bluuebunny/crossref_metadata_2025 huggingface dataset:
Adjustment Scales for Children and Adolescents: Factorial Validity Generalization with Hispanic/Latino Youths
Authors: Canivez Gary L. , Sprouls Katie
Published: November 2009

Replication of the Adjustment Scales for Children and Adolescents (ASCA) core syndrome factor structure with a sample of 124 randomly selected Hispanic/Latino youths is reported. The six ASCA core syndromes produced the identical two-factor solution observed in other samples. Principal-axis exploratory factor analysis using multiple factor extraction criteria and varimax, direct oblimin, and promax rotations produced nearly identical factor structure coefficients. Consistent with earlier studies, the ASCA was observed to measure two independent dimensions of youth psychopathology (Overactivity and Underactivity) that are similar to the conduct problems/ externalizing and withdrawal/internalizing dimensions typically found in the child psychopathology assessment literature.
Confirmatory Factor Analysis of the School Refusal Assessment Scale-Revised in an African American Community Sample
Authors: Lyon Aaron R.
Published: November 2009

The current study used confirmatory factor analysis techniques to investigate the construct validity of the child version of the School Refusal Assessment Scale—Revised (SRAS-R) in a community sample of low socioeconomic status (SES), urban, African American, fifth and sixth graders ( n = 174). The SRAS-R is the best-researched measure of school refusal behavior in youth and typically yields four functional dimensions. Results of the investigation suggested that a modified version of the four-factor model, in which three items from the tangible reinforcement dimension are removed, may have construct validity in the current sample of youth. In addition, youth endorsement of the dimension measuring avoidance of social and/or evaluative situations was positively associated with unexcused absences. Implications for further psychometric research and early identification and prevention of problematic absenteeism in low SES, ethnic minority, community samples are highlighted.
Anticlastogenic effect of caffeic acid phenethyl ester on cisplatin-induced chromosome aberrations in rat bone marrow cells
Authors: Ramazan Yılmaz H. , Uz Efkan , Altunbaşak Ayşe , Sakallı Esin , Özçelik Nurten
Published: November 2009

Caffeic acid phenethyl ester (CAPE) is an antioxidant that can scavenge free radicals and protect cellular macromolecules, including DNA and proteins, from oxidative damage induced by various agents. The protective effect of CAPE on cisplatin-induced chromosome aberrations has been determined in rat bone marrow cells. The animals were pretreated with a single dose of CAPE (10 μmol/kg body weight [b.w.]) injected intraperitoneally (i.p.) 24 hours before the administration of cisplatin and then sacrificed 24 hours after the cisplatin administration. Cisplatin was administered to rats either alone (5 mg/kg b.w., i.p.) or after CAPE treatment. CAPE has led to a statistically significant decrease in the total number of chromosomal aberrations and abnormal metaphases induced by cisplatin when compared with only cisplatin given groups. We have concluded that CAPE could prevent cisplatin-induced chromosome aberrations by establishing a potent free radical scavenger effect.
Necrotizing lymphadenitis: Kikuchi—Fujimoto disease alias lupus lymphadenitis?
Authors: Cramer JP , Schmiedel S. , Alegre NG , Schäfer H. , Burchard GD , Merz H.
Published: November 2009

Differentiation between lymphadenopathy in potentially life-threatening systemic lupus erythematosus (SLE) and self-limiting necrotizing lymphadenitis, also called Kikuchi— Fujimoto disease (KFD), is difficult. In the past, co-occurrence of SLE and KFD has been described repeatedly in case reports. Here, we report a case of necrotizing lymphadenitis, describe the clinical and histopathologic features in detail and discuss the current literature. KFD may in fact be a histopathologic characteristic of SLE supporting the hypothesis that KFD is a rare manifestation of SLE. To clarify whether KFD is the same entity as lupus lymphadenitis, more cases with SLE and lymphadenopathy should be examined in detail. Lupus (2010) 19, 89—92.
Effect of Electrode Pattern on the Actuator Performance of Cellulose Electro-Active Paper
Authors: Ridley Dudley R. , Williams Frances R. , Song Kyo D. , Yun S.R. , Kang K.S. , Kim Jaehwan
Published: November 2009

The effect of electrode patterns on the actuator performance of electro-active paper (EAPap) is studied. A rectangular electrode pattern has been typically used for EAPap actuator. Since the electrical field can be concentrated at the edge of electrodes, the electrode patterns of EAPap can influence the actuator performance. Thus, a fishbone pattern electrode was designed and fabricated on EAPap materials and its actuation characteristics were compared with the rectangular electrode ones. Two EAPap materials, DCell, which is made by dissolving cellulose pulp with N,N-Dimethylacetamide and LiCl followed by curing process, and cellophane were used. Bending displacements and the resonance frequencies of EAPap actuators were investigated. Although the bending displacements of the fishbone patterned EAPap actuators were slightly lower than the rectangular patterned actuators, the resonance frequencies of the fishbone patterned actuators were higher than the rectangular patterned actuators. Electrical field concentration around the edge of fishbone pattern electrode might result in increased bending stiffness of the actuator and electrical power consumption. Electrical power consumption and electrode damage of the fishbone pattern electrode were addressed.
Creating Procedural Discourse and Knowledge for Software Users: Beyond Translation and Transmission
Authors: Rush Hovde Marjorie
Published: November 2009

