Search PubMed⌕ Search

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.

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

At least 1,045 records · Page 58Linked to original sources
PubMed2000

An evaluation of terminal-restriction fragment length polymorphism (T-RFLP) analysis for the study of microbial community structure and dynamics.

A systematic evaluation of the value and potential of terminal-restriction fragment length polymorphism (T-RFLP) analysis for the study of microbial community structure has been undertaken. The reproducibility and robustness of the method has been assessed using environmental DNA samples isolated directly from PCB-polluted or pristine soil, and subsequent polymerase chain reaction (PCR) amplification of total community 16S rDNA. An initial investigation to assess the variability both within and between different polyacrylamide gel electrophoresis (PAGE) runs showed that almost identical community profiles were consistently produced from the same sample. Similarly, very little variability was observed as a result of variation between replicate restriction digestions, PCR amplifications or between replicate DNA isolations. Decreasing concentrations of template DNA produced a decline in both the complexity and the intensity of fragments present in the community profile, with no additional fragments detected in the higher dilutions that were not already present when more original template DNA was used. Reducing the number of cycles of PCR produced similar results. The greatest variation between profiles generated from the same DNA sample was produced using different Taq DNA polymerases, while lower levels of variability were found between PCR products that had been produced using different annealing temperatures. Incomplete digestion by the restriction enzyme may, as a result of the generation of partially digested fragments, lead to an overestimation of the overall diversity within a community. The results obtained indicate that, once standardized, T-RFLP analysis is a highly reproducible and robust technique that yields high-quality fingerprints consisting of fragments of precise sizes, which, in principle, could be phylogenetically assigned, once an appropriate database is constructed.

DNA Primers↗
PubMed2003

Determining diversity of freshwater fungi on decaying leaves: comparison of traditional and molecular approaches.

Traditional microscope-based estimates of species richness of aquatic hyphomycetes depend upon the ability of the species in the community to sporulate. Molecular techniques which detect DNA from all stages of the life cycle could potentially circumvent the problems associated with traditional methods. Leaf disks from red maple, alder, linden, beech, and oak as well as birch wood sticks were submerged in a stream in southeastern Canada for 7, 14, and 28 days. Fungal biomass, estimated by the amount of ergosterol present, increased with time on all substrates. Alder, linden, and maple leaves were colonized earlier and accumulated the highest fungal biomass. Counts and identifications of released conidia suggested that fungal species richness increased, while community evenness decreased, with time (up to 11 species on day 28). Conidia of Articulospora tetracladia dominated. Modifications of two molecular methods-denaturing gradient gel electrophoresis (DGGE) and terminal restriction fragment length polymorphism (T-RFLP) analysis-suggested that both species richness and community evenness decreased with time. The dominant ribotype matched that of A. tetracladia. Species richness estimates based on DGGE were consistently higher than those based on T-RFLP analysis and exceeded those based on spore identification on days 7 and 14. Since traditional and molecular techniques assess different aspects of the fungal organism, both are essential for a balanced view of fungal succession on leaves decaying in streams.

Biomass↗
PubMed2006

Geographic structure of pollinator communities, reproductive assurance, and the evolution of self-pollination.

