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At least 469 records · Page 26Linked to original sources
PubMed2002

Macroecological patterns of phytoplankton in the northwestern North Atlantic Ocean.

Many issues in biological oceanography are regional or global in scope; however, there are not many data sets of extensive areal coverage for marine plankton. In microbial ecology, a fruitful approach to large-scale questions is comparative analysis wherein statistical data patterns are sought from different ecosystems, frequently assembled from unrelated studies. A more recent approach termed macroecology characterizes phenomena emerging from large numbers of biological units by emphasizing the shapes and boundaries of statistical distributions, because these reflect the constraints on variation. Here, I use a set of flow cytometric measurements to provide macroecological perspectives on North Atlantic phytoplankton communities. Distinct trends of abundance in picophytoplankton and both small and large nanophytoplankton underlaid two patterns. First, total abundance of the three groups was related to assemblage mean-cell size according to the 3/4 power law of allometric scaling in biology. Second, cytometric diversity (an ataxonomic measure of assemblage entropy) was maximal at intermediate levels of water column stratification. Here, intermediate disturbance shapes diversity through an equitable distribution of cells in size classes, from which arises a high overall biomass. By subsuming local fluctuations, macroecology reveals meaningful patterns of phytoplankton at large scales.

Animals↗
PubMed1984

Postmarketing drug surveillance by record linkage in Tayside.

The feasibility of conducting postmarketing drug surveillance by record linkage in Tayside was assessed. The key feature of the method is that all hospital discharge data are already computerised by the area health board and may be accessed through the unique community health number (CHNo) which has been allocated to all Tayside residents. The 12 861 prescriptions for cimetidine dispensed in Tayside over a nine month period were collected and the CHNo identified for 76%. These corresponded to 3802 individuals and their discharge data, together with those for an equal number of controls matched by age, sex, and general practitioner were retrieved from the computer. The expected excess of those diseases for which cimetidine is prescribed (peptic ulcer and oesophagitis) was observed. Other drug-disease associations were observed but may have been due to confounding and emphasise the inadequacy of community based controls. The major advantages of record linkage are, firstly, the low cost of the method, the present study costing just over pounds 12 000, and, secondly, the duration of patient follow up which may may be extended for as many years as required simply by rerunning the computer programs. To assemble large patient cohorts the study would have to be extended to other area health boards that are currently developing similar computer systems. Record linkage may provide a cost effective method for the follow up of patients to identify serious adverse drug reactions, particularly those that take several years to develop.

Cimetidine↗
PubMed1980

European concepts on the use of laboratory animals in relationship with animal welfare problems.

Within the Council of Europe which consists of 21 European countries, a draft convention for the protection of animals used for experimental purposes, based on Recommendation 621 (1971) of its Parliamentary Assembly, is being drawn up in Strasbourg (France) by the Committee of Experts for the Protection of Animals. Regulations (e.g.: refinement of experimental procedures), techniques (e.g.: restrictions of experiments) and ethics (e.g.: use of replacement methods) are subject to international discussions among repreentatives of member states and observers from the European Economic Community and the United States of America, in order to propose equitable national provisions and prevent later economic distortions. European concepts that concern all human activities which deal with the use of live laboratory animals, experimental and administrative procedures (e.g.: registration, authorization, licensing, supervision) and compliance with a Code of Ethics governing experiments, should obtain the uninamous support of countries using laboratory animals. Furthermore, European countries emphasize the importance of: staff training and qualifications; public information; setting up advisory committees with scientists and animal welfare societies; using animals bred for experimental purposes; prohibiting unnecessary experiments; and the importance of veterinary supervision in implementing regulations in European countries.

Animals↗
PubMedDate not supplied

Legislative Cardiovascular Health Check: a multidisciplinary health promotion experience for South Carolina lawmakers.

