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PubMed2026

Metagenomics Reveals Microbial Community Shifts Associated With Contrasting Anthropogenic Impacts in Freshwater Sources of A Coastal Protected Area in Southeastern Brazil.

This study aimed to characterize freshwater microbial communities, environmental drivers, and anthropogenic impact patterns across three sites on Marambaia Island (southeastern Brazil) using metagenomics. Samples collected from freshwater sources used for human consumption were processed through concentration, nucleic acid extraction, and sequencing on the Illumina NextSeq 2000 platform. A total of 67.2 million reads were assembled into 89,230 bacterial contigs, mostly attributed to Gammaproteobacteria, Alphaproteobacteria, and Betaproteobacteria. Sites under lower anthropogenic influence exhibited higher microbial diversity, whereas impacted sites showed enrichment of opportunistic and fecal-associated genera. A heterogeneous anthropogenic impact profile was observed across sites, corroborated by the proposed Anthropogenic Impact Index (AII). Fourteen antimicrobial resistance genes conferring resistance to beta-lactams, quinolones, sulfonamides, tetracyclines, and macrolides were detected predominantly in sewage-impacted areas, indicating potential diffuse contamination. Redundancy analysis revealed that environmental variables explained 88.1% of microbial community variation, with conductivity, salinity, and turbidity as key drivers. These findings demonstrate the applicability of metagenomics as a powerful tool for assessing microbial diversity, ecological dynamics, and contamination risks in vulnerable freshwater systems.

Brazil↗

PubMed1987

Pollution episodes at Venice related to weather types: an analysis for a better predictability.

In order to obtain a rational strategy for the control and management of emissions from the industrial area of Venice, determination of the air quality is made from different perspectives. A source-receptor oriented approach shows a remarkable scatter of data due to the complex source field and variability of atmospheric conditions at a coastal site. As many pollution episodes are initiated by local diffusion potentials induced by the interaction between topographic irregularities (i.e. Alpine chain and Adriatic Sea) and the mesoscale atmospheric circulation system, a correlation between pollution events and synoptic conditions is made. Two periods of two years each were considered, the former characterized by very frequent, moderate episodes, the latter by more rare but potentially more severe episodes, although the emission rate was reduced. Four different criteria (i.e. weather types as classified by the U.K. Meteorological Office, by Borghi and Giuliacci, and by Urbani, and the passage of fronts) are considered and compared in order to describe the synoptic conditions and to make a reasonable prediction of the local dynamic climatology. A risk index (RI) is computed for each weather type. The U.K. classification appears to be the most suitable as it classifies the maximum number of synoptic maps and has the greatest spread of RI, thus making a more sound prediction. The analysis shows that the pollution episodes are associated with instability phenomena, i.e. passage of fronts or the onset of moderate to fresh winds, and not with stationary conditions. Also, the areal extension over which the highest pollution levels are recorded is related to particular weather types. The statistics of the meteorological weather types occurring during the pollution events give satisfactory results for some weather types, especially for those correlating highly or poorly with pollution events.

Air Pollution↗

PubMed2006

Moving from evidence to practice in the care of patients who have acute coronary syndrome.

Both acute management and secondary prevention for patients presenting with the spectrum of ACS have evolved greatly during the last decade, as evidenced by the multitude of clinical trials and the development of CPGs. The goal of the next decade is to ensure the accurate, equal,and timely application of these therapies and management strategies in clinical practice. In the emergency department, initiation of guideline-based management is especially challenging given the dynamic process of risk stratification that must take place to ensure properly directed care. It is clear, however, that application of such therapies leads to improved outcomes. Lessons learned from previous and ongoing quality improvement initiatives will provide the tools needed to ensure that widespread adoption of guideline-based therapy is complete.

Combined Modality Therapy↗

PubMed2005

Getting to the point: developing IT for the sharp end of healthcare.

