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PubMed2006

Biodiversity of bacterial ecosystems in traditional Egyptian Domiati cheese.

Bacterial biodiversity occurring in traditional Egyptian soft Domiati cheese was studied by PCR-temporal temperature gel electrophoresis (TTGE) and PCR-denaturing gradient gel electrophoresis (DGGE). Bands were identified using a reference species database (J.-C. Ogier et al., Appl. Environ. Microbiol. 70:5628-5643, 2004); de novo bands having nonidentified migration patterns were identified by DNA sequencing. Results reveal a novel bacterial profile and extensive bacterial biodiversity in Domiati cheeses, as reflected by the numerous bands present in TTGE and DGGE patterns. The dominant lactic acid bacteria (LAB) identified were as follows: Leuconostoc mesenteroides, Lactococcus garvieae, Aerococcus viridans, Lactobacillus versmoldensis, Pediococcus inopinatus, and Lactococcus lactis. Frequent non-LAB species included numerous coagulase-negative staphylococci, Vibrio spp., Kocuria rhizophila, Kocuria kristinae, Kocuria halotolerans, Arthrobacter spp./Brachybacterium tyrofermentans. This is the first time that the majority of these species has been identified in Domiati cheese. Nearly all the dominant and frequent bacterial species are salt tolerant, and several correspond to known marine bacteria. As Domiati cheese contains 5.4 to 9.5% NaCl, we suggest that these bacteria are likely to have an important role in the ripening process. This first systematic study of the microbial composition of Domiati cheeses reveals great biodiversity and evokes a role for marine bacteria in determining cheese type.

Biodiversity↗

PubMed2003

Development and validation of a nested-PCR-denaturing gradient gel electrophoresis method for taxonomic characterization of bifidobacterial communities.

The taxonomic characterization of a bacterial community is difficult to combine with the monitoring of its temporal changes. None of the currently available identification techniques are able to visualize a "complete" community, whereas techniques designed for analyzing bacterial ecosystems generally display limited or labor-intensive identification potential. This paper describes the optimization and validation of a nested-PCR-denaturing gradient gel electrophoresis (DGGE) approach for the species-specific analysis of bifidobacterial communities from any ecosystem. The method comprises a Bifidobacterium-specific PCR step, followed by purification of the amplicons that serve as template DNA in a second PCR step that amplifies the V3 and V6-V8 regions of the 16S rRNA gene. A mix of both amplicons is analyzed on a DGGE gel, after which the band positions are compared with a previously constructed database of reference strains. The method was validated through the analysis of four artificial mixtures, mimicking the possible bifidobacterial microbiota of the human and chicken intestine, a rumen, and the environment, and of two fecal samples. Except for the species Bifidobacterium coryneforme and B. indicum, all currently known bifidobacteria originating from various ecosystems can be identified in a highly reproducible manner. Because no further cloning and sequencing of the DGGE bands is necessary, this nested-PCR-DGGE technique can be completed within a 24-h span, allowing the species-specific monitoring of temporal changes in the bifidobacterial community.

Animals↗

PubMed2005

Construction, analysis, and beta-glucanase screening of a bacterial artificial chromosome library from the large-bowel microbiota of mice.

A metagenomic (community genomic) library consisting of 5,760 bacterial artificial chromosome clones was prepared in Escherichia coli DH10B from DNA extracted from the large-bowel microbiota of BALB/c mice. DNA inserts detected in 61 randomly chosen clones averaged 55 kbp (range, 8 to 150 kbp) in size. A functional screen of the library for beta-glucanase activity was conducted using lichenin agar plates and Congo red solution. Three clones with beta-glucanase activity were detected. The inserts of these three clones were sequenced and annotated. Open reading frames (ORF) that encoded putative proteins with identity to glucanolytic enzymes (lichenases and laminarinases) were detected by reference to databases. Other putative genes were detected, some of which might have a role in environmental sensing, nutrient acquisition, or coaggregation. The insert DNA from two clones probably originated from uncultivated bacteria because the ORF had low sequence identity with database entries, but the genes associated with the remaining clone resembled sequences reported in Bacteroides species.

Amino Acid Sequence↗

PubMed2006

Genetic diversity of norovirus among children with gastroenteritis in São Paulo State, Brazil.

