bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bayesian Classification of Microbial Communities Based on 16S rRNA Metagenomic Data
Authors: Bahadorinejad Arghavan , Ivanov Ivan , Lampe Johanna W , Hullar Meredith AJ , Chapkin Robert S , Braga-Neto Ulisses M 
Published: June 2018

AbstractWe propose a Bayesian method for the classification of 16S rRNA metagenomic profiles of bacterial abundance, by introducing a Poisson-Dirichlet-Multinomial hierarchical model for the sequencing data, constructing a prior distribution from sample data, calculating the posterior distribution in closed form; and deriving an Optimal Bayesian Classifier (OBC). The proposed algorithm is compared to state-of-the-art classification methods for 16S rRNA metagenomic data, including Random Forests and the phylogeny-based Metaphyl algorithm, for varying sample size, classification difficulty, and dimensionality (number of OTUs), using both synthetic and real metagenomic data sets. The results demonstrate that the proposed OBC method, with either noninformative or constructed priors, is competitive or superior to the other methods. In particular, in the case where the ratio of sample size to dimensionality is small, it was observed that the proposed method can vastly outperform the others.Author summaryRecent studies have highlighted the interplay between host genetics, gut microbes, and colorectal tumor initiation/progression. The characterization of microbial communities using metagenomic profiling has therefore received renewed interest. In this paper, we propose a method for classification, i.e., prediction of different outcomes, based on 16S rRNA metagenomic data. The proposed method employs a Bayesian approach, which is suitable for data sets with small ration of number of available instances to the dimensionality. Results using both synthetic and real metagenomic data show that the proposed method can outperform other state-of-the-art metagenomic classification algorithms.
Proteogenomic view of cancer epigenetics: the impact of DNA methylation on the cancer proteome
Authors: Magzoub Majed Mohamed , Prunello Marcos , Brennan Kevin , Gevaert Olivier 
Published: June 2018

AbstractAberrant DNA methylation disrupts normal gene expression in cancer and broadly contributes to oncogenesis. We previously developed MethylMix, a model-based algorithmic approach to identify epigenetically regulated driver genes. MethylMix identifies genes where methylation likely executes a functional role by using transcriptomic data to select only methylation events that can be linked to changes in gene expression. However, given that proteins more closely link genotype to phenotype recent high-throughput proteomic data provides an opportunity to more accurately identify functionally relevant abnormal methylation events. Here we present ProteoMix, which refines nominations for epigenetic driver genes by leveraging quantitative high-throughput proteomic data to select only genes where DNA methylation is predictive of protein abundance. Applying our algorithm across three cancer cohorts we find that ProteoMix narrows candidate nominations, where the effect of DNA methylation is often buffered at the protein level. Next, we find that ProteoMix genes are enriched for biological processes involved in cancer including functions involved in epithelial and mesenchymal transition. ProteoMix results are also enriched for tumor markers which are predictive of clinical features like tumor stage and we find clustering on ProteoMix genes captures cancer subtypes.
Pediatric Cancer Variant Pathogenicity Information Exchange (PeCanPIE): A Cloud-based Platform for Curating and Classifying Germline Variants
Authors: Edmonson Michael N. , Patel Aman N. , Hedges Dale J. , Wang Zhaoming , Rampersaud Evadnie , Kesserwan Chimene A. , Zhou Xin , Liu Yanling , Newman Scott , Rusch Michael C. , McLeod Clay L. , Wilkinson Mark R. , Rice Stephen V. , Becksfort Jared B. , Nichols Kim E. , Robison Leslie L. , Downing James R. , Zhang Jinghui 
Published: June 2018

AbstractVariant interpretation in the era of next-generation sequencing (NGS) is challenging. While many resources and guidelines are available to assist with this task, few integrated end-to-end tools exist. Here we present “PeCanPIE” – the Pediatric Cancer Variant Pathogenicity Information Exchange, a web- and cloud-based platform for annotation, identification, and classification of variations in known or putative disease genes. Starting from a set of variants in Variant Call Format (VCF), variants are annotated, ranked by putative pathogenicity, and presented for formal classification using a decision-support interface based on published guidelines from the American College of Medical Genetics and Genomics (ACMG). The system can accept files containing millions of variants and handle single-nucleotide variants (SNVs), simple insertions/deletions (indels), multiple-nucleotide variants (MNVs), and complex substitutions. PeCanPIE has been applied to classify variant pathogenicity in cancer predisposition genes in two large-scale investigations involving >4,000 pediatric cancer patients, and serves as a repository for the expert-reviewed results. While PeCanPIE’s web-based interface was designed to be accessible to non-bioinformaticians, its back end pipelines may also be run independently on the cloud, facilitating direct integration and broader adoption. PeCanPIE is publicly available and free for research use.
The passion and the interests in life science venturing
Authors: Styhre Alexander , Norbäck Maria 
Published: June 2018

