bluuebunny/crossref_metadata_2025_split huggingface dataset:
Influence of a Minimum-Length Limit Regulation on Wild Brown Trout: an Example of Recruitment and Growth Overfishing
Authors: Sánchez-Hernández Javier , Shaw Stephanie L. , Cobo Fernando , Allen Mike S. 
Published: August 2016

Abstract
The relative abundance of the largest size-classes of individuals within a fish population has an important influence on recruitment success. Fishing regulations with a basis in size (e.g., minimum-length limits) can directly impact the abundance of these larger individuals and thus potentially influence recruitment. We analyzed whether recruitment of exploited native Brown Trout Salmo trutta populations was affected via the extraction of large individuals (&gt;220 mm, i.e., minimum-length limit). The study was replicated temporally (2007–2009) and spatially across seven recreational fishing sections (four exploited and three catch-and-release sections) within the River Tormes located in central Spain. Catch-and-release sections were used as reference points to compare with exploited sections. We tested the hypothesis that minimum-length limit regulations would adversely affect fish recruitment through fishing-induced mortality of large individuals. Spawning stock (measured as fish &gt;220 mm) and young-of-the-year abundances were estimated using multiple-pass depletion methods. We modeled the relationship between spawning stock and subsequent recruitment using a nonparametric approach (generalized additive models) to fit the best stock–recruit relationship. Additionally, von Bertalanffy growth and yield-per-recruit models were generated to evaluate the potential for growth and recruitment overfishing. The restrictive length limits used to regulate harvest in the study area limited both recruitment and adult abundance. The present study provides evidence that the use of minimum-length limit regulations in the management of recreational fisheries has the potential to adversely affect the species’ recruitment. Such adverse impacts could be occurring via both recruitment overfishing and growth overfishing, exemplifying that the removal of the larger size-classes of individuals through recreational fishing could have important consequences for recruitment. Management actions should be directed to protect large individuals (e.g., via harvest slots) rather than promote their removal, thereby reducing the chances of overfishing.
Received November 25, 2015; accepted April 18, 2016Published online August 24, 2016
PhenomeScape: a cytoscape app to identify differentially regulated sub-networks using known disease associations
Authors: Soul Jamie , Dunn Sara L. , Hardingham Tim E. , Boot-Handford Ray P. , Schwartz Jean-Marc 
Published: August 2016

Summary: PhenomeScape is a Cytoscape app which provides easy access to the PhenomeExpress algorithm to interpret gene expression data. PhenomeExpress integrates protein interaction networks with known phenotype to gene associations to find active sub-networks enriched in differentially expressed genes. It also incorporates cross-species phenotypes and associations to include results from animal models of disease. With expression data imported into PhenomeScape, the user can quickly generate and visualise interactive sub-networks. PhenomeScape thus enables researchers to use prior knowledge of a disease to identify differentially regulated sub-networks and to generate an overview of altered biologically processes specific to that disease.
Availability and Implementation: Freely available for download at https://github.com/soulj/PhenomeScape
Contact: jamie.soul@postgrad.manchester.ac.uk or jean-marc.schwartz@manchester.ac.uk
KScons: a Bayesian approach for protein residue contact prediction using the knob-socket model of protein tertiary structure
Authors: Li Qiwei , Dahl David B. , Vannucci Marina , Joo Hyun , Tsai Jerry W. 
Published: August 2016

Motivation: By simplifying the many-bodied complexity of residue packing into patterns of simple pairwise secondary structure interactions between a single knob residue with a three-residue socket, the knob-socket construct allows a more direct incorporation of structural information into the prediction of residue contacts. By modeling the preferences between the amino acid composition of a socket and knob, we undertake an investigation of the knob-socket construct’s ability to improve the prediction of residue contacts. The statistical model considers three priors and two posterior estimations to better understand how the input data affects predictions. This produces six implementations of KScons that are tested on three sets: PSICOV, CASP10 and CASP11. We compare against the current leading contact prediction methods.
Results: The results demonstrate the usefulness as well as the limits of knob-socket based structural modeling of protein contacts. The construct is able to extract good predictions from known structural homologs, while its performance degrades when no homologs exist. Among our six implementations, KScons MST-MP (which uses the multiple structure alignment prior and marginal posterior incorporating structural homolog information) performs the best in all three prediction sets. An analysis of recall and precision finds that KScons MST-MP improves accuracy not only by improving identification of true positives, but also by decreasing the number of false positives. Over the CASP10 and CASP11 sets, KScons MST-MP performs better than the leading methods using only evolutionary coupling data, but not quite as well as the supervised learning methods of MetaPSICOV and CoinDCA-NN that incorporate a large set of structural features.
Contact: qiwei.li@rice.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
An analysis of the operative capacity of non-governmental organizations in the Southern region of Punjab Province, Pakistan
Authors: Jabeen Sadia , Yasmin Nighat 
Published: August 2016

