bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gene-associated markers can assign origin in a weakly structured fish, Atlantic herring
Authors: Bekkevold Dorte , Helyar Sarah J. , Limborg Morten T. , Nielsen Einar E. , Hemmer-Hansen Jakob , Clausen Lotte A. W. , Carvalho Gary R. 
Published: February 2015

AbstractRegulations on the exploitation of populations of commercially important fish species and the ensuing consumer interest in sustainable products have increased the need to accurately identify the population of origin of fish and fish products. Although genomics-based tools have proven highly useful, there are relatively few examples in marine fish displaying accurate origin assignment. We synthesize data for 156 single-nucleotide polymorphisms typed in 1039 herring, Clupea harengus L., spanning the Northeast Atlantic to develop a tool that allows assignment of individual herring to their regional origin. We show the method's suitability to address specific biological questions, as well as management applications. We analyse temporally replicated collections from two areas, the Skagerrak (n = 81, 84, 66) and the western Baltic (n = 52, 52). Both areas harbour heavily fished mixed-origin stocks, complicating management issues. We report novel genetic evidence that herring from the Baltic Sea contribute to catches in the North Sea, and find support that western Baltic feeding aggregations mainly constitute herring from the western Baltic with contributions from the Eastern Baltic. Our study describes a general approach and outlines a database allowing individual assignment and traceability of herring across a large part of its East Atlantic distribution.
Preparation of monoPEGylated Cyanovirin-N’s derivative and its anti-influenza A virus bioactivity in vitro and in vivo
Authors: Wu Chongchao , Chen Wei , Chen Jia , Han Bo , Peng Zhou , Ge Feng , Wei Bo , Liu Mingxian , Zhang Meiying , Qian Chuiwen , Hou Zhibo , Liu Ge , Guo Chaowan , Wang Yifei , Kitazato Kaio , Yu Guoying , Zou Chunbin , Xiong Sheng 
Published: February 2015

Abstract
Influenza A virus (IAV) has been raising public health and safety concerns worldwide. Cyanovirin-N (CVN) is a prominent anti-IAV candidate, but both cytotoxicity and immunogenicity have hindered the development of this protein as a viable therapy. In this article, linker-CVN (LCVN) with a flexible and hydrophilic polypeptide at the N-terminus was efficiently produced from the cytoplasm of Escherichia coli at a &gt;15-l scale. PEGylation at the N-terminal α-amine of LCVN was also reformed as 20 kDa PEGylated linkered Cyanovirin-N (PEG20k–LCVN). The 50% effective concentrations of PEG20k–LCVN were 0.43 ± 0.11 µM for influenza A/HK/8/68 (H3N2) and 0.04 ± 0.02 µM for A/Swan/Hokkaido/51/96 (H5N3), dramatically lower than that of the positive control, Ribavirin (2.88 ± 0.66 × 103 µM and 1.79 ± 0.62 × 103 µM, respectively). A total of 12.5 µM PEG20k–LCVN effectively inactivate the propagation of H3N2 in chicken embryos. About 2.0 mg/kg/day PEG20k–LCVN increased double the survival rate (66.67%, P = 0.0378) of H3N2 infected mice, prolonged the median survival period, downregulated the mRNA level of viral nuclear protein and decreased (attenuated) the pathology lesion in mice lung. A novel PEGylated CVN derivative, PEG20k–LCVN, exhibited potent and strain-dependent anti-IAV activity in nanomolar concentrations in vitro, as well as in micromolar concentration in vivo.
Effectiveness of Single-Digit IOP Targets on Decreasing Global and Localized Visual Field Progression After Filtration Surgery in Eyes With Progressive Normal-Tension Glaucoma
Authors: Iverson Shawn M. , Schultz Scott K. , Shi Wei , Feuer William J. , Greenfield David S. 
Published: February 2015

Purpose:
To examine the effectiveness of achieving single-digit intraocular pressure (IOP) targets with filtration surgery on decreasing global and localized visual field (VF) progression in eyes with progressive normal-tension glaucoma (NTG).

