bluuebunny/crossref_metadata_2025 huggingface dataset:
The Independent Association Between 25‐Hydroxyvitamin D and Adiponectin and Its Relation With BMI in Two Large Cohorts: The NHS and the HPFS
Authors: Vaidya Anand , Williams Jonathan S. , Forman John P.
Published: July 2011

Low 25‐hydroxyvitamin D (25(OH)D) and adiponectin levels are both associated with obesity and cardiovascular disease. Cross‐sectional studies have suggested that 25(OH)D concentrations are positively associated with adiponectin, and that this relation may strengthen with increasing BMI. However, these studies had small samples sizes and did not account for many known confounders of adiponectin levels. We evaluated whether 25(OH)D was independently associated with circulating adiponectin in two large populations, and whether BMI modified this relationship. Cross‐sectional analyses were performed on 1,206 women from the Nurses' Health Study I (NHS) and 439 men from the Health Professionals Follow‐Up Study. Multivariable linear regression was used to analyze the independent association between 25(OH)D and adiponectin after controlling for potential confounders. Effect modification by BMI was examined by creating interaction terms between vitamin D and BMI. 25(OH)D concentrations were positively associated with circulating adiponectin in univariate analyses, and also independently associated with adiponectin after multivariable adjustments in both populations (women: β = 0.06, P < 0.001; men: β = 0.07, P < 0.05). BMI did not significantly modify the relation between 25(OH)D and adiponectin in either population. Higher 25(OH)D concentrations were independently associated with higher adiponectin concentrations in large populations of women and men. Since lower levels of 25(OH)D and adiponectin are associated with higher cardio‐metabolic risk, assessing the effect of vitamin D supplementation on adiponectin levels is warranted.
Regulation of Wnt/β‐Catenin Signaling by CCAAT/Enhancer Binding Protein β During Adipogenesis
Authors: Chung Sung Soo , Lee Ji Seon , Kim Min , Ahn Byung Yong , Jung Hye Seung , Lee Hak Mo , Kim Jae‐Woo , Park Kyong Soo
Published: July 2011

Activation of the Wnt/β‐catenin signaling pathway inhibits adipogenesis, while disruption of Wnt signaling leads to spontaneous adipogenesis. CCAAT/enhancer binding protein β (C/EBPβ) is rapidly induced in early stages of adipogenesis and is responsible for transcriptional induction of two major adipogenic transcription factors, peroxisome proliferator‐activated receptor γ (PPARγ) and C/EBPα. In this study, we examined whether C/EBPβ is involved in the suppression of Wnt/β‐catenin signaling during adipogenesis. Knockdown of C/EBPβ expression not only inhibited adipogenesis but also maintained active Wnt/β‐catenin signaling, after addition of adipogenic inducers. In contrast, overexpression of C/EBPβ substantially inhibited Wnt signaling. Interestingly, our data showed that C/EBPβ is involved in the expression of Wnt10b, a major Wnt ligand in preadipocytes, even though C/EBPβ is not an essential factor to regulate Wnt10b expression during adipogenesis, and that C/EBPβ inhibits Wnt10b promoter activity by directly binding to specific regions of the promoter. These results suggest a dual function of C/EBPβ: stimulating expression of adipogenic genes and inhibiting Wnt signaling.
Relationship Between Treatment Preference and Weight Loss in the Context of a Randomized Controlled Trial
Authors: Borradaile Kelley E. , Halpern Scott D. , Wyatt Holly R. , Klein Samuel , Hill James O. , Bailer Brooke , Brill Carrie , Stein Richard I. , Miller‐III Bernard V. , Foster Gary D.
Published: July 2011

Randomized controlled trials (RCTs) are considered the gold standard used to assess the efficacy of treatment. While a well implemented RCT can produce an unbiased estimate of the relative difference between treatment groups, the generalizability of these findings may be limited. Specific threats to the external validity include treatment preference. The purposes of this study were to: (i) assess whether receiving one's treatment preference was associated with weight loss and retention and (ii) whether receiving one's treatment preference modified the relationship between the treatments and weight loss. Treatment preference was assessed in 250 subjects prior to but independent of randomization into either low‐carbohydrate or low‐fat diets. Treatment preference was a predictor of weight loss (P = 0.002) but not retention (P = 0.90). Participants who received their preference lost less weight (−7.7 kg, 95% confidence interval (CI): −9.3 to −6.1) than participants who did not receive their preference (−9.7 kg, 95% CI: −11.4 to −8.1) and participants who did not report a strong preference at baseline (−11.2 kg, 95% CI: −12.6 to −9.7) (P = 0.04 and P = 0.0004, respectively). Treatment preference did not modify the effect of the treatment on weight loss. Contrary to conceptual predictions, this study failed to identify an interaction between treatment preference and weight loss in the setting of a randomized trial. Until treatment preference effects are definitively ruled out in this domain, future studies might consider stratifying their randomization procedure by treatment preference rather than excluding participants with strong treatment preferences.
Patients' Preferred Terms for Describing Their Excess Weight: Discussing Obesity in Clinical Practice
Authors: Volger Sheri , Vetter Marion L. , Dougherty Megan , Panigrahi Eva , Egner Rebecca , Webb Victoria , Thomas J. Graham , Sarwer David B. , Wadden Thomas A.
Published: July 2011

