AS2TS system for protein structure modeling and analysis

We present a set of programs and a website designed to facilitate protein structure comparison and protein structure modeling efforts. Our protein structure analysis and comparison services use the LGA (local-global alignment) program to search for regions of local similarity and to evaluate the level of structural similarity between compared protein structures. To facilitate the homology-based protein structure modeling process, our AL2TS service translates given sequence–structure alignment data into the standard Protein Data Bank (PDB) atom records (coordinates). For a given sequence of amino acids, the AS2TS (amino acid sequence to tertiary structure) system calculates (e.g. using PSI-BLAST PDB analysis) a list of the closest proteins from the PDB, and then a set of draft 3D models is automatically created. Web services are available at

Diurnal cortisol and obesity in adolescents with and without Down syndrome

BackgroundThe prevalence of obesity in adolescents with Down syndrome (DS) far exceeds that in the general population. Cortisol, an adrenal hormone, can be obesogenic when dysregulated. However, the diurnal patterns of this hormone have not been examined among individuals with DS. Variations in adiposity may also mediate cortisol regulation. This study sought to examine diurnal cortisol patterns in adolescents with DS as well as associations between cortisol function and obesity.MethodA total of 32 adolescents, including 16 with DS and 16 controls with typical development (TD) of similar sex, age and Tanner pubertal stage (P > 0.05), participated in this preliminary study. Participants completed a dual‐energy X‐ray absorptiometry scan to measure body composition and collected saliva samples for cortisol measurements in the morning, afternoon and night. Linear mixed models with random intercepts and repeated measures were used to examine the daily trajectory of log‐transformed cortisol concentrations between adolescents with and without DS. A second model examined the interaction between DS and presence of elevated body fatness.ResultsAdolescents with DS had higher morning cortisol concentrations (intercept = 0.37 μg/dL), but this was not significantly different than in TD (0.35 μg/dL, P = 0.16). Cortisol significantly declined across hours (b = −0.026 μg/dL/h, P  0.05; d = 0.30).ConclusionsThis study is the first to examine diurnal cortisol in DS but is limited in sample size. These preliminary findings suggest that diurnal cortisol patterns are not significantly different between adolescents with DS and TD and that cortisol levels are not associated with adiposity in this population. Despite these non‐significant differences, youth with DS continue to be an ‘at‐risk’ population for paediatric obesity in need of clinical intervention.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/151976/1/jir12682_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/151976/2/jir12682.pd

MannDB – A microbial database of automated protein sequence analyses and evidence integration for protein characterization

BACKGROUND: MannDB was created to meet a need for rapid, comprehensive automated protein sequence analyses to support selection of proteins suitable as targets for driving the development of reagents for pathogen or protein toxin detection. Because a large number of open-source tools were needed, it was necessary to produce a software system to scale the computations for whole-proteome analysis. Thus, we built a fully automated system for executing software tools and for storage, integration, and display of automated protein sequence analysis and annotation data. DESCRIPTION: MannDB is a relational database that organizes data resulting from fully automated, high-throughput protein-sequence analyses using open-source tools. Types of analyses provided include predictions of cleavage, chemical properties, classification, features, functional assignment, post-translational modifications, motifs, antigenicity, and secondary structure. Proteomes (lists of hypothetical and known proteins) are downloaded and parsed from Genbank and then inserted into MannDB, and annotations from SwissProt are downloaded when identifiers are found in the Genbank entry or when identical sequences are identified. Currently 36 open-source tools are run against MannDB protein sequences either on local systems or by means of batch submission to external servers. In addition, BLAST against protein entries in MvirDB, our database of microbial virulence factors, is performed. A web client browser enables viewing of computational results and downloaded annotations, and a query tool enables structured and free-text search capabilities. When available, links to external databases, including MvirDB, are provided. MannDB contains whole-proteome analyses for at least one representative organism from each category of biological threat organism listed by APHIS, CDC, HHS, NIAID, USDA, USFDA, and WHO. CONCLUSION: MannDB comprises a large number of genomes and comprehensive protein sequence analyses representing organisms listed as high-priority agents on the websites of several governmental organizations concerned with bio-terrorism. MannDB provides the user with a BLAST interface for comparison of native and non-native sequences and a query tool for conveniently selecting proteins of interest. In addition, the user has access to a web-based browser that compiles comprehensive and extensive reports. Access to MannDB is freely available at

