bluuebunny/crossref_metadata_2025 huggingface dataset:
Trends in the Use of Service Learning With Students With Disabilities
Authors: Dymond Stacy K. , Renzaglia Adelle , Slagor Michael T.
Published: March 2010

Peer-reviewed journal articles published between 1990 and 2007 examining service-learning (SL) and students with disabilities were reviewed. Thirty-four articles were coded according to type of SL (inclusive, segregated, both), grade level and disability of the students, type of article (general description, program description, research-based), and date of publication. The findings indicate that the literature on SL focuses primarily on program descriptions involving students with learning disabilities, behavior disorders, and severe disabilities at the middle and high school levels. Descriptions of inclusive and segregated SL were approximately equal although the percentage of articles focused on inclusive SL gradually increased over time. A framework is presented to suggest directions for future research on the use of SL with students with disabilities.
Building Oral Reading Fluency With Peer Coaching
Authors: Marr Mary Beth , Algozzine Bob , Nicholson Kelly , Keller Dugan Katherine
Published: March 2010

Fluent oral reading is an essential literacy skill, and data suggest that it is a consistent and persistent problem for many elementary school children. Peer-mediated instruction in which students work together to support each other is an evidence-based practice for improving performance in a variety of academic areas. In this study, we investigated the effectiveness of a peer-mediated fluency-building intervention for struggling readers in second grade. The intervention was provided to small groups of students referred to as difficult-to-remediate, treatment resisters, nonresponders, or lower responders in similar research. Oral reading fluency performance for students who received supplemental intervention ( n = 17) was statistically significantly better than that for their peers who received only typical classroom instruction ( n = 17). The effects of enhanced fluency instruction were evident across multiple benchmarks, and significant relationships were evident between oral reading fluency and comprehension. The authors discuss the findings in the context of similar peer-mediated interventions and the emerging development of targeted interventions to support response-to-intervention practices.
Evaluation of a Second-Tier Classroom-Based Assignment Completion Strategy for Middle School Students in a Resource Context
Authors: Ness Bryan Michael , Sohlberg McKay Moore , Albin Richard W.
Published: March 2010

Students who struggle academically often struggle with assignment completion. Poor assignment completion is attributable to both student cognitive and motivational barriers. This study evaluates the effectiveness of an intervention designed to improve assignment completion for middle school students who struggle academically. Seventh graders with diverse educational and behavioral profiles in a resource room context learned to use an organization system to facilitate assignment management while in the resource classroom. The intervention was applied at the classroom level to address implementation barriers encountered while piloting the system with individual students. Using a single-subject design methodology, we demonstrated a functional relation between the intervention and assignment completion skills for two of three participants. Classroom-wide application facilitated implementation and positive effects were maintained 1 month postintervention. Additional implementation and intervention implications are discussed.
A Case of PANDAS Treated With Tetrabenazine and Tonsillectomy
Authors: Fusco Francesca Romana , Pompa Alessandra , Bernardi Giorgio , Ottaviani Fabrizio , Giampà Carmela , Laurenti Daunia , Morello Maria , Bernardini Sergio , Nuccetelli Marzia , Sabatini Umberto , Paolucci Stefano
Published: March 2010

PANDAS (pediatric autoimmune neuropsychiatric disorders associated with streptococcal infections) is a rare clinical syndrome characterized by the presence of tics, Tourette syndrome, obsessive-compulsive disorder, or chorea in the context of an immediately precedent streptococcal infection. In this report, we describe the case of an 11-year-old boy who developed PANDAS with severe choreic movements. The criteria for PANDAS diagnosis were met. Moreover, serum antibrain antibodies were present. The patient was initially treated with tetrabenazine 12.5 mg twice daily with remission of the neurological symptoms. Subsequently, the patient underwent tonsillectomy and has been asymptomatic since, with antistreptolysin O titer levels in range.
Neurodevelopmental Outcomes in Neonates With Seizures: A Numerical Score of Background Encephalography to Help Prognosticate
Authors: Nagarajan Lakshmi , Palumbo Linda , Ghosh Soumya
Published: March 2010

There is a high incidence of mortality and neurodevelopmental sequelae in babies with neonatal seizures. The electroencephalography (EEG) background has been shown to be an excellent predictor of outcome by most studies, with a few suggesting limited value in prognostication. Previous studies suggest poor prognosis with severely abnormal backgrounds, but prediction was difficult with moderate abnormalities. The proposed numerical scoring system for the EEG background provides an objective method of evaluation with improved reproducibility, categorization, and prognostication. Our study showed that the numerical score of EEG background was a good predictor of outcome. Higher numerical scores reflecting greater abnormality of background EEG were associated with increasing incidence of mortality, neurodevelopmental impairment, cerebral palsy, vision and hearing impairment, and epilepsy. The numerical score also correlated with neuroimaging abnormalities. A numerical EEG score can help target interventional strategies for neonatal seizures.
Intraventricular Meningioma After Cranial Irradiation for Childhood Leukemia
Authors: Ney Douglas E. , Huse Jason T. , Dunkel Ira J. , Steinherz Peter G. , Haque Sofia , Khakoo Yasmin
Published: March 2010