The increasing prevalence of obesity has become one of the most challenging problems facing healthcare providers. Despite recommendations from the US Preventive Services Task Force, many health professionals fail to discuss obesity with their patients. This study sought to identify terms that obese individuals who were treated in primary care would find the most and least acceptable for describing their excess weight. Three‐hundred ninety obese adult primary care patients in the Philadelphia area were administered the Weight Preferences Questionnaire from January 2008 through February 2009. Ratings of 11 terms used to describe excess weight were transformed to a 5‐point scale, ranging from “very desirable” (+2) to neutral (0) to “very undesirable” (−2). The term “fatness” (mean score −1.1 ± 1.3) was rated as significantly more undesirable than all other descriptors (P < 0.001). The terms “excess fat” (−0.6 ± 1.3), “large size” (−0.6 ± 1.3), “obesity” (−0.5 ± 1.4), and “heaviness” (−0.4 ± 1.2) were rated as significantly more undesirable then the remaining terms, which included weight problem, BMI, and excess weight (P < 0.001). In contrast, the term “weight” was viewed as the most desirable term for characterizing excess weight. Patients' preferences for terms were not significantly influenced by gender, race/ethnicity, or a BMI ≥40 kg/m2. Practitioners who treat obesity are encouraged to avoid undesirable terms when discussing this condition with their patients. Instead practitioners may want to consider broaching the topic using more patient‐friendly terms such as “weight,” “BMI,” “weight problem,” or “excess weight.”
Total Tooth Loss and Systemic Correlates of Inflammation: Role of Obesity
Authors: Meisel Peter , Wilke Peter , Biffar Reiner , Holtfreter Birte , Wallaschofski Henry , Kocher Thomas
Published: July 2011

Obesity and edentulism are both associated with multiple systemic disorders with an inflammatory background including periodontal diseases. This study aimed to evaluate the different impact of obesity on inflammation in dentate and toothless subjects. The data came from the population‐based, cross‐sectional study SHIP (Study of Health in Pomerania). We determined anthropometric measures including BMI, waist‐to‐hip ratio (WHR), diagnostic periodontal parameters, and systemic metabolites. It was shown that measures of systemic markers of inflammation and lipid or glucose metabolism (P < 0.001) were increased with higher WHR. When adjusted for age, sex, smoking, diabetes, education, physical activity, and last dentist's appointment, C‐reactive protein (CRP), fibrinogen, and leukocyte count were significantly related to WHR increasing from the first to the fourth WHR quartile (P < 0.001) as well as to the BMI. In both dentate and edentulous subjects higher WHR contributes significantly to increasing systemic CRP and fibrinogen with sex differences. In toothless subjects, while still dependent on increasing WHR, the inflammatory markers CRP and fibrinogen were higher than in dentate subjects, thereby revealing effect modification between sex and edentulism (P < 0.010). In conclusion, subjects with total tooth loss, although devoid of periodontal inflammation, may exhibit increased levels of systemic inflammatory mediators. Possible implications are discussed with respect to obesity and its relationship to inflammation.
Testing and Beyond: Strategies and Tools for Evaluating and Assessing Infants and Toddlers
Authors: Crais Elizabeth R.
Published: July 2011

Purpose

This article is a condensation of the recent American Speech-Language-Hearing Association (ASHA) document entitled
Roles and Responsibilities of Speech-Language Pathologists in Early Intervention: Guidelines
(ASHA, 2008). The article presents information on recommended and evidence-based practices related to the screening, evaluation, and assessment of infants and toddlers with, or at risk for, communication deficits. It is intended to be used by clinicians to enhance their practices.

Method

The
Guidelines
document was developed using the available research evidence, expert clinical perspectives, and, when possible, family perspectives related to the screening, evaluation, and assessment process. The current article includes key definitions and an overview of recommended practices in screening, evaluation, assessment, and results interpretation.

Implications

The article provides important and timely information for professionals and families related to the screening, evaluation, and assessment of infants and toddlers with, or at risk for, communication deficits. Speech-language pathologists, other professionals, and family members can use the information to implement recommended and evidence-based practices when screening, evaluating, and assessing young children for communication deficits.
Peeling the Onion of Auditory Processing Disorder: A Language/Curricular-Based Perspective
Authors: Wallach Geraldine P.
Published: July 2011

Purpose

This article addresses auditory processing disorder (APD) from a language-based perspective. The author asks speech-language pathologists to evaluate the functionality (or not) of APD as a diagnostic category for children and adolescents with language-learning and academic difficulties. Suggestions are offered from a curriculum-relevant/strategic-based language approach that places APD symptoms within a broader framework and takes into account the complex interaction among the language knowledge, skills, and strategies needed for academic success.

Method

Using the metaphor of peeling an onion to get to its core, the author demonstrates how auditory perceptual processing is influenced by and dependent on language abilities. Examples of curricular content are used to highlight the language savvy needed by students with language-learning disabilities (LLDs) to access the curriculum.