Abstract
This study explores the operative capacity of non-governmental organizations (NGOs) in the Southern region of Punjab Province, Pakistan. Data from all functional NGOs registered with the Social Welfare and the Bait-ul-Maal Department, Punjab under the provisions of the Voluntary Social Welfare Agencies (Registration and Control) Ordinance, 1961 were collected. A questionnaire based on basic information about NGOs, namely about membership, elections, services offered and opportunities for capacity building, was used for data collection. The results of the study identify education, health, and vocational and technical training as the three major areas of activity for NGOs in the Southern region. The study also found that NGOs do not have an adequate democratic process for elections. Women’s participation is less than men’s in general and in particular regarding membership of executive bodies. The core areas where gaps in capacity building were found are in governance and leadership, financial and human resource management, record maintenance and reporting. On the basis of the findings of this study, it is suggested that NGOs should extend their areas of operation and field of services, and that the democratic process could be ensured by concerned departments through proper monitoring and surveillance.
Le Vieux de la Montagne, ou les vertus du contre-exemple: Le
Roman des Sept Sages
,
Barlaam et Josaphat
, Le
Décaméron
Authors: Uhlig Marion 
Published: August 2016

Résumé

À l’occasion d’une réflexion sur les adaptations littéraires médiévales de l’histoire du Vieux de la Montagne, l’article interroge le potentiel de vérité de la littérature, et notamment les capacités de la fiction à séduire et à subvertir. Le propos est nourri par l’analyse de trois fables qui résonnent avec cette trame légendaire et sont enchâssées dans trois ‘récits à tiroirs’ d’importance majeure: ‘L’Exemple du Haschischin’ dans le
Roman des sept sages
(version M:
L’Ystoire de la male marastre
, fin du treizième ou début du quatorzième siècle); ‘La Séduction’ dans
Barlaam et Josaphat
(rédaction du treizième siècle); et la nouvelle des ‘Oies du père Philippe’ dans le
Décaméron
de Boccace, dans l’adaptation française du quinzième siècle réalisée par Laurent de Premierfait. L’enjeu est double: il s’agit en premier lieu de mettre en valeur la quête de vérité qui habite la littérature exemplaire ou plutôt, en l’occurrence, contre-exemplaire; de manière subsidiaire, on souhaite révéler le lien, jusqu’ici insu, qui relie les fables de
Barlaam et Josaphat
et du
Décaméron
à celle des
Sept sages
et, à travers elle, au mythe du Vieux de la Montagne.
Renoir’s Automaton, Vigo’s Puppet: Automatism and Movement in
La Règle du jeu
and
L’Atalante
Authors: ffrench Patrick 
Published: August 2016

Abstract

Jean Renoir’s 1939 film
La Règle du jeu
incorporates several automata as indexes of the alienated status of the class it depicts, including the orchestrion that the main protagonist Robert de La Chesnaye unveils as the ultimate piece in his collection. This focus on machines is as much an expression of the film’s eighteenth-century philosophical and aesthetic references as it is a revelation of an anachronistic relation to the machine as such, and to the form of movement it embodies. In a key scene the display of the orchestrion falters, revealing a deathly repetition that the moribund pseudo-aristocracy cannot accommodate. The opposition drawn by Lacan between automaton and
tuchē
in his eleventh seminar, as well as Deleuze’s intimation of the ‘crack’ in the filmic crystal that Renoir’s cinema deploys, illuminate this moment as an event of pure repetition. In contrast, Jean Vigo’s 1934 film
L’Atalante
depicts a human–machine relation that allows for forms of connection and innovation of a more organic nature. Across these representations of automatism and movement, the cinema of the 1930s explores patterns of alienation and of historicity, for which the theses of Walter Benjamin provide a powerful interpretative framework.
If it does not kill them, it makes them stronger: collisional evolution of star clusters with tidal shocks
Authors: Gieles Mark , Renaud Florent 
Published: August 2016

