bluuebunny/crossref_metadata_2025_split huggingface dataset:
Upstream Movement of Juvenile Coho Salmon in Relation to Environmental Conditions in a Culvert Test Bed
Authors: Johnson Gary E. , Pearson Walter H. , Southard Susan L. , Mueller Robert P. 
Published: October 2012

AbstractWe measured the upstream passage success of juvenile coho salmon Oncorhynchus kisutch in relation to select experimental factors in a culvert test bed at a salmon rearing facility on the Skookumchuk River in western Washington State. Passage success, the term used for the response variable, was defined as the number of fish in the headwater tank at the end of the test divided by the number of fish released in the tailwater pool at the beginning of the test (2‐ to 17‐h test periods). Passage success was higher for large (139 mm fork length [FL]) than small (55 mm FL) fish, was higher at night than during the day, was not affected by shading, decreased as tailwater pool depth increased (22.9–53.3 cm), and did not differ significantly among the fish densities tested in the tailwater pool (35–141 fish/m3). There was a clear, negative exponential trend in the response relationship between transformed (arcsine of the square root) passage success and culvert discharge (0.028–0.099 m3/s; mean velocities, 0.59–0.98 m/s). The horizontal distribution of fish moving upstream that successfully exited the culvert into the headwater tank was skewed to the right side of the inlet where the reduced‐velocity zone (RVZ) was located. This observation supported the RVZ hypothesis about upstream movement of juvenile salmon in a culvert—fish accomplish upstream movements in roughened culverts via pathways in the low‐velocity, low‐turbulence boundary layer. To facilitate salmonid passage at road crossings, the preferred resource management alternatives are bridges or stream simulation, but in situations where these approaches are constrained by cost or logistics, the hydraulic design of culverts may be appropriate. The findings from these experiments in the culvert test bed are applicable to hydraulic designs of culverts where upstream passage of juvenile salmon is a concern.
Investigating eating disorders in elite gymnasts: Conceptual, ethical and methodological issues
Authors: Tan Jacinta , Bloodworth Andrew , McNamee Mike , Hewitt Jeanette 
Published: October 2012

AbstractElite gymnastics, and other sports where athletes and coaches are particularly concerned with aesthetic considerations, weight and shape, are fields within which the risk of eating disorders may be unusually high. Adolescent gymnasts, developing their own sense of self, at a time of life where body image concerns are common, often compete at the very top of the sport with a need to maintain a body shape and weight optimal for elite performance. Research into this field should address the range of sociological and ethical aspects of eating disorders in elite sport, their prevalence as well as the ethos of the sport itself. This paper addresses a range of conceptual, ethical and methodological issues relevant to conducting research in this sensitive yet important field.
Multinomial modeling and an evaluation of common data-mining algorithms for identifying signals of disproportionate reporting in pharmacovigilance databases
Authors: Johnson Kjell , Guo Cen , Gosink Mark , Wang Vicky , Hauben Manfred 
Published: October 2012

AbstractMotivation: A principal objective of pharmacovigilance is to detect adverse drug reactions that are unknown or novel in terms of their clinical severity or frequency. One method is through inspection of spontaneous reporting system databases, which consist of millions of reports of patients experiencing adverse effects while taking one or more drugs. For such large databases, there is an increasing need for quantitative and automated screening tools to assist drug safety professionals in identifying drug–event combinations (DECs) worthy of further investigation. Existing algorithms can effectively identify problematic DECs when the frequencies are high. However these algorithms perform differently for low-frequency DECs.Results: In this work, we provide a method based on the multinomial distribution that identifies signals of disproportionate reporting, especially for low-frequency combinations. In addition, we comprehensively compare the performance of commonly used algorithms with the new approach. Simulation results demonstrate the advantages of the proposed method, and analysis of the Adverse Event Reporting System data shows that the proposed method can help detect interesting signals. Furthermore, we suggest that these methods be used to identify DECs that occur significantly less frequently than expected, thus identifying potential alternative indications for these drugs. We provide an empirical example that demonstrates the importance of exploring underexpected DECs.Availability: Code to implement the proposed method is available in R on request from the corresponding authors.Contact: kjell@arboranalytics.com or Mark.M.Gosink@Pfizer.comSupplementary information: Supplementary data are available at Bioinformatics online.
A counting renaissance: combining stochastic mapping and empirical Bayes to quickly detect amino acid sites under positive selection
Authors: Lemey Philippe , Minin Vladimir N. , Bielejec Filip , Kosakovsky Pond Sergei L. , Suchard Marc A. 
Published: October 2012