Conclusion

At the heart of the article is the question of what is (or are) the most effective way(s) to treat problems defined as “auditory” in nature. The article concludes with 10 suggestions that remind clinicians to consider the usefulness of viewing auditory processing problems as isolated events that can be “fixed.” Practical guidelines for creating authentic and functional intervention targets at school-age levels are also provided.
Auditory Processing Disorder and Auditory/Language Interventions: An Evidence-Based Systematic Review
Authors: Fey Marc E. , Richard Gail J. , Geffner Donna , Kamhi Alan G. , Medwetsky Larry , Paul Diane , Ross-Swain Deborah , Wallach Geraldine P. , Frymark Tobi , Schooling Tracy
Published: July 2011

Purpose

In this systematic review, the peer-reviewed literature on the efficacy of interventions for school-age children with auditory processing disorder (APD) is critically evaluated.

Method

Searches of 28 electronic databases yielded 25 studies for analysis. These studies were categorized by research phase (e.g., exploratory, efficacy) and ranked on a standard set of quality features related to methodology and reporting.

Results

Some support exists for the claim that auditory and language interventions can improve auditory functioning in children with APD and those with primary spoken language disorder. There is little indication, however, that observed improvements are due to the auditory features of these programs. Similarly, evidence supporting the effects of these programs on spoken and written language functioning is limited.

Conclusion

The evidence base is too small and weak to provide clear guidance to speech-language pathologists faced with treating children with diagnosed APD, but some cautious skepticism is warranted until the record of evidence is more complete. Clinicians who decide to use auditory interventions should be aware of the limitations in the evidence and take special care to monitor the spoken and written language status of their young clients.
The Role of the Speech-Language Pathologist in Identifying and Treating Children With Auditory Processing Disorder
Authors: Richard Gail J.
Published: July 2011

Purpose

The purpose of this prologue is to provide a historical perspective regarding the controversial issues surrounding auditory processing disorder (APD), as well as a summary of the current issues and perspectives that will be discussed in the articles in this forum.

Method

An evidence-based systematic review was conducted to examine treatment efficacy data in regard to APD, with inconclusive results. The review raised several issues and highlighted the differences in how various professionals approach APD. Consequently, experts who were members of an ad hoc American Speech-Language-Hearing Association committee charged with delineating the role of the speech-language pathologist in addressing APD attempted to describe in more detail their individual author perspectives on the topic.

Conclusion

Despite concerted efforts by researchers and clinical professionals, minimal concrete evidence is available to guide practicing professionals responsible for the diagnosis and treatment of APD. The role of the speech-language pathologist in diagnosing and treating APD remains under discussion, with varying perspectives advocated by individuals based on their research and clinical experience.
Collaborative Consultation in Natural Environments: Strategies to Enhance Family-Centered Supports and Services
Authors: Woods Juliann J. , Wilcox M. Jeanne , Friedman Mollie , Murch Trudi
Published: July 2011

Purpose

This article presents current information on recommended practices related to the delivery of early intervention (EI) supports and services to infants and toddlers with, or at risk for, communication deficits and their families.

Method

The focus is on presenting the changing paradigm for speech-language pathologists (SLPs) working in EI based on the best available research evidence and expert opinion. The article includes a brief review of the recommended and promising practices for early communication intervention and applies the content to the role of the SLP as a consultant to caregivers. It provides strategies for “how to” join into the everyday activities/routines and places with the caregiver and child in order to facilitate caregiver-implemented intervention that will enhance caregiver–child interactions and promote the child’s participation and learning. The importance of, and strategies for, collaborative consultation with diverse caregivers within a family-centered approach is presented.

Implications

This article provides important and timely information for professionals and families related to family-centered EI practices, caregiver-implemented interventions, adult teaching strategies, and collaborative consultation with families of infants and toddlers with, or at risk for, communication deficits. SLPs can use the information presented to inform their practices when working with these young children and their families.
The Diagnosis and Management of Auditory Processing Disorder
Authors: Moore David R.
Published: July 2011

Purpose

To provide a personal perspective on auditory processing disorder (APD), with reference to the recent clinical forum on APD and the needs of clinical speech-language pathologists and audiologists.

Method

The Medical Research Council–Institute of Hearing Research (MRC-IHR) has been engaged in research into APD and auditory learning for 8 years. This commentary is informed by and describes that and other research.

Results

Currently, APD is ill defined, and training-based interventions appear to have limited effectiveness. However, there remains a huge clinical and caregiver appetite for evidence-based information about children’s listening difficulties and how they might be managed. MRC-IHR research suggests that both the problem and the solution revolve around auditory cognition and, in particular, working memory and attention. Children who are poor listeners tend to have a range of cognitive difficulties. But, results of training studies within and beyond auditory science indicate that training primarily influences sustained attention (focus) rather than more basic sensory detection or discrimination.

Conclusion

Providing logical and rigorous scientific information on the nature and alleviation of listening difficulties in children should remain a high priority for speech, language, and hearing research. We should be optimistic that collaboration between clinicians and researchers will result in much greater understanding and improved management of listening disorders in the near future.
The Role of the Speech-Language Pathologist in Identifying and Treating Children With Auditory Processing Disorder
Authors: Richard Gail J.
Published: July 2011

Purpose

A summary of issues regarding auditory processing disorder (APD) is presented, including some of the remaining questions and challenges raised by the articles included in the clinical forum.

Method

Evolution of APD as a diagnostic entity within audiology and speech-language pathology is reviewed. A summary of treatment efficacy results and issues is provided, as well as the continuing dilemma for speech-language pathologists (SLPs) charged with providing treatment for referred APD clients.