Reproductive assurance is often invoked as an explanation for the evolution of self-fertilization in plants. However, key aspects of this hypothesis have received little empirical support. In this study, I use geographic surveys of pollinator communities along with functional studies of floral trait variation to examine the role of pollination ecology in mating system differentiation among populations and subspecies of the annual plant Clarkia xantiana. A greenhouse experiment involving 30 populations from throughout the species' range indicated that variation in two floral traits, herkogamy and protandry, was closely related to levels of autofertility and that trait variation was partitioned mainly among populations. Emasculation experiments in the field showed that autonomous selfing confers reproductive assurance by elevating fruit and seed production. Surveys of pollinator communities across the geographic range of the species revealed that bee pollinator abundance and community composition differed dramatically between populations of the outcrossing subspecies xantiana and the selfing subspecies parviflora despite their close proximity. Specialist bee pollinators of Clarkia were absent from selfing populations, but they were the most frequent visitors to outcrossing populations. Moreover, within the outcrossing subspecies xantiana, there was a close correspondence between specialist abundance and population differentiation in herkogamy, a key mating system trait. This spatial covariation arose, in part, because geographically peripheral populations had reduced herkogamy, higher autofertility, and lower pollinator abundance compared to central populations of xantiana. Finally, I detected strong spatial structure to bee communities both across the range of the species and within the outcrossing subspecies. In both cases, spatial structure was stronger for specialist bees compared to generalist bees, and pollinator communities varied in parallel with population variation in herkogamy. These results provide evidence that mating system differentiation parallels spatial variation in pollinator abundance and community composition at both broad and more restricted spatial scales, consistent with the hypothesis that pollinator abundance and reproductive assurance are important drivers of plant mating system evolution.

Adaptation, Biological↗
PubMed2004

The role of self-report questionnaire in the screening of postnatal depression- a community sample survey in central Tokyo.

BACKGROUND: Numerous studies have shown that health care professionals often experience difficulty in detecting postnatal depression. In Japan, where mental illness has traditionally been stigmatized, detection seems even more difficult. This study investigates the prevalence of postnatal depression in the community and its relation to screening methodology. METHODS: The Edinburgh Postnatal Depression Scale (EPDS) was distributed at community health centers in a district in central Tokyo. The results from both non-identifiable questionnaires and identifiable questionnaires were compared. Screening by EPDS and clinical judgment by community nurses were compared. RESULTS: Making the questionnaire identifiable did not change the score distribution pattern. Among mothers with 3- to 4-month-old babies in the community, 13.9% scored high (9 or above) on EPDS. In 51.1% of high scorers,nurses did not detect postnatal depression. Clinically, postnatal depression can be easily missed in the community health-check setting especially when there was hitherto no report of obstetric abnormality during pregnancy or delivery. CONCLUSION: The prevalence of high scorers is comparable to those reported in other countries. The use of the questionnaire was helpful in drawing the attention of mothers and health care professionals to issues of mental health.

Adult↗
PubMed2001

Sampling of kidneys from cattle and pigs for cadmium analysis.

Cadmium accumulates in proximal tubule cells causing a gradient of cadmium through the kidney, which is important to consider when sampling kidney tissue for cadmium analysis. In this study different sampling techniques of cattle and pig kidneys have been tested. Cadmium was determined by dry ashing-FAAS (detection limit 6.0 micrograms l-1, BCR (Community Bureau of Reference) No. 186 3.1 +/- 0.17 mg kg-1 (mean +/- s), laboratory quality sample (LQS) 495 +/- 17 micrograms kg-1) and microwave digestion-graphite furnace AAS (detection limit 0.24 microgram l-1, BCR No. 186 2.7 +/- 0.16 mg kg-1, LQS 444 +/- 14 micrograms kg-1) in homogenates, slices, and in cortex, intermediate and medulla zones of bovine and porcine kidneys. The bovine kidney lobulus cortex, intermediate zone, and medulla contained 70, 28 and 2% of the total cadmium content, and the relative weights of the zones were 53, 35 and 12%, respectively. The cadmium concentration in bovine cortex, intermediate zone and medulla was 1.37 +/- 7, 0.79 +/- 0.06 and 0.10 +/- 0.06 times the calculated homogenate concentration. Pig renal cortex, intermediate zone and medulla, contained 73, 26 and 0.5% respectively of the total cadmium content, and the relative weights were 63, 36 and 2.4%, respectively. The cadmium concentration in porcine cortex, intermediate zone and medulla was 1.14 +/- 0.05, 0.78 +/- 0.09 and 0.23 +/- 0.11 times the calculated homogenate concentration. Freezing of pig kidney caused a slight redistribution of cadmium from cortex to medulla. The results show that sampling technique is of greater importance for the determination of cadmium in bovine kidney than in pig kidney. A well described method for sampling of kidney is necessary to make it possible to compare results. To detect small differences in renal Cd levels between groups, as, e.g., in the case of biological monitoring of Cd exposure, sampling of the outer cortex is suggested as an optimal method.