Abstract
Motivation: Statistical methods for comparing relative rates of synonymous and non-synonymous substitutions maintain a central role in detecting positive selection. To identify selection, researchers often estimate the ratio of these relative rates () at individual alignment sites. Fitting a codon substitution model that captures heterogeneity in across sites provides a reliable way to perform such estimation, but it remains computationally prohibitive for massive datasets. By using crude estimates of the numbers of synonymous and non-synonymous substitutions at each site, counting approaches scale well to large datasets, but they fail to account for ancestral state reconstruction uncertainty and to provide site-specific estimates.
Results: We propose a hybrid solution that borrows the computational strength of counting methods, but augments these methods with empirical Bayes modeling to produce a relatively fast and reliable method capable of estimating site-specific values in large datasets. Importantly, our hybrid approach, set in a Bayesian framework, integrates over the posterior distribution of phylogenies and ancestral reconstructions to quantify uncertainty about site-specific estimates. Simulations demonstrate that this method competes well with more-principled statistical procedures and, in some cases, even outperforms them. We illustrate the utility of our method using human immunodeficiency virus, feline panleukopenia and canine parvovirus evolution examples.
Availability: Renaissance counting is implemented in the development branch of BEAST, freely available at http://code.google.com/p/beast-mcmc/. The method will be made available in the next public release of the package, including support to set up analyses in BEAUti.
Contact: philippe.lemey@rega.kuleuven.be or msuchard@ucla.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Novel acid resistance genes from the metagenome of the Tinto River, an extremely acidic environment
Authors: Guazzaroni María‐Eugenia , Morgante Verónica , Mirete Salvador , González‐Pastor José E. 
Published: October 2012

SummaryMicroorganisms that thrive in acidic environments are endowed with specialized molecular mechanisms to survive under this extremely harsh condition. In this work, we performed functional screening of six metagenomic libraries from planktonic and rhizosphere microbial communities of the Tinto River, an extremely acidic environment, to identify genes involved in acid resistance. This approach has revealed 15 different genes conferring acid resistance to Escherichia coli, most of which encoding putative proteins of unknown function or previously described proteins not known to be related to acid resistance. Moreover, we were able to assign function to one unknown and three hypothetical proteins. Among the recovered genes were the ClpXP protease, the transcriptional repressor LexA and nucleic acid‐binding proteins such as an RNA‐binding protein, HU and Dps. Furthermore, nine of the retrieved genes were cloned and expressed in Pseudomonas putida and Bacillus subtilis and, remarkably, most of them were able to expand the capability of these bacteria to survive under severe acid stress. From this set of genes, four presented a broad‐host range as they enhance the acid resistance of the three different organisms tested. These results expand our knowledge about the different strategies used by microorganisms to survive under extremely acid conditions.
Role of nitric oxide and endothelin in endothelial maintenance of vasoconstrictor responses in aortas of diabetic female rats (一氧化氮与内皮素对糖尿病雌性大鼠主动脉血管内皮维持血管收缩反应的影响)
Authors: Sartoretto Simone M. , Santos‐Eichler Rosângela , de Cássia A. Tostes Rita , Carvalho Maria Helena C. , Akamine Eliana H. , Fortes Zuleica B. 
Published: October 2012