Conclusion

The role of the SLP in diagnosing and treating APD remains under discussion, despite lack of efficacy data supporting auditory intervention and questions regarding the clinical relevance and validity of APD.
Pathways to Assessment of Learning: A Family-Centered, Culturally Responsive Approach to Transdisciplinary Assessment in Early Childhood
Authors: Moore Susan , Hyde-Smith Anne , Pratt Camilla , McKight Rosemary
Published: July 2011

Parental engagement in all aspects of the assessment process of their young child increases the reliability and validity of information gathered and shared. This article will describe a transdisciplinary assessment team framework that effectively engages each and every family in all aspects of the assessment process using person-centered planning strategies. The framework facilitates effective planning for next steps, strategies, and resources for the child and family in intervention and/or educational planning.
Speech-Language Pathologists Collaborating With Head Start To Improve Children’s Early Language and Literacy Skills: Efficacy and Intensity Effects
Authors: Moyle Maura Jones , Berman S. Sue
Published: July 2011

The current study examined the efficacy of a speech-language pathologist–designed and implemented emergent literacy program for Head Start preschoolers and the influence of intensity of intervention on children’s gains. Results indicated that children who participated in the intervention program exhibited greater gains than the control group on oral language, phonological awareness, and alphabet/print knowledge. Children who received a higher dosage of intervention made greater gains on vocabulary and oral language compared to the lower intensity group. Speech-language pathologists may be valuable collaborators in promoting emergent literacy skills in at-risk children.
Interprofessional Collaborative Practice: Preparing Future Professionals To Use the ICF-CY
Authors: Self Trisha , Coufal Kathy L. , Francois Jennifer
Published: July 2011

The global call to action has been communicated from the World Health Organization (WHO), addressed to health care providers and higher education programs. The expressed need is to mobilize a workforce that is “collaborative practice-ready” (WHO, 2010, p. 7), prepared to work as members of an interprofessional team. Although the context of the WHO statement explicitly targets health care professionals, it also addresses the need for services to be contextually based and culturally appropriate and to involve the families, communities, and individuals for whom services are directed. This article will explore the key elements and mechanisms of interprofessional collaborative practice in early childhood service delivery for health care and early intervention specialists from a number of professional perspectives.
Theoretical study of Cl−RG (rare gas) complexes and transport of Cl− through RG (RG = He–Rn)
Authors: Withers Carolyn D. , Wright Timothy G. , Viehland Larry A. , Grossman Leonid , Kirkpatrick Charles C. , Lee Edmond P. F.
Published: July 2011

We present a systematic investigation of the accuracy of the various theories and basis sets that can be applied to study the interaction of Cl− ions with Ar atoms. It is conclusively shown that gaseous ion mobility can distinguish among theoretical ion-neutral interaction potentials. Based on the conclusions, high-level ab initiopotential energy curves are obtained for all of the Cl−–RG (RG = He–Rn) complexes. Spectroscopic constants have been derived from these potentials and are compared to a range of theoretical and experimental data, to which they generally show good agreement. General trends are discussed in comparison to other halogen-rare gas complexes previously studied. The potentials also have been tested by using them to calculate transport coefficients for Cl− moving through a bath of RG atoms.
Rigorous non-Born-Oppenheimer theory: Combination of explicitly correlated Gaussian method and nuclear orbital plus molecular orbital theory
Authors: Hoshino Minoru , Nishizawa Hiroaki , Nakai Hiromi
Published: July 2011

The present study proposes a rigorous non-Born-Oppenheimer theory combining between the explicitly correlated Gaussian (ECG) method and the nuclear orbital plus molecular orbital (NOMO) method. The new method, called ECG-NOMO, adopts the ECG functions between the electronic and nuclear coordinates and, therefore, is capable of describing the nucleus-electron correlation effect accurately. The basic formalism of the ECG-NOMO method is close to the NOMO method, which starts with the Hartree-Fock type equations for NOs and MOs. The present method requires more computational cost than the original NOMO method. However, its cost is significantly smaller than that of the ECG method. The numerical tests was performed for hydrogen-like atoms (H-Ne9+) and dihydrogen cations (H2+, D2+ and T2+), and clarified that the ECG-NOMO method shows the sufficient accuracy.
Effects of reagent vibrational excitation on the dynamics of the H + CHD3 → H2 + CD3 reaction: A seven-dimensional time-dependent wave packet study
Authors: Zhou Yong , Wang Chunrui , Zhang Dong H.
Published: July 2011

Seven-dimensional time-dependent wave packet calculations were carried out to study the title reaction on the potential energy surface constructed recently by the group [Y. Zhou, B. Fu, C. Wang, M. A. Collins, and D. H. Zhang, J. Chem. Phys. 134, 064323 (2011)10.1063/1.3552088]. Total reaction probabilities and integral cross sections were calculated for a number of initial vibration states. It is found that the fundamental C–H stretching excitation can promote the reaction dramatically. At E = 1.53 eV, it enhances the integral cross section by a factor of 13.2, which is in good agreement with the quasiclassical trajectory result on the ZBB1 potential energy surface, but larger than that on the the EG-2002 potential energy surface. The thermal rate constants were obtained for the title reaction by taking into account the contributions from all relevant initial vibration states. It is found that the ground initial state has a dominant contribution to the thermal rate constant at low temperature region. As the temperature increases, the relative contribution to the thermal rate constant from the ground initial state decreases quickly, and those from the stretching and bending excited states increases substantially. It is estimated that the C–H stretching mode contributes about 40% of the thermal rate constant at T = 1000 K despite the fact that the overall population for stretching excited states is tiny.
A new species of deep-sea Dendronotus Alder & Hancock (Mollusca:Nudibranchia) from California, with an expanded phylogeny of the genus
Authors: Stout Carla C. , Wilson Nerida G. , Valdés Ángel
Published: July 2011

