bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cost Effective Acoustic Monitoring of Biodiversity and Bird Populations in Kenya
Authors: wa Maina Ciira , Muchiri David , Njoroge Peter 
Published: September 2016

AbstractWith the increasing need to effectively monitor a growing number of ecosystems of interest due to risks posed to these ecosystems by human activity and climate change, novel approaches to biodiversity monitoring are needed. In this work we demonstrate the application of low cost acoustic recorders based on the Raspberry Pi microprocessor to biodiversity monitoring. The recorders are capable of capturing audio recordings from which we can compute acoustic indices of biodiversity and identify bird species of interest. We compare the acoustic indices of biodiversity and results of point counts aimed at determining bird species presence and find that the acoustic complexity index has a significant positive correlation to point count results. In addition, we show that the presence of the Hartlaub’s Turaco, a ubiquitous species in montane forests in Kenya with a distinct call, can be automatically determined using recordings obtained using our setup. Montane species are of interest for long-term automatic monitoring since they are particularly vulnerable to the effects of climate change. Our system is able to deal with the large amounts of data generated by the acoustic recorders. The automatic screening of approximately five hours of recordings for presence of the Hartlaub’s Turaco call is achieved in approximately three minutes representing a large time saving that makes use of audio recordings for species identification feasible.
dms2dfe: Comprehensive Workflow for Analysis of Deep Mutational Scanning Data
Authors: Dandage Rohan , Chakraborty Kausik 
Published: September 2016

SummaryHigh throughput genotype to phenotype (G2P) data is increasingly being generated by widely applicable Deep Mutational Scanning (DMS) method. dms2dfe is a comprehensive end-to-end workflow that addresses critical issue with noise reduction and offers variety of crucial downstream analyses. Noise reduction is carried out by normalizing counts of mutants by depth of sequencing and subsequent dispersion shrinkage at the level of calculation of preferential enrichments. In downstream analyses, dms2dfe workflow provides identification of relative selection pressures, potential molecular constraints and generation of data-rich visualizations.Availabilitydms2dfe is implemented as a python package and it is available athttps://kc-lab.github.io/dms2dfe.Contactkausik@igib.in,rohan@igib.inSupplementary informationSupplementary data are available at Bioinformatics online.
Targeted reconstruction of T cell receptor sequence from single cell RNA-sequencing links CDR3 length to T cell differentiation state
Authors: Afik Shaked , Yates Kathleen B. , Bi Kevin , Darko Samuel , Godec Jernej , Gerdemann Ulrike , Swadling Leo , Douek Daniel C. , Klenerman Paul , Barnes Eleanor J. , Sharpe Arlene H. , Haining W. Nicholas , Yosef Nir 
Published: September 2016

ABSTRACTThe T cell compartment must contain diversity in both TCR repertoire and cell state to provide effective immunity against pathogens1,2. However, it remains unclear how differences in the TCR contribute to heterogeneity in T cell state at the single cell level because most analysis of the TCR repertoire has, to date, aggregated information from populations of cells. Single cell RNA-sequencing (scRNA-seq) can allow simultaneous measurement of TCR sequence and global transcriptional profile from single cells. However, current protocols to directly sequence the TCR require the use of long sequencing reads, increasing the cost and decreasing the number of cells that can be feasibly analyzed. Here we present a tool that can efficiently extract TCR sequence information from standard, short-read scRNA-seq libraries of T cells: TCR Reconstruction Algorithm for Paired-End Single cell (TRAPeS). We apply it to investigate heterogeneity in the CD8+T cell response in humans and mice, and show that it is accurate and more sensitive than previous approaches3,4. We applied TRAPeS to single cell RNA-seq of CD8+T cells specific for a single epitope from Yellow Fever Virus5. We show that the recently-described "naive-like" memory population of YFV-specific CD8+T cells have significantly longer CDR3 regions and greater divergence from germline sequence than do effector-memory phenotype CD8+T cells specific for YFV. This suggests that TCR usage contributes to heterogeneity in the differentiation state of the CD8+T cell response to YFV. TRAPeS is publicly available, and can be readily used to investigate the relationship between the TCR repertoire and cellular phenotype.
Schizophrenia and human self-domestication: an evolutionary linguistics approach
Authors: Benítez-Burraco Antonio , Pietro Lorena Di , Barba Marta , Lattanzi Wanda 
Published: September 2016

