bluuebunny/crossref_metadata_2025_split huggingface dataset:
Irruptive prey dynamics following the groundfish collapse in the Northwest Atlantic: an illusion?
Authors: Frank Kenneth T. , Leggett William C. , Petrie Brian D. , Fisher Jonathan A. D. , Shackell Nancy L. , Taggart Christopher T. 
Published: August 2013

Abstract
Frank, K. T., Leggett, W. C., Petrie, B., Fisher, J. A. D., Shackell, N. L., and Taggart, C. T. 2013. Pelagic fish outbreak in the Northwest Atlantic - reality or illusion? – ICES Journal of Marine Science, 70: . The collapse of Northwest Atlantic groundfish in the early 1990s yielded a “natural experiment” within which to explore responses of ecosystems to a major perturbation. The “Pelagic Outburst” hypothesis was developed to explain an up to 900% increase in the abundance of small-bodied forage fishes and macroinvertebrates following this collapse and a subsequent trophic cascade extending across four trophic levels. Recently, this theory has been challenged and an alternative “Suprabenthic Habitat Occupation” (SHO) hypothesis has been advanced; it proposes the prey outburst associated with the forage fish component was an illusion created by changes in the vertical distribution of small pelagic fishes after the cod collapse in favour of a more bottom-oriented distribution that increased their vulnerability to bottom trawls. We evaluated the SHO hypothesis as it applied to the relationship between changes in the biomass of cod and the vertical distribution of herring and sand lance, the major small pelagic species of the Scotian Shelf ecosystem off eastern Nova Scotia. Contrary to predictions of the SHO hypothesis our initial conclusion that a pelagic outburst occurred in that ecosystem was confirmed and we found no evidence of a predator effect on vertical distributions of these species. We also explored the acoustic survey design and execution that generated the data that form the cornerstone of the SHO hypothesis, and the coherence between the behaviour depicted in these data and catch rates in the surface-oriented purse-seine fishery for herring operating at the time of these surveys. In combination, the results of our re-analysis of the population dynamics and behaviour of herring on the eastern Scotian Shelf, lead us to conclude that the SHO hypothesis, at least as it relates to the post-cod collapse dynamics of the affected Northwest Atlantic ecosystems, is not supported.
Socio-economic and institutional incentives influencing fishers' behaviour in relation to fishing practices and discard
Authors: Eliasen Søren Q. , Papadopoulou K.-Nadia , Vassilopoulou Vassiliki , Catchpole Tom L. 
Published: August 2013

Abstract
Discard of unwanted catches are common in European fisheries, but reducing or banning this has been given high priority in the proposal for the reform of the Common Fisheries Policy. Although many technical regulations have been introduced to limit unwanted catches, there is little understanding of the underlying socio-economic and institutional incentives causing discard at the fisher level. The paper presents an approach which views discards as a result of decisions made both on deck and at earlier stages of the fishing planning and implementation process. Decisions made by fishers resulting in a more selective fishery are considered “selective behaviour”. It is argued that fishing practices are institutionally embedded within three institutional spheres: “state”, “market”, and “community”, which together with “natural conditions” create incentives and frameworks for discard and selective behaviour. A comprehensive list of factors which may influence discards and selective behaviour is developed and applied to three case studies—all trawl fisheries—in Denmark, Greece, and England. The paper discusses cross-case findings of how the identified factors may create drivers for discard. Finally, a refined list of factors is presented in a tree structure and the usefulness of the list as a tool for analysing drivers for discard and selective behaviour, in a context of developing mitigating measures, is discussed.
Is size-dependent pricing prevalent in fisheries? The case of Norwegian demersal and pelagic fisheries
Authors: Zimmermann Fabian , Heino Mikko 
Published: August 2013

