A Constraint Solver for Flexible Protein Model

This paper proposes the formalization and implementation of a novel class of constraints aimed at modeling problems related to placement of multi-body systems in the 3-dimensional space. Each multi-body is a system composed of body elements, connected by joint relationships and constrained by geometric properties. The emphasis of this investigation is the use of multi-body systems to model native conformations of protein structures---where each body represents an entity of the protein (e.g., an amino acid, a small peptide) and the geometric constraints are related to the spatial properties of the composing atoms. The paper explores the use of the proposed class of constraints to support a variety of different structural analysis of proteins, such as loop modeling and structure prediction. The declarative nature of a constraint-based encoding provides elaboration tolerance and the ability to make use of any additional knowledge in the analysis studies. The filtering capabilities of the proposed constraints also allow to control the number of representative solutions that are withdrawn from the conformational space of the protein, by means of criteria driven by uniform distribution sampling principles. In this scenario it is possible to select the desired degree of precision and/or number of solutions. The filtering component automatically excludes configurations that violate the spatial and geometric properties of the composing multi-body system. The paper illustrates the implementation of a constraint solver based on the multi-body perspective and its empirical evaluation on protein structure analysis problems.

[Capsule endoscopy in children: which are the best indications?]

BACKGROUND AND STUDY AIMS

Capsule endoscopy (CE) is a novel and noninvasive means of investigating the small bowel. In children, the best CE indications have not yet been fully appraised. The aim of this study was to evaluate the diagnostic yield of CE in different pediatric pathologies.

PATIENTS AND METHODS

We retrospectively reviewed every CE performed in children in two French pediatric hospitals between March 2002 and June 2009. Seventy-nine CEs were performed on 70 children (mean age, 10.6 years; range, 2.2-18.0); 52 boys and 18 girls. The indications were iron deficiency anemia (24%), obscure gastrointestinal bleeding (14%), polyposis syndromes (16%), suspected Crohn disease (15%), unresponsive Crohn disease (10%), graft-versus-host disease (10%), and other (10%).

RESULTS

Of the 79 CEs, 69 reached the cecum (87%). Only one occlusion occurred in a case of stenosing Crohn disease, requiring surgical removal. In addition, technical difficulties led to an incomplete small bowel study in 12 cases (16%). The CE showed small bowel lesions in 42 cases (53%). The diagnostic yield was 27% in obscure gastrointestinal bleeding, 37% in iron-deficiency anemia, 42% in suspected Crohn disease, 88% in unresponsive Crohn disease, 62% in polyposis syndromes, and 88% in graft-versus-host disease.

CONCLUSION

In children, CE is well tolerated and can be performed in children as young as 2.2 years of age. Its diagnostic yield is highest in polyposis syndromes, unresponsive Crohn disease, and graft-versus-host disease.

Fecal expression of human β-defensin-2 following birth

BACKGROUND

Newborns display high intestinal permeability and a naive adaptive immune system, but infections are rare, indicating strong innate defense mechanisms.

OBJECTIVE

To measure the kinetics of fecal β-defensin-2 (HBD2), an inducible endogenous antimicrobial peptide produced by intestinal epithelial cells, in full-term and preterm infants.

METHODS

As a first step of this bicentric study, we enrolled 30 healthy full-term infants and 20 healthy preterm infants, with fecal samples collected at days 3, 7, 12 and 30 in full-term infants and at days 15, 30 and 60 in preterm infants. As a second step, we enrolled 10 preterm infants with intestinal distress, either necrotizing enterocolitis (NEC) Bell's stage III (n = 3) or isolated rectal bleeding (n = 7) and 20 controls, cross-matched for gestational age and age at sampling.

RESULTS

HBD2 decreased significantly from day 3 to day 7 (227 ng/g; 14-440 vs. 117 ng/g; 30-470, p = 0.01) then moderately until day 30 (84 ng/g; 10-500) in healthy full-term infants. Healthy preterm infants showed similar high levels between days 15 and 60 (82 ng/g; 30-154 and 85 ng/g; 26-390, respectively). No significant variation of fecal HBD2 levels was observed between infants with clinical features of intestinal distress (77 ng/g, 2-1,271) and cross-matched controls (56 ng/g, 31-164). However, 2/3 infants with NEC and 1/7 infants with isolated rectal bleeding had HBD2 levels above the maximal level observed in controls.

CONCLUSIONS

The kinetics of fecal HBD2 in the neonatal period indicate that this inducible defensin can be detected at high level in the feces of full-term and preterm infants, independently of gestational age or mode of feeding. The potential role of fecal HBD2 in detecting NEC is suggested.

Anemia impairs small intestinal absorption measured by intestinal permeability in children

OBJECTIVE

To determine the effect of anemia and iron status on intestinal permeability in children.

DESIGN

A routine prospective study was performed in 64 children with symptoms suggesting cow's milk allergy (CMA) (11.8 +/- 16 mo, 2-94 mo). They exhibited a negative cow's milk challenge upon the ESPGHAN criteria. Hemoglobin (Hb), mean corpuscular volume (MCV), blood iron (Fe) and ferritin (Fer) concentrations were studied in all. Permeability was measured as percent of urinary excretion of lactitol (L,%) and mannitol (M,%) (oral absorption, 0.1 g/Kg for each sugar) and determination of the L/M ratio (L/M,%).

RESULTS

L/M was significantly higher in anemic children than in non-anemic ones, 2.45, (median), 1.92-3.43 (extremes), n = 29, vs. 1.72, 1.56-2.18, n = 35, p = 0.03. Hb correlated negatively with L/M (p = 0.0001) and L (p = 0.05) and positively with M (p = 0.03). Also, L/M correlated negatively with MCV (p = 0.001) and Fe (p = 0.04).

