GeneHunt for rapid domain-specific annotation of glycoside hydrolases.

The identification of glycoside hydrolases (GHs) for efficient polysaccharide deconstruction is essential for the development of biofuels. Here, we investigate the potential of sequential HMM-profile identification for the rapid and precise identification of the multi-domain architecture of GHs from various datasets. First, as a validation, we successfully reannotated >98% of the biochemically characterized enzymes listed on the CAZy database. Next, we analyzed the 43 million non-redundant sequences from the M5nr data and identified 322,068 unique GHs. Finally, we searched 129 assembled metagenomes retrieved from MG-RAST for environmental GHs and identified 160,790 additional enzymes. Although most identified sequences corresponded to single domain enzymes, many contained several domains, including known accessory domains and some domains never identified in association with GH. Several sequences displayed multiple catalytic domains and few of these potential multi-activity proteins combined potentially synergistic domains. Finally, we produced and confirmed the biochemical activities of a GH5-GH10 cellulase-xylanase and a GH11-CE4 xylanase-esterase. Globally, this "gene to enzyme pipeline" provides a rationale for mining large datasets in order to identify new catalysts combining unique properties for the efficient deconstruction of polysaccharides.

Assessment of conversational pragmatics: A screening tool for pragmatic language impairment in a control population of children aged 6-12 years.

Pragmatics can be defined as the way in which language is used to communicate in a given social context. Although there is a lack of a standardized assessment, healthcare professionals find themselves confronted with pragmatic language skill impairments in children with neurodevelopmental disorders or brain injuries. The characterization of language use causes problems in social interactions, which has clinical implications in daily life. However, this is still underestimated because there is currently no quick, easy-to-use screening device to rank these deficits. We have developed a pragmatic deficits screening chart that has been tested on a control population of children aged 6-12 years. The chart comprises 26 items exploring seven areas of pragmatics (intentionality, governance of exchange, organization of information, adaptation strategies, conversational implicit language, nonverbal skills, and paralinguistic aspects). Parents select one of four possible answers to describe how frequently their child demonstrates each type of behavior ("never, rarely, sometimes, often"). We distributed 1666 charts; 760 were returned, of which 552 could be analyzed. Internal consistency as measured with Cronbach's alpha coefficient (0.88) was satisfactory. There was no influence of age on total score, nor of the department/type of schooling. The population distribution was non-Gaussian so the results are presented in percentiles. We propose a first-line screening tool that is quick and easy to complete by family, which facilitates referral to specialists for further investigations into the etiological implications of pragmatic language impairment.

Evaluation of broad-spectrum beta-lactam prescriptions (except carbapenems) in a French teaching hospital.

OBJECTIVES: We aimed to assess broad-spectrum beta-lactam prescriptions (except carbapenems) in a French teaching hospital and the impact of controlled dispensing, antimicrobial management team, and antibiotic treatment reassessment on Day 2-3. PATIENTS AND METHODS: We performed a point-prevalence study in all hospital units and analyzed curative antibiotic broad-spectrum beta-lactam prescriptions. The assessment focused on indication, dosing, combinations, revaluation on Day 2-3, and treatment duration. RESULTS: Sixty-seven broad-spectrum beta-lactam prescriptions were identified. The main prescriptions were amoxicillin-clavulanic acid (37%, n=25), ceftriaxone (36%, n=24), and piperacillin-tazobactam (16%, n=11). Indications, doses, combinations, and reassessment on Day 2-3 were appropriate, respectively 90% (n=60), 96% (n=64), 94% (33/35 combinations), and 88% (n=59). However, appropriate treatment durations amounted to only 63% (n=42). The benefit of controlled dispensing was observed in terms of overall antibiotic treatment duration: 86% versus 51% adequacy for uncontrolled dispensing of beta-lactams (P=0.02). The antimicrobial management team improved the antibiotic treatment duration: 73% of appropriate durations versus 44% for beta-lactams not monitored by the team, but this difference was not significant. CONCLUSION: Broad-spectrum beta-lactams were usually well prescribed but the adequacy of treatment duration could be improved, especially by reinforcing the monitoring of prescriptions.

