bluuebunny/crossref_metadata_2025_split huggingface dataset:
Extracting fish and water velocity from Doppler profiler data
Authors: Zedel Len , Cyr-Racine Francis-Yan 
Published: June 2009

Abstract
Zedel, L., and Cyr-Racine, F-Y. 2009. Extracting fish and water velocity from Doppler profiler data. – ICES Journal of Marine Science, 66: 1846–1852. Doppler current profilers are optimized for measuring water velocities, but have the demonstrated capability to measure fish swimming speeds. This is possible when fish form schools that are large enough for all multiple Doppler sonar beams to sample the fish speeds at the same time. In situations where fish are not present in at least three acoustic beams, it is impossible to extract fish velocity with the data-processing algorithms normally used to extract water velocity. We present an alternative method of analysing Doppler sonar data that treats data from individual acoustic beams independently, so that velocities can be extracted when fish appear intermittently in the sonar beams. The method determines the variance for each velocity estimate so that data averaging can be adjusted to achieve the desired accuracy. The algorithm is applied to extract both water and fish velocities from Doppler profiler observations of overwintering Atlantic cod (Gadus morhua) in Smith Sound, Newfoundland. Currents in this enclosed coastal area are slow (∼10 cm s−1), and the fish appear to move passively with the water much of the time. However, there are times when the fish have velocities different from those of the water, and profiles averaged over 20 d show clear differences in fish and water velocities.
Oscillating reproductive strategies of herring in the western Atlantic in response to changing environmental conditions
Authors: Melvin Gary D. , Stephenson Robert L. , Power Michael J. 
Published: June 2009

Abstract
Melvin, G. D., Stephenson, R. L., and Power, M. J. 2009. Oscillating reproductive strategies of herring in the western Atlantic in response to changing environmental conditions. – ICES Journal of Marine Science, 66: 1784–1792. Herring are broadly distributed in the western Atlantic, but reproductive activity is restricted to the central portion, from Cape Cod to northern Newfoundland. Spawning extends from early spring to late autumn. Two spawning types are recognized: spring spawners and autumn spawners. At the southern extreme, spawning occurs almost exclusively in autumn, whereas in the north, spring spawners prevail. Mid-range, both strategies are common, with spawning occurring throughout the entire season. We postulate that the temporal intra-stock dominance of spawning type is an adaptive reproductive strategy to changing environmental conditions. A conceptual model is presented to describe how reproductive success can oscillate between spawning strategies. In most years, environmental conditions appear to favour one type or the other, although strong year classes can co-occur when conditions are right. The recent change in environmental conditions, characterized by a general warming trend, favours autumn spawners and is consistent with our model. At the distributional extremes, stocks are restricted to a single spawning strategy, and broad-scale environmental changes can introduce large interannual variability and limit the reproductive and recovery potential of a stock. The dependence of a stock on a single spawning season may result in longer times to recover to target levels.
Dispersal and settlement of sea scallop larvae spawned in the fishery closed areas on Georges Bank
Authors: Tian Rucheng C. , Chen Changsheng , Stokesbury Kevin D. E. , Rothschild Brian J. , Cowles Geoffrey W. , Xu Qichun , Hu Song , Harris Bradley P. , Marino Michael C. 
Published: June 2009

Abstract
Tian, R. C., Chen, C., Stokesbury, K. D. E., Rothschild, B. J., Cowles, G. W., Xu, Q., Hu, S., Harris, B. P., and Marino II, M. C. 2009. Dispersal and settlement of sea scallop larvae spawned in the fishery closed areas on Georges Bank. – ICES Journal of Marine Science, 66: 2155–2164. Three fishery closed areas in the Georges Bank (GB) region were implemented in 1994 to protect depleted groundfish stocks for population replenishment. However, the drift and ultimate destination of larvae spawned in the closed areas have not been analysed specifically within the framework of ocean currents. To assess the efficiency of the closed areas as population replenishment sources, we conducted a simulation-based analysis on the dispersal and settlement of sea scallop larvae spawned in the closed areas from 1995 to 2005 using circulation fields computed by the Finite-Volume Coastal Ocean Model, scallop survey data, and a population dynamics model. Closed area I located in the Great Southern Channel (GSC) had a persistently high rate of larval retention (86% on average). For closed area II located on eastern GB, a considerable quantity of larvae was dispersed out of the domain. For the Nantucket Lightship Closed Area located on Nantucket Shoals, larvae consistently drifted away from the region during the 11 years simulated. Our simulation revealed three high-retention regions that are the most suitable for closed-area selection and rotational fishery management in terms of larval supply to the GB–GSC region.
Adrenomedullin treatment reduces intestinal inflammation and maintains epithelial barrier function in mice administered dextran sulphate sodium
Authors: Ashizuka Shinya , Inagaki‐Ohara Kyoko , Kuwasako Kenji , Kato Johji , Inatsu Haruhiko , Kitamura Kazuo 
Published: June 2009