Healthcare demonstrates the same properties of risk, complexity, uncertainty, dynamic change, and time-pressure as other high hazard sectors including aviation, nuclear power generation, the military, and transportation. Unlike those sectors, healthcare has particular traits that make it unique such as wide variability, ad hoc configuration, evanescence, resource constraints, and governmental and professional regulation. While healthcare's blunt (management) end is more easily understood, the sharp (operator) end is more difficult to research the closer one gets to the sharp end's point. Understanding sharp end practice and cognitive work can improve computer-based systems resilience, which is the ability to perform despite change and challenges. Research into actual practice at the sharp end of healthcare will provide the basis to understand how IT can support clinical practice. That understanding can be used to develop computer-based systems that will act as team players, able to support both individual and distributed cognitive work at healthcare's sharp end.

Artificial Intelligence↗

PubMed2025

SARS-CoV-2 genomic diversity and within-host evolution in individuals with persistent infection in the UK: an observational, longitudinal, population-based surveillance study.

BACKGROUND: Persistent SARS-CoV-2 infections in hospitalised immunocompromised individuals are known to facilitate accelerated within-host viral evolution, potentially contributing to the emergence of highly divergent variants. However, little is known about the evolutionary dynamics and transmission risks of persistent infections in the general population. We aimed to characterise the within-host evolution of SARS-CoV-2 during persistent infections identified through a large community surveillance study. METHODS: We used data from the Office for National Statistics COVID-19 Infection Survey (ONS-CIS), a large-scale, longitudinal, population-based surveillance study conducted in the UK from April, 2020, to March, 2023. For this analysis, we focused on infections with high viral load (cycle threshold ≤30) and available genome sequences, from seven major SARS-CoV-2 lineages (alpha, delta, BA.1, BA.2, BA.4, BA.5, and XBB). ONS-CIS participants were randomly selected from the general population and tested regularly by RT-PCR, regardless of symptoms. We defined persistent infections as those with sustained or rebounding high viral RNA titres for 26 days or longer. We examined associated host characteristics and used raw sequence data to identify de novo mutations and estimate within-host synonymous and non-synonymous evolutionary rates across the SARS-CoV-2 genome. FINDINGS: Between Nov 2, 2020, and March 21, 2023, we identified 576 persistent infections with at least two sequences, including 11 alpha, 106 delta, 102 BA.1, 204 BA.2, 16 BA.4, 133 BA.5, and 4 XBB. Persistent infections were more common in males than females (p<0·0001) and individuals older than 60 years (p=0·0027). The median within-host genome-wide evolutionary rate was 7·9 × 10-4 substitutions per site per year (IQR 7·0-9·0 × 10-4), with high inter-individual variability driven largely by non-synonymous mutations, particularly in the N-terminal and receptor-binding domains of the spike protein. Longer infection duration was associated with higher evolutionary rates, while no associations were found with age, sex, vaccination status, previous infection, or virus lineage. We found no clear evidence of transmission beyond the first month of infection in any of the 84 persistent infections lasting 56 days or longer. In total, we identified 379 recurrent mutations, including many with known or predicted negative fitness effects and low prevalence at the population level, as well as de novo reversions to the Wuhan-Hu-1 reference sequence, which were likely under positive selection within those individuals. INTERPRETATION: This study highlights the heterogeneous nature of within-host SARS-CoV-2 evolution in individuals with persistent infection in the community. Notably, a small subset of persistent infections with high viral loads underwent accelerated viral evolution or recurrently acquired hallmark mutations found in novel variants. In addition, onward transmission from a persistent infection during the later stages of infection is likely to be rare. These insights have important implications for prioritising genomic surveillance and managing patients with persistent infections. FUNDING: Department of Health and Social Care.

Humans↗

PubMed2006

Transmission of a pestivirus infection in a population of Pyrenean chamois.

