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PubMed2006

Metagenomic analysis of coastal RNA virus communities.

RNA viruses infect marine organisms from bacteria to whales, but RNA virus communities in the sea remain essentially unknown. Reverse-transcribed whole-genome shotgun sequencing was used to characterize the diversity of uncultivated marine RNA virus assemblages. A diverse assemblage of RNA viruses, including a broad group of marine picorna-like viruses, and distant relatives of viruses infecting arthropods and higher plants were found. Communities were dominated by distinct genotypes with small genome sizes, and we completely assembled the genomes of several hitherto undiscovered viruses. Our results show that the oceans are a reservoir of previously unknown RNA viruses.

Animals↗
PubMed1976

Legislation relevant to perinatal care.

The legislative process is one route to follow in the attempt to change and improve perinatal care. Payment by the State Crippled Children's Service for medical care of certain costly high-risk neonatal conditions, only to qualified specialists and in centers meeting acceptable standards has had a snowball effect on upgrading neonatal care in this state. Not only has a large network of neonatal care centers and infant transport systems been developed, but there has been a rush especially on the part of nurses, to get special training in neonatal care. This has included not only the care of the sick neonate, but a look at newborn evaluation and resuscitation in the delivery and newborn areas. It is expected that this same center development and education and training process will now be extended to obstetrical care, as there is renewed interest in special care for high-risk mothers because of Assembly Bill 1326. The new hospital perinatal regulations mandate improvement of care in community hospitals where the majority of deliveries take place. The emphasis is on a larger and better educated staff, more concern with patients rights, and provision of a more humanistic family centered care as well as continual evaluation of maternal and neonatal outcome. The greatest limitation has been lack of Health Department staff to provide adequate consultation and surveillance of these services for compliance with the new laws. There has been an approximate 10 per cent reduction in the number of hospitals with maternity services- from 416 in 1968 to 369 today. While much of this consolidation may have been due to the fall in birth rate, these regulations have also contributed to the process. Most important of all, these laws have kept perinatal care constantly in the consciousness of California health care providers and consumers.

California↗
PubMed2026

Community-driven updates for comprehensive long-read metagenomics and enhanced binning in nf-core/mag v5.

SUMMARY: nf-core/mag is a reproducible Nextflow pipeline for best-practice metagenomic de novo assembly and binning within the nf-core framework. Here we present a major update that adds support for long-read-only assembly and bin refinement, includes five new binning tools, expands taxonomic classification to viruses and eukaryotes, and improves bin quality evaluation with new tools and latest databases. Through sustained community-driven development spanning seven years and four primary curator teams, nf-core/mag remains actively developed as an open source workflow for metagenomic analysis, benefiting from contributions from across the broader metagenomics, nf-core, and Nextflow ecosystem. AVAILABILITY AND IMPLEMENTATION: The source code of nf-core/mag v5 is available on GitHub (https://github.com/nf-core/mag) under the open source MIT license, with v5.5.0 source code archived on Zenodo (https://zenodo.org/records/21735731). Documentation is viewable on the nf-core website (https://nf-co.re/mag).

Metagenomics↗
PubMed2000

Central mutation databases--a review.

The Internet has been a key component in the coordination of the diverse group of scientists involved in the Human Genome Project. Nowhere has this contribution been more critical than in the maintenance and exchange of information about genetic variation and mutation. Whereas the majority of DNA sequence is generated and stored by a relatively few sites, a far greater number of researchers investigate the variations in that sequence from sites scattered worldwide. It falls to central databases to utilize the Internet to assemble data from these sites and make them available to the greater human genomic community.

Databases, Factual↗
PubMed2005

Semi-synthetic mammalian gene regulatory networks.