Analysis of Variance↗
PubMed1996

The abuse of dextromethorphan-based cough syrup: a pilot study of the community of Waynesboro, Pennsylvania.

Drug abuse has been a national social problem in the United States for decades and is often complicated by the emergence of new types of abused drugs or new forms of abuse. In the late 1980s, the community of Waynesboro, Pennsylvania began to detect behavior among its teenagers that suggested a new form of drug abuse and thus a new social problem. The drug was dextromethorphan, used in cough syrup-principally Robitussin DM. The form of abuse is often referred to as "roboing" or "robo-copping." This paper presents the results of the first phase of a comprehensive investigation of this phenomenon in the Waynesboro school district. Data from a survey of school personnel indicate that abuse of cough syrup (Robitussin or other brands) has increased over the years and is increasingly perceived as a problem by the community.

Adolescent↗
PubMed2026

Antimicrobial resistance surveillance through wastewater: methodological considerations for metagenomic approaches and public health perspectives.

Antimicrobial resistance (AMR) is a recognised global threat with substantial predicted impact on lives, agriculture, and the economy. Metagenomic sequencing is being increasingly used for AMR surveillance and detection, given its capacity for community-level AMR profiling with high-level resolution. This technology has seen an explosion of surveillance efforts and data generation; however, the variation between workflows has direct implications on the sequencing results and their interpretation. In this Personal View, we summarise aspects of the sequencing workflow that need to be considered during metagenomic study design, for meaningful and reliable population-based surveillance. We reflect on the vital role of standardisation for capturing the ground truth of AMR and data comparability and reproducibility, and in addition, review the limitations of the various phenotypic and genotypic methods of AMR detection. We further highlight complex mechanisms of resistance to antimicrobials that could hinder our ability to confidently assess the true AMR burden in the environment and those that are often overlooked during surveillance.

Metagenomics↗
PubMed2006

Neonatal hearing screening: modelling cost and effectiveness of hospital- and community-based screening.

BACKGROUND: Children with congenital hearing impairment benefit from early detection and management of their hearing loss. These and related considerations led to the recommendation of universal newborn hearing screening. In 2001 the first phase of a national Newborn Hearing Screening Programme (NHSP) was implemented in England. Objective of this study was to assess costs and effectiveness for hospital and community-based newborn hearing screening systems in England based on data from this first phase with regard to the effects of alterations to parameter values. METHODS DESIGN: Clinical effectiveness analysis using a Markov Model. OUTCOME MEASURE: quality weighted detected child months (QCM). RESULTS: Both hospital and community programmes yielded 794 QCM at the age of 6 months with total costs of 3,690,000 pound sterling per 100,000 screened children in hospital and 3,340,000 pound sterling in community. Simulated costs would be lower in hospital in 48% of the trials. Any statistically significant difference between hospital and community in prevalence, test sensitivity, test specificity and costs would result in significant differences in cost-effectiveness between hospital and community. CONCLUSION: This modelling exercise informs decision makers by a quantitative projection of available data and the explicit and transparent statements about assumptions and the degree of uncertainty. Further evaluation of the cost-effectiveness should focus on the potential differences in test parameters and prevalence in these two settings.

Community Health Services↗
PubMed2006

Cyanobacterial ecotypes in the microbial mat community of Mushroom Spring (Yellowstone National Park, Wyoming) as species-like units linking microbial community composition, structure and function.

We have investigated microbial mats of alkaline siliceous hot springs in Yellowstone National Park as natural model communities to learn how microbial populations group into species-like fundamental units. Here, we bring together empirical patterns of the distribution of molecular variation in predominant mat cyanobacterial populations, theory-based modelling of how to demarcate phylogenetic clusters that correspond to ecological species and the dynamic patterns of the physical and chemical microenvironments these populations inhabit and towards which they have evolved adaptations. We show that putative ecotypes predicted by the theory-based model correspond well with distribution patterns, suggesting populations with distinct ecologies, as expected of ecological species. Further, we show that increased molecular resolution enhances our ability to detect ecotypes in this way, though yet higher molecular resolution is probably needed to detect all ecotypes in this microbial community.

