bluuebunny/crossref_metadata_2025_split huggingface dataset:
Expansion of the CRISPR toolbox in an animal with tRNA-flanked Cas9 and Cpf1 gRNAs
Authors: Port Fillip , Bullock Simon L 
Published: April 2016

AbstractWe present vectors for producing multiple CRISPR gRNAs from a single RNA polymerase II or III transcript inDrosophila. The system, which is based on liberation of gRNAs by processing of flanking t †RNAs, permits highly efficient multiplexing of Cas9-based mutagenesis. We also demonstrate that the †RNA-gRNA system markedly increases the efficacy of conditional gene disruption by Cas9 and can promote editing by the recently discovered RNA-guided endonuclease Cpf1.
Evaluating performance of metagenomic characterization algorithms usingin silicodatasets generated with FASTQSim
Authors: Shcherbina Anna , Ricke Darrell O. , Chiu Nelson 
Published: April 2016

AbstractBackgroundIn silicobacterial, viral, and human truth datasets were generated to evaluate available metagenomics algorithms. Sequenced datasets include background organisms, creating ambiguity in the true source organism for each read. Bacterial and viral datasets were created with even and staggered coverage to evaluate organism identification, read mapping, and gene identification capabilities of available algorithms. These truth datasets are provided as a resource for the development and refinement of metagenomic algorithms. Algorithm performance on these truth datasets can inform decision makers on strengths and weaknesses of available algorithms and how the results may be best leveraged for bacterial and viral organism identification and characterization.Source organisms were selected to mirror communities described in the Human Microbiome Project as well as the emerging pathogens listed by the National Institute of Allergy and Infectious Diseases. The sixin silicodatasets were used to evaluate the performance of six leading metagenomics algorithms: MetaScope, Kraken, LMAT, MetaPhlAn, MetaCV, and MetaPhyler.ResultsAlgorithms were evaluated on runtime, true positive organisms identified to the genus and species levels, false positive organisms identified to genus and species level, read mapping, relative abundance estimation, and gene calling. No algorithm out performed the others in all categories, and the algorithm or algorithms of choice strongly depends on analysis goals. MetaPhlAn excels for bacteria and LMAT for viruses. The algorithms were ranked by overall performance using a normalized weighted sum of the above metrics, and MetaScope emerged as the overall winner, followed by Kraken and LMAT.ConclusionsSimulated FASTQ datasets with well-characterized truth data about microbial community composition reveal numerous insights about the relative strengths and weaknesses of the metagenomics algorithms evaluated. The simulated datasets are available to download from the Sequence Read Archive (SRP062063).
Looking for Energy in Population Data: How to Detect Self-Organization in Human Community Distribution
Authors: Casas-Busquet Josep M , Poch-Parés Agustí 
Published: April 2016

AbstractIn the present work we study the relationship between population allocation and the combined effects of urban size and energy consumption, for two given areas and through a major part of the twentieth century. Along these lines a general application model is laid down which relates city-growth rates to initial inhabitants and to exosomatic energy increment, the deviations from it showing order in space and time, as shown in a series of maps which hint at unaccounted socioeconomic factors. The study of the maps by means of spectral analysis allows finding patterns which reinforce over time, in such a manner that spatial frequencies can be determined whose weight increases up so granting surface evolution estimation.HighlightsThe regressions can be considered as a way to quantifying the population’s distributionSlopes correlate well with commercial primary energy increments to a 0.9 coefficientThis result couples demography to energy and posits the emergence of self-orderOur model’s unexplained deviations show continuity in spaceThe topography of the maps has been typified through the methodology exposed herein
OncoPhase: Quantification of somatic mutation cellular prevalence using phase information
Authors: Chedom-Fotso Donatien , Ahmed Ahmed Ashour , Yau Christopher 
Published: April 2016

AbstractThe impact of evolutionary processes in cancer and its implications for drug response, biomarker validation and clinical outcome requires careful consideration of the evolving mutational landscape of the cancer. Genome sequencing allows us to identify mutations but the prevalence of those mutations in heterogeneous tumours must be inferred. We describe a method that we call OncoPhase to compute the prevalence of somatic point mutations from genome sequencing analysis of heterogeneous tumours that combines information from nearby phased germline variants. We show using simulations that the use of phased germline information can give improved prevalence estimates over the use of somatic variants only.
Control of Transposon-mediated Activation of theglpFKOperon ofEscherichia coliby two DNA binding Proteins
Authors: Zhang Zhongge , Saier Milton H. 
Published: April 2016