In recent years gene network engineers have celebrated spectacular success: Genetic devices such as epigenetic toggle switches and oscillating networks have been engineered and pioneered a new ever-increasing scientific community known as synthetic biology. While synthetic biology was until recently restricted to network assembly and testing in prokaryotes, decisive advances have been achieved in eukaryotic systems based on current availability of different human-compatible transgene control technologies. Most prominent examples include the epigenetic gene network enabling metastable fully inheritable transgene expression states in mice, artificial regulatory cascades managing multi-level expression control and Boolean-type BioLogic gates supporting near-digital expression readout. The majority of transgene control networks available to date are fully synthetic and integrate artificial extracellular signals in a desired host metabolism-independent manner. Yet, in order to develop their full anticipated therapeutic potential, synthetic transgene control circuits need to be well interconnected with the host cell's regulatory networks in order to enable physiologic control of prosthetic molecular expression units. We have designed three semi-synthetic transcription control networks able to integrate physiologic oxygen levels and artificial antibiotic signals to produce expression readout with NOT IF or NOR-type Boolean logic or discrete multi-level control of several intracellular and secreted model product proteins. Subtle differences in the regulation performance of the endogenous oxygen-sensing system in CHO-K1 and human HT-1080 switched the semi-synthetic network's readout from a classic four-level (high, medium, low, basal) regulatory cascade to a network enabling six discrete transgene expression levels. These findings are in excellent correspondence with a mathematical model. Prosthetic networks, precisely embedded in host regulatory networks and co-fine-tuned by physiologic as well as pharmacologic input signals, will foster future advances in gene therapy and tissue engineering.

Animals↗
PubMed2006

Predicting life expectancy in men with clinically localized prostate cancer.

PURPOSE: The choice of appropriate management for localized prostate cancer depends in part on the estimated life expectancy of a man. Little is known about the accuracy of existing rules for deriving these estimates. We developed a new prediction rule and examined the accuracy of 2 others in our data set. MATERIALS AND METHODS: A retrospective cohort was assembled, consisting of 506 men who were diagnosed or received initial treatment at a community based, tertiary care health center between 1987 and 1989 for clinically localized prostate cancer (stages A, B, I, II or T1-2N0M0) and had at least 13 years of followup. Most patients did not have prostate specific antigen levels available. Proportional hazards regression was used to create a nomogram for deriving survival estimates. Discrimination of the new and external prediction rules was assessed by the c-statistic. Calibration curves compared predicted to actual survival at 10 years. RESULTS: Estimates for survival at 5, 10 and 15 years, and for median life expectancy were determined. Discrimination was modest with a c-statistic of 0.73. The rules of Albertsen and Tewari et al had comparable discrimination in our data with a c-statistic of 0.71 and 0.70, respectively. Predicted life expectancy according to our rule and that of Tewari approximated actual survival experience. Predictions according to the Albertsen study underestimated actual survival in our group but in consistent fashion. CONCLUSIONS: Overall life expectancy can be predicted with a moderate degree of accuracy, sufficient for informing patient-clinician discussions but inadequate as the only determinant of the optimal management approach.

Aged↗
PubMed1993

Conjugal gene transfer to aquatic bacteria detected by the generation of a new phenotype.

An experimental approach based on the assembly of genes of a catabolic pathway was used to detect transconjugants in aquatic communities. Resistance to phenylmercury acetate was established in transconjugants when wide-host-range conjugal plasmids containing merB, the gene encoding organomercurial lyase, were transferred to strains from aquatic communities that had been acclimated to inorganic mercury and thus enriched for populations containing merA, the gene encoding mercuric reductase (T. Barkay, Appl. Environ. Microbiol. 53:2725-2732, 1987). Conjugation was confirmed by using the plasmids' encoded antibiotic resistance patterns and by hybridization with a eukaryotic gene. Three merB-conjugal plasmids, belonging to incompatibility groups W (pGTE16), P1 (pGTE26), and N (pGTE25), were prepared. Transfers by filter matings of pGTE16 and pGTE26 from Pseudomonas aeruginosa PA01 to indigenous strains were at efficiencies of 4.5 x 10 and 4.8 x 10 transconjugant per potential recipient, respectively. These efficiencies were from 1 to 2 orders of magnitude below those observed for intraspecies matings with genetically marked recipients. The third plasmid, pGTE25, was not stably maintained in P. aeruginosa donors, and its transfer from Escherichia coli donors was below the level of detection. Characterized transconjugant strains were shown to be Pseudomonas spp. Potential applications of the described experimental approach in the creation of bacterial populations with new catabolic capabilities in hazardous waste sites and in the detection of transfer of recombinant DNA from engineered microorganisms to indigenous bacteria are discussed.

