SEARCH · Search PubMed

Results for “Community Detection”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,315 records · Page 73Linked to original sources

PubMed2000

Molecular detection of bacterial and streptomycete chitinases in the environment.

Sets of PCR primers were designed to amplify bacterial chitinases at different levels of specificity. The bacterial chitinase group primers were successful in targeting enzymes classified within the group A glycosyl hydrolases of family 18. The widespread occurrence of group A bacterial chitinases in actinomycetes was demonstrated. Streptomycete chitinase specific primers were designed and a collection of type strains of species changed in the genes Streptomyces were screened and shown to have at least one and usually multiple chitinase genes. The presence of the gene for the chitin binding protein was also demonstrated within the streptomycete type strains. These data indicate that streptomycetes are well equipped to degrade chitin. The detection of group A chitinases in total community DNA is described and a sandy soil shown to contain more than 10 different genes using DGGE to indicate genetic diversity.

Actinomycetales↗

PubMed2006

Malaria early warnings based on seasonal climate forecasts from multi-model ensembles.

The control of epidemic malaria is a priority for the international health community and specific targets for the early detection and effective control of epidemics have been agreed. Interannual climate variability is an important determinant of epidemics in parts of Africa where climate drives both mosquito vector dynamics and parasite development rates. Hence, skilful seasonal climate forecasts may provide early warning of changes of risk in epidemic-prone regions. Here we discuss the development of a system to forecast probabilities of anomalously high and low malaria incidence with dynamically based, seasonal-timescale, multi-model ensemble predictions of climate, using leading global coupled ocean-atmosphere climate models developed in Europe. This forecast system is successfully applied to the prediction of malaria risk in Botswana, where links between malaria and climate variability are well established, adding up to four months lead time over malaria warnings issued with observed precipitation and having a comparably high level of probabilistic prediction skill. In years in which the forecast probability distribution is different from that of climatology, malaria decision-makers can use this information for improved resource allocation.

Animals↗

PubMed1997

Integration of schistosomiasis-control activities into the primary-health-care system in the Gizan region, Saudi Arabia.

A few decades ago, the prevalence of Schistosoma haematobium infection in the human inhabitants of the Gizan region of Saudi Arabia was very high (43%-91%). A vertical programme for the control of the disease, by case finding, treatment of infected individuals and by chemical snail control, was begun in 1974 and led to significant reductions in prevalence in most areas. In 1989 the control activities were gradually integrated into the primary-health-care (PHC) system. Several schools in the area recently participated in the detection of ova (among schoolchildren and neighbouring communities) and organized health-education sessions. The records taken during the vertical and PHC programmes indicate that there were more diagnoses and higher chemotherapy coverage in the latter. The PHC programme has maintained the overall prevalence of infection at an extremely low level (< 1%) and the infection has been completely eradicated in several areas. The participation of schools proved to be particularly useful in terms of population coverage and health education.

Animals↗

PubMed2004

Endoscopic treatment of Barrett's oesophagus.

Barrett's oesophagus develops as a consequence of severe gastro-oesophageal reflux. The importance of Barrett's oesophagus lies in the small risk of developing high-grade dysplasia and subsequent adenocarcinoma. Because of poor treatment results in patients with advanced adenocarcinoma, surveillance of patients with Barrett's oesophagus for the development of dysplasia, although not uncontroversial, is widely practised in the gastroenterological community. The aim of surveillance is to detect adenocarcinoma in an early stadium where surgical cure is possible. In recent years several endoscopic treatments for both high-grade dysplasia and intramucosal adenocarcinoma have been developed. In this review some basic aspects of Barrett's oesophagus are discussed together with endoscopic treatments such as endoscopic mucosal resection, local thermal treatments and photodynamic therapy. Although surgical resection is probably the treatment of choice in fit patients, local endoscopic treatments should be considered in patients with high-grade dysplasia or intramucosal carcinoma who are unfit or unwilling to have surgery.