Although most theorists agree that discourse creates meaning, they have not adequately described how this process emerges within the creation of procedural knowledge. This article explores how technical communicators in diverse settings based discourse decisions on their knowledge of (a) users, (b) organizational image and constraints, (c) software structure and features, and (d) genre conventions in order to create communication artifacts designed to help users develop procedural knowledge. The transformations in which they engaged indicated that these technical communicators were skilled in forming images in these four areas and then using these images as they created meaning in procedural discourse. In this process, they moved beyond merely translating or transmitting technical knowledge.
Foregrounding Positive Problem-Solving Teamwork: Awareness and Assessment Exercises for the First Class and Beyond
Authors: Rehling Lu
Published: November 2009

In an advanced technical and professional writing course, a pair of in-class exercises integrates the teaching of teamwork with other class topics of project management and observation-based research. The first exercise introduces teamwork in a positive way, by raising awareness of strategies for solving problems successfully. The second exercise follows up on the first, focusing on assessment of problem-solving teamwork. The pair of exercises is memorable and effective, showing students in an engaging, thought-provoking way that they have control and responsibility for the success of their teamwork. The materials for conducting the exercises, provided here, encourage reflection and discussion.
A Pilot Study Assessing the Impact of a Learner-Centered Adult Asthma Self-Management Program on Psychological Outcomes
Authors: Tousman Stuart , Zeitz Howard , Taylor Linda D.
Published: November 2009

The purpose of the research was to determine if an adult asthma self-management program could significantly improve psychological outcomes for participants. Small groups of adults met for 2 hours for 7 consecutive weeks. Intervention techniques included interactive discussions, problem solving, social support, and a behavior modification procedure. The behavior modification procedure consisted of homework assignments in which participants were asked to self-monitor and record asthma-specific behaviors (peak expiratory flow monitoring, avoidance/removal of asthma triggers, and controller medication adherence) and general lifestyle behaviors (drinking water, washing hands, and exercising). Paired sample t tests indicated statistically significant improvements for the outcomes of quality of life, depression, and self-efficacy. Significant increases were found in knowledge and behaviors, such as peak-flow monitoring and frequency of daily exercise. These results provide initial evidence that our program was effective, although the small sample size and lack of control group indicate the need for further research.
The Great São Paulo Homicide Drop
Authors: Goertzel Ted , Kahn Tulio
Published: November 2009

The homicide rates in the city and state of São Paulo were cut in half in the years from 2001 to 2007. The decline in the city of São Paulo was especially striking and parallels the decline in New York City in the 1990s. It can be confirmed with a number of independent data sources and was significantly larger than in other Brazilian cities. The decline may be attributed to more effective policing methods including the better enforcement of strict gun-control legislation. It demonstrates that effective measures can be taken to reduce lethal crime in a developing country without waiting to solve underlying socioeconomic problems.
Integrated Review of the Association of Cytokines With Fibromyalgia and Fibromyalgia Core Symptoms
Authors: Menzies Victoria , Lyon Debra E.
Published: November 2009

Fibromyalgia (FMS) is a chronic widespread pain (CWP) and fatigue syndrome that affects three to six million adults in the United States. Core symptoms of FMS include pain, fatigue, and mood and sleep disturbances. To date, consensus has not been reached among researchers regarding the pathogenesis of FMS nor the specific role of cytokine activation on the neuroendocrine—immune response patterns in persons with FMS. The purpose of this article is to describe and synthesize the results of research studies focused on the relationship between cytokines and FMS and among cytokines and core symptoms of FMS. There is some support in the literature for relationships among FMS symptoms and cytokines; however, there are discrepant findings related to whether proinflammatory and anti-inflammatory cytokines are elevated or reduced in persons with FMS and whether their levels correlate with the core symptoms of this disorder. Although the use of cytokine biomarkers must be considered exploratory at this time due to the lack of consistent empirical findings, biobehavioral research focused on understanding the relationship of FMS with cytokines may lead to a better understanding of this complex syndrome. This knowledge may ultimately contribute to the development of interventions for symptom management that address not only the symptom manifestation but also a biological mediator of symptoms.
Steering teachers
Authors: Brennan Marie
Published: November 2009

