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PubMed2005

Parasite species coexistence and limiting similarity: a multiscale look at phylogenetic, functional and reproductive distances.

The factors that control biodiversity have been the focus of numerous recent investigations; these include species interactions, speciation, environmental gradients and heterogeneity, all of these operating differently at each observation scale. We used a null model to examine the influence of two forces shaping the community structure of Dactylogyrus species parasitic on roach (Rutilus rutilus) gills: interspecific competition that might prevent the coexistence of the most similar species and environmental filters that might result in the most similar species coexisting together. The study was carried out on two sets of fish from two different localities in the Morava river basin (Czech Republic) to evaluate the consistency of the results across host populations, and at three different scales of observation to test for the scale dependence of assembly rules. In decreasing order, from largest to smallest, the three spatial scales investigated were: the individual fish, the individual gill arch and individual sections of each gill arch. The similarity between pairs of parasite species was measured using three different criteria: (1) phylogeny, (2) quantitative functional traits consisting of parasite size and morphometric measurements of the attachment organ's sclerotized parts and (3) qualitative attributes of reproductive organs. First, our study reveals a strong conservatism of ecological characters for the nine Dactylogyrus parasite species, in particular regarding the attributes of their copulatory organs. Second, our study did not find any limitation of similarity among coexisting Dactylogyrus species due to interspecific competition, irrespective of the scale and the similarity measures considered. Conversely, our results support the niche filtering hypothesis, preventing the co-occurrence of species too dissimilar from one another. This process is particularly apparent at the scale of the individual fish and for functional traits associated with the hard parts of the parasites' attachment organs. In both localities, the Dactylogyrus species that occur on the same fish individuals tend to have similar values for the haptor dimensions. Our study supports previous studies on monogenean parasite communities indicating a weak influence of competition as a structuring force, but it goes a step further by identifying environmental filtering as a key process shaping these communities.

Animals↗

PubMed2026

nf-core/magmap: Map metatranscriptomes to large collections of genomes.

SUMMARY: The lack of publicly available reference genomes has forced annotation of metatranscriptomes to either use direct alignment of sequence reads to reference databases or de novo assembly. As more and more natural environments are covered by metagenomic surveys, this is rapidly changing. This opens up the possibility of genome-resolved studies of prokaryotic metatranscriptomes by mapping to genomes from public repositories or metagenome-assembled genomes derived from the same environment. Here, we present the nf-core/magmap pipeline that provides a reproducible, easy-to-access, and well-documented workflow for selecting reference genomes, mapping to them, and quantifying features. Genomes can be drawn from public sources or originate from private collections. The pipeline is primarily aimed at prokaryotic communities but can, together with collections of reference mature gene sequences, also be applied to eukaryotes. AVAILABILITY AND IMPLEMENTATION: The nf-core/magmap pipeline is implemented in Nextflow and part of the nf-core collaboration. The pipeline is available at the nf-core website (https://nf-co.re/magmap) and GitHub (https://github.com/nf-core/magmap).

Software↗

PubMed1989

Research design and analysis issues.

The overall perspective of this article is the need for researchers of school-based health promotion to make more progressive use of existing statistical methods to improve both the rigor and the efficiency of school-based experiments. Investigative teams working in the school setting have an advantage over health education researchers working in communities or worksites in that they have greater choice of the experimental unit and usually easier access to large clusters of units. They are, therefore, in a position to make optimal use of a wide variety of experimental designs and observation strategies. In order to make full use of this advantage, however, researchers in this field need to assemble multidisciplinary teams, including researchers from other fields who are not restricted by the traditional approaches evident in many of the current school studies. Such teams should include statisticians and epidemiologists who have broadly-based experimental design and survey experience to work with the health educators and other behavioral and biomedical scientists.

Data Interpretation, Statistical↗

PubMed1990

Communication and health--health as an ecosystem.