AbstractSchizophrenia (SZ) is a pervasive neurodevelopmental disorder entailing social and cognitive deficits, including marked problems with language. Its complex multifactorial etiopathogenesis, including genetic and environmental factors, is still widely uncertain. SZ incidence has always been high and quite stable in human populations, across time and regardless of cultural implications, due to unclear reasons. It has been hypothesised that SZ pathophysiology may involve the biological components that changed during the recent human evolutionary history and led to our distinctive mode of cognition, which includes language skills. In this paper we explore this possibility, focusing on the self-domestication of the human species. This has been claimed to account for many human-specific distinctive traits, including aspects of our behaviour and cognition, and to favour the emergence of complex languages through cultural evolution. The “domestication syndrome” in mammals comprises the constellation of traits exhibited by domesticated strains, seemingly resulting from the hypofunction of the neural crest. It is our intention to show that people with SZ exhibit more marked domesticated traits at the morphological, physiological, and behavioural levels. We also show that genes involved in domestication and neural crest development and function comprise nearly 20% SZ candidates, most of which exhibit altered expression profiles in the brain of SZ patients, specifically in areas involved in language processing. Based on these observations, we conclude that SZ may represent an abnormal ontogenetic itinerary for the human faculty of language, resulting, at least in part, from changes in genes important for the “domestication syndrome” and, primarily involving the neural crest.
Contig annotation tool CAT robustly classifies assembled metagenomic contigs and long sequences
Authors: Cambuy Diego D. , Coutinho Felipe H. , Dutilh Bas E. 
Published: September 2016

AbstractIn modern-day metagenomics, there is an increasing need for robust taxonomic annotation of long DNA sequences from unknown micro-organisms. Long metagenomic sequences may be derived from assembly of short-read metagenomes, or from long-read single molecule sequencing. Here we introduce CAT, a pipeline for robust taxonomic classification of long DNA sequences. We show that CAT correctly classifies contigs at different taxonomic levels, even in simulated metagenomic datasets that are very distantly related from the sequences in the database. CAT is implemented in Python and the required scripts can be freely downloaded from Github.
Dissecting the genetics of complex traits using summary association statistics
Authors: Pasaniuc Bogdan , Price Alkes L. 
Published: September 2016

AbstractDuring the past decade, genome-wide association studies (GWAS) have successfully identified tens of thousands of genetic variants associated with complex traits and diseases. These studies have produced vast repositories of genetic variation and trait measurements across millions of individuals, providing tremendous opportunities for further analyses. However, privacy concerns and other logistical considerations often limit access to individual-level genetic data, motivating the development of methods that analyze summary association statistics. Here we review recent progress on statistical methods that leverage summary association data to gain insights into the genetic basis of complex traits and diseases.
Selective constraints on coding sequences of nervous system genes are a major determinant of duplicate gene retention in vertebrates
Authors: Roux Julien , Liu Jialin , Robinson-Rechavi Marc 
Published: September 2016

AbstractThe evolutionary history of vertebrates is marked by three ancient whole-genome duplications: two successive rounds in the ancestor of vertebrates, and a third one specific to teleost fishes. Biased loss of most duplicates enriched the genome for specific genes, such as slow evolving genes, but this selective retention process is not well understood. To understand what drives the long-term preservation of duplicate genes, we characterized duplicated genes in terms of their expression patterns. We used a new method of expression enrichment analysis, TopAnat, applied toin situhybridization data from thousands of genes from zebrafish and mouse. We showed that the presence of expression in the nervous system is a good predictor of a higher rate of retention of duplicate genes after whole-genome duplication. Further analyses suggest that purifying selection against the toxic effects of misfolded or misinteracting proteins, which is particularly strong in non-renewing neural tissues, likely constrains the evolution of coding sequences of nervous system genes, leading indirectly to the preservation of duplicate genes after whole-genome duplication. Whole-genome duplications thus greatly contributed to the expansion of the toolkit of genes available for the evolution of profound novelties of the nervous system at the base of the vertebrate radiation.
Beyond the iron triangle: reflections of an early career academic
Authors: Turner Michelle 
Published: September 2016

Purpose
The Rethinking Project Management (RPM) research agenda has been influential in multiple domains. These include industry, education and research. In response to the call for papers for this special issue, the purpose of this paper is to consider RPM with a particular focus on the human side of project management.

