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PubMed2025

Characterization of microbial dark matter at scale with MetaSBT and taxonomy-aware Sequence Bloom Trees.

Metagenomics has become a powerful tool for studying microbial communities, allowing researchers to investigate microbial diversity within complex environmental samples. Recent advances in sequencing technology have enabled the recovery of near-complete microbial genomes directly from metagenomic samples, also known as metagenome-assembled genomes (MAGs). However, accurately characterizing these genomes remains a significant challenge due to the presence of sequencing errors, incomplete assembly, and contamination. Here we present MetaSBT, a new tool for organizing, indexing, and characterizing microbial reference genomes and MAGs. It is able to identify clusters of genomes at all seven taxonomic levels, from the kingdom all the way down to the species level, using the Sequence Bloom Tree (SBT) data structure that relies on Bloom Filters (BFs) to index massive amounts of genomes based on their k-mers composition. We have built an initial set of databases composed of over 190 thousand viral genomes from NCBI GenBank and public sources grouped into sequence consistent clusters at different taxonomic levels, making it the first software solution for the classification of viruses at different ranks, including still unknown ones. This results in the definition of over 40 thousand species clusters where ~80% do not match with any known viral species in reference databases to date. Furthermore, we show how our databases can be used as a new basis for existing quantitative metagenomic profilers to unlock the detection of unknown microbes and the estimation of their abundance in metagenomic samples. Finally, the framework is released open-source and, along with its public databases, is fully integrated into the Galaxy Platform enabling broad accessibility.

metagenome-assembled genomes↗

PubMed2005

Metagenomics for studying unculturable microorganisms: cutting the Gordian knot.

More than 99% of prokaryotes in the environment cannot be cultured in the laboratory, a phenomenon that limits our understanding of microbial physiology, genetics, and community ecology. One way around this problem is metagenomics, the culture-independent cloning and analysis of microbial DNA extracted directly from an environmental sample. Recent advances in shotgun sequencing and computational methods for genome assembly have advanced the field of metagenomics to provide glimpses into the life of uncultured microorganisms.

Genetics, Microbial↗

PubMed1982

Maternal nutrition in the 1980s.

Tight money, limited resources, and stringent accountability will characterize maternal nutrition in the 1980s. Our communities will continue to need the best available services. But those needs will have to be much better defined so that funds can be allocated more wisely. The urgency of the times requires that we assemble our baseline data on health and nutrition as rapidly as possible so that we can consolidate the achievements of the 1970s with a minimum of loss. Only then can we generate plans and expectations that fit the years ahead.

Cost-Benefit Analysis↗

PubMed1998

Part I. A look at population-based medical care.

Recent trends toward managed health care have generated interest in developing strategies to manage the health care of a population as a whole. Population-based medicine places the individual patient within the context of the larger community, which is composed of both sick and well individuals; when viewed in these terms, only a small proportion of the people who consult a primary care physician are at risk for substantial morbidity. However, the physician serves as the central figure for delivering population-based health care to the entire community. Many strategies for population-based care contain the following 4 basic elements: 1. Identifying the health and disease states that are likely to be responsive to population-based care, 2. Applying principles of epidemiology to define the population-of-interest, 3. Assembling a multidisciplinary team, and 4. Building information systems to support ongoing surveillance of population-based care. To date, most of the published examples of population-based management have been conducted in managed care environments, but population-based management may also be used by a single physician practice or a small group practice. Programs aimed at health promotion or disease prevention are among the easiest to implement. By examining the results of an entire population with a given condition, physicians and their teams may begin to identify ways to improve the overall delivery of care, either by establishing new procedures or improving old ones.

Community Health Planning↗

PubMed1993

A preliminary study of reproductive outcomes of female maquiladora workers in Tijuana, Mexico.