ABSTRACTHyperactivation and hyperpermeability of the intestinal epithelium is a hallmark of IBD. AM has been shown to reduce the severity of colitis in the acetic acid and TNBS‐induced colitis model, however the mechanism of the therapeutic effect of AM against the colitis has not been clarified. Here, we show that the protective capability of AM is associated with suppression of inflammation and maintenance of the intestinal epithelial barrier function. In the DSS‐induced colitis model, intra‐rectal AM‐treated mice showed a reduction in loss of body weight and severity of colitis. AM‐treatment suppressed phosphorylation of STAT1 and STAT3 in the colonic epithelium, and altered the cytokine balance in the intestinal T cells, with lower levels of IFN‐γ and TNF‐α but higher levels of TGF‐β. Expression of the epithelial intercellular junctions such as tight and adherence junctions were sustained in the AM‐treated mice. In contrast, the epithelial junctions were down‐regulated in the control mice, leading to loss of epithelial barrier integrity and enhanced permeability. Collectively, these data indicate a broad spectrum of AM‐induced effects with respect to protection against DSS‐induced colitis, and suggest a potential therapeutic value of this treatment for IBD.
Identification of PAK4 as a putative target gene for amplification within 19q13.12‐q13.2 in oral squamous‐cell carcinoma
Authors: Begum Asma , Imoto Issei , Kozaki Ken‐ichi , Tsuda Hitoshi , Suzuki Emina , Amagasa Teruo , Inazawa Johji 
Published: June 2009

Amplification of chromosomal DNA is thought to be one of the mechanisms activating cancer‐related genes in tumors. To identify the most likely target for amplification in the region 19q13.12‐q13.2, detected previously in SKN‐3 cells by a genome‐wide screening of DNA copy‐number aberrations in a panel of oral squamous‐cell carcinoma (OSCC) cell lines, we determined the extent of the amplicon, analyzed a panel of cell lines for the expression of candidate genes within the amplicon, and then evaluated growth‐suppressive effects by knocking down genes of interest. Reported information about the function and/or expression of each gene, remarkable overexpression in SKN‐3 cells and relatively frequent overexpression in additional OSCC lines compared with an immortalized normal oral epithelial cell line, and expression level–dependent proliferation‐promoting activity led us to conclude that the p21‐activated kinase 4 (PAK4) gene was the most likely target. An immunohistochemical analysis of primary tumors from 105 cases of head and neck SCC including 50 cases of OSCC demonstrated the overexpression of PAK4 to be significantly associated with a poorer prognosis. These findings reveal that the PAK4 overexpression through amplification or other mechanisms promotes the proliferation and/or survival of OSCC cells, and that PAK4 might be a good diagnostic and/or therapeutic target. (Cancer Sci 2009; 100: 1908–1916)
Inhibitory effects of epigallocatechin‐3 gallate, a polyphenol in green tea, on tumor‐associated endothelial cells and endothelial progenitor cells
Authors: Ohga Noritaka , Hida Kyoko , Hida Yasuhiro , Muraki Chikara , Tsuchiya Kunihiko , Matsuda Kohei , Ohiro Yoichi , Totsuka Yasunori , Shindoh Masanobu 
Published: June 2009

