bluuebunny/crossref_metadata_2025 huggingface dataset:
Short template switch events explain mutation clusters in the human genome
Authors: Löytynoja Ari , Goldman Nick
Published: April 2017

Resequencing efforts are uncovering the extent of genetic variation in humans and provide data to study the evolutionary processes shaping our genome. One recurring puzzle in both intra- and inter-species studies is the high frequency of complex mutations comprising multiple nearby base substitutions or insertion-deletions. We devised a generalized mutation model of template switching during replication that extends existing models of genome rearrangement and used this to study the role of template switch events in the origin of short mutation clusters. Applied to the human genome, our model detects thousands of template switch events during the evolution of human and chimp from their common ancestor and hundreds of events between two independently sequenced human genomes. Although many of these are consistent with a template switch mechanism previously proposed for bacteria, our model also identifies new types of mutations that create short inversions, some flanked by paired inverted repeats. The local template switch process can create numerous complex mutation patterns, including hairpin loop structures, and explains multinucleotide mutations and compensatory substitutions without invoking positive selection, speculative mechanisms, or implausible coincidence. Clustered sequence differences are challenging for current mapping and variant calling methods, and we show that many erroneous variant annotations exist in human reference data. Local template switch events may have been neglected as an explanation for complex mutations because of biases in commonly used analyses. Incorporation of our model into reference-based analysis pipelines and comparisons of de novo assembled genomes will lead to improved understanding of genome variation and evolution.
Nonrandom domain organization of the Arabidopsis genome at the nuclear periphery
Authors: Bi Xiuli , Cheng Ying-Juan , Hu Bo , Ma Xiaoli , Wu Rui , Wang Jia-Wei , Liu Chang
Published: April 2017

The nuclear space is not a homogeneous biochemical environment. Many studies have demonstrated that the transcriptional activity of a gene is linked to its positioning within the nuclear space. Following the discovery of lamin-associated domains (LADs), which are transcriptionally repressed chromatin regions, the nonrandom positioning of chromatin at the nuclear periphery and its biological relevance have been studied extensively in animals. However, it remains unknown whether comparable chromatin organizations exist in plants. Here, using a strategy using restriction enzyme–mediated chromatin immunoprecipitation, we present genome-wide identification of nonrandom domain organization of chromatin at the peripheral zone of Arabidopsis thaliana nuclei. We show that in various tissues, 10%–20% of the regions on the chromosome arms are anchored at the nuclear periphery, and these regions largely overlap between different tissues. Unlike LADs in animals, the identified domains in plants are not gene-poor or A/T-rich. These domains are enriched with silenced protein-coding genes, transposable element genes, and heterochromatic marks, which collectively define a repressed environment. In addition, these domains strongly correlate with our genome-wide chromatin interaction data set (Hi-C) by largely explaining the patterns of chromatin compartments, revealed on Hi-C maps. Moreover, our results reveal a spatial compartment of different DNA methylation pathways that regulate silencing of transposable elements, where the CHH methylation of transposable elements located at the nuclear periphery and in the interior are preferentially mediated by CMT2 and DRM methyltransferases, respectively. Taken together, the results demonstrate functional partitioning of the Arabidopsis genome in the nuclear space.
Transverse gradient in Apple-type undulators
Authors: Calvi M. , Camenzuli C. , Prat E. , Schmidt Th.
Published: April 2017

Apple-type undulators are globally recognized as the most flexible devices for the production of variable polarized light in the soft X-ray regime, both at synchrotron and free-electron laser facilities. Recently, the implementation of transverse gradient undulators has been proposed to enhance the performance of new generation light sources. In this paper it is demonstrated that Apple undulators do not only generate linear and elliptical polarized light but also variable transverse gradient under certain conditions. A general theoretical framework is introduced to evaluate the K-value and its transverse gradient for an Apple undulator, and formulas for all regular operational modes and different Apple types (including the most recent Delta type and Apple X) are calculated and critically discussed.
5-Hydroxy-2-phenyl-7-(prop-2-yn-1-yloxy)-4H-chromen-4-one
Authors: Yang Fan , Li Yang , Zhou Shu-Jing
Published: April 2017

In the title compound, C18H12O4, the essentially planar chromenone ring system [the maximum deviation = 0.016 (2) Å] is nearly co-planar with the phenyl ring [dihedral angle = 3.85 (8)°]. An intramolecular O—H...O hydrogen bond occurs. In the crystal, weak C—H...O hydrogen bonds and π–π stacking interactions link the molecules into a three-dimensional supramolecular network.
(Benzylthiolato-κS)phenylmercury(II)
Authors: Nath Paras , Bharty Manoj K. , Gupta Sushil K. , Butcher Ray J. , Jasinski Jerry P.
Published: April 2017