Outbreaks of a previously unrecorded disease have recently affected Pyrenean chamois (Rupicapra pyrenaica pyrenaica) populations across the mountain range. A pestivirus was hypothesized to be the cause of this emerging disease and this type of virus can cross the species barrier and be transmitted to or from wildlife. Using an epidemiological survey conducted from 1995 to 2004 at Orlu, France, we characterized the virus and analyzed its transmission. A phylogenetic analysis of viral sequences and virus neutralization tests showed that the virus belonged to the newly described border disease virus-4 group. The increase of seroprevalence with age indicated that infection can occur at any age and resulted in lifelong immunity. Overall, 70.3% of 323 samples were positive for anti-p80 antibodies and 10.2% of 167 samples showed viremia, as demonstrated by either positive ELISA antigen test or RT-PCR. Infection has thus been widespread in this population since 1995, whereas no mass mortality or clinical signs have been observed. Incidence and seroprevalence varied seasonally and according to number of individuals aged less than 2 years old in the population, so viral transmission was dependent on host population age structure. We propose that the virus is now endemic in this population and is likely detrimental for reproduction and juveniles. Further investigation is needed to estimate the impact of pestivirus on host population dynamics and the risk of cross-transmission to farm animals.

Animals↗

PubMed2026

Perfluorooctane sulfonate drives the synergistic dissemination of antimicrobial resistance and pathogenicity during sludge anaerobic digestion.

Per- and polyfluoroalkyl substances, one of the most prevalent and persistent emerging contaminants in sludge, may drive the dissemination of antimicrobial resistance and pathogenicity during sludge treatment. However, the mechanisms underlying perfluorooctane sulfonate (PFOS)-mediated propagation of antibiotic resistance genes (ARGs) and virulence factors (VFs) remain poorly understood. This study investigated the effects of PFOS (1 and 10 μg/g-dw) on ARGs dynamics and virulence risks. Quantitative PCR and metagenomic analysis revealed that PFOS stress led to the widespread enrichment of ARGs, the total abundance of mobile genetic elements (MGEs) and VFs also increased by 33.22-37.62% and 6.71-8.41%, respectively. Metagenomic binning results demonstrated that most metagenome-assembled genomes carrying ARGs or VFs simultaneously harbored MGEs. Mechanistically, excessive reactive oxygen species production and enhanced substrate-level phosphorylation for ATP generation may contribute to the increased horizontal transfer potential of ARGs under PFOS stress, which further facilitated the convergence of antimicrobial resistance and virulence traits within pathogens. Furthermore, PFOS may have hindered the negative regulation of the RhlI/RhlR quorum sensing system on the Type III secretion system, stimulating the secretion of VFs. This study elucidates the mechanisms by which PFOS promotes the dissemination of ARGs and pathogenicity during anaerobic digestion, highlighting the potentially overlooked environmental health risks of PFOS during sludge disposal.

Alkanesulfonic Acids↗

PubMed1984

Left ventricular dysfunction after acute myocardial infarction: results of a prospective multicenter study.

In a multicenter prospective study of 866 patients who survived the coronary care unit phase of an acute myocardial infarction, variables reflecting left ventricular function were examined to assess their impact on 2 year survival. Single variables that reflected left ventricular dysfunction before infarction and in the acute and recovery phases were, respectively, history of prior myocardial infarction, rales in the coronary care unit dichotomized at greater than bibasilar and predischarge radionuclide ejection fraction dichotomized at less than 0.40. When combined in a stepwise fashion, patients lacking these three risk characteristics had a 2 year 4.2% mortality rate, whereas patients possessing all three characteristics had a 45% mortality rate. Rales in the coronary care unit and predischarge ejection fraction act independently, and each contributes to mortality. Fifty-two patients with advanced rales but an ejection fraction of 0.40 or greater had a 21% mortality rate. Similarly, 208 patients with few rales but an ejection fraction of less than 0.40 had a 15% mortality rate. These data suggest that the mortality risk imposed by those factors that assess permanent left ventricular damage is independent of and additive to the mortality risk contributed by dynamic, acute phase dysfunction. These data fit the hypothesis that acute phase dysfunction is, in part, due to transient ischemia that, on reversal, can restore function toward normal. The results suggest 1) that assessment of left ventricular function during the acute and recovery phases of myocardial infarction is necessary to define prognostic characteristics of an individual patient, and 2) that of particular importance is the identification of patients whose postinfarction course is consistent with reversible ischemia.