Dendronotus patricki, sp. nov. is a new species collected from a whalefall in the Monterey Canyon, California. This new species is characterised by having a small number of dorsal appendages compared with similarly sized species of Dendronotus Alder & Hancock, 1845. Anatomically, D. patricki, sp. nov. has a small prostate with just a few alveoli, a very small seminal receptacle situated near the distal end of the vagina, and a relatively short and small ampulla. The rachidian radular teeth of D. patricki, sp. nov. are unique among Dendronotus as they have a well differentiated, conical cusp with very small denticles on either side, but most denticles are located on the sides of the teeth, rather than on the sides of the cusp. Dendronotus patricki, sp. nov., is genetically distinct from other species of Dendronotus for which sequence data are available. A phylogenetic analysis of Dendronotus based on COI, 16S, and H3 sequence data reveals that D. patricki, sp. nov. forms a polytomy with Dendronotus orientalis (Baba, 1932) and a clade of the shallow temperate and cold water species. The tropical Indo-Pacific species D. regius Pola & Stout, 2008 is the sister group to all other Dendronotus species.
The Impact of Product Name on Dieters’ and Nondieters’ Food Evaluations and Consumption
Authors: Irmak Caglar , Vallen Beth , Robinson Stefanie Rosen
Published: July 2011

This research explores the impact of merely altering the name of a food on dieters’ and nondieters’ evaluations of the food’s healthfulness and taste, as well as consumption. Four studies demonstrate that when a food is identified by a relatively unhealthy name (e.g., pasta), dieters perceive the item to be less healthful and less tasty than do nondieters. When the identical food is assigned a relatively healthy name (e.g., salad), however, dieting tendency has no effect on product evaluations. This effect, which results in differences in actual food consumption, is explained by nondieters’ insensitivity to food cues as well as dieters’ reliance on cues indicating a lack of healthfulness and tendency to employ heuristic information processing when evaluating foods. These findings contribute to the body of literature that explores both individual and contextual factors that influence food evaluation and consumption.
How Much Does the Supplemental Nutrition Assistance Program Reduce Food Insecurity?
Authors: Ratcliffe Caroline , McKernan Signe-Mary , Zhang Sisi
Published: July 2011

Nearly 15% of all U.S. households and 40% of near‐poor households were food insecure in 2009. The Supplemental Nutrition Assistance Program (SNAP) is the cornerstone of federal food assistance programs and serves as the first line of defense against food‐related hardship. This paper measures the effectiveness of SNAP in reducing food insecurity using an instrumental variables approach to control for selection. Our results suggest that receipt of SNAP benefits reduces the likelihood of being food insecure by roughly 30% and reduces the likelihood of being very food insecure by 20%.
A Model of Labeling with Horizontal Differentiation and Cost Variability
Authors: Saak Alexander E.
Published: July 2011

We study optimal disclosure of variety by a multiproduct firm with random costs. The prices for labeled varieties are increasing functions of the cost differential and do not reveal which variety is cheaper to produce. Nondisclosure is most common under moderate uncertainty about costs and not too much idiosyncrasy in valuations and quality asymmetry. Mandatory disclosure decreases expected welfare when cost variability is large and quality asymmetry is small. The cheaper variety tends to be oversupplied (undersupplied) when disclosure is voluntary (mandatory). Competition among multiproduct firms that source inputs in the same upstream market may not lead to more disclosure.
DECOD: fast and accurate discriminative DNA motif finding
Authors: Huggins Peter , Zhong Shan , Shiff Idit , Beckerman Rachel , Laptenko Oleg , Prives Carol , Schulz Marcel H. , Simon Itamar , Bar-Joseph Ziv
Published: July 2011

Motivation: Motif discovery is now routinely used in high-throughput studies including large-scale sequencing and proteomics. These datasets present new challenges. The first is speed. Many motif discovery methods do not scale well to large datasets. Another issue is identifying discriminative rather than generative motifs. Such discriminative motifs are important for identifying co-factors and for explaining changes in behavior between different conditions.

Results: To address these issues we developed a method for DECOnvolved Discriminative motif discovery (DECOD). DECOD uses a k-mer count table and so its running time is independent of the size of the input set. By deconvolving the k-mers DECOD considers context information without using the sequences directly. DECOD outperforms previous methods both in speed and in accuracy when using simulated and real biological benchmark data. We performed new binding experiments for p53 mutants and used DECOD to identify p53 co-factors, suggesting new mechanisms for p53 activation.

