bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid metagenomic next-generation sequencing during an investigation of hospital-acquired human parainfluenza virus 3 infections
Authors: Greninger Alexander L. , Zerr Danielle M , Qin Xuan , Adler Amanda L. , Englund Janet A. , Jerome Keith R. 
Published: September 2016

AbstractMetagenomic next-generation sequencing (mNGS) is increasingly used for the unbiased detection of viruses, bacteria, fungi, and eukaryotic parasites in clinical samples. Whole genome sequencing (WGS) of clinical bacterial isolates has been shown to inform hospital infection prevention practices, but the use of this technology during potential respiratory virus outbreaks has not been taken advantage of. Here, we report on the use of mNGS to inform the real-time infection prevention response to a cluster of hospital-acquired human parainfluenza 3 virus (HPIV3) infections at a children’s hospital. Isolates from 3 patients with hospital-acquired HPIV3 identified over a 12-day period on a general medical unit and 10 temporally-associated isolates from patients with community-acquired of HPIV3 were analyzed. Our sample-to-sequencer time was <24 hours while our sample-to-answer turn-around time was <60 hours with a hands-on time of approximately 6 hours. Eight (2 case isolates and 6 control isolates) of 13 samples had sufficient sequencing coverage to yield whole genomes for HPIV3, while 10 (2 cases and 8 controls) of 13 samples gave partial genomes and all 13 samples had >1 read to HPIV3. Phylogenetic clustering revealed the presence of identical HPIV3 genomic sequence in the two of the cases with hospital-acquired infection, consistent with the concern for recent transmission within the medical unit. Adequate sequence coverage was not recovered for the third case. This work demonstrates the promise of mNGS to provide actionable information for infection control in addition to microbial detection.
Genome-wide reconstruction of complex structural variants using read clouds
Authors: Spies Noah , Weng Ziming , Bishara Alex , McDaniel Jennifer , Catoe David , Zook Justin M. , Salit Marc , West Robert B. , Batzoglou Serafim , Sidow Arend 
Published: September 2016

AbstractRecently developed methods that utilize partitioning of long genomic DNA fragments, and barcoding of shorter fragments derived from them, have succeeded in retaining long-range information in short sequencing reads. These so-called read cloud approaches represent a powerful, accurate, and cost-effective alternative to single-molecule long-read sequencing. We developed software, GROC-SVs, that takes advantage of read clouds for structural variant detection and assembly. We apply the method to two 10x Genomics data sets, one chromothriptic sarcoma with several spatially separated samples, and one breast cancer cell line, all Illumina-sequenced to high coverage. Comparison to short-fragment data from the same samples, and validation by mate-pair data from a subset of the sarcoma samples, demonstrate substantial improvement in specificity of breakpoint detection compared to short-fragment sequencing, at comparable sensitivity, and vice versa. The embedded longrange information also facilitates sequence assembly of a large fraction of the breakpoints; importantly, consecutive breakpoints that are closer than the average length of the input DNA molecules can be assembled together and their order and arrangement reconstructed, with some events exhibiting remarkable complexity. These features facilitated an analysis of the structural evolution of the sarcoma. In the chromothripsis, rearrangements occurred before copy number amplifications, and using the phylogenetic tree built from point mutation data we show that single nucleotide variants and structural variants are not correlated. We predict significant future advances in structural variant science using 10x data analyzed with GROC-SVs and other read cloud-specific methods.
Distributed representation of context by intrinsic subnetworks in prefrontal cortex
Authors: Waskom Michael L. , Wagner Anthony D. 
Published: September 2016