Cardiac Output↗

PubMed2006

Challenging and changing gender attitudes among young men in Mumbai, India.

This article presents findings from a pilot intervention in 2005-6 to promote gender equity among young men from low-income communities in Mumbai, India. The project involved formative work on gender, sexuality and masculinity, and educational activities with 126 young men, aged 18-29, over a six-month period. The programme of activities was called Yari-dosti, which is Hindi for friendship or bonding among men, and was adapted from a Brazilian intervention. Pre- and post-intervention surveys, including measures of attitudes towards gender norms using the Gender Equitable Men (GEM) Scale and other key outcomes, qualitative interviews with 31 participants, monitoring and observations were used as evaluation tools. Almost all the young men actively participated in the activities and appreciated the intervention. It was often the first time they had had the opportunity to discuss and reflect on these issues. The interviews showed that attitudes towards gender and sexuality, as reported behaviour in relationships, had often changed. A survey two months later also showed a significant decrease in support for inequitable gender norms and sexual harassment of girls and women. The results suggest that the pilot was successful in reaching and engaging young men to critically discuss gender dynamics and health risk, and in shifting key gender-related attitudes.

Adolescent↗

PubMed2002

Mammographic tissue, breast cancer risk, serial image analysis, and digital mammography. Part 1. Tissue and related risk factors.

This work is presented as a sequence of two parts. In this leading section, a review of the breast tissue-risk research is provided. Although controversy remains, there is substantial evidence indicating that dense mammographic tissue (a) is a breast cancer risk factor that is at least similar, if not greater, in magnitude with the other known breast cancer risk factors and (b) may be a partial biomarker for some of the other risk factors. Understanding these influences may provide a mechanism for measuring the dynamics of breast cancer risk. The totality of this work is to provide support for an automated serial mammography study under way at the authors' institution, where digital mammographic images are acquired with a full-field digital mammography system. This is a filmless imaging system, where the image is acquired in digital format. This electronic imaging acquisition system provides a prime opportunity to easily couple and manipulate the image data with patient information such as risk probability analysis or other pertinent personal history data for improved automated decision making. In this leading section, the main focus is on understanding elements that will assist in fusing risk probability analysis with automated computer-aided diagnosis. The evidence indicates that there are many factors that influence breast tissue at any given time and thus have the ability to alter the associated radiographic image appearance over time. At the initiation of the serial study it was clear that the authors did not fully understand the nature of the problem: automatically comparing similar mammographic scenes acquired at different times. In the second part of this sequence, the more time-related tissue influences are reviewed.

Breast↗

PubMed2002

Mammographic tissue, breast cancer risk, serial image analysis, and digital mammography. Part 2. Serial breast tissue change and related temporal influences.

The work presented herein is the second part of a review of breast tissue-related cancer-risk research. Briefly, in part 1, the tissue-risk research is discussed. In this part, factors that influence temporal breast tissue change are reviewed. Since breast composition is correlated with some of the known risk factors, understanding these influences may provide a mechanism for measuring the dynamics of breast cancer risk. The purpose of this work is to provide support for an automated serial mammography study under way at the authors' institution, where the digital mammographic images are acquired with a full-field digital mammography imaging system. At the initiation of the serial study, it was clear that the authors did not fully understand the nature of the problem: automatically comparing similar mammographic scenes acquired at different times. The evidence indicates that there are many factors that influence breast tissue at any given time and thus have the ability to alter the associated radiographic appearance over time. In general, the topics considered herein include aging; involution; breast development; exogenous and endogenous hormonal interactions such as hormone replacement therapy, oral contraceptive use, and menstrual timing; screening sensitivity issues and interval cancers; tumor growth rates; sojourn times; and lifestyle factors such as diet and exercise. Throughout this work, commentaries and suggestive strategies for automated serial image analysis are provided.

Aging↗

PubMed2005

The origin of bursts and heavy tails in human dynamics.