The title complex, [Hg(C6H5)(C7H7S)], was synthesized from benzyl 4-methylpiperidine-1-carbodithioate. In the complex, the HgIIcation binds to a C atom of a phenyl ring and the S atom of a benzylthiolate ligand in a linear coordination geometry. The molecule is bent at the methylene C atom and the S atom, resulting in asynconformation with respect to the benzyl and phenyl rings. The dihedral angle between the phenyl and benzyl rings is 64.6 (2)°. The crystal structure is stabilized by intermolecular Hg...S [3.290 (3) Å] contacts and C—H...π interactions, generating a three-dimensional network.
4-[(1H-Imidazol-1-yl)methyl]-1-(4-nitrobenzyl)-1H-1,2,3-triazole
Authors: Sahbi Azzeddine , Mague Joel T. , Ben-Tama Abdeslem , El Hadrami El Mestafa , Gaamoussi Issam , Ouzidan Younes
Published: April 2017

The title molecule, C13H12N6O2, adopts a slightly twisted zigzag conformation in the crystal, with the dihedral angles between the central triazole ring and the 4-nitrophenyl and imidazole rings being 79.81 (11) and 81.21 (13)°, respectively. The packing features weak C—H...O and C—H...N hydrogen bonds, as well as unusual N=O...π stacking interactions.
4-{[5-Methyl-2-(propan-2-yl)phenoxy]methyl}-1-(4-nitrobenzyl)-1H-1,2,3-triazole
Authors: Sahbi Azzeddine , Mague Joel T. , Ben-Tama Abdeslem , El Hadrami El Mestafa , El Aroussi Fatima , Ouzidan Younes
Published: April 2017

The asymmetric unit of the title compound, C20H22N4O3, comprises two independent molecules (AandB) with markedly different conformations as the C—H bonds of the imidazole rings point in opposite directions. In the crystal, C—H...N hydrogen bonds form chains of molecules extending along theb-axis direction, while C—H...O hydrogen bonds form zigzag chains alonga. Additional intermolecular N...; O...π(ring) contacts form parallel chains of like molecules alonga. The structure was refined as a two-component twin.
Linking disaster risk reduction, climate change, and the sustainable development goals
Authors: Kelman Ilan
Published: April 2017

Purpose

The purpose of this paper is to better link the parallel processes yielding international agreements on climate change, disaster risk reduction, and sustainable development.

Design/methodology/approach

This paper explores how the Paris Agreement for climate change relates to disaster risk reduction and sustainable development, demonstrating too much separation amongst the topics. A resolution is provided through placing climate change within wider disaster risk reduction and sustainable development contexts.

Findings

No reason exists for climate change to be separated from wider disaster risk reduction and sustainable development processes.

Research limitations/implications

Based on the research, a conceptual approach for policy and practice is provided. Due to entrenched territory, the research approach is unlikely to be implemented.

Originality/value

Using a scientific basis to propose an ending for the silos separating international processes for climate change, disaster risk reduction, and sustainable development.
First responder well-being following the 2011 Canterbury earthquake
Authors: Shepherd Daniel , McBride David , Lovelock Kirsten
Published: April 2017

Purpose

The role of first responders in mitigating the effects of earthquakes is vital. Unlike other disasters, earthquakes are not single events, and exposure to dangerous and trauma-inducing events may be ongoing. Understanding how first responders cope in the face of such conditions is important, for both their own well-being as well as the general public whom they serve. The paper aims to discuss these issues.

Design/methodology/approach

Using questionnaires, this study measured posttraumatic stress disorder (PTSD), psychological resilience, and reactive coping styles in a sample of first responders active during the 2011 Canterbury earthquake in New Zealand.

Findings

The prevalence of PTSD was similar to that reported in the literature. Psychological resilience, but not disaster exposure, was found to be associated with PTSD. Maladaptive coping strategies best predicted resiliency, but there were significant gender differences.

Originality/value

These findings can inform those managing first responder disaster workers through the consideration of preventive and treatment interventions.
Academic entrepreneurial intention: the role of gender
Authors: Miranda F. Javier , Chamorro-Mera Antonio , Rubio Sergio , Pérez-Mayo Jesús
Published: April 2017

Purpose

The purpose of this study is firstly to analyze whether the determining factors of the entrepreneurial intention of academics are the same for men and women and test whether their degree of importance varies depending on gender, and secondly to test whether the lesser entrepreneurial intention of women detected in previous studies is because of the lesser presence of the determining factors of entrepreneurial intention among women or, on the contrary, is determined by the existence of implicit barriers that do not depend on these factors.

Design/methodology/approach

After conducting a survey on a sample of 1,178 academics, the results of a linear regression model confirm the hypothesis that female academics have less of an entrepreneurial intention.

Findings

Moreover, through the Blinder–Oaxaca decomposition, it is observed that this lesser female entrepreneurial behavior is not because of the absence of any of the factors considered as determinants of entrepreneurial intention, but instead is related to the existence of implicit barriers for women that influence their entrepreneurial intention.