Norovirus (NoV) is one of the most common causes of acute gastroenteritis in children and adults. To study the prevalence and genetic variability of NoV in children with acute gastroenteritis in São Paulo State, Brazil, we examined 234 stool samples from children with or without gastroenteritis during a 5-year period (1995 to 1999). NoV RNA was detected by reverse transcription-PCR and confirmed by DNA sequence analysis. We used two different oligonucleotide primer sets targeting the 3' end of the RNA polymerase gene (region B), as well a partial capsid region at the 3' end of the VP1 gene (region D). A total of 78 (33.3%) of the samples tested positive for NoV, and in region B, of the 66 strains sequenced, 4 (6.1%) belonged to GI, 52 (78.7%) belonged to GII, and five samples (7.6%) contained a mixture of the GI and GII genotypes. Phylogenetic analysis showed that the majority (40 of 66 [60.6%]) of the strains belonged to genotype GII.4. The nucleotide sequence identity of three strains was lower than 77.9% compared to a region B reference sequence database but showed 85.3 to 88.8% identity with GII.2 Melksham strain in region D, indicating the circulation of a possible recombinant NoV strain. One sample (GII.3) was sequenced only in region D. In conclusion, we have a total of 67 sequenced strains. This is the first report that describes the predominance of GII.4 NoV strains in children visiting the ambulatory of different hospitals in São Paulo State, Brazil, and we show that mixtures of different strains can be found in individual samples, including some possible new recombinant strains.

Child, Preschool↗

PubMed1996

A systematic review of physical activity promotion strategies.

We have reviewed randomised controlled trials of physical activity promotion to provide recent and reliable information on the effectiveness of physical activity promotion. Computerised databases and references of references were searched. Experts were contacted and asked for information about existing work. Studies assessed were randomised controlled trials of healthy, free living, adult subjects, where exercise behaviour was the dependent variable. Eleven trials were identified. No United Kingdom based studies were found. Interventions that encourage walking and do not require attendance at a facility are most likely to lead to sustainable increases in overall physical activity. Brisk walking has the greatest potential for increasing overall activity levels of a sedentary population and meeting current public health recommendations. The small number of trials limits the strength of any conclusions and highlights the need for more research.

Adult↗

PubMed1996

Prevalence of potentially inappropriate long term prescribing in general practice in the United Kingdom, 1980-95: systematic literature review.

OBJECTIVE: To determine the prevalence of potentially inappropriate long term prescribing in general practice in the United Kingdom. DESIGN: Review of 62 studies of the appropriateness of prescribing identified from seven electronic databases, from reference lists, and by hand searching of journals. A nominal group of 10 experts helped to define the appropriateness of prescribing. SETTING: General practice in the United Kingdom. MAIN OUTCOME MEASURES: Prevalences of 19 indicators of inappropriate long term prescribing representing five dimensions: indication, choice of drug, drug administration, communication, and review. RESULTS: Prevalences of potentially inappropriate prescribing varied by indicator and chronic condition, but drug dosages outside the therapeutic range consistently recorded the highest rates. The lowest rates were generally associated with indicators of the choice of the drug, except cost minimisation. Communication is studied less frequently than other dimensions of prescribing appropriateness. CONCLUSIONS: The evidence base to support allegations of widespread inappropriate prescribing in general practice is unsound. Although inappropriate prescribing has occurred, the scale of the problem is unknown because of limitations associated with selection of a standard, publication bias, and uncertainty about the context of prescribing decisions. Opportunities for cost savings and effectiveness gains are thus unclear. Indicators applicable to individual patients could yield evidence of prescribing appropriateness.

Communication↗

PubMed2000

A systematic review of treatments for settling problems and night waking in young children.