The dynamics of many social, technological and economic phenomena are driven by individual human actions, turning the quantitative understanding of human behaviour into a central question of modern science. Current models of human dynamics, used from risk assessment to communications, assume that human actions are randomly distributed in time and thus well approximated by Poisson processes. In contrast, there is increasing evidence that the timing of many human activities, ranging from communication to entertainment and work patterns, follow non-Poisson statistics, characterized by bursts of rapidly occurring events separated by long periods of inactivity. Here I show that the bursty nature of human behaviour is a consequence of a decision-based queuing process: when individuals execute tasks based on some perceived priority, the timing of the tasks will be heavy tailed, with most tasks being rapidly executed, whereas a few experience very long waiting times. In contrast, random or priority blind execution is well approximated by uniform inter-event statistics. These finding have important implications, ranging from resource management to service allocation, in both communications and retail.

Behavior↗

PubMed2026

Long-read proteogenomic atlas of human neuronal differentiation reveals isoform diversity informing neurodevelopmental risk mechanisms.

RNA splicing shapes neuronal identity and disease risk, yet current maps lack the developmental resolution and depth to resolve this complexity. Here, we integrate deep long-read RNA sequencing and proteomics in induced pluripotent stem cell-derived cortical neurons to generate a high-resolution proteogenomic atlas of human neuron development. We identify 182,371 mRNA isoforms (over half previously unknown) and provide direct peptide evidence for the translation of hundreds of novel protein-coding sequences. Population genetics demonstrates that variants affecting novel exons and splice sites are under negative selection, underscoring the potential significance of these isoforms. During neuronal maturation, we observe that autism risk genes undergo dynamic isoform switching, including microexon inclusion and intron retention, that remodel key protein domains and regulatory regions. Furthermore, we uncover widespread, long-range coordination between alternative transcript processing events, including transcription start sites, exon splicing, and polyadenylation. Finally, our atlas enables variant reinterpretation in autism, highlighting the value of an isoform-centric view for interpreting pathogenic variation in neurodevelopment.

Humans↗

PubMed2006

Predicting hospitalization and mortality in end-stage renal disease (ESRD) patients using an Index of Coexisting Disease (ICED)-based risk stratification model.

We evaluated the use of an additive Index of Coexisting Diseases (ICED)-based stratification schema to determine subsequent hospitalization and mortality in a hemodialysis population. Patients from five commercial health plans were stratified into low-, medium-, and high-risk groups and followed for up to 1 year. Patients were reassessed and restratified at 90-day intervals and censored when disease management ceased. Outcome measures collected through selfreports and health plan records were captured in an active database. Survival to first hospitalization/ mortality was compared by Kaplan Meier curves, survivor function differences by the Wilcoxon test, and group comparisons by ANOVA and chi square. Population characteristics included mean age of 63.0, 57.7% male, and 58.8% diabetic. Mortality was 13.0% per patient year (standardized mortality ratio 0.43) and the hospitalization rate was 0.59 per patient year (standardized hospitalization ratio 0.24). Survival curves demonstrated differences in mortality and hospitalization between the patients in different initial risk categories (p < 0.01). Mean hospitalizations were 0.81 +/- 1.53 per patient year (high risk), 0.45 +/- 0.99 (medium risk), and 0.15 +/- 0.51 for the low-risk group (p < 0.001). Stratification was dynamic; 47.3% decreased and 4.7% increased risk level between the first and second assessment. These changes were associated with survival differences for initial low (p = 0.06) or medium patients (p < 0.01), and hospital-free survival for initial medium (p = 0.08) or high patients (p < 0.05). In conclusion, this ICED-based stratification schema predicted mortality and hospitalization for hemodialysis patients participating in our disease management program.

Analysis of Variance↗

PubMed1992

Mortality trends in a cohort of homosexual men in New York City, 1978-1988.

