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PubMed1990

Malaria among gold miners in southern Pará, Brazil: estimates of determinants and individual costs.

As malaria grows more prevalent in the Amazon frontier despite increased expenditures by disease control authorities, national and regional tropical disease control strategies are being called into question. The current crisis involving traditional control/eradication methods has broadened the search for feasible and effective malaria control strategies--a search that necessarily includes an investigation of the roles of a series of individual and community-level socioeconomic characteristics in determining malaria prevalence rates, and the proper methods of estimating these links. In addition, social scientists and policy makers alike know very little about the economic costs associated with malarial infections. In this paper, I use survey data from several Brazilian gold mining areas to (a) test the general reliability of malaria-related questionnaire response data, and suggest categorization methods to minimize the statistical influence of exaggerated responses, (b) estimate three statistical models aimed at detecting the socioeconomic determinants of individual malaria prevalence rates, and (c) calculate estimates of the average cost of a single bout of malaria. The results support the general reliability of survey response data gathered in conjunction with malaria research. Once the effects of vector exposure were controlled for, individual socioeconomic characteristics were only weakly linked to malaria prevalence rates in these very special miners' communities. Moreover, the socioeconomic and exposure links that were significant did not depend on the measure of malaria adopted. Finally, individual costs associated with malarial infections were found to be a significant portion of miners' incomes.

Brazil↗
PubMed2025

Discovery of diverse anellovirus sequences in Thai human sequencing data.

UNLABELLED: Anelloviruses are part of the normal human viral flora. Although their diversity in humans has been investigated in many countries, and despite their initial detection in Thailand in 1999, knowledge of Thai anelloviruses remains very limited. This study analyzed 1,175 whole-genome sequencing data sets from Thai individuals to mine for potential anellovirus sequences. Our analyses detected anellovirus sequences in 149 data sets (12.68%), uncovering 434 partial anellovirus sequences and 77 complete genome sequences, characterized by the presence of terminal redundancy, complete orf1, and the conserved untranslated region upstream of the orf1 gene. Sequence analyses indicated that these viruses belong to seven genera, including Alphatorquevirus, Betatorquevirus, Gammatorquevirus, Hetorquevirus, Lamedtorquevirus, Samektorquevirus, and Yodtorquevirus. Notably, Hetorquevirus, Lamedtorquevirus, Samektorquevirus, and Yodtorquevirus had not previously been reported in Thailand. Phylogenetic analysis of ORF1 protein sequences showed that Thai anelloviruses form multiple phylogenetic clusters with non-Thai anelloviruses, indicating frequent cross-country transmission and multiple origins of the virus in Thailand. Furthermore, sequence similarity network analysis identified 33 potentially novel anellovirus species in our data set. Our findings greatly expand the knowledge of anellovirus diversity in Thailand and demonstrate the potential of human whole-genome sequencing data as a valuable resource for viral discovery. Lastly, we highlight and discuss some challenges with the use of the current pairwise sequence similarity-based classification scheme, in particular, how gaps can influence similarity calculation and potentially lead to inconsistencies with a phylogenetic-based classification scheme. IMPORTANCE: Anelloviruses are widespread in humans, yet their diversity remains poorly characterized in many regions, including Thailand. Here, we demonstrate that human sequencing data sets, originally generated without the intention for virome research, can be effectively mined for anellovirus sequences, including complete genomes. Our findings reveal a substantial number of previously unreported anelloviruses in Thailand, significantly expanding the known diversity of the virus. We also highlight potential limitations of the current anellovirus species classification scheme, which is based on pairwise orf1 sequence similarity analysis with a hard threshold cutoff at 69%. Our results reveal that the current scheme can sometimes yield taxonomic groupings that are inconsistent with phylogenetic relationships, particularly when significant alignment gaps are present. Overall, our results show that existing human sequencing data can be effectively repurposed for virus discovery research and suggest the need for more robust and phylogenetically informed classification frameworks as viral sequence databases continue to expand.

Humans↗
PubMedDate not supplied

Does coal mine dust present a risk for lung cancer? A case-control study of U.S. coal miners.