PurposePassion and interest are the two principal drivers of competitive capitalism, and reconciling the two is conducive to a dynamic and welfare-generating economic system. On the level of the individual, the same categories can be applied to examining, for example, career choices, at times violating propositions regarding rational expectations as some categories of work include lower economic compensation or higher levels of risk than would be attractive to the median job applicant. The purpose of this paper is to examine how venture workers, employees of life, thinly capitalize science ventures, justify their career choices and how they act in order to create economic security for themselves and their families.Design/methodology/approachThe study is based on a qualitative data collection methodology and reports on empirical research material from a study of co-workers at life science start-ups. The sample includes salaried employees working at venture capital-backed start-up companies in the life science sector.FindingsThe study indicates that passionate preferences regarding, for example, meaningful work in collaboration with peers, and the ability to participate in the creation of a new venture, have overshadowed the downside risks and the lower level of economic compensationvis-à-viscomparable work. Such findings indicate that deeply meaningful work is a useful analytical category, and that combinations of the favorable market pricing of skills and experiences, as well as state-funded welfare mechanisms, cushioning some of the market risk that employees are exposed to, will provide opportunities for venture labor, i.e. work done at thinly capitalized firms, such as start-ups,per secontributing to a dynamic industry.Originality/valueThe study contributes to the innovation management literature as it examines the key role of salaried venture workers, i.e. workers that do not hold contracts, granting them the right to compensation when venture capital investors make an exit. In addition, the study also discusses the literature on deeply meaningful work, stressing that this is a useful analytical category.
Conflict management in family businesses
Authors: Caputo Andrea , Marzi Giacomo , Pellegrini Massimiliano Matteo , Rialti Riccardo 
Published: June 2018

PurposeThe purpose of this study is to map the intellectual structure of the field of conflict management and the field of family business to the investigation of conflicts in family firms, with the aim of contributing to the further integration of knowledge between the two fields.Design/methodology/approachFamily conflicts and work–family balance issues also received a lot of attention, yet studies in conflict management still seem to overlook a thorough investigation of conflict in family businesses. Conflict is a major aspect of family businesses, which differs highly from non-family businesses, and offers an important research avenue for conflict management scholars to contribute to the investigation of major characteristics of organisations that constitute a large part of the value created in the world.FindingsThe results of a bibliometric analysis and systematic literature review show that studies concerning conflict in family business aggregate around three clusters: organisational conflicts; firm growth and conflicts; and family control, performance and conflicts. An interpretative framework is also developed to interpret how antecedents, conflicts and growth dynamics in family business influence performances. Findings show how family conflicts and work–family balance issues received a lot of attention, yet studies in conflict management still seem to miss a thorough investigation of conflict in family businesses.Originality/valueThis paper contributes to the field of conflict management and family business by providing a systematic analysis of knowledge and family firms. This paper can be a starting point for researchers interested in understanding how conflicts affect family businesses.
Nobody understands me! The need for empathy
Authors: Topaloglu Omer , Erkaya Yusuf 
Published: June 2018

Purpose
This paper aims to explore the mind-set of consumers with negative mood states during mundane consumption activities.

Design/methodology/approach
The authors conducted in-depth interviews with 17 informants who have recently experienced severe yet temporary medical problems.

Findings
Consumers with severe medical problems experience an increased need for empathy during mundane business interactions, and their reaction to service failures is aggravated.

Originality/value
Although previous research has investigated the relationship between empathy and satisfaction in healthcare services, the current research provides a novel perspective by studying the mind-set of customers with medical problems during regular consumption activities. Further, previous research has called for a need for qualitative work in empathy research. This gap is also addressed by the current research.
What is the stock of the situation? A bibliometric analysis on social and environmental accounting research in public sector
Authors: Fusco Floriana , Ricci Paolo 
Published: June 2018

