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PubMed2006

New threshold and confidence estimates for terminal restriction fragment length polymorphism analysis of complex bacterial communities.

Terminal restriction fragment length polymorphism (T-RFLP) analysis has the potential to be useful for comparisons of complex bacterial communities, especially to detect changes in community structure in response to different variables. To do this successfully, systematic variations have to be detected above method-associated noise, by standardizing data sets and assigning confidence estimates to relationships detected. We investigated the use of different standardizing methods in T-RFLP analysis of PCR-amplified 16S rRNA genes to elucidate the similarities between the bacterial communities in 17 soil and sediment samples. We developed a robust method for standardizing data sets that appeared to allow detection of similarities between complex bacterial communities. We term this the variable percentage threshold method. We found that making conclusions about the similarities of complex bacterial communities from T-RFLP profiles generated by a single restriction enzyme (RE) may lead to erroneous conclusions. Instead, the use of multiple REs, each individually, to generate multiple data sets allowed us to determine a confidence estimate for groupings of apparently similar communities and at the same time minimized the effects of RE selection. In conjunction with the variable percentage threshold method, this allowed us to make confident conclusions about the similarities of the complex bacterial communities in the 17 different samples.

Bacteria↗
PubMed1997

Cognitive predictors of dementia in elderly community residents.

Detection of subjects with a high risk of developing dementia is a major goal of epidemiological research. Among the potential predictors, minor cognitive impairments detected by psychometric methods could be important precursors. A total of 2,726 elderly nondemented subjects, aged 65 and over, randomly selected from the general population of Gironde (south-western France) were followed up for 3 years. During this time, 84 developed an incident dementia, diagnosed as Alzheimer's disease (AD) in 59. The relationships between cognitive performance (Mini Mental State Examination, Benton Visual Retention Test and Isaacs Set Test) measured at the baseline screening of the cohort and the risk of dementia or AD were studied with a discrete Cox proportional hazard model. After adjustment for age and educational level, the three test scores remained strongly related to the risk of dementia or AD. Psychometric performance can be used to screen subjects at risk of developing dementia or AD and allow pharmacological intervention at an early stage.

Activities of Daily Living↗
PubMed1990

Atlantoaxial instability in Down syndrome--guidelines for screening and detection.

A community survey was conducted in all adults with Down syndrome living in three health districts to see if there was any correlation between radiological and neurological abnormalities which could indicate the presence of atlantoaxial instability. There was no difference in the proportion of individuals with neurological abnormalities in the group with radiological abnormalities suggestive of atlantoaxial instability (6/14) compared with individuals with normal X-rays (50/123) as determined by the chi square test (0.01463: not significant). The clinical and ethical implications for screening of people with Down syndrome living in the community are discussed in view of these findings.

Adult↗
PubMed1992

Cancer: improving early detection and prevention. A community practice randomised trial.

OBJECTIVE: To test the impact of physician education and facilitator assisted office system interventions on cancer early detection and preventive services. DESIGN: A randomised trial of two interventions alone and in combination. SETTING AND SUBJECTS: Physicians in 98 ambulatory care practices in the United States. INTERVENTIONS: The education intervention consisted of a day long physician meeting directed at improving knowledge, attitudes, and skills relevant to cancer prevention and early detection. The office system intervention consisted of assistance from a project facilitator in establishing routines for providing needed services. These routines included division of responsibilities for providing services among physicians and their staff and the use of medical record flow sheets. MAIN OUTCOME MEASURES: The proportions of patients provided the cancer prevention and early detection services indicated annually according to the US National Cancer Institute. RESULTS: Based on cross sectional patient surveys, the office system intervention was associated with an increase in mammography, the recommendation to do breast self examination, clinical breast examination, faecal occult blood testing, advice to quit smoking, and the recommendation to decrease dietary fat. Education was associated only with an increase in mammography. Record review for a patient cohort confirmed cross sectional survey findings regarding the office system for mammography and faecal occult blood testing. CONCLUSION: Community practices assisted by a facilitator in the development and implementation of an office system can substantially improve provision of cancer early detection and preventive services.

Adult↗
PubMedDate not supplied

Morton Plat ties its brand to an ambitious public health campaign.