AbstractEscherichia colicells deleted for the cyclic AMP (cAMP) receptor protein (Crp) gene (Δcrp) cannot utilize glycerol because cAMP-Crp is a required positive activator of glycerol utilization operonglpFK. We have previously shown that a transposon, Insertion Sequence 5 (IS5), can reversibly insert into the upstream regulatory region of the operon so as to activateglpFKand enable glycerol utilization. GlpR, which repressesglpFKtranscription, binds to theglpFKupstream region near the site of IS5insertion, and prevents insertion. We here show that the cAMP-Crp complex, which also binds to theglpFKupstream regulatory region, also inhibits IS5hopping into the activating site. This finding allowed us to identify conditions under which wild type cells can acquireglpFK-activating IS5insertions. Maximal rates of IS5insertion into the activating site require the presence of glycerol as well as a non-metabolizable sugar analogue that lowers cytoplasmic cAMP concentrations. Under these conditions, IS5insertional mutants accumulate and outcompete the wild type cells. Because of the widespread distribution of glucose analogues in nature, this mechanism of gene activation could have evolved by natural selection.
Automated population identification and sorting algorithms for high-dimensional single-cell data
Authors: Anchang Benedict , Plevritis Sylvia K. 
Published: April 2016

AbstractCell sorting or gating homogenous subpopulations from single-cell data enables cell-type specific characterization, such as cell-type genomic profiling as well as the study of tumor progression. This highlight summarizes recently developed automated gating algorithms that are optimized for both population identification and sorting homogeneous single cells in heterogeneous single-cell data. Data-driven gating strategies identify and/or sort homogeneous subpopulations from a heterogeneous population without relying on expert knowledge thereby removing human bias and variability. We further describe an optimized cell sorting strategy called CCAST based on Clustering, Classification and Sorting Trees which identifies the relevant gating markers, gating hierarchy and partitions that define underlying cell subpopulations. CCAST identifies more homogeneous subpopulations in several applications compared to prior sorting strategies and reveals simultaneous intracellular signaling across different lineage subtypes under different experimental conditions.
Delivering a water treatment plant project using a collaborative project procurement approach
Authors: Walker Derek H.T. , Rahmani Farshid 
Published: April 2016

Purpose
The purpose of this paper is to explore an interesting complex infrastructure construction case study project in which the initiation/design and delivery phases were managed differently, with diverse assumptions and workplace culture. It uses a recently developed collaboration and relationship-based procurement taxonomy to analyse the decision to commence a project and to deliver the project. The taxonomy tool reveals underlying assumptions and helps explain actions taken. The paper provides a window into the decision-making process. It also illustrates levels of innovation applied at the design and delivery phases.

Design/methodology/approach
A case study was undertaken, primarily using recorded and transcribed interviews, with five key senior participants in the project. This gathered a client, designer and contractor perspective that was subsequently analysed using a sense-making approach.

Findings
It is possible to start a project adopting a highly collaborative approach that maximises innovation, understanding complexity and developing a design that can then be delivered using a more traditional approach. The taxonomy used demonstrates that it is a useful visualisation tool for this purpose.

Research limitations/implications
The research was limited to the perspectives of only five individuals even though they were key decision-makers and had a robust overview of the project as a whole. The delivery phase was chosen as a matter of policy without the ability to break loose from that policy. The implications for beginning the initiation and design process in a highly collaborative hands-on mode influenced the understanding of all parties involved in the project in a positive direction. The case study was based in Australia, which has extensive experience of collaborative project delivery approaches.

Practical implications
The taxonomy and its ability to provide visualisation of the experienced collaboration presents a powerful tool in helping us understand how it may be useful and what limitations to collaboration exists.

Social implications
The paper illustrates the value of social interactions as alliance forms tend to consider triple bottom line issues and stakeholder engagement more highly than traditional, transnational approaches to project design and delivery.

Originality/value
The case study was unusual in its technical complexity; however, the main value of the paper is the application of the taxonomy and visualisation tool as a way to better understand how a project is being managed from a collaboration perspective.
Hybrid project delivery processes observed in constructor BIM innovation adoption
Authors: Gledson Barry J. 
Published: April 2016