Maquiladoras are plants on the Mexican side of the United States-Mexico border which are used largely by U.S. manufacturers to assemble premanufactured parts. We examined reproductive outcomes of women employed in electronics (N = 120) and garment (N = 121) maquiladora work compared to women employed in the service sector (N = 119) in Tijuana, Mexico. Women recruited by community health workers were interviewed about their reproductive history, sociodemographic characteristics, health behaviors, and characteristics of their current job. Length of regular menstrual cycle in the past year as well as time of conception and rates of fetal loss in the most recent pregnancy were similar across occupational groups. However, infants of garment maquiladora workers were 653 g lighter (95% confidence interval [CI]: -1,041 g, -265 g) and infants of electronic maquiladora workers were 337 g lighter (95% CI: -682 g, 9 g) than infants of service workers after adjusting for potential confounders. The cause of these differences remains unclear.

Abortion, Spontaneous↗

PubMed2005

[Validity of clinical records and information systems in studies of health-care delivery in primary care].

OBJECTIVES: To examine how well the clinical process was recorded in the clinical history (CH), and care delivery on the activity sheet (AS). To assemble a series of recommendations on the validity of these documents for recording health care delivery. DESIGN: Multi-centred, observational, and cross-sectonal study. SETTING: Four medical clinics at 12 health centres in the Community of Valencia, Spain. PARTICIPANTS: There were 2051 attendances, with 284 CH and 407 AS involved. Main measurements and results. The information recorded by doctors in the CH and on the AS was validated by external observers who collected directly at the consultation the working day's entire care activity. The following was analysed: 1) in the CH, filling out of the "SOAP" form (basic info.); 2) on the AS, mean per professional per day of scheduled and on-demand patients, home visits and length of consultations; 3) information in the documents validated on the organisation of consultations; 4) analysis of care delivery according to how predictable it is and its clinical content; 5) clinical practice guidelines with validity and clinical usefulness indicators and reliability index (kappa). CONCLUSIONS: The documents validated do not properly reflect the reality of health care demand. There was an under-recording bias and validity problems that may limit their usefulness as sources of information for health care planning and management.

Cross-Sectional Studies↗

PubMed1983

Consumerism in hospitals--hospitals are, or should be, for people.

The factory situation: are people seen as number patients or are they handled with care and compassion? Hospital care should aim at treatment of the whole person--role of non clinical services within hospitals, partnership with community--role of parents; better communication needed between treating professionals and patients--would reduce complaints and possible litigation; people wish to be partners with health professionals in their own treatment and recovery not articles on an assembly line; rights of patients to be given full facts of their illness and prospects for recovery. Who "pays the piper"? Medical audit, accountability, peer review; iatrogenesis or "doctor induced" illness e.g. adverse reaction to prescribed drugs, hospital induced infections, malnutrition, faulty diagnosis or failure to diagnose. Who motivates the provider and support personnel and how? Institutionalisation and its effects on treatment and recovery, attitudes by providers and receptors. New trends in treatment patterns and delivery facilities: high technology, birthing centers, is there a role for alternative professions within hospitals? Who looks after the consumer? Ombudsman , medical boards, licensing authorities, Australian Council on Hospital Standards.

Australia↗

PubMed2005

Ultrasonically controlled release of ciprofloxacin from self-assembled coatings on poly(2-hydroxyethyl methacrylate) hydrogels for Pseudomonas aeruginosa biofilm prevention.