Look to stake out a market position in the Tampa Bay area, Morton Plant Mease didn't just claim it cared about community health. It launched a 10-step "action plan" that included white papers, press conferences and a coordinated ad campaign aimed at education, prevention and early detection.

Community Health Services↗
PubMed2002

Changes in soil microbial community structure and function in an alpine dry meadow following spring snow melt.

Previous work in an alpine dry meadow in the Front Range of the Rocky Mountains has shown that microbial biomass is high during winter and declines rapidly as snow melts in the spring, and that this decline is associated with changes in temperature regime and substrate availability. In this study we tested the hypothesis that the summer and winter microbial communities differ in function and composition. Shifts in species composition between pre- and post-snowmelt communities were detected using reciprocal hybridization of community DNA; DNA extracted from soils sampled at different times was significantly less homologous relative to spatial replicates sampled at the same time. Fungal/bacterial ratios, as measured by direct microscopic counts and by substrate-induced respiration experiments with specific inhibitors, were higher in winter soils. Specific activity of cellulase (absolute cellulase activity per unit microbial biomass C) was higher in the winter soils than in summer soils, while specific amylase activity was not different between winter and summer. Based on most-probable number measurements, the use of the phenolic compound vanillic acid was highest in the winter, while the use of the amino acid glycine was lowest in the winter. Winter and summer soil respiration responded differently to temperature; at 0 degrees C, winter soils respired at a higher proportion of the 22 degrees C rate than did summer soils.

Biomass↗
PubMed2001

Evaluation of the MRSA-Screen Test in detecting oxacillin resistance in community and hospital isolates of Staphylococcus aureus.

The MRSA-Screen Test (Denka Seiken Co., Japan), a latex agglutination test to detect penicillin-binding protein 2a, was compared with PCR for the detection of oxacillin resistance in Staphylococcus aureus. A total of 77 oxacillin-sensitive and 269 oxacillin-resistant (ORSA) isolates were evaluated. Of the ORSA isolates, 186 were non-multiresistant (NORSA), defined as being resistant to two or fewer antibiotics other than beta-lactams. Eighty-three were multiresistant ORSA (MORSA) strains. If PCR is considered the gold standard test, then the sensitivity, specificity, positive and negative predictive values of the MRSA-Screen Test were 100, 99, 99 and 100%, respectively. The endpoint was hard to read with NORSA strains that took longer than 60 s to react. MORSA strains took a median 12 s (range 5-60 s) to give a positive reaction with the MRSA-Screen Test, whereas NORSA strains took a median 30 s (range 5-180 s), a difference which was significantly different (P < 0.0001, two-tailed Mann-Whitney unpaired two sample test). NORSA strains had an MIC50 of 128 mg/l and MIC90 of 256mg/l, whereas MORSA strains had an MIC50 and MIC90 of >256mg/l. The time that the MRSA-Screen Test took to agglutinate with ORSA strains correlated weakly with the MIC (r2 = 0.26). Detection of methicillin resistance cost AUD$9 per isolate with the MRSA-Screen Test, compared with AUD$13 per isolate with mecA PCR. The MRSA-Screen Test gave excellent sensitivity and specificity, and was quicker and cheaper than PCR. The full 3 min should be allowed to elapse before calling a test negative. Organisms giving indeterminate reactions should be tested for the mecA gene by PCR.

Antibodies, Monoclonal↗
PubMed2006

Development of a polymerase chain reaction assay for the detection of antibiotic resistance genes in community DNA.

Many methods are used to detect antibiotic resistance genes in samples. The objective of the study reported here was to compare polymerase chain reaction (PCR) analysis of community DNA with fecal culturing for detecting antibiotic resistance genes in cattle samples. In the laboratory-based portion of this study, known concentrations of an Escherichia coli strain with 3 antibiotic resistance genes (cmy-2, flo, and cat) were added to feces from dairy cattle. These genes were used to assess the effect of various primer pairs, chromosomally versus plasmid-encoded genes, and gene copy number on the sensitivity of PCR amplification. Gene-specific PCR amplification was performed on the community DNA extracted from the feces. Feces were cultured for the inoculated strain. In the field-based portion of the study, 80 cattle fecal samples of unknown gene status were compared by use of similar methods. Culture and PCR amplification from community DNA extractions produced variable results, and this variability was most noticeable at dilutions that approached the detection limit of the assay. Typically, PCR amplification had a higher sensitivity than did culture for detecting the gene of interest. However, the sensitivity of culture was improved by plating on selective media containing antibiotics. The community DNA approach enables assessment of bacterial communities in complex samples such as feces, a task that can be prohibitive by budget or time constraints associated with culture methods. Through a strategic combination of culture and community DNA approaches, the relationship between specific selection pressures and the persistence and dissemination of specific resistance genes can be elucidated.