Adaptation, Biological↗
PubMed2002

Minimally invasive spectroscopic system for intraocular drug detection.

A novel, minimally invasive measurement technique has been developed for the detection of drugs in the anterior chamber of the eye. Presently there is no satisfactory, real-time detection method available to the ophthalmic community. Accurate determination of drug concentrations in the eye would be of great value and assistance to researchers and manufacturers of ophthalmic drugs and ocular implants, to enable a better understanding of intraocular pharmacokinetics. At present researchers use techniques of direct sampling of the aqueous humor from laboratory animal eyes into which the drug has been introduced topically or systemically. Rabbit eyes are frequently used in this context. Sampling via paracentesis is invasive, and does not yield a continuous measurement. Our approach to addressing this measurement requirement is, in effect, to turn the eye into a cuvette and use optical absorbance spectroscopy measurements to detect drug concentrations. A novel contact lens has been designed using commercial, off-the-shelf, optical design software. The lenses have been optimized to direct light across the anterior chamber of a rabbit's eye. Practical demonstration and characterization of light propagation across the eye have been undertaken and are reported. Preliminary results of the identification of drug compounds introduced into model eyes are also reported.

Adrenergic alpha-Agonists↗
PubMed1998

An assessment of asthmatic patients at four Western Cape community pharmacies.

OBJECTIVES: To identify the profile of asthmatic patients visiting community pharmacies and to assess the appropriateness of their current asthma therapy. DESIGN: Patients were identified as either chronic, newly diagnosed or undiagnosed. Asthma status was assessed from their current symptom and medication profiles and from performance in an airways responsiveness test. Reversibility of > 15% was suggestive of probable airflow obstruction and such patients were referred to a medical practitioner. SETTING: Four community pharmacies located in different socio-economic areas, viz. Khayelitsha, Wynberg, Mitchell's Plain and Vrijzee, were selected. SUBJECTS: Participants over the age of 6 years, who suffered from recurrent cough, wheeze, chest tightness and/or breathlessness and used over-the-counter (OTC) and/or asthma medications, completed a questionnaire and participated in the airways responsiveness test. OUTCOME MEASURES: Effective control of asthma based on minimal symptoms, appropriate use of bronchodilator and anti-inflammatory therapies and absence of airflow obstruction. RESULTS: Of the 220 participants, 120 were identified as chronic, 7 as newly diagnosed and 93 as undiagnosed. Chronic asthmatics suffered daily symptoms and used inadequate prophylactic anti-inflammatory therapy. Many undiagnosed asthmatics were unaware of their symptoms and took OTC medication indiscriminately. Based on peak expiratory flow rate measurements, > 50% of the screened patients displayed a reversibility of > 15%. CONCLUSIONS: Chronic and many undiagnosed asthmatic patients frequent community pharmacies for their medication. Such patients suffer recurrent asthma symptoms and use medication inappropriately, which results in suboptimal lung function. Pharmacists should play a more participatory role in the detection and management of asthma in the community.

Adolescent↗
PubMed1996

Screening for dementia of the alzheimer type in the community: the utility of the Clock Drawing Test.

This study reports the sensitivity and specificity of the Clock Drawing Test (CDT) for detecting dementia of the Alzheimer type in a community-dwelling sample of elderly subjects. Forty-two patients with clinically diagnosed Alzheimer's disease and 237 cognitively intact subjects were administered the CDT as part of an epidemiological study of aging and dementia. Three individual measures of clock drawing performance (quantitative score, qualitative score, and combined quantitative and qualitative score) were determined for each participant. When qualitative elements such as errors and strategies were incorporated into the CDT score, the sensitivity was 84% and the specificity was 72%. The findings suggest that a CDT score which evaluates qualitative and quantitative features provides reasonably good discrimination between normal elderly individuals and DAT patients. However, the CDT appears to have limited utility as a single screening instrument in the community. Instruments such as the Dementia Rating Scale (Mattis, 1976) provide better discrimination of DAT, indicating that functions such as memory and verbal fluency need to be assessed during screening.

