bluuebunny/crossref_metadata_2025_split huggingface dataset:
Beware the Jaccard: the choice of metric is important and non-trivial in genomic colocalisation analysis
Authors: Salvatore Stefania , Rand Knut Dagestad , Grytten Ivar , Ferkingstad Egil , Domanska Diana , Holden Lars , Gheorghe Marius , Mathelier Anthony , Glad Ingrid , Sandve Geir Kjetil 
Published: November 2018

AbstractBackgroundThe generation and systematic collection of genome-wide data is ever-increasing. This vast amount of data has enabled researchers to study relations between a variety of genomic and epigenomic features, including genetic variation, gene regulation, and phenotypic traits. Such relations are typically investigated by comparatively assessing genomic co-occurrence. Technically, this corresponds to assessing the similarity of pairs of genome-wide binary vectors. A variety of metrics have been proposed for this problem in other fields like ecology. However, while several of these metrics have been employed for assessing genomic co-occurrence, their appropriateness for the genomic setting has never been investigated.ResultsWe show that the choice of metric may strongly influence results and propose two alternative modelling assumptions that can be used to guide this choice. On both simulated and real genomic data, the Jaccard index is strongly affected by dataset size and should be used with caution. The Forbes coefficient (fold change) and tetrachoric correlation are less affected by dataset size, but one should be aware of increased variance for small datasets.AvailabilityAll results on simulated and real data can be inspected and reproduced athttps://hyperbrowser.uio.no/sim-measure
The embryonic transcriptome ofArabidopsis thaliana
Authors: Hofmann Falko , Schon Michael A. , Nodine Michael D. 
Published: November 2018

AbstractCellular differentiation is associated with changes in transcript populations. Accurate quantification of transcriptomes during development can thus provide global insights into differentiation processes including the fundamental specification and differentiation events operating during plant embryogenesis. However, multiple technical challenges have limited the ability to obtain high quality early embryonic transcriptomes, namely the low amount of RNA obtainable and contamination from surrounding endosperm and seed-coat tissues. We compared the performance of three low-input mRNA sequencing (mRNA-seq) library preparation kits on 0.1 to 5 nanograms (ng) of total RNA isolated fromArabidopsis thaliana(Arabidopsis) embryos and identified a low-cost method with superior performance. This mRNA-seq method was then used to profile the transcriptomes of Arabidopsis embryos across eight developmental stages. By comprehensively comparing embryonic and post-embryonic transcriptomes, we found that embryonic transcriptomes do not resemble any other plant tissue we analyzed. Moreover, transcriptome clustering analyses revealed the presence of four distinct phases of embryogenesis which are enriched in specific biological processes. We also compared zygotic embryo transcriptomes with publicly available somatic embryo transcriptomes. Strikingly, we found little resemblance between zygotic embryos and somatic embryos derived from late-staged zygotic embryos suggesting that the molecular basis of somatic and zygotic embryogenesis are distinct from each other. In addition to the biological insights gained from our systematic characterization of the Arabidopsis embryonic transcriptome, we provide a data-rich resource for the community to explore.Key MessageArabidopsis embryos possess unique transcriptomes relative to other plant tissues including somatic embryos, and can be partitioned into four transcriptional phases with characteristic biological processes.
CNApp: quantification of genomic copy number alterations in cancer and integrative analysis to unravel clinical implications
Authors: Franch-Expósito Sebastià , Bassaganyas Laia , Vila-Casadesús Maria , Hernández-Illán Eva , Esteban-Fabró Roger , Díaz-Gay Marcos , Lozano Juan José , Castells Antoni , Llovet Josep M. , Castellví-Bel Sergi , Camps Jordi 
Published: November 2018

ABSTRACTSomatic copy number alterations (CNAs) are a hallmark of cancer. Although CNA profiles have been established for most human tumor types, their precise role in tumorigenesis as well as their clinical and therapeutic relevance remain largely unclear. Thus, computational and statistical approaches are required to thoroughly define the interplay between CNAs and tumor phenotypes. Here we developed CNApp, a user-friendly web tool that offers sample- and cohort-level computational analyses, allowing a comprehensive and integrative exploration of CNAs with clinical and molecular variables. By using purity-corrected segmented data from multiple genomic platforms, CNApp generates genome-wide profiles, computes CNA scores for broad, focal and global CNA burdens, and uses machine learning-based predictions to classify samples. We applied CNApp to a pan-cancer dataset of 10,635 genomes from TCGA showing that CNA patterns classify cancer types according to their tissue-of-origin, and that broad and focal CNA scores positively correlate in samples with low amounts of whole-chromosome and chromosomal arm-level imbalances. Moreover, using the hepatocellular carcinoma cohort from the TCGA repository, we demonstrate the reliability of the tool in identifying recurrent CNAs, confirming previous results. Finally, we establish machine learning-based models to predict colon cancer molecular subtypes and microsatellite instability based on broad CNA scores and specific genomic imbalances. In summary, CNApp facilitates data-driven research and provides a unique framework for the first time to comprehensively assess CNAs and perform integrative analyses that enable the identification of relevant clinical implications. CNApp is hosted at http://cnapp.bsc.es.
A Statistical Procedure for Genome-wide Detection of QTL Hotspots Using Public Databases with Application to Rice
Authors: Yang Man-Hsia , Wu Dong-Hong , Kao Chen-Hung 
Published: November 2018