OBJECTIVES: To assess the efficacy of treatments for settling problems and night waking in young children. DESIGN: A systematic review of randomised controlled trials of interventions for settling problems and night waking in young children. SETTING: Electronic bibliographic databases and references on identified papers, hand searches, and personal contact with specialists. SUBJECTS: Children aged 5 years or less who had established settling problems or night waking. INTERVENTIONS: Interventions had to be described and a placebo, waiting list, or another intervention needed to have been used as a comparison. Interventions comprised drug trials or non-drug trials. MAIN OUTCOME MEASURES: Number of wakes at night, time to settle, or number of nights in which these problems occurred. RESULTS: Drugs seemed to be effective in treating night waking in the short term, but long term efficacy was questionable. In contrast, specific behavioural interventions showed both short term efficacy and possible longer term effects for dealing with settling problems and night waking. CONCLUSIONS: Given the prevalence and persistence of childhood sleep problems and the effects they can have on children and families, treatments that offer long lasting benefits are appealing and these are likely to be behavioural interventions.

Behavior Therapy↗

PubMed2003

Systematic review of role of bisphosphonates on skeletal morbidity in metastatic cancer.

OBJECTIVE: To review the evidence for the use of bisphosphonates to reduce skeletal morbidity in cancer patients with bone metastases. DATA SOURCES: Electronic databases, scanning reference lists, and consultation with experts and pharmaceutical companies. Foreign language papers were included. STUDY SELECTION: Included trials were randomised controlled trials of patients with malignant disease and bone metastases who were treated with oral or intravenous bisphosphonate compared with another bisphosphonate, placebo, or standard care. All trials measured at least one outcome of skeletal morbidity. RESULTS: 95 articles were identified; 30 studies fulfilled inclusion criteria. In studies that lasted > or = 6 months, compared with placebo bisphosphonates significantly reduced the odds ratio for fractures (vertebral 0.69, 95% confidence interval 0.57 to 0.84, P < 0.0001; non-vertebral 0.65, 0.54 to 0.79, P < 0.0001; combined 0.65, 0.55 to 0.78, P < 0.0001), radiotherapy (0.67, 0.57 to 0.79, P < 0.0001), and hypercalcaemia (0.54, 0.36 to 0.81, P = 0.003) but not for orthopaedic surgery (0.70, 0.46 to 1.05, P = 0.086) or spinal cord compression (0.71, 0.47 to 1.08, P = 0.113). The reduction in orthopaedic surgery was significant in studies that lasted over a year (0.59, 0.39 to 0.88, P = 0.009). Use of bisphosphonates significantly increased time to first skeletal related event but did not increase survival. Subanalyses showed that most evidence supports use of intravenous aminobisphosphonates. CONCLUSIONS: In people with metastatic bone disease bisphosphonates significantly decrease skeletal morbidity, except for spinal cord compression and increased time to first skeletal related event. Treatment should start when bone metastases are diagnosed and continue until it is no longer clinically relevant.

Bone Neoplasms↗

PubMed2006

Efficacy and safety of exogenous melatonin for secondary sleep disorders and sleep disorders accompanying sleep restriction: meta-analysis.

OBJECTIVE: To conduct a systematic review of the efficacy and safety of exogenous melatonin in managing secondary sleep disorders and sleep disorders accompanying sleep restriction, such as jet lag and shiftwork disorder. DATA SOURCES: 13 electronic databases and reference lists of relevant reviews and included studies; Associated Professional Sleep Society abstracts (1999 to 2003). STUDY SELECTION: The efficacy review included randomised controlled trials; the safety review included randomised and non-randomised controlled trials. QUALITY ASSESSMENT: Randomised controlled trials were assessed by using the Jadad Scale and criteria by Schulz et al, and non-randomised controlled trials by the Downs and Black checklist. DATA EXTRACTION AND SYNTHESIS: One reviewer extracted data and another reviewer verified the data extracted. The inverse variance method was used to weight studies and the random effects model was used to analyse data. MAIN RESULTS: Six randomised controlled trials with 97 participants showed no evidence that melatonin had an effect on sleep onset latency in people with secondary sleep disorders (weighted mean difference -13.2 (95% confidence interval -27.3 to 0.9) min). Nine randomised controlled trials with 427 participants showed no evidence that melatonin had an effect on sleep onset latency in people who had sleep disorders accompanying sleep restriction (-1.0 (-2.3 to 0.3) min). 17 randomised controlled trials with 651 participants showed no evidence of adverse effects of melatonin with short term use (three months or less). CONCLUSIONS: There is no evidence that melatonin is effective in treating secondary sleep disorders or sleep disorders accompanying sleep restriction, such as jet lag and shiftwork disorder. There is evidence that melatonin is safe with short term use.

