bluuebunny/crossref_metadata_2025_split huggingface dataset:
Recurrence after surgery for equinus foot deformity in children with cerebral palsy: Assessment of predisposing factors for recurrence in a long-term follow-up study
Authors: Joo Sun Young , Knowtharapu Durga N. , Rogers Kenneth J. , Holmes Laurens , Miller Freeman 
Published: June 2011

Background Despite the large number of studies on the recurrence after surgery for equinus foot deformity in cerebral palsy (CP) patients, only a few investigations have reported long-term recurrence rates. Furthermore, little is known on the interval between the recurrent surgeries and the factors that lead to early recurrence. This study aimed to assess the overall recurrence after surgery for equinus foot deformity in patients with CP and to assess the factors associated with recurrence. We also aimed to determine the predisposing factors for early recurrence. Methods The medical records of 186 patients (308 feet) were reviewed in order to determine the recurrence after surgery for equinus foot deformity. The type of CP, type of surgery, age at surgery, functional mobility, passive dorsiflexion of the ankle at the last follow-up visit, and subsequent treatment were recorded. Kaplan–Meier survival analysis was employed, with the end point defined as reoperation. Results The mean age at surgery was 6.8 ± 2.5 years (range, 2.2–13.1). With the mean follow-up period of 11.3 years (range, 7.2–17.7), the overall recurrence rate was 43.8%. The recurrence rate was highest among patients with hemiplegia (62.5%). The Kaplan–Meier survival without repeat surgery estimate was shown to be 88.6% at 5 years and 59.6% at 10 years. Among children with hemiplegia and diplegia, the younger children (≤8 years of age) showed a higher rate of recurrence compared with the older children ( P = 0.04 and P = 0.01, respectively). In 41 feet (30.4%), reoperations were performed within 5 years after the primary surgery. Early recurrence was most prevalent among children with hemiplegia (50.0%). In children with diplegia and quadriplegia, the younger children underwent the secondary operation later than the older children ( P = 0.04 and P = 0.02, respectively). Conclusion Recurrence after surgery for equinus foot deformity is common and the age at surgery has a significant influence on recurrence. Recurrence can occur at any age while the child is still growing; therefore, it is advised to follow those patients until they reach skeletal maturity. Level of Evidence Level III, therapeutic study.
Confirmatory Factor Analysis of the Patient Health Questionnaire‐9: A Study of the Participants From the Spinal Cord Injury Model Systems
Authors: Krause James S. , Saunders Lee L. , Bombardier Charles , Kalpakjian Claire 
Published: June 2011

ObjectiveTo examine the factor structure of the Patient Health Questionnaire‐9, a measure of depression, in persons with spinal cord injury (SCI).DesignCross‐sectional, confirmatory factor analytic study.SettingCommunity.ParticipantsData for 7296 persons with an SCI who had sustained their injury at least 1 year prior to assessment and who had complete Patient Health Questionnaire‐9 data collected at a follow‐up interview were drawn from the National Spinal Cord Injury Statistical Center Database.InterventionsNone.Main outcome measuresFactor structure of the Patient Health Questionnaire‐9.ResultsConfirmatory factor analysis indicated a marginal fit for the single factor solution (root mean square error of approximation [RMSEA] = 0.086), whereas the solution with 5 somatic items and 4 nonsomatic items had the best fit (RMSEA = 0.054) among 2‐factor models that used all 9 items. Of the models that used fewer than 9 items, the best fit was for the 6‐item solution with 3 somatic items (sleep, appetite, and fatigue) and 3 nonsomatic items (feeling down, feeling bad about self, and suicidal ideation; RMSEA = 0.043). Similar results were found across the strata except for the Hispanic group (for whom no model fit well).ConclusionsGiven the results of this analysis that support a 2‐factor structure of the Patient Health Questionnaire‐9 in persons with SCI, the next step in this line of research is to validate each of these dimensions against other ways of measuring depression.
Optimal design of a class of generalized symmetric Gough–Stewart parallel manipulators with dynamic isotropy and singularity-free workspace
Authors: Tong Zhizhong , He Jingfeng , Jiang Hongzhou , Duan Guangren 
Published: June 2011