The importance of communication in public health is described with reference to recent experiences in Australia where good progress has been made with certain major public health problems. There has been a 30% fall in road accident deaths and a 40% fall in deaths from coronary heart disease, and a smoke free environment has been established in public places and in the work place. These successes depended on effective communication based on appropriate data. Evaluation data have also been used to keep the public informed and to reinforce the message. The cooperation of the media has been most important in stimulating a new awareness of health and the opportunities for self help and community initiatives. In central Australia, new initiatives involving the Central Australian Aboriginal Congress have led to an improvement in the health of Aborigines, the training of Aborigines as health workers and the development of a Centre for Appropriate Technology at the Alice Springs College of Technical and Further Education. At the international level, Australia sponsored a World Health Assembly resolution in 1986 calling for the elimination of iodine deficiency disorders. With the support of the Australian International Development Assistance Bureau and the United Nations Children's Fund (UNICEF), an international expert group of scientists and public health professionals, the International Council for Control of Iodine Deficiency Disorders (ICCIDD), based in Adelaide, has been able to work with the World Health Organization (WHO) and UNICEF in the development of an international public health programme aimed at eliminating iodine deficiency disorders by the year 2000. The ICCIDD is a new model for communication and action in international health which is now being advocated for other areas.

Breath Tests↗

PubMed1976

Rape evidence kit: simplified procedures for the emergency department.

The crime of rape requires medical evaluation and therapy concomitant with the collection of legal evidence for potential prosecution. A practical, inexpensive evidence kit has been disigned that meets the needs of the local health department, police department, hospital emergency centers, and district attorney personnel. Costs of assembly and specimen analysis are assumed by the police department. Chain of custody is assured through tamper-proof bags, appropriate reporting forms and police involvement in specimen pick-up. Victims participate in chain of custody by sharing in collection and authorization. The requirement for physician appearance in court is thus lessened. Standardization of examination and reporting prompts all community hospitals to share in examinations, preventing over loading of a single, busy facility. Six months' experience had borne out the anticipated simplification of collection, standardization of reporting, and reduction of physician involvement in legal procedures.

Emergency Service, Hospital↗

PubMed2006

StellaBase: the Nematostella vectensis Genomics Database.

StellaBase, the Nematostella vectensis Genomics Database, is a web-based resource that will facilitate desktop and bench-top studies of the starlet sea anemone. Nematostella is an emerging model organism that has already proven useful for addressing fundamental questions in developmental evolution and evolutionary genomics. StellaBase allows users to query the assembled Nematostella genome, a confirmed gene library, and a predicted genome using both keyword and homology based search functions. Data provided by these searches will elucidate gene family evolution in early animals. Unique research tools, including a Nematostella genetic stock library, a primer library, a literature repository and a gene expression library will provide support to the burgeoning Nematostella research community. The development of StellaBase accompanies significant upgrades to CnidBase, the Cnidarian Evolutionary Genomics Database. With the completion of the first sequenced cnidarian genome, genome comparison tools have been added to CnidBase. In addition, StellaBase provides a framework for the integration of additional species-specific databases into CnidBase. StellaBase is available at http://www.stellabase.org.

Animals↗

PubMed1988

CHA task force prepares report on care of elderly.

The CHA Task Force on Long Term Care Policy is examining social, spiritual, and economic factors related to America's growing elderly population and to the ways in which society will respond to their special needs. The task force is working to: Articulate the Church's theological and ethical basis for interest in the needs of the elderly, and describe related justice implications Identify the concerns of the elderly, with emphasis on healthcare Identify the Church community's existing approaches to meeting the needs Identify existing resources in the larger community Identify ways in which the Church community can coordinate resources in service of the elderly Identify and recommend for advocacy private and public sector mechanisms for financing long-term healthcare for the frail elderly The task force expects to present a final draft of recommendations to the CHA board in April. The book will be presented to the public at the 73rd Annual Catholic Health Assembly in Nashville, TN, June 19 to 22.

Activities of Daily Living↗

PubMed2026

An integrated global resource of wetland microbiomes linking environmental metadata, community profiles, and genome-resolved metabolic traits.

Wetlands are biogeochemical hotspots pivotal to global carbon and nutrient cycling, yet genome-resolved studies across diverse wetland types remain limited. To address this, we constructed a global wetland metagenomic dataset, integrating environmental metadata, community profiles, and genome-resolved metabolic traits. This dataset comprises 1,962 samples-including 129 newly sequenced field-collected samples-from lakes, rivers, paddies, marshes, and coastal wetlands, spanning water, soil, and sediment habitats. We generated comprehensive taxonomic profiles for all 1,962 samples, and used 251 samples to reconstruct 5,704 sample-specific metagenome-assembled genomes (MAGs). These MAGs were subsequently dereplicated to establish a normalized, non-redundant catalog of 4,164 representative genomes. We further mapped gene repertoires to 549 KEGG modules to decode the metabolic potential of all 5,704 MAGs. This dataset depicts an overview of microbial genomic diversity across global wetlands and provides a comprehensive resource for understanding the metabolic capabilities, ecology, and evolution of wetland microbiomes.