Indwelling prostheses and subcutaneous delivery devices are now routinely and indispensably employed in medical practice. However, these same devices often provide a highly suitable surface for bacterial adhesion and colonization, resulting in the formation of complex, differentiated, and structured communities known as biofilms. The University of Washington Engineered Biomaterials group has developed a novel drug delivery polymer matrix consisting of a poly(2-hydroxyethyl methacrylate) hydrogel coated with ordered methylene chains that form an ultrasound-responsive coating. This system was able to retain the drug ciprofloxacin inside the polymer in the absence of ultrasound but showed significant drug release when low-intensity ultrasound was applied. To assess the potential of this controlled drug delivery system for the targeting of infectious biofilms, we monitored the accumulation of Pseudomonas aeruginosa biofilms grown on hydrogels with and without ciprofloxacin and with and without exposure to ultrasound (a 43-kHz ultrasonic bath for 20 min daily) in an in vitro flow cell study. Biofilm accumulation from confocal images was quantified and statistically compared by using COMSTAT biofilm analysis software. Biofilm accumulation on ciprofloxacin-loaded hydrogels with ultrasound-induced drug delivery was significantly reduced compared to the accumulation of biofilms grown in control experiments. The results of these studies may ultimately facilitate the future development of medical devices sensitive to external ultrasonic impulses and capable of treating or preventing biofilm growth via "on-demand" drug release.

Anti-Infective Agents↗

PubMed2006

Reducing under-five mortality through Hôpital Albert Schweitzer's integrated system in Haiti.

BACKGROUND: The degree to which local health systems contribute to reductions in under-five mortality in severely impoverished settings has not been well documented. The current study compares the under-five mortality in the Hôpital Albert Schweitzer (HAS) Primary Health Care Service Area with that for Haiti in general. HAS provides an integrated system of community-based primary health care services, hospital care and community development. METHODS: A sample of 10% of the women of reproductive age in the HAS service area was interviewed, and 2390 live births and 149 child deaths were documented for the period 1995-99. Under-five mortality rates were computed and compared with rates for Haiti. In addition, available data regarding inputs, processes and outputs for the HAS service area and for Haiti were assembled and compared. RESULTS: Under-five mortality was 58% less in the HAS service area, and mortality for children 12-59 months of age was 76% less. These results were achieved with an input of fewer physicians and hospital beds per capita than is available for Haiti nationwide, but with twice as many graduate nurses and auxiliary nurses per capita than are available nationwide, and with three cadres of health workers that do not exist nationwide: Physician Extenders, Health Agents and Community Health Volunteers. The population coverage of targeted child survival services was generally 1.5-2 times higher in the HAS service area than in rural Haiti. DISCUSSION: These findings support the conclusion that a well-developed system of primary health care, with outreach services to the household level, integrated with hospital referral care and community development programmes, can make a strong contribution to reducing infant and child mortality in severely impoverished settings.

Adolescent↗

PubMed2005

Ruthenium-catalyzed reactions--a treasure trove of atom-economic transformations.

The demand for new chemicals spanning the fields of health care to materials science combined with the pressure to produce these substances in an environmentally benign fashion pose great challenges to the synthetic chemical community. The maximization of synthetic efficiency by the conversion of simple building blocks into complex targets remains a fundamental goal. In this context, ruthenium complexes catalyze a number of non-metathesis conversions and allow the rapid assembly of complex molecules with high selectivity and atom economy. These complexes often exhibit unusual reactivity. Careful consideration of the mechanistic underpinnings of the transformations can lead to the design of new reactions and the discovery of new reactivity.

Alkenes↗

PubMed1999

Fire and resprouting in Mediterranean ecosystems: insights from an external biogeographical region, the mexical shrubland.

We investigated modes of regeneration of dominant species of the mexical vegetation after fire. The mexical shrubland shows a remarkable structural, morphological, and floristic similarity to Mediterranean-type vegetation and is considered a relict of the Madro-Tertiary Geoflora under a non-Mediterranean climate. This vegetation provides an ideal scenario to test the role of fire in Mediterranean ecosystems because historical fire occurrence is absent and the species assembly is constituted mostly by Madro-Tertiary elements and Neotropical species (some of them, endemic species from Mexico). The existence of congeneric species of the California chaparral allows us to determine the regeneration ability of these communities after fire in relation to resprouting and seeding strategies, which are widespread modes reported in the Mediterranean-type vegetation. By the experimental application of fire in the two biogeographical groups of species, we tested the hypothesis that low resprouting ability of California congeneric species (Madro-Tertiary species) after fire would indicate that fire has played an important selective force in the resprouting habit. A low resprouting ability in the Neotropical group of species would suggest that fire has molded the set of species dominating fire-prone environments.Our results indicated that resprouting is a widespread trait in the mexical species characterized by the presence of lignotubers and burls. Resprouting can be considered an ancient trait, probably linked to losses of aboveground biomass, that became a pre-adaptation in Mediterranean fire-prone communities. The Neotropical group of species showed less ability to regenerate after fire, and small plants were more likely to die after disturbance in this group than in the Madro-Tertiary group. The resprouting feature and the seeder strategy of other species after a fire in the mexical shrubland are similar to Mediterranean-type ecosystems, emphasizing their common origin and the relevance of phylogenetic and biogeographical studies to explain current patterns of vegetation.