This paper evaluates the relationship between the risk of lung cancer mortality and coal mine dust exposure under control by cigarette smoking status. Two case-control studies based on 317 white male lung cancer mortality cases are presented. A one-to-one matched-case design allows examination of the risk of coal mine dust exposure and cigarette smoking. A two-to-one matched-case design was employed to examine the lung cancer risk of coal mine dust exposure independent of cigarette smoking. Based upon these data, no evidence of a coal mine dust exposure-lung cancer risk was found, although the expected increased risk for lung cancer in cigarette smokers was observed. There was no evidence of an interactive effect between cigarette smoking and coal mine dust exposure.

Coal Mining↗
PubMed2024

Haplotype-resolved genome assembly and implementation of VitExpress, an open interactive transcriptomic platform for grapevine.

Haplotype-resolved genome assemblies were produced for Chasselas and Ugni Blanc, two heterozygous Vitis vinifera cultivars by combining high-fidelity long-read sequencing and high-throughput chromosome conformation capture (Hi-C). The telomere-to-telomere full coverage of the chromosomes allowed us to assemble separately the two haplo-genomes of both cultivars and revealed structural variations between the two haplotypes of a given cultivar. The deletions/insertions, inversions, translocations, and duplications provide insight into the evolutionary history and parental relationship among grape varieties. Integration of de novo single long-read sequencing of full-length transcript isoforms (Iso-Seq) yielded a highly improved genome annotation. Given its higher contiguity, and the robustness of the IsoSeq-based annotation, the Chasselas assembly meets the standard to become the annotated reference genome for V. vinifera. Building on these resources, we developed VitExpress, an open interactive transcriptomic platform, that provides a genome browser and integrated web tools for expression profiling, and a set of statistical tools (StatTools) for the identification of highly correlated genes. Implementation of the correlation finder tool for MybA1, a major regulator of the anthocyanin pathway, identified candidate genes associated with anthocyanin metabolism, whose expression patterns were experimentally validated as discriminating between black and white grapes. These resources and innovative tools for mining genome-related data are anticipated to foster advances in several areas of grapevine research.

Vitis↗
PubMed1992

The derivation of estimated dust exposures for U.S. coal miners working before 1970.

A number of reports on the prevalence of coal workers' pneumoconiosis in U.S. coal miners have been published, yet very little is known about the relationship between dust exposure and pneumoconiosis levels in the U.S. This report describes the derivation of cumulative dust exposure estimates by back-extrapolation of data processed by the Mine Safety and Health Administration after 1970 by using a ratio of dust concentrations based on information collected during environmental surveys at certain U.S. mines by the Bureau of Mines between 1968 and 1969. Cumulative personal dust exposure estimates were calculated by using occupational histories obtained from the miners and job-specific estimates of dust concentration. In other reports, the resulting estimated exposures have been shown to correlate well with various measures of respiratory morbidity.

Adult↗
PubMed1984

Comparison of mass concentrations determined with personal respirable coal mine dust samplers operating at 1.2 liters per minute and the Casella 113A gravimetric sampler (MRE).

Measuring respirable dust concentrations in coal mine environments is currently done using approved personal respirable dust sampling equipment operating at a flow rate of 2.0 liters per minute (Lpm). Measurements made with approved coal mine dust sampling equipment are converted to equivalent concentrations that would be obtained with a Mining Research Establishment (MRE) instrument known as the Casella 113A gravimetric sampler, using a conversion factor of 1.38. NIOSH has recently recommended that coal mine dust samplers (CMDS) used to measure respirable dust levels in mine environments be operated at 1.2 Lpm and measured concentrations be multiplied by 0.91 to obtain an equivalent MRE concentration. The purpose of this recommendation is to reduce systematic error caused by the variation in mine dust distributions. This paper presents and discusses data collected in the laboratory and in underground coal mines to evaluate the recommended 1.2 Lpm flow rate and 0.91 conversion factor. Comparative measurements were obtained in the laboratory with the CMDS operating at 2.0 and 1.2 liters per minute and the MRE, using aerosols of coal and limestone dust of varying particle size distribution. Similar comparative measurements were made in a number of underground coal mines at locations with environments having particle size distributions representative of different underground mining operations. It was concluded from this study that there is no significant change in the variability associated with the constant factor used to convert respirable dust measurements, obtained with approved respirable CMDS, to equivalent MRE measurements when the flow rate of the CMDS is reduced from 2.0 to 1.2 Lpm.