Wetlands↗

PubMed2003

Could control of soil-transmitted helminthic infection influence the HIV/AIDS pandemic.

In May 2001, the World Health Assembly (WHA) estimated that two billion people were infected by soil-transmitted helminths (S-THs) and schistosomiasis, worldwide. The WHA urged member states to recognise that there can be synergy between public health control programmes for S-THs, schistosomiasis and other diseases. This is particularly relevant to the new dimension created by the HIV/AIDS epidemics in the same impoverished communities and countries where helminthiasis is hyperendemic. Immunological adaptation between humans and parasitic helminths has developed during evolution. Review of 109 research papers, 76% (83/109) of which, were published between 1995 and February 2002, revealed increasing evidence that this relationship may have created an opportunity for more rapid infection by the human immunodeficiency virus (HIV), as well as quicker progression to AIDS. Moreover, the efficacy of some vaccines against HIV is likely to be impaired by chronic helminthiasis. For this, there is strong, indirect evidence. There is an urgent need for parasitologists, epidemiologists, immunologists and virologists to undertake comprehensive, transdisciplinary research. On the other hand, there is no current evidence that immunosuppression by HIV facilitates helminthic infection. The situation in regard to strongyloidiasis, however, is not yet clear.

Animals↗

PubMed2025

Uncertainty Modeling Outperforms Machine Learning for Microbiome Data Analysis.

Microbiome sequencing measures relative rather than absolute abundances, providing no direct information about total microbial load. Normalization methods attempt to compensate, but rely on strong, often untestable assumptions that can bias inference. Experimental measurements of load (e.g., qPCR, flow cytometry) offer a solution, but remain costly and uncommon. A recent high-profile study proposed that machine learning could bypass this limitation by predicting microbial load from sequencing data alone. To evaluate this claim, we assembled mutt, the largest public database of paired sequencing and load measurements, spanning 35 studies and over 15,000 samples. Using mutt, we show that published machine learning models fail to generalize: on average they perform worse than a naive baseline that always predicted the training set mean. These failures stem from covariate shift-limited shared taxa between studies, differences in community composition, and differences in preprocessing pipelines-that silently derail model inputs. In contrast, Bayesian partially identified models do not attempt to impute microbial load, but instead propagate scale uncertainty through downstream analyses. Across 30 benchmark datasets, Bayesian partially identified models consistently outperformed normalization and machine learning approaches, providing a principled and reproducible foundation for microbiome inference.

16S rRNA-seq↗

PubMed1995

Experience in the development of a postmarketing surveillance network: the pharmacy medication monitoring program.

OBJECTIVE: To describe the pilot and early implementation phase of a system for assembling and recruiting cohorts of patients taking selected prescription medications and prospectively monitoring them for new health events. DESIGN: Prospective observational study, based on telephone interviews, of 1475 patients filling prescriptions for a nonsteroidal antiinflammatory drug (NSAID). Patients were interviewed by telephone using trained interviewers at a central site. Hospitalizations and deaths were followed up and reviewed by an independently physician. SETTING: Community setting in a region of Hamilton, Ontario, Canada. PARTICIPANTS: All consenting patients filling new or repeat prescriptions for NSAIDs at participating pharmacies. MAIN OUTCOME MEASURES: The authors report on the development and assessment of systems for: (1) ongoing recruitment of patients through community pharmacies; (2) data transfer from pharmacies to the coordinating center; (3) surveying patients; (4) classifying, coding, and evaluating new health events; and (5) following up on new serious adverse events. RESULTS: Fifty-one percent of patients approached were recruited, and 83% of these provided completed interviews. For patients picking up their own medications, pharmacy workload varied from 4 to 10 minutes per patient approached. Nineteen percent of patients reported having a new health problem or unusual symptom at the initial telephone interview. Reported health-related events were similar to those described in other studies of NSAIDs. CONCLUSIONS: Most aspects of the monitoring system performed well. One limitation was the low recruitment rate for patients who did not directly drop off or pick up their own prescriptions. Even so, this method of patient accrual may complement alternative monitoring programs.