Barrett Esophagus↗

PubMed2006

New low-temperature applications of anaerobic wastewater treatment.

Low-temperature or psychrophilic (<20 degrees C) anaerobic biological treatment of simple industrial wastewaters has recently been proven feasible as an alternative to more expensive mesophilic (ca. 37 degrees C) technology. We implemented novel expanded granular sludge bed (EGSB)-based bioreactor designs for 27 psychrophilic anaerobic digestion (PAD) trials for the treatment of a broad range of simple and complex synthetic wastewaters representing dairy, food-processing and pharmaceutical sector effluents. A variety of operating parameters, such as hydraulic retention time, organic and volumetric loading rates and upflow velocity, were tested. Chemical oxygen demand (COD) removal efficiencies were recorded, which were comparable to previous mesophilic trials. Specific methanogenic activity, toxicity and biodegradability batch assays were employed to monitor the metabolic capabilities of microbial consortia in anaerobic reactors. The prevalence of psychrotolerant communities was observed and psychrophilic populations were detected in two of the reactors. The potential of PAD with respect to global sustainable development is discussed.

Anaerobiosis↗

PubMed2005

SIMAP--the similarity matrix of proteins.

MOTIVATION: Sequence similarity searches are of great importance in bioinformatics. Exhaustive searches for homologous proteins in databases are computationally expensive and can be replaced by a database of pre-calculated homologies in many cases. Retrieving similarities from an incrementally updated database instead of repeatedly recalculating them should provide homologs much faster and frees computational resources for other purposes. RESULTS: We have implemented SIMAP-a database containing the similarity space formed by almost all amino acid sequences from public databases and completely sequenced genomes. The database is capable of handling very large datasets and allows incremental updates. We have implemented a powerful backbone for similarity computation, which is based on FASTA heuristics. By providing WWW interfaces as well as web services, we make our data accessible to the worldwide community. We have also adapted procedures to detect putative orthologs as example applications. AVAILABILITY: The SIMAP portal page providing links to SIMAP services is publicly available: http://mips.gsf.de/services/analysis/simap/. The web services can be accessed under http://mips.gsf.de/proj/hobitws/services/RPCSimapService?wsdl and http://mips.gsf.de/proj/hobitws/services/DocSimapService?wsdl

Algorithms↗

PubMed2004

The analysis of methyl salicylate and salicylic acid from Chinese herbal medicine ingestion.

This paper presents a multi-drug fatality in which methyl salicylate was ingested. It is presented to inform the toxicological community that a particularly expeditious method of detection for methyl salicylate exists. Previously published methods for the analysis of methyl salicylate include a gas chromatographic-mass spectrometric method and an alkaline/acidic extraction followed by high-performance liquid chromatographic (HPLC) analysis. This article describes a method for analyzing methyl salicylate using HPLC, in which a simple, rapid extraction procedure is used. Using a previously published HPLC method, methyl salicylate and salicylic acid were easily identified in biological specimens. Methyl salicylate and salicylic acid were detected using an extraction solution of acetonitrile coupled with internal standard and then analyzed by HPLC-diode-array detection. Because of its concentrated liquid form, methyl salicylate ingestion can cause rapid onset salicylate toxicity. As the potentially fatal methyl salicylate forms are readily available and easily found on drugstore shelves, the need to rapidly detect and quantitate salicylic acid concentrations that are due to methyl salicylate ingestion may arise. In the case presented, the peripheral blood concentration of salicylic acid from methyl salicylate ingestion was 320 mg/L, and the concentration in gastric contents was 820 mg. It alone was not the cause of death, however. The discovery of the ability to detect and quantitate methyl salicylate was due to its suspected ingestion.

Acetonitriles↗

PubMed1991

Post-viral fatigue syndrome. Epidemiology: lessons from the past.