Journal Article↗
PubMed1998

Use of focus groups to identify health promotion strategies for the early detection of diabetic retinopathy.

BACKGROUND: People with diabetes do not regularly utilise eye services for the early prevention of vision loss due to diabetic eye disease. A community-based screening program has been initiated in Victoria to address this issue. To encourage people to take preventive eye health care measures, the most effective health promotion strategies were identified. METHODS: Thirty-three health professionals were invited to attend focus groups. A sample of 35 people with diabetes was approached by their GPs or diabetes educators because of their motivation to participate in diabetes activities. Each group consisted of 10 members. Discussion points included the type of education messages available to people with diabetes; use of eye services among the participants with diabetes; and strategies required promoting the screening service. RESULTS: Five focus groups were conducted. The discussions highlighted that a great deal could be achieved by using local community networks to promote the benefits of early detection of diabetic retinopathy and local screening program. The group members recommended that particular attention be directed to general practitioners and their distribution of materials to patients. Key issues for planning and implementing the program were highlighted. The groups urged development of strategies to encourage people with diabetes in rural Victoria to participate in a program for the early detection of diabetic retinopathy.

Diabetic Retinopathy↗
PubMed2001

Sorption and metabolism of selected herbicides in river biofilm communities.

In the present study, biofilms were grown in rotating annular bioreactors with river water as inoculum and sole source of nutrients. The herbicides atrazine and diclofop methyl were applied to the bioreactors, while an identical reactor acted as a control. Biofilm structure was visualized using specific fluorescent probes in conjunction with confocal laser scanning microscopy. The concentration of both herbicides in the bulk water phase followed the pattern of application. Atrazine and metabolites were detected in biofilm samples using direct insertion probe tandem mass spectrometry (DIP-MS/MS) and only trace levels were detected after the addition phase. Monoclonal antibody (MAb) studies indicated that sorption of atrazine was associated with a unique microcolony type. In contrast, diclofop and metabolites reached a maximum level in the biofilm at the end of the addition phase and persisted in the biofilm. Experiments with 14C-labeled atrazine and diclofop methyl indicated that mineralization of these compounds to CO2 (<1%) occurred in the river biofilms. Thus, both herbicides were sorbed and metabolized by the river biofilm community and detected in biofilms when they were not detected in the bulk water phase. These results indicate that biofilms and specific community members may act as a sink for herbicides, and that this should be taken into account in terms of both sampling and studies of the environmental chemodynamics of contaminants.

Adsorption↗
PubMed2003

[Portable echocardiographs: useful or futile?].

Echocardiographic systems which are the size of a laptop computer are currently available. These hand-held ultrasound units are very easy to use at patient bedside in various clinical settings. According to the miniaturized devices, spectral Doppler may not be available and power Doppler may replace true color Doppler. Validation studies of hand-held echocardiography have been conducted in critically ill patients, in patients hospitalized in ward, but also in outpatients and as a screening tool for the detection of cardiac abnormalities in the community. Hand-held echocardiography appears to have important limitations in specific clinical settings, such as shock, pulmonary hypertension, assessment of valvulopathy or valvular prosthesis, dynamic left outflow tract obstruction, left ventricular restriction or construction. The miniaturized system with spectral Doppler capability has not yet been properly validated in these indications. At its present stage of development, hand-carried ultrasound units do not allow to perform a comprehensive examination which relies on the use of a full-feature system, especially when a precise hemodynamic evaluation is required. Diagnostic ability of hand-held echocardiography is similar to that of upper-end platforms for diagnoses based on two-dimensional imaging: left ventricular systolic function, detection of wall motion abnormalities, size of cardiac chambers, identification of pericardial or pleural effusions. Hand-carried ultrasound devices may be considered as a "visual stethoscope" which provides an extension of the physical examination, but not as a potential alternative to standard transthoracic echocardiography. Its large potential clinical field of use raises the concern of taylored training programs to intensivists which could be focused on goal-directed echocardiographic examinations.