Adolescent↗

PubMed2006

Effectiveness of hip protectors for preventing hip fractures in elderly people: systematic review.

OBJECTIVES: To present the updated results of systematic review of the current evidence for the effectiveness of hip protectors from reports of completed randomised trials, and to explore the evolution of that evidence. DESIGN: Systematic review with meta-analysis. DATA SOURCES: Cochrane Bone, Joint, and Muscle Trauma Group trials register (January 2005), Cochrane central register of controlled trials (Cochrane Library Issue 1, 2005), Medline (1966 to January 2005), Embase (1988 to January 2005), and CINAHL (1982 to December 2004). Other databases and reference lists of relevant articles were searched and some trialists were contacted. REVIEW METHODS: Randomised or quasirandomised controlled trials reporting the incidence of hip fractures, pelvic fractures, and other fractures in elderly people offered hip protectors compared with a control group that was not. RESULTS: Outcomes for fracture were available from 14 randomised and quasirandomised trials. Pooling of data from 11 trials carried out in nursing or residential care settings, including six cluster randomised studies, showed evidence of a marginally statistically significant reduction in incidence of hip fracture (relative risk 0.77, 95% confidence interval 0.62 to 0.97). Pooling of data from three individually randomised trials of 5135 community dwelling participants showed no reduction in hip fracture incidence with provision of hip protectors (1.16, 0.85 to 1.59). No evidence was found of any significant effect of hip protectors on incidence of pelvic or other fractures. No important adverse effects of hip protectors were reported, but compliance, particularly in the long term, was poor. CONCLUSIONS: On the basis of early reports of randomised trials, hip protectors were advocated. Accumulating evidence indicates that hip protectors are an ineffective intervention for those living at home and that their effectiveness in an institutional setting is uncertain.

Aged↗

PubMed2006

Strength of evidence for perioperative use of statins to reduce cardiovascular risk: systematic review of controlled studies.

OBJECTIVE: To determine the strength of evidence underlying recommendations for use of statins during the perioperative period to reduce the risk of cardiovascular events. DESIGN: Systematic review of studies with concurrent control groups. DATA SOURCES: Four electronic databases, the references of identified studies, international experts on perioperative medicine, and the authors of the primary studies. Review methods Two reviewers independently extracted data from studies that reported acute coronary syndromes or mortality in patients receiving or not receiving statins during the perioperative period. MAIN OUTCOME MEASURE: Random effects summary odds ratios for death or acute coronary syndrome during the perioperative period. RESULTS: 18 studies--two randomised trials (n=177), 15 cohort studies (n=799,632), and one case-control study (n=480)--assessed whether statins provide perioperative cardiovascular protection; 12 studies enrolled patients undergoing non-cardiac vascular surgery, four enrolled patients undergoing coronary bypass surgery, and two enrolled patients undergoing various surgical procedures. In the randomised trials the summary odds ratio for death or acute coronary syndrome during the perioperative period with statin use was 0.26 (95% confidence interval 0.07 to 0.99) and the summary odds ratio in the cohort studies was 0.70 (0.57 to 0.87). Although the pooled cohort data provided a statistically significant result, statins were not randomly allocated, results in retrospective studies were larger (odds ratio 0.65, 0.50 to 0.84) than those in the prospective cohorts (0.91, 0.65 to 1.27), and dose, duration, and safety of statin use was not reported. CONCLUSION: The evidence base for routine administration of statins to reduce perioperative cardiovascular risk is inadequate.

Case-Control Studies↗

PubMed2000

A systematic review of treatment of settling problems and night waking in young children

OBJECTIVE: To assess the efficacy of treatment of settling problems and night waking in young children. DESIGN: A systematic review of randomized controlled trials of interventions. SETTING: Electronic bibliographic databases and references on identified papers, hand searches, and personal contact with specialists. SUBJECTS: Children aged 5 years or younger who had established settling problems or night waking. INTERVENTIONS: Interventions had to be described and a placebo, waiting list, or another intervention needed to have been used as a comparison. Interventions comprised drug trials or nondrug trials. Main outcome measures Number of wakes at night, time to settle, or number of nights in which these problems occurred. RESULTS: Drugs seemed to be effective in treating night waking in the short term, but long-term efficacy was questionable. In contrast, specific behavioral interventions showed both short-term efficacy and possible longer term effects for dealing with settling problems and night walking. CONCLUSIONS: Given the prevalence and persistence of childhood sleep problems and the effects they can have no children and families, treatments that offer long-lasting benefits are more appealing, and these are likely to be behavioral interventions.