Abstract
Zimmermann, F., and Heino, M. 2013. Is size-dependent pricing prevalent in fisheries? The case of Norwegian demersal and pelagic fisheries. – ICES Journal of Marine Science, 70: . It is commonly acknowledged that body weight of fish is a key factor in determining market value of landed catch, thus influencing optimal harvest strategies. However, in management strategy evaluations and bioeconomic modelling, body size is often an overlooked economic parameter, and there are no systematic studies on the prevalence of size-dependent pricing. Here we assess the presence and magnitude of size-dependent pricing in ex-vessel prices of fish in Norwegian fisheries. The data encompass landings of four pelagic and four demersal stocks in Norway in 2000–2010. Linear mixed models and generalized additive models were used to determine the dependence of unit price on weight class as well as on total yield and time (year). The results show a significant positive relationship between weight class and price for seven out of the eight examined fish stocks. The relative effect of body weight on price was the strongest for cod, Greenland halibut, Norwegian spring-spawning herring and mackerel, lesser for North Sea herring and saithe, and negligible for horse mackerel. These findings demonstrate that size-dependent pricing is common in Norwegian fisheries, and is therefore of high relevance for resource economics and fisheries management.
Towards a comprehensive strategy to recover river herring on the Atlantic seaboard: lessons from Pacific salmon
Authors: Bowden Alison A. 
Published: August 2013

Abstract
River herring (alewife, Alosa pseudoharengus, and blueback herring, Alosa aestivalis) are anadromous alosines that play important ecological roles and comprised major US fisheries in the past. Stocks are at historically low levels Atlantic coast-wide and river herring are being considered for listing as threatened species under the Endangered Species Act. A comprehensive, linked freshwater and marine approach to restoring these important species is proposed, informed by a “life cycle” strategy for the recovery of an Endangered Pacific salmon species. The California coho salmon strategy entails identifying core populations stratified by biological units, assessing threats and developing site-specific and range-wide recovery actions to restore habitat and abate threats to all life stages. Protecting and strengthening core populations, combined with marine strategies, is likely key to the recovery of the species at scale. A case study is presented from the Taunton River, a ∼1300-km2 watershed in Massachusetts (USA) that hosts one of the largest river herring runs in New England. This watershed and its river herring populations possess multiple characteristics that indicate resilience and thus it could be an example of a river herring core habitat, critical for the recovery of the species at scale. A watershed-wide protection and restoration initiative is underway. Site-based strategies including dam removal, low impact development retrofits, and land protection are linked to policy efforts such as establishing streamflow standards and easing permitting of restoration projects to protect and improve connectivity, flow, and water quality. These watershed-based strategies are linked to regional scale research and fisheries management to set sustainable directed harvest targets and reduce the bycatch of river herring in ocean fisheries. Core habitats for river herring need to be identified range-wide and investments in those places prioritized to secure resilient source populations.
Growth forms of Leymus chinesis (Poaceae) at the different developmental stages of the natural population
Authors: Zhang Ji‐Tao , Li Xiu‐Jun , Liu Zhuang , Li Xiao‐Yu , Gao Zhan‐Wu , Mu Chun‐Sheng 
Published: August 2013

AbstractThe manner in which the density of Leymus chinensis increases from a single plant to a dominant population can be understood by tracing the development of a population from early to late stages. Parent shoot density, above‐ground dry weight, spike density, heading rate and spike dry weight, density of spreading shoots (buds/daughter shoots in apical/axillary rhizomes) and clumping shoots (buds/daughter shoots in axillary parent shoots), and young rhizome length and weight were investigated in the same quadrats for a low density/early stage (LE) population and a high density/late stage (HL) population. Clonal growth (buds/daughter shoots formation) and sexual reproduction (spikes formation) increased while rhizome storage (young rhizome weight) decreased during the transition from LE to HL. In a LE population an outward occupation strategy was employed, with a high proportion of spreading shoots. As the population density gradually increased until HL, an inward consolidation strategy increasing shoot amount in previously occupied areas, was adopted. This was characterized by a high proportion of clumping shoots. Interestingly, the trade‐off between spreading and clumping shoots can be adjusted by the duration of young rhizome elongation during a growth season. In other words, compared with a HL population, a LE population shortened the duration of young rhizome elongation during the growth season, which resulted in more time for the production of axillary spreading shoots along the rhizomes, and high amounts and proportions of total spreading shoots. The special growth patterns, that is, trade‐offs among growth forms, allow L. chinensis to establish dominant populations throughout the eastern Eurasian Steppe.
Th17 Cells in Immunopathogenesis and treatment of rheumatoid arthritis
Authors: Azizi Gholamreza , Jadidi‐Niaragh Farhad , Mirshafiey Abbas 
Published: August 2013