AbstractBackgroundDiabetes differentially affects the vascular system in males and females. Although various results have been reported, very few studies have focused on responses in females. In the present study, we investigated contractile responses to norepinephrine in aortas of alloxan‐diabetic female rats and evaluated endothelial modulation of these responses.MethodsConcentration–response curves were constructed to norepinephrine in the absence or presence of NG‐nitro‐l‐arginine methyl ester (l‐NAME), indomethacin, losartan, tezosentan, and calphostin C; pre‐pro‐endothelin mRNA expression was evaluated; and norepinephrine‐stimulated expression of phosphorylated (p‐) Akt Ser473, p‐endothelial nitric oxide synthase (eNOS) Ser1177, and p‐eNOS Ser633 was determined in endothelial cells incubated in the presence of low (5 mmol/L) or high (25 mmol/L) glucose concentrations.ResultsSimilar maximal responses (Rmax) to norepinephrine were seen in control and diabetic endothelium‐intact aortas; however, Rmax was reduced in diabetic endothelium‐denuded aortas. Incubation of endothelium‐intact aortas with 100 μmol/L l‐NAME increased Rmax in the control group only. Inhibition of cyclo‐oxygenase (10 μmol/L indomethacin) and blockade of angiotensin II receptors (10 μmol/L losartan) reduced Rmax in endothelium‐intact aortas in both the control and diabetic groups. Blockade of endothelin receptors (0.1 μmol/L tezosentan) and inhibition of protein kinase C (PKC; 0.1 μmol/L calphostin C) reduced Rmax only in endothelium‐intact aortas from diabetic rats. Pre‐pro‐endothelin mRNA expression was increased in aortas from diabetic female rats. Finally, p‐Akt Ser473, p‐eNOS Ser1177, and p‐eNOS Ser633 levels were enhanced after norepinephrine stimulation only in low glucose‐treated endothelial cells.ConclusionsIn aortas of diabetic female rats, reductions in smooth muscle contractile responses to norepinephrine are counterbalanced by the endothelium via reduced eNOS activation and increased endothelin release and PKC activation.
Telephone Support to Rural and Remote Patients with Heart Failure: The Chronic Heart Failure Assessment by Telephone (CHAT) study
Authors: Krum Henry , Forbes Andrew , Yallop Julie , Driscoll Andrea , Croucher Jo , Chan Bianca , Clark Robyn , Davidson Patricia , Huynh Luan , Kasper Edward K. , Hunt David , Egan Helen , Stewart Simon , Piterman Leon , Tonkin Andrew 
Published: October 2012

SummaryBackgroundHeart failure (HF) remains a condition with high morbidity and mortality. We tested a telephone support strategy to reduce major events in rural and remote Australians with HF, who have limited healthcare access. Telephone support comprised an interactive telecommunication software tool (TeleWatch) with follow‐up by trained cardiac nurses.MethodsPatients with a general practice (GP) diagnosis of HF were randomized to usual care (UC) or UC and telephone support intervention (UC+I) using a cluster design involving 143 GPs throughout Australia. Patients were followed up for 12 months. The primary endpoint was the Packer clinical composite score. Secondary endpoints included hospitalization for any cause, death or hospitalization, as well as HF hospitalization.ResultsFour hundred and five patients were randomized to CHAT. Patients were well matched at baseline for key demographic variables. The primary endpoint of the Packer score was not different between the two groups (P = 0.98), although more patients improved with UC+I. There were fewer patients hospitalized for any cause (74 vs. 114, adjusted HR 0.67 [95% CI 0.50–0.89], P = 0.006) and who died or were hospitalized (89 vs. 124, adjusted HR 0.70 [95% CI 0.53–0.92], P = 0.011), in the UC+I vs. UC group. HF hospitalizations were reduced with UC+I (23 vs. 35, adjusted HR 0.81 [95% CI 0.44–1.38]), although this was not significant (P = 0.43). There were 16 deaths in the UC group and 17 in the UC+I group (P = 0.43).ConclusionsAlthough no difference was observed in the primary endpoint of CHAT (Packer composite score), UC+I significantly reduced the number of HF patients hospitalized among a rural and remote cohort. These data suggest that telephone support may be an efficacious approach to improve clinical outcomes in rural and remote HF patients.
The Effect of Prethrombolytic Cyclosporine‐A Injection on Clinical Outcome of Acute Anterior ST‐Elevation Myocardial Infarction
Authors: Ghaffari Samad , Kazemi Babak , Toluey Mehdi , Sepehrvand Nariman 
Published: October 2012