Changes in public sector management need to be unpacked for different sectors to understand their impact in a particular country. This article focuses on the governance of the feminized profession of teaching in Australia, the single largest professional grouping in the country. Neoliberal assumptions have been built into teachers’ work through policy change in three related ‘waves’. The first wave in the 1980s installed managerialism in public education by recentralizing curriculum policy, establishing ‘self-managing’ schools, and downsizing infrastructure. The second wave in the 1990s steered teachers’ work through federal intervention into curriculum, and individualization of teachers’ work in contexts of marketization; this wave consolidated a national political role in education. The third wave in the 2000s emphasized the codification of knowledge through establishment of standards and criteria for teacher employment and promotion. The article concludes that the governance efforts to steer teachers’ work by neoliberal assumptions have been significantly, but not totally, effective.
The ‘return to community’
Authors: Fawcett Barbara , Hanlon Maurice
Published: November 2009

In Australia and the United Kingdom over the past two decades, the way human service professionals have been involved in ‘communities’, whether defined by ‘place’, ‘interest’ or ‘exclusion’, has varied with the political complexion of the government in power. This has resulted in both opportunities for and constraints on human services practice and community participation. In this article, the terminology and the conceptual frames associated with work both in and with communities are critically scrutinized. However, it is also contended that spatial analysis and social entrepreneurship can enable those working in the field to respond productively to the New Public Management and ‘Third Way’ approaches that have shaped the policy context of human services practice. It is argued that a form of spatial analysis and of social entrepreneurship can be used to facilitate meaningful participation in decision-making processes in a variety of communities and to re-forge social connections at a range of levels.
A case of mistaken identity
Authors: Healy Karen
Published: November 2009

Social welfare professions have been highly exposed to the corrosive effects of New Public Management (NPM) on professional identity and influence. In this article, I argue that ambivalence from within the social welfare professions, and in society more generally, towards professional recognition of these occupations enables NPM to enact an agenda of de-professionalization. Further, gendered assumptions about professional identity, and particularly about the caring professions in which there is a high concentration of women workers, are pivotal to the destabilization of the professional social welfare workforce. I draw on examples from the Queensland Department of Child Safety workforce reforms to illustrate how NPM discourse intersects with, and is enabled by, well-established ambivalence towards professional recognition within and outside the social welfare professions. I suggest that a gender analysis can deepen our understanding of the substantial impact of NPM on social welfare professions and can enable these professions to develop effective responses to the substantial threats they now face.
Managing health care under New Public Management
Authors: Newman Stuart , Lawler Jocalyn
Published: November 2009

The drive to reform the public health care system became a common feature of Australia’s political and economic landscape from the early 1980s. Health care reform in Australia has been underpinned by New Public Management (NPM) which was promoted as providing more transparent policy and empowering managers to manage service delivery. However, these claims are a fallacy and nursing and nursing care have been affected adversely and severely. General (generic) management structures have replaced established nursing management structures and the distance between politics (politicians) and health service managers has narrowed to the extent that there is now an unprecedented level of political interference in the daily management of health services, in direct contrast to the tenets of NPM. This article reports on the ‘reformed’ health care environment as experienced by nurse managers. They reported that their ability to manage nursing services and provide professional and clinical leadership has been seriously diminished, as has their work satisfaction, motivation and commitment. They also report uncertainty about their future as well as the future of nursing itself.
Should the nurse change the light globe?
Authors: Sawyer Anne-Maree , Green David , Moran Anthony , Brett Judith
Published: November 2009

Over the last two decades New Public Management, de-institutionalization and the growth of community care have radically altered the landscape of human service delivery in Australia. As a consequence of these changes, human service agencies have been compelled to develop mechanisms for regulating and managing the risks involved in frontline community care — and the management of risk is now pivotal to the practices of professional workers in this field. British research suggests that the emphasis on risk gives rise to greater monitoring and administrative supervision of workers and a focus on managerial rather than therapeutic skills. This article presents some early findings from an Australian study that finds a very different picture. Based on interviews with 24 social workers and nurses employed in community care, we found that these workers expressed a strong sense of agency when interpreting and negotiating the risk management policies of their respective organizations, and were focused primarily on the needs of their clients rather than bureaucratic procedures.
Gendered organizational dynamics
Authors: Schofield Toni
Published: November 2009

Australian governments have reported an impending ‘crisis’ with workforce shortages in the health sector expected to deepen over the next decade. The allied health professions, however, have barely rated a mention despite the fact their retention rates are low and they are expected to play an expanded and more preventive role in the future. This article examines current Australian public policy approaches to the allied health professions in relation to workforce shortages. It identifies the dominance of technocratic representations of the problem, noting that these have become more pervasive and robust with the New Public Management (NPM). Recent Australian sociological discussion suggests that technocratic ‘framing’ of allied health workforce shortages is limited by its failure to address the role of organizational and institutional dynamics. Such an analysis advances prevailing policy-based problematizations of allied health workforce shortages, but is itself constrained by the lack of acknowledgement of the gendered character of Australian health services organization and the role this may play in allied health workforce shortages.
Admission Trends Over 8 Years for Diabetic Foot Ulceration in a Specialized Diabetes Unit in Cameroon
Authors: Kengne Andre Pascal , Djouogo Catherine F. T. , Dehayem Mesmin Y. , Fezeu Leopold , Sobngwi Eugene , Lekoubou Alain , Mbanya Jean-Claude
Published: November 2009