Meningiomas are among the most common brain tumors in adults. They are most commonly located over the cerebral convexities and are infrequently found in an intraventricular location. Ionizing cranial radiation is a risk factor for late occurrence of meningiomas within the radiation field. While pathologic grading of meningiomas is straightforward, significant variability often exists between pathologists in applying standard grading criteria. This has implications for prognosis. Radiation-induced meningiomas may also have predilection to recur. The authors describe a case of an intraventricular meningioma occurring 23 years after cranial irradiation for childhood acute lymphoblastic leukemia.
Development and Evaluation of In Situ Gel-forming System for Sustained Delivery of Insulin
Authors: Dhawan Sanju , Kapil Rishi , Kapoor Deepak N.
Published: March 2010

Phase-sensitive in situ gel-forming controlled release formulations of insulin were prepared using poly(lactide-co-glycolide) and a solvent system consisting of various proportions of benzyl benzoate and benzyl alcohol. The in vitro release samples of formulations were assayed for insulin content by enzyme linked immunosorbent assay. Sodium dodecyl sulfate polyacrylamide gel electrophoresis and circular dichroism spectroscopy studies of released insulin confirmed its conformational stability. The stability of insulin in the formulation was assessed using Fourier transform infrared spectroscopy. Rheological properties of the formulations, assessed under isothermal conditions, showed dilatant behavior of all the formulations. In vivo studies were carried out on the optimized formulations vis-à-vis pure insulin in mice and blood glucose levels were monitored for 15 days. Mean percentage reduction in blood glucose levels was calculated in all the animals and the results analyzed using ANOVA. The studies construed better pharmacodynamic response for the two optimized formulations in controlling the blood glucose levels vis-à-vis routine once-a-day administration of insulin. The subcutaneous tissues, further subjected to scanning electron microscopy studies and histopathological examinations, ascertained the biocompatibility of the formulation.
Temporary Employment and Perceived Employability: Mediation by Impression Management
Authors: De Cuyper Nele , De Witte Hans
Published: March 2010

Perceived employability (PE) has been advanced as the upcoming resource for career development, particularly for temporary workers. The question is how temporary workers become employable. Our hypothesis is that temporary workers more than permanent workers use impression management to become employable, both on the internal and the external labor market. This hypothesis was tested with a sample of 371 Belgian temporary and permanent workers from the educational sector and using structural equation modeling (SEM). The results suggest that (a) temporary workers were more likely than permanent workers to use impression management; (b) impression management related positively to the worker’s perception of being employable, both on the internal and the external labor market, which; (c) in turn, related to the perception of availability of better job opportunities. That is to say, impression management is an important mechanism available to temporary workers to first secure their labor market position and then for career advancement.
Developing librarians as teachers: A study of their pedagogical knowledge
Authors: Bewick Laura , Corrall Sheila
Published: March 2010

The widespread involvement of librarians in information literacy education has raised concerns about their development as teachers, but there is little research on their acquisition and application of pedagogical knowledge. A questionnaire was used to collect mainly quantitative data about the teaching roles, pedagogical knowledge and professional development of subject librarians in 82 UK higher education institutions. Two expert interviews and a literature review informed the design and contextualized the findings. The survey showed postholders were engaged in a variety of teaching-related activities, regarded as central to their work. Contrary to assumptions, most felt confident about teaching and thought their knowledge sufficient, giving examples of pedagogical theory gained via courses informing their teaching practice. Although on-the-job development was common, the majority had undertaken a short course and/or extended programme. Respondents favoured incorporating a teaching module into initial professional education and providing tailored programmes for librarians with substantial teaching roles.
Outlier detection for a hierarchical Bayes model in a study of hospital variation in surgical procedures
Authors: Farrell Patrick J , Groshen Susan , MacGibbon Brenda , Tomberlin Thomas J
Published: March 2010

One of the most important aspects of profiling healthcare providers or services is constructing a model that is flexible enough to allow for random variation. At the same time, we wish to identify those institutions that clearly deviate from the usual standard of care. Here, we propose a hierarchical Bayes model to study the choice of surgical procedure for rectal cancer using data previously analysed by Simons et al.1 Using hospitals as random effects, we construct a computationally simple graphical method for determining hospitals that are outliers; that is, they differ significantly from other hospitals of the same type in terms of surgical choice.
Segmented relationships to model erosion of regression effect in Cox regression
Authors: Muggeo Vito MR , Attanasio Massimo
Published: March 2010

In this article we propose a parsimonious parameterisation to model the so-called erosion of the covariate effect in the Cox model, namely a covariate effect approaching to zero as the follow-up time increases. The proposed parameterisation is based on the segmented relationship where proper constraints are set to accomodate for the erosion. Relevant hypothesis testing is discussed. The approach is illustrated on two historical datasets in the survival analysis literature, and some simulation studies are presented to show how the proposed framework leads to a test for a global effect with good power as compared with alternative procedures. Finally, possible generalisations are also presented for future research.
Finite Element Implementation of a Multivariant Shape Memory Alloy Model
Authors: Vigliotti Andrea
Published: March 2010