AbstractHuman prefrontal cortex supports flexible decision-making by representing abstract information about task context. The organizational basis of these context representations, and of representations underlying other higher-order processes, is unknown. Here, we use multivariate decoding and analyses of spontaneous correlations to show that context representations are distributed across subnetworks within prefrontal cortex. Examining targeted prefrontal regions, we found that pairs of voxels with similar context preferences exhibited spontaneous correlations that were approximately twice as large as those between pairs with opposite context preferences. This subnetwork organization was stable across task-engaged and resting states, suggesting that abstract context representations are constrained by an intrinsic functional architecture. These results reveal a principle of fine-scaled functional organization in association cortex.
Director trading, or lack thereof, and acquiring firm performance
Authors: Hossain Md Mosharraf , Heaney Richard Arthur , Koh SzeKee 
Published: September 2016

Purpose
This paper aims to address the question of whether acquiring firm directors trading, prior to a merger or acquisition (M&A) announcement, predicts the share market reaction on M&A announcement.

Design/methodology/approach
Event studies and cross-section regression were used in this analysis.

Findings
This paper finds that acquiring firms with no director trading and firms with net director purchases in the 12 months prior to the M&A announcement earn positive abnormal returns. It is also found that share market reaction to M&A announcements is considerably larger for acquiring firms whose directors do not trade relative to those companies with directors who do trade over the prior 12 months. This director non-trading result is further born out in regression analysis.

Research limitations/implications
The absence of pre-M&A announcement director trading could reflect lower agency costs for the acquiring firm and this might explain to stronger announcement day effect for this group of firms.

Practical implications
The fact that directors choose not to trade in their shares prior to a M&A transaction appears to be viewed as good news by the market.

Social implications
Director trading is value relevant for the acquiring firm and so it is critical that director trading is transparent.

Originality/value
To the best of the authors' knowledge, this question has not been addressed in the literature before, particularly the finding for firms with no director trading in the period prior to the M&A announcement.
Not just a pretty picture: visual literacy education through art for young children
Authors: Lopatovska Irene , Hatoum Sarah , Waterstraut Saebra , Novak Lisa , Sheer Sara 
Published: September 2016

Purpose
The purpose of this paper is to understand young children’s knowledge of visual literacy elements as well as their ability to comprehend newly introduced visual literacy concepts. The study also examined existing support for visual literacy programs from parents and educators.

Design/methodology/approach
The study explored the knowledge of basic visual literacy elements of young children enrolled in two private schools in the New York City metropolitan area. The authors interviewed 17 children, aged four to six years old, about fine art paintings using a semi-structured interview format. Children’s responses were qualitatively analyzed to determine their initial level of visual literacy and their ability to learn and retain the concepts of visual literacy after receiving basic instruction. The children’s educators and parents completed online questionnaires that were quantitatively analyzed to determine their level of support for visual literacy programs.

Findings
The findings show that young children exhibited extensive knowledge of simple visual literacy elements (color, shape, line), and limited understanding of more abstract elements (perspective and salience). Children’s knowledge of visual elements improved after instruction. Parents and educators expressed support for incorporating visual literacy instruction in early childhood education.

Research limitations/implications
The study relied on a sample of children and adults drawn from two private schools. The sample’s demographics might have affected study findings. More studies are needed using a larger and more diverse sample.

Practical implications
The study suggests that young children are ready to receive instruction on visual literacy elements using art images. Children reacted positively to the images and were engaged in the discussions about them, supporting the use of fine art paintings as an instrument to introduce visual literacy concepts to young children. Survey of children’s parents and teachers indicated strong interest in, and support for such programs.

Social implications
With the increase of visual information production and consumption, it is important to introduce visual literacy early in life. The study advances research in methods for developing visual literacy instruction for young children.