Adverse Drug Reaction Reporting Systems↗

PubMed2006

A new proposed guidance system for beverage consumption in the United States.

The Beverage Guidance Panel was assembled to provide guidance on the relative health and nutritional benefits and risks of various beverage categories. The beverage panel was initiated by the first author. The Panel's purpose is to attempt to systematically review the literature on beverages and health and provide guidance to the consumer. An additional purpose of the Panel is to develop a deeper dialog among the scientific community on overall beverage consumption patterns in the United States and on the great potential to change this pattern as a way to improve health. Over the past several decades, levels of overweight and obesity have increased across all population groups in the United States. Concurrently, an increased daily intake of 150-300 kcal (for different age-sex groups) has occurred, with approximately 50% of the increased calories coming from the consumption of calorically sweetened beverages. The panel ranked beverages from the lowest to the highest value based on caloric and nutrient contents and related health benefits and risks. Drinking water was ranked as the preferred beverage to fulfill daily water needs and was followed in decreasing value by tea and coffee, low-fat (1.5% or 1%) and skim (nonfat) milk and soy beverages, noncalorically sweetened beverages, beverages with some nutritional benefits (fruit and vegetable juices, whole milk, alcohol, and sports drinks), and calorically sweetened, nutrient-poor beverages. The Panel recommends that the consumption of beverages with no or few calories should take precedence over the consumption of beverages with more calories.

Alcohol Drinking↗

PubMed2026

Flavobacteria consume nitrous oxide produced by partial denitrifiers in coastal sediments.

Nearly one-fifth of global emissions of the potent greenhouse gas nitrous oxide (N2O) originate from the ocean, particularly from nutrient-polluted coastal regions. Permeable (sandy) sediments, which cover half of the continental shelf worldwide, are potential sources of N2O due to increasing nutrient inputs from urbanization and agriculture. Yet, the microbial processes determining N2O emissions in these dynamic and unique ecosystems remain understudied. Here, we combined environmental measurements, bacterial cultivation, and genomic analyses to understand the microbes and processes controlling N2O cycling in permeable sediments from Port Phillip Bay (Australia). We established a genomic resource comprising 249 metagenome-assembled genomes and 95 new isolate genomes. Genome-based metabolic reconstructions and culture-based gas measurements revealed that diverse bacteria in these sediments produce N2O through incomplete denitrification pathways. However, these bacteria co-occurred with highly abundant clade II N2O-reducing bacteria from the Flavobacteriaceae family. Kinetic profiling showed that both clade II nosZ flavobacterial isolates and whole sand communities exhibited a low apparent affinity for N2O under the tested experimental conditions, expanding the currently limited kinetic data available for N2O reducing microorganisms from coastal permeable sediments, including flavobacterial clade II N2O reducers. Collectively, these findings indicate that abundant N₂O reducing communities can substantially consume N2O within permeable sediments, thus limiting N2O accumulation despite active N2O production. Together with previous hydrodynamic models predicting low N2O release from permeable sediments, our results highlight the important role of specialized microbial communities in regulating N2O cycling under increasing nutrient pollution.

Nitrous Oxide↗

PubMed2002

Using virtual reality technology for aircraft visual inspection training: presence and comparison studies.

The aircraft maintenance industry is a complex system consisting of several interrelated human and machine components. Recognizing this, the Federal Aviation Administration (FAA) has pursued human factors related research. In the maintenance arena the research has focused on the aircraft inspection process and the aircraft inspector. Training has been identified as the primary intervention strategy to improve the quality and reliability of aircraft inspection. If training is to be successful, it is critical that we provide aircraft inspectors with appropriate training tools and environment. In response to this need, the paper outlines the development of a virtual reality (VR) system for aircraft inspection training. VR has generated much excitement but little formal proof that it is useful. However, since VR interfaces are difficult and expensive to build, the computer graphics community needs to be able to predict which applications will benefit from VR. To address this important issue, this research measured the degree of immersion and presence felt by subjects in a virtual environment simulator. Specifically, it conducted two controlled studies using the VR system developed for visual inspection task of an aft-cargo bay at the VR Lab of Clemson University. Beyond assembling the visual inspection virtual environment, a significant goal of this project was to explore subjective presence as it affects task performance. The results of this study indicated that the system scored high on the issues related to the degree of presence felt by the subjects. As a next logical step, this study, then, compared VR to an existing PC-based aircraft inspection simulator. The results showed that the VR system was better and preferred over the PC-based training tool.