High rates of foot complications have been reported in people with diabetes in sub-Saharan Africa (SSA). However, there is a paucity of data in support of the changing pattern with time. We report here data on trends in hospitalization for foot ulceration over an 8-year consecutive period in a specialized diabetes unit in SSA. Admission and discharge registers of the diabetes and endocrine unit of the Yaounde Central hospital, Cameroon, were reviewed for the period 2000 through 2007. Data were collected on the status for diabetes, presence of foot ulcer, age, sex, duration of hospitalization, amputation, and deaths.We found that 1841 patients with diabetes were admitted during the study period. The prevalence of foot ulceration was 13% (95% confidence interval [CI] = 11%-15%) and varied significantly by year of study ( P = .001). The mean duration of hospitalization significantly decreased with time. Foot ulcer was associated with 115% (95% CI = 87%-148%) more bed use than other conditions in diabetes. Foot ulcer was associated with a nonsignificantly lower risk of death or dropout, with evidence of some attenuation with time. With one exception, the amputation rate of 16% (95% CI = 11%-20%) was similar across years. Foot ulcer is a major cause of hospital admission and bed use for diabetes in Cameroon.
Successful Pharmacological Treatment and Treatment of Large Soft-Tissue Ulceration With Split-Thickness Skin Graft in a Chronically Critical Ischemic Leg
Authors: Firat Cemal , Kenan Coban Y.
Published: November 2009

The authors present the results of preoperative and postoperative prostacyclin analog treatment with skin grafting in a large ulceration of a chronic critical ischemic leg in a man who had lost his contralateral extremity 5 years ago. Healing was uneventful at the 6-month follow-up.
Futility interim monitoring with control of type I and II error probabilities using the interim Z-value or confidence limit
Authors: Lachin John M
Published: November 2009

Background It is highly desirable to terminate a clinical trial early if the emerging data suggests that the experimental treatment is ineffective, or substantially less effective than the level the study was designed to detect. Many studies have used a conditional power calculation as the basis for termination for futility. However, in order to compute conditional power one must posit an assumption about the distribution of the future data yet to be observed, such as that the original design assumptions will apply, or that the future data will have the same treatment effect as that estimated from the current ‘trend’ in the data. Each such assumption will yield a different conditional power value.

Purpose The assessment of futility is described in terms of the observed quantities alone, specifically the interim Z-value or the interim confidence limit on the magnitude of the treatment effect, such that specified type I and II error probabilities are achieved. No assumption is required regarding the distribution of the future data yet to be observed.

Methods Lachin [1] presents a review of futility stopping based on assessment of conditional power and evaluates the statistical properties of a futility stopping rule. These methods are adapted to futility stopping using only the observed data without any assumption about the future data yet to be observed.

Results The statistical properties of the futility monitoring plan depend specifically on the corresponding boundary value for the interim Z-value. These include the probability of interim stopping under the null or under a specific alternative hypothesis, and the resulting type I and II error probabilities. Thus, the stopping rule can be uniquely specified in terms of a boundary for the interim Z-value. Alternately, the stopping rule can be specified in terms of a boundary on the upper confidence limit for the treatment group effect (favoring treatment). Herein it is shown that this approach is equivalent to a boundary on the test Z-value, from which the operating characteristics of the stopping rule can then be calculated.

Limitations While the statistical properties described herein strictly apply to a pre-specified futility boundary, it is also shown that these methods can be applied in an ad-hoc manner. In the event that a sequence of interim assessments for futility is desired, other sequential methods with an outer effectiveness boundary and inner futility boundary would be preferred.

Conclusions These methods allow the design of clinical trials that have specified operating characteristics with a pre-specified futility analysis based only on the interim quantities that have been observed. Examples are presented. Clinical Trials 2009; 6: 565—573. http://ctj.sagepub.com
Folk Culture and Political Power
Authors: Sarmento Clara
Published: November 2009

This article analyses the painted panels of the moliceiro boat, a traditional working boat of the Ria de Aveiro region of Por tugal. The ar ticle examines how the painted panels have been invented and reinvented over time. The boat and its panels are contextualized both within the changing socio-economic conditions of the Ria de Aveiro region, and the changing socio-political conditions of Portugal throughout the 20th century and until the present day. The article historically analyses the social significance of ‘ moliceiro culture’, examining in particular the power relations it expresses and its ambiguous past and present relationships with the political and the economic powers of the Portuguese state. The article unpacks some of the complexity of the relations that have pertained between public and private, local and national, folk culture and ‘art’, and popular and institutional in the Ria de Aveiro region in particular, and Portugal more generally.
Effectiveness of pharmacotherapy and behavioral interventions for smoking cessation in actual clinical practice
Authors: Rovina Nikoletta , Nikoloutsou Ioanna , Katsani Georgia , Dima Efrossini , Fransis Konstantinos , Roussos Charis , Gratziou Christina
Published: November 2009

Objectives: This study evaluated the effectiveness of behavioral interventions (brief counseling, nonspecific psychological support in groups — NSGS and cognitive behavioral group therapy — CBGT) in combination with bupropion SR for smoking cessation in the field, through a smoking cessation clinic.