Originality/value
There are no previously reported studies that have examined pre-kindergarten children’s knowledge of basic visual literacy elements and reactions to visual literacy instruction.
Information seeking and searching strategies as plans and patterns of action
Authors: Savolainen Reijo 
Published: September 2016

PurposeThe purpose of this paper is to elaborate the picture of strategies for information searching and seeking by reviewing the conceptualizations on this topic in the field of library and information science (LIS).Design/methodology/approachThe study draws on Henry Mintzberg’s idea of strategy as plan and strategy as pattern in a stream of actions. Conceptual analysis of 57 LIS investigations was conducted to find out how researchers have approached the above aspects in the characterizations of information search and seeking strategies.FindingsIn the conceptualizations of information search and information seeking strategies, the aspect of strategy as plan is explicated most clearly in text-book approaches describing the steps of rational web searching. Most conceptualizations focus on the aspect of strategy as pattern in a stream of actions. This approach places the main emphasis on realized strategies, either deliberate or emergent. Deliberate strategies indicate how information search or information seeking processes were oriented by intentions that existed previously. Emergent strategies indicate how patterns in information seeking and seeking developed in the absence of intentions, or despite them.Research limitations/implicationsThe conceptualizations of the shifts in information seeking and searching strategies were excluded from the study. Similarly, conceptualizations of information search or information retrieval tactics were not examined.Originality/valueThe study pioneers by providing an in-depth analysis of the ways in which the key aspects of strategy are conceptualized in the classifications and typologies of information seeking and searching strategies. The findings contribute to the elaboration of the conceptual space of information behaviour research.
The impact of intellectual capital on start-up expectations
Authors: Matricano Diego 
Published: September 2016

PurposeAccording to an emerging research trend, which seeks to apply the concept of intellectual capital (IC) to the field of entrepreneurship, the purpose of this paper is to test whether IC can affect the start-up expectations of aspiring entrepreneurs.Design/methodology/approachBinary logistic regression models, based on empirical data derived from the Global Entrepreneurship Monitor website and referring to Italy over the years 2005-2010, are used to test the influence of IC (comprising human, structural and relational capital) on start-up expectations.FindingsBinary logistic regression models reveal robust results. Human, structural and relational capitals affect start-up expectations in Italy. Only in 2010 did structural capital fail to do so.Research limitations/implicationsThis study has three main limitations. The first concerns the need for further research to confirm the influence of IC on start-up expectations. The second concerns in-depth, more exhaustive analyses that cannot be carried out due to the use of second- hand data. The third deals with the reference only to Italy, over a limited time-span (2005-2010).Originality/valueTo the best knowledge of the author, this is one of the first empirical studies that investigate whether IC can affect start-up expectations. Results revealed by the regression models might steer other scholars’ interest toward this research path (linking IC and entrepreneurship) that has not yet been properly considered.
Towards environmental management accounting for trade-offs
Authors: Christ Katherine Leanne , Burritt Roger , Varsei Mohsen 
Published: September 2016

PurposeEnvironmental Management Accounting (EMA) information has become synonymous with win-win decision settings, but this paper aims to consider how EMA support can be extended to company managers who face the dynamics of win-wins and trade-offs.Design/methodology/approachBased on extant literature, the paper suggests an important extension of the use of EMA in support of management decision-making. The need for extended consideration and use of EMA to help overcome trade-offs is illustrated using the case of a wine bottling plant location decision by an Australian company in a global supply chain transporting wine from Australia to North America and Europe.FindingsResults confirm the need to add to the broader use of EMA to assist managers attempting to solve real world trade-off problems between economic performance, carbon equivalent emissions reduction and water risk reduction.Research limitations/implicationsGeneralisation of the single wine company case illustration to other companies and similar industry settings remains to be investigated.Practical implicationsTrade-offs are considered between economic benefit and two environmental performance matters of concern to the company, carbon equivalent emissions reduction and water risk reduction.Originality/valueThe paper introduces the notion of extending the use of EMA as a pragmatic way for managers to assess trade-off situations with environmental alternatives where no optimal solution is available. Value is added through the real case study of an Australian wine company.
Modelling effects of nonbreeders on population growth estimates
Authors: Lee Aline M. , Reid Jane M. , Beissinger Steven R. 
Published: September 2016

Summary

Adult individuals that do not breed in a given year occur in a wide range of natural populations. However, such nonbreeders are often ignored in theoretical and empirical population studies, limiting our knowledge of how nonbreeders affect realized and estimated population dynamics and potentially impeding projection of deterministic and stochastic population growth rates.