In this article a finite element implementation of a multivariant constitutive model of shape memory alloys for a mono-dimensional element is presented. The model has been implemented by writing the kinetic law and the equilibrium equation in the rate form and integrating this equation along the thermomechanical load path. The implemented model allows to simulate both the operation in isothermal condition, in full or partial pseudoelastic recover and the behavior of shape memory alloy’s wire in mixed thermal and mechanical load application such as in cyclic activations of a wire against a structure. The developed model is suitable for integration in structural finite element program allowing to simulate the action of SMA wires in integrated in complex structure. A number of numerical cases for the developed model are showed in order to verify the ability to reproduce expected typical SMA behaviors.
Damage Detection Using Piezoelectric Admittance Approach with Inductive Circuitry
Authors: Wang X. , Tang J.
Published: March 2010

The impedance/admittance-based damage detection has been recognized to be sensitive to small-sized damage due to its high frequency measurement capability. Low-cost measurement circuit has previously been explored to extract the piezoelectric impedance/ admittance curves by using a resistor that is serially connected with the piezoelectric transducer, which enables a self-contained sensor unit. In this research, an innovative admittance-based damage detection scheme is proposed, which combines the key features of the low-cost impedance/admittance measurement circuit with those of the piezoelectric circuitry dynamics. In the new scheme, the piezoelectric transducer is integrated with an inductive circuit. The resonant effect of the inductive circuitry can greatly increase the measurement amplitude. Moreover, when the inductance is properly tuned, very significant dynamic interaction between the mechanical structure being monitored and the electrical circuitry will occur. This results in an order-of-magnitude amplification of the admittance change upon the occurrence of damage, which can yield much increased damage detection sensitivity. Extensive numerical and experimental investigations are carried out to demonstrate the new sensing system development.
Three-dimensional Stability Analysis of Piezoelectric Antisymmetric Angle-Ply Laminates Using Finite Layer Method
Authors: Akhras G. , Li W.C.
Published: March 2010

The finite layer method is the most efficient numerical method for 3D analysis of simply supported rectangular plates. In this method, the plate is divided into a number of finite layers. Within each finite layer, trigonometric functions are used for the in-plane interpolations of displacements, whereas polynomials are employed for the interpolations in the thickness direction. Thus, the 3D analysis is transformed into a series of 1D analyses, and the efficiency is enhanced significantly. In the present study, the finite layer method is extended to the stability analysis of piezoelectric antisymmetric angle-ply laminates, which may be also combined with some symmetrical cross-plies. Numerical results are presented to verify the proposed method. The effects of side-to-thickness ratio, aspect ratio, number of plies, fiber-orientation, and electrical conditions on stability behaviors of some piezoelectric laminates are investigated.
Timing of Impairment and Health-Promoting Lifestyles in Women With Disabilities
Authors: Harrison Tracie C. , Umberson Deborah , Lin Li-Chen , Cheng Hsui-Rong
Published: March 2010

The purpose of this study was to develop a substantive theory to explain how the timing of impairment in women’s lives influenced health-promoting lifestyles among 45 women age 43 to 79 years with impairments of varying onset across the life course. From this grounded theory exploration, we suggest that women created health-related lifestyles that were comprised of changing abilities, roles, and rituals in support of perceived self. The ultimate goal of a healthy lifestyle was healthy aging, which was self-determination in the support of positive relationships. Environment and resources had direct influence on the perceived self. Our proposed substantive theory provides an understanding of how women develop a healthy lifestyle after the onset of permanent sensory or physical impairment. It also takes steps toward an understanding of how timing of impairment influences the perceptions women have of themselves and their health behaviors.
Sustainability of a Targeted Intervention Package: First Step to Success in Oregon
Authors: Loman Sheldon L. , Rodriguez Billie Jo , Horner Robert H.
Published: March 2010

Variables affecting the sustained implementation of evidence-based practices are receiving increased attention. A descriptive analysis of the variables associated with sustained implementation of First Step to Success (FSS), a targeted intervention for young students at risk for behavior disorders, is provided. Measures based on a conceptual model of sustainability were used with personnel from 29 schools from 13 Oregon school districts to describe variables that promote the sustainability of FSS. Results indicate that 28% of the school districts continued to implement FSS up to 10 years after initial implementation. Six critical features were perceived by school personnel to promote sustainability: (a) dedicated resources, (b) training and orientation activities, (c) district-level coordination, (d) selection of students who are a good fit for the intervention, (e) highly qualified coaches, and (f) administrative support. Clinical relevance and future directions for research addressing sustainability are presented.
South Asian Immigrant Women Who Have Survived Child Sexual Abuse: Resilience and Healing
Authors: Singh Anneliese A. , Hays Danica G. , Chung Y. Barry , Watson Laurel
Published: March 2010

The current study is a phenomenological examination of the resilience strategies of South Asian immigrant women in the United States who survived child sexual abuse. Semistructured interviews ( N = 5) and a focus group ( N = 8) were analyzed to gain a deep structural understanding of participants’ experiences of child sexual abuse and resilience. Findings included four subthemes of South Asian context (strict gender socialization, maintenance of family image, influence of ethnic identity, acculturative stressors) and five subthemes of resilience strategies (use of silence, sense of hope, South Asian social support, social advocacy, intentional self-care). Research and practice implications are discussed.
Why Do Women Take Self-Defense Classes?
Authors: Hollander Jocelyn A.
Published: March 2010