Journal Article↗

PubMed1995

Randomised controlled trials of physical activity promotion in free living populations: a review.

OBJECTIVES: To review evidence on the effectiveness of trials of physical activity promotion in healthy, free living adults. To identify the more effective intervention programmes. METHODS: Computerised databases and references were searched. Experts were contacted and asked for information about existing work. INCLUSION CRITERIA: Randomised controlled trials of healthy, free living adult subjects, where exercise behaviour was the dependent variable were included. CONCLUSIONS: Ten trials were identified. The small number of trials limits the strength of any conclusions and highlights the need for more research. No UK based studies were found. Previously sedentary adults can increase activity levels and sustain them. Promotion of these changes requires personal instruction, continued support, and exercise of moderate intensity which does not depend on attendance at a facility. The exercise should be easily included into an existing lifestyle and should be enjoyable. Walking is the exercise most likely to fulfil these criteria.

Adult↗

PubMed1999

A meta-analysis of acupuncture techniques for smoking cessation.

OBJECTIVE: To determine the effectiveness of acupuncture for smoking cessation and to examine whether any individual aspect of trials is associated with an effect. DATA SOURCES: All randomised controlled trials of acupuncture for smoking cessation that were listed in computerised databases or reference lists of relevant articles. STUDY SELECTION: All randomised single-blind studies that compared acupuncture with sham acupuncture. DATA EXTRACTION: Methodological data were extracted for quality assessment. Outcome data were extracted for rates of total smoking cessation at three intervals: early after treatment and after six and 12 months follow up. DATA SYNTHESIS: Results were expressed as odds ratios of success over failure in intervention over control groups. The combined odds ratio for all studies was calculated. Repeated meta-analyses were subsequently performed on subsets of studies combined according to defined characteristics: acupuncture technique, number of attendances, country of origin, status of journal, and control procedure. The overall quality of studies was poor. The combined odds ratio for smoking cessation calculated for the earliest results after the end of treatment was 1.20 (95% confidence intervals (95% CIs) = 0.98 to 1.48). The combined odds ratio for smoking cessation after six months was 1.29 (95% CI = 0.82 to 2.01), and after 12 months was 1.03 (95% CI = 0.73 to 1.46). There were no significant effects of relevance among subsets of studies grouped according to defined characteristics. CONCLUSIONS: Acupuncture was not superior to sham acupuncture for smoking cessation; no particular aspect of acupuncture technique was associated with a positive effect. The conclusions are limited by methodological inadequacies of studies and by the absence of testable hypotheses; design of future trials should avoid these deficiencies.

Acupuncture Therapy↗

PubMed2003

Forensics and mitochondrial DNA: applications, debates, and foundations.

Debate on the validity and reliability of scientific methods often arises in the courtroom. When the government (i.e., the prosecution) is the proponent of evidence, the defense is obliged to challenge its admissibility. Regardless, those who seek to use DNA typing methodologies to analyze forensic biological evidence have a responsibility to understand the technology and its applications so a proper foundation(s) for its use can be laid. Mitochondrial DNA (mtDNA), an extranuclear genome, has certain features that make it desirable for forensics, namely, high copy number, lack of recombination, and matrilineal inheritance. mtDNA typing has become routine in forensic biology and is used to analyze old bones, teeth, hair shafts, and other biological samples where nuclear DNA content is low. To evaluate results obtained by sequencing the two hypervariable regions of the control region of the human mtDNA genome, one must consider the genetically related issues of nomenclature, reference population databases, heteroplasmy, paternal leakage, recombination, and, of course, interpretation of results. We describe the approaches, the impact some issues may have on interpretation of mtDNA analyses, and some issues raised in the courtroom.

DNA, Mitochondrial↗

PubMed2005

Urgent clinical challenges in children with ischemic stroke: analysis of 1065 patients from the 1-800-NOCLOTS pediatric stroke telephone consultation service.