Originality/value

To the best of the authors’ knowledge, this is the first time that a study of this nature has been conducted internationally. Unlike other studies on academic entrepreneurship, the authors do not restrict the sample to one or two universities but rather aim the study at all universities in Spain and, therefore, at all academics from all branches of knowledge.
Factors affecting health tourism and international health-care facility choice
Authors: Aydin Gökhan , Karamehmet Bilge
Published: April 2017

Purpose

Health-care tourism has become a major industry in the past decade. Following the increasing activity in health-care tourism, the decision-making process of consumers in choosing an international health-care facility has become increasingly important to the related parties. The present study aims to offer a holistic model of international health-care facility choice that incorporates the important dimensions by assessing the growth drivers and the alternative factors proposed in the literature and by validating them via a survey study.

Design/methodology/approach

The factors deemed important in the existing literature were used as the basis of a study in Turkey. In total, 65 structured interviews were conducted with health-care professionals and international health tourists to understand the perspective of the two important parties that affect policymaking.

Findings

The findings of the study support the significance of the majority of the variables proposed as important factors affecting international health-care facility choice.

Research limitations/implications

The study was carried out in four large hospital chains in Turkey; however, this creates a limitation in scope and may have limited representativeness of the overall market. The model has yet to be tested on a larger scale.

Practical implications

There are significant differences in the opinions of professionals and international health-care tourists in terms of choice criteria. This indicates problems with health professionals’ understanding of the consumer decision process.

Originality/value

The study provides a model that can be used to gain insights on the consumer decision process and also provides the policymakers and stakeholders of the international health-care industry with a sound theoretical foundation to build further studies upon. Only a limited number of studies was carried out in Turkey that focus on international health-care tourism, and the present study will fill a substantial research gap.
Factors influencing the choice of private and public hospitals: empirical evidence from Ghana
Authors: Bamfo Bylon Abeeku , Dogbe Courage Simon Kofi
Published: April 2017

Purpose

The study aims to examine the factors influencing the choice of private and public hospitals in Ghana.

Design/methodology/approach

Purposive and convenient sampling techniques were used in selection of 225 respondents for the study. An independent samples t-test was used in ascertaining the significant difference in the opinions of both groups. Finally, binary logistics regression was used in ascertaining the factors that significantly influenced the choice of hospitals in Ghana.

Findings

In Ghana, patients’ choice of private or public hospital was significantly influenced by service quality, word-of-mouth, type of ailment and National Health Insurance Scheme (NHIS). Patients who made choice decision based on service quality were more likely to attend a private hospital. Word-of-mouth influenced the choice of public hospitals more than private hospitals. Patients preferred visiting public hospitals for more complicated ailments such as spinal defects, HIV/AIDS, heart-related problems, etc. Patients registered under the NHIS also preferred visiting public hospital to private hospital. Although services from private hospitals were more expensive, patients were more satisfied with services provided, as compared to patients from the public hospital. Cost of service and patient satisfaction, however, did not have a statistically significant effect on the choice of hospital.

Originality/value

Most comparative studies done on private and public hospitals studied in isolation focused on service quality, customer satisfaction, national health insurance and cost of health care or a combination of them. This study, however, considered all these selection criteria and extended it by adding word-of-mouth and the type of ailments suffered. The study, thus, provided a more comprehensive hospital selection criteria. The use of logistics regression in this particular area of study was also quite unique.
2016 top trends and issues in Jamaican academic libraries
Authors: Harris Sasekea
Published: April 2017

Purpose

Biennially, the Association of College & Research Libraries (ACRL), a division of the American Library Association, publishes a report on the top trends and issues affecting academic libraries in higher education. Harris (2016) used the trends and issues reported by the ACRL to inform a document and thematic analysis of publications written on Jamaican academic librarianship 2010-2016, to investigate the trends and issues in Jamaican academic librarianship. Harris’ (2016) paper however noted that a survey of the chief librarian in each library, regarding their perceptions of the trends and issues would be a useful follow-up to her study, and cited this as a limitation/implication of her paper. The purpose of this paper is to address the above limitation and is therefore the follow-up to Harris’ (2016) paper.

Design/methodology/approach

The chief librarians in five of the six local university libraries were surveyed to provide insights into the trends and issues in Jamaican academic libraries at the university level.

Findings

Acquisitions, budget, staffing, communicating value, digital preservation and curation, mobile environment, collaboration, scholarly communication, information technology, space, higher education, user behaviour and expectations and information literacy are the top trends and issues in Jamaican academic libraries at the university level.

Research limitations/implications

This survey seeks to complement rather than contest Harris’ (2016) research. Perhaps a useful follow-up to both papers would be biennial updates. Additionally, a survey of the trends and issues in all types of academic libraries throughout the English-speaking Caribbean would be a useful follow-up.

Originality/value

This paper is of value, as it is the first survey of trends and issues in Jamaican academic librarianship. It enriches the existing document and thematic analytical research on trends and issues in Jamaican academic libraries by adding an empirical component. It also increases the number of publications, on trends and issues in Jamaican academic librarianship, from one to two, and allows voices from the English-speaking Caribbean (Jamaica) to be incorporated into the literature dedicated to trends and issues in academic libraries.
An assessment of the information needs and information-seeking behaviour of Members of Parliament (MPs) in Bangladesh
Authors: Hossain Md Uzzal , Hossain Md Arman , Islam Md Shariful
Published: April 2017

Purpose

The purpose of this paper is to assess the information needs and information-seeking behaviour of Members of Parliament (MPs) in Bangladesh. It aimed at determining the information sources, preferred information format, frequency of seeking information and access to information and communication technology and online information services by the MPs. The study also intended to assess the role of parliament library for satisfying the information needs of the MPs.