Methods: Two-hundred-and-five smokers were enrolled in a 19-week course during 2007/ 2008, and were randomly assigned to: bupropion SR combined with brief counseling (group A), bupropion SR combined with NSGS (group B), bupropion SR combined with CBGT (group C), or CBGT as the only approach (group D).

Results: Continuous abstinence rates at the end of therapy were 53.2% for group A, 62.9% for group B, 50.0% for group C, and 22.2% (p < 0.05) for group D. Sustained abstinence rates in 12 months were 29.6%, 28.1%, 34.3% and 19.4% (p > 0.05), respectively.

Conclusions: Bupropion SR is an effective aid for smoking cessation in clinical practice. NSGT increased the chances for success at the end of therapy when combined with bupropion SR, while CBGT as monotherapy was less effective compared with the approaches including pharmacotherapy. It is suggested that smoking cessation interventions in real-life healthcare settings should be implemented through comprehensive programs using pharmacotherapy where applicable, combined with NSGT, and integrated by specialized healthcare professionals.
Intrapleural hemorrhage after administration of tPA: a case report and review of the literature
Authors: Goralski Jennifer L. , Bromberg Philip A. , Haithcock Benjamin
Published: November 2009

Objective: Intrapleural fibrinolytic enzymes have been used for over 60 years in the treatment of complicated pleural effusions to lyse loculations and promote resolution. Despite this extensive history of use, however, little is known about complications that may arise with the use of this therapy. Here we discuss a patient with chronic renal failure on hemodialysis who developed an intrapleural hemorrhage after the administration of intrapleural tPA to treat a complicated parapneumonic effusion. A review of the literature examines the efficacy and safety of this therapy, focusing on bleeding complications. Specific attention is paid to patients who have underlying coagulopathies or who are receiving anticoagulation.

Data sources: A review of the literature, as indexed in PubMed, was undertaken using the following search terms in combination: tPA, pleural effusion, complications of thrombolytics, and intrapleural hemorrhage. The search was inclusive of patients under the age of 18, but was limited by English language and human subjects.

Study selection/data extraction: All relevant articles identified during the search were reviewed. Those studies that reported on bleeding complications, or lack thereof, were included in this review. Limitations of each article are noted in the text.

Conclusions: Multiple studies, including a 2000 ACP consensus statement and a 2008 Cochrane review, indicate the need for further investigations to evaluate the safety and efficacy of intrapleural thrombolytics for the treatment of complicated pleural effusions and empyemas. Limited studies specifically address bleeding complications, especially in subpopulations of patients receiving concurrent anticoagulant therapy.
Spontaneous pneumomediastinum: an algorithm for diagnosis and management
Authors: Takada Kazuto , Matsumoto Shuuichi , Hiramatsu Tetsuo , Kojima Eiji , Shizu Masato , Okachi Shoutarou , Ninomiya Kiyoko , Morioka Hiroshi
Published: November 2009

Spontaneous pneumomediastinum (SPM) is a rare disorder most often affecting young males which is generally self-limiting. Despite the benign prognosis with few complications and little morbidity, it frequently confuses clinicians in primary settings, who may have difficulty differentiating SPM from other serious organ ruptures, especially oesophageal rupture (the so-called Boerhaave syndrome), which may lead to mediastinitis and may be fatal, even with appropriate interventions. An overview of adult SPM is provided, reviewing 17 studies (414 patients), including our clinical experience, and finally an algorithm for diagnosis and management of SPM is proposed, based on the characteristics of SPM.
Comparison of eukaryotic phylogenetic profiling approaches using species tree aware methods
Authors: Ruano-Rubio Valentín , Poch Olivier , Thompson Julie D
Published: November 2009

Background

Phylogenetic profiling encompasses an important set of methodologies for in silico high throughput inference of functional relationships between genes. The simplest profiles represent the distribution of gene presence-absence in a set of species as a sequence of 0's and 1's, and it is assumed that functionally related genes will have more similar profiles. The methodology has been successfully used in numerous studies of prokaryotic genomes, although its application in eukaryotes appears problematic, with reported low accuracy due to the complex genomic organization within this domain of life. Recently some groups have proposed an alternative approach based on the correlation of homologous gene group sizes, taking into account all potentially informative genetic events leading to a change in group size, regardless of whether they result in a de novo group gain or total gene group loss.

Results

We have compared the performance of classical presence-absence and group size based approaches using a large, diverse set of eukaryotic species. In contrast to most previous comparisons in Eukarya, we take into account the species phylogeny. We also compare the approaches using two different group categories, based on orthology and on domain-sharing. Our results confirm a limited overall performance of phylogenetic profiling in eukaryotes. Although group size based approaches initially showed an increase in performance for the domain-sharing based groups, this seems to be an overestimation due to a simplistic negative control dataset and the choice of null hypothesis rejection criteria.