Availability: The source code and binaries for DECOD are available at http://www.sb.cs.cmu.edu/DECOD

Contact:  zivbj@cs.cmu.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
PDBpaint, a visualization webservice to tag protein structures with sequence annotations
Authors: Fournier David , Andrade-Navarro Miguel A.
Published: July 2011

Summary: Protein features are often displayed along the linear sequence of amino acids that make up that protein, but in reality these features occupy a position in the folded protein's 3D space. Mapping sequence features to known or predicted protein structures is useful when trying to deduce the function of those features and when evaluating sequence or structural predictions. To facilitate this goal, we developed PDBpaint, a simple tool that displays protein sequence features gathered from bioinformatics resources on top of protein structures, which are displayed in an interactive window (using the Jmol Java viewer). PDBpaint can be used either with existing protein structures or with novel structures provided by the user. The current version of PDBpaint allows the visualization of annotations from Pfam, ARD (detection of HEAT-repeats), UniProt, TMHMM2.0 and SignalP. Users can also add other annotations manually.

Availability and Implementation: PDBpaint is accessible at http://cbdm.mdc-berlin.de/~pdbpaint. Code is available from http://sourceforge.net/projects/pdbpaint. The website was implemented in Perl, with all major browsers supported.

Contact:  david.fournier@mdc-berlin.de
The Irish Sea data-enhancement project: comparison of self-sampling and national data-collection programmes—results and experiences
Authors: Hoare Deirdre , Graham Norman , Schön Pieter-Jan
Published: July 2011

Hoare, D., Graham, N., and Schön, P-J. 2011. The Irish Sea data-enhancement project: comparison of self-sampling and national data-collection programmes—results and experiences. – ICES Journal of Marine Science, 68: 1778–1784. The Irish Sea Data Enhancement Pilot (ISDEP) was initiated by the UK and Irish fishing sectors, with the objective of improving the precision of commercial catch data (landings and discards) from vessels engaged in demersal trawling in the Irish Sea (ICES Division VIIa). The programme was supported by the Irish and UK Governments and managed by national laboratories. The experience of establishing and managing such a programme, including logistical, data-quality, and participation issues, is discussed. By contrasting with parallel national programmes, it is shown that the new data are robust and have improved precision. Experience has also shown that it is preferable to involve a few vessels in providing frequent samples, but that positive incentives are needed to maintain the participation.
First Report of Soybean Rust Caused by Phakopsora pachyrhizi on Pachyrhizus erosus in the United States
Authors: Delaney M. A. , Sikora E. J. , Delaney D. P. , Palm M. E. , Roscoe J. , Haudenshield J. S. , Hartman G. L.
Published: July 2011

Soybean rust, caused by the fungus Phakopsora pachyrhizi, was detected on jicama (Pachyrhizus erosus L. Urban) for the first time in the United States in November 2009. The pathogen was observed on leaves of a single, potted jicama plant grown outdoors in a residential area and on leaves of all plants in a 12-m2 demonstration plot located at the Auburn University Teaching Garden in Auburn, AL. Symptoms on the upper leaf surfaces were isolated chlorotic areas near the leaf edges in the lower part of the canopy. The abaxial surface was first observed to exhibit brown lesions and subsequently produced volcano-shaped uredinia. These symptoms are consistent with a rust previously described on jicama in Mexico (1). Representative symptomatic plant tissue was sent to the USDA National Identification Services (Mycology) Laboratory in Beltsville, MD for diagnostic confirmation at both the Urbana, IL lab and the USDA National Plant Germplasm and Biotechnology Laboratory for DNA testing. From an infected leaf, samples of approximately 5 mm2 were excised from a microscopically observed rust lesion and an apparently noninfected area. Total DNA was purified with the FastDNA Spin Kit (MP Biomedicals, Solon, OH) followed by the E.Z.N.A. MicroElute DNA Clean-Up Kit (Omega Bio-tek, Inc, Doraville, GA) per manufacturer's instructions. Detection of P. pachyrhizi and P. meibomiae DNA was achieved by quantitative PCR using the method of Frederick et al. (2) and a DNA standard of previously prepared P. pachyrhizi spores. The observed rust pustule was found to contain P. pachyrhizi DNA in excess of 28,000 genomes, while no P. pachyrhizi DNA was observed from the asymptomatic sample. Both samples were negative for P. meibomiae. The fungal structures present were confirmed to be Phakopsora spp. DNA was extracted from sori aseptically removed from leaves with a Qiagen (Valencia, CA) DNeasy Plant Mini Kit and amplified with primers Ppa1 and NL4. The resulting partial ITS2 and 28S ribosomal RNA sequences were 100% identical to GenBank entry DQ354537 P. pachyrhizi internal transcribed spacer 2 and 28S ribosomal RNA gene, partial sequence. Sequences from jicama from Alabama were deposited in GenBank. Voucher specimens were deposited in the USDA Agricultural Research Service, National Fungus Collection (BPI). To our knowledge, this is the first report of the disease on jicama in the United States.