Adult↗

PubMed1985

Prejudice and neurotic symptomatology among white South Africans.

Van der Spuy and Shamley (1978) have assembled evidence suggesting chronically elevated levels of neurotic symptomatology among both white and black South Africans. They have argued that these elevated levels could be attributed to the experience of racial discrimination and prejudice. New data obtained from a reasonably representative national sample of white South Africans (N = 782) did reveal symptom scores substantially and significantly higher than scores previously reported for a large community sample in the United States. On the other hand, partial correlational analyses did not indicate any consistent pattern of association between antiblack prejudice and symptom scores among white South Africans. Therefore, intergroup conflict in a sharply stratified society may affect symptomatic levels in individuals by influencing the general quality of social life.

Adolescent↗

PubMed1996

AB 3632 mental health entitlement for special education students in California: aspects of the Los Angeles experience.

California Assembly Bill (AB) 3632, passed in 1984, ushered in an era of entitlement to mental health services for schoolchildren with serious emotional disturbances. This article examines the development of the law, the children's public mental health context in Los Angeles County, and the significant impact of the legislation on distribution of mental health services in Los Angeles County and in one Los Angeles area community mental health center. Countywide and agency data are presented that document AB 3632 and regular mental health service provision differences in gender, age, ethnic, income, and language domains and, at the agency level, an increasing proportion of AB 3632 clients. Implications of AB 3632 service provision in relation to provision of mental health services to children in general are reviewed.

Adolescent↗

PubMed2003

TRAP: Tandem Repeat Assembly Program produces improved shotgun assemblies of repetitive sequences.

The software commonly used for assembly of shotgun sequence data has several limitations. One such limitation becomes obvious when repetitive sequences are encountered. Shotgun assembly is a difficult task, even for non-repetitive regions, but the use of quality assessments of the data and efficient matching algorithms have made it possible to assemble most sequences efficiently. In the case of highly repetitive sequences, however, these algorithms fail to distinguish between sequencing errors and single base differences in regions containing nearly identical repeats. None of the currently available fragment assembly programs are able to correctly assemble highly similar repetitive data, and we, therefore, present a novel shotgun assembly program, Tandem Repeat Assembly Program (TRAP). The main feature of this program is the ability to separate long repetitive regions from each other by distinguishing single base substitutions as well as insertions/deletions from sequencing errors. This is accomplished by using a novel multiple-alignment based analysis method. Since repeats are a common complication in most sequencing projects, this software should be of use for the whole sequencing community.

Algorithms↗

PubMed2005

Neutralizing antibodies against poliovirus serotypes among children in southwest Nigeria.

In May 1988, the World Health Assembly resolved to eradicate poliomyelitis globally by the year 2000. Despite the reported success in national immunization days, acute flaccid paralysis surveillance and accelerated efforts to meet the deadline including 'mopping-up' were executed in 1999 and subsequent years. Nigeria remains one of the major reservoirs for wild poliovirus transmission. Neutralizing antibody titre to the three poliovirus serotypes was determined among children from different communities in southwest of Nigeria, and analysed by age, gender and location. About 0.5-2 ml of blood sample was collected by venepuncture from each child. Aliquot of serum from each blood sample was inactivated prior to neutralization test by the beta method for poliovirus antibodies. A total of 347 (59.6 per cent) out of 500 and 82 children enrolled for the study had at least antibody titre of 1:8 against each of the three poliovirus serotypes. Immunity level to the three poliovirus serotypes increased with age and peaked in children aged 4-6 years. Seven (53.8 per cent) out of 13 unvaccinated children tested in the study had detectable neutralizing antibody to the three serotypes. Immunity pattern of P2 > P1 and P3 was observed but no correlation between gender and antibody to the poliovirus serotypes. The populations had 59.6 per cent herd immunity for the three poliovirus serotypes. In a country with high incidence of poliomyelitis this situation leaves a high number of non-immunized children at the risk of infection with one or more poliovirus serotypes.

Antibodies, Viral↗