AbstractRheumatoid arthritis (RA) is a chronic inflammatory disease characterized by the sequestration of various leukocyte subpopulations within both the developing pannus and synovial space. The chronic nature of this disease results in inflammation of multiple joints, with subsequent destruction of the joint cartilage and erosion of bone. Identification of T helper (Th)17 cells led to breaking the dichotomy of the Th1/Th2 axis in immunopathogenesis of autoimmune diseases such as RA, and its experimental model, collagen‐induced arthritis (CIA). Th17 cells produce cytokines, including interleukin (IL)‐17, IL‐6, IL‐21, IL‐22 and tumor necrosis factor (TNF)‐α, with pro‐inflammatory effects, which appear to have a role in immunopathogenesis of RA. Regarding the wide ranging production of pro‐inflammatory cytokines and chemokines by Th17 cells, it is expected that Th17 cell could be a potent pathogenic factor in disease immunopathophysiology. Thus the identification of effector mechanisms used by Th17 cells in induction of disease lesions may open new prospects for designing a new therapeutic strategy for treatment of RA.
Association of N‐terminal domain polymorphisms of the porcine glucocorticoid receptor with carcass composition and meat quality traits
Authors: Reyer Henry , Ponsuksili Siriluck , Wimmers Klaus , Murani Eduard 
Published: August 2013

SummaryThe glucocorticoid receptor (GR) is a ubiquitously acting transcription factor that is responsible for mediating the physiological response to stress and adaptation to environmental conditions. Genetic variation of a GR gene (NR3C1) may therefore contribute to multiple phenotypic alterations and influence relevant traits of animal production. Here, we examined effects of two non‐synonymous mutations of the porcine NR3C1, leading to amino acid exchanges p.Glu13Asp (c.39A>C) and p.Val19Leu (c.55G>C) in the N‐terminal domain of the GR, on meat quality and carcass composition. In addition, we explored their influence on transcriptional activity of GR in vitro. A commercial crossbreed Pietrain × (German Large White × German Landrace) herd (n = 545) in which genotypes and relevant traits had been collected was used to perform the association analysis. The single nucleotide polymorphism (SNP) c.55G>C was significantly associated with conductivity and meat color scores. These effects were highly consistent considering the physiological relationship between these traits. Association analysis of SNP c.39A>C also revealed significant effects on closely connected meat quality traits. In addition, SNP c.55G>C showed association with carcass traits, mainly those related to muscle deposition. The molecular mechanism of action of both amino acid substitutions remains obscure because neither showed significant influence on transcriptional activity of GR. Our study emphasizes NR3C1 as an important candidate gene for muscle‐related traits in pigs, but further work is necessary to clarify the molecular background of the identified associations.
Genome‐wide association with delayed puberty in swine
Authors: Nonneman D. , Lents C. , Rohrer G. , Rempel L. , Vallet J. 
Published: August 2013

SummaryAn improvement in the proportion of gilts entering the herd that farrow a litter would increase overall herd performance and profitability. A significant proportion (10–30%) of gilts that enter the herd never farrow a litter; reproductive reasons account for approximately a third of gilt removals, with anestrous and failure to conceive the most common reasons for culling. Tools to select gilts for reproductive longevity through genomics or alternative phenotypes would be of great benefit to the producer. Ninety‐one gilts that failed to display behavioral estrus by 240 days (cases) and 127 pubertal littermates (controls) were genotyped with the Illumina Porcine SNP60 Beadchip. One hundred and seventy‐four SNPs with the most significant associations were genotyped in an additional 86 cases and 103 controls. Twelve of these associations were significant in the final analysis. The most significant (P < 1.5 × 10−14) region associated with failure to attain puberty was on chromosome 4 surrounding the NHLH2 gene. Delayed pubertal development and age at first estrus have been associated with NHLH2 in mice. Because attainment of puberty is a complex trait, identifying genes that affect pubertal age would greatly contribute to our knowledge of reproductive development as well as overall fertility.
Preliminary time‐course study of antiinflammatory macrophage infiltration in crush‐injured skeletal muscle
Authors: Shono Jun‐ichi , Sakaguchi Shohei , Suzuki Takahiro , Do Mai‐Khoi Q. , Mizunoya Wataru , Nakamura, Mako , Sato Yusuke , Furuse Mitsuhiro , Yamada Koji , Ikeuchi Yoshihide , Tatsumi Ryuichi 
Published: August 2013