We present and analyse a general modelling framework for systems where breeders and nonbreeders differ in key demographic rates, incorporating different forms of nonbreeding, different life histories and frequency‐dependent effects of nonbreeders on demographic rates of breeders.

Comparisons of estimates of deterministic population growth rate, λ, and demographic variance, , from models with and without distinct nonbreeder classes show that models that do not explicitly incorporate nonbreeders give upwardly biased estimates of , particularly when the equilibrium ratio of nonbreeders to breeders, , is high. Estimates of λ from empirical observations of breeders only are substantially inflated when individuals frequently re‐enter the breeding population after periods of nonbreeding.

Sensitivity analyses of diverse parameterizations of our model framework, with and without negative frequency‐dependent effects of nonbreeders on breeder demographic rates, show how changes in demographic rates of breeders vs. nonbreeders differentially affect λ. In particular, λ is most sensitive to nonbreeder parameters in long‐lived species, when , and when individuals are unlikely to breed at several consecutive time steps.

Our results demonstrate that failing to account for nonbreeders in population studies can obscure low population growth rates that should cause management concern. Quantifying the size and demography of the nonbreeding section of populations and modelling appropriate demographic structuring is therefore essential to evaluate nonbreeders' influence on deterministic and stochastic population dynamics.
The emerging role of calmodulin regulation of RyR2 in controlling heart rhythm, the progression of heart failure and the antiarrhythmic action of dantrolene
Authors: Walweel Kafa , Oo Ye Win , Laver Derek R 
Published: September 2016

SummaryCardiac output and rhythm depend on the release and the take‐up of calcium from the sarcoplasmic reticulum (SR). Excessive diastolic calcium leak from the SR due to dysfunctional calcium release channels (RyR2) contributes to the formation of delayed after‐depolarizations, which underlie the fatal arrhythmias that occur in heart failure and inherited syndromes. Calmodulin (CaM) is a calcium‐binding protein that regulates target proteins and acts as a calcium sensor. CaM is comprised of two calcium‐binding EF‐hand domains and a flexible linker. CaM is an accessory protein that partially inhibits RyR2 channel activity. CaM is critical for normal cardiac function, and altered CaM binding and efficacy may contribute to defects in SR calcium release. The present paper reviews CaM binding to RyR2 and how it regulates RyR2 channel activity. It then goes on to review how mutations in the CaM amino acid sequence give rise to inherited syndromes such as Catecholaminergic Polymorphic Ventricular Tachychardia (CPVT) and long QT syndrome (LQTS). In addition, the role of reduced CaM binding to RyR2 that results from RyR2 phosphorylation or from oxidation of either RyR2 or CaM contributes to the progression of heart failure is reviewed. Finally, this manuscript reviews recent evidence that CaM binding to RyR2 is required for the inhibitory action of a pharmaceutical agent (dantrolene) on RyR2. Dantrolene is a clinically used muscle relaxant that has recently been found to exert antiarrhythmic effects against SR Ca2+ overload arrhythmias.
The impact of ovarian stimulation on the outcome of intrauterine insemination treatment: an analysis of 8893 cycles
Authors: Liu Jinyong , Li Tin‐Chiu , Wang Jing , Wang Wei , Hou Zhen , Liu Jiayin 
Published: September 2016