Abstract
The radii of young (≲100 Myr) star clusters correlate only weakly with their masses. This shallow relation has been used to argue that impulsive tidal perturbations, or ‘shocks’, by passing giant molecular clouds (GMCs) preferentially disrupt low-mass clusters. We show that this mass–radius relation is in fact the result of the combined effect of two-body relaxation and repeated tidal shocks. Clusters in a broad range of environments including those like the solar neighbourhood evolve towards a typical radius of a few parsecs, as observed, independent of the initial radius. This equilibrium mass–radius relation is the result of a competition between expansion by relaxation and shrinking due to shocks. Interactions with GMCs are more disruptive for low-mass clusters, which helps to evolve the globular cluster mass function (GCMF). However, the properties of the interstellar medium in high-redshift galaxies required to establish a universal GCMF shape are more extreme than previously derived, challenging the idea that all GCs formed with the same power-law mass function.
Positive and Negative Thinking in Tinnitus: Factor Structure of the Tinnitus Cognitions Questionnaire
Authors: Handscomb Lucy E. , Hall Deborah A. , Shorter Gillian W. , Hoare Derek J. 
Published: August 2016

Objectives:Researchers and clinicians consider thinking to be important in the development and maintenance of tinnitus distress, and altering thoughts or thinking style is an object of many forms of psychological therapy for tinnitus. Those working with people with tinnitus require a reliable, psychometrically robust means of measuring both positive and negative thinking related to it. The Tinnitus Cognitions Questionnaire (TCQ) was designed as such a measure and its authors showed it to be reliable, with good psychometric properties. However, no research teams have yet carried out independent validation. This study aimed to use the TCQ to investigate thinking amongst members of the general population with both bothersome and nonbothersome tinnitus and also to verify its factor structure.Design:Three hundred forty-two members of the public with tinnitus completed the TCQ online or on paper. They also rated their tinnitus on a scale as “not a problem,” “a small problem,” “a moderate problem,” “a big problem,” or a “very big problem.” The authors tested the original factor structure of the TCQ using confirmatory factor analysis and then calculated the mean scores for each item, comparing mean total scores across “problem categories” for the full questionnaire and for the positive and negative subscales.Results:The original two-factor structure of the TCQ was a good fit to the data when the correlation between positive and negative factors was fixed at zero (root mean square error of approximation = 0.064, 90% confidence interval = 0.058 to 0.070). Items pertaining to wishing the tinnitus would go away and despairing that it would ever get better had the highest mean scores. The mean total score for the “no problem” group (M = 31.17, SD = 16.03) was not significantly different from the mean total score for the “small problem” group (M = 34.00, SD = 12.44,p= 0.99). Differences between mean scores for all other groups were statistically significant. For the negative subscale, differences were statistically significant between all problem categories. For the positive subscale, the differences between mean scores were only statistically significant for the “no problem” group (M = 28.40, SD = 17.11) compared with the “moderate problem” group (M = 18.55, SD = 8.64,p= 0.02) and for the “moderate problem” group compared with the “very big problem” group (M = 26.79, SD = 11.66,p= 0.002). Positive and negative factors were uncorrelated (ρ= −0.03.)Conclusions:The TCQ is a valid measure of positive and negative thinking in tinnitus, and the authors recommend its use in research and therapeutic settings. Negative thinking appears to be associated with more problematic tinnitus, but positive thinking is not associated with unproblematic tinnitus, suggesting that reducing negative thinking may be more important than teaching positive thinking in therapy.
Aberrant immune response with consequent vascular and connective tissue remodeling – causal to scleroderma and associated syndromes such as Raynaud phenomenon and other fibrosing syndromes?
Authors: Durmus Nedim , Park Sung-Hyun , Reibman Joan , Grunig Gabriele 
Published: August 2016