CONCLUSION

IP depends on anemia and iron status. The interpretation of IP should be taken cautiously into account in the diagnosis of CMA in case of anemia or iron deficiency.

Acquisition nosocomiale de bactéries multirésistantes dans un service de néonatologie : étude prospective et analyse des facteurs de risque

A systematic analysis of weekly nasal and rectal swabs was carried out in a neonatal unit in order to detect colonization with multiresistant bacteria (MRB).

PATIENTS AND METHODS

During a 6-month period, rectal and nasal samples were taken in 187 consecutively hospitalized newborns, the day of the admission (day 0) and every week until discharge, in order to detect MRB, mainly methicillin-resistant coagulase negative staphylococci (MRCoNS), Staphylococcus aureus and multi-resistant Gram-negative bacilli.

RESULTS

Among 187 infants, 50 were already colonized at entrance and excluded from the study. In others, 49 (35%) were colonized by at least one MRB, with a total of 71 strains isolated. The most frequent was MRCoNS, especially Staphylococcus epidermidis (66.1%). Gram-negative bacilli accounted for 9.8%. Colonization began earlier with MRCoNS than with Gram-negative bacilli, 7.8 +/- 6 vs. 15.5 +/- 16 days, P=0.004, and finished earlier 22.7 +/- 15 vs. 38.5 +/- 16 days, P=0.03. Colonized children exhibited by univariate analysis a lower birth weight, more frequent parenteral nutrition or previous hospitalization in a neonatal unit and a younger age at admission. Odds ratio for colonization were 4.06 for prematurity and 43.83 for a previous hospitalization. MRCoNS at days 15 (P <0.05) and 22 (P <0.05) were correlated with the empiric use of antibiotics. No nosocomial infection occurred during the study.

CONCLUSION

A high rate of newborns were colonized with MRB in our unit, especially MRCoNS, acquired earlier than Gram-negative bacilli, with a favoring action of empiric antibiotherapy.

High faecal calprotectin concentrations in newborn infants

BACKGROUND

Calprotectin, a major component of soluble cytosolic proteins in human neutrophil granulocytes, is excreted in excess in stools during inflammatory bowel disease in adults and children. Faecal calprotectin concentrations are also higher during the first year of life than in adults.

OBJECTIVES

To measure faecal calprotectin concentrations in the neonatal period and define reference values according to the mode of feeding: standard infant formula, prebiotic infant formula (Calisma, Blédina SA, France), or breast feeding.

PATIENTS AND METHODS

A prospective study was carried out over three months in 69 full term, healthy newborns with a median gestational age of 39.8 weeks (range 37-41.5) and a birth weight of 3300 g (range 2600-4460). Three groups were formed depending on the mode of feeding: group 1 (n = 18) received a standard infant formula, group 2 (n = 19) the prebiotic infant formula, and group 3 (n = 32) was breast fed. One stool sample was taken from each newborn on day 4 (3-7), and faecal calprotectin analysed using a commercial enzyme linked immunoassay (Calprest, Eurospital, Italy).

RESULTS

Faecal calprotectin concentrations (median 167 micro g/g) were higher than reference values in healthy adults. The concentration was below the upper reference limit for adults (50 micro g/g) for three infants only, one fed the standard formula and two fed the prebiotic formula. Concentrations did not differ significantly according to method of feeding.

CONCLUSIONS

Compared with healthy adults, newborns have high calprotectin concentrations in the first days of life. There is no obvious influence of the mode of feeding.

Nutrition trophique et maturation du tube digestif de l’enfant prématuré

Maturation of gastrointestinal function in neonates is stimulated by enteral nutrition whereas parenteral nutrition induces gastrointestinal atrophy and malfunction. Trophic feeding is the practice of feeding minute volumes of milk in order to stimulate the development of the immature gastrointestinal tract of the preterm infant. The provision of trophic feeding to the metabolically stable premature infant appears to result in multiple nutritional benefits and in minimum risk of complications. Further studies are, however, needed before recommending this practice routinely.

Low levels of pancreatic elastase 1 in stools of preterm infants

The amount of faecal pancreatic enzyme elastase 1 was significantly lower in 42 preterm newborns than in 12 full term babies at day 2 (89 (3-539) v 354 (52-600) microg/g, p<0.0007) and day 5 (164 (3-600) v 600 (158-600) microg/g, p<0.05) and correlated positively with total nutrient intake during the first week of life in preterm infants. This should probably be taken into account during early feeding.

[Rectal self-mutilation, rectal bleeding and Prader-Willi syndrome]

Prader-Willi syndrome is a genetic disorder characterized by infantile hypotonia, obesity, hypogonadism and mental retardation. Individuals with Prader-Willi syndrome manifest a severe skin picking behavior, including rectal picking.

CASE REPORT

We report the case of a girl (12 years old) with this syndrome in whom rectal picking resulted in rectal bleeding and solitary rectal ulcer.

CONCLUSION

Caregivers of children with Prader-Willi syndrome should be aware of a potential rectal picking behavior, which results in significant bleeding. Early recognition of such a behavior helps to avoid misdiagnosis.

Clarithromycin resistance and eradication of Helicobacter pylori in children

Outcome of Helicobacter pylori infection was analyzed in 61 children treated with a triple therapy including clarithromycin. Bacterial eradication was obtained in all children with clarithromycin-susceptible strains but not in children with clarithromycin-resistant ones (P = 0.0001). H. pylori antimicrobial susceptibility is mandatory before choosing a treatment, and clarithromycin should be avoided in case of resistance.