Design/methodology/approach

A survey method was adopted for data collection; the respondents were interviewed by the researchers with the guidance of a structured questionnaire. The questionnaire was read out for the respondents and filled up by the interviewers based on the answers they received. Fifty MPs were selected for the study using simple random sampling. The data were analysed with the help of weighted mean.

Findings

The study found that the MPs mainly seek information to make a parliamentary request/inquiry, to make a speech and to make a decision. The most important sources of information were minutes of sessions, mass media, personal letters and information networks; and they preferred printed formats rather than online documents. The result also showed that only a few MPs were aware of the information services provided by the parliament library and were satisfied with the services they received.

Originality/value

There has been no study carried out on the information needs and information-seeking behaviour of MPs in Bangladesh prior to this research. The study will help the policymakers to improve the library services for MPs in Bangladesh.
Internet attacks and intrusion detection system
Authors: Singh Raman , Kumar Harish , Singla Ravinder Kumar , Ketti Ramachandran Ramkumar
Published: April 2017

Purpose

The paper addresses various cyber threats and their effects on the internet. A review of the literature on intrusion detection systems (IDSs) as a means of mitigating internet attacks is presented, and gaps in the research are identified. The purpose of this paper is to identify the limitations of the current research and presents future directions for intrusion/malware detection research.

Design/methodology/approach

The paper presents a review of the research literature on IDSs, prior to identifying research gaps and limitations and suggesting future directions.

Findings

The popularity of the internet makes it vulnerable against various cyber-attacks. Ongoing research on intrusion detection methods aims to overcome the limitations of earlier approaches to internet security. However, findings from the literature review indicate a number of different limitations of existing techniques: poor accuracy, high detection time, and low flexibility in detecting zero-day attacks.

Originality/value

This paper provides a review of major issues in intrusion detection approaches. On the basis of a systematic and detailed review of the literature, various research limitations are discovered. Clear and concise directions for future research are provided.
Twenty years of readership of library and information science literature under Mendeley’s microscope
Authors: Pooladian Aida , Borrego Ángel
Published: April 2017

Purpose

Altmetric indicators have been proposed as a complement to citation counts in research evaluation. Conceivably, they might also be used to supplement other methods for estimating journal readership. The purpose of this paper is to explore the use of Mendeley reference management software to characterize the features of the readership of library and information science (LIS) literature.

Design/methodology/approach

The authors used the Social Sciences Citation Index to retrieve 54,655 articles and reviews published between 1995 and 2014 and indexed in the category “Information Science & Library Science”. Each record was then searched in Mendeley to obtain the number of bookmarks of the paper and the academic status of the users.

Findings

Mendeley covers 61 per cent of the LIS literature published in the last 20 years. In all, 75 per cent of the papers published in the last five years had been bookmarked at least once in Mendeley whereas just 55 per cent had been cited in Web of Science. Reviews are bookmarked more frequently than articles, and papers in English have more bookmarks than papers in any other language. Most users of LIS literature are PhD and postgraduate students.

Originality/value

The study shows that altmetrics can be used as a source of data in information behaviour studies. Reference management software provides an unobtrusive means of capturing reading habits in the scholarly literature. Compared to citation counts, bookmarks are rapidly available and also reflect usage outside the academic community.
Principles to guide reliable and ethical research evaluation using metric-based indicators of impact
Authors: Webster Berenika M.
Published: April 2017

Purpose

The purpose of this paper is to summarize and provide context to the recently published Leiden Manifesto, a document written by leading bibliometric researchers, which proposes ten principles that should guide the use of bibliometric tools and indicators in research evaluation.

Design/methodology/approach

This paper is an opinion piece based on the Leiden Manifesto.

Findings

This paper addresses the phenomenon of increasing provision of bibliometric services by research university libraries and argues that their mission should be to advocate the responsible use of bibliometric methods for research evaluation in their institutions, in line with Leiden Manifesto principles.

Originality/value

This is an original piece.
An altmetric analysis of ResearchGate profiles of physics researchers
Authors: Shrivastava Rishabh , Mahajan Preeti
Published: April 2017

Purpose

The purpose of this paper is to carry out an altmetric analysis of faculty members and research scholars of Department of Physics and Astrophysics, University of Delhi (India) (Univ.Delhi P&A) who are members of the academic social networking site ResearchGate. ReserachGate is a rich source of altmetric indictors such as publications, reads, profile views, citations, impact points, RGScore, followers and following, etc. The RGScore, unique to ResearchGate, was further explored in depth in the study.