Given the positive benefits of self-defense training for women, it is important to understand how women come to enroll in self-defense classes. Using data from a longitudinal study of university women, I explore the reasons women give for taking a self-defense class. I find that friends’ recommendations, visions of the “possible selves” they could become, and fear of violence were the most frequently reported reasons; having experienced a past assault was rarely cited as a reason for enrolling. In addition, many women who had never enrolled in a self-defense class reported having considered doing so. I explore barriers to learning self-defense and find that logistical issues such as time, money, and availability of classes were the most frequently reported reasons for not enrolling.
Intimate Partner Violence and Posttraumatic Stress Disorder Among High-Risk Women: Does Pregnancy Matter?
Authors: Stampfel Caroline C. , Chapman Derek A. , Alvarez Andrea E.
Published: March 2010

Interviews from 655 women participating in the Chicago Women’s Health Risk Study (CWHRS) were used to assess prevalence and factors associated with intimate partner violence (IPV) and posttraumatic stress disorder (PTSD). Black women had the highest rate of IPV overall and among pregnant women, and had decreased odds of PTSD compared to Black nonpregnant women. Hispanic pregnant women, however, had decreased odds of IPV and PTSD compared to Hispanic nonpregnant women. Disparities in IPV by race/ ethnicity and pregnancy status complicate the study of IPV and PTSD and have implications for the public health community.
Comparison of multifocal visual evoked potential, standard automated perimetry and optical coherence tomography in assessing visual pathway in multiple sclerosis patients
Authors: Laron Michal , Han Cheng  , Bin Zhang  , Schiffman Jade S , Tang Rosa A , Frishman Laura J
Published: March 2010

Background: Multifocal visual evoked potentials (mfVEP) measure local response amplitude and latency in the field of vision.

Objective: To compare the sensitivity of mfVEP, Humphrey visual field (HVF) and optical coherence tomography (OCT) in detecting visual abnormality in multiple sclerosis (MS) patients.

Methods: mfVEP, HVF, and OCT (retinal nerve fiber layer [RNFL]) were performed in 47 MS-ON eyes (last optic neuritis [ON] attack ≥6 months prior) and 65 MS-no-ON eyes without ON history. Criteria to define an eye as abnormal were: (1) mfVEP amplitude/latency — either amplitude or latency probability plots meeting cluster criteria with 95% specificity; (2) mfVEP amplitude or latency alone (specificity: 97% and 98%, respectively); and (3) HVF and OCT, mean deviation and RNFL thickness meeting p < 0.05, respectively.

Results: MfVEP (amplitude/latency) identified more abnormality in MS-ON eyes (89%) than HVF (72%), OCT (62%), mfVEP amplitude (66%) or latency (67%) alone. Eighteen percent of MS-no-ON eyes were abnormal for both mfVEP (amplitude/latency) and HVF compared with 8% with OCT. Agreement between tests ranged from 60% to 79%. mfVEP (amplitude/latency) categorized an additional 15% of MS-ON eyes as abnormal compared with HVF and OCT combined. Conclusions: mfVEP, which detects both demyelination (increased latency) and neural degeneration (reduced amplitude), revealed more abnormality than HVF or OCT in MS patients.
Angiotensin II type 1 receptor gene A1166C polymorphism and essential hypertension in Chinese: a meta-analysis
Authors: Wang Jia-Li , Li Xue  , Hao Pan-Pan , Feng Xu  , Chen Yu-Guo , Yun Zhang
Published: March 2010

Introduction. We performed a meta-analysis with the aim of assessing the association of the angiotensin II type 1 (AT1) receptor gene A1166C polymorphism with essential hypertension in Chinese case-control studies. Methods. Studies were searched from the Chinese Biomedicine Database, the China National Knowledge Infrastructure platform, Pubmed and Medline, using the search terms ‘hypertension’, ‘angiotensin II type 1 receptor’, ‘AT1R’, ‘polymorphism’, ‘China’ and ‘Chinese’, without limiting to any specific language. The strength of the association between the A1166C polymorphism and hypertension was evaluated by the odds ratio (OR) with the corresponding 95% confidence interval (CI). The analyses were performed with Cochrane RevMan software version 4.2.

Results. Overall, the variant genotype AC/CC was associated with a statistically increased essential hypertension risk with the pooled OR 1.48 (95% CI: 1.20—1.83). In the subgroup analyses, the association was also significant among studies using Northern populations, Southern populations, Han Chinese and hospital-based controls. The age did not influence the relationship between the AT1receptor A1166C polymorphism and hypertension in the subgroup analyses.