BACKGROUND AND PURPOSE: Clinical trials are lacking in pediatric stroke. As a result, physicians caring for children with stroke face significant challenges. The patient characteristics and specific nature of clinical challenges facing practicing clinicians can inform the design of and priorities for developing relevant clinical trials. METHODS: Physicians consulted the 1-800-NOCLOTS toll-free pediatric stroke telephone consultation service on children (birth to 18 years) with ischemic stroke. Pediatric neurologist or hematologists provided telephone consultation and documented caller and patient characteristics, antithrombotic treatments and callers' questions for entry into a computerized database. Children referred from January 1, 1995 to January 1, 2004, comprised the study cohort. RESULTS: Stroke consults were completed on 1065 children located predominantly in the United States (76%). Children had arterial ischemic stroke (AIS; 679; 64%) or cerebral sinovenous thrombosis (CSVT; 386; 36%) and were 54% male and 16% neonates. Risk factors and antithrombotic agents (none, aspirin, warfarin, and heparins) differed by stroke type. In 60% of patients, callers had not initiated antithrombotic therapy. Callers' questions for both stroke types usually concerned treatment selection (83%), but for AIS, questions more frequently (P<0.0001) concerned the selection and interpretation of etiological investigations. CONCLUSIONS: Research is urgently needed in pediatric stroke to provide direction for management in "real-life" settings. Research efforts should address the unique challenges within different stroke types and include observational studies addressing investigation of the child with AIS. For AIS and CSVT, randomized controlled trials investigating the efficacy of antithrombotic treatment are urgently needed.

Adolescent↗

PubMed2001

Exercise therapy for arm function in stroke patients: a systematic review of randomized controlled trials.

OBJECTIVE: Assessment of the available evidence for the effectiveness of exercise therapy to improve arm function in patients who have suffered from a stroke. METHODS: A systematic search of bibliographical databases and reference checking were performed to identify publications on randomized controlled trials (RCTs) which evaluated the effect of exercise therapy on arm function in stroke patients. The methodological quality was assessed systematically by two raters, based on a standardized list of methodological criteria. Study characteristics, such as the chronicity and severity of impairment of the patient population, the amount and duration of interventions, and specific methodological criteria, were related to reported effects. RESULTS: Thirteen RCTs were identified, six of which reported positive results on an arm function test. In five of these six studies there was a contrast in amount or duration of exercise therapy between groups. Methodological scores ranged from 5 to 15 (maximum possible score: 19 points). CONCLUSION: Insufficient evidence made it impossible to draw definitive conclusions about the effectiveness of exercise therapy on arm function in stroke patients. The difference in results between studies with and without contrast in the amount or duration of exercise therapy between groups suggests that more exercise therapy may be beneficial.

Arm↗

PubMed2005

Schizophrenia and suicide: systematic review of risk factors.

BACKGROUND: Suicide risk is greatly increased in schizophrenia. Detection of those at risk is clinically important. AIMS: To identify risk factors for suicide in schizophrenia. METHOD: The international literature on case-control and cohort studies of patients with schizophrenia or related conditions in which suicide was reported as an outcome was systematically reviewed. Studies were identified through searching electronic databases and reference lists, and by consulting experts. RESULTS: Twenty-nine eligible studies were identified. Factors with robust evidence of increased risk of suicide were previous depressive disorders (OR=3.03, 95% CI 2.06-4.46), previous suicide attempts (OR=4.09, 95% CI 2.79-6.01), drug misuse (OR=3.21, 95% CI 1.99-5.17), agitation or motor restlessness (OR=2.61, 95% CI 1.54-4.41), fear of mental disintegration (OR=12.1, 95% CI 1.89-81.3), poor adherence to treatment (OR=3.75, 95% CI 2.20-6.37) and recent loss (OR=4.03, 95% CI 1.37-11.8). Reduced risk was associated with hallucinations (OR=0.50, 95% CI 0.35-0.71). CONCLUSIONS: Prevention of suicide in schizophrenia is likely to result from treatment of affective symptoms, improving adherence to treatment, and maintaining special vigilance in patients with risk factors, especially after losses.

Depressive Disorder↗