Journal Article↗
PubMed2022

Preparation of Nucleosome Core Particles Complexed with DNA Repair Factors for Cryo-Electron Microscopy Structural Determination.

DNA repair in the context of chromatin is poorly understood. Biochemical studies using nucleosome core particles, the fundamental repeating unit of chromatin, show most DNA repair enzymes remove DNA damage at reduced rates as compared to free DNA. The molecular details on how base excision repair (BER) enzymes recognize and remove DNA damage in nucleosomes have not been elucidated. However, biochemical BER data of nucleosomal substrates suggest the nucleosome presents different structural barriers dependent on the location of the DNA lesion and the enzyme. This indicates the mechanisms employed by these enzymes to remove DNA damage in free DNA may be different than those employed in nucleosomes. Given that the majority of genomic DNA is assembled into nucleosomes, structural information of these complexes is needed. To date, the scientific community lacks detailed protocols to perform technically feasible structural studies of these complexes. Here, we provide two methods to prepare a complex of two genetically fused BER enzymes (Polymerase β and AP Endonuclease1) bound to a single-nucleotide gap near the entry-exit of the nucleosome for cryo-electron microscopy (cryo-EM) structural determination. Both methods of sample preparation are compatible for vitrifying quality grids via plunge freezing. This protocol can be used as a starting point to prepare other nucleosomal complexes with different BER factors, pioneer transcription factors, and chromatin-modifying enzymes.

Chromatin↗
PubMed2005

[The unfinished agenda for child survival: what role for the integrated management of childhood illness?].

The endorsement by the United Nations General Assembly of the Millennium Development Goals (MDG) and the growing acknowledgment by the international community that child survival is an unfinished agenda created a new momentum for rapid scaling up of effective child health interventions. In this review, the authors discuss the environment in which child health programs are being implemented and the potential role of the integrated management of childhood illness (IMCI) strategy in country efforts to achieve the MDGs. The discussion is based on the conclusions of a multi-country analytic review of the IMCI strategy conducted jointly by DFID, UNICEF, USAID, and WHO as well as the results of another multi-country evaluation coordinated by the WHO on IMCI costs, effectiveness, and impact. The article concludes on the need to increase child health investments and on the potential importance of IMCI in improving child survival. However, the MDGs may not be reached if IMCI is not implemented in conjunction with other strategies to reduce mortality during the first days of life and to strengthen the health system. The authors also stress the need to increase research on mechanisms to scale up delivery of existing public health interventions.

Child↗
PubMed2000

Burger King, Dunkin Donuts and community mental health care.

This paper describes the patchwork of cottage industries and human warehousing composing Montréal's 'community mental health care' system. It examines the ways in which this system's clients assemble a collage of ad hoc facilities including homeless shelters, rooming houses, food banks and soup kitchens through which they pursue the fragmented task of daily survival. In their various forms of transit around the city, released psychiatric patients, who rotate in and out of the local psychiatric wards, construe the grammar of urban space. In examining their use of key city sites - malls, fast food outlets, churches and the streets - it becomes apparent that the 'mad' have a particular relationship to these places which they pass through and use on certain terms. Examining the nature of their journeys, the scenes on which they are set and the social relationships of space in play, it is evident that the 'mad' have a particular (dialogical) relationship to the city: a relationship which they share with other, multiply disenfranchised people. This raises significant social questions concerning the politics of city space, and the kinds of fragmented lives and forms of subjectivity that they produce.

Adolescent↗
PubMed2026

Benchmarking DNA extraction protocols across use cases for culture-independent Nanopore metagenomics.