The polyphenol epigallocatechin‐3 gallate (EGCG) in green tea suppresses tumor growth by direct action on tumor cells and by inhibition of angiogenesis, but it is not known whether it specifically inhibits tumor angiogenesis. We examined the anti‐angiogenic effect of EGCG on tumor‐associated endothelial cells (TEC), endothelial progenitor cells (EPC), and normal endothelial cells (NEC). EGCG suppressed the migration of TEC and EPC but not NEC. EGCG also inhibited the phosphorylation of Akt in TEC but not in NEC. Furthermore, vascular endothelial growth factor‐induced mobilization of EPC into circulation was inhibited by EGCG. MMP‐9 in the bone marrow plasma plays key roles in EPC mobilization into circulation. We observed that expression of MMP‐9 mRNA was downregulated by EGCG in mouse bone marrow stromal cells. In an in vivo model, EGCG suppressed growth of melanoma and reduced microvessel density. Our study showed that EGCG has selective anti‐angiogenic effects on TEC and EPC. It is suggested that EGCG could be a promising angiogenesis inhibitor for cancer therapy. (Cancer Sci 2009; 100: 1963–1970)
Phase I clinical study of a peptide vaccination for hepatitis C virus‐infected patients with different human leukocyte antigen‐class I‐A alleles
Authors: Yutani Shigeru , Komatsu Nobukazu , Shichijo Shigeki , Yoshida Kazumi , Takedatsu Hiroko , Itou Minoru , Kuromatu Ryoko , Ide Tatsuya , Tanaka Masatoshi , Sata Michio , Yamada Akira , Itoh Kyogo 
Published: June 2009

Hepatitis C virus (HCV) infection has a high risk of liver cirrhosis and hepatocellular carcinoma at later stages. We recently identified a peptide derived from the HCV core protein capable of inducing both cellular and humoral responses to nearly all HCV‐positive patients in Japan with different human leukocyte antigen (HLA)‐class I‐A alleles. To assess the safety and immune responses to this novel peptide, we conducted a phase I dose‐escalation study of the vaccination for 26 HCV‐positive patients who were either non‐responders to the interferon‐based therapy (n = 23) or refused it (n = 3). The regimen was well tolerated, with no severe vaccine‐related toxicity. Twenty‐five and 22 patients completed the first and second cycle vaccination (6 and 12 vaccine injections), respectively. After a series of six vaccine injections, peptide‐specific CTL activity was augmented in peripheral blood mononuclear cells from 15 of 25 patient samples, with an expected optimal dose of 1 mg peptide. After 12 vaccine injections, peptide‐specific IgG production was augmented in plasma from the majority of patients (15 of 22 patients) tested, but not in a dose‐dependent fashion. There were two HCV RNA responders with >1 log declines. Among patients whose pre‐vaccination levels of alanine aminotransferase and alpha feto‐protein exceeded the normal ranges, a <30% decrease was found in 7 of 24 and three of six patients, respectively. Because of its tolerability and higher rate of immune boosting, this protocol is recommended for a phase II study to investigate its clinical efficacy. (Cancer Sci 2009; 100: 1935–1942)
Prostaglandin E2, Wnt, and BMP in gastric tumor mouse models
Authors: Oshima Hiroko , Oguma Keisuke , Du Yu‐Chen , Oshima Masanobu 
Published: June 2009

The development of gastric cancer is closely associated with Helicobacter pylori (H. pylori) infection. The expression of cylooxigenase‐2 (COX‐2), a rate‐limiting enzyme for prostaglandin biosynthesis, is induced in H. pylori‐associated chronic gastritis, which thus results in the induction of proinflammatory prostaglandin, PGE2. The COX‐2/PGE2 pathway plays a key role in gastric tumorigenesis. On the other hand, several oncogenic pathways have been shown to trigger gastric tumorigenesis. The activation of Wnt/β‐catenin signaling is found in 30–50% of gastric cancers, thus suggesting that Wnt signaling plays a causal role in gastric cancer development. Mutations in the bone morphogenetic protein (BMP) signaling pathway are responsible for the subset of juvenile polyposis syndrome (JPS) that develops hamartomas in the gastrointestinal tract. BMP suppression appears to contribute to gastric cancer development because gastric cancer risk is increased in JPS. Wnt signaling is important for the maintenance of gastrointestinal stem cells, while BMP promotes epithelial cell differentiation. Accordingly, it is possible that both Wnt activation and BMP suppression can cause gastric tumorigenesis through enhancement of the undifferentiated status of epithelial cells. Recent mouse model studies have indicated that induction of the PGE2 pathway is required for the development of both gastric adenocarcinoma and hamartoma in the Wnt‐activated and BMP‐suppressed gastric mucosa, respectively. This article reviews the involvement of the PGE2, Wnt, and BMP pathways in the development of gastric cancer, and gastric phenotypes that are found in transgenic mouse models of PGE2 induction, Wnt activation, BMP suppression, or a combination of these pathways. (Cancer Sci 2009; 100: 1779–1785)
Cellular characterization of the peritumoral edema zone in malignant brain tumors
Authors: Engelhorn Tobias , Savaskan Nic E. , Schwarz Marc A. , Kreutzer Jürgen , Meyer Eric P. , Hahnen Eric , Ganslandt Oliver , Dörfler Arnd , Nimsky Christopher , Buchfelder Michael , Eyüpoglu Ilker Y. 
Published: June 2009