Design/methodology/approach
Prior to joining academia, the author worked as a project manager for 15 years. This provided an opportunity for the author to consider the influence of RPM from three viewpoints: project practitioner; project educator; and researcher in project management.

Findings
Resources originating from project management bodies of knowledge and professional associations relating to the human side of project management are limited. This serves to emphasize the importance of the RPM-inspired research and its influence on the teaching and education of project professionals. The RPM agenda has also served to endorse a research agenda which is wide ranging and one that seeks to better understand and support the human element of project management.

Originality/value
RPM has encouraged researchers to consider project management beyond classical project management and the iron triangle of time, cost and quality. In doing so, there has emerged a rich and diverse body of knowledge which underpins the human element of project management and positively impacts the skills development of project professionals and the practice of project management.
Project studies and engaged scholarship
Authors: Geraldi Joana , Söderlund Jonas 
Published: September 2016

PurposeIn 2006, the “Rethinking Project Management” network called for a paradigm shift in project research, and proposed five research directions. The directions inspired research and marked a milestone in the development of the field. The purpose of this paper is to reflect on the past decade and to rejuvenate these research directions.Design/methodology/approachThe authors propose the umbrella term: “project studies” to denote the research related to projects and temporary organizing. Project studies is conceived not only as a body of research, but also as a social process embedded in research communities, and contemporary Zeitgeist. Based on Sandberg’s interpretative approach to the fit between work and works (in this case research-researcher) and Habermas’ three types of human interests: technical, practical, and emancipatory, the authors develop a conceptual framework circumscribing three types of research in project studies.FindingsThe conceptual framework is used to craft future research directions, in the lines proposed by Winteret al.(2006b).Research limitations/implicationsThe authors conclude by proposing for a sixth theme on the practice of theorizing, and call for engaged, ambidextrous scholars, who’s “job” goes beyond the writing of articles and research applications, and includes shaping discourses of project research, nurturing new project scholars, contributing to project practice and carefully considering the legacy of projects and project studies in society.Originality/valueThis paper positions research as a social process, and the role of researchers as actors shaping research in project studies.
Rethinking project practice: emerging insights from a series of books for practitioners
Authors: Dalcher Darren 
Published: September 2016

Purpose
The purpose of this paper is to identify the major trends and contributions published in the Advances in Project Management book series and place them in the context of the findings and outputs from the Rethinking Project Management Network. A key aim is to address the concerns of project practitioners and explore the alternatives to the assumed linear rationality of project thinking. The paper further offers a guided catalogue to some of the key ideas, concepts and approaches offered to practitioners through the series.

Design/methodology/approach
This is a conceptual review paper that reflects on the main areas covered in a book series aimed at improving modern project practice and explores the implications on practice, knowledge and the relationship between research and practice. The topics are addressed through the prism of the Rethinking Project Management Network findings.

Findings
The paper explores new advances in project management practice aligning them with key trends and perspectives identified as part of the Rethinking Project Management initiative. It further delineates new areas of expertise augmenting those mentioned in the disciplinary canons of knowledge.

Research limitations/implications
The paper offers a new understanding of how knowledge is created in, for and by practice. Improving the relationship between theory and practice may demand a new appreciation of the role of practitioners and the value of their reflection in context.

Practical implications
The primary implication is to explore the new directions and perspectives covered by authors in the Advances in Project Management series, and identify main areas and topics that feature in the emerging discourse about project management practice. In addition, new conceptualisations of the role of practitioners in making sense of project realities are offered and considered.

Originality/value
New areas of interest and activity are identified and examined, offering a catalogue of new writing and perspectives in project practice. Reflection on the relationship between research and practice encourages fresh thinking about the crucial role of practitioner knowledge and reflection.
The determinants of export performance: a review of the literature 2006-2014
Authors: Chen Jieke , Sousa Carlos M.P. , He Xinming 
Published: September 2016

Purpose
The purpose of this paper is to synthesize and evaluate recent studies on determinants of export performance.

Design/methodology/approach
Using a vote-counting technique this paper reviews 124 papers published between 2006 and 2014 to assess the determinants of export performance.

Findings
The results indicate that significant progress has been made during these nine years and that: numerous new determinants are identified, data quality and statistical biases have received considerable attention, and interaction and indirect relationships are considered. However, at the same time, the research of export performance is still limited by a lack of synthetic theoretical basis, inconsistent empirical test results, and insufficiency in the research framework and statistical methodologies.