Oxford Nanopore Technologies (ONT) sequencing offers several advantages for metagenomics, including long reads, rapid turnaround, low upfront cost, scalability and portability. However, for ONT metagenomics, DNA yield, quality and integrity are important considerations when selecting an extraction method. Many metagenomic extraction methods use harsh lysis conditions to extract a wide range of species and provide an accurate community composition, but these conditions can compromise DNA fragment length. Therefore, extraction methods for ONT metagenomics must balance DNA shearing and recovery with representative community lysis. We systematically evaluated DNA extraction methods for ONT metagenomic sequencing using a use case-oriented framework. Among nearly 50 extraction methods screened, 7 were selected for detailed comparison based on suitability for metagenomics, variation in methodology, availability, cost and processing time: Norgen BioTek Corp's Stool DNA Isolation (NG), Zymo Research's ZymoBIOMICS Quick-DNA HMW MagBead (ZMG), Qiagen's DNeasy Blood and Tissue (QBT), Macherey-Nagel's NucleoMag DNA Microbiome (MN), Zymo Research's ZymoBIOMICS DNA Mini Prep (ZMI), Qiagen's DNeasy PowerSoil/QIAamp PowerFecal Pro (PS) and Qiagen's QIAamp Fast DNA Stool Mini (QIA). Methods were tested using Zymo Research's ZymoBIOMICS Microbial Community Standard (MCS), a matrix-free mock community with known composition. DNA extracts were sequenced on an ONT PromethION using the Rapid Barcoding Kit, except QIA due to insufficient DNA yield. Metrics for the method, DNA extracts, sequencing and genomes were evaluated, revealing trade-offs between methods. The two magnetic bead methods, MN and ZMG, produced the highest mean read length N50 values (13.9 and 16.5 kb, respectively) but showed apparent community compositions skewed towards Gram-negative bacteria. In contrast, ZMI and PS maintained a community composition close to expected, with reduced mean read length N50 values (4.5 vs. 7.5 kb). Performance across various metrics is presented in the context of the following use cases: maximizing genome coverage and assembly completeness, preserving composition accuracy, targeting specific species and limiting required resources (equipment, time or budget). The metrics and use case considerations presented offer practical guidance for informed selection of DNA extraction methods for ONT metagenomics. For accurate community composition, ZMI or PS are recommended, while PS and ZMG perform best at maximizing genome coverage and assembly completeness. NG and QBT may be the most economical options, though performance trade-offs were observed. Finally, PS may be the preferred method for time-sensitive diagnostic or field applications.

Metagenomics↗
PubMed2006

Condom and sexual abstinence talk in the Malawi National Assembly.

BACKGROUND: Correct and consistent use of condoms has been reported as effective in the prevention of transmission of HIV. There have been many studies reporting on attitudes (perceptions) of communities on condoms and other aspects of HIV and AIDS and yet there is paucity of data on the perception towards condoms and abstinence by law makers. OBJECTIVE: To determine perceptions of Members of Parliament in Malawi towards condoms. METHODS: A qualitative study utilising parliamentary Hansards to describe the discussions about condoms and abstinence in the National Assembly 1999-2004. Content and discourse analyses were used. RESULTS: In general, Members of Parliament had negative attitudes towards extra- and/or pre-marital sexual intercourse, condom promotion and use. Sexual abstinence amongst non-married persons was preferred as opposed to condom use. Condom use was not perceived as an effective way of controlling the spread of HIV. Some MPs though called for a change in mind-set so as to allow use of condoms in prisons, in order to prevent transmission of infection from prisoners to the general community once the prisoners were released. CONCLUSION: This study confirms that health interventions such as condoms are not perceived neutrally and may be construed as the enemy of society.

Adult↗
PubMed2006

Vertical transmission of diverse microbes in the tropical sponge Corticium sp.