[Course and progression of children admitted before 4 years of age in a French child welfare center]. / Parcours et devenir de 128 enfants admis avant l'âge de quatre ans en pouponnière sociale.

AIM: The purpose of this study was to determine the institutional trajectory and future of young children in child welfare. MATERIALS AND METHODS: A catamnestic study - based on data from the child welfare office in Maine and Loire, France, from 1994 to 2001 - was conducted by a child psychiatrist and a psychologist. Medical, judicial, and educational data (development, health, pathways in child protection services) were collected and analyzed regarding the status of these children 15 years later, adding information gathered by interviewing the child welfare and foster family consultant. RESULTS: We included 128 children admitted to the child welfare office before 4 years of age. Admission to the child welfare system suffers from care delays (a mean of 13.1 months between the first child protection referral and placement) with an average entry age of 17 months and frequent cases of child abuse (e.g., seven Silverman syndrome cases). The physical and mental health status of these children was poor (poorly monitored pregnancies, prematurity, low birth weight). More than one third of the children had growth failure at admission, with catch-up in half of the cases. The average length of stay in the child welfare system was 13.2±4.6 years. At the end of the follow-up, there were specific measures to safeguard vulnerable adults: "young adult" (24 cases), "major protection" (eight cases) and "disabled living allowance" (nine cases). One hundred and sixteen children suffered from psychiatric disorders at entry and 98 at the end. The general functioning of children as assessed by the Children's Global Assessment Scale (CGAS) showed a statistically significant improvement. One out of two young adults showed problems integrating socially with chaotic pathways: many foster placements, unsuccessful return to the family, and academic failures. CONCLUSION: The clinical situations of children in the child welfare office and their long-term progression confirm the importance of this public health problem. Although the measures can greatly improve their physical and psychological recovery, with evidence of thriving, this remains limited: only a few of these children are well integrated socially and academically.

Prevalence, demographics, and complications of cleft palate surgery.

INTRODUCTION: Current published data on the demographics of cleft lip and palate is sparse and differs intranationally in reported incidence, demographics, and complication rates, making accurate local data both valuable and useful. We investigate the prevalence, demographics, and complications of cleft palate correction surgery in the inpatient setting over a 15-year period. METHODS: A retrospective review of The California Hospital Discharge Data sets of all pediatric patients who underwent cleft palate repair or cleft palate revision from 1997 to 2011. Children's hospitals (CHs) were analyzed as a separate group. For each record, age, gender, ethnicity, length of stay, total charges, principal payer, complications, and disposition were analyzed. RESULTS: 10,450 correction surgeries were performed during 1997-2011. This was an annual case-volume of 697 and annual population-adjusted rate of 2.0, neither of which changed over time (p=0.9 and 0.06, respectively). Of all surgeries, 21.5% were revisions, 48.3% were performed in CHs, 56.2% were performed on males, and 65.5% were performed on Caucasians. The median length of stay was 1 day, which did not change over time (p=1.0). The median total charges increased from $9.074 to $35,643 over the studied period (p<0.001). Admission to CHs was associated with shorter stay (1-3 days vs. 1-4 days) and higher total charges ($15,560 vs. $13,242; both p<0.001). Complications occurred in 393 (3.8%) of the surgeries. This percentage did not change over time (p=0.2). The most common complication was fistula/abscess/infection, which occurred in 159 cases (1.5%). Respiratory complications requiring ventilation occurred 66 cases (0.6%). Complications were more common in CHs (4.8% vs. 2.8%; p<0.001). Mortality rate was <0.1%. CONCLUSIONS: Our study constitutes the entire surgical cohort within a state, allowing for an accurate representation of the true perioperative complication rate of these procedures. The prevalence, demographics, and outcomes of the cleft palate correction surgery have remained unchanged during 1997-2011. Collectively, our data suggest that primary and secondary palatoplasty present low perioperative risk.

[Nutritional assessment in primary practice in elderly patients]. / Approche ambulatoire de la dénutrition chez la personne âgée.