Design/methodology/approach

The data were collected manually by visiting the profile pages of all the members who had an account in ResearchGate under Univ.Delhi P&A during the first week of July, 2016. The authors found a total of 173 members in ResearchGate from the department. Data were collected for publications, reads, profile views, citations, impact points, RGScore, followers and following from the profile pages of the members. Correlations were calculated amongst the metrics provided by ResearchGate to seek the nature of the relationship amongst the various ResearchGate metrics.

Findings

The analysis revealed that the publications added by researchers to their profiles were relatively low, as 28.32 per cent of the members had not added even a single publication to their profiles. Average reads acquired per person was found to be 909.49 and the median value of reads was found to be 95. Average citation per member in ResearchGate was found to be 414.60 and the median value was found to be 7. Majority of the researchers (45.09 per cent) had impact points in the range of 0.2-50. Most of the members (35.84 per cent) had followers in the range of 1-10. Majority of the members (52.02 per cent) had profile views in the range of 1-100. Most of the members (26.01 per cent) had RGScore equivalent to 0.01. The highest correlation of RGScore was found with publications added by researchers to their profiles, followed by correlation between RGScore and reads, correlation between RGscore and profile views, correlation between RGScore and number of Full Texts and correlation between RGScore and number of followers of a researcher.

Originality/value

Not much research has been conducted in the area of altmetrics, especially using ResearchGate as a source of altmetrics. The findings of the study help in understanding the validity of ResearchGate as a source of altmetrics for research evaluation in a developing country such as India. Also, the novel ResearchGate indicator RGScore has been evaluated in great depth and its relationship with other ResearchGate altmetric and bibliometric indicators has been established.
Supporting the research feedback loop
Authors: Tattersall Andy
Published: April 2017

Purpose

The purpose of this paper is to explore the opportunities altmetrics offer to library and information professionals as part of their research support provision. This paper examines what altmetrics are and how they can offer another useful metric to help academics engage with a variety of interested parties over the web.

Design/methodology/approach

The paper considers the emergence of altmetrics as a research measurement and scholarly communication tool and the impact on academic libraries. It also identifies existing metrics and explores their shortcomings as well as how these can be bridged by altmetrics.

Findings

Altmetrics offer a wealth of opportunities for library and information professionals to make better strategic decisions, explore their own institution’s research output and provide scholarly communications intelligence to their research community.

Originality/value

The value in this paper lies in encouraging academic librarians and information professionals to explore altmetrics for themselves and align any new knowledge with existing services and skills, in particular around metrics and digital media.
Defining community recommended practice for altmetrics
Authors: Carpenter Todd A. , Lagace Nettie M.
Published: April 2017

Purpose

In 2013, the National Information Standards Organization launched a three-year project to identify areas of potential community consensus around these new metrics and then develop recommended practices in those areas. The paper aims to discuss these issues.

Design/methodology/approach

After collecting community input on potential activities, NISO surveyed the community to prioritize five areas of work around which to develop community consensus.

Findings

The NISO Working Groups produced a set of recommended practices that included: definitions and use cases for alternative metrics, applications of metrics for non-traditional scholarly outputs, collections of persistent identifiers around which metrics can be built, and a Code of Conduct for metrics providers.

Originality/value

The development of standards and recommended practices around altmetrics will encourage adoption of these new metrics forms and will add to the trust in those metrics for the academy.
A model‐based data‐driven dictionary learning for seismic data representation
Authors: Yarman Can Evren , Kumar Rajiv , Rickett James
Published: April 2017

Planar waves events recorded in a seismic array can be represented as lines in the Fourier domain. However, in the real world, seismic events usually have curvature or amplitude variability, which means that their Fourier transforms are no longer strictly linear but rather occupy conic regions of the Fourier domain that are narrow at low frequencies but broaden at high frequencies where the effect of curvature becomes more pronounced. One can consider these regions as localised “signal cones”. In this work, we consider a space–time variable signal cone to model the seismic data. The variability of the signal cone is obtained through scaling, slanting, and translation of the kernel for cone‐limited (C‐limited) functions (functions whose Fourier transform lives within a cone) or C‐Gaussian function (a multivariate function whose Fourier transform decays exponentially with respect to slowness and frequency), which constitutes our dictionary. We find a discrete number of scaling, slanting, and translation parameters from a continuum by optimally matching the data. This is a non‐linear optimisation problem, which we address by a fixed‐point method that utilises a variable projection method with ℓ1 constraints on the linear parameters and bound constraints on the non‐linear parameters. We observe that slow decay and oscillatory behaviour of the kernel for C‐limited functions constitute bottlenecks for the optimisation problem, which we partially overcome by the C‐Gaussian function. We demonstrate our method through an interpolation example. We present the interpolation result using the estimated parameters obtained from the proposed method and compare it with those obtained using sparsity‐promoting curvelet decomposition, matching pursuit Fourier interpolation, and sparsity‐promoting plane‐wave decomposition methods.
A real‐time PCR assay for improved rapid, specific detection of Cryphonectria parasitica
Authors: Rubio S. , Barnes A. , Webb K. , Hodgetts J.
Published: April 2017