Conclusions. The present meta-analysis suggests that the AT1receptor 1166 AC/CC genotype is associated with susceptibility to hypertension in the Chinese population.
Genomics Education Training Needs of U.S. Health Educators
Authors: Chen Lei-Shih , Goodson Patricia
Published: March 2010

As genomic advances have turned the promise of personalized prevention and health promotion into a concrete possibility in the near future, scholars and the Centers for Disease Control and Prevention have begun to call for U.S. health educators to develop their genomic competencies. This advocacy, however, begs the question whether health educators feel the need for further genomic training. Using an emergent design, the authors analyze qualitative data obtained from in-depth interviews with 24 health educators in the United States. Data are searched for salient, emergent themes (salience is determined by the frequency of a theme’s occurrence across interviews). Findings indicate that although the majority (78.3%) of health educators have received minimal or no genomic education, 81.0% acknowledge the importance of adding some type of training to their future professional development. Participants suggest conference presentations, workshops, and symposia (54.5%) as the most preferable approach for delivering such training. The four most frequently desired training topics include applied genetics/genomics (85.7%), basic genetics/genomics (42.9%), current and future developments in genetics/genomics (28.6%), and genetic testing and screening (19.0%). Findings from this qualitative study can become catalysts for future examinations of this topic and provide the conceptual basis for developing genomics training materials specifically for health educators.
Bridging the Qualitative-Quantitative Software Divide
Authors: Annechino Rachelle , Antin Tamar M. J. , Lee Juliet P.
Published: March 2010

To compare and combine qualitative and quantitative data collected from respondents in a mixed-methods study, the research team developed a relational database to merge survey responses stored and analyzed in SPSS and semi-structured interview responses stored and analyzed in the qualitative software package ATLAS.ti. The process of developing the database as well as practical considerations for researchers who may wish to use similar methods are explored.
Prioritised research agenda for prevention and control of chronic respiratory diseases
Authors: Bousquet J. , Kiley J. , Bateman E.D. , Viegi G. , Cruz A.A. , Khaltaev N. , Aït Khaled N. , Baena-Cagnani C.E. , Barreto M.L. , Billo N. , Canonica G.W. , Carlsen K-H. , Chavannes N. , Chuchalin A. , Drazen J. , Fabbri L.M. , Gerbase M.W. , Humbert M. , Joos G. , Masjedi M.R. , Makino S. , Rabe K. , To T. , Zhi L.
Published: March 2010

The 2008–2013 World Health Organization (WHO) action plan on noncommunicable diseases (NCDs) includes chronic respiratory diseases as one of its four priorities. Major chronic respiratory diseases (CRDs) include asthma and rhinitis, chronic obstructive pulmonary disease, occupational lung diseases, sleep-disordered breathing, pulmonary hypertension, bronchiectiasis and pulmonary interstitial diseases. A billion people suffer from chronic respiratory diseases, the majority being in developing countries. CRDs have major adverse effects on the life and disability of patients. Effective intervention plans can prevent and control CRDs, thus reducing morbidity and mortality. A prioritised research agenda should encapsulate all of these considerations in the frame of the global fight against NCDs. This requires both CRD-targeted interventions and transverse NCD programmes which include CRDs, with emphasis on health promotion and disease prevention.
Influence of genetic ancestry on the risk of obstructive sleep apnoea syndrome
Authors: Guindalini C. , Colugnati F.A.B. , Pellegrino R. , Santos-Silva R. , Bittencourt L.R.A. , Tufik S.
Published: March 2010

The aim of the present study was to evaluate the influence of ethnicity on the risk of developing obstructive sleep apnoea syndrome (OSAS) using genomic analysis methods to estimate ancestry.

DNA samples were obtained from 1,010 individuals participating in the São Paulo Epidemiologic Sleep Study, who underwent full-night polysomnography. A total of 31 genetic ancestry-informative markers were selected in order to estimate individual admixture proportions.

Of patients with a diagnosis of OSAS, a higher number self-reporting Caucasian ethnicity (65.3%), as well as an increased percentage of European ancestry (78.2±16.7%) and lower percentage of West African ancestry (16.1±15.3%), than among individuals without OSAS (53.6, 73.5±18.1 and 20.1±16.8%, respectively) (p<0.001) was observed. Moreover, after correcting for sex, age, body mass index and socioeconomic status, logistic regression demonstrated that European ancestry was significantly associated with an increased risk of manifesting OSAS (OR 2.80, 95% CI 1.11–7.09). Conversely, West African ancestry was associated with a reduced risk of the OSAS phenotype (OR 0.26, 95% CI 0.09–0.72).

This is the first study to incorporate genomic analysis methods to measure the influence of ethnicity on the risk of OSAS. Since genetically determined ancestry may not capture unmeasured cultural and lifestyle differences, the contribution of environmental factors to the current findings should not be disregarded.
Unified translation repression mechanism for microRNAs and upstream AUGs
Authors: Ajay Subramanian S , Athey Brian D , Lee Inhan
Published: March 2010

Background

MicroRNAs (miRNAs) are endogenous small RNAs that modulate gene expression at the post-transcriptional level by binding complementary sites in the 3'-UTR. In a recent genome-wide study reporting a new miRNA target class (miBridge), we identified and validated interactions between 5'-UTRs and miRNAs. Separately, upstream AUGs (uAUGs) in 5'-UTRs are known to regulate genes translationally without affecting mRNA levels, one of the mechanisms for miRNA-mediated repression.