The South Carolina Department of Health and Environmental Control has conducted a Legislative Cardiovascular Health Check for the past 4 years. The primary purpose of the event, held in the lobby of the State Capitol Building, is to increase the awareness of State legislators about the leading causes of death in South Carolina and about community-based health promotion services that are available. The health check emphasizes the relationship between modifiable risk factors and the development of heart disease, cancer, and stroke. These legislative events are organized by State health department staff members, but they are conducted by local health department personnel from throughout South Carolina. This approach is intended to build the capacity of these local staff members to communicate more effectively with their legislators and to carry out similar events at the county or community level. The health check is staffed by a trained multidisciplinary team, including persons designated as legislative liaisons. The liaison people contact legislators prior to the event and provide them with health status data specific to their respective districts. The Legislative Cardiovascular Health Checks have been attended by members of the General Assembly and their staffs, members of the Governor's staff and the Lieutenant Governor's office, and other employees of the State Capitol. An average of 380 people have participated annually. Screening activities have included blood pressure and blood cholesterol checks, with risk factor counseling and educational materials provided to each screened participant. During the past year, activities were expanded to include a variety of interactive exhibits related to nutrition, exercise, and smoking. Feedback from participants has been positive. The Legislative Cardiovascular Health Check is encouraged and supported by the upper management of the State health department and is now established as an annual event of mutual benefit to legislators and to State and local health department staff members.

Blood Pressure↗
PubMedDate not supplied

Implications of chemical mixtures in public health practice.

The Agency for Toxic Substances and Disease Registry (ATSDR) is a federal public health agency that investigates and strives to prevent human health problems produced by exposure to toxic chemicals and their mixtures in the environment. Most human exposures involving toxic chemicals or mixtures are thought to originate from environmental and occupational sources; however, concurrent exposures are also likely from other sources, such as prescription and nonprescription drugs, indoor air pollutants, alcohol, and tobacco smoke. Thus, in evaluating the potential hazard following exposure to environmental mixtures, ATSDR not only considers the inherent joint toxicity of the mixture but also the influence of environmental, demographic, occupational, and lifestyle factors. To foster these goals, ATSDR has pursued a Mixtures Research and Assessment Program that consists of three component efforts: trend analysis, joint toxicity assessment, and experimental testing. Through trend analysis, ATSDR sets priorities for environmental mixtures of concern for which joint toxicity assessments are conducted as needed. If data are not available to conduct appropriate assessments, a research agenda is pursued through established extramural mechanisms. Ultimately, the data generated are used to support ATSDR's work at sites involving exposure to chemical mixtures. This pragmatic approach allows testable hypotheses or research needs to be identified and resolved and enhances our understanding of the mechanisms of joint toxicity. Several collaborative and cooperative efforts with national and international organizations such as the Toxicology and Nutrition Office, the Netherlands, and the Department of Energy are being pursued as part of these activities. ATSDR also develops guidance manuals to consistently and accurately apply current methodologies for the joint toxicity assessment of chemicals. Further, expert panels often are assembled to resolve outstanding scientific issues or obtain expert advice on pertinent issues. Recently, the need for studies on chemical mixtures has been proposed as one of the six priority areas the agency identified in its agenda for public health environmental research. This has been reinforced through the agency's close work with communities whose leaders have spoken passionately about their concern for information on exposures to chemical mixtures. The five other priority research areas the agency identified are exposure, susceptible populations, communities and tribal involvement, evaluation/surveillance of health effects, and health promotion/prevention.

Algorithms↗
PubMed2025

GRUMB: a genome-resolved metagenomic framework for monitoring urban microbiomes and diagnosing pathogen risk.