Sponges are host to extremely diverse bacterial communities, some of which appear to be spatiotemporally stable, though how these consistent associations are assembled and maintained from one sponge generation to the next is not well understood. Here we report that a diverse group of microbes, including both bacteria and archaea, is consistently present in aggregates within embryos of the tropical sponge Corticium sp. The major taxonomic groups represented in bacterial 16S rRNA sequences amplified from the embryos are similar to those previously described in a variety of marine sponges. Three selected bacterial taxa, representing proteobacteria, actinobacteria, and a clade including recently described sponge-associated bacteria, were tested and found to be present in all adult samples tested over a 3-year period and in the embryos throughout development. Specific probes were used in fluorescence in situ hybridization to localize cells of the three types in the embryos and mesohyl. This study confirms the vertical transmission of multiple, phylogenetically diverse microorganisms in a marine sponge, and our findings lay the foundation for future work on exploring vertical transmission of specific, yet diverse, microbial assemblages in marine sponges.

Animals↗
PubMed2006

Cancer chemoprevention and cancer preventive vaccines--a call to action: leaders of diverse stakeholder groups present strategies for overcoming multiple barriers to meet an urgent need.

The emerging field of cancer prevention through chemoprevention agents and cancer vaccines offers significant promise for reducing suffering and death from cancer. However, that promise may not be kept unless major barriers to progress are lowered or eliminated. Among the most significant barriers are the relatively small investment from government and industry in research and development of cancer preventive agents; a predominant emphasis of translational cancer research on therapeutic interventions for metastatic or advanced cancer; complexities of prevention trial design; a relatively uncharted Food and Drug Administration (FDA) approval process for preventive agents; insufficient public and patient understanding of the importance and potential for cancer preventive measures, with consequent unpredictable public and patient willingness to take preventive agents; an uncertain reimbursement from payors; and limitations in patent law, liability protection, and data package exclusivity that undermine the opportunity for recouping investment. Viewed individually or collectively, each of these barriers serves as a substantial deterrent to intellectual and financial investment by all sectors of the cancer community. In an effort to ultimately overcome these barriers, a Cancer Prevention Research Summit was assembled June 12-13, 2006 in Bethesda, Maryland, organized by C-Change with support from the AACR. The Summit brought together some 120 leaders from private, public, and not-for-profit entities, including cancer researchers and clinicians; federal health officials; regulatory agency representatives; pharmaceutical, biotech, and food industry leaders; patent attorneys; economists; public and private provider group executives; and advocates. Participants engaged in a detailed process to more carefully define the major barriers, identify potential solutions, and formulate initial priorities and recommendations for action. At the conclusion of this dialogue among experts, the following recommended actions were outlined: define policy solutions to patent, intellectual property, and liability law barriers; create an advisory document about the approval process for cancer chemopreventive agents and vaccines for the FDA; develop new design models for cancer chemopreventive clinical trials; outline the business case for chemopreventive agents and vaccines for federal research agencies, payors and investors; and implement a communications strategy to increase public awareness about the importance of chemoprevention and cancer preventive vaccines.

Anticarcinogenic Agents↗
PubMed1999

Comorbidity in arthritis.

OBJECTIVE: To describe the relative frequency of selected comorbidities in 2 population based prevalence cohorts of patients with rheumatoid arthritis (RA) and osteoarthritis (OA) compared to age and sex matched community controls. METHODS: Using the population based data resources of the Rochester Epidemiology Project, we assembled 3 prevalence cohorts of all residents of Olmsted County, Minnesota, with RA (1987 American College of Rheumatology criteria) and age and sex matched controls without arthritis on January 1, 1965, January 1, 1975, and January 1, 1985. Cases and controls were followed longitudinally through their complete (inpatient and outpatient) medical records beginning 10 years prior to the prevalence (or index) date until death, migration from the county, or January 1, 1995. Comorbidity was assessed yearly using the Charlson Comorbidity Index and the Index of Co-existent Diseases (ICED). Descriptive statistics were used to illustrate the baseline characteristics of the study population and the frequency of individual comorbidities in each of the 3 groups over the followup period. Cox proportional hazards modeling was used to assess the risk for each individual comorbidity among patients with arthritis compared to controls and to identify significant predictors of an increase in comorbidity level over time. RESULTS: Our study population included 450 RA, 441 OA, and 891 control subjects. The age and sex distributions of cases and their controls were similar. Over the followup period, patients with RA had a higher likelihood of developing congestive heart failure, chronic pulmonary disease, dementia, and peptic ulcer disease, while cases with OA had a significantly higher risk of developing peptic ulcer disease and renal disease. Among patients with either RA or OA, age, male sex, and baseline comorbidity were significant predictors of a rise in comorbidity. The presence of RA was a highly significant predictor of a rise in comorbidity from one year to the next, even after controlling for the effects of age, sex, and baseline comorbidity (p = 0.0004 for the Charlson and p = 0.006 for the ICED). CONCLUSION: These data indicate that the burden of illness among people with arthritis is higher than for nonarthritics and that this burden appears to be increasing over time, particularly in RA. These results suggest that specialized chronic disease care will be increasingly important for the future health care needs of people with RA.