PurposeExploratory research was undertaken focusing upon an innovation adoption decision taken by a regional UK division of a large international contracting organisation implementing building information modelling (BIM) into their project delivery processes. The purpose of this paper was to gain new insights through observations of the process and analysis of the views of employees about organisational BIM adoption during the implementation stage of the innovation-decision process.Design/methodology/approachCase study research was performed focussing on initial BIM projects delivered by an early adopter organisation. Observations and semi-structured interviews were used as part of a data collection strategy, and an iterative research approach was adopted.FindingsDuring implementation stages of BIM innovation adoption, organisations may have to make use of hybrid project delivery methods on initial adopter projects while also working concomitantly with existing systems, processes and personnel not yet ready to adapt to BIM methodology.Originality/valueThe work captures previously unseen phenomena of how such an organisation and its staff have adapted to BIM innovation adoption during a programme of organisational change. The identification of hybrid project delivery processes has generated further implications for practice and research into the effectiveness of construction production information management.
“Chasing a passion”: first-generation college graduates at work
Authors: Olson Joann S. 
Published: April 2016

Purpose
– The purpose of this paper is to describe the college-to-work transition as experienced by first-generation college (FGC) graduates. First-generation graduates are often adjusting to workplaces that are significantly different from parents’ work environments.

Design/methodology/approach
– This phenomenological study explored the early-career learning experiences of six FGC graduates from the USA. All participants were working full-time and had graduated two to six years earlier.

Findings
– Three themes were identified: starting the job, being in the job, and releasing the past. Participants highlighted unanticipated aspects of their college-to-work transition, including dealing with workplace politics and family dynamics. They also described ambivalence between their current work and the desire to pursue a more compelling career or vocational passion.

Research limitations/implications
– All participants were white and from similar (rural) settings in one region of the USA. The qualitative nature of the study restricts generalization.

Practical implications
– This study suggests, given the distinction between first-generation students’ post-college work environments and that of their parents, that educators’ efforts to assist FGC students might appropriately extend to topics beyond graduation. FGC graduates should be alerted to the impact of shifts in social and cultural norms, and informed about changing family dynamics that may continue after leaving school.

Originality/value
– Previous research has highlighted the challenges facing FGC students. This is one of few studies that explores the experiences of FGC graduates in the workplace following graduation.
The rise and fall of the Australian DBA
Authors: Kortt Michael A. , Pervan Simon J , Hogan Owen 
Published: April 2016

Purpose
– The purpose of this paper is to identify and discuss the drivers behind the rise and fall of the Australian Doctor of Business Administration (DBA) and to assess its future.

Design/methodology/approach
– Data covering the period 1993-2013 was sourced from the Commonwealth Department of Education and Training to provide a comprehensive analysis of the rise and fall of the Australian DBA.

Findings
– In Australia, the DBA was introduced in 1993. In the first 11 years of the programme, enrolments increased from only nine candidates in 1993 to 1,505 candidates in 2004. However, by 2013, the number of candidates had fallen to 869 candidates. The authors argue that the principal rationale for the dramatic fall in enrolments points to the challenges and issues of managing overseas candidates by second tier and regional universities rather than a decline in the market per se.

Practical implications
– The challenge for universities is to determine whether they can or are able to offer the DBA under a quality framework that requires academic rigour equal to the PhD.

Originality/value
– This paper presents – for the first time – the most comprehensive description of trends in the Australian DBA programme from its inception to the present day. It also offers valuable insights and cautionary lessons for other countries thinking of introducing or expanding their current DBA programmes.
IFRS and value relevance: evidence based on Canadian adoption
Authors: Okafor Oliver N. , Anderson Mark , Warsame Hussein 
Published: April 2016

Purpose
– The purpose of this paper is to investigate whether financial information prepared and disclosed under International Financial Reporting Standards (IFRS) has incremental value relevance vs information prepared under generally accepted accounting principles (GAAP) in Canada.

Design/methodology/approach
– The authors employ a difference in differences methodology and estimate value relevance using: first, the adjusted R2 of regressions of stock price on book value and earnings; second, the adjusted R2 of regressions of stock returns on earnings and changes in earnings; and third, a time series incremental association return estimation. The authors use multiple models including a model similar to the Ohlson (1995) model and a modified Balachandran and Mohanram (2011) model to investigate value relevance in the period 2008-2013.

Findings
– The authors provide empirical evidence, based on unique Canadian environment, that accounting information prepared and disclosed under IFRS exhibits higher price and returns value relevance than accounting information prepared previously under local GAAP. Sensitivity analyses and yearly trends regressions produce collaborating evidence.