Animals↗
PubMedDate not supplied

Skin cancer detection and prevention: a community program promoting sun safe behaviors.

New cases of skin cancer will be diagnosed over one million times in the United States in 1999. Basal and squamous cell types can cause significant cosmetic morbidity. Malignant melanoma can cause serious morbidity and mortality. Thus, early detection and prevention efforts are crucial for all skin cancers. Studies have identified genetic, hereditary, and environmental factors associated with increased risk of developing skin cancer. In this article, the incidence and risk factors are reviewed. The Howard County Skin Cancer Awareness Project, established in 1996, is presented as a community based program that aims to increase public awareness about the prevention and early detection of skin cancer. Future directions are also addressed.

Basal Cell Carcinoma↗
PubMedDate not supplied

[Validation of a screening questionnaire for stroke detection in Spanish-speaking communities].

OBJECTIVE: To evaluate the accuracy of an screening questionnaire for stroke detection in speaking-speaking communities. PATIENTS AND METHODS: We performed a door-to-door survey in Atahualpa (a rural community in coastal Ecuador) using a modified version of the Spanish translation of the OMS questionnaire for stroke detection. Subjects suspected of having a stroke as well as a 2% sample of negative subjects were evaluated by neurologists to evaluate sensitivity, specificity, and predictive value of the questionnaire and that of each of its questions. RESULTS: We found 18 possible cases among 1,568 individuals around 15 years old. Of these, 10 were confirmed stroke patients and 8 were false-positive (crude stroke prevalence of 6.38 per 1,000). We did not find false-negative cases. Sensitivity of the questionnaire was 100%, specificity was 99.5%, positive predictive value was 0.55 and negative predictive value was 1. The accuracy of each question as well as the number of questions answered as affirmative were different between patients and false-positive cases. CONCLUSIONS: The current questionnaire is highly sensitive but its positive predictive value is poor. This causes problems in large-scale studies, as the detection of many false-positives may compromise its viability. We propose a modification of the questionnaire that will turn it more accurate.

Adult↗
PubMed2002

[Evaluation of Streptococcus pneumoniae-urinary antigen detection kit in patients with community acquired pneumonia].

We evaluated a new rapid urinary antigen detection kit. NOW Streptococcus pneumoniae (Binax Inc., USA) that detected S. pneumoniae antigen by immunochromatographic membrane assay, with 66 Japanese adult patients of community acquired pneumonia. Twenty-two (33.3%) patients were found to be positive with the kit and S. pneumoniae was isolated from six patients (27.3%) of these 22 patients. S. pneumoniae was not isolated from eight of the 22 patients by blood or sputum culture. Analysis of clinical laboratory data showed that the levels of C-reactive protein (CRP) in the serum were significantly higher in the urine-antigen positive group than those in the urine-antigen negative group. There were no significant difference between the two groups including renal function, urinalysis, clinical symptom, and severity of pneumonia. Our study suggests that more cases of community acquired pneumonia are caused by S. pneumoniae than conventional tests can currently confirm. Since it is not technically complex, does not require equipment, and detects within as quickly as in 15 minutes, the S. pneumoniae urinary antigen kit is useful for rapid diagnosis of community acquired pneumonia in adults.

Adult↗
PubMed2002

Community-level disruptions among zooplankton of pond mesocosms treated with a neem (azadirachtin) insecticide.