Cryphonectria parasitica, an ascomycete fungus, is the causal agent of chestnut blight. This highly destructive disease of chestnut trees causes significant losses, and is therefore a regulated pathogen in Europe. Existing methods for the detection of C. parasitica include morphological identification following culturing, or PCR; however, these are time‐consuming resulting in delays to diagnosis. To allow improved detection, a new specific real‐time PCR assay was designed to detect C. parasitica directly from plant material and fungal cultures, and was validated according to the European Plant Protection Organisation (EPPO) standard PM 7/98. The analytical specificity of the assay was tested extensively using a panel of species taxonomically closely related to Cryphonectria, fungal species associated with the hosts and healthy plant material. The assay was found to be specific to C. parasitica, whilst the analytical sensitivity of the assay was established as 2 pg µL−1 of DNA. Comparative testing of 63 samples of naturally infected plant material by the newly developed assay and traditional morphological diagnosis demonstrated an increased diagnostic sensitivity when using the real‐time PCR assay. Furthermore the assay is able to detect both virulent and hypovirulent strains of C. parasitica. Therefore the new real‐time PCR assay can be used to provide reliable, rapid, specific detection of C. parasitica to prevent the accidental movement of the disease and to monitor its spread.
Further evidence on mandatory partner rotation and audit pricing: a supply‐side perspective
Authors: Ferguson Andrew , Lam Peter , Ma Nelson
Published: April 2017

This study examines effects of mandatory partner rotation (MPR) on audit fees of Australian‐listed companies. Using a fee changes approach, evidence of fee increases in year of the MPR driven by smaller offices of non‐Big 4 auditors is found, consistent with supply‐side resource constraint arguments. Broadly consistent findings are observed using a fee levels approach. Appointment of inexperienced partners to MPR engagements has no discernible effect on fees. Additional analysis of audit reporting lag indicates fee increases reflect additional audit effort as opposed to a pricing strategy. Overall, the evidence supports recent moves by policy‐makers to soften MPR requirements.
The ‘cognitive footprint’ of psychiatric and neurological conditions: cross‐sectional study in the UK Biobank cohort
Authors: Cullen B. , Smith D. J. , Deary I. J. , Evans J. J. , Pell J. P.
Published: April 2017

Objective

We aimed to quantify the prevalence of cognitive impairment in adults with a history of mood disorder, schizophrenia, multiple sclerosis or Parkinson's disease, within a large general population cohort.

Method

Cross‐sectional study using UK Biobank data (n = 502 642). Psychiatric and neurological exposure status was ascertained via self‐reported diagnoses, hospital records and questionnaires. Impairment on reasoning, reaction time and memory tests was defined with reference to a single unexposed comparison group. Results were standardised for age and gender. Sensitivity analyses examined the influence of comorbidity, education, information sources and missing data.

Results

Relative to the unexposed group, cognitive impairment was least common in major depression (standardised prevalence ratios across tests = 1.00 [95% CI 0.98, 1.02] to 1.49 [95% CI 1.24, 1.79]) and most common in schizophrenia (1.89 [95% CI 1.47, 2.42] to 3.92 [95% CI 2.34, 6.57]). Prevalence in mania/bipolar was similar to that in multiple sclerosis and Parkinson's disease. Estimated population attributable prevalence of cognitive impairment was higher for major depression (256 per 100 000 [95% CI 130, 381]) than for all other disorders.

Conclusion

Although the relative prevalence of cognitive impairment was lowest in major depression, the population attributable prevalence was highest overall for this group.
Diagnostic tools in ocular allergy
Authors: Leonardi A. , Doan S. , Fauquert J. L. , Bozkurt B. , Allegri P. , Marmouz F. , Rondon C. , Jedrzejczak M. , Hellings P. , Delgado L. , Calder V.
Published: April 2017

Ocular allergy (OA) includes a group of common and less frequent hypersensitivity disorders frequently misdiagnosed and not properly managed. The diagnosis of OA is usually based on clinical history and signs and symptoms, with the support of in vivo and in vitro tests when identification of the specific allergen is required. To date, no specific test is available for the diagnosis of the whole spectrum of the different forms of OA. The lack of recommendations on diagnosis of OA is considered a medical need not only for allergists but also for ophthalmologists. This position paper aims to provide a comprehensive overview of the currently available tools for diagnosing OA to promote a common nomenclature and procedures to be used by different specialists. Questionnaires, sign and symptom grading scales, tests, and potential biomarkers for OA are reviewed. We also identified several unmet needs in the diagnostic tools to generate interest, increase understanding, and inspire further investigations. Tools, recommendations, and algorithms for the diagnosis of OA are proposed for use by both allergists and ophthalmologists. Several unmet needs in the diagnostic tools should be further improved by specific clinical research in OA.
Laparoscopic versus open resection for transverse and descending colon cancer: Short‐term and long‐term outcomes of a multicenter retrospective study of 1830 patients
Authors: Yamaguchi Shigeki , Tashiro Jo , Araki Ryuichiro , Okuda Junji , Hanai Tsunekazu , Otsuka Koki , Saito Shuji , Watanabe Masahiko , Sugihara Kenichi
Published: April 2017

Introduction

Previous randomized controlled trials demonstrated similar oncological outcomes between laparoscopic and open colectomies, except for cases involving transverse colon and splenic flexure colon cancer. The objective of this study was to confirm the oncological safety and advantages of the short‐term results of laparoscopic surgery for transverse and descending colon cancer in comparison with open surgery.