Conclusion

Presence-absence profiling represents a more accurate classifier of related versus non-related profile pairs, when the profiles under consideration have enough information content. Group size based approaches provide a complementary means of detecting domain or family level co-evolution between groups that may be elusive to presence-absence profiling. Moreover positive correlation between co-evolution scores and functional links imply that these methods could be used to estimate functional distances between gene groups and to cluster them based on their functional relatedness. This study should have important implications for the future development and application of phylogenetic profiling methods, not only in eukaryotic, but also in prokaryotic datasets.
Diverse MHC IIB allele repertoire increases parasite resistance and body condition in the Long-tailed giant rat (Leopoldamys sabanus)
Authors: Lenz Tobias L , Wells Konstans , Pfeiffer Martin , Sommer Simone
Published: November 2009

Background

Genes of the major histocompatibility complex (MHC) code for key functions in the adaptive immune response of vertebrates and most of them show exceptionally high polymorphism. This polymorphism has been associated with the selection by diverse and changing parasite communities. We analysed MHC class IIB diversity, gastrointestinal parasite load and body condition in the wild ranging tropical rat Leopoldamys sabanus (Thomas, 1887) under natural selection conditions in a highly variable rainforest environment in Borneo to explore the mechanisms that maintain these high levels of genetic polymorphism.

Results

Allelic diversity was determined via SSCP and sequencing, and parasite screening was done through non-invasive faecal egg count. The detected alleles showed expected high levels of polymorphism and balancing selection. Besides a clear advantage for more diverse MHC genotypes in terms of number of alleles, reflected in better body condition and resistance against helminth infection, our data also suggested a positive effect of MHC allele divergence within an individual on these parameters.

Conclusion

In accordance with the heterozygote advantage hypothesis, this study provides evidence for an advantage of more diverse MHC genotypes. More specifically, the potential negative relation between individual allele divergence and number of parasite species is in line with the 'divergent allele advantage' hypothesis.
Cytogenetic studies in Eigenmannia virescens (Sternopygidae, Gymnotiformes) and new inferences on the origin of sex chromosomes in the Eigenmannia genus
Authors: Silva Danillo S , Milhomem Susana SR , Pieczarka Julio C , Nagamachi Cleusa Y
Published: November 2009

Background

Cytogenetic studies were carried out on samples of Eigenmannia virescens (Sternopygidae, Gymnotiformes) obtained from four river systems of the Eastern Amazon region (Para, Brazil).

Results

All four populations had 2n = 38, with ZZ/ZW sex chromosomes (Z, acrocentric; W, submetacentric). Constitutive heterochromatin (CH) was found at the centromeric regions of all chromosomes. The W chromosome had a heterochromatic block in the proximal region of the short arm; this CH was positive for DAPI staining, indicating that it is rich in A-T base pairs. The nucleolar organizer region (NOR) was localized to the short arm of chromosome pair 15; this result was confirmed by fluorescent in situ hybridization (FISH) with human 45S rDNA, and CMA3 staining indicated that the region is G-C rich. FISH with telomeric probes did not show any evidence of interstitial telomeric sequences (ITS).

Conclusion

Previous studies have shown that the species Eigenmannia sp. 2 and E. virescens have differentiated sex chromosomes, and diverse sex chromosome systems have been described for E. virescens specimens obtained from different Brazilian rivers. A comparative analysis of the present data and prior reports suggests that the sex chromosomes of Eigenmannia may have arisen independently in the different populations.
De novo 454 sequencing of barcoded BAC pools for comprehensive gene survey and genome analysis in the complex genome of barley
Authors: Steuernagel Burkhard , Taudien Stefan , Gundlach Heidrun , Seidel Michael , Ariyadasa Ruvini , Schulte Daniela , Petzold Andreas , Felder Marius , Graner Andreas , Scholz Uwe , Mayer Klaus FX , Platzer Matthias , Stein Nils
Published: November 2009

Background

De novo sequencing the entire genome of a large complex plant genome like the one of barley (Hordeum vulgare L.) is a major challenge both in terms of experimental feasibility and costs. The emergence and breathtaking progress of next generation sequencing technologies has put this goal into focus and a clone based strategy combined with the 454/Roche technology is conceivable.

Results

To test the feasibility, we sequenced 91 barcoded, pooled, gene containing barley BACs using the GS FLX platform and assembled the sequences under iterative change of parameters. The BAC assemblies were characterized by N50 of ~50 kb (N80 ~31 kb, N90 ~21 kb) and a Q40 of 94%. For ~80% of the clones, the best assemblies consisted of less than 10 contigs at 24-fold mean sequence coverage. Moreover we show that gene containing regions seem to assemble completely and uninterrupted thus making the approach suitable for detecting complete and positionally anchored genes.