References: (1) A. Cárcamo Rodriguez et al. Plant Dis. 90:1260, 2006. (2) R. D. Frederick et al. Phytopathology 92:217, 2002.
Toward Fungicidal Management of Laurel Wilt of Avocado
Authors: Ploetz Randy C. , Pérez-Martínez José M. , Evans Edward A. , Inch Sharon A.
Published: July 2011

Laurel wilt threatens commercial and residential production of avocado (Persea americana) in Florida. Laurel wilt on redbay (P. borbonia) was controlled previously with macroinfusions (injections) of Alamo, an injectable formulation of propiconazole. To determine whether Alamo macroinfusion would be cost effective in commercial avocado production, economic analyses were conducted for various macroinfusion scenarios and a standardized production situation in southern Florida. Under prevailing conditions, macroinfusion was not cost effective. In the interest of identifying alternative means to manage the disease, other fungicides and application measures were evaluated. In all, 20 fungicides in 15 chemical groups and 10 fungicide groups were examined in vitro. In vitro inhibition of the radial growth of the pathogen Raffaelea lauricola was determined on fungicide-amended malt extract agar; demethylation inhibitors (DMIs; fenarimol, myclobutanil, propiconazole, prothioconazole, triadimenol, triadimefon, and triticonazole), quinone outside inhibitors (azoxystrobin, pyraclostrobin, and fluoxastrobin), and a quinone inside inhibitor (fluazinam) had the greatest impact on radial growth (the concentration at which growth was reduced by 50% was ≥0.1 μg ml–1). In greenhouse studies, the most inhibitory products in vitro, plus thiabendazole and two products that were not tested in vitro, flutriafol and a potassium salts mixture of phosphorus acid, were tested for disease suppression on artificially inoculated, potted ‘Simmonds,’ a susceptible avocado cultivar. In general, soil drench applications of the above DMIs and thiabendazole but not azoxystrobin, pyraclostrobin, fluazinam, or the phosphorus acid salt provided significant control of disease (P < 0.05). Topical branch or trunk applications of propiconazole, and triadimenol in 2% Pentrabark, a bark-penetrating surfactant, were also effective at lower rates than were used in drench applications. Comparable levels of disease suppression were achieved when propiconazole was applied at 11% of the rates that were used in soil drenches. Although topical fungicide applications in bark-penetrating surfactants would be a less expensive practice than macroinfusion, moving sufficient concentrations of propiconazole or other fungicides into host xylem will be difficult in trees that are larger than the potted plants that were tested in these trials. Ongoing work examines means by which this goal might be met on fruit-bearing trees in the field.
Pediatric Capsule Endoscopy
Authors: Cohen Stanley A. , Ephrath Hagit , Lewis Jeffery D. , Klevens Alan , Bergwerk Ari , Liu Steven , Patel Dinesh , Reed‐Knight Bonney , Stallworth Angela , Wakhisi Tamara , Gold Benjamin D.
Published: July 2011

Background and Objective:

Because capsule endoscopy (CE) avoids ionizing radiation, deep sedation, and general anesthesia, CE may be valuable in pediatrics. We report a single pediatric center's experience with the use and safety of CE.

Methods:

In a retrospective review of consecutive CE studies, 284 CE studies were performed in 277 patients with a mean age of 15 (±3.7) years during a 5‐year period. The youngest to swallow the capsule was 4.6 years old. Twenty capsules were placed. Overall, 245 (86%) patients underwent CE for suspected (184, 65%) or confirmed (61, 21%) Crohn disease (CD); 27 (9.5%) anemia or gastrointestinal bleeding; 6 (2%) polyposis; and 4 (1.4%) celiac disease.

Results:

Positive findings were observed in 205 (72%) of the studies, with 152 (54%) having small bowel findings. Of these, 72 (47%) were diagnostic. Gastric (95, 33%) and colonic (31, 11%) abnormalities were also identified. Five CE studies (1.8%) resulted in retention of the capsule in nonsurgical patients. A patency capsule before CE in 23 patients allowed 19 CE to proceed with only 1 retained capsule. In 65 (21%) patients, the video capsule did not enter the colon before the video's end. Of these, 36 (65%) had significant findings, including 27 (49%) documenting small bowel (SB) CD.

Conclusions:

CE is useful to diagnose SB disease in children. Even in a study population with a high prevalence of confirmed and suspected CD, the risk of retention remains small. The patency capsule may lessen that risk. CE may identify gastric or colonic disease even when SB lesions are not present.
Effect of a 10‐week Weight Loss Camp on Fatty Liver Disease and Insulin Sensitivity in Obese Danish Children
Authors: Grønbæk Henning , Lange Aksel , Birkebæk Niels H. , Holland‐Fischer Peter , Solvig Jan , Hørlyck Arne , Kristensen Kurt , Rittig Søren , Vilstrup Hendrik
Published: July 2011

Background and Objective:

Childhood nonalcoholic fatty liver disease (NAFLD) associated with insulin resistance and obesity is a growing problem and increases the risk of cirrhosis, type 2 diabetes mellitus, and cardiovascular complications. We examined the effects of a 10‐week “weight loss camp” residency in obese children on the prevalence and degree of NAFLD and insulin sensitivity with 12‐month follow‐up.

Methods:

At the camp, 117 obese white children (body mass index 28.0 ± 3.6 kg/m2, age 12.1 ± 1.3 years) exercised moderately for 1 hour/day and restricted their energy intake to induce weight loss. NAFLD was diagnosed and graded using ultrasound and transaminasemia. Insulin sensitivity and glucose tolerance were assessed using homeostasis model assessment and oral glucose tolerance test. We performed anthropometric measurements and determined body composition using bioimpedance. Data were collected from 71 of 117 children at entry, after the 10 weeks at the camp, and 12 months after the camp ended.

Results:

The children showed an average weight loss of 7.1 ± 2.7 kg during the camp. At baseline, 43% had ultrasonographic liver steatosis, 50% elevated transaminases (>25 IU/L), and reduced insulin sensitivity. These abnormalities were mutually related and improved significantly during the camp (P ≤ 0.05). Liver fat improvement was sustained at 12 months. At the 12‐month follow‐up, 17 of 71 (24%) children maintained the body weight.