MannDB: A microbial annotation database for protein characterization

MannDB was created to meet a need for rapid, comprehensive automated protein sequence analyses to support selection of proteins suitable as targets for driving the development of reagents for pathogen or protein toxin detection. Because a large number of open-source tools were needed, it was necessary to produce a software system to scale the computations for whole-proteome analysis. Thus, we built a fully automated system for executing software tools and for storage, integration, and display of automated protein sequence analysis and annotation data. MannDB is a relational database that organizes data resulting from fully automated, high-throughput protein-sequence analyses using open-source tools. Types of analyses provided include predictions of cleavage, chemical properties, classification, features, functional assignment, post-translational modifications, motifs, antigenicity, and secondary structure. Proteomes (lists of hypothetical and known proteins) are downloaded and parsed from Genbank and then inserted into MannDB, and annotations from SwissProt are downloaded when identifiers are found in the Genbank entry or when identical sequences are identified. Currently 36 open-source tools are run against MannDB protein sequences either on local systems or by means of batch submission to external servers. In addition, BLAST against protein entries in MvirDB, our database of microbial virulence factors, is performed. A web client browser enables viewing of computational results and downloaded annotations, and a query tool enables structured and free-text search capabilities. When available, links to external databases, including MvirDB, are provided. MannDB contains whole-proteome analyses for at least one representative organism from each category of biological threat organism listed by APHIS, CDC, HHS, NIAID, USDA, USFDA, and WHO. MannDB comprises a large number of genomes and comprehensive protein sequence analyses representing organisms listed as high-priority agents on the websites of several governmental organizations concerned with bio-terrorism. MannDB provides the user with a BLAST interface for comparison of native and non-native sequences and a query tool for conveniently selecting proteins of interest. In addition, the user has access to a web-based browser that compiles comprehensive and extensive reports

Percentile reference values for anthropometric body composition indices in European children from the IDEFICS study

INTRODUCTION: To characterise the nutritional status in children with obesity or wasting conditions, European anthropometric reference values for body composition measures beyond the body mass index (BMI) are needed. Differentiated assessment of body composition in children has long been hampered by the lack of appropriate references. OBJECTIVES: The aim of our study is to provide percentiles for body composition indices in normal weight European children, based on the IDEFICS cohort (Identification and prevention of Dietary-and lifestyle-induced health Effects in Children and infantS). METHODS: Overall 18 745 2.0-10.9-year-old children from eight countries participated in the study. Children classified as overweight/obese or underweight according to IOTF (N = 5915) were excluded from the analysis. Anthropometric measurements (BMI (N = 12 830); triceps, subscapular, fat mass and fat mass index (N = 11 845-11 901); biceps, suprailiac skinfolds, sum of skinfolds calculated from skinfold thicknesses (N = 8129-8205), neck circumference (N = 12 241); waist circumference and waist-to-height ratio (N = 12 381)) were analysed stratified by sex and smoothed 1st, 3rd, 10th, 25th, 50th, 75th, 90th, 97th and 99th percentile curves were calculated using GAMLSS. RESULTS: Percentile values of the most important anthropometric measures related to the degree of adiposity are depicted for European girls and boys. Age-and sex-specific differences were investigated for all measures. As an example, the 50th and 99th percentile values of waist circumference ranged from 50.7-59.2 cm and from 51.3-58.7 cm in 4.5-to < 5.0-year-old girls and boys, respectively, to 60.6-74.5 cm in girls and to 59.9-76.7 cm in boys at the age of 10.5-10.9 years. CONCLUSION: The presented percentile curves may aid a differentiated assessment of total and abdominal adiposity in European children

Does High BMI Influence Hospital Charges in Children Undergoing Adenotonsillectomy?