A natural, plant-derived insecticide, neem, is being evaluated as an alternative insect pest control product for forestry in Canada. As part of the process to investigate the environmental safety of neem-based insecticides, a mesocosm experiment was conducted to assess the effects of neem on natural zooplankton communities. Replicate (n=5), shallow (<1 m) forest pond enclosures were treated with Neemix 4.5, at concentrations of 0.035 (the expected environmental concentration), 0.18, 0.70, and 1.75 mg/l active ingredient, azadirachtin. Zooplankton communities were quantitatively sampled over a 4-month experimental period in treated and control enclosures, and water samples were collected to track azadirachtin concentrations. Concentrations in water declined linearly with estimated DT(50) values of 25-29 days. Trends in abundance over time among populations of cladocerans, copepods, and rotifers were found to differ significantly among treatments. At the two highest test concentrations, adverse effects were obvious with significant reductions in several cladoceran species, and near elimination of the three major copepod species present. More subtle effects at the two lowest test concentrations were determined by comparing the community structure of enclosures across treatment levels and over time through an analytical process based on the multivariate statistical software, PRIMER. Significant effects on community structure were detected at both of these lower concentrations, including the expected environmental concentration of 0.035 mg/l azadirachtin. Differential responses among species (some increases, some decreases) caused detectable disruptions in community structure among zooplankton of treated enclosures. Perturbations to zooplankton communities were sufficient to cause measurable differences in system-level metabolism (midday dissolved oxygen concentrations) at all but the lowest test concentration.

Animals↗
PubMed2006

Modularity and community structure in networks.

Many networks of interest in the sciences, including social networks, computer networks, and metabolic and regulatory networks, are found to divide naturally into communities or modules. The problem of detecting and characterizing this community structure is one of the outstanding issues in the study of networked systems. One highly effective approach is the optimization of the quality function known as "modularity" over the possible divisions of a network. Here I show that the modularity can be expressed in terms of the eigenvectors of a characteristic matrix for the network, which I call the modularity matrix, and that this expression leads to a spectral algorithm for community detection that returns results of demonstrably higher quality than competing methods in shorter running times. I illustrate the method with applications to several published network data sets.

Journal Article↗
PubMed1999

Evaluation of the shell vial technique for detection of ocular adenovirus. Community Ophthalmologists of Pittsburgh, Pennsylvania.

PURPOSE: The shell vial technique is a cell culture method that uses centrifugation and immunofluorescence to decrease the time required for a positive test. The authors evaluated the shell vial technique as a diagnostic test to detect adenovirus in conjunctival specimens of patients with adenoviral conjunctivitis. DESIGN: Retrospective and prospective case series. PARTICIPANTS: Forty-six patients with adenoviral culture-positive ocular infection. METHODS: The minimum time of incubation (days) that was required for testing clinical isolates with the shell vial was determined with adenovirus serotypes 5 and 8. In a masked retrospective study, 25 true-positive (frozen clinical samples) and 25 true-negative specimens were tested for the presence of adenovirus using the shell vial technique. The 25 true-negative samples included herpes simplex virus, Chlamydia trachomatis, Haemophilus influenzae, Streptococcus pneumoniae, and Staphylococcus aureus. In a prospective study, 21 patients who later tested positive in cell culture for adenovirus were concurrently tested with shell vial. MAIN OUTCOME MEASURES: The time of incubation was determined in days, and the sensitivity, specificity, positive and negative predictive values, and the efficacy of the shell vial test were determined. RESULTS: The minimal time of incubation for testing ocular samples by shell vial was 3 days. In the retrospective study, the sensitivity, specificity, positive predictive value, negative predictive value, and efficacy were 92%, 100%, 100%, 93%, and 96%, respectively. Comparably (P = 0.99), in the prospective study the sensitivity, specificity, positive predictive value, negative predictive value, and efficacy were 95%, 100%, 100%, 96%, and 97%, respectively. The shell vial (93%, 43 of 46) was equivalent (P = 0.42) to cell culture (100%, 46 of 46) for detecting adenovirus, but a positive result was obtained in significantly less time (3 days versus 9.41 +/- 6.23 days) (P = 0.00001). CONCLUSIONS: The shell vial technique was found to be a definitive method for identifying adenovirus from ocular specimens. A clear benefit for the ophthalmologist is that the test can provide a faster positive result (3 days) compared with conventional cell culture, which can take 1 to 3 weeks for adenovirus isolation.

Adenovirus Infections, Human↗
PubMed1994

Community screening for diabetes. Low detection rate in a low-risk population.