Methods:
A retrospective chart review was conducted to identify NTG patients who underwent trabeculectomy with mitomycin C between 2006 and 2010 for progressive VF loss with preoperative IOP≤15 mm Hg during the 12 months before surgery. All eyes had glaucomatous optic neuropathy and progressive VF loss, uncontrolled IOP on maximum therapy, and a minimum of 2 baseline preoperative and 4 postoperative VF examinations. VF progression was assessed using Guided Progression Analysis (GPA) and Progressor software.

Results:
Fifteen eyes of 14 patients (mean age 71.8±7.5 y) were enrolled with mean follow-up of 71±26 months. Mean postoperative IOP (8.5±3.5 mm Hg) was significantly (P<0.001) reduced compared with preoperatively (13.1±1.5 mm Hg). The probability of achieving an IOP goal ≤10 mm Hg was 66% at 4 years’ follow-up. The overall rate of postoperative VF progression using any method was 13.3% (1 eye using Progressor; 1 eye using GPA and Progressor). Average postoperative slope of MD (−0.25±0.86 dB/y) and pattern SD (0.49±0.83 dB/y) were improved (P=0.05 and 0.07) compared with the preoperative slopes (−1.05±0.66 and 1.21±0.71 dB/y).

Conclusions:
Achieving single-digit IOP targets with filtration surgery has a beneficial effect on reducing global and localized rates of VF progression in NTG eyes with progression at low IOP.
Clinical Outcomes of Ahmed Glaucoma Valve Implantation With or Without Intravitreal Bevacizumab Pretreatment for Neovascular Glaucoma: A Systematic Review and Meta-Analysis
Authors: Zhou Minwen , Xu Xun , Zhang Xiulan , Sun Xiaodong 
Published: February 2015

Purpose:To evaluate the efficacy and tolerability of Ahmed glaucoma valve (AGV) implantation with intravitreal bevacizumab injection (IVB) pretreatment in the treatment of neovascular glaucoma (NVG).Methods:A comprehensive literature search was performed according to the Cochrane collaboration methodology to identify controlled clinical trials comparing AGV implantation with (IVB group) or without IVB (control group) pretreatment for NVG. The main outcome measures were the weighted mean differences (WMDs) for intraocular pressure reduction, a reduction in glaucoma medications, odds ratio (OR) for complete success rates, and qualified success rates. Tolerability estimates were measured by OR for adverse events.Results:The WMD of the intraocular pressure reduction when comparing the IVB group with the control group was 3.30 (−1.21 to 7.80). The IVB group was associated with numerically greater but nonsignificant IOP lowering efficacy compared with the control group (P=0.152). Both groups were comparable in the reduction of glaucoma medication, with a WMD of 0.28 (−0.03 to 0.59) at the follow-up endpoint (P=0.077). The IVB group was associated with significant greater complete success rates compared with the control group, with a pooled OR of 3.18 (1.41 to 7.19). However, it did not show a significant difference for the qualified success rate between them, with a pooled OR of 2.00 (0.95 to 4.21). The IVB group was associated with a significantly lower frequency of hyphema than the control group, with a pooled OR of 0.15 (0.07 to 0.32).Conclusion:The use of IVB pretreatment for NVG is a safe and effective additional step during AGV implantation surgery.
Exome Sequencing and Prediction of Long-Term Kidney Allograft Function
Authors: Mesnard L. , Muthukumar T. , Burbach M. , Li C. , Shang H. , Dadhania D. , Lee J. R , Sharma V. K. , Xiang J. , Suberbielle C. , Carmagnat M. , Ouali N. , Rondeau E. , Friedewald J. J. , Abecassis M. M. , Suthanthiran M. , Campagne F. 
Published: February 2015