SUMMARY: Urban infrastructure hosts dynamic microbial communities that complicate biosurveillance and AMR monitoring. Existing tools rarely combine genome-resolved reconstruction with ecological modeling and batch-aware analytics tailored to infrastructure-scale studies. We present GRUMB (Genome-Resolved Urban Microbiome Biosurveillance), an open-source, SLURM-compatible pipeline that reconstructs high-quality metagenome-assembled genomes (MAGs) from shotgun sequencing reads and integrates taxonomic/functional annotation (CARD, VFDB), batch-aware normalization, ecological diagnostics and machine learning classification of environment types with uncertainty and risk scoring. GRUMB accepts either SRA project accessions or paired-end FASTQ files with metadata, and produces assemblies, MAGs, taxonomic and functional profiles, ecological outputs and risk-informed classification. Its modular design enables reproducible, infrastructure-scale biosurveillance across diverse environments. AVAILABILITY AND IMPLEMENTATION: GRUMB is freely available under the MIT License at: https://github.com/SuleimanAminu/genome-resolved-urban-microbiome-biosurveillance; Zenodo DOI: https://doi.org/10.5281/zenodo.15505402. Requirements: Linux (Ubuntu 20.04+), Python 3.11, R 4.2+, SLURM. Issues and feature requests are tracked on GitHub.

Microbiota↗
PubMed2026

Gut microbiome composition and predicted functions relate to growth and behavior in a Japanese preschool cohort.

Early childhood is a period of rapid brain maturation and gut microbiome assembly, when emerging behavioral difficulties can shape later mental health and learning trajectories. Microbiota-gut-brain communication has been implicated in neurodevelopment through microbial metabolites and immune signaling. However, most pediatric evidence comes from high-risk or clinically referred cohorts, and gut microbiome-related correlates of typical behavioral variation in community-based preschool children remain poorly defined. In a cross-sectional sample of typically developing Japanese preschool children, we observed exploratory nominal associations between behavioral variation within normative ranges and gut microbiome composition and predicted functions. Internalizing domains showed candidate links with taxa and predicted pathways related to inflammatory potential and nucleotide biosynthesis, whereas somatic complaints and withdrawn behavior showed nominal associations with lower predicted respiratory and fermentative activity. Sleep-related difficulties showed multiple representative nominal pathway-level associations, including pathways related to methyl-donor and heme biosynthesis, while externalizing domains showed candidate links with predicted cell-envelope and carbohydrate-remodeling pathways. In contrast, age, height, and weight tracked expected maturation-related microbiome features, indicating that behavioral associations were not simple proxies of growth. Together, these findings provide an exploratory profile of microbiome-behavior correlations in a low-risk Japanese preschool cohort and highlight pathway-level candidates that may interface with neurodevelopment.

Humans↗
PubMed2006

Are ectoparasite communities structured? Species co-occurrence, temporal variation and null models.

1. We studied temporal variation in the structure of flea communities on small mammalian hosts from eastern Slovakia using null models. We asked (a) whether flea co-occurrences in infracommunities (in the individual hosts) in different hosts as well as in the component communities (in the host species) demonstrate a non-random pattern; (b) whether this pattern is indicative of either positive or negative flea species interactions; (c) whether this pattern varies temporally; and (d) whether the expression of this pattern is related to population size of either fleas or hosts or both. 2. We constructed a presence/absence matrix of flea species for each temporal sample of a host species and calculated four metrics of co-occurrence, namely the C-score, the number of checkerboard species pairs, the number of species combinations and the variance ratio (V-ratio). Then we compared these metrics with the respective indices calculated for 5000 null matrices that were assembled randomly using two algorithms, namely fixed-fixed (FF) and fixed-equiprobable (FE). 3. Most co-occurrence metrics calculated for real data did not differ significantly from the metrics calculated for simulated matrices using the FF algorithm. However, the indices observed for 42 of 75 presence/absence matrices differed significantly from the null expectations for the FE models. Non-randomness was detected mainly by the C-score and V-ratio metrics. In all cases, the direction of non-randomness was the same, namely the aggregation, not competition, of flea species in host individuals and host species. 4. The inclusion or exclusion of the uninfested hosts in the FE models did not affect the results for individual host species. However, exclusion of the uninfested host species led to the acceptance of the null hypothesis for only six of 13 temporal samples of the component flea communities for which non-randomness was detected when the uninfested hosts were included in the analysis. 5. In most host species, the absolute values of the standardized size effect of both the C-score and V-ratio increased with an increase in host density and a concomitant decrease in flea abundance and prevalence. 6. Results of this study demonstrated that (a) flea assemblages on small mammalian hosts were structured at some times, whereas they appeared to be randomly assembled at other times; (b) whenever non-randomness of flea co-occurrences was detected, it suggested aggregation but never segregation of flea species in host individuals or populations; and (c) the expression of structure in flea assemblages depended on the level of density of both fleas and hosts.