Results

Using sequence data from whole-genome cDNA alignments we identified 1418 uAUG sequences on the 5'-UTR that specifically interact with 3'-ends of conserved miRNAs. We computationally identified miRNAs that can target six genes through their uAUGs that were previously reported to suppress translation. We extended this meta-analysis by confirming expression of these miRNAs in cell-lines used in the uAUG studies. Similarly, seven members of the KLF family of genes containing uAUGs were computationally identified as interacting with several miRNAs. Using KLF9 as an example (whose protein expression is limited to brain tissue despite the mRNA being expressed ubiquitously), we show computationally that miRNAs expressed only in HeLa cells and not in neuroblastoma (N2A) cells can bind the uAUGs responsible for translation inhibition. Our computed results demonstrate that tissue- or cell-line specific repression of protein translation by uAUGs can be explained by the presence or absence of miRNAs that target these uAUG sequences. We propose that these uAUGs represent a subset of miRNA interaction sites on 5'-UTRs in miBridge, whereby a miRNA binding a uAUG hinders the progression of ribosome scanning the mRNA before it reaches the open reading frame (ORF).

Conclusions

While both miRNAs and uAUGs are separately known to down-regulate protein expression, we show that they may be functionally related by identifying potential interactions through a sequence-specific binding mechanism. Using prior experimental evidence that shows uAUG effects on translation repression together with miRNA expression data specific to cell lines, we demonstrate through computational analysis that cell-specific down-regulation of protein expression (while maintaining mRNA levels) correlates well with the simultaneous presence of miRNA and target uAUG sequences in one cell type and not others, suggesting tissue-specific translation repression by miRNAs through uAUGs.
Whole genome evaluation of horizontal transfers in the pathogenic fungus Aspergillus fumigatus
Authors: Mallet Ludovic V , Becq Jennifer , Deschavanne Patrick
Published: March 2010

Background

Numerous cases of horizontal transfers (HTs) have been described for eukaryote genomes, but in contrast to prokaryote genomes, no whole genome evaluation of HTs has been carried out. This is mainly due to a lack of parametric methods specially designed to take the intrinsic heterogeneity of eukaryote genomes into account. We applied a simple and tested method based on local variations of genomic signatures to analyze the genome of the pathogenic fungusAspergillus fumigatus.

Results

We detected 189 atypical regions containing 214 genes, accounting for about 1 Mb of DNA sequences. However, the fraction of atypical DNA detected was smaller than the average amount detected in the same conditions in prokaryote genomes (3.1% vs 5.6%). It appeared that about one third of these regions contained no annotated genes, a proportion far greater than in prokaryote genomes. When analyzing the origin of these HTs by comparing their signatures to a home made database of species signatures, 3 groups of donor species emerged: bacteria (40%), fungi (25%), and viruses (22%). It is to be noticed that though inter-domain exchanges are confirmed, we only put in evidence very few exchanges between eukaryotic kingdoms.

Conclusions

In conclusion, we demonstrated that HTs are not negligible in eukaryote genomes, bearing in mind that in our stringent conditions this amount is a floor value, though of a lesser extent than in prokaryote genomes. The biological mechanisms underlying those transfers remain to be elucidated as well as the biological functions of the transferred genes.
A comparative epidemiologic analysis of SARS in Hong Kong, Beijing and Taiwan
Authors: Lau Eric HY , Hsiung C Agnes , Cowling Benjamin J , Chen Chang-Hsun , Ho Lai-Ming , Tsang Thomas , Chang Chiu-Wen , Donnelly Christl A , Leung Gabriel M
Published: March 2010

Background

The 2002-2003 Severe Acute Respiratory Syndrome (SARS) outbreak infected 8,422 individuals leading to 916 deaths around the world. However, there have been few epidemiological studies of SARS comparing epidemiologic features across regions. The aim of this study is to identify similarities and differences in SARS epidemiology in three populations with similar host and viral genotype.

Methods

We present a comparative epidemiologic analysis of SARS, based on an integrated dataset with 3,336 SARS patients from Hong Kong, Beijing and Taiwan, epidemiological and clinical characteristics such as incubation, onset-to-admission, onset-to-discharge and onset-to-death periods, case fatality ratios (CFRs) and presenting symptoms are described and compared between regions. We further explored the influence of demographic and clinical variables on the apparently large differences in CFRs between the three regions.

Results

All three regions showed similar incubation periods and progressive shortening of the onset-to-admission interval through the epidemic. Adjusted for sex, health care worker status and nosocomial setting, older age was associated with a higher fatality, with adjusted odds ratio (AOR): 2.10 (95% confidence interval: 1.45, 3.04) for those aged 51-60; AOR: 4.57 (95% confidence interval: 3.32, 7.30) for those aged above 60 compared to those aged 41-50 years. Presence of pre-existing comorbid conditions was also associated with greater mortality (AOR: 1.74; 95% confidence interval: 1.36, 2.21).