Conclusions:

This short‐term diet and exercise program induced weight loss, markedly improved all aspects of the threatening condition of NAFLD, and reduced insulin sensitivity in childhood obesity; 24% of the children maintained weight loss at least until the 12‐month follow‐up.
Significance of Abnormalities in Systems Proximal and Distal to the Obstructed Site of Duodenal Atresia
Authors: Alatas Fatima S. , Masumoto Kouji , Esumi Genshiro , Nagata Kouji , Taguchi Tomoaki
Published: July 2011

Background:

Duodenal atresia (DA) is a well‐known neonatal intestinal disease. Even after surgery, the proximal segment can continue to be severely dilated with hypoperistalsis, resulting in intestinal dysmotility problems in later life. No data have been published regarding the morphologic differences between the proximal and distal regions of obstructed sites of the intramural components in DA.

Methods:

Operative duodenal samples (N = 12) from cases with DA (age 1–3 days) were used. Age‐matched controls (N = 2) were used. All of the specimens were immunohistochemically stained with antibodies to S‐100 protein, α‐smooth muscle actin, and c‐kit protein.

Results:

At the proximal segments of the obstructed site in DA, the number of neuronal cells decreased in size and number. The circular musculature was moderately to severely hypertrophic. Unusual ectopic smooth muscle bundles were also identified. The innermost layer of the circular musculature was thinner. Interstitial cells of Cajal are decreased, even around the myenteric plexus. All of the staining in the distal segments in DA was similar to the control tissues.

Conclusions:

Proximal and distal segments in DA differ in the neural cells, musculature, and distributions of the interstitial cells of Cajal. Based on the present study, these morphologic changes may contribute to the onset of postoperative duodenal dysmotility.
Comparison of rhinovirus A infection in human primary epithelial and HeLa cells
Authors: Amineva S. P. , Aminev A. G. , Gern J. E. , Palmenberg A. C.
Published: July 2011

HeLa cells are used to study the life cycles of many different viruses, including the human rhinoviruses (HRV) in the family Picornaviridae. Although the natural targets of HRV are human bronchial epithelial cells (hBE), it is generally more difficult to obtain and maintain the relevant primary cell cultures, relative to HeLa cells. Given that the HRV are now identified as a major cause of human asthma exacerbations, it becomes important to document how much of the virus biology learned from HeLa cells is common also to natural primary cells. When compared directly in matched infections using A01a virus, the kinetics of RNA replication, the synthesis and processing of viral proteins and the general subcellular localization of key non-structural proteins were resembled in hBE and HeLa cells. Viral-induced shutoff of host cell processes (e.g. nucleo-cytoplasmic trafficking) was also comparable.
Glycoprotein J of infectious laryngotracheitis virus is required for efficient egress of infectious virions from cells
Authors: Mundt Alice , Mundt Egbert , Hogan Robert J. , García Maricarmen
Published: July 2011

Glycoprotein J (gJ) of infectious laryngotracheitis virus (ILTV) represents a major viral antigen and is dispensable for replication in cell culture and chickens. We generated gJ deletion mutants derived from the United States Department of Agriculture standard challenge strain (USDA-ch), a GFP-expressing mutant GΔgJ, a gJ deletion mutant void of any foreign DNA insertion (BΔgJ) and a gJ rescue mutant gJR with US5 restored. GΔgJ, BΔgJ and gJR were characterized in cell culture and embryonated eggs. Entry kinetic assays showed that the gJ deletion mutants did not differ in their entry kinetics from gJR. Replication kinetics strongly indicated that gJ plays an important role during egress of the virus. Differences in the abilities of the mutants to replicate in chorioallantoic membranes of chicken embryos and to release infectious virus into the allantoic fluid supported a function of gJ during the egress of ILTV from infected cells.
Characterization of a cluster of oncogenic mutations in E6 of a human papillomavirus 83 variant isolated from a high-grade squamous intraepithelial lesion
Authors: Cannavo Isabelle , Benchetrit Maxime , Loubatier Céline , Michel Gregory , Lemichez Emmanuel , Giordanengo Valérie
Published: July 2011

We previously isolated human papillomavirus 83 (HPV83m) from a cervical smear. Sequence analysis of E6 and E7 proteins highlighted five mutations located in the second putative zinc-finger region of E6 (E6m), an important domain for protein–protein or protein–DNA interactions. Here, we show that E6m of HPV83m can trigger human primary cell proliferation and anchorage-independent growth properties, similarly to E6 of HPV16, a high-risk HPV (HR-HPV). Interestingly, we demonstrate that, in contrast to E6 of HPV16, E6m corrupts neither p53 stability nor telomerase activity, but acts as a specific modulator of the transcriptional machinery. By studying E6m reversion mutants, we confirmed the importance of the second zinc-finger domain in triggering the observed upregulation of cell growth and of the transcriptional machinery. Reversion of these mutations in E6m (to yield strain E6r) fully abolished the oncogenic potential of E6m, transforming the phenotype of E6 from a high-risk to a low-risk phenotype. Importantly, our data define the importance of a cluster of mutations in the second zinc finger of E6m in increasing the oncogenic potential of HPV83.