Animals↗
PubMed2005

Diverse evolutionary trajectories characterize a community of RNA-cleaving deoxyribozymes: a case study into the population dynamics of in vitro selection.

Two parallel in vitro selections (denoted Selection A and Selection B) were conducted under different selection-pressure regimes, yielding a diverse community of RNA-cleaving deoxyribozymes. In Selection A, the reaction time was reduced four times (from 5 h to 5 s) over the course of 24 generations, while in Selection B the reaction time was maintained at 5 h for 30 rounds of selective amplification. Sequence alignment was conducted on more than 800 clones assembled from 18 generations that span both selections. Many prominent catalytic sequence classes, including some that extend across both selections, were identified and used to construct fitness landscapes depicting their rise and fall over time. The landscapes from both selections exhibit similar global trends despite differences in population dynamics. Some deoxyribozymes were predominant in the early rounds of selection but gave way to other species that dominated in the middle rounds. Ultimately, these middle classes disappeared from the landscape in favor of new and presumably more fit deoxyribozyme sequence classes. The shape of these landscapes alludes to the presence of many latent deoxyribozymes in the initial library, which can only be accessed by changes in the selection pressure and/or by adaptive mutations. Basic computer simulations provide theoretical corroboration of the experimentally observed pattern of staggered sequence-class transitions across the fitness landscapes. These simulations model the influence of one or more contributing factors, including catalytic rate, folding efficiency, PCR amplification efficiency, and random mutagenesis. This is the first study which thoroughly documents the topography of a deoxyribozyme fitness landscape over many generations of in vitro selection.

Base Sequence↗
PubMed1997

Predicting discharge outcomes of VA nursing home residents.

This article's purpose was to identify predictors of discharge outcomes of VA nursing home stays. Using data tapes, diagnostic and assessment data were assembled on elderly individuals admitted to VA nursing homes nationwide during Fiscal Year 1987. Six-month outcomes for 3 groups were considered: all residents (n = 5,895), and those remaining in care after 6 (n = 2,815) and 12 months (n = 1,812), respectively. Logistic regression was used to evaluate predictors of death and community discharge. Limited activities of daily living (ADL) dependency, younger age, and receipt of rehabilitation services most consistently predicted community discharge. ADL dependency, older age, oxygen use, terminally ill prognosis, malignancy, and congestive heart failure most consistently predicted mortality. For both dependent variables, predictive ability declined as stay length increased. Predicting death and community discharge become increasingly problematic as stay lengthens. Comparing observed versus expected discharge outcomes has limited usefulness as a quality-improvement tool.

Activities of Daily Living↗
PubMed2004

Disease eradication, elimination and control: the need for accurate and consistent usage.

This article seeks to clarify the terminology associated with disease control, elimination and eradication programmes. There are several global activities under way, which are initiated and guided by resolutions of the World Health Assembly. Scrutiny of the feasibility of achieving eradication goals by bodies such as the International Task Force for Disease Eradication has identified diseases that could be eradicated. The criteria for this attribution as eradicable, the definitions guiding policy, and examples of programmes and strategies are provided here. This article pleads for scientific, health policy and editorial communities to be more consistent in the use of the terms control, elimination and eradication, and to adhere to published definitions.

Animals↗
PubMed2003

The interpretation of biological surveys.

Biological surveys provide the raw material for assembling ecological patterns. These include the properties of parameters such as range, abundance, dispersion, evenness and diversity; the relationships between these parameters; the relationship between geographical distributions and landscape structure; and the co-occurrence of species. These patterns have often been used in the past to evaluate the role of ecological processes in structuring natural communities. In this paper, I investigate the patterns produced by simple neutral community models (NCMs) and compare them with the output of systematic biological surveys. The NCM generates qualitatively, and in some cases quantitatively, the same patterns as the survey data. It therefore provides a satisfactory general theory of diversity and distribution, although what patterns can be used to distinguish neutral from adaptationist interpretations of communities, or even whether such patterns exist, remains unclear.