Originality/value
– The study provides early empirical evidence that value relevance increases in mandatory IFRS adoption, based on unique Canadian adoption. The Canadian adoption is unique because Canada: first, is the first G7 non-European country to adopt IFRS; second, had pursued a dual strategy of harmonizing with the US GAAP while supporting IFRS convergence; third, provided information environment that mitigates the problems associated with measuring the effects of IFRS adoption in the European countries where IFRS or its predecessor – international accounting standards – had permeated the reporting environment prior to the mandatory adoption in 2005; and fourth, allowed firms listed on the US exchanges to continue to use or adopt the US GAAP for financial reporting and thus, provided a group of benchmark firms drawn from the same social-political and economic environment as the treatment firms. The study clarifies prior inconsistent results from European samples.
FASB and IASB diverging perspectives on the new lessee accounting
Authors: Beckman Judy Kay 
Published: April 2016

Purpose
– The purpose of this paper is to demonstrate the expected effect of diverging accounting requirements and practices on firms in two industries – construction and retailing – which typically undertake different types of leases, namely, equipment and real estate, respectively. The paper also discusses how the new standards will provide expanded disclosures to aid this financial statement analysis.

Design/methodology/approach
– The research demonstrates how to estimate information comparable to that produced under IFRS from US GAAP financial statements and estimates the significance of the impact on key financial statement ratios.

Findings
– Key profitability ratios – return on assets and return on equity – generally improve over the time period 2007-2013 while interest coverage drastically deteriorates particularly for retailing firms. This finding contrasts with what some view as the Financial Accounting Standards Board’s reason for its choice of income statement presentation – to avoid the front-end loading of costs that ensues from accounting for leases as one would any other long-lived asset acquired through long-term financing.

Practical implications
– Current IFRS and US GAAP requirements do not provide sufficient information to estimate lease accounting changes for those firms which have no long-term debt other than long-term leases. Therefore, the estimates presented in this analysis are limited below what will be possible to do under new accounting requirements.

Originality/value
– The research covers a current topic of new divergence between US GAAP and IFRS requirements for leases. In addition, improvements over analysis techniques currently required that will be possible with new financial statement disclosures also are discussed.
The effect of mandatory XBRL and IFRS adoption on audit fees
Authors: Shan Yuan George , Troshani Indrit 
Published: April 2016

Purpose
– The purpose of this paper is to evaluate the impact of the International Financial Reporting Standards (IFRS) and eXtensible Business Reporting Language (XBRL) on audit fees based on evidence from listed companies operating in an emerging economy. Whilst IFRS constitute high-quality accounting standards, XBRL represents a technology standard that can enhance the usability of IFRS and overall financial reporting transparency.

Design/methodology/approach
– Multivariate analyses are used on a sample of 1,798 firm-year observations between 2000 and 2011 from companies listed in the Shanghai Stock Exchange that were subject to XBRL and IFRS adoption mandates.

Findings
– The main results suggest that XBRL has a main negative effect on audit fees which is weaker for larger firms. Additionally, the authors find that IFRS increases audit fees for all companies. Whilst this effect is positive for firms of different sizes, it is weaker for larger firms.

Research limitations/implications
– Whilst the findings are applicable to the selected sample and may or may not be generaliseable to other economies, they can provide important implications for both regulators and companies that are undertaking IFRS convergence and XBRL implementation projects in developing economies around the world.

Originality/value
– This study offers a timely assessment of the economic consequences of IFRS and XBRL on listed companies operating in an emerging economy, in addition to providing an important basis upon which further research can be designed in order to extend the analysis.
Followership and job satisfaction in the public sector
Authors: Jin Myung , McDonald Bruce , Park Jaehee 
Published: April 2016

Purpose– The purpose of this paper is to explicate the role of followership behavior on employee job satisfaction as well as the conditions that may moderate its impact.Design/methodology/approach– This study uses a largensurvey data from federal agencies and investigates an additive moderation model in which two situational factors, perceived supervisor support (PSS) and performance-oriented culture (POC), interact with followership behavior.Findings– Employees high on active followership perceived greater job satisfaction when PSS was high, rather than low. On the other hand, employees high on active followership perceived greater job satisfaction when POC was low, rather than high.Research limitations/implications– This is, to the knowledge, the first empirical study based on a cross-sectional survey that tests how the effects of active followership on employee job satisfaction may vary depending on the different types of situational factors. As such, more studies are needed to validate the causal directions of the findings.Practical implications– The present findings show that active engagement had greater association with job satisfaction when leader involvement was high and performance orientation was low. For highly engaged employees, leaders are encouraged to show higher degree of involvement in their work but with less emphasis on the performance orientation of the organization.Originality/value– This study contributes to the broader literature in public sector leadership in two ways. First, research on the relationship between followership and job satisfaction has been sparse. Second, and most importantly, this study is the first empirical study that tests the moderating roles of situational (organizational) factors on the relationship between followership and employee attitude (job satisfaction).