AbstractMuscle damage induces massive macrophage infiltration of the injury site, in which activated pro‐inflammatory and anti‐inflammatory phenotypes (currently classified as M1 and M2, respectively) have been documented as distinct functional populations predominant at different times after the conventional acute injury by intramuscular injection of snake venoms (cardiotoxin, notexin) or chemicals (bupivacaine hydrochloride, barium chloride). The present study employed a muscle‐crush injury model that may better reflect the physiologic damage and repair processes initiated by contusing a gastrocnemius muscle in the lower hind‐limb of adult mice with hemostat forceps, and examined the time‐course invasion of M1 and M2 macrophages during muscle regeneration by immunocytochemistry of CD197 and CD206 marker proteins. CD197‐positive M1 macrophages were observed exclusively at 1–4 days after crush followed by the alternative prevalence of CD206‐positive M2 at 7 days of myogenic differentiation, characterized by increasing levels of myogenin messenger RNA expression. Preliminary PCR analysis showed that M2 may produce hepatocyte growth factor (HGF) in culture, providing additional benefit to understanding that M2 populations actively promote regenerative myogenesis (muscle fiber repair) and moto‐neuritogenesis (re‐attachment of motoneuron terminals onto damaged fibers) through their time‐specific infiltration and release of growth factor at the injury site early in muscle regeneration.
The evaluation of children with prolonged cough accompanied by American College of Chest Physicians guidelines
Authors: Karabel Müsemma , Kelekçi Selvi , Karabel Duran , Gürkan Mehmet Fuat 
Published: August 2013

AbstractIntroductionIn children, coughs lasting longer than 4 weeks are considered to be chronic, with etiological factors varying widely.ObjectiveThis study included children with chronic cough who were followed for 1 year. All cases were evaluated with the guidance of the American College of Chest Physicians (ACCP), and etiological factors were analyzed.MethodsThe study included 270 children between the ages of 2 months and 14 years. Their presenting symptoms, physical examination findings and laboratory data were recorded. All patients underwent laboratory tests including direct chest X‐ray and spirometric measurements. Several patients required additional advanced examinations such as a sweat test, determination of immunoglobulin levels and bronchoscopy. Patients were reevaluated according to ACCP recommendations, and etiological factors were investigated.ResultsThe total of 270 patients were included in the study included 43.3% (n = 153) females with a mean age of 6.5 ± 2.3 years (7 months to 17 years). After a 1‐year follow‐up of patients, we determined that the most common etiologic factors were asthma (27%), asthma‐like syndrome (15.5%) and gastroesophageal reflux (10%). Other etiological factors included upper airway cough syndrome and protracted bronchitis, respectively.ConclusionThe use of a standardized clinical approach such as the ACCP increases the possibility for fast and accurate diagnosis during the treatment of children with chronic cough, and the use of these guidelines should be required.
Neuroprotection and reduction of glial reaction by cannabidiol treatment after sciatic nerve transection in neonatal rats
Authors: Perez Matheus , Benitez Suzana U. , Cartarozzi Luciana P. , del Bel Elaine , Guimarães Francisco S. , Oliveira Alexandre L. R. 
Published: August 2013