Animals↗
PubMed2005

Global Pseudomonas aeruginosa biodiversity as reflected in a Belgian river.

The biodiversity of the bacterium Pseudomonas aeruginosa in an aquatic environment (the Woluwe River, Brussels, Belgium) was analysed. Surface water was sampled bimonthly over a 1-year period (2000-2001) at seven sites evenly dispersed over the river. Total bacterial counts were performed and P. aeruginosa strains were isolated on a selective medium. A weighed out sample of 100 randomly chosen presumptive P. aeruginosa isolates was further analysed. A set of data consisting of the nucleotide sequence of the oprL gene, a DNA-based fingerprint (amplified fragment length polymorphism, AFLP), serotype, pyoverdine type and antibiogram (MICs of 21 clinically relevant antibiotics) was assembled. These data were integrated with those previously obtained for 73 P. aeruginosa clinical and environmental isolates collected across the world. The combined results were analysed and compared using biological data analysis software. Our findings indicate a positive relationship between the extent of pollution and the prevalence of P. aeruginosa. Surprisingly, the Woluwe River P. aeruginosa community was almost as diverse as the global P. aeruginosa population. Indeed, the Woluwe River harboured members of nearly all successful clonal complexes. With the exception of one multidrug-resistant (MDR) strain, belonging to a ubiquitous and clinically relevant serotype O11 clone, antibiotic resistance levels were relatively low. These findings illustrate the significance of river water as a reservoir and source of distribution of potentially pathogenic P. aeruginosa strains and could have repercussions on antinosocomial infection strategies.

Anti-Bacterial Agents↗
PubMed2003

Identification of conserved regulatory elements by comparative genome analysis.

BACKGROUND: For genes that have been successfully delineated within the human genome sequence, most regulatory sequences remain to be elucidated. The annotation and interpretation process requires additional data resources and significant improvements in computational methods for the detection of regulatory regions. One approach of growing popularity is based on the preferential conservation of functional sequences over the course of evolution by selective pressure, termed 'phylogenetic footprinting'. Mutations are more likely to be disruptive if they appear in functional sites, resulting in a measurable difference in evolution rates between functional and non-functional genomic segments. RESULTS: We have devised a flexible suite of methods for the identification and visualization of conserved transcription-factor-binding sites. The system reports those putative transcription-factor-binding sites that are both situated in conserved regions and located as pairs of sites in equivalent positions in alignments between two orthologous sequences. An underlying collection of metazoan transcription-factor-binding profiles was assembled to facilitate the study. This approach results in a significant improvement in the detection of transcription-factor-binding sites because of an increased signal-to-noise ratio, as demonstrated with two sets of promoter sequences. The method is implemented as a graphical web application, ConSite, which is at the disposal of the scientific community at http://www.phylofoot.org/. CONCLUSIONS: Phylogenetic footprinting dramatically improves the predictive selectivity of bioinformatic approaches to the analysis of promoter sequences. ConSite delivers unparalleled performance using a novel database of high-quality binding models for metazoan transcription factors. With a dynamic interface, this bioinformatics tool provides broad access to promoter analysis with phylogenetic footprinting.

Algorithms↗
PubMed2006

Ipratropium bromide versus long-acting beta-2 agonists for stable chronic obstructive pulmonary disease.