By comparing the assemblies of four clones to their complete reference sequences generated by the Sanger method, we evaluated the distribution, quality and representativeness of the 454 sequences as well as the consistency and reliability of the assemblies.

Conclusion

The described multiplex 454 sequencing of barcoded BACs leads to sequence consensi highly representative for the clones. Assemblies are correct for the majority of contigs. Though the resolution of complex repetitive structures requires additional experimental efforts, our approach paves the way for a clone based strategy of sequencing the barley genome.
Genome reannotation of Escherichia coli CFT073 with new insights into virulence
Authors: Luo Chengwei , Hu Gang-Qing , Zhu Huaiqiu
Published: November 2009

Background

As one of human pathogens, the genome of Uropathogenic Escherichia coli strain CFT073 was sequenced and published in 2002, which was significant in pathogenetic bacterial genomics research. However, the current RefSeq annotation of this pathogen is now outdated to some degree, due to missing or misannotation of some essential genes associated with its virulence. We carried out a systematic reannotation by combining automated annotation tools with manual efforts to provide a comprehensive understanding of virulence for the CFT073 genome.

Results

The reannotation excluded 608 coding sequences from the RefSeq annotation. Meanwhile, a total of 299 coding sequences were newly added, about one third of them are found in genomic island (GI) regions while more than one fifth of them are located in virulence related regions pathogenicity islands (PAIs). Furthermore, there are totally 341 genes were relocated with their translational initiation sites (TISs), which resulted in a high quality of gene start annotation. In addition, 94 pseudogenes annotated in RefSeq were thoroughly inspected and updated. The number of miscellaneous genes (sRNAs) has been updated from 6 in RefSeq to 46 in the reannotation. Based on the adjustment in the reannotation, subsequent analysis were conducted by both general and case studies on new virulence factors or new virulence-associated genes that are crucial during the urinary tract infections (UTIs) process, including invasion, colonization, nutrition uptaking and population density control. Furthermore, miscellaneous RNAs collected in the reannotation are believed to contribute to the virulence of strain CFT073. The reannotation including the nucleotide data, the original RefSeq annotation, and all reannotated results is freely available via
http://mech.ctb.pku.edu.cn/CFT073/.

Conclusion

As a result, the reannotation presents a more comprehensive picture of mechanisms of uropathogenicity of UPEC strain CFT073. The new genes change the view of its uropathogenicity in many respects, particularly by new genes in GI regions and new virulence-associated factors. The reannotation thus functions as an important source by providing new information about genomic structure and organization, and gene function. Moreover, we expect that the detailed analysis will facilitate the studies for exploration of novel virulence mechanisms and help guide experimental design.
Annotation and expression of carboxylesterases in the silkworm, Bombyx mori
Authors: Yu Quan-You , Lu Cheng , Li Wen-Le , Xiang Zhong-Huai , Zhang Ze
Published: November 2009

Background

Carboxylesterase is a multifunctional superfamily and ubiquitous in all living organisms, including animals, plants, insects, and microbes. It plays important roles in xenobiotic detoxification, and pheromone degradation, neurogenesis and regulating development. Previous studies mainly used Dipteran Drosophila and mosquitoes as model organisms to investigate the roles of the insect COEs in insecticide resistance. However, genome-wide characterization of COEs in phytophagous insects and comparative analysis remain to be performed.

Results

Based on the newly assembled genome sequence, 76 putative COEs were identified in Bombyx mori. Relative to other Dipteran and Hymenopteran insects, alpha-esterases were significantly expanded in the silkworm. Genomics analysis suggested that BmCOEs showed chromosome preferable distribution and 55% of which were tandem arranged. Sixty-one BmCOEs were transcribed based on cDNA/ESTs and microarray data. Generally, most of the COEs showed tissue specific expressions and expression level between male and female did not display obvious differences. Three main patterns could be classified, i.e. midgut-, head and integument-, and silk gland-specific expressions. Midgut is the first barrier of xenobiotics peroral toxicity, in which COEs may be involved in eliminating secondary metabolites of mulberry leaves and contaminants of insecticides in diet. For head and integument-class, most of the members were homologous to odorant-degrading enzyme (ODE) and antennal esterase. RT-PCR verified that the ODE-like esterases were also highly expressed in larvae antenna and maxilla, and thus they may play important roles in degradation of plant volatiles or other xenobiotics.

Conclusion

B. mori has the largest number of insect COE genes characterized to date. Comparative genomic analysis suggested that the gene expansion mainly occurred in silkworm alpha-esterases. Expression evidence indicated that the expanded genes were specifically expressed in midgut, integument and head, implying that these genes may have important roles in detoxifying secondary metabolites of mulberry leaves, contaminants in diet, and odorants. Our results provide some new insights into functions and evolutionary characteristics of COEs in phytophagous insects.
Proteins with an Euonymus lectin-like domain are ubiquitous in Embryophyta
Authors: Fouquaert Elke , Peumans Willy J , Vandekerckhove Tom TM , Ongenaert Maté , Van Damme Els JM
Published: November 2009

Background

Cloning of the Euonymus lectin led to the discovery of a novel domain that also occurs in some stress-induced plant proteins. The distribution and the diversity of proteins with an Euonymus lectin (EUL) domain were investigated using detailed analysis of sequences in publicly accessible genome and transcriptome databases.