SummaryIntroductionReperfusion injury reduces the benefits of early reperfusion therapies after acute ST‐elevation myocardial infarction (STEMI). Cyclosporine‐A (CsA) is a potent inhibitor of opening of the mitochondrial permeability transition pore, which has been shown to play a key role in myocardial reperfusion injury. The impact of this treatment on clinical outcomes of acute STEMI remains unknown. Our aim was to investigate the clinical outcomes of using this drug in patients with acute anterior STEMI receiving thrombolytic treatment (TLT).MethodsIn this double‐blinded randomized clinical trial, 101 patients with acute anterior STEMI who were candidate for TLT, were enrolled and randomly assigned into treatment or control groups. Patients in the treatment group received an intravenous bolus injection of 2.5 mg/kg of CsA immediately before TLT. The patients in the control group received an equivalent volume of normal saline. Infarct size, occurrence of major arrhythmias, heart failure, left ventricular ejection fraction (LVEF), TLT‐related complications, in‐hospital and 6‐month mortality rates were investigated.ResultsThere were no significant differences among the demographics, myocardial enzyme release, occurrence of major arrhythmias [9 (18%) vs. 12 (23.5%), P = 0.80], heart failure [18 (36%) vs. 19 (38.3%), P = 0.83], LVEF at first day [34.7 ± 9.9% vs. 33.5 ± 8.1%, P = 0.50] or at discharge [37.7 ± 10% vs. 36.1 ± 8.2%, P = 0.43], and in‐hospital [4 (8%) vs. 6 (11.8%), P = 0.74] or 6‐month mortality rates [9 (18%) vs. 10 (19.6%), P = 0.99] between the CsA vs. the control group.ConclusionIn this study, the prethrombolytic administration of CsA was not associated with a reduction in the infarct size or any improvement in clinical outcomes.
Gene expression analysis of mTOR pathway: association with human longevity
Authors: Passtoors Willemijn M. , Beekman Marian , Deelen Joris , van der Breggen Ruud , Maier Andrea B. , Guigas Bruno , Derhovanessian Evelyna , van Heemst Diana , de Craen Anton J. M. , Gunn David A. , Pawelec Graham , Slagboom Pieternella E. 
Published: October 2012

SummarymTOR signalling is implicated in the development of disease and in lifespan extension in model organisms. This pathway has been associated with human diseases such as diabetes and cancer, but has not been investigated for its impact on longevity per se. Here, we investigated whether transcriptional variation within the mTOR pathway is associated with human longevity using whole‐blood samples from the Leiden Longevity Study. This is a unique cohort of Dutch families with extended survival across generations, decreased morbidity and beneficial metabolic profiles in middle‐age. By comparing mRNA levels of nonagenarians and middle‐aged controls, the mTOR signalling gene set was found to associate with old age (P = 4.6 × 10−7). Single gene analysis showed that seven of 40 mTOR pathway genes had a significant differential expression of at least 5%. Of these, the RPTOR (Raptor) gene was found to be differentially expressed also when the offspring of nonagenarians was compared with their spouses, indicating association with familial longevity in middle‐age. This association was not explained by variation between the groups in the prevalence of type 2 diabetes and cancer or glucose levels. Thus, the mTOR pathway not only plays a role in the regulation of disease and aging in animal models, but also in human health and longevity.
Deficiency of ovarian ornithine decarboxylase contributes to aging‐related egg aneuploidy in mice
Authors: Tao Yong , Liu X. Johné 
Published: October 2012

SummaryIt has been known for more than four decades that during mammalian estrous cycles, luteinizing hormone stimulates a transitory rise in the ovaries of ornithine decarboxylase (ODC) activity and its enzymatic product putrescine, concurrent with oocyte maturation in vivo. Inhibition of this transitory ODC/putrescine rise, however, does not appear to affect oocyte maturation or ovulation. Using several mouse models and combining in vitro and in vivo approaches, we demonstrated that deficiency of ODC during oocyte maturation is correlated with increased levels of egg aneuploidies. These results suggest that the transitory ovarian ODC rise in late proestrus is important for ensuring proper chromosome segregation during oocyte maturation. Older mice (8 months of age) exhibited about 1/3 that of young mice in LH‐stimulated ovarian ODC activity and a corresponding increase in egg aneuploidies. Moreover, a combination of putrescine supplementation in mouse drinking water leading up to oocyte retrieval and in oocyte maturation medium reduced egg aneuploidies of the older mice from 12.7% to 5.3%. Therefore, ovarian ODC deficiency might be an important etiology of maternal aging‐related aneuploidies, and peri‐ovulatory putrescine supplementation might reduce the risk of aneuploid conceptions in older women.
Adherence of Streptococcus mutans to orthodontic band cements
Authors: Gonzalez‐Perez JC , Scougall‐Vilchis RJ , Contreras‐Bulnes R , De La Rosa‐Gómez I , Uematsu S , Yamaguchi R 
Published: October 2012