ABSTRACTGenome-wide detection of quantitative trait loci (QTL) hotspots underlying variation in many molecular and phenotypic traits has been a key step in various biological studies since the QTL hotspots are highly informative and can be linked to the genes for the quantitative traits. Several statistical methods have been proposed to detect QTL hotspots. These hotspot detection methods rely heavily on permutation tests performed on summarized QTL data or individual-level data (with genotypes and phenotypes) from the genetical genomics experiments. In this article, we propose a statistical procedure for QTL hotspot detection by using the summarized QTL (interval) data collected in public web-accessible databases. First, a simple statistical method based on the uniform distribution is derived to convert the QTL interval data into the expected QTL frequency (EQF) matrix. And then, to account for the correlation structure among traits, the QTLs for correlated traits are grouped together into the same categories to form a reduced EQF matrix. Furthermore, a permutation algorithm on the EQF elements or on the QTL intervals is developed to compute a sliding scale of EQF thresholds, ranging from strict to liberal, for assessing the significance of QTL hotspots. With grouping, much stricter thresholds can be obtained to avoid the detection of spurious hotspots. Real example analysis and simulation study are carried out to illustrate our procedure, evaluate the performances and compare with other methods. It shows that our procedure can control the genome-wide error rates at the target levels, provide appropriate thresholds for correlated data and is comparable to the methods using individual-level data in hotspot detection. Depending on the thresholds used, more than 100 hotspots are detected in GRAMENE rice database. We also perform a genome-wide comparative analysis of the detected hotspots and the known genes collected in the Rice Q-TARO database. The comparative analysis reveals that the hotspots and genes are conformable in the sense that they co-localize closely and are functionally related to relevant traits. Our statistical procedure can provide a framework for exploring the networks among QTL hotspots, genes and quantitative traits in biological studies. The R codes that produce both numerical and graphical outputs of QTL hotspot detection in the genome are available on the worldwide webhttp://www.stat.sinica.edu.tw/~chkao/.
Investigations of thermal sprayed HAP and HAP-TiO2composite coatings for biomedical applications
Authors: Kaur Sarbjit , Bala Niraj , Khosla Charu 
Published: November 2018

PurposeThe biomaterials are natural or synthetic materials used to improve quality of life either by replacing tissue/organ or assisting their function in medical field. The purpose of the study is to analyze the hydroxyapatite (HAP), HAP-TiO2(25 percent) composite coatings deposited on 316 LSS by High Velocity Flame Spray (HVFS) technique.Design/methodology/approachThe coatings exhibit almost uniform and dense microstructure with porosity (HAP = 0.153 and HAP-TiO2composite = 0.138). Electrochemical corrosion testing was done on the uncoated and coated specimens in Ringer solution (SBF). As-sprayed coatings were characterized by XRD, SEM/EDS and cross-sectional X-ray mapping techniques before and after dipping in Ringer solution. Microhardness of composite coating (568.8 MPa) was found to be higher than HAP coating (353 MPa).FindingsDuring investigations, it was observed that the corrosion resistance of steel was found to have increased after the deposition of HAP and HAP-TiO2composite coatings. Thus, coatings serve as an effective diffusion barrier to prohibit the diffusion of ions from the SBF into the substrate. Composite coatings have been found to be more corrosion resistant as compared to HAP coating in the simulated body fluid.Research limitations/implicationsIt has been concluded that corrosion resistance of HAP as well as composite coating is because of the desirable microstructural changes such as low porosity high microhardness and flat splat structures in coatings as compared to bare specimen.Practical implicationsThis study is useful in the selection of biomedical implants.Social implicationsThis study is useful in the field of biomaterials.Originality/valueNo reported literature on corrosion behavior of HAP+ 25%- TiO2has been noted till now using flame spray technique. The main focus of the study is to investigate the HAP as well as composite coatings for biomedical applications.
When is silence golden? The use of strategic silence in crisis communication
Authors: Le Phuong D. , Teo Hui Xun , Pang Augustine , Li Yuling , Goh Cai-Qin 
Published: November 2018

Purpose
Scholars have discouraged using silence in crises as it magnifies the information vacuum (see Pang, 2013). The purpose of this paper is to argue for its viability and explore the type of silence that can be used.