Purpose of reviewScleroderma and other autoimmune-induced connective tissue diseases are characterized by dysfunctions in the immune system, connective tissue and the vasculature. We are focusing on systemic sclerosis (SSc)-associated pulmonary hypertension, which remains a leading cause of death with only a 50–60% of 2-year survival rate.Recent findingsMuch research and translational efforts have been directed at understanding the immune response that causes SSc and the networked interactions with the connective tissue and the vasculature. One of the unexpected findings was that in some cases the pathogenic immune response in SSc resembles the immune response to helminth parasites. During coevolution, means of communication were developed which protect the host from over-colonization with parasites and which protect the parasite from excessive host responses. One explanation for the geographically clustered occurrence of SSc is that environmental exposures combined with genetic predisposition turn on triggers of molecular and cellular modules that were once initiated by parasites.SummaryFuture research is needed to further understand the parasite-derived signals that dampen the host response. Therapeutic helminth infection or treatment with parasite-derived response modifiers could be promising new management tools for autoimmune connective tissue diseases.
Myopathy in scleroderma and in other connective tissue diseases
Authors: Paik Julie J. 
Published: August 2016

Purpose of review
This review discusses the most updated literature of myopathy in scleroderma and other connective tissue diseases.

Recent findings
In the past year, studies have demonstrated that myopathy in scleroderma is associated with poor outcomes such as disability and mortality. In addition, muscle histopathology in scleroderma continues to reveal that it is a heterogeneous entity, and that necrosis and acute neurogenic atrophy may be a more prevalent histopathologic feature in muscle biopsies than previously reported. In other connective tissue diseases such as SLE, the onset of overlap myositis typically does not occur simultaneously as it does in scleroderma or rheumatoid arthritis.

Summary
Myopathy in scleroderma is heterogeneous and given that it is associated with poor outcomes, it is imperative that optimal diagnostic strategies and therapies including a classification criterion be developed. In other connective tissue diseases, such as rheumatoid arthritis and systemic lupus erythematosus, myopathy is even more poorly defined and requires more robust studies to clarify both the clinical features and muscle histopathology in this group.
The role of myokines in muscle health and disease
Authors: Lightfoot Adam P. , Cooper Robert G. 
Published: August 2016

Purpose of review
This article updates on the concept that muscle-derived cytokines (myokines) play important roles in muscle health and disease.

Recent findings
Interleukin-6 (IL-6) is released from normal skeletal muscle in response to exercise, mediating both anti-inflammatory responses and metabolic adaptations, actions contradictory to the prevailing view that IL-6 is a proinflammatory cytokine that is inducing and propagating disease. The anti-inflammatory effects of IL-6 result from its trans-membrane signalling capability, via membrane-bound receptors, whereas its proinflammatory effects result instead from signalling via the soluble IL-6 receptor and gp130. IL-15 is elevated following exercise, promoting muscle fibre hypertrophy in some circumstances, while inducing fibre apoptosis in others. This functional divergence appears because of variations in expression of IL-15 receptor isoforms. Decorin, a recently described myokine, is also elevated following exercise in normal muscle, and promotes muscle fibre hypertrophy by competitively binding to, and thus inhibiting, myostatin, a negative regulator of muscle protein synthesis. Exercise-induced myostatin downregulation thus promotes muscle fibre growth, prompting recent trials of a biological myostatin inhibitor in inclusion body myositis.

Summary
Myokines appear to exert diverse beneficial effects, though their mechanistic roles in myositis and other myopathologies remain poorly understood.
Laparoscopic prolapse surgery: types and evidence
Authors: Wattiez Arnaud , Nasir Razan , Al Maamari Basma , Schindler Larissa 
Published: August 2016

Purpose of review
Recommendations for the surgical treatment of pelvic organ prolapse have undergone significant changes over the last few decades.
First described to be too difficult, the laparoscopic technique has gained popularity but is still controversial. The recent warning on vaginal mesh was the sign of revival and we start now to have many articles published on results and on techniques for laparoscopic prolapse repair.