Results

Comprehensive in silico analyses indicate that the recently identified Euonymus europaeus lectin domain represents a conserved structural unit of a novel family of putative carbohydrate-binding proteins, which will further be referred to as the Euonymus lectin (EUL) family. The EUL domain is widespread among plants. Analysis of retrieved sequences revealed that some sequences consist of a single EUL domain linked to an unrelated N-terminal domain whereas others comprise two in tandem arrayed EUL domains. A new classification system for these lectins is proposed based on the overall domain architecture. Evolutionary relationships among the sequences with EUL domains are discussed.

Conclusion

The identification of the EUL family provides the first evidence for the occurrence in terrestrial plants of a highly conserved plant specific domain. The widespread distribution of the EUL domain strikingly contrasts the more limited or even narrow distribution of most other lectin domains found in plants. The apparent omnipresence of the EUL domain is indicative for a universal role of this lectin domain in plants. Although there is unambiguous evidence that several EUL domains possess carbohydrate-binding activity further research is required to corroborate the carbohydrate-binding properties of different members of the EUL family.
Quality of life and mortality from a nephrologist's view: a prospective observational study
Authors: Han Seung Seok , Kim Ki Woong , Na Ki Young , Chae Dong-Wan , Kim Yon Su , Kim Suhnggwon , Chin Ho Jun
Published: November 2009

Background

Although health-related quality of life (HRQOL) is a potential independent predictor of mortality, nephrologists have shown little interest in HRQOL with respect to mortality in chronic kidney disease (CKD). The aim of this article is to evaluate the impact of HRQOL on mortality in the elderly, who are likely to develop or already have CKD.

Methods

Among 1,000 randomly sampled participants aged more than 65 years (sourced from the Korean Longitudinal Study on Health and Ageing), 944 subjects were evaluated for HRQOL. HRQOL was assessed using a 36-item Short-Form health survey (SF36). A cumulative survival rate was calculated according to tertiles of SF36 scores and classified by the presence of CKD (estimated GFR <60 ml/min/1.73 m2).

Results

Among 944 subjects, 46.6% had CKD. CKD patients had lower total and physical component scores compared with subjects without CKD. The 3-year cumulative survival rate was 90.0% (non-CKD vs. CKD: 92.6% vs. 87.4%, P = 0.005 by log rank test). After adjusting for multiple variables, a reduced SF36 score (physical and mental components) was a strong predictor of all-cause mortality. Physical components were consistently able to predict mortality after CKD classification, but mental components were statistically significant only in the CKD group.

Conclusion

In addition to traditional risk factors of mortality, nephrologists should be aware of HRQOL as a predictor of mortality and should make efforts to improve HRQOL in CKD patients.
The effect of low-level laser irradiation (In-Ga-Al-AsP - 660 nm) on melanoma in vitro and in vivo
Authors: Frigo Lúcio , Luppi Juliana SS , Favero Giovani M , Maria Durnavei A , Penna Sócrates C , Bjordal Jan M , Bensadoun Rene J , Lopes-Martins Rodrigo AB
Published: November 2009

Background

It has been speculated that the biostimulatory effect of Low Level Laser Therapy could cause undesirable enhancement of tumor growth in neoplastic diseases. The aim of the present study is to analyze the behavior of melanoma cells (B16F10) in vitro and the in vivo development of melanoma in mice after laser irradiation.

Methods

We performed a controlled in vitro study on B16F10 melanoma cells to investigate cell viability and cell cycle changes by the Tripan Blue, MTT and cell quest histogram tests at 24, 48 and 72 h post irradiation. The in vivo mouse model (male Balb C, n = 21) of melanoma was used to analyze tumor volume and histological characteristics. Laser irradiation was performed three times (once a day for three consecutive days) with a 660 nm 50 mW CW laser, beam spot size 2 mm2, irradiance 2.5 W/cm2 and irradiation times of 60s (dose 150 J/cm2) and 420s (dose 1050 J/cm2) respectively.

Results

There were no statistically significant differences between the in vitro groups, except for an increase in the hypodiploid melanoma cells (8.48 ± 1.40% and 4.26 ± 0.60%) at 72 h post-irradiation. This cancer-protective effect was not reproduced in the in vivo experiment where outcome measures for the 150 J/cm2 dose group were not significantly different from controls. For the 1050 J/cm2 dose group, there were significant increases in tumor volume, blood vessels and cell abnormalities compared to the other groups.

Conclusion

LLLT Irradiation should be avoided over melanomas as the combination of high irradiance (2.5 W/cm2) and high dose (1050 J/cm2) significantly increases melanoma tumor growth in vivo.