Conclusion

The large discrepancy in crude fatality ratios across the three regions can only be partly explained by epidemiological and clinical heterogeneities. Our findings underline the importance of a common data collection platform, especially in an emerging epidemic, in order to identify and explain consistencies and differences in the eventual clinical and public health outcomes of infectious disease outbreaks, which is becoming increasingly important in our highly interconnected world.
Quantitative methylation profiling in tumor and matched morphologically normal tissues from breast cancer patients
Authors: Van der Auwera Ilse , Bovie Catherine , Svensson Cecilia , Trinh Xuan B , Limame Ridha , van Dam Peter , van Laere Steven J , van Marck Eric A , Dirix Luc Y , Vermeulen Peter B
Published: March 2010

Background

In the present study, we determined the gene hypermethylation profiles of normal tissues adjacent to invasive breast carcinomas and investigated whether these are associated with the gene hypermethylation profiles of the corresponding primary breast tumors.

Methods

A quantitative methylation-specific PCR assay was used to analyze the DNA methylation status of 6 genes (DAPK, TWIST, HIN-1, RASSF1A, RARβ2andAPC) in 9 normal breast tissue samples from unaffected women and in 56 paired cancerous and normal tissue samples from breast cancer patients.

Results

Normal tissue adjacent to breast cancer displayed statistically significant differences to unrelated normal breast tissues regarding the aberrant methylation of theRASSF1A(P = 0.03),RARβ2(P = 0.04) andAPC(P = 0.04) genes. Although methylation ratios for all genes in normal tissues from cancer patients were significantly lower than in the cancerous tissue from the same patient (P ≤ 0.01), in general, a clear correlation was observed between methylation ratios measured in both tissue types for all genes tested (P < 0.01). When analyzed as a categorical variable, there was a significant concordance between methylation changes in normal tissues and in the corresponding tumor for all genes tested butRASSF1A. Notably, in 73% of patients, at least one gene with an identical methylation change in cancerous and normal breast tissues was observed.

Conclusions

Histologically normal breast tissues adjacent to breast tumors frequently exhibit methylation changes in multiple genes. These methylation changes may play a role in the earliest stages of the development of breast neoplasia.
Targeting mTORC2 inhibits colon cancer cell proliferation in vitro and tumor formation in vivo
Authors: Roulin Didier , Cerantola Yannick , Dormond-Meuwly Anne , Demartines Nicolas , Dormond Olivier
Published: March 2010

The mammalian target of rapamycin (mTOR), which exists in two functionally distinct complexes, mTORC1 and mTORC2 plays an important role in tumor growth. Whereas the role of mTORC1 has been well characterized in this process, little is known about the functions of mTORC2 in cancer progression. In this study, we explored the specific role of mTORC2 in colon cancer using a short hairpin RNA expression system to silence the mTORC2-associated protein rictor. We found that downregulation of rictor in HT29 and LS174T colon cancer cells significantly reduced cell proliferation. Knockdown of rictor also resulted in a G1 arrest as observed by cell cycle analysis. We further observed that LS174T cells deficient for rictor failed to form tumors in a nude mice xenograft model. Taken together, these results show that the inhibition of mTORC2 reduces colon cancer cell proliferation in vitro and tumor xenograft formation in vivo. They also suggest that specifically targeting mTORC2 may provide a novel treatment strategy for colorectal cancer.
Neighborhood sampling: how many streets must an auditor walk?
Authors: McMillan Tracy E , Cubbin Catherine , Parmenter Barbara , Medina Ashley V , Lee Rebecca E
Published: March 2010

This study tested the representativeness of four street segment sampling protocols using the Pedestrian Environment Data Scan (PEDS) in eleven neighborhoods surrounding public housing developments in Houston, TX. The following four street segment sampling protocols were used (1) all segments, both residential and arterial, contained within the 400 meter radius buffer from the center point of the housing development (the core) were compared with all segments contained between the 400 meter radius buffer and the 800 meter radius buffer (the ring); all residential segments in the core were compared with (2) 75% (3) 50% and (4) 25% samples of randomly selected residential street segments in the core. Analyses were conducted on five key variables: sidewalk presence; ratings of attractiveness and safety for walking; connectivity; and number of traffic lanes. Some differences were found when comparing all street segments, both residential and arterial, in the core to the ring. Findings suggested that sampling 25% of residential street segments within the 400 m radius of a residence sufficiently represents the pedestrian built environment. Conclusions support more cost effective environmental data collection for physical activity research.
Intraductal papilloma of ectopic breast tissue in axillary lymph node of a patient with a previous intraductal papilloma of ipsilateral breast: a case report and review of the literature
Authors: Dzodic Radan , Stanojevic Boban , Saenko Vladimir , Nakashima Masahiro , Markovic Ivan , Pupic Gordana , Buta Marko , Inic Momcilo , Rogounovitch Tatiana , Yamashita Shunichi
Published: March 2010

The presence of ectopic breast tissue in axillary lymph nodes (ALN) is a benign condition that must be differentiated from primary or metastatic carcinoma. Here we report a patient who underwent excision of enlarged ALN 10 years after she had received surgical treatment of ipsilateral breast for an intracystic intraductal papilloma (IDP). Histological examination of the removed ALN revealed that the proliferative lesion consisted of papillary and tubular structures lined by luminal cuboidal cells and a distinct outer layer of myoepithelial cells resembling IDP of the breast. Immunostaining with a set of immunohistochemical markers including AE/AE3, alpha-smooth muscle actin and p63 in combination with estrogen and progesterone receptors confirmed the diagnosis of ectopic IDP.