Arthritis, Rheumatoid↗
PubMed1992

A statistical analysis of successional patterns in carrion-arthropod assemblages: implications for forensic entomology and determination of the postmortem interval.

A set of statistical protocols is proposed for analyzing carrion-arthropod succession in forensic entomology investigations. A total of 23 carrion-arthropod data sets from temperate, tropical, desert, and coastal environments were assembled in a standard format and analyzed using randomization tests and methods derived from quantitative community ecology. The data were analyzed in three ways. First, patterns of arthropod visitation on nonhuman carcasses were analyzed in each of the 23 cases. Analysis revealed two groups of taxa: those that persist on the carcass over a single time interval (= nonreoccurring taxa, 80% of the taxa) and those that appear, leave, and reappear over time on the carcass (= reoccurring taxa, 20%). Reoccurring taxa, which can confound estimation of the postmortem interval (PMI), were found in 6 classes, 12 orders, and 29 taxonomic families of arthropods, including some forensically important taxa (for example, calliphorids, sarcophagids, histerids). The recognition that reoccurring taxa exist and that they are found in forensically important groups is an early step toward factoring in their potential importance in future entomological investigations. Second, temporal changes in the taxonomic composition of the carrion-arthropod community were studied by quantifying the degree of taxonomic similarity between pairwise combinations of time-specific samples of the succession. In 13 of the 18 illustrated cases, the midsuccessional samples, owing to their higher species richness, were taxonomically more similar to all other pairwise samples, on the average, than early and late successional samples which were poorer in species. Variability in taxonomic composition is the norm for most periods of the succession; however, in 17 of the 23 cases, some successional periods (particularly endpoint samples) revealed no changes in arthropod species composition (= matching sample-pairs). When applied to medicolegal cases, it is suggested that data sets with large fractions of matching sample-pairs should produce wider-ranging PMI estimates, on the average, than data sets with smaller fractions of matching sample-pairs. Third, Monte Carlo simulation was applied to each of the 23 assemblages to test specific hypotheses about community-wide patterns of arthropod visitation times on nonhuman carcasses. Simulation results revealed that arthropod residence times in the majority of cases (13 or 56%) followed a "clumped" succession model, whereas, the remaining 10 cases (44%) showed a more "uniform" spacing pattern of residence times on carcasses. Comparison of species accumulation curves for observed and simulated data further revealed that among the 13 "clumped" cases, most (9 or 69%) followed a "clumped, early" model (rather than "clumped, midterm" or "clumped, late" models).(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗
PubMedDate not supplied

Evaluation of the British Columbia AIDS Information Line.

We evaluated implementation of the British Columbia AIDS Information Line during its initial 15 weeks of operation. Data collected during daily operation of the line included call frequency, caller characteristics, response patterns, caller concerns and community referrals. Information on activities and resources required to implement the AIDS Line was also assembled. The study concluded that the advertising campaign sponsored by the provincial government and other AIDS-related media events had a strong impact on the frequency of calls made to the AIDS Line. However, the effect of both advertising and media events was of relatively short duration, suggesting that utilization of an AIDS information line is dependent on continuing promotional activities. The evaluation results demonstrate the importance of continuous collection of data online utilization, to track public awareness of and response to AIDS-related issues, and to facilitate planning of public education.

Acquired Immunodeficiency Syndrome↗