Methods

The study data were retrospectively collected from the databases of 45 hospitals. Patients with transverse or descending colon cancer who underwent laparoscopic or open R0 resection were registered. The primary end‐points were the 3‐year overall survival and relapse‐free survival rates according to pathological stage. The secondary end‐points were the short‐term results, including blood loss, operative time, diet intake, hospital stay, and postoperative complications.

Results

Of the 1830 eligible patients, 872 underwent open colectomy and 958 underwent laparoscopic colectomy. The median follow‐up period was 38.4 months. The conversion rate to open resection was 4.5%. The 3‐year overall survival rate of the laparoscopic group was significantly higher than that of the open group for stage I patients (96.2% vs 99.2%; P = 0.04); it was also higher for stage II (94.0% vs 95.5%) and stage III (87.4% vs 90.2%) patients, but there were no significant differences. The 3‐year relapse‐free survival rate of the laparoscopic group was significantly higher than that of the open group for stage I patients; there were no differences between the open and laparoscopic groups among the stage II and III patients. In the multivariate analyses, laparoscopic resection was a significant factor in relapse‐free survival. Laparoscopic patients had significantly lower blood loss and a significantly longer operative time than the open groups. Also, postoperative hospital stay was significantly shorter and postoperative morbidity was significantly lower in the laparoscopic group.

Conclusion

Although this retrospective study has limitations, we can conclude that laparoscopic surgery for transverse and descending colon cancer is oncologically safe and yields better short‐term results than open surgery.
Large scale studies assessing anti‐factor VIII antibody development in previously untreated haemophilia A: what has been learned, what to believe and how to learn more
Authors: Iorio Alfonso , Fischer Kathelijn , Makris Michael
Published: April 2017

Minimizing the risk of inhibitor development by acting on modifiable risk factors remains a sensible goal for treatment optimization in haemophilia A. By critically appraising published studies assessing inhibitor development, this review addresses the role of studies in previously untreated patients (PUPs) for establishing the immunogenicity of new concentrates, suggest novel research design to be adopted in future studies and discuss clinical practice implications of the reported differential immunogenicity of Kogenate Bayer and Advate factor VIII concentrates. Three considerations are relevant here: (i) all of the existing concentrates, when tested following the International Society on Thrombosis and Haemostasis Scientific and Standardization Committee recommendation, were shown to be safe; as a consequence, (ii) when considering using any newly introduced product, one should be aware that it could, in future, turn out to be as immunogenic as Kogenate Bayer, and (iii) at the population level, it might be wiser not to use Kogenate Bayer in PUPs, if the choice is against Advate. When presenting the risk of developing inhibitors to the individual patient (or their family), the message remains that the risk can be as high as 40%, without any efficient instrument to predict individual inhibitor risk. Patients should be invited to enrol into a randomized registry trial, including random assignment to trials with new investigational products.
Aberrant intracellular metabolism of T‐DM1 confers T‐DM1 resistance in human epidermal growth factor receptor 2‐positive gastric cancer cells
Authors: Wang Hongbin , Wang Wenqian , Xu Yongping , Yang Yong , Chen Xiaoyan , Quan Haitian , Lou Liguang
Published: April 2017

Trastuzumab emtansine (T‐DM1), an antibody–drug conjugate (ADC) consisting of human epidermal growth factor receptor 2 (HER2)‐targeted mAb trastuzumab linked to antimicrotubule agent mertansine (DM1), has been approved for the treatment of HER2‐positive metastatic breast cancer. Acquired resistance has been a major obstacle to T‐DM1 treatment, and mechanisms remain incompletely understood. In the present study, we established a T‐DM1‐resistant N87‐KR cell line from HER2‐positive N87 gastric cancer cells to investigate mechanisms of acquired resistance and develop strategies for overcoming it. Although the kinetics of binding, internalization, and externalization of T‐DM1 were the same in N87‐KR cells and N87 cells, N87‐KR was strongly resistant to T‐DM1, but remained sensitive to both trastuzumab and DM1. T‐DM1 failed to inhibit microtubule polymerization in N87‐KR cells. Consistently, lysine‐MCC‐DM1, the active T‐DM1 metabolite that inhibits microtubule polymerization, accumulated much less in N87‐KR cells than in N87 cells. Furthermore, lysosome acidification, achieved by vacuolar H+‐ATPase (V‐ATPase), was much diminished in N87‐KR cells. Notably, treatment of sensitive N87 cells with the V‐ATPase selective inhibitor bafilomycin A1 induced T‐DM1 resistance, suggesting that aberrant V‐ATPase activity decreases T‐DM1 metabolism, leading to T‐DM1 resistance in N87‐KR cells. Interestingly, HER2‐targeted ADCs containing a protease‐cleavable linker, such as hertuzumab‐vc‐monomethyl auristatin E, were capable of efficiently overcoming this resistance. Our results show for the first time that a decrease in T‐DM1 metabolites induced by aberrant V‐ATPase activity contributes to T‐DM1 resistance, which could be overcome by HER2‐targeted ADCs containing different linkers, including a protease‐cleavable linker. Accordingly, we propose that V‐ATPase activity in lysosomes is a novel biomarker for predicting T‐DM1 resistance.
The effect of chrysin‐loaded nanofiber on wound healing process in male rat
Authors: Mohammadi Zoheyr , Sharif Zak Mohsen , Majdi Hasan , Seidi Khaled , Barati Meisam , Akbarzadeh Abolfazl , Latifi Ali Mohammad
Published: April 2017