Brain edema is a hallmark of human malignant brain tumors and contributes to the clinical course and outcome of brain tumor patients. The so‐called perifocal edema or brain swelling imposes in T2‐weighted MR scans as high intensity areas surrounding the bulk tumor mass. The mechanisms of this increased fluid attraction and the cellular composition of the microenvironment are only partially understood. In this study, we focus on imaging perifocal edema in orthotopically implanted gliomas in rodents and correlate perifocal edema with immunohistochemical markers. We identified that areas of perifocal edema not only include the tumor invasion zone, but also are associated with increased glial fibrillary acidic protein (GFAP) and aquaporin‐4 expression surrounding the bulk tumor mass. Moreover, a high number of activated microglial cells expressing CD11b and macrophage migration inhibitory factor (MIF) accumulate at the tumor border. Thus, the area of perifocal edema is mainly dominated by reactive changes of vital brain tissue. These data corroborate that perifocal edema identified in T2‐weighted MR scans are characterized with alterations in glial cell distribution and marker expression forming an inflammatory tumor microenvironment. (Cancer Sci 2009; 100: 1856–1862)
Efficacy of methotrexate in Crohn’s disease and ulcerative colitis patients unresponsive or intolerant to azathioprine /mercaptopurine
Authors: WAHED M. , LOUIS‐AUGUSTE J. R. , BAXTER L. M. , LIMDI J. K. , MCCARTNEY S. A. , LINDSAY J. O. , BLOOM S. L. 
Published: June 2009

SummaryBackground  Despite the wide use of azathioprine/mercaptopurine (AZA/MP) therapy in the management of both Crohn’s disease (CD) and ulcerative colitis (UC), approximately 20% of patients cannot tolerate the drugs and 30% do not respond.Aim  To examine the efficacy and safety profile of methotrexate (MTX) in patients with CD or UC who are either intolerant or non‐responsive to AZA/MP.Methods  A total of 131 patients with IBD treated with MTX were identified. Retrospective data were obtained by case note review. Clinical response (defined as steroid withdrawal, normalization of previously raised CRP or physician’s clinical assessment of improvement) was assessed at 6 months.Results  Clinical response in Crohn’s disease occurred in 18 of 29 patients (62%) refractory to AZA/MP and 42 of 70 patients (60%) intolerant to AZA/MP, with no difference between the groups (P = 1.0). In UC, clinical response was seen in 7 of 9 (78%) patients refractory to AZA/MP and 15 of 23 (65%) intolerant to thiopurines. MTX was well tolerated in a majority of individuals.Conclusions  Methotrexate appears effective in both CD and UC patients who fail to respond to or are intolerant to AZA/MP therapy.
Irritable bowel syndrome is strongly associated with generalized anxiety disorder: a community study
Authors: LEE S. , WU J. , MA Y. L. , TSANG A. , GUO W.‐J. , SUNG J. 
Published: June 2009

SummaryBackground  No previous study has examined the comorbidity of Irritable Bowel Syndrome (IBS) and Generalized Anxiety Disorder (GAD) in a general population using standardized diagnostic methods.Aim  To examine the prevalence, comorbidity and risk correlates of IBS and GAD in a general population.Methods  A random community‐based telephone survey was conducted. The questionnaire covered symptoms of IBS, GAD, core depressive symptoms, help‐seeking behaviour and functional impairment on the Sheehan Disability Scale.Results  A total of 2005 participants completed the interview. The current prevalence of IBS was 5.4% and the 12‐month prevalence of GAD was 4%. GAD was five times more common among IBS respondents than non‐IBS respondents (OR: 5.84, P < 0.001), whereas IBS was 4.7 times more common among GAD respondents than among non‐GAD respondents (OR: 6.32, P < 0.001). Core depressive symptoms (OR: 6.25, P < 0.01) and education level (OR: 5.918, P = 0.021) were risk correlates of GAD among IBS respondents. Comorbid respondents were more impaired than respondents having either disorder alone, but were not more likely to seek professional help than IBS‐only respondents.Conclusion  Irritable Bowel Syndrome and GAD comorbidity was common and added to impairment in the community. The strong association between psychiatric morbidity and IBS observed in referral centres was not a consequence of increased help‐seeking behaviour.
Systematic review: secondary prevention with band ligation, pharmacotherapy or combination therapy after bleeding from oesophageal varices
Authors: CHEUNG J. , ZEMAN M. , Van ZANTEN S. V. , TANDON P. 
Published: June 2009