SUMMARYIn this paper, the definition of generalized symmetric Gough–Stewart parallel manipulators is presented. The concept of dynamic isotropy is proposed and the singular values of the bandwidth matrix are introduced to evaluate dynamic isotropy and solved analytically. Considering the payload's mass-geometry characteristics, the formulations for completely dynamic isotropy are derived in close form. It is proven that a generalized symmetric Gough–Stewart parallel manipulator is easer to achieve dynamic isotropy and applicable in engineering applications. An optimization procedure based on particle swarm optimization is proposed to obtain better dexterity and large singularity-free workspace, which guarantees the optimal solution and gives mechanically feasible realization.
The role of drinking water in the transmission of antimicrobial-resistantE. coli
Authors: COLEMAN B. L. , SALVADORI M. I. , McGEER A. J. , SIBLEY K. A. , NEUMANN N. F. , BONDY S. J. , GUTMANIS I. A. , McEWEN S. A. , LAVOIE M. , STRONG D. , JOHNSON I. , JAMIESON F. B. , LOUIE M. ,   ARO Water Study Group
Published: June 2011

SUMMARYTo determine whether drinking water contaminated with antimicrobial-resistantE. coliis associated with the carriage of resistantE. coli, selected households sending water samples to Ontario and Alberta laboratories in 2005–2006 were asked to participate in a cross-sectional study. Household members aged ⩾12 years were asked to complete a questionnaire and to submit a rectal swab. In 878 individuals, 41% carried a resistant strain ofE. coliand 28% carried a multidrug-resistant strain. The risk of carriage of resistantE. coliwas 1·26 times higher for users of water contaminated with resistantE. coli. Other risk factors included international travel [prevalence ratio (PR) 1·33], having a child in nappies (PR 1·33), being male (PR 1·33), and frequent handling of raw red meats (PR 1·10). Protecting private water sources (e.g. by improving systems to test and treat them) may help slow the emergence of antimicrobial resistance inE. coli.
Right bundle branch block as a marker for interatrial septal abnormalities
Authors: Bakalli Aurora , Koçinaj Dardan , Georgievska-Ismail Ljubica , Bekteshi Tefik , Pllana Ejup , Sejdiu Basri 
Published: June 2011

AbstractBackgroundInteratrial septal anomalies, which include atrial septal defect, patent foramen ovale, and atrial septal aneurysm, are common disorders among adult patients. Early detection of interatrial septal anomalies is important in order to prevent haemodynamic consequences and/or thromboembolic events. Electrocardiogram offers some clues that should serve as hints for detection of interatrial abnormalities. The aim of our study was to analyse the interatrial septum by transoesophageal echocardiography in patients with electrocardiogram signs of right bundle branch block and in those without right bundle branch block.Methods and resultsIn a prospective study, 87 adult patients were included, that is, 41 with electrocardiogram signs of right bundle branch block forming the first group and 46 without right bundle branch block forming the second group. Interatrial septal anomalies were present in 80.5% of the patients with right bundle branch block, with patent foramen ovale (39.02%) being the most prevalent disorder, followed by atrial septal aneurysm (21.9%) and atrial septal defect (19.5%). Interatrial septal abnormalities were significantly more frequent in the first group compared with the second group (80.5% versus 6.5%, p value less than 0.001). Independently, patent foramen ovale was significantly more prevalent in patients with right bundle branch block (39.02% versus 4.3%, p value less than 0.001), as were atrial septal aneurysm (21.9% versus 2.2%, p value equal 0.01) and atrial septal defect (19.5% versus 0%, p value equal 0.004).ConclusionsRight bundle branch block should serve as a valuable indicator to motivate a detailed search for interatrial septal abnormalities.
Objectively assessed physical activity and sedentary behaviour does not differ between children and adolescents with and without a congenital heart defect: a pilot examination
Authors: Ewalt Lauren A. , Danduran Michael J. , Strath Scott J. , Moerchen Victoria , Swartz Ann M. 
Published: June 2011