Undernutrition is frequent and often underdiagnosed among older adults in every setting (home, nursing home, hospital), and is associated with increased morbidity and mortality. In this context, a systematic periodical nutritional assessment is proposed in patients aged 75 years and over. Without a consensus, the most widely used diagnostic criteria is an unintentional weight loss of 5% over a month or 10% over 6 months. When undernutrition is present, multimodal interventions are provided to address each potentially contributing comorbid condition and to promote increased caloric intake. Follow-up and adaptation of interventions after 3 months are required.

[Preoperative assessment in elderly patients]. / Evaluation préopératoire des patients ages.

Age-related physiological changes and comorbidities affect older patients' tolerance to surgery. Pre-operative assessment in these patients requires, beside the usual physical evaluation, the systematic screening of common geriatric syndromes. Cognitive, gait and balance, nutritional, and functional impairments, all flag patients at higher risk for per- and postoperative complications. Preoperative assessment is an opportunity to detect these syndromes and propose preventative interventions (physical therapy, nutritional and cognitive support measures) likely to reduce the incidence of postoperative morbidity.

[Bacteremia and French computerized disease surveillance system: financial valorisation of an infectious diseases specialist in a hospital]. / Bactériémies et Programme de médicalisation des systèmes d'information : valorisation financière de l'infectiologue à l'hôpital.

OBJECTIVE: Bacteremia surveillance is a mission assumed by the referent person for antimicrobial therapy. We propose an original financial valorization of this activity, using the computerized disease surveillance system (CDSS). MATERIAL AND METHODS: A database collecting community-acquired and care-associated bacteremia was created on January 1, 2009 at the Bethune Hospital, France, using EPI-Info software (EPI Data). This database was used to complete missing data (presence of bacteremia, origin [community-acquired or care-associated], site of infection) in CDSS codes of patients hospitalized in surgical and medical wards (410 beds) during 2009. Financial benefit was assessed by the difference of funds allocated on the basis of CDSS, before and after completion of the missing data. RESULTS: In 2009, 383 out of the 35,000 patients presented with bacteremia. When missing CDSS codes were added, a financial gain of 229,291 euros was obtained, concerning 64 patients. CONCLUSION: Bacteremia surveillance is a transversal task based on quality of care, which may have a positive financial impact. This study may be helpful for clinicians with transversal activities, for whom financial valorization is difficult to implement in the CDSS, particularly without hospitalization beds. The lack of complete notification in the CDSS may cause a substantial financial loss.

Tobacco use in India: prevalence and predictors of smoking and chewing in a national cross sectional household survey.

OBJECTIVE: To estimate the prevalence and the socioeconomic and demographic correlates of tobacco consumption in India. DESIGN: Cross sectional, nationally representative population based household survey. SUBJECTS: 315 598 individuals 15 years or older from 91 196 households were sampled in National Family Health Survey-2 (1998-99). Data on tobacco consumption were elicited from household informants. Measures and methods: Prevalence of current smoking and current chewing of tobacco were used as outcome measures. Simple and two way cross tabulations and multivariate logistic regression analysis were the main analytical methods. RESULTS: Thirty per cent of the population 15 years or older-47% men and 14% of women-either smoked or chewed tobacco, which translates to almost 195 million people-154 million men and 41 million women in India. However, the prevalence may be underestimated by almost 11% and 1.5% for chewing tobacco among men and women, respectively, and by 5% and 0.5% for smoking among men and women, respectively, because of use of household informants. Tobacco consumption was significantly higher in poor, less educated, scheduled castes and scheduled tribe populations. The prevalence of tobacco consumption increased up to the age of 50 years and then levelled or declined. The prevalence of smoking and chewing also varied widely between different states and had a strong association with individual's sociocultural characteristics. CONCLUSION: The findings of the study highlight that an agenda to improve health outcomes among the poor in India must include effective interventions to control tobacco use. Failure to do so would most likely result in doubling the burden of diseases-both communicable and non-communicable-among India's teeming poor. There is a need for periodical surveys using more consistent definitions of tobacco use and eliciting information on different types of tobacco consumed. The study also suggests a need to adjust the prevalence estimates based on household informants.