SummaryBackground  Variable methods are available for secondary prevention after oesophageal variceal bleeding (EVB).Aim  To compare band ligation (BL), pharmacotherapy (PT) and BL+PT for EVB secondary prevention.Methods  A systematic search of databases, references and meeting abstracts was conducted for randomized trials of BL, PT or BL+PT. The outcomes were mortality, rebleeding and adverse events. A random‐effects model was used for meta‐analyses.Results  Twelve trials were included (6 BL vs. PT, 4 BL+PT vs. BL, 2 BL+PT vs. PT). All trials used beta‐blockers ± isosorbide mononitrate (ISMN) as PT. Mortality was not significantly different among trials. Rebleeding was not significantly different for BL vs. PT (RR 1.00, 95% CI 0.73–1.37). BL reduced rebleeding compared with PT for trials with mean beta‐blocker dose <80 mg/day (RR 0.67, 95% CI 0.49–0.91). There were nonsignificant differences in rebleeding for BL+PT vs. BL (RR 0.57, 95% CI 0.31–1.08) and BL+PT vs. PT (RR 0.76, 95% CI 0.56–1.03). There was no difference in adverse events between BL vs. PT, but was higher with BL+PT vs. BL.Conclusion  Band ligation and PT alone are comparable for secondary prevention of rebleeding after EVB. Further trials with adequate PT dosing are required to determine the efficacy of combination BL+PT therapy.
Transmitochondrial embryonic stem cells containing pathogenic mtDNA mutations are compromised in neuronal differentiation
Authors: Kirby D. M.  , Rennie K. J.  , Smulders‐Srinivasan T. K.  , Acin‐Perez R.  , Whittington M.  , Enriquez J.‐A.  , Trevelyan A. J.  , Turnbull D. M.  , Lightowlers R. N.  
Published: June 2009

AbstractObjectives:  Defects of the mitochondrial genome (mtDNA) cause a series of rare, mainly neurological disorders. In addition, they have been implicated in more common forms of movement disorders, dementia and the ageing process. In order to try to model neuronal dysfunction associated with mitochondrial disease, we have attempted to establish a series of transmitochondrial mouse embryonic stem cells harbouring pathogenic mtDNA mutations.Materials and methods:  Transmitochondrial embryonic stem cell cybrids were generated by fusion of cytoplasts carrying a variety of mtDNA mutations, into embryonic stem cells that had been pretreated with rhodamine 6G, to prevent transmission of endogenous mtDNA. Cybrids were differentiated into neurons and assessed for efficiency of differentiation and electrophysiological function.Results:  Neuronal differentiation could occur, as indicated by expression of neuronal markers. Differentiation was impaired in embryonic stem cells carrying mtDNA mutations that caused severe biochemical deficiency. Electrophysiological tests showed evidence of synaptic activity in differentiated neurons carrying non‐pathogenic mtDNA mutations or in those that caused a mild defect of respiratory activity. Again, however, neurons carrying mtDNA mutations that resulted in severe biochemical deficiency had marked reduction in post‐synaptic events.Conclusions:  Differentiated neurons carrying severely pathogenic mtDNA defects can provide a useful model for understanding how such mutations can cause neuronal dysfunction.
Service user participation in diverse child protection contexts: principles for practice
Authors: Healy Karen , Darlington Yvonne 
Published: June 2009

ABSTRACTPromoting the participation of children and parents in child protection practice is one of the most complex and sensitive areas of social work practice. Increasingly, child protection legislation and policy in many parts of the world enshrines ideals of service user participation. Yet, with the exception of extensive discussion about family group conferencing, the principles and methods for achieving participatory practices in child protection work remain underdeveloped. We use the term ‘child protection’ to refer to a broad spectrum of child and family welfare services aimed at prevention of (or intervention to address) child abuse and neglect. This spectrum of services includes intensive family support, family support, domestic violence, statutory child protection and child and family advocacy services. In this paper, we present findings from the first phase of a 3‐year study into participatory practice in child protection. In this paper, we present findings from a qualitative analysis of interviews with 28 child protection practitioners across five domains of child protection work. Our analysis reveals three core principles of participatory practice underpinning these practitioners' accounts as well as contextual differences among them. We conclude with a discussion of the educational implications of our findings.