AbstractCurrent strategies to improve graft outcome following kidney transplantation consider information at the HLA loci. Here, we used exome sequencing of DNA from ABO compatible kidney graft recipients and their living donors to determine recipient and donor mismatches at the amino acid level over entire exomes. We estimated the number of amino acid mismatches in transmembrane proteins, more likely to be seen as foreign by the recipient’s immune system, and designated this tally as the allogenomics mismatch score (AMS). The AMS can be measured prior to transplantation with DNA for potential donor and recipient pairs. We examined the degree of relationship between the AMS and post-transplantation kidney allograft function by linear regression. In a discovery cohort, we found a significant inverse correlation between the AMS and kidney graft function at 36 months post-transplantation (n=10 recipient/donor pairs; 20 exomes) (r2>=0.57, P<0.05). The predictive ability of the AMS persists when the score is restricted to regions outside of the HLA loci. This relationship was validated using an independent cohort of 24 recipient donor pairs (n=48 exomes) (r2>=0.39, P<0.005). In an additional cohort of living and mostly intra-familial recipient/donor pairs (n=19, 38 exomes), we validated the association after controlling for donor age at time of transplantation. Finally, a model that controls for donor age, HLA mismatches and time post-transplantation yields a consistent AMS effect across these three independent cohorts (P<0.05). Taken together, these results show that the AMS is a strong predictor of long-term graft function in kidney transplant recipients.One Sentence SummaryPrediction of long-term kidney graft function with exome sequencing
Protein Domain Hotspots Reveal Functional Mutations across Genes in Cancer
Authors: Miller Martin L. , Reznik Ed , Gauthier Nicholas P. , Aksoy Bülent Arman , Korkut Anil , Gao Jianjion , Ciriello Giovanni , Schultz Nikolaus , Sander Chris 
Published: February 2015

ABSTRACTIn cancer genomics, frequent recurrence of mutations in independent tumor samples is a strong indication of functional impact. However, rare functional mutations can escape detection by recurrence analysis for lack of statistical power. We address this problem by extending the notion of recurrence of mutations from single genes to gene families that share homologous protein domains. In addition to lowering the threshold of detection, this sharpens the functional interpretation of the impact of mutations, as protein domains more succinctly embody function than entire genes. Mapping mutations in 22 different tumor types to equivalent positions in multiple sequence alignments of protein domains, we confirm well-known functional mutation hotspots and make two types of discoveries: 1) identification and functional interpretation of uncharacterized rare variants in one gene that are equivalent to well-characterized mutations in canonical cancer genes, such as uncharacterizedERBB4(S303F) mutations that are analogous to canonicalERRB2(S310F) mutations in the furin-like domain, and 2) detection of previously unknown mutation hotspots with novel functional implications. With the rapid expansion of cancer genomics projects, protein domain hotspot analysis is likely to provide many more leads linking mutations in proteins to the cancer phenotype.
Historical and clinical items of the HCR-20 as predictors of risk within an intellectual disability population
Authors: Chaplin Eddie , Eyeoyibo Mo , Wright Steve , Xenitidis Kiriakos , McCarthy Jane 
Published: February 2015

Purpose
– The use of violence risk assessment measures within intellectual disabilities (ID) services is now the norm and a growing target for research. The purpose of this paper is to examine the clinical utility of the historical and clinical factors of the HCR-20 in predicting violence.

Design/methodology/approach
– The study took place within a national low secure service for adults with ID examining all completed admissions over a six-year period, (N=22). Clinical records covering the first three months of admission were examined along with historical reports and incident data recorded at three, six, nine and 12 months admission using the Modified Overt Aggression Scale (MOAS).

Findings
– Significant positive relationship between Historical score and total number of incidents was established. Patients with challenging behaviour less likely to have a previous history of violence, and more likely to be older at first violent incident than patients without challenging behaviour. Incidents involving patients with autism were less severe and those with no additional psychiatric diagnosis were significantly more likely to have substance misuse problems than those with a diagnosis.

Originality/value
– The study found the Historical section was predictive of violent incidents and whilst the study is too small to draw any firm conclusions, the significant positive relationship between the Historical Score and number of incidents for those without additional diagnosis needs to be investigated further as well as the potential positive clinical impact of using the HCR-20 in routine clinical practice.
Intellectual disability, personality disorder and offending: a systematic review
Authors: Rayner Kelly , Wood Harry , Beail Nigel , Nagra Maninder Kaur 
Published: February 2015