AbstractObjectivesTo objectively evaluate and describe physical activity levels in children with a stable congenital heart defect and compare those levels with children who do not have a congenital heart defect.MethodsWe matched 21 pairs of children for gender and grade in school and gave them an accelerometer-based motion sensor to wear for 7 consecutive days.ResultsPhysical activity levels did not differ between children with and without a congenital heart defect. During the 7 days of monitoring, children in this study spent most of their time in sedentary behaviours, that is, 6.7 hours of the 13 monitored hours, 54 minutes in moderate-intensity physical activity, and 12 minutes in vigorous-intensity physical activity. Less than one-fifth of all participants, with or without a congenital heart defect, accumulated sufficient physical activity to meet current physical activity recommendations for children and adolescents.ConclusionChildren with a stable congenital heart defect have activity behaviours that are similar to children without a congenital heart defect. Habitual physical activity in children with a congenital heart defect should be encouraged early on in life to develop strong physical activity habits that will hopefully follow them across their lifespan.
Symptomatic myocardial bridges in children: a case report with review of literature
Authors: Sharma Jayendra , Hellenbrand William , Kleinman Charles , Mosca Ralph 
Published: June 2011

AbstractMyocardial bridge is a rare congenital coronary anomaly in children, usually seen in the setting of hypertrophic cardiomyopathy and in left ventricular hypertrophy. Most myocardial bridges are believed to represent a benign anatomical variant; however, symptomatic myocardial bridge is a distinct subgroup of pathological variant, linked to myocardial ischaemia, ventricular arrhythmia, and sudden cardiac death. We present a case of a symptomatic myocardial bridge in a 5-year-old boy with mild hypertrophic cardiomyopathy who underwent supra-arterial myotomy, automatic defibrillator placement, and long-term Beta-blocker therapy. We also present 10 years of follow-up with a review of literature regarding symptomatic myocardial bridges in the paediatric age group.
The Healthy Eating Index and the Alternate Healthy Eating Index as predictors of 10-year CHD risk in Cuban Americans with and without type 2 diabetes
Authors: Huffman Fatma G , Zarini Gustavo G , Mcnamara Elizabeth , Nagarajan Aarthi 
Published: June 2011

AbstractObjectiveTo examine the relationship between dietary patterns, as measured by the Healthy Eating Index (HEI) and the Alternate Healthy Eating Index (AHEI), and 10-year predicted CHD risk in Cuban Americans with and without type 2 diabetes (T2D).DesignIn a cross-sectional study participants were selected from two randomly generated mailing lists of individuals with and without T2D. HEI and AHEI scores were calculated from a self-reported FFQ. CHD risk was determined using the 10-year CHD risk calculator of the Adult Treatment Panel III.SettingMiami Dade and Broward Counties, FL, USA.SubjectsCuban Americans (n358) aged ≥30 years.ResultsParticipants with T2D had a higher waist circumference (P= 0·001) and 10-year CHD risk score (P= 0·008) compared with those without T2D. Participants without T2D had a higher energy intake (P= 0·034), total blood cholesterol (P= 0·007), HDL cholesterol (P= 0·001) and HEI score (P= 0·006) compared with participants with T2D. AHEI score was a significant predictor of 10-year CHD risk (F(1,351)= 4·44,P= 0·036). An association between AHEI and 10-year CHD risk was found only for participants with T2D (β= −0·244,se= 0·049,P= 0·001).ConclusionThe present study showed that only participants with T2D with significantly higher AHEI scores had lower scores for 10-year predicted CHD risk. No association was found between HEI score and CHD risk among Cuban Americans. Individuals with T2D are advised to follow the AHEI dietary pattern.
Structure and Chemistry across Interfaces at Nanoscale of a Ge Quantum Well Embedded within Rare Earth Oxide Layers
Authors: Das Tanmay , Bhattacharyya Somnath 
Published: June 2011

AbstractStructure and chemistry across the rare earth oxide-Ge interfaces of a Gd2O3-Ge-Gd2O3 heterostructure grown on p-Si (111) substrate using encapsulated solid phase epitaxy method have been studied at nanoscale using various transmission electron microscopy methods. The structure across both the interfaces was investigated using reconstructed phase and amplitude at exit plane. Chemistry across the interfaces was explored using elemental mapping, high-angle annular dark-field imaging, electron energy loss spectroscopy, and energy dispersive X-ray spectrometry. Results demonstrate the structural and chemical abruptness of both the interfaces, which is most essential to maintain the desired quantum barrier structure.
Biophysical visual virtual reality in retinotopic visual areas
Authors: Bókkon István , Tuszynski Jack , Salari Vahid 
Published: June 2011