This chapter outlines the recorded epidemiological history of PVFS (including the early epidemics of myalgic encephalomyelitis) and the development of the concept, including the realisation that endemic cases also occur. Cases of PVFS are still not recorded by the Surveillance Centre for Communicable Diseases, so it is very difficult to detect and monitor any outbreak in the community, since each GP may only have two or three such patients and would, therefore, not be aware of an epidemic in the community as a whole if it occurred. Epidemiological issues raised by the early epidemics, including the delineation of the syndrome, the question of bias, the role of hysteria and the role of depression; the issue of symptom distribution, and its implications for aetiology; and a multiaxial framework for understanding the association with psychological symptoms are discussed. The value of a future multidisciplinary research programme designed to disentangle direct and predisposing causes of PVFS is emphasised.

Disease Outbreaks↗

PubMed1988

Screening for fecal occult blood in Israel. Different approaches to recruitment.

Invitations to participate in a screening program for fecal occult blood were sent or given directly to 20,251 people in Israel aged 40 years or above. We received 11,985 requests for stool testing kits, and ultimately we received 7,096 stool specimens (35% response). The highest response was from subjects using their own initiative to participate in the program (62%), followed by members of 23 communal farms, where 59% of subjects submitted specimens. The lowest response came from a low-middle class urban neighborhood (10%), and an intermediate response from an upper middle-class neighborhood (17%). Subsequent to the mail campaigns, a series of local newspaper articles yielded 6,519 specimens. Over all, 59% of subjects requesting kits returned specimens. Among the 7,096 specimens submitted, 145 (2%) were positive for occult blood. One hundred and twelve subjects were evaluated colonoscopically. Sixteen malignancies (14%) and 34 benign growths (30%) were found and resected. The prevalence of benign and malignant large bowel lesions was 7.0 and 7.2 per 1000 specimens in the screened urban and farm communities, respectively. In communities with limited resources for early cancer detection programs, efforts should be directed toward subgroups at risk who are most likely to respond.

Adult↗

PubMed2006

Fatal pneumonia caused by Panton-Valentine Leucocidine-positive methicillin-resistant Staphylococcus aureus (PVL-MRSA) transmitted from a healthy donor in living-donor liver transplantation.

Severe infections are the most dangerous complications in liver transplantation and their prevention is one of the major goals. A 60-year-old Saudi-Arabian female with decompensated hepatitis C liver cirrhosis received a right-lobe liver graft from her healthy daughter. After 9 days, the patient developed a rapidly progressive necrotizing pneumonia that was fatal in spite of extracorporal lung assist. The pneumonia was due to a Panton-Valentine Leucocidine-positive (PVL) methicillin-resistant Staphylococcus aureus (MRSA), or "community-acquired" MRSA, that had not been detectable in the patient preoperatively. The same strain of PVL-MRSA could be demonstrated in the nares of the asymptomatic donor, but not of other relatives, patients, or medical staff. These findings strongly suggest transmission of PVL-MRSA from the donor to the recipient. This case demonstrates a previously unknown, and potentially fatal, risk in living-donor liver transplantation: transmission of a severe infection from a healthy donor to the recipient.

Adult↗

PubMed1991

The herald waves of influenza virus infections detected in Sendai and Yamagata cities in 1985-1990.

The community surveillance of respiratory virus infections performed during 1985-1987 in Sendai and 1988-1990 in Yamagata has identified a total of five herald waves of influenza virus infections: A/H3N2 virus infections in 1985 and 1989, A/H1N1 virus infections in 1986 and 1988, and type B virus infections in 1989. To investigate the antigenic and genetic relationships between the herald wave and epidemic strains, influenza A/H1N1 viruses isolated during the 1986 and 1988 herald waves were compared with those isolated during the 1986-1987 and 1988-1989 epidemic seasons, respectively, utilizing hemagglutination inhibition tests with anti-hemagglutinin monoclonal antibodies and oligonucleotide mapping of total viral RNAs. The results showed that multiple variants differing in antigenic and genetic properties were cocirculating during the 1986 herald wave as well as during each of the two epidemics (only one strain was isolated in the 1988 herald wave). It was also observed that viruses which had the antigenic and/or genetic characteristics closely similar to those of the viruses circulating in the 1986 and 1988 herald waves, were isolated during the winters of 1986-1987 and 1988-1989, respectively.