Design/methodology/approach
Eight international cases were analyzed to examine how silence was adopted, sustained and broken.

Findings
The findings uncovered three intention-based typologies of strategic silence: delaying, avoiding and hiding silences. Among such, avoiding/hiding silence intensified crises and adversely affected post-silence organizational image when forcefully broken, while delaying silence helped preserve/restore image with primary stakeholders if successfully sustained and broken as planned.

Research limitations/implications
First, these findings may lack generalizability due to the limited number of cases studied. Second, local sentiments may not be fully represented in the English-language news examined as they may be written for a different audience. Finally, a number of cases studied were still ongoing at the time of writing, so the overall effectiveness of the strategy employed might be compromised as future events unfold.

Practical implications
A stage-based practical guide to adopting delaying silence is proposed as a supporting strategy before the execution of crisis response strategies.

Originality/value
This is one of the few studies to examine the role of silence in crisis communication as silence is not recognized as a type of response in dominant crisis theories – be it the situational crisis communication theory or the image repair theory (An and Cheng, 2010; Benoit, 2015; Benoit and Pang, 2008; Xu and Li, 2013).
Artificial intelligence-based training learning from application
Authors: Upadhyay Ashwani Kumar , Khandelwal Komal 
Published: November 2018

Purpose
This paper aims to discuss the rationale, theoretical foundation, application, and future of artificial intelligence (AI)-based training.

Design/methodology/approach
A review of relevant research papers, articles and case studies is done to highlight developments in research and practice.

Findings
AI-based training systems are smart, intelligent and expert in handling queries. These systems can curate content, grade, evaluate, and provide feedback to trainee, thus making learning adaptive and contextual.

Practical implications
Application of AI is vital in the field of training, as it helps personalization and customization of training programs to increase the effectiveness of training.

Originality/value
Executives and researchers can save time by reading relevant information on the linkage, and its contribution to AI is discussed and summarized in an easy to read format.
Women leaders and organizational diversity: their critical role in promoting diversity in organizations
Authors: Gupta Anuja 
Published: November 2018

Purpose
The purpose of this paper is to analyze the role of women leaders in enhancing and managing diversity in organizations.

Design/methodology/approach
The approach of this paper is to combine the findings of two fields of research, namely, effectiveness of women leaders, and organizational diversity, and propose that women leaders have a critical role to play in enhancing organizational diversity and its effectiveness.

Findings
The main findings of the paper are that women leaders outperform their male counterparts in many of the necessary skills and competencies required to create democratic and inclusive organizations. Their leadership style is also best suited to effectively manage and take advantage of diversity in organizations.

Practical implications
Women leaders can create a very significant impact on creating inclusive environments in which diversity is valued and on organizational performance overall. Thus, it is imperative for firms to overcome gender bias and create meritocracies in which women leaders can be hired, retained, and promoted.

Social implications
Societies need to create grassroots change where perceptions of women in the workplace change.

Originality/value
The study creates a connection between two bodies of literature: one that explores the effectiveness of women leaders on leadership competencies and the second that looks at diversity in organizations, and how organizations can take advantage of this diversity. It shows that women leaders are well suited to promote and manage diversity in organizations by virtue of their skills and leadership style.
Expansion decision: HC Securities and Investment
Authors: Choucri Ali H. , Dietterich Anne , Gillern Victoria , Ivy Julia 
Published: November 2018

Learning outcomes
Expected learning outcomes: To respond to the case question, students would analyze macro- and microeconomic differences to determine HC Securities’ preferred global strategy and appropriate market entry mode. The case demonstrates how instability in a local market, in this case Egypt, can force a company to go global. It also demonstrates how two superficially similar markets, Singapore and Hong Kong, provide different opportunities for HC Securities and require different global strategies: Singapore provides a jumping-off point to its predominantly Muslim neighbors Malaysia and Indonesia, whereas Hong Kong gives access to China and could provide a new customer base of Asian investors willing to invest in Africa and the Middle East.

Case overview/synopsis
Brief overview of the case: The case introduces the Egyptian investment company HC Securities, which is facing challenges related to Egypt’s political instability and economic slowdown. HC Securities’ CEO, Mr. Choucri, feels expansion to one of the Asia-Pacific countries could help with the company’s growth and stability. He identifies Hong Kong and Singapore as the most compelling locations because of their sophisticated economies and growth potential in the investments industry. This case provides information about each market, allowing students to respond to the question “What should Choucri do to assure a market-based solution for his company?”