Clinical Trials as Topic↗
PubMed2000

A prospective study of laboratory and clinical measures of postural stability to predict community-dwelling fallers.

BACKGROUND: The identification of specific risk factors for falls in community-dwelling elderly persons is required to detect early changes and permit a preventative approach to management. This study determines the ability of various laboratory measures and clinical tests of postural stability to prospectively predict fallers in community-dwelling elderly women. METHODS: One hundred elderly women (65-86 years, mean age 73 +/- 5 years) performed a reaction-time step task, a limits of stability, and a quiet stance balance task. Postural muscle timing and movement speed were recorded during the step task. Center of pressure (COP) motion was recorded in quiet stance and at the limits of stability. Four common clinical balance tests were performed, and balance confidence, medical and activity history questionnaires were completed. Subjects were followed up regularly for a 6-month period following testing to determine the frequency and characteristics of any falls that occurred. Predictive capabilities of the balance measures to determine fallers were determined through logistic regression models. RESULTS: The clinical balance tests investigated were not able to predict fallers in this community-dwelling elderly population. A combination of variables from the laboratory tasks provided the best overall prediction rate (77%) of fallers (sensitivity 51%) and nonfallers (specificity 91%) from laboratory measures. Of these, step movement time and gluteus medius onset times were the factors best able to predict fallers. Alone, measures of COP motion in quiet stance and at the limits of stability had a poor ability to predict fallers, although they could correctly identify most nonfallers. Prediction was not significantly improved when clinical balance test results were added to the most predictive laboratory measures. CONCLUSIONS: Not all older adults with a reduction in balance ability reported a fall over a 6-month period. Of those who did, a combination of measures reflective of different aspects of mediolateral postural stability during a rapid step task, quiet stance, and movement to the limits of stability were best able to predict faller status, with nonfallers better predicted than fallers. These results emphasize the importance of the multifactorial nature of falls in the community-dwelling elderly population in that the clinical and laboratory measures did not predict a high proportion of fallers.

Accidental Falls↗
PubMedDate not supplied

[Diversity of bacteria at various depths in the southern part of lake Baikal as detected by 16S rRNA sequencing].

Phylogenetic analysis of the bacterial community inhabiting the water of Lake Baikal was performed on the basis of 16S rRNA sequencing. The composition of the bacterial community was shown to vary significantly with depth. Cyanobacteria were dominant species at the surface of the lake. At a moderate depth (400 m), actinomycete relatives were most abundant. At a great depth and near the bottom, the community was composed mainly of proteobacteria and cyanobacteria (the latter are probably brought from the surface layers by vertical near-shore water fluxes). Most of the bacterial 16S rRNA sequences detected exhibited low similarity to those known and formed separate clusters in the phylogenetic tree, which may indicate the endemic nature of the corresponding bacteria.

Bacteria↗
PubMedDate not supplied

Environmental radiation levels in central Florida's phosphate mining district.

Environmental levels of radionuclides and gamma radiation were measured in two communities located near active phosphate mining areas in Florida. Activated carbon canisters and alpha track detectors were used to measure indoor air levels of radon in approximately 100 private homes. Elevated levels of radon (> 4 picocuries per liter [pCi/L]) were detected in 8 of 27 homes in a community built on reclaimed land that had been previously mined. In a nearby community built on unmined land, elevated levels of radon were detected in 1 of 69 homes. All of the homes with elevated levels of radon were built on concrete slabs. Outdoor gamma radiation levels were significantly greater in the reclaimed area than in the unmined area. Air particulates collected from outdoor ambient air at three locations did not contain elevated levels of radionuclides.

Air Pollution, Indoor↗