Antibodies, Monoclonal↗

PubMed2004

[Evaluation of a new chromogenic medium for isolation of MRSA].

Methicillin-resistant Staphylococcus aureus (MRSA) is responsible for an increasing number of serious nosocomial and community-acquired infections, and accurate methods to detect such strains are needed. We tested the susceptibility of 3 kinds of MRSA isolation medium, MRSA Screen Agar, Oxacillin Resistance Screening Agar and CHROMagar MRSA. Both sensitivity and specificity of CHROMagar MRSA were 100%. The sensitivity and specificity of both MRSA Screen Agar and Oxacillin Resistance Screening Agar were 100% and 91.5%, respectively. It is suggested that CHROMagar MRSA is a useful medium to detect MRSA including mecA positive and oxacillin susceptible strains.

Color↗

PubMed2003

Community-level physiological profiling performed with an oxygen-sensitive fluorophore in a microtiter plate.

Community-level physiological profiling based upon fluorometric detection of oxygen consumption was performed on hydroponic rhizosphere and salt marsh litter samples by using substrate levels as low as 50 ppm with incubation times between 5 and 24 h. The rate and extent of response were increased in samples acclimated to specific substrates and were reduced by limiting nitrogen availability in the wells.

Biosensing Techniques↗

PubMed2004

Novel sulfonolipid in the extremely halophilic bacterium Salinibacter ruber.

Salinibacter ruber is an extremely halophilic bacterium, phylogenetically affiliated with the Flavobacterium/Cytophaga branch of the domain Bacteria. Electrospray mass analyses (negative ion) of the total lipid extract of a pure culture of S. ruber shows a characteristic peak at m/z 660 as the most prominent peak in the high-mass range of the spectrum. A novel sulfonolipid, giving rise to the molecular ion [M-H]- of m/z 660, has been identified. The sulfonolipid isolated and purified by thin-layer chromatography was shown by chemical degradation, mass spectrometry, infrared spectroscopy, and nuclear magnetic resonance analysis to have the structure 2-carboxy-2-amino-3-O-(13'-methyltetradecanoyl)-4-hydroxy-18-methylnonadec-5-ene-1-sulfonic acid. This lipid represents about 10% of total cellular lipids, and it appears to be a structural variant of the sulfonolipids found as main components of the cell envelope of gliding bacteria of the genus Cytophaga and closely related genera (W. Godchaux and E. R. Leadbetter, J. Bacteriol. 153:1238-1246, 1983) and of diatoms (R. Anderson, M. Kates, and B. E. Volcani, Biochim. Biophys. Acta 528:89-106, 1978). Since this sulfonolipid has never been observed in any other extreme halophilic microorganism, we consider the peak at m/z 660 the lipid signature of Salinibacter. This study suggests that this novel sulfonolipid may be used as a chemotaxonomic marker for the detection of Salinibacter within the halophilic microbial community in saltern crystallizer ponds and other hypersaline environments.

Bacteroidetes↗

PubMed2004

Culture-independent analysis of fecal enterobacteria in environmental samples by single-cell mRNA profiling.