Originality/value
Export performance has received increasing attention over recent decades, but the area is still characterized by fragmentation and diversity hindering theoretical and practical development. This paper integrates the findings of recent studies on export performance and provides further discussion from both theoretical and methodological aspects, and points out the directions for future research.
The governance-performance relationship: evidence from Ghana
Authors: Owusu Andrews , Weir Charlie 
Published: September 2016

PurposeThe purpose of this paper is to investigate the impact corporate governance, measured by a governance index, on the performance of listed firms in a developing economy, Ghana. It also evaluates the effect of the introduction of a code of corporate governance on compliance rates across Ghanaian firms as well as assessing the impact of the code’s introduction on firm performance for the study period 2000-2009.Design/methodology/approachThe paper develops a Ghanaian corporate governance index (GCGI) containing 33 provisions to measure corporate governance quality during the pre-code and the post-code sub-periods. The authors use a panel data analytical framework and fixed effects regressions to analyse the governance-performance relationships.FindingsAfter controlling for endogeneity, the authors find a statistically significant and positive relationship between the GCGI and firm performance. The analysis shows evidence of a statistically significant increase in the degree of compliance with the Ghanaian Code from the pre-2003 sub-period to the post-2003 sub-period. The authors also find that the introduction of the code has led to improved firm performance. However, not all elements of corporate governance appear to have a significant effect on firm performance.Research limitations/implicationsOne limitation of this study is the development of a corporate governance index. The binary coding used to construct the GCGI may not reflect the relative importance of the different corporate governance provisions. This means that all elements included in the index are given equal weighting. Future research may assign weights to each of the corporate governance provisions but this may have the disadvantage of making subjective judgements relative to the importance of each corporate governance provision recommended by the Ghanaian Code.Practical implicationsThese results have important implications for both policy makers and companies. For policy makers, it is encouraging for the development of a code of corporate governance to regulate firms rather than enforcing rigid laws that may not be value relevant. For companies, the improvement in compliance with a code of corporate governance can provide a means of achieving improved performance.Originality/valueThis paper adds to the limited evidence on the governance-performance relationship in developing economies and in particular it analyses the role of a governance index. It is also the first paper to compare the pre- and the post-code governance index-performance relationship in an African or developing country.
Using international standards as a complement to overcome the unachieved nature of local GAAPs
Authors: Klibi Mohamed Faker 
Published: September 2016

Purpose
In recent years, Tunisian listed companies have been preparing their financial statements under a hybrid set of accounting standards; a mixture of national and international standards. The purpose of this paper is to empirically verify to what extent this particular form of de facto compliance with IAS/IFRS (which are not authorized in Tunisia) is used among listed companies. The paper further analyzes accounting professionals’ perception of the current state of Tunisian standards and their attitudes in the absence of relevant national Generally Accepted Accounting Principles (GAAPs).

Design/methodology/approach
Two methodological approaches were used to answer the paper’s research questions: a document analysis approach and a survey questionnaire.

Findings
The document analysis revealed that a growing number of listed companies complement local GAAPs by standards they select among IAS/IFRS. The perception study indicated that Tunisian Accounting Standards are, indeed, less suitable for listed companies’ needs. Accordingly, when there is no local standard to measure a specific transaction or event, accounting professionals seem to have no problem in using some IAS/IFRS as a complement to overcome the unachieved nature of local GAAPs. However, the overall findings are likely to suggest that international standards used must not conflict with the Tunisian conceptual framework’s provisions. This means that the use of IAS/IFRS in conjunction with local GAAPs is generally perceived as being beneficial to the quality of financial statements.

Research limitations/implications
This study may be of interest to many developing countries that have not continued the harmonization of their accounting standards with IAS/IFRS. Future research should focus on the reasons which have led to this unachieved harmonization and the consequences of the normative gap which might emerge.

Practical implications
Previous research has often shown how difficult it is to apply international accounting standards in developing countries, especially when they do not correspond to the companies’ needs. Difficulties could occur when local standard-setters do not accurately know which new international standards are suitable to the market needs. The study gives some insights suggesting that corporate accounting practices should be analyzed to understand the real needs for new standards.

Originality/value
The paper highlights the beginning of a de facto convergence with international accounting standards without any support of national de jure convergence. Consideration of this phenomenon may contribute to the understanding of the malaise that characterizes the current accounting standard-setting in developing countries.