Recent findings
If nothing is new in the comparison of the routes including vaginal mesh placement, the new articles are very interesting in terms of technical information and recommendations. Those articles are very important and help us understand some failures in the laparoscopic approach mainly in the anterior compartment.

Summary
New models have been created and eventually in the future, we will be able to simulate the repair on our own patients and to assess virtually the mobility of each compartment preoperatively. This will allow us to adjust and tailor the treatment to each patient.
Eating disorders in children and adolescents: what does the gynecologist need to know?
Authors: Sieke Erin H. , Rome Ellen S. 
Published: August 2016

Purpose of reviewThe purpose of this review is to discuss the diagnosis, medical complications, and treatment of eating disorders as defined by the newly released Diagnostic and Statistical Manual, 5th edition.Recent findingsWith the introduction of the Diagnostic and Statistical Manual, 5th edition, the diagnostic criteria for anorexia nervosa and bulimia nervosa have been revised to better capture the varied presentations of patients with eating disorders. In addition, new eating disorder diagnoses including binge-eating disorder, characterized by recurrent bingeing without associated compensatory behaviors, and avoidant/restrictive food intake disorder, characterized by a restrictive eating pattern without associated body dysmorphism, allow for increased recognition, diagnosis, and treatment of disordered eating patterns. In addition to a high mortality rate, eating disorders are associated with serious medical sequelae secondary to malnutrition and disordered behaviors, including disturbances of the cardiovascular, neurologic, gastrointestinal, reproductive, and skeletal systems. Early diagnosis and family-based treatment are associated with improved outcomes in children and adolescents.SummaryEating disorders are illnesses with biological, psychological, and social implications that commonly present in childhood and adolescence. Gynecologists are on the front line for the screening and diagnosis of eating disorders in adolescent women.
Prosthetic Aortic Valve Fixation Study: 48 Replacement Valves Analyzed Using Digital Pressure Mapping
Authors: Lee Candice Y. , Wong Joshua K. , Ross Ronald E. , Liu David C. , Khabbaz Kamal R. , Martellaro Angelo J. , Gorea Heather R. , Sauer Jude S. , Knight Peter A. 
Published: August 2016

Objective Prostheses attachment is critical in aortic valve replacement surgery, yet reliable prosthetic security remains a challenge. Accurate techniques to analyze prosthetic fixation pressures may enable the use of fewer sutures while reducing the risk of paravalvular leaks (PVL). Methods Customized digital thin film pressure transducers were sutured between aortic annulus models and 21-mm bioprosthetic valves with 15 × 4-mm, 12 × 4-mm, or 9 × 6-mm-wide pledgeted mattress sutures. Simulating open and minimally invasive access, 4 surgeons, blinded to data acquisition, each secured 12 valves using manual knot-tying (hand-tied [HT] or knot-pusher [KP]) or automated titanium fasteners (TFs). Real-time pressure measurements and times were recorded. Two-dimensional (2D) and 3D pressure maps were generated for all valves. Pressures less than 80 mm Hg were considered at risk for PVL. Results Pressures under each knot (intrasuture) fell less than 80 mm Hg for 12 of 144 manual knots (5/144 HT, 7/144 KP) versus 0 of 288 TF (P < 0.001). Pressures outside adjacent sutures (extrasuture) were less than 80 mm Hg in 10 of 60 HT, zero of 60 KP, and zero of 120 TF sites for 15 × 4-mm valves; 17 of 48 HT, 25 of 48 KP, and 12 of 96 TF for 12 × 4-mm valves; and 15 of 36 HT, 17 of 36 KP and 9 and 72 TF for 9 × 6-mm valves; P < 0.001 all manual versus TF. Annular areas with pressures less than 80 mm Hg ranged from 0% of the sewing-ring area (all open TF) to 31% (12 × 4 mm, KP). The average time per manual knot, 46 seconds (HT, 31 seconds; KP, 61 seconds), was greater than TF, 14 seconds (P < 0.005). Conclusions Reduced operative times and PVL risk would fortify the advantages of surgical aortic valve replacement. This research encourages continued exploration of technical factors in optimizing prosthetic valve security.