Journal Article↗

PubMed2026

De novo assembly and authentication of ancient DNA metagenomes with nf-core/mag.

Ancient DNA provides a direct window into the evolutionary processes that have shaped living microbial species today, as well as their now extinct relatives. Advances in both sequencing methods and de novo assembly techniques have not only resulted in a flood of modern metagenomic sequencing data, but they have also allowed palaeogenomicists to retrieve vast amounts of ancient DNA from past microorganisms, including species and strains without modern reference genomes. However, the degraded nature of ancient DNA means that the standard techniques of genome assembly developed for modern DNA are unlikely to perform effectively, unless heavily modified. This hinders the incorporation of ancient data into broader metagenomic studies that would otherwise benefit from having deep time information on the evolution of different microbial species. In this primer and protocol paper, we provide guidance on ways to adapt existing metagenomic de novo assembly processes, including data input, tools, and settings, in order to perform more robustly and effectively on ancient DNA. After assembly, we then further describe how ancient DNA contigs can be identified and validated. The key steps of ancient metagenomic assembly are now integrated in a dedicated ancient DNA mode in the established pipeline nf-core/mag. By introducing support for ancient DNA data in nf-core/mag, we aim to improve the ability of researchers to more regularly integrate de novo assembled ancient microbial data into broader metagenomics studies of microbial ecology and evolution.

DNA, Ancient↗

PubMed1995

Strategic planning futurists need to be capitation-specific and epidemiological.

Strategic planning has always been a proposition of envisioning an organization's future state, then working backward, quarter by quarter, year by year, to plot a course of action. The surer the vision, the surer the course. In our burgeoning capitated environment, the successful provider will clarify a singular vision: to manage health care for a defined population. The key will be to understand the changing needs of covered lives and to prepare the organization to serve those needs. Gone are the days when mere responsiveness to market needs and preferences could secure a hospital's competitive advantage. Nimble, surefooted, practically clairvoyant--the emerging health care leader will listen to reliable epidemiologic information and custom-design its future. Timing is everything. Depending only your market's readiness for capitation, epidemiologic research and planning techniques may not prove critical to your organization for five to seven years. Good thing, too, because a few years may be just the head start many hospitals and health care systems need. Now is the time to lay the groundwork, to cultivate new planning techniques that will work under capitation, and to jettison any outdated modes of strategic thinking. Assemble all the talent and knowledge you need, then give your best minds ample room to do their work.

Capitation Fee↗

PubMed1979

Speak up for children!

During 1979, the International Year of the Child, the United Nations General Assembly has asked its member nations to examine and improve their services for children.

Accident Prevention↗

PubMed2024

Microbial diversity and metabolic pathways linked to benzene degradation in petrochemical-polluted groundwater.