AbstractPreviously, we have pointed out that biophoton production can be a controlled process that originates from regulated redox/radical reactions. Our biophoton experiments support the notion that various visual related phenomena such as discrete retinal noise, retinal phosphenes as well as negative afterimages are due to biophotons. We have also suggested a new model, stating that the brain is able to create biophysical pictures in retinotopic visual areas via redox regulated biophotons of synchronized neurons. According to our interpretation, visualization (imagery) is a special kind of representation i.e., visual imagery requires peculiar inherent biophysical processes. Our idea of biophysical visual virtual reality in retinotopic areas may be a possible biophysical basis of Kosslyn's reality simulation principle in the case of visual imagery. Long-term visual memories are not stored as biophysical pictures but as epigenetic codes. During visual imagery, top-down processes control the epigenetic encoded long-term visual information. Then, according to retrieved epigenetic information, synchronized retinotopic neurons generate dynamic patterns of biophotons via redox reactions that can produce biophysical pictures. We have also presented an iterative model involving a biophysical picture-representation without homunculus during visual imagery.
Enriching targeted sequencing experiments for rare disease alleles
Authors: Edwards Todd L. , Song Zhuo , Li Chun 
Published: June 2011

Abstract
Motivation: Next-generation targeted resequencing of genome-wide association study (GWAS)-associated genomic regions is a common approach for follow-up of indirect association of common alleles. However, it is prohibitively expensive to sequence all the samples from a well-powered GWAS study with sufficient depth of coverage to accurately call rare genotypes. As a result, many studies may use next-generation sequencing for single nucleotide polymorphism (SNP) discovery in a smaller number of samples, with the intent to genotype candidate SNPs with rare alleles captured by resequencing. This approach is reasonable, but may be inefficient for rare alleles if samples are not carefully selected for the resequencing experiment.
Results: We have developed a probability-based approach, SampleSeq, to select samples for a targeted resequencing experiment that increases the yield of rare disease alleles substantially over random sampling of cases or controls or sampling based on genotypes at associated SNPs from GWAS data. This technique allows for smaller sample sizes for resequencing experiments, or allows the capture of rarer risk alleles. When following up multiple regions, SampleSeq selects subjects with an even representation of all the regions. SampleSeq also can be used to calculate the sample size needed for the resequencing to increase the chance of successful capture of rare alleles of desired frequencies.
Software: http://biostat.mc.vanderbilt.edu/SampleSeq
Contact: chun.li@vanderbilt.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Identification of novel transcripts in annotated genomes using RNA-Seq
Authors: Roberts Adam , Pimentel Harold , Trapnell Cole , Pachter Lior 
Published: June 2011

Abstract
Summary: We describe a new ‘reference annotation based transcript assembly’ problem for RNA-Seq data that involves assembling novel transcripts in the context of an existing annotation. This problem arises in the analysis of expression in model organisms, where it is desirable to leverage existing annotations for discovering novel transcripts. We present an algorithm for reference annotation-based transcript assembly and show how it can be used to rapidly investigate novel transcripts revealed by RNA-Seq in comparison with a reference annotation.
Availability: The methods described in this article are implemented in the Cufflinks suite of software for RNA-Seq, freely available from http://bio.math.berkeley.edu/cufflinks. The software is released under the BOOST license.
Contact: cole@broadinstitute.org; lpachter@math.berkeley.edu
Supplementary Information: Supplementary data are available at Bioinformatics online.
A procedure to statistically evaluate agreement of differential expression for cross-species genomics
Authors: Pounds Stan , Gao Cuilan Lani , Johnson Robert A. , Wright Karen D. , Poppleton Helen , Finkelstein David , Leary Sarah E. S. , Gilbertson Richard J. 
Published: June 2011