Purpose– This review seeks to systematically review studies where personality disorder has been explored as a descriptive or possible predictive factor in offending behaviour in people with an intellectual disability. The papar aims to discuss this issue.Design/methodology/approach– A systematic search of several databases was conducted and 15 studies met the inclusion criteria and were included in this review.Findings– Methodological limitations and problems in accurate diagnosis within this client group preclude firm conclusions being reached.Originality/value– It is concluded that further research should be conducted, with particular attention paid to the conceptualisation and assessment of personality disorder.
Attachment behavior in children with Autistic Spectrum Disorders
Authors: Kahane Lital , El-Tahir Mohamed 
Published: February 2015

Purpose
– Significance of attachment relationship to the development and impairments among children with autism has been studied. The purpose of this paper is to analyze the literature for studies completed on the attachment and assess the effect of autism on attachment development. Different moderators of attachment are also reviewed.

Design/methodology/approach
– Systematic reviews were searched for in different databases to establish the necessity and relevance of the current paper. The last systematic review on the topic was published in 2004 so studies done after that year were searched for in electronic databases and experts on the filed were also contacted before choosing the ten studies selected for this review.

Findings
– Attachment is present among children with Autistic Spectrum Disorders (ASD), however not prevalent as in normally developing children. The security and organization of attachment behavior are affected by the severity of the diagnosis of Autism and the co-morbidities associated. Maternal sensitivity and insightfulness support the development of secure attachment in children with ASD while impairments in joint attention and symbolic play proved to be risk factors for insecurity and disorganization of attachment.

Originality/value
– The review contributes to the relatively understudied topic of attachment behavior in autism spectrum disorders focussing on the influence brought to the bonding connection by different influencing factors like: mothers’ sensitivity, insightfulness and attachment style, parenting style and symbolic play levels.
User-visible cryptography in email and web scenarios
Authors: Brooke Phil , Paige Richard 
Published: February 2015

Purpose– This paper aims to classify different types of “user-visible cryptography” and evaluate the value of user-visible cryptographic mechanisms in typical email and web scenarios for non-expert IT users.Design/methodology/approach– The authors review the existing literature, and then identify user stories typical to their users of interest. They analyse the risks, mitigations of risks and the limits of those mitigations in the user stories.Findings– The scenarios identified suggest that background, opportunistic encryption has value, but more explicit, user-visible cryptographic mechanisms do not provide any further mitigation. Other mechanisms beyond technological mitigations provide the required mitigation for the users.Research limitations/implications– Further work should be carried out on the trust issues with trusted third parties, as they are intrinsic to global, automated cryptographic mechanisms. The authors suggest that deployed systems should rely on automation rather than explicit user involvement; further work on how best to involve users effectively remains valuable.Practical implications– Deployed systems should rely on automation rather than explicit user dialogues. This follows from recognised aspects of user behaviour, such as ignoring dialogues and unconsciously making a holistic assessment of risk that is mostly mitigated by social factors.Social implications– The user populations concerned rely significantly on the existing legal and social infrastructure to mitigate some risks, such as those associated with e-commerce. Guarantees from third parties and the existence of fallback procedures improve user confidence.Originality/value– This work uses user stories as a basis for a holistic review of the issues surrounding the use of cryptography. The authors concentrate on a relatively large population (non-expert IT users) carrying out typical tasks (web and email).
Secular and Islamic feminist entrepreneurship in Turkey
Authors: Özkazanç-Pan Banu 
Published: February 2015

Purpose– This paper aims to highlight secular and Islamic feminist approaches to entrepreneurship as potential means to challenge gender inequality in the Turkish context. In Turkey, gender equality remains elusive in a nation where secular and Islamic ideologies compete and produce different solutions to ongoing economic, socio-cultural and political issues. Women’s entrepreneurship has emerged as an important solution toward gender equality and economic development.Design/methodology/approach– Using two women’s organizations that exemplify secular and Islamic feminist ideologies, the author examines whether the entrepreneurship activities they promote give way to challenging patriarchal norms, values and practices widespread in Turkish society.Findings– Through their distinct practices and engagement with entrepreneurship, both secular and Islamic feminist positions allow for praxis and represent an ethico-political commitment to dismantling neo-liberal development ideologies in the Turkish context that perpetuate gender inequality.Social implications– Secular and Islamic feminist practices and entrepreneurship practices have different implications for achieving gender equality including changes in gender norms, economic development policies and women’s empowerment in a Muslim-majority country. In addition, it raises questions around the popular notion of “entrepreneurship as women’s empowerment”.Originality/value– This paper is of value to scholars who want to understand secular and Islamic feminisms and their implications for challenging gender inequality. The Turkish context with its traditional and modern societal norms and values provides a rich case study to examine these issues through the exemplars of entrepreneurship. It is also of value to scholars who want to understand structural constraints associated with gender equality beyond individual-level challenges.
The Affordable Care Act: triumphs and tribulations
Authors: Goldberg Ilene 
Published: February 2015