PurposeThe purpose of this paper is to provide a picture of the state of the art in social and environmental accounting research applied to the public sector, highlighting different streams and the main gaps in current literature and providing input for future research.Design/methodology/approachA bibliometric method was used to analyse the characteristics, citation patterns and content of 38 papers published in international academic journals.FindingsThe findings show that the research on social and environmental reporting in the public sector is still at an early stage. Current investigations, although slowly on the increase, are still very few and localised. Most papers are about the reasons why public organisations report, what and how they report, but there are so many aspects that need to be investigated more in-depth or require extra validation in order to open new directions for future research, among which the relationship with and the differences between other non-financial type of reporting, namely ICR and IR.Research limitations/implicationsThe study shows some limitations, mainly related to the adoption of the bibliometric method. Indeed, it does not take into account books and chapters but only papers published in international and academic journals. This leads to exclude a significant part of the existing literature and other relevant contributions on the field.Originality/valueSocial and environmental reporting practices are quickly spreading in the public sector. The field is particularly interesting, given the specific connotations of this kind of organisations. However, the literature is clearly not exhaustive and there is not a comprehensive and systematic review of the state of the art on the subject.
Uncertainty, agency costs and investment behavior in the Euro area and in the USA
Authors: Strobel Johannes , Salyer Kevin D. , Lee Gabriel S. 
Published: June 2018

PurposeThe purpose of this paper is to analyze the credit channel effects on investment behavior for the US and the Euro area.Design/methodology/approachThis paper uses the dynamic stochastic general equilibrium model and calibrates a version of the Carlstrom and Fuerst’s (1997) agency cost model of business cycles with time-varying uncertainty in the technology shocks that affect capital production. To highlight the differences between the US and European financial sectors, the paper focuses on two key components of the lending channel: the risk premium associated with bank loans and the bankruptcy rates.FindingsThis paper shows that the effects of minor differences in the credit market translate into large, persistent and asymmetric fluctuations in real and financial variables and depend on the type of shocks. The results imply that the Euro areas supply elasticities for capital are less elastic than that of the USA following a technology shock. Finally, the authors find that the adverse impact of uncertainty shocks is heterogeneous across countries and amplified by the steady-state bankruptcy rate and risk premium.Originality/valueThis paper quantifies the effects of uncertainty shocks when there is a credit channel due to asymmetric information between lenders and borrowers for the Euro area countries, and then compares the results to that of the USA. This paper shows that financial accelerator mechanism could potentially play a significant role in business cycles in the Euro area. This result directly lends one to conclude the following: the credit channel that affects the financial sector does indeed matter for macroeconomic behavior, and that policy makers should be attentive in smoothing out uncertainties if the economic policies are to lower the business and financial cycle volatilities.
The short and long run effects of debt reduction
Authors: Gamel Kelsey , Van Pham Hoang 
Published: June 2018

Purpose
The purpose of this paper is to estimate benefits to debt reduction by using the natural experiment provided by the debt relief programs: the Heavily Indebted Poor Countries Initiative launched by the International Monetary Fund and World Bank in 1996 and the Multilateral Debt Relief Initiative extension in 2005.

Design/methodology/approach
The authors apply a time-shifted difference-in-differences strategy to evaluate the effects of this intervention. The date of each country’s decision to participate in the program is used as one treatment point while the date of the completion of the debt relief program is used as another treatment point. The exercise compares different economic outcomes such as domestic and foreign investment, schooling, and employment of the treated observations to the counterfactual of untreated country-years. The period between the decision and completion points is a short run while the period after the completion point is considered a long run.

Findings
The authors found that debt relief increased capital investment as much as 1.63 percent in the short run and 5.79 percent in the long run. However, there was no effect on foreign direct investment suggesting that debt overhang does not affect incentives of foreign investors. Output and schooling enrollment increased both in the short and long run.

Originality/value
This paper exploits a natural experiment of debt relief in a number of developing countries to shed light on the possible benefits to debt reduction. The authors are able to separate the short- and long-run effects of debt reduction. The finding that domestic but not foreign investment responds to debt reduction is suggestive of the differences in incentives across these two sources of investment.
Duality of knowledge, singularity of method
Authors: Schinckus Christophe , Akdere Cinla 
Published: June 2018

PurposeHow a micro-founded discipline such as economics could deal with the increasing global economic reality? This question has been asked frequently since the last economic crisis that appeared in 2008. In this challenging context, some commentators have turned their attention to a new area of knowledge coming from physics: econophysics which mainly focuses on a macro-analysis of economic systems. By showing that concepts used by econophysicists are consistent with an existing economic knowledge (developed by J.S. Mill), the purpose of this paper is to claim that an interdisciplinary perspective is possible between these two communities.Design/methodology/approachThe authors propose a historical and conceptual analysis of the key concept of emergence to emphasize the potential bridge between econophysics and economics.FindingsSix methodological arguments will be developed in order to show the existence of conceptual bridges as a necessary condition for the elaboration of a common language between economists and econophysics which would not be superfluous, in this challenging context, to clarify the growing complexity of economic phenomena.Originality/valueAlthough the economics and econophysics study same the complex economic phenomena, very few collaborations exist between them. This paper paves a conceptual/methodological path for more collaboration between the two fields.
Emotional intelligence testing for headteachers: globalization or lost in translation
Authors: Cliffe Joanne 
Published: June 2018

