolio returns are affected by the human capital in the Indian context. Third, the study period and methodology used are completely different from the previous studies.
Beyond Brexit’s uncertainty: the foreseeable Britain’s innovative stagnation
Authors: Padilla Alcides J. , Garrido Alexander 
Published: July 2018

Purpose
The purpose of this paper is to explore the causes that determine the UK’s civilian research and development (R&D) expenditure to forecast its possible evolution in a post-Brexit scenario.

Design/methodology/approach
The authors use the Johansen’s co-integration analysis for time series.

Findings
The authors find a co-integration relationship between R&D and variables such as exports, military expenditure, patents, EU GDP per capita and USA GDP per capita. The authors also observed a stagnation in the foreseen R&D expenditure over the next five years.

Research limitations/implications
The authors warned that the results can only be viewed as a glance into the understanding of the complex elements that undergird the UK’s civilian, scientific and technological policy-making. But the authors see them as an interesting starting point for scrutinizing current shortcomings in policy-making, while providing clues for corrective action that would otherwise lead the UK to a structural crisis in its economic performance.

Originality/value
This study constitutes a first attempt to account for the loss of the UK’s innovative influence all over the world.