BACKGROUND: Chronic obstructive pulmonary disease (COPD) is a condition associated with high morbidity, mortality and cost to the community. Patients often report symptomatic improvement with long acting beta-2 agonists (LABAs) and anticholinergic bronchodilator medications, both of which are recommended in COPD guidelines. These medications have different mechanisms of action and therefore theoretically could have an additive effect when combined. As these medications are prescribed in COPD as long term therapy, it is important to assemble reliable evidence on their relative and additive effects. OBJECTIVES: To compare the relative efficacy and safety of regular long term use (at least four weeks) of ipratropium bromide and LABA in patients with stable COPD. Comparisons were made between single agents and in combination versus LABAs alone. SEARCH STRATEGY: We searched the Cochrane Airways Group Specialised Register of Trials (August 2005) and reference lists of articles. We also contacted drug companies for relevant trial data. SELECTION CRITERIA: All randomised controlled trials comparing treatment for at least four weeks with an anticholinergic agent (ipratropium bromide) alone or in combination with LABA versus LABA alone, delivered via metered dose inhaler or nebuliser, in non-asthmatic adult subjects with stable COPD. DATA COLLECTION AND ANALYSIS: Three review authors independently performed data extraction and study quality assessment. We contacted study authors and pharmaceutical companies for missing data. MAIN RESULTS: Seven studies met the inclusion criteria of the review (2652 participants). Monotherapy comparison (six studies): There was a significantly greater change in favour of salmeterol in morning PEF and FEV1. There were no significant differences in quality of life, exacerbations, or symptoms. Formoterol appeared to confer some benefits over ipratropium treatment in terms of morning peak flow. Combination comparison (three studies): There was a significant improvement in post-bronchodilator lung function, supplemental short-acting beta-agonist use and HRQL in favour of combination therapy compared with salmeterol alone. AUTHORS' CONCLUSIONS: The available data from the trials suggest that there is little difference between regular long term use of IpB alone and salmeterol if the aim is to improve COPD symptoms and exercise tolerance. However, salmeterol was more effective in improving lung function variables. In terms of post-bronchodilator lung function, combination therapy conferred modest benefits and a significant improvement in HRQL, and reduced supplemental short-acting beta-agonist requirement, although this effect was not consistent. Additional studies are needed to assess the relative effects of combining therapies, using validated subjective measurements, and should consider concordance and the convenience of people having to use different inhaler devices.

Adrenergic beta-Agonists↗
PubMed2025

From sporulation to village differentiation: The shaping of the social microbiome over rural-to-urban lifestyle transition in Indonesia.

Despite established roles in human health and profound global diversity, microbiome datasets remain biased toward Western urban cohorts, with especial under-representation of Southeast Asia. Here, we present a gut microbiome dataset from 116 Indonesians spanning transitional hunter-gatherer, rural agricultural, and urban lifestyles. We identify 1,304 species and 3,258 subspecies by assembling 11,070 metagenome-assembled genomes, revealing substantial species- (15%) and subspecies- (50%) level novelty. Novel taxa are rare, often village specific, and depleted for sporulation genes, revealing a link between bacterial physiology, transmission, prevalence, and discovery. We identify rural-to-urban clines across multiple levels of biological organization, from species abundance to microbiome composition and diversity. Furthermore, between-community, but not within-community, diet variation is strongly predictive of microbiome composition, suggesting that microbiome divergence is driven by community-level differences. Our work highlights the interplay of host lifestyle, population structure, and bacterial physiology in shaping microbiome diversity and biogeography, at the key scale of human communities.

Humans↗
PubMedDate not supplied

Microbial genomics: from sequence to function.

The era of genomics (the study of genes and their function) began a scant dozen years ago with a suggestion by James Watson that the complete DNA sequence of the human genome be determined. Since that time, the human genome project has attracted a great deal of attention in the scientific world and the general media; the scope of the sequencing effort, and the extraordinary value that it will provide, has served to mask the enormous progress in sequencing other genomes. Microbial genome sequencing, of particular interest to the community studying emerging infectious diseases, prompted the series of articles presented in the following pages. These articles review technological and scientific advances that have occurred since publication of the Haemophilus influenzae genome sequence in July 1995; that was the first demonstration that an entire genome sequence could be deciphered by a "shotgun" approach, i.e., the sequencing and assembly of random fragments of the genome. This is now the method of choice for sequencing of most other genomes, including human (as performed by Celera Genomics).

Genome, Bacterial↗