The rapid advance in shotgun metagenome sequencing has enabled us to identify uncultivated functional microorganisms in polluted environments. While aerobic petrochemical-degrading pathways have been extensively studied, the anaerobic mechanisms remain less explored. Here, we conducted a study at a petrochemical-polluted groundwater site in Henan Province, Central China. A total of twelve groundwater monitoring wells were installed to collect groundwater samples. Benzene appeared to be the predominant pollutant, detected in 10 out of 12 samples, with concentrations ranging from 1.4 μg/L to 5,280 μg/L. Due to the low aquifer permeability, pollutant migration occurred slowly, resulting in relatively low benzene concentrations downstream within the heavily polluted area. Deep metagenome sequencing revealed Proteobacteria as the dominant phylum, accounting for over 63 % of total abundances. Microbial α-diversity was low in heavily polluted samples, with community compositions substantially differing from those in lightly polluted samples. dmpK encoding the phenol/toluene 2-monooxygenase was detected across all samples, while the dioxygenase bedC1 was not detected, suggesting that aerobic benzene degradation might occur through monooxygenation. Sequence assembly and binning yielded 350 high-quality metagenome-assembled genomes (MAGs), with 30 MAGs harboring functional genes associated with aerobic or anaerobic benzene degradation. About 80 % of MAGs harboring functional genes associated with anaerobic benzene degradation remained taxonomically unclassified at the genus level, suggesting that our current database coverage of anaerobic benzene-degrading microorganisms is very limited. Furthermore, two genes integral to anaerobic benzene metabolism, i.e, benzoyl-CoA reductase (bamB) and glutaryl-CoA dehydrogenase (acd), were not annotated by metagenome functional analyses but were identified within the MAGs, signifying the importance of integrating both contig-based and MAG-based approaches. Together, our efforts of functional annotation and metagenome binning generate a robust blueprint of microbial functional potentials in petrochemical-polluted groundwater, which is crucial for designing proficient bioremediation strategies.

Groundwater↗

PubMed1995

Construction and validation of risk assessments in a six-year follow-up of forensic patients: a tridimensional analysis.

Evaluations of risk were conducted for 162 Canadian mentally disordered criminal defendants through the assembly of actuarial data, scores from special-to-purpose psychometric instruments, and scaled global predictions of dangerousness to others by clinicians and nonclinical raters. Violent conduct by participants was tracked across legal and medical institutions and the community for a subsequent 6 years, with aggregate violence base rates reaching 62%. Decisions about risk were strongly associated with participant attributes and presentations during forensic interviews, but neither linear regression equations involving background and scale items nor direct discretionary judgments could account for more than 25% of variance in the frequency of outcome violence. Predictive accuracy maximized after 3 years, and was strongest for hospital-based violence. Professional clinicians were no more accurate than nonclinical raters. Implications of these findings for the sociolegal control of violence, and for the resurgent "second generation" of risk research, are explored.

Adult↗

PubMed1995

Case study. Columbia/HCA in Florida: a national strategy played out in a $47 billion market.

The world's largest health management company controls a fourth of Florida's hospital beds and is assembling a full-fledged integrated system, including physician investors. HSL looks at Columbia's key strategies, from geographic encirclement to overwhelming purchasing power. And we listen to critics who warn that Columbia "skims the cream" and abandons communities to maximize profits.

Catchment Area, Health↗

PubMed2006

RetrOryza: a database of the rice LTR-retrotransposons.

Long terminal repeat (LTR)-retrotransposons comprise a significant portion of the rice genome. Their complete characterization is thus necessary if the sequenced genome is to be annotated correctly. In addition, because LTR-retrotransposons can influence the expression of neighboring genes, the complete identification of these elements in the rice genome is essential in order to study their putative functional interactions with the plant genes. The aims of the database are to (i) Assemble a comprehensive dataset of LTR-retrotransposons that includes not only abundant elements, but also low copy number elements. (ii) Provide an interface to efficiently access the resources stored in the database. This interface should also allow the community to annotate these elements. (iii) Provide a means for identifying LTR-retrotransposons inserted near genes. Here we present the results, where 242 complete LTR-retrotransposons have been structurally and functionally annotated. A web interface to the database has been made available (http://www.retroryza.org/), through which the user can annotate a sequence or search for LTR-retrotransposons in the neighborhood of a gene of interest.

Databases, Nucleic Acid↗