Complexity academic level
Student level and proposed courses: The case is appropriate for use in undergraduate courses in international business or strategic management.

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
International Business.
Lump, breather and solitary wave solutions to new reduced form of the generalized BKP equation
Authors: Kaur Lakhveer , Wazwaz Abdul-Majid 
Published: November 2018

Purpose
The purpose of this paper is to explore new reduced form of the (3 + 1)-dimensional generalized B-type Kadomtsev-Petviashvili (BKP) equation by considering its bilinear equations, derived from connection between the Hirota’s transformation and Bell polynomials.

Design/methodology/approach
Based on the bilinear form of new reduced form of the (3 + 1)-dimensional generalized BKP equation, lump solutions with sufficient and necessary conditions to guarantee analyticity and rational localization of the solutions are discovered. Also, extended homoclinic approach is applied to considered equation for finding solitary wave solutions.

Findings
A class of the bright-dark lump waves are fabricated for studying different attributes of (3 + 1)-dimensional generalized BKP equation and some new exact solutions including kinky periodic solitary wave solutions and line breathers periodic are also obtained by Following the extended homoclinic approach.

Research limitations/implications
The paper presents that the implemented methods have emerged as a promising and robust mathematical tool to manage (3 + 1)-dimensional generalized BKP equation by using the Hirota’s bilinear equation.

Practical implications
By considering important characteristics of lump and solitary wave solutions, one can understand the shapes, amplitudes and velocities of solitons after the collision with another soliton.

Social implications
The analysis of these higher-dimensional nonlinear wave equations is not only of fundamental interest but also has important practical implications in many areas of mathematical physics and ocean engineering.

Originality/value
To the best of the authors’ knowledge, the acquired solutions given in various cases have not been reported for new reduced form of the (3 + 1)-dimensional generalized BKP equation in the literature. These obtained solutions are advantageous for researchers to know objective laws and grab the indispensable features of the development of the mathematical physics.
Teamwork of temporary employees: multiple perspectives
Authors: Chakraborty Saikat , Chakravarti Sushmita 
Published: November 2018

Purpose
The purpose of this study is to understand the teamwork of temporary employees by taking into consideration the impact and role of the management’s perspective, temporary employee’s perspective and contextual perspective.

Design/methodology/approach
Based on reviews of workplace literature pertaining to temporary employments, conversations with managers and temporary and permanent employees of organizations engaging temporary employees on a perennial basis have been thematically analyzed.

Findings
Multiple perspectives of teamwork of temporary employees exist in organizations. However, one rarely finds the interaction and collective treatment of these perspectives, which are critical to understanding teamwork of temporary employees. The paper reports on these perspectives.

Practical implications
With rise in temporary employments in organizations and teamwork being crucial to participative work cultures, organizations need to consider multiple perspectives of the phenomenon before making an informed decision.

Originality/value
There is limited research that delves into teamwork of temporary employees despite the phenomenon becoming increasingly significant in organizations. This paper offers an approach to look at teamwork of temporary employees through multiple perspectives.
The drivers and challenges of improving the energy efficiency performance of listed pre-1919 housing
Authors: Rispoli Maria , Organ Samantha 
Published: November 2018

Purpose
Concerns about climate change and the availability of energy has resulted in countries setting targets to improve energy efficiency and reduce carbon emissions. A large proportion of energy is consumed by existing housing. Europe has a large proportion of historic housing, some of which also represent significant value in relation to historical, cultural and/or architectural importance. Upgrading their energy efficiency whilst retaining their significance is crucial for the sustainability of heritage buildings. The purpose of this paper is to focus on the challenges and barriers to improving the energy efficiency of listed pre-1919 housing.

Design/methodology/approach
The research utilised semi-structured interviews to explore the debates surrounding sustainability and conservation, identifying the key drivers and barriers to achieving a balance between these concepts.

Findings
Concern about climate change and the desire to preserve a heritage asset were the main drivers to balancing sustainability with conservation through energy efficiency improvements. The main challenges included the risk of detrimentally affecting the significance of the building, the lack of communication and collaboration between stakeholders, the availability of adequately skilled professionals and the lack of appropriate energy efficiency solutions for heritage buildings. The cost of improvements was found to be both a barrier and driver.

Originality/value
Heritage buildings perform differently to their modern counterparts and therefore the measures the authors apply to these historic properties must be done with sufficient understanding of this difference. Such measures must be compatible with these buildings in line with conservation principles. Further, the discussion of developing an alternative version of energy calculation for these buildings should be entered into.