AbstractBackground:  The aim of this study was to quantitatively determine the adherence of Streptococcus mutans to orthodontic band cements.Methods:  Two hundred and ten blocks of seven different band cements for orthodontic prescription were made using a Teflon mould (4 × 4 × 1 mm). The obtained blocks were slightly polished and cleansed ultrasonically. Certified S. mutans ATCC 25175 were cultured with conventional methods for growth in Petri dishes and trypticase soy broth. Quantitative analysis was carried out with radioactive markers to codify the bacteria (3H). Subsequently, a combustion system was used to capture the residues, the radioactivity of the samples was measured, and the values recorded in disintegrations per minute (dpm). One‐way analysis of variance (ANOVA) with a Scheffé test for multiple comparisons was realized with a significance level of ≤0.05.Results:  Significant differences were found among different band cement materials (p < 0.001). Two band cement materials showed statistically lower values than the others (Transbond Plus Band Cem and Ketac Cem). In contrast, GC Fuji Ortho Band presented the highest adherence of S. mutans.Conclusions:  Among the cements evaluated, Transbond Plus Band Cem and Ketac Cem showed lower adherence of S. mutans.
Female Genital Cutting and HIV Transmission: Is There an Association?
Authors: Diouf Khady , Nour Nawal 
Published: October 2012

Female Genital Cutting (FGC) refers to the practice of surgically removing all or part of the female external genitalia for non‐medical purposes. It is a common practice in many countries in Africa, the Middle East, and to a lesser extent, Asia. Over 130 million women worldwide have undergone this procedure, and over 2 million women and girls are subject to it every year. Various complications have been described, including infection, hemorrhage, genitourinary and obstetric complications, as well as psychological sequelae. Since the beginning of the HIV epidemic, a few reports have also described a potentially elevated risk of HIV transmission among women with FGC. In this report, we aim to review the evidence and identify unanswered questions and research gaps regarding a potential association between FGC and HIV transmission.
The rASRM score and the Enzian classification for endometriosis: their strengths and weaknesses
Authors: HAAS DIETMAR , SHEBL OMAR , SHAMIYEH ANDREAS , OPPELT PETER 
Published: October 2012

AbstractThe revised American Society for Reproductive Medicine (rASRM) score is currently the best‐known classification of endometriosis and is the one most widely used throughout the world. It is relatively easy to use, but it does not take into account the involvement of retroperitoneal structures with deeply infiltrating endometriosis. For this reason, the Enzian classification was developed as a supplement to the rASRM score, in order to provide a morphologically descriptive classification of deeply infiltrating endometriosis. The Enzian classification currently has a poor level of international acceptance and is mainly used in the German‐speaking countries. It was revised in 2011 and is now also easier to use. This article describes the strengths and weaknesses of the rASRM score and the Enzian classification and their common potential for classifying endometriosis.
Effect of play‐based summer break exercise on cardiovascular function in adolescents
Authors: Meucci Marco , Curry Chelsea D , Baldari Carlo , Guidetti Laura , Cook Carol , Collier Scott R 
Published: October 2012

AbstractAimTo compare the effects of 4 and 8 weeks of play‐based, supervised exercise during summer break versus an unsupervised break on cardiovascular function in adolescent children.MethodsTwenty‐two subjects were divided into a 4‐week exercise group (age 10.1 ± 1.3 years), an 8‐week exercise group (age 9.4 ± 1.7 years) or a control group (age 10.0 ± 1.3 years). The activity groups participated in a supervised summer camp for 6 h/day, 5 days/week including a discontinuous play‐based physical activity program and a healthy lifestyle, while the control group were told to keep their regular summer break routines. Anthropometrics, pulse wave velocity, augmentation index, blood pressure and peak oxygen consumption were evaluated before and after the intervention.ResultsNormalized augmentation index (75 beats/min) significantly decreased after 4 and 8 weeks in the active groups (p = 0.04) while pulse wave velocity showed no significant changes in all groups. Mean arterial pressure decreased (p = 0.003) and peak oxygen consumption increased (p = 0.001) significantly in the 8 week group.ConclusionThese data suggest that 8 weeks of supervised play‐based activity yield several cardio‐beneficial results in adolescents, which may act as a clinical prophylaxis throughout their lifetime.