OBJECTIVE: To evaluate glucose-based community screening for diabetes with regard to detection rate. RESEARCH DESIGN AND METHODS: A retrospective analysis of a community-screening questionnaire data base that included a screening for blood glucose. Referred subjects had fasting glucose levels > 6.4 mM (115 mg/dl) or postprandial levels > or = 8.9 mM (160 mg/dl). An attempt was made to contact referred subjects and to ascertain whether follow-up was undertaken and current status. A random sample of subjects not meeting the glucose criteria (nonreferred) also was contacted in an analogous fashion to referred subjects. RESULTS: In 2,016 questionnaires, glucose-based referral criteria were exhibited by 148 (7.3%) individuals, and subsequent evaluation data were available for 111. Of those 111 individuals, 37 (33%) knew they had diabetes before the screening, and 39 (36%) did not seek further evaluation. Of the remaining 35 subjects, 6 (13%) were told of their new diagnosis of diabetes, and 29 were told they did not have diabetes. Three of 50 nonreferred subjects knew of their diabetes before screening. Thirty percent (14 out of 47) of nonreferred subjects underwent subsequent evaluation, although they were not told to do so. A single new case of diabetes occurred in the nonreferred group. CONCLUSIONS: Community screening for diabetes that is based on measured glucose is of low yield. The known problems of glucose-based screening, coupled with its low yield, make a glucose-based approach difficult to justify. These results indicate that glucose-based community screening should be done only under the careful supervision of a health professional who is trained both in glucose measurement instrumentation and in screening.

Adolescent↗
PubMed2004

Application of PCR for Mycoplasma pneumoniae detection in children with community-acquired pneumonia.

Between April 2002 and March 2003, to detect Mycoplasma pneumoniae by polymerase chain reaction (PCR), a primer set designed for the 16S rRNA gene was used to examine clinical samples from 369 children with community-acquired pneumonia. Samples were collected from 12 Japanese institutions participating in a study group concerning acute respiratory infectious diseases. The sensitivity of primers--2 CFU per reaction tube, using M. pneumoniae M129, a standard strain--was calculated to represent 1.1 x 10(3) M. pneumoniae organisms adherent to the tip of the swab used to collect clinical samples. Results for PCR were obtained within 2.6 h. Cases identified by PCR, cultures, and serologic tests were 68 (18.4%), 53 (14.4%), and 76 (20.6%) respectively. Among 57 PCR-positive patients tested serologically, 56 showed a significant elevation or rise in antibody titer. PCR positivity was high among patients prescribed beta-lactam antibiotics (86.7%) or no antibiotic (87.0%) before PCR analysis, but was low among patients receiving macrolides, new quinolones, or tetracyclines (37.5%). We concluded that the PCR constructed by us had a high probability for confirming a diagnosis of M. pneumoniae pneumonia and for guiding antibiotic choice for patients not yet treated.

Adolescent↗
PubMed1993

Rapid detection of pneumococcal antigen in pleural fluid of patients with community acquired pneumonia.

BACKGROUND: Detection of pneumococcal antigen may help to increase the rate of diagnosis of pneumococcal pneumonia. This study was designed to determine the value of rapid detection of pneumococcal antigen in pleural fluid from patients with community acquired pneumonia. METHODS: Thoracentesis was performed in patients suspected of having empyema and in patients with pneumonia of unknown aetiology. Pneumococcal capsular antigen was detected by latex agglutination and this method was compared with Gram staining and culture, specimens of pleural fluid being examined in parallel by the three methods. RESULTS: Pleural fluid was radiographically identified in 63 of 135 patients with community acquired pneumonia. In nine of 45 patients with pneumococcal pneumonia and pleural fluid pneumococci were identified by Gram stain in two and by culture in one specimen of pleural fluid, whereas antigen was detected in eight of these specimens. In 12 of 33 patients with pneumonia of other known aetiology only one pleural fluid specimen was antigen positive, providing a specificity of 92% for this test. Pleural fluid obtained from 12 of 58 patients with pneumonia of unknown aetiology yielded detectable antigen in seven cases. CONCLUSIONS: Detection of pneumococcal antigen by latex agglutination in pleural fluid may yield important and rapid information in patients with community acquired pneumonia.

Antigens, Bacterial↗