This case shows that even though benign proliferative change in ectopic breast tissue is an extremely rare phenomenon, this possibility should be taken into account for correct diagnosis.
Risk factors for multidrug resistant bacteria and optimization of empirical antibiotic therapy in postoperative peritonitis
Authors: Augustin Pascal , Kermarrec Nathalie , Muller-Serieys Claudette , Lasocki Sigismond , Chosidow Denis , Marmuse Jean-Pierre , Valin Nadia , Desmonts Jean-Marie , Montravers Philippe
Published: March 2010

Introduction

The main objective was to determine risk factors for presence of multidrug resistant bacteria (MDR) in postoperative peritonitis (PP) and optimal empirical antibiotic therapy (EA) among options proposed by Infectious Disease Society of America and the Surgical Infection Society guidelines.

Methods

One hundred patients hospitalised in the intensive care unit (ICU) for PP were reviewed. Clinical and microbiologic data, EA and its adequacy were analysed. The in vitro activities of 9 antibiotics in relation to the cultured bacteria were assessed to propose the most adequate EA among 17 regimens in the largest number of cases.

Results

A total of 269 bacteria was cultured in 100 patients including 41 episodes with MDR. According to logistic regression analysis, the use of broad-spectrum antibiotic between initial intervention and reoperation was the only significant risk factor for emergence of MDR bacteria (odds ratio (OR) = 5.1; 95% confidence interval (CI) = 1.7 - 15; P = 0.0031). Antibiotics providing the best activity rate were imipenem/cilastatin (68%) and piperacillin/tazobactam (53%). The best adequacy for EA was obtained by combinations of imipenem/cilastatin or piperacillin/tazobactam, amikacin and a glycopeptide, with values reaching 99% and 94%, respectively. Imipenem/cilastin was the only single-drug regimen providing an adequacy superior to 80% in the absence of broad spectrum antibiotic between initial surgery and reoperation.

Conclusions

Interval antibiotic therapy is associated with the presence of MDR bacteria. Not all regimens proposed by Infectious Disease Society of America and the Surgical Infection Society guidelines for PP can provide an acceptable rate of adequacy. Monotherapy with imipenem/cilastin is suitable for EA only in absence of this risk factor for MDR. For other patients, only antibiotic combinations may achieve high adequacy rates.
A hybrid scheme for absorbing edge reflections in numerical modeling of wave propagation
Authors: Liu Yang , Sen Mrinal K.
Published: March 2010

We propose an efficient scheme to absorb reflections from the model boundaries in numerical solutions of wave equations. This scheme divides the computational domain into boundary, transition, and inner areas. The wavefields within the inner and boundary areas are computed by the wave equation and the one-way wave equation, respectively. The wavefields within the transition area are determined by a weighted combination of the wavefields computed by the wave equation and the one-way wave equation to obtain a smooth variation from the inner area to the boundary via the transition zone. The results from our finite-difference numerical modeling tests of the 2D acoustic wave equation show that the absorption enforced by this scheme gradually increases with increasing width of the transition area. We obtain equally good performance using pseudospectral and finite-element modeling with the same scheme. Our numerical experiments demonstrate that use of 10 grid points for absorbing edge reflections attains nearly perfect absorption.
A Maternal “Junk Food” Diet in Pregnancy and Lactation Promotes Nonalcoholic Fatty Liver Disease in Rat Offspring
Authors: Bayol Stéphanie A. , Simbi Bigboy H. , Fowkes Robert C. , Stickland Neil C.
Published: March 2010

With rising obesity rates, nonalcoholic fatty liver disease is predicted to become the main cause of chronic liver disease in the next decades. Rising obesity prevalence is attributed to changes in dietary habits with increased consumption of palatable junk foods, but maternal malnutrition also contributes to obesity in progeny. This study examines whether a maternal junk food diet predisposes offspring to nonalcoholic fatty liver disease. The 144 rat offspring were fed either a balanced chow diet alone or with palatable junk foods rich in energy, fat, sugar, and/or salt during gestation, lactation, and/or after weaning up to the end of adolescence. Offspring fed junk food throughout the study exhibited exacerbated hepatic steatosis, hepatocyte ballooning, and oxidative stress response compared with offspring given free access to junk food after weaning only. These offspring also displayed sex differences in their hepatic molecular metabolic adaptation to diet-induced obesity with increased expression of genes associated with insulin sensitivity, de novo lipogenesis, lipid oxidation, and antiinflammatory properties in males, whereas the gene expression profile in females was indicative of hepatic insulin resistance. Hepatic inflammation and fibrosis were not detected indicating that offspring had not developed severe steatohepatitis by the end of adolescence. Hepatic steatosis and increased oxidative stress response also occurred in offspring born to junk food-fed mothers switched to a balanced chow diet from weaning, highlighting a degree of irreversibility. This study shows that a maternal junk food diet in pregnancy and lactation contributes to the development of nonalcoholic fatty liver disease in offspring.