Coal↗
PubMed1977

Cancer in asbestos-mining and other areas of Quebec.

Employing incidence data from the Quebec Tumor Registry, we examined the relative risks of cancer of all sites for the years 1969-73 in the asbestos-mining, rural, and metropolitan counties of Quebec Province, Canada. Generally, rates for males exceeded those for females, and the relative risks in the asbestos-mining counties for 7-10 different sites of cancer, all of low incidence, were from 1.50 to 8.08 times those of other rural counties of the Province for both sexes. Metropolitan counties exhibited equally high risk for many of these sites. We discovered higher risks among males in asbestos-mining counties for cancer of the pleura, peritoneum, lip, tongue, salivary gland, mouth, and small intestine and higher risks among females for cancer of the pleura, lip, kidney, salivary gland, and for melanoma. Because of the likelihood of a long latent period for asbestos-related cancers, the risks we observed were possibly the product of since-altered occupational and environmental conditions existing 20-30 years ago in the asbestos-mining areas. The similarities in risks for most cancers in asbestos-mining and urban areas were noteworthy.

Asbestos↗
PubMed1992

Occupational diseases in South African mines--a neglected epidemic?

A major difficulty in assessing incidence and prevalence of occupational diseases among the workforce employed on South African mines is the lack of epidemiological data. Published and unpublished data were collated and analysed for the period 1915-1988 in order to provide insights into occupational disease trends. Using proxies for incidence rates, it was demonstrated that the rates of silicosis and tuberculosis were likely to be high. In the case of silicosis among black miners, disease was contracted in a relatively short period on average. The stabilisation of the black workforce on the mines, which started in 1975 and continues, is an important factor likely to lead to an increase in occupational disease rates. Recommendations for improved data reporting and research are made, in particular the need to identify occupational groups at high risk and the calculation of prevalences.

Adult↗
PubMed2025

Seq2Saccharide: Discovering Oligosaccharides and Aminoglycosides Natural Products by Integrating Computational Mass Spectrometry and Genome Mining.

Natural oligosaccharides and aminoglycosides are important sources of new drug candidates, especially in the development of antibiotics. In the past, discovering novel saccharides has been time-consuming and costly. However, the rapid expansion of high-throughput data, including genomic and mass spectrometry data sets, has greatly increased opportunities for natural saccharide discovery. Yet, due to the complex biosynthesis pathways of saccharides, no existing method can predict their structures with high precision. To address this, we introduce Seq2Saccharide, a tool designed to automate saccharide natural product discovery by integrating both genomic and mass spectrometry data. To enhance accuracy, Seq2Saccharide predicts hundreds or thousands of putative structures for each gene cluster. The correct structure is then identified from these predictions using a mass spectral search. Benchmarks against saccharides in the MiBIG database show that Seq2Saccharide outperforms existing methods in predicting the structure of saccharides. Furthermore, mass spectrometry analysis indicates that the variable search module can correct mispredictions from genome mining. By searching genomic and mass spectrometry data of microbial strains, Seq2Saccharide correctly identified the biosynthetic gene cluster for the polysaccharide oligosaccharide trestatin B.

Aminoglycosides↗
PubMedDate not supplied

UTAB: a computer database on residues of xenobiotic organic chemicals and heavy metals in plants.

The UTAB Database contains information concerned with the uptake/accumulation, translocation, adhesion, and biotransformation of both xenobiotic organic chemicals and heavy metals by vascular plants. UTAB can be used to estimate the accumulation of chemicals in vegetation and their subsequent movement through the food chain. The database contains actual data from papers in the published literature dating from 1926 for organic chemicals and from 1976 for heavy metals. At present the database is comprised of more than 37,000 records pertaining to 900 different organic chemicals, 21 heavy metals, and over 350 plant species. Each record contains information on a single combination of species, chemical, and dose. Other information includes the application and destination sites, amount accumulated, rates of uptake or translocation, products and sites of biotransformation, experimental condition parameters, and the source paper. Thus, the database can be used to quickly obtain specific data pertaining to a chemical, plant species, