bluuebunny/crossref_metadata_2025_split huggingface dataset:
Retention of PIT and T-Bar Anchor Tags in Blue Catfish
Authors: Bodine Kristopher A. , Fleming Paul 
Published: February 2014

Abstract
We quantified retention of PIT and T-bar anchor tags in Blue Catfish Ictalurus furcatus. Eighty-one fish (364–1,005 mm TL) were injected with a PIT tag in the dorsal musculature immediately posterior to the dorsal fin and a T-bar anchor tag below the dorsal fin between the pterygiophores. Fish were held in a 0.24-ha earthen pond and retention was evaluated at 2, 4, and 6 months. Retention of PIT tags was 100% over the duration of the study. T-bar anchor tag retention was about 94% at 2 months and 76% at 6 months and was linearly related to time. We estimated that by 25 months, all T-bar tags would be lost. Our results suggest PIT tags can effectively be used in long-term studies (&gt;6 months), whereas T-bar anchor tags are suited for short-term experiments.
Received July 29, 2013; accepted October 15, 2013
Published online January 24, 2014
Assessing single nucleotide variant detection and genotype calling on whole-genome sequenced individuals
Authors: Cheng Anthony Youzhi , Teo Yik-Ying , Ong Rick Twee-Hee 
Published: February 2014

Abstract
Motivation: Whole-genome sequencing (WGS) is now routinely used for the detection and identification of genetic variants, particularly single nucleotide polymorphisms (SNPs) in humans, and this has provided valuable new insights into human diversity, population histories and genetic association studies of traits and diseases. However, this relies on accurate detection and genotyping calling of the polymorphisms present in the samples sequenced. To minimize cost, the majority of current WGS studies, including the 1000 Genomes Project (1 KGP) have adopted low coverage sequencing of large number of samples, where such designs have inadvertently influenced the development of variant calling methods on WGS data. Assessment of variant accuracy are usually performed on the same set of low coverage individuals or a smaller number of deeply sequenced individuals. It is thus unclear how these variant calling methods would fare for a dataset of ∼100 samples from a population not part of the 1 KGP that have been sequenced at various coverage depths.
Results: Using down-sampling of the sequencing reads obtained from the Singapore Sequencing Malay Project (SSMP), and a set of SNP calls from the same individuals genotyped on the Illumina Omni1-Quad array, we assessed the sensitivity of SNP detection, accuracy of genotype calls made and variant accuracy for six commonly used variant calling methods of GATK, SAMtools, Consensus Assessment of Sequence and Variation (CASAVA), VarScan, glfTools and SOAPsnp. The results indicate that at 5× coverage depth, the multi-sample callers of GATK and SAMtools yield the best accuracy particularly if the study samples are called together with a large number of individuals such as those from 1000 Genomes Project. If study samples are sequenced at a high coverage depth such as 30×, CASAVA has the highest variant accuracy as compared with the other variant callers assessed.
Availability and implementation:
Contact: twee_hee_ong@nuhs.edu.sg
Supplementary information: Supplementary data are available at Bioinformatics online.
A further study of superoutbursts and superhumps in SU UMa stars by the Kepler light curves of V1504 Cygni and V344 Lyrae
Authors: Osaki Yoji , Kato Taichi 
Published: February 2014

Abstract
We made a supplementary study of the superoutbursts and superhumps in SU UMa stars by using the recently released Kepler public data of V1504 Cyg and V344 Lyr. One of the superoutbursts in V1504 Cyg was preceded by a precursor normal outburst which was well separated from the main superoutburst. The superhump first appeared during the descending branch of the precursor normal outburst and it continued into its quiescence (the deep dip between the precursor and the main superoutburst), and it began to grow in amplitude with the development of the main superoutburst after the quiescence ended. A similar phenomenon was also observed in V344 Lyr. This observation very clearly demonstrates that the superoutburst was triggered by the superhump (i.e., by the tidal instability), supporting the thermal tidal instability model. Smak (2013, Acta Astron., 63, 109) criticized our previous paper (Osaki & Kato, 2013, PASJ, 65, 50) and challenged our main conclusion that various lines of observational evidence of V1504 Cyg support the thermal tidal instability model for the superoutbursts of SU UMa stars. We present our detailed accounts to all of his criticisms by offering clear explanations. We conclude that the thermal tidal instability model is, after all, only the viable model for the superoutbursts and superhumps in SU UMa stars.
Use of Nanocrystalline Hydroxyapatite With Autologous BMA and Local Bone in the Lumbar Spine
Authors: Robbins Stephen , Lauryssen Carl , Songer Matthew N. 
Published: February 2014

Study Design:
A retrospective, multicenter, medical record review and independent analysis of computed tomographic scans was performed in 46 patients to determine radiographic arthrodesis rates after 1-segment, 2-segment, or 3-segment instrumented posterolateral fusions (PLF) using autograft, bone marrow aspirate (BMA), and a nanocrystalline hydroxyapatite bone void filler (nHA).

Objective:
To determine the radiographic arthrodesis rates after instrumented lumbar PLF using local autograft, BMA, and nHA.

Summary of Background Data:
The use of iliac crest autograft in posterolateral spine fusion carries real and significant risks. Many forms of nanocrystalline hydroxyapatite have been studied in various preclinical models, but no human studies have reviewed its efficacy as a bone graft supplement in PLF.

Methods:
Posterolateral arthrodesis progression was documented approximately 12 months postoperatively using a computed tomographic scan and evaluated by an independent radiologist for the presence of bridging bone. One-year postoperative clinical outcomes were assessed using the PROLO score.

Results:
Radiographically, 91% patients treated exhibited bilateral or unilateral posterolateral bridging bone. Ninety-four percent of the segments treated exhibited bilateral or unilateral posterolateral bridging bone, whereas 6% segments exhibited no posterolateral bridging bone on either side. A total of 93% individual sites treated exhibited posterolateral bridging bone. In 1-segment, 2-segment, and 3-segment arthrodesis, 88%, 93%, and 100%, respectively, of individual sites exhibited radiographic bridging bone. One-year postoperative PROLO scores for 77% patients were excellent or good. There were no complications related to the posterolateral graft mass and no symptomatic nonunions.

Conclusions:
The arthrodesis rates after instrumented lumbar fusion using local autograft mixed with BMA and the nHA is equivalent to the rates reported for iliac crest autograft in these indications, including stringent indications, such as 3-segment procedures. By approximately 12 months postoperatively, there was no significant difference in the rates of bridging bone between the 1-segment, 2-segment, and 3-segment procedures.
Economic and Operational Implications of a Standardized Approach to Hemodynamic Support Therapy Using Percutaneous Cardiac Assist Devices
Authors: Wohns David , Muthusamy Purushothaman , Davis Alan T. , Khan Mohsin , Postma Joseph K. , Williams Elbert E. , Gile Cynthia M. , Scotti Dennis J. , Gregory David 
Published: February 2014

Objective Impella 2.5 has been shown to reduce major adverse events for patients undergoing elective high-risk percutaneous coronary intervention. We performed a single-center retrospective study to compare the costs and resource use of Impella 2.5 and intra-aortic balloon pump (IABP) support. Methods All high-risk patients who received Impella 2.5 (n = 35) and IABP (n = 295) support from December 2008 to July 2011 were included. Propensity score matching identified a balanced 1:1 matched cohort (35 Impella vs 35 IABP) based on indications for implantation, preimplantation hemodynamics, and age. Diagnostic, procedural, financial, and resource use data were collected. Results As compared with IABP, Impella offered a more predictable course of treatment/resource consumption and was not associated with any extreme cost outliers (17.1% vs 0.0%, respectively; P = 0.025). The mean admission and 90-day episode of care total costs for Impella were 5.5% ($67,681 vs $71,608, P = 0.79) and 4.2% ($70,680 vs $73,476, P = 0.85) lesser than that for IABP, respectively. Although not statistically significant, Impella patients had a trend toward lower rehospitalization rates (11.4% vs 20%), lesser mean index length of hospital stay (11.2 vs 13.7), and 90-day (11.7 vs 14.2) episode of care length of hospital stay. Conclusions Impella support was associated with consistent course of treatment/resource consumption with significantly fewer 90-day extreme cost outliers than was IABP. The lower index and 90-day follow-up cost trends observed for Impella were driven by shorter length of hospital stay and fewer rehospitalizations. As providers strive to improve quality of care by reducing variability, these findings have implications for the development of hemodynamic support algorithms.
HTSeq – A Python framework to work with high-throughput sequencing data
Authors: Anders Simon , Pyl Paul Theodor , Huber Wolfgang 
Published: February 2014

ABSTRACTMotivation:A large choice of tools exists for many standard tasks in the analysis of high-throughput sequencing (HTS) data. However, once a project deviates from standard work flows, custom scripts are needed.Results:We present HTSeq, a Python library to facilitate the rapid development of such scripts. HTSeq offers parsers for many common data formats in HTS projects, as well as classes to represent data such as genomic coordinates, sequences, sequencing reads, alignments, gene model information, variant calls, and provides data structures that allow for querying via genomic coordinates. We also present htseq-count, a tool developed with HTSeq that preprocesses RNA-Seq data for differential expression analysis by counting the overlap of reads with genes.Availability:HTSeq is released as open-source software under the GNU General Public Licence and available fromhttp://www-huber.embl.de/HTSeqor from the Python Package Indexhttps://pypi.python.org/pypi/HTSeq.Contact:sanders@fs.tum.de
No evidence that natural selection has been less effective at removing deleterious mutations in Europeans than in West Africans
Authors: Do Ron , Balick Daniel , Li Heng , Adzhubei Ivan , Sunyaev Shamil , Reich David 
Published: February 2014

AbstractNon-African populations have experienced major bottlenecks in the time since their split from West Africans, which has led to the hypothesis that natural selection to remove weakly deleterious mutations may have been less effective in non-Africans. To directly test this hypothesis, we measure the per-genome accumulation of deleterious mutations across diverse humans. We fail to detect any significant differences, but find that archaic Denisovans accumulated non-synonymous mutations at a higher rate than modern humans, consistent with the longer separation time of modern and archaic humans. We also revisit the empirical patterns that have been interpreted as evidence for less effective removal of deleterious mutations in non-Africans than in West Africans, and show they are not driven by differences in selection after population separation, but by neutral evolution.
Mapping the structure of drosophilid behavior
Authors: Berman Gordon J. , Choi Daniel M. , Bialek William , Shaevitz Joshua W. 
Published: February 2014

AbstractMost animals possess the ability to actuate a vast diversity of movements, ostensibly constrained only by morphology and physics. In practice, however, a frequent assumption in behavioral science is that most of an animal’s activities can be described in terms of a small set of stereotyped motifs. Here we introduce a method for mapping the behavioral space of organisms, relying only upon the underlying structure of postural movement data to organize and classify behaviors. We find that six different drosophilid species each perform a mix of non-stereotyped actions and over one hundred hierarchically-organized, stereotyped behaviors. Moreover, we use this approach to compare these species’ behavioral spaces, systematically identifying subtle behavioral differences between closely-related species.
A GWAS platform built on iPlant cyber-infrastructure
Authors: Wang Liya , Ware Doreen , Lushbough Carol , Merchant Nirav , Stein Lincoln 
Published: February 2014

AbstractWe demonstrated a flexible Genome-Wide Association Study (GWAS) platform built upon the iPlant Collaborative Cyber-infrastructure. The platform supports big data management, sharing, and large scale study of both genotype and phenotype data on clusters. End users can add their own analysis tools, and create customized analysis workflows through the graphical user interfaces in both iPlant Discovery Environment and BioExtract server.
Momentum building for more women in senior appointments
Authors: J. Hurn Brian 
Published: February 2014

Purpose
– The purpose of this paper is to review the encouraging progress and increased momentum in both business and Government for more women to be appointed to senior positions. It traces this momentum since the author's last article: “Are cracks now appearing in the boardroom glass ceiling?” in Industrial and Commercial Training, Vol. 45 No. 4, 2013.

Design/methodology/approach
– Critical review of recent initiatives by both government and business.

Findings
– The article highlights the positive momentum towards greater gender equality in the workplace. It emphasises the need for more career guidance beginning early in school for girls and to change the male-dominated culture found in many areas of business.

Research limitations/implications
– Review of literature and media articles in the past 12 months.

Practical implications
– The increased antipathy towards quotas and the need for greater career guidance in both schools and colleges, together with work experience placements for women. Recruitment and selection should be gender-free, based on ability and experience and carried out by selection panels of both sexes.

Originality/value
– Highlights and analyses the recent encouraging trends and increasing awareness of the value women bring to a company board.
Modern trends in learning architecture
Authors: Little Bob , Knihova Ladislava 
Published: February 2014

Purpose
– The purpose of this paper is to examine current practice in blended learning – notably the view of blended learning as a synthesis of different approaches to the delivery of learning in order to create high impact learning.

Design/methodology/approach
– An exploration of the development of blended learning over the years, especially how it is being affected by developments in learning delivery technology and learning design.

Findings
– Learning architecture and design ought to be enhanced by the thoughtful use of various new tools, strategies and delivery platforms working in harmony. Only then can the learning process finally become highly attractive for new generations of learners.

Research limitations/implications
– New trends driving virtual learning prescribe the use of a portfolio of new tools. This, therefore, is producing changes in e-learning architecture, including the need for multi-device learning solutions, along with the need to implement multimedia formats in producing virtual learning solutions. Simultaneously, for educators, there have been changes in learning solutions' design based on the emergence of the self-determined and autonomous learner, as described by the concept of heutagogy.

Practical implications
– The complexities of creating an appropriate blend along with the most effective learning solutions for each learner – including the use of mobile platforms and social learning – have never been more challenging.

Originality/value
– Customising learning is in its early stages but, with the advent of new delivery technology and the growth of self-determined learners, it will become unavoidable.
What kills innovation? Your role as a leader in supporting an innovative culture
Authors: H. Soken Nelson , Kim Barnes B. 
Published: February 2014

Purpose
– The purpose of this paper is to suggest a set of leadership practices that can help to build and sustain a culture of innovation.

Design/methodology/approach
– The article is based on the authors' many years of consulting and facilitating learning experiences in innovation management in a broad range of organizations. The authors have observed that specific leadership and management practices seem to be strongly related to the success or failure of organizations in building self-renewing innovation environments.

Findings
– Leadership and management behaviors that engender fear, a lack of focus and communication about organizational innovation strategy, a paucity of resources (time, money, encouragement) are among the factors that make innovation less likely or less successful. A clearly communicated purpose, the ability to accept and use failure, and an accessible process for getting a hearing on ideas are among the supportive factors.

Practical implications
– Many leaders understand that innovation is key to their organization's ability to survive in a connected and competitive business environment. Fewer understand and/or are willing to make the changes that will create and sustain a culture of innovation. Leaders who are willing to adopt some of these practices are likely to achieve better results in encouraging talented people to contribute their capabilities, ideas and efforts to strategic innovation initiatives.

Originality/value
– Successful innovation is not created through magic and good fortune. It is the product of strategic thinking, a supportive culture, great talent, managers who know when to be involved and when to step back, and leaders who listen, support risk, and learn from failure.
The rebirth of dependence – offering an alternative understanding of financial crisis
Authors: Hackett Ciara 
Published: February 2014

Purpose
– This article aims to contribute to the re-evaluation of the global market system using a Marxist inspired theory of development, dependency.

Design/methodology/approach
– This article draws on dependency theory as an alternative means of understanding global relationships. Building on existing literature, it modifies dependency to encapsulate technological developments and trends in the global market.

Findings
– Re-evaluating the global market and the relationships that underpin it, through an alternative theory, highlights the fragility of markets and associated relationships. Increasingly, nation states are becoming irrelevant. This presents a problem as the main actors in the global market today are “above” inter-state relations, yet the organs that regulate their behaviour still are grounded in inter-state rhetoric. The relationship between development and underdevelopment remains.

Research limitations/implications
– The financial crisis has propagated a wealth of interest in the relationships between states, between multi-national corporations (MNCs) and between MNCs and state. Using this broad theory of modified dependency, it can be applied to a range of different relationships. In the wake of financial crisis, there is the opportunity to raise awareness of these ingrained issues and initiate discussions at national, regional and international levels to alleviate some of the conditions of dependence.

Practical implications
– Regardless of the work of national governments and NGOs to instigate development in lesser-developed regions through policy and regulations, unless there is a conscientious commitment from MNCs operating in that region to contribute to development, the result will be the development of underdevelopment and the underdevelopment of development. CSR can help alleviate the conditions of the dependence on capital generated by MNCs, but this is not a solution to an ingrained problem, capitalism.

Originality/value
– This article introduces a modified theory of dependency for the first time. It applies the theory to the financial crisis and to the continent of Africa. It considers the role that CSR can play in alleviating the conditions of dependence.
Secure inpatient services: a needs assessment
Authors: Hall Ian , Yacoub Evan , Boast Neil , Bates Robert , Stamps Rebekah , Holder Sarah , Beadman Matthew 
Published: February 2014

Purpose
– The purpose of this paper is to complete a thorough needs assessment that would enable the development of a robust pathway of care for adults with a learning disability requiring secure care, and to assist commissioners to make informed planning decisions.

Design/methodology/approach
– The paper identified people with a learning disability originating from London who were in secure care, and collected data about them. The paper used reference groups to inform the analysis.

Findings
– The paper identified 249 people in secure services and was able to include 136 patients in the analysis. In all, 64 were in NHS provision and 72 in independent sector provision; 109 (80.1 per cent) were male and 27 (19.9 per cent) female; on average, patients were cared for 61.5 miles away from their homes; NHS patients were far closer to home; 69.1 per cent had a mild learning disability; 82.3 per cent had a history of violence; approximately one in six patients could not progress due to a lack of an appropriate ward, facility, resource and/or intervention.

Practical implications
– Secure care for this population is a major public health issue. Many are placed a long way from home. Local services should be developed, and there should be sufficiently robust “step down” places for patients to be discharged to.

Originality/value
– Systematic identification of the needs of a marginalised group to enable better more appropriate care pathways to be developed in the future.
Economic analysis of aprepitant‐containing regimen to prevent chemotherapy‐induced nausea and vomiting in patients receiving highly emetogenic chemotherapy in Hong Kong
Authors: Chan Stephen L , Jen Jason , Burke Thomas , Pellissier James 
Published: February 2014

AbstractAimWe aim to evaluate the cost effectiveness of aprepitant‐containing regimens for the prevention of chemotherapy‐induced nausea and vomiting (CINV) among patients receiving high emetogenic chemotherapy (HEC) in Hong Kong.MethodsBoth cost‐effectiveness and cost‐utility analyses were conducted utilizing a decision‐analytic model to measure the economic costs and clinical outcomes associated with the aprepitant‐containing regimen versus a standard regimen in the prevention of CINV. Analyses were conducted on the basis of four published double‐blind randomized clinical trials involving different usages of serotonin receptor antagonists.ResultsThe use of aprepitant‐containing regimens is associated with an improvement in quality‐adjusted life years (QALYs) compared with non‐aprepitant regimens. For cisplatin‐based chemotherapy, the incremental cost per QALY gained is HKD 239 644 (1 USD approximates HKD 7.8) when ondansetron is administered on day 1 only. The incremental cost per QALY is HKD 440 950 when ondansetron is used on day 1 to 4. For anthracycline and cyclophosphamide chemotherapy, the aprepitant‐containing regimen is associated with incremental cost of HKD 195 442 per QALY gained. Similar results were obtained when other 5HT3 receptor antagonists are used. The use of aprepitant was associated with higher cost of drug but lower costs of emesis‐related management. With the cost‐effectiveness threshold set at the World Health Organization endorsed criteria of three times gross domestic product (GDP) per capita (three times GDP per capita in Hong Kong in 2011 is HKD 798 078), the current analyses showed that the aprepitant‐containing regimen was cost‐effective.ConclusionsIn patients undergoing HEC, the use of aprepitant as the anti‐emetic is cost‐effective in Hong Kong.