Trends in mortality related to infection by human immunodeficiency virus type 1 (HIV-1) and to other causes were examined from 1978 to 1988 in a cohort of 8,906 homosexual men who participated in studies of hepatitis B virus infection in the late 1970s in New York City. HIV-related mortality rates increased from 1 per 10,000 person-years in 1980 to 181 per 10,000 person-years in 1986, followed by a plateau from 1986 to 1988. The standardized mortality ratio among white men in the cohort was 3.7 (95% confidence interval (Cl) 3.4-3.9) as compared with white men from across the United States. Higher HIV-related mortality rates were associated with a higher number of sexual partners, a history of gonorrhea and/or syphilis, and serologic markers of infection with hepatitis B virus. After adjustment for demographics and sexual behaviors, the relative risk of mortality for Hispanic men as compared with white men was 1.5 (95% Cl 1.1-1.9). This study illustrates the large excess in mortality among homosexual men over the last decade, with the excess accounted for by deaths from HIV-related diseases. The recent plateau in mortality may be due to the effect of new treatments and/or the decline in new HIV-1 infections among homosexual men. The excess in HIV-related mortality among Hispanic homosexual men was not explained by differences in demographics and factors associated with the sexual transmission of HIV-1.

Adult↗

PubMed1989

Radiological health effects models for nuclear power plant accident consequence analysis.

Improved health effects models have been developed for assessing the early effects, late somatic effects and genetic effects that might result from low-LET radiation exposures to populations following a major accident in a nuclear power plant. All the models have been developed in such a way that the dynamics of population risks can be analyzed. Estimates of life years lost and the duration of illnesses were generated and a framework recommended for summarizing health impacts. Uncertainty is addressed by providing models for upper, central and lower estimates of most effects. The models are believed to be a significant improvement over the models used in the U.S. Nuclear Regulatory Commission's Reactor Safety Study, and they can easily be modified to reflect advances in scientific understanding of the health effects of ionizing radiation.

Accidents↗

PubMed1999

Some problems in the skeletal dosimetry of bone-seeking radionuclides.

There are fundamental problems with the calculation of radiation doses to the skeleton from internal emitters deposited in bone. Some of these include dose inhomogeneities, identity of cells at risk and their dynamics, changing deposition patterns of bone-seeking radionuclides with time after exposure, seemingly unique responses of the skeleton to each deposited radionuclide, the role of radioactive progeny produced by deposited emitters and their individual dynamics and effects, different responses of mammals of different ages at exposure to identical dosages, different responses to different chemical forms of a given radionuclide, and different responses to an identical dose from a given radionuclide at different dose-rates. This situation makes it necessary to choose some common dose parameter that will allow the overall effects of different radionuclides to be compared directly so that projected effects of each of them in humans can be estimated. For radiation protection purposes, it appears premature to abandon the concept of average skeletal dose (which appears to be a practical compromise for use) until an undelusive, non-artificial and uncontrived method of calculating absorbed dose to the appropriate cells in bone is developed that fulfills the requirement of equal cancer response for equal skeletal dose for all circumstances.

Age Factors↗

PubMed2006

Interactive effects of environmental stress and inbreeding on reproductive traits in a wild bird population.

1. Conservation biologists are concerned about the interactive effects of environmental stress and inbreeding because such interactions could affect the dynamics and extinction risk of small and isolated populations, but few studies have tested for these interactions in nature. 2. We used data from the long-term population study of song sparrows Melospiza melodia on Mandarte Island to examine the joint effects of inbreeding and environmental stress on four fitness traits that are known to be affected by the inbreeding level of adult birds: hatching success, laying date, male mating success and fledgling survival. 3. We found that inbreeding depression interacted with environmental stress to reduce hatching success in the nests of inbred females during periods of rain. 4. For laying date, we found equivocal support for an interaction between parental inbreeding and environmental stress. In this case, however, inbred females experienced less inbreeding depression in more stressful, cooler years. 5. For two other traits, we found no evidence that the strength of inbreeding depression varied with environmental stress. First, mated males fathered fewer nests per season if inbred or if the ratio of males to females in the population was high, but inbreeding depression did not depend on sex ratio. Second, fledglings survived poorly during rainy periods and if their father was inbred, but the effects of paternal inbreeding and rain did not interact. 6. Thus, even for a single species, interactions between the inbreeding level and environmental stress may not occur in all traits affected by inbreeding depression, and interactions that do occur will not always act synergistically to further decrease fitness.

Animals↗