Purpose
– This paper aims to discuss key provisions of the Affordable Care Act (ACA) and the obstacles faced by the federal government in achieving its goal. The ACA is designed to provide most Americans with an access to affordable health care.

Design/methodology/approach
– Using data obtained from government sources, case law and current literature, the paper first discusses the history and background of the ACA. It evaluates the law’s current status, the benefits it achieved and the legal, economic, political and social challenges that lie ahead.

Findings
– Although the Supreme Court upheld most of the ACA’s provisions, opponents at the federal and state level are still attempting to overturn or undercut it. The ACA itself is so complicated that it has generated confusion among employers, consumers and even those who are charged with enforcing it. The extent to which the ACA can be successfully implemented is unclear, and adjustments must be made as the federal government struggles to implement key components.

Originality/value
– This paper should be of interest to academics, health-care and legal professionals, and to anyone who needs clarification and analysis of a still-evolving law that is certain to have an impact on most Americans.
Is a public interest test for workplace whistleblowing in society’s interest?
Authors: Lewis David 
Published: February 2015

Purpose– The aim of the paper is to consider the efficacy of requiring a public interest test to be satisfied before protection is afforded to workers who blow the whistle under Part IVA of the Employment Rights Act 1996 (ERA 1996).Design/methodology/approach– Not all definitions of whistleblowing require there to be a public interest in the disclosure of information. To illustrate how the expression “public interest” has been used in this context, the common law defence to an action for breach of confidence is outlined. The paper then explains how the concept of “public interest whistleblowing” evolved in other jurisdictions. It also examines the jurisprudence of the European Court of Human Rights to see if it helps us to apply the public interest test. Finally, this test is considered in the context of UK legislation.Findings– Several sources of uncertainty are identified. These include the fact that personal and public interest matters may be intertwined and that an organization may encourage the internal reporting of concerns about wrongdoing that do not have a public dimension to further its private interests. One obvious result of uncertainty is that those who are not legally required to report wrongdoing may choose not to do so and society may be denied important information; for example, about serious health and safety risks or financial scandals.Originality/value– It is suggested that the public interest test should be removed from Part IVA ERA 1996. However, this test is likely to remain for a while, so nine recommendations about how it should be interpreted are made.
Spatial variation in age structure among colonies of a marine snake: the influence of ectothermy
Authors: Bonnet Xavier , Brischoux François , Pinaud David , Michel Catherine Louise , Clobert Jean , Shine Richard , Fauvel Thomas 
Published: February 2015

Abstract

Several tetrapod lineages that have evolved to exploit marine environments (e.g. seals, seabirds, sea kraits) continue to rely upon land for reproduction and, thus, form dense colonies on suitable islands.

In birds and mammals (endotherms), the offspring cannot survive without their parents. Terrestrial colonies contain all age classes. In reptiles (ectotherms), this constraint is relaxed, because offspring are independent from birth. Hence, each age class has the potential to select sites with characteristics that favour them.

Our studies of sea snakes (sea kraits) in the lagoon of New Caledonia reveal marked spatial heterogeneity in age structure among colonies.

Sea krait colonies exhibit the endothermic ‘seal–seabird’ pattern (mixed‐age classes within populations) only where the lagoon is narrow. Where the lagoon is wide, most snake colonies are comprised primarily of a single age cohort. Nurseries are located near the coast, adult colonies offshore and mixed colonies in‐between.

We suggest that ectothermy allows individuals to utilize habitats that are best suited to their own ecological requirements, a flexibility not available to endothermic marine taxa with obligate parental care.