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/93757/1/oby.2008.234.pd

Lactobacillus casei strain GG in the treatment of infants with acute watery diarrhea: A randomized, double-blind, placebo controlled clinical trial [ISRCTN67363048]

BACKGROUND: Adjuvant therapy to ORT with probiotic bacteria for infants with acute watery diarrhea has been under active investigation. Most studies have been done in the developed world showing benefit only for viral mild gastroenteritis. We evaluated the effect of a milk formula containing one billion (10(9)) cfu/ml of Lactobacillus casei strain GG (LGG) upon duration and severity of diarrhea in infants in an environment with more severe acute diarrhea, where etiologic agents other than rotavirus are involved more frequently, and where mixed infections are more prevalent. METHODS: Male infants aged 3–36 months brought for treatment of acute watery diarrhea of less than 48 hours were eligible. After rehydration was completed with the WHO's oral rehydration solution, patients were randomly assigned to receive a milk formula either containing LGG or not. Stool volume was periodically measured using a devise suited to collect stools separate from urine. Duration of diarrhea was estimated based on stools physical characteristics. RESULTS: Eighty nine patients received the placebo milk formula and ninety received the LGG containing formula. Both groups were comparable in their baseline characteristics. Total stool output was significantly larger (p = 0.047) in the LGG group (247.8 ml/kg) than in the placebo group (195.0 ml/kg). No significant differences were found in duration of diarrhea (58.5 hours with LGG vs. 50.4 hours with placebo), rate of treatment failure (21.1% with LGG vs. 18.0% with placebo), and proportion of patients with unresolved diarrhea after 120 hours (12.2% with LGG vs. 12.5% with placebo). The rate of stools with reducing substances after 24 hours of treatment increased significantly in both groups (from 41.4% to 72.2% with LGG and from 45.9% to 68.0% with placebo). CONCLUSION: This study did not show a positive effect of LGG on the clinical course of acute watery diarrhea. Positive beneficial effects of LGG, as had been reported elsewhere, could have been masked in our study by worsening diarrhea due to transient lactose malabsorption. Further studies with low-lactose or non-lactose conveyors of LGG are desirable

Recruitment into diabetes prevention programs : what is the impact of errors in self-reported measures of obesity?

BackgroundError in self-reported measures of obesity has been frequently described, but the effect of self-reported error on recruitment into diabetes prevention programs is not well established. The aim of this study was to examine the effect of using self-reported obesity data from the Finnish diabetes risk score (FINDRISC) on recruitment into the Greater Green Triangle Diabetes Prevention Project (GGT DPP).MethodsThe GGT DPP was a structured group-based lifestyle modification program delivered in primary health care settings in South-Eastern Australia. Between 2004&ndash;05, 850 FINDRISC forms were collected during recruitment for the GGT DPP. Eligible individuals, at moderate to high risk of developing diabetes, were invited to undertake baseline tests, including anthropometric measurements performed by specially trained nurses. In addition to errors in calculating total risk scores, accuracy of self-reported data (height, weight, waist circumference (WC) and Body Mass Index (BMI)) from FINDRISCs was compared with baseline data, with impact on participation eligibility presented.ResultsOverall, calculation errors impacted on eligibility in 18 cases (2.1%). Of n&thinsp;=&thinsp;279 GGT DPP participants with measured data, errors (total score calculation, BMI or WC) in self-report were found in n&thinsp;=&thinsp;90 (32.3%). These errors were equally likely to result in under- or over-reported risk. Under-reporting was more common in those reporting lower risk scores (Spearman-rho&thinsp;=&thinsp;&minus;0.226, p-value&thinsp;&lt;&thinsp;0.001). However, underestimation resulted in only 6% of individuals at high risk of diabetes being incorrectly categorised as moderate or low risk of diabetes.ConclusionsOverall FINDRISC was found to be an effective tool to screen and recruit participants at moderate to high risk of diabetes, accurately categorising levels of overweight and obesity using self-report data. The results could be generalisable to other diabetes prevention programs using screening tools which include self-reported levels of obesity.<br /