A culture-independent method called mRNA profiling has been developed for the analysis of fecal enterobacteria and their physiological status in environmental samples. This taxon-specific approach determines the single-cell content of selected gene transcripts whose abundance is either directly or inversely proportional to growth state. Fluorescence in situ hybridization using fluorochrome-labeled oligonucleotide probes was used to measure the cellular concentration of fis and dps mRNA. Relative levels of these transcripts provided a measure of cell growth state and the ability to enumerate fecal enterobacterial cell number. Orthologs were cloned by inverse PCR from several major enterobacterial genera, and probes specific for fecal enterobacteria were designed using multiple DNA sequence alignments. Probe specificity was determined experimentally using pure and mixed cultures of the major enterobacterial genera as well as secondary treated wastewater samples seeded with pure culture inocula. Analysis of the fecal enterobacterial community resident in unseeded secondary treated wastewater detected fluctuations in transcript abundance that were commensurate with incubation time and nutrient availability and demonstrated the utility of the method using environmental samples. mRNA profiling provides a new strategy to improve wastewater disinfection efficiency by accelerating water quality analysis.

Bacterial Outer Membrane Proteins↗

PubMed2001

Molecular epidemiology of outbreak of respiratory syncytial virus within bone marrow transplantation unit.

During the winter of 1995-1996, eight of nine bone marrow transplantation (BMT) unit patients were infected with the same strain of respiratory syncytial virus (RSV). This RSV strain was not detected in 20 hospitalized patients from the community, suggesting that the BMT unit infections did not occur by independent incidents of transmission from the community.

Bone Marrow Transplantation↗

PubMed2002

Molecular epidemiology of tuberculosis in a rural area of high prevalence in South India: implications for disease control and prevention.

Molecular and conventional epidemiologic techniques were used to study the mechanisms and risk factors for tuberculosis transmission in a rural area with high prevalence in south India. Restriction fragment length polymorphism analysis with IS6110 and direct repeat probes was performed with 378 Mycobacterium tuberculosis isolates from patients. Forty-one percent of M. tuberculosis isolates harbored a single copy of IS6110. Of 378 patients, 236 had distinct strains; 142 (38%) shared a strain with other patients, indicating recent infection. Older patients, those detected by a house-to-house community survey, and those hospitalized in a sanatorium were more likely to have had a recent infection. These findings suggest that the majority of the tuberculosis cases in south India were due to reactivation; therefore, efforts to control tuberculosis should be sustained.

Adult↗

PubMed1994

Ceftriaxone in the treatment of chronic donovanosis in central Australia.

OBJECTIVES: To determine the effectiveness of intramuscular (IM) ceftriaxone sodium in the treatment of chronic donovanosis, and the acceptability to patients and staff of supervised outpatient treatment in rural clinics. METHODS: We collected demographic and sexual health data from participants using a standard questionnaire, and recorded their donovanosis lesions at baseline using genital diagrams. Treatment consisted of a single daily IM injection of 1 g ceftriaxone diluted in 2 ml of 1% lignocaine. Clinic staff followed patients for between three and 12 months, enabling the detection of late recurrences. SETTING: Rural Aboriginal communities in central Australia. PARTICIPANTS: The study describes eight women and four men with chronic donovanosis in detail, and summarises the outcome in 12 additional cases. All cases presented with advanced lesions which had failed to heal on the standard oral antibiotic regimens used in the region. RESULTS: The mean duration of infection was 3.0 years (SD 1.9 years), and between four and ten courses of antibiotics had been prescribed for six of the 12 patients. Patients received between 7-26g of ceftriaxone sodium. Clinical improvement was dramatic in most lesions, and four patients healed completely without recurrence after a total 7-10g of ceftriaxone. Mild recurrences responded to further ceftriaxone or short courses of oral antibiotics. Treatment was well tolerated, and both patient and staff compliance high. CONCLUSION: Donovanosis is an important cause of chronic genital ulceration in central Australia, and is potentially an important risk factor for HIV transmission in Aboriginal communities. The pharmacokinetics and safety profile of ceftriaxone make it a useful and cost-effective agent in the ambulatory management of donovanosis, especially in remote communities. Supervised multidrug regimens of two or more long-acting agents may provide the best answer in donovanosis, administered through the existing health care infrastructure.

Adult↗