ObjectiveTo evaluate the impact of ovarian stimulation on the outcome of intrauterine insemination (IUI).DesignRetrospective analysis.SettingA single university‐based centre.PopulationA total of 5109 couples with 8893 cycles.MethodsThe outcome of IUI with different protocols for ovarian stimulation was examined.Main outcome measuresThe live birth rate (LBR), twin pregnancy rate and ovarian hyperstimulation syndrome (OHSS).ResultsIn ovulatory women without ovarian stimulation, the LBR was 7.6%. Stimulation with clomifene citrate (CC), letrozole (LE), human menopausal gonadotrophin (HMG), CC or LE combined with HMG achieved LBRs of 6.1, 5, 7.9, 8 and 12.2%, respectively. LE combined with HMG achieved a significantly improved LBR compared with no stimulation. HMG stimulation was associated with a higher rate of twins (7.4%) than no stimulation (0%, P < 0.01). In ovulatory women, the LBR appeared lower in CC and LE compared with no stimulation (P > 0.05). In anovulatory women, ovarian stimulation with CC, LE, HMG, CC or LE combined with HMG achieved LBRs of 11.3, 5.1, 11.8, 12.6 and 13.6%, respectively. No significant difference was observed. There were no triplet pregnancies or OHSS in stimulated cycles.ConclusionsIn ovulatory women, ovarian stimulation with LE combined with HMG achieved a significantly improved live birth rate. HMG stimulation resulted in a high risk for twins.Tweetable abstractIn ovulatory women, ovarian stimulation with letrozole and HMG resulted in a significantly improved LBR.
Trade law and alcohol regulation: what role for a global Alcohol Marketing Code?
Authors: Mitchell Andrew D. , Casben Jessica 
Published: September 2016

AbstractBackground and aimsFollowing calls for restrictions and bans on alcohol advertising, and in light of the tobacco industry's challenge to Australia's tobacco plain packaging measure, a tobacco control measure finding support in the World Health Organization (WHO) Framework Convention on Tobacco Control, this paper considers what role, if any, an international alcohol marketing code might have in preventing or reducing the risk of challenges to domestic alcohol marketing restrictions under trade rules.MethodsNarrative review of international trade and health instruments and international trade court judgements regarding alcohol products and marketing restrictions.FindingsThe experience of European trade courts in the litigation of similar measures suggests that World Trade Organization rules have sufficient flexibility to support the implementation of alcohol marketing restrictions. However, the experience also highlights the possibility that public health measures have disproportionate and unjustifiable trade effects and that the ability of a public health measure to withstand a challenge under trade rules will turn on its particular design and implementation.ConclusionMeasures implemented pursuant to international public health instruments are not immune to trade law challenges. Close collaboration between health policymakers, trade officials and lawyers, from as early as the research stage in the development of a measure to ensure a robust evidence base, will ensure the best chance of regulatory survival for an international marketing code.
Three‐dimensional culture system can induce expression of casein in immortalized bovine mammary epithelial cells
Authors: Zhan Kang , Lin Miao , Liu MingMei , Sui YangNan , Babekir Haitham Mohammed , Zhao GuoQi 
Published: September 2016

AbstractPrimary bovine mammary epithelial cells (BMECs) are not ideal models for long‐term studies of lactation mechanisms because these cells in a monolayer culture system cannot be polarized to simulate the physiological functions in vitro. We investigate the effects of different culture models and karyotypes on casein expression in a three‐dimensional (3D) culture system. The immortalized cells' karyotypes were analyzed at passages 10, 20, 30 and 40 to detect the effects of chromosome stability. Western blotting examined that whether or not the immortalized cells at passages 5, 10, 20, 30, 40 and 50 could induce expression of casein in a 3D culture system. The proper polarization of the acinar structures was monitored. BMECs were successfully immortalized. The cell karyotype at passage 30 remained at 60 chromosomes and the average value was 57.1 ± 0.40 after passage 40. The polarized protein's levels were up‐regulated in 3D culture compared to 2D culture. Expression of αs1, β and κ‐casein could be detectable in a passage range in 3D culture. Expression of αs2‐casein was undetectable in all experimental groups. However, all casein expressions were barely detectable in traditional 2D culture system. Therefore, 3D culture system is an important tool for the long‐term study of lactation mechanisms in vitro.