Genetic evidence on the origins of Indian caste populations.

The origins and affinities of the approximately 1 billion people living on the subcontinent of India have long been contested. This is owing, in part, to the many different waves of immigrants that have influenced the genetic structure of India. In the most recent of these waves, Indo-European-speaking people from West Eurasia entered India from the Northwest and diffused throughout the subcontinent. They purportedly admixed with or displaced indigenous Dravidic-speaking populations. Subsequently they may have established the Hindu caste system and placed themselves primarily in castes of higher rank. To explore the impact of West Eurasians on contemporary Indian caste populations, we compared mtDNA (400 bp of hypervariable region 1 and 14 restriction site polymorphisms) and Y-chromosome (20 biallelic polymorphisms and 5 short tandem repeats) variation in approximately 265 males from eight castes of different rank to approximately 750 Africans, Asians, Europeans, and other Indians. For maternally inherited mtDNA, each caste is most similar to Asians. However, 20%-30% of Indian mtDNA haplotypes belong to West Eurasian haplogroups, and the frequency of these haplotypes is proportional to caste rank, the highest frequency of West Eurasian haplotypes being found in the upper castes. In contrast, for paternally inherited Y-chromosome variation each caste is more similar to Europeans than to Asians. Moreover, the affinity to Europeans is proportionate to caste rank, the upper castes being most similar to Europeans, particularly East Europeans. These findings are consistent with greater West Eurasian male admixture with castes of higher rank. Nevertheless, the mitochondrial genome and the Y chromosome each represents only a single haploid locus and is more susceptible to large stochastic variation, bottlenecks, and selective sweeps. Thus, to increase the power of our analysis, we assayed 40 independent, biparentally inherited autosomal loci (1 LINE-1 and 39 Alu elements) in all of the caste and continental populations (approximately 600 individuals). Analysis of these data demonstrated that the upper castes have a higher affinity to Europeans than to Asians, and the upper castes are significantly more similar to Europeans than are the lower castes. Collectively, all five datasets show a trend toward upper castes being more similar to Europeans, whereas lower castes are more similar to Asians. We conclude that Indian castes are most likely to be of proto-Asian origin with West Eurasian admixture resulting in rank-related and sex-specific differences in the genetic affinities of castes to Asians and Europeans.

Critical factors associated with the successful supported employment placement of patients with severe traumatic brain injury.

A number of investigations have recently demonstrated the effectiveness of supported employment programmes in improving the vocational status of clients with traumatic brain injuries. The present study investigated a sample of 39 individuals participating in a return to work programme emphasizing a supported employment approach to identify key functional characteristics which differentiated successful and unsuccessful clients. Clinical ratings of employment specialists were used to identify two groups of individuals rated least and most difficult to place and maintain. Results indicated that the two groups differed markedly on key employment outcomes. Individuals rated most difficult tended to be younger, possess functional limitations such as visual and fine motor impairments, and display significant deficits in numerous work-related skills. Recommendations are made for applying these findings to assessment, placement, and training activities within vocational rehabilitation programmes for persons with traumatic brain injuries.

Implementation of a home-based program for early detection of clinical deterioration in cystic fibrosis.

A statistical decision-making system, based on daily self measurements obtained at home, has been developed that will predict the clinical status of a patient with cystic fibrosis (CF). The data for the study were collected from patients randomly selected from those served by the University of Minnesota CF Center. Participants recorded four daily measurements (weight, vital capacity, breathing rate, and resting pulse) and one weekly measurement (height) and returned completed diaries to the coordinating center each week. The goal of the rule was to determine whether each patient's clinical status was deteriorating, remaining stable, or improving at the time of the most recent set of weekly measurements. This early detection and intervention criterion (EDIC) is being used in the clinical setting to aid in the management of patients with cystic fibrosis. The computer hardware and software, particularly the relational database, have provided an efficient basis for the continued use of EDIC.