Purpose
The emotional labor of headteachers and teachers is complex. The purpose of this paper is to explore the relevance of the use of the Mayer-Salovey-Caruso Emotional Intelligence test (MSCEIT) (Mayer, Caruso & Salovey, 2000) when assessing the emotional intelligence of headteachers as part of an investigation which aimed to reveal the ways in which female secondary school leaders were emotionally intelligent and whether it was possible to test for emotional intelligence.

Design/methodology/approach
Seven female headteachers’ MSCEIT reports are investigated. Semi-structured interviews were held pre- and post-test to explore the headteachers’ emotional labor. In addition, teachers serving under the headteachers were interviewed.

Findings
The accuracy of the MSCEIT is questioned, rather than taking the results at face value, attention is given to its content, language and cultural differences. The MSCEIT originates from the USA and is used globally. The findings of this investigation suggest it is possible the MSCEIT represents a deficit model due to the test takers’ interpretation of nuanced language. The findings show a disparity in relation to MSCEIT scores and self-reported emotional responses.

Research limitations/implications
Although the sample size is small and therefore cannot claim generalization from the findings, the use of emotional intelligence tests should be used with caution. Emotional responses are best understood through life experience as the headteachers attach retrospective meaning to their leadership actions.

Originality/value
Headteachers’ work is multifaceted because emotion is integral to the processes of teaching and learning. The emotional labor of headteachers and teachers impacts and has relevance to their roles as educational landscapes continue to shift.
Lost in migration: document quality for batch conversion to PDF/A
Authors: Suri Roland Erwin , El-Saad Mohamed 
Published: June 2018

Purpose
Changes in file format specifications challenge long-term preservation of digital documents. Digital archives thus often focus on specific file formats that are well suited for long-term preservation, such as the PDF/A format. Since only few customers submit PDF/A files, digital archives may consider converting submitted files to the PDF/A format. The paper aims to discuss these issues.

Design/methodology/approach
The authors evaluated three software tools for batch conversion of common file formats to PDF/A-1b: LuraTech PDF Compressor, Adobe Acrobat XI Pro and 3-HeightsTM Document Converter by PDF Tools. The test set consisted of 80 files, with 10 files each of the eight file types JPEG, MS PowerPoint, PDF, PNG, MS Word, MS Excel, MSG and “web page.”

Findings
Batch processing was sometimes hindered by stops that required manual interference. Depending on the software tool, three to four of these stops occurred during batch processing of the 80 test files. Furthermore, the conversion tools sometimes failed to produce output files even for supported file formats: three (Adobe Pro) up to seven (LuraTech and 3-HeightsTM) PDF/A-1b files were not produced. Since Adobe Pro does not convert e-mails, a total of 213 PDF/A-1b files were produced. The faithfulness of each conversion was investigated by comparing the visual appearance of the input document with that of the produced PDF/A-1b document on a computer screen. Meticulous visual inspection revealed that the conversion to PDF/A-1b impaired the information content in 24 of the converted 213 files (11 percent). These reproducibility errors included loss of links, loss of other document content (unreadable characters, missing text, document part missing), updated fields (reflecting time and folder of conversion), vector graphics issues and spelling errors.

Originality/value
These results indicate that large-scale batch conversions of heterogeneous files to PDF/A-1b cause complex issues that need to be addressed for each individual file. Even with considerable efforts, some information loss seems unavoidable if large numbers of files from heterogeneous sources are migrated to the PDF/A-1b format.
Collaborating to improve access of video for all
Authors: Keenan Teressa M. 
Published: June 2018

PurposeThe purpose of this paper is to illustrate one library’s role in the development of a new collaborative captioning service to provide accessible media for classroom use. This pilot project created a new workflow for on-demand captioning of videos.Design/methodology/approachThrough collaboration and iteration, university and library personnel addressed the challenges involved in building new and improved services related to accessible media resources. Circulation and acquisition data were collected via Alma Analytics.FindingsWorking collaboratively enabled the expansion and improvement of specialized services to the deaf and hard of hearing community on campus.Originality/valueWhile many libraries provide captioning for their communities, little is found in the literature to help others establish a similar service. This study demonstrates how collaborative planning can efficiently and effectively use resources and expertise to create a sustainable service, and it may provide an example that could be followed by other institutions with limited budgets.