Wound healing is an inflammatory process. Chrysin, a natural flavonoid found in honey, has been recently investigated to have anti‐inflammatory and antioxidant effects. In this work, the effects of chrysin‐loaded nanofiber on the expressions of genes that are related to wound healing process such as P53, TIMPs, MMPs, iNOS, and IL‐6 in an animal model study were evaluated. The electrospinning method was used for preparation the different concentrations of chrysin‐loaded PCL‐PEG nanofiber (5%, 10%, and 20% [w/w]) and characterized by FTIR and SEM. The wound healing effects of chrysin‐loaded PCL‐PEG nanofiber were in vivo investigated in rats, and the expressions of genes related to wound healing process were evaluated by real‐time PCR. The study results showed chrysin‐loaded PLC‐PEG compared to chrysin ointment and control groups significantly increase IL‐6, MMP‐2, MMP‐8, MMP‐9, TIMP‐1, and TIMP‐2 (p < .05). On the other hand, nanofibers containing chrysin significantly decreased p53 and iNOS expression compared to chrysin ointment and control groups (p < .05). According to the results, chrysin‐loaded PCL‐PEG‐PCL nanofibers have positive effects on the expression of the genes that have pivotal role in wound healing.
Exploring the RNA‐bound and RNA‐free human Argonaute‐2 by molecular dynamics simulation method
Authors: Kong Ren , Xu Lei , Piao Lianhua , Zhang Dawei , Hou Ting‐Jun , Chang Shan
Published: April 2017

Argonaute 2 (Ago2) protein is the major vehicle of microRNAs (miRNAs)‐guided gene repression and silencing processes. Although the crystal structure of human Ago2 (hAgo2) has recently been disclosed, the information of dynamically structural character of protein–RNA recognition is still lacking. Molecular dynamics simulations were used to systematically explore hAgo2 in the presence and absence of RNA duplex. Stable direct and water‐mediated hydrogen bonds were observed between guide RNA backbone atoms and hAgo2, especially for nucleotides 2–7. In addition, water‐mediated hydrogen bonds are indicated to be critical in the specific recognition between hAgo2 and the conserved adenine in position 1 of target RNA. The core domains (N, PAZ, MID, and PIWI) possess rigid body movements during the simulations. The motions of N‐PAZ and PIWI‐MID are negatively correlated with or without RNA binding and PAZ domain is identified as the most mobile domain in both systems. The reorientation of PAZ domain not only influences the binding of helix‐7 and RNA duplex, the initial pairing process, but also the shape of N‐PAZ cleft, where the supplemental base pairing occurs. It is speculated that PAZ domain could be a key regulator in hAgo2‐mediated miRNA‐induced gene regulation.
Self‐Concepts, Self‐Esteem, and Academic Achievement of Minority and Majority North American Elementary School Children
Authors: Cvencek Dario , Fryberg Stephanie A. , Covarrubias Rebecca , Meltzoff Andrew N.
Published: April 2017

Minority and majority elementary school students from a Native American reservation (N = 188; K–fifth grade; 5‐ to 10‐year‐olds) completed tests of academic self‐concepts and self‐esteem. School grades, attendance, and classroom behavior were collected. Both minority and majority students exhibited positive self‐esteem. Minority students demonstrated lower academic self‐concepts and lower achievement than majority students. Two age‐related patterns emerged. First, minority students had lower academic achievement than majority students, and this effect was stronger in older (Grades 3–5) than in younger (Grades K–2) students. Second, children's actual achievement was related to their academic self‐concepts for older students but more strongly linked to self‐esteem in younger students. The authors offer a developmental account connecting students’ developing self‐representations to their school achievement.
Falling Out of Time: The Challenges of Synchrony for Children with Incarcerated Fathers
Authors: Oldrup Helene
Published: April 2017

Using a temporal lens, the article shows how fathers’ incarceration leads to a loss of attunement to the temporal rhythms of their children's everyday lives. This lack of synchrony has implications for both the being and the becoming of the child. Through in‐depth interviews, the article draws on data from a Danish study of mothers and children, aged 5–27, whose father/stepfather was incarcerated. Findings show the significance of a multifaceted understanding of time showing the implications of fathers’ imprisonment for children, suggesting that policy initiatives would be enriched by a focus on challenges to synchrony from the child's perspective.