AbstractIn neonatal rats, the transection of a peripheral nerve leads to an intense retrograde degeneration of both motor and sensory neurons. Most of the axotomy‐induced neuronal loss is a result of apoptotic processes. The clinical use of neurotrophic factors is difficult due to side effects and elevated costs, but other molecules might be effective and more easily obtained. Among them, some are derived from Cannabis sativa. Cannabidiol (CBD) is the major non‐psychotropic component found on the surface of such plant leaves. The present study aimed to investigate the neuroprotective potential of CBD. Thus, 2‐day‐old Wistar rats were divided into the following experimental groups: sciatic nerve axotomy + CBD treatment (CBD group), axotomy + vehicle treatment (phosphate buffer group) and a control group (no‐treatment group). The results were analysed by Nissl staining, immunohistochemistry and terminal deoxynucleotidyl transferase dUTP nick end labeling at 5 days post‐lesion. Neuronal counting revealed both motor and sensory neuron rescue following treatment with CBD (15 and 30 mg/kg). Immunohistochemical analysis (obtained by synaptophysin staining) revealed 30% greater synaptic preservation within the spinal cord in the CBD‐treated group. CBD administration decreased the astroglial and microglial reaction by 30 and 27%, respectively, as seen by glial fibrillary acidic protein and ionised calcium binding adaptor molecule 1 immunolabeling quantification. In line with such results, the terminal deoxynucleotidyl transferase dUTP nick end labeling reaction revealed a reduction of apoptotic cells, mostly located in the spinal cord intermediate zone, where interneurons promote sensory–motor integration. The present results show that CBD possesses neuroprotective characteristics that may, in turn, be promising for future clinical use.
Development of a Children's Version of the SCORE Index of Family Function and Change
Authors: Jewell Tom , Carr Alan , Stratton Peter , Lask Judith , Eisler Ivan 
Published: August 2013

The Systemic Clinical Outcome and Routine Evaluation (SCORE) Index of Family Function and Change is a recently developed outcome measure. It was designed to be acceptable to adults and children aged 12 and over. Thus far no research has been conducted using the SCORE in children under the age of 12. The aim of this study was to pilot a children's version of the SCORE. An existing 29‐item version of the SCORE was completed by a sample of seven children aged 8–10. Time was allowed for group discussion with the children. Feedback from this stage of the study was used to develop a draft version of the SCORE for children. An expert panel of clinicians and researchers were also consulted. A pilot version of the Child SCORE was administered to 80 children aged 7–10 in an inner London primary school. Thirty‐five children also completed the measure for a second time, 1 week later. Findings suggested that the Child SCORE was acceptable to children in the 8–11 age range. Values for internal reliability and test–retest reliability were good. The Child SCORE appears to be a promising instrument. Further research is required to confirm its acceptability to clinical populations, and to demonstrate sensitivity to change.
The transporter–opsin–G protein‐coupled receptor (TOG) superfamily
Authors: Yee Daniel C. , Shlykov Maksim A. , Västermark Åke , Reddy Vamsee S. , Arora Sumit , Sun Eric I. , Saier Milton H. 
Published: August 2013

Visual rhodopsins are recognized members of the large and diverse family of G protein‐coupled receptors (GPCRs), but their evolutionary origin and relationships to other proteins are not known. In a previous paper [Shlykov MA, Zheng WH, Chen JS & Saier MH Jr (2012) Biochim Biophys Acta 1818, 703–717], we characterized the 4‐toluene sulfonate uptake permease (TSUP) family of transmembrane proteins, and showed that these 7‐transmembrane segment (TMS) or 8‐TMS proteins arose by intragenic duplication of a gene encoding a 4‐TMS protein, sometimes followed by loss of a terminal TMS. In this study, we show that the TSUP, GPCR and microbial rhodopsin families are related to each other and to six other currently recognized transport protein families. We designate this superfamily the transporter/opsin/G protein‐coupled receptor (TOG) superfamily. Despite their 8‐TMS origins, the members of most constituent families exhibit 7‐TMS topologies that are well conserved, and these arose by loss of either the N‐terminal TMS (more frequent) or the C‐terminal TMS (less frequent), depending on the family. Phylogenetic analyses revealed familial relationships within the superfamily and protein relationships within each of the nine families. The results of the statistical analyses leading to the conclusion of homology were confirmed using hidden Markov models, Pfam and 3D superimpositions. Proteins functioning by dissimilar mechanisms (channels, primary active transporters, secondary active transporters, group translocators and receptors) are interspersed on a phylogenetic tree of the TOG superfamily, suggesting that changes in the transport and energy‐coupling mechanisms occurred multiple times during evolution of this superfamily.