Abstract
Motivation: Animal models play a pivotal role in translation biomedical research. The scientific value of an animal model depends on how accurately it mimics the human disease. In principle, microarrays collect the necessary data to evaluate the transcriptomic fidelity of an animal model in terms of the similarity of expression with the human disease. However, statistical methods for this purpose are lacking.
Results: We develop the agreement of differential expression (AGDEX) procedure to measure and determine the statistical significance of the similarity of the results of two experiments that measure differential expression across two groups. AGDEX defines a metric of agreement and determines statistical significance by permutation of each experiment's group labels. Additionally, AGDEX performs a comprehensive permutation-based analysis of differential expression for each experiment, including gene-set analyses and meta-analytic integration of results across studies. As an example, we show how AGDEX was recently used to evaluate the similarity of the transcriptome of a novel model of the brain tumor ependymoma in mice to that of a subtype of the human disease. This result, combined with other observations, helped us to infer the cell of origin of this devastating human cancer.
Availability: An R package is currently available from www.stjuderesearch.org/site/depts/biostats/agdex and will shortly be available from www.bioconductor.org.
Contact: stanley.pounds@stjude.org
Supplementary information: Supplementary data are available at Bioinformatics online.
In-depth annotation of SNPs arising from resequencing projects using NGS-SNP
Authors: Grant Jason R. , Arantes Adriano S. , Liao Xiaoping , Stothard Paul 
Published: June 2011

Abstract
Summary: NGS-SNP is a collection of command-line scripts for providing rich annotations for SNPs identified by the sequencing of whole genomes from any organism with reference sequences in Ensembl. Included among the annotations, several of which are not available from any existing SNP annotation tools, are the results of detailed comparisons with orthologous sequences. These comparisons can, for example, identify SNPs that affect conserved residues, or alter residues or genes linked to phenotypes in another species.
Availability: NGS-SNP is available both as a set of scripts and as a virtual machine. The virtual machine consists of a Linux operating system with all the NGS-SNP dependencies pre-installed. The source code and virtual machine are freely available for download at http://stothard.afns.ualberta.ca/downloads/NGS-SNP/.
Contact: stothard@ualberta.ca
Supplementary information: Supplementary data are available at Bioinformatics online.
MetaABC—an integrated metagenomics platform for data adjustment, binning and clustering
Authors: Su Chien-Hao , Hsu Ming-Tsung , Wang Tse−Yi , Chiang Sufeng , Cheng Jen-Hao , Weng Francis C. , Kao Cheng−Yan , Wang Daryi , Tsai Huai-Kuang 
Published: June 2011

Abstract
Summary: MetaABC is a metagenomic platform that integrates several binning tools coupled with methods for removing artifacts, analyzing unassigned reads and controlling sampling biases. It allows users to arrive at a better interpretation via series of distinct combinations of analysis tools. After execution, MetaABC provides outputs in various visual formats such as tables, pie and bar charts as well as clustering result diagrams.
Availability: MetaABC source code and documentation are available at http://bits2.iis.sinica.edu.tw/MetaABC/
Contact: dywang@gate.sinica.edu.tw; hktsai@iis.sinica.edu.tw
Supplementary information: Supplementary data are available at Bioinformatics online.
SNPman: a program for genotype calling using run data from TaqMan allelic discrimination
Authors: Konopac Martin , Dusatkova Petra , Cinek Ondrej 
Published: June 2011

Abstract
Summary: The SNPman program calls the genotypes of single nucleotide polymorphisms (SNP) from TaqMan allelic discrimination assays. It utilizes the fluorescence data collected over the whole PCR run, rather than relying on the end point fluorescence measurements that is the basis of the genotype calling process in most software solutions sold with the real-time instruments. This inspection of run data facilitates genotype calls in difficult sample sets, especially in those containing various concentrations of DNA or inhibitors, as indicated by results of a reanalysis of 3738 genotyping samples. The program works with data from three different widely used PCR instruments.
Availability: The compiled program is available online at http://sourceforge.net/projects/snpman/files/, along with its user documentation and demonstration data files. It is free of charge for non-commercial users.
Contact: Ondrej.Cinek@Lfmotol.cuni.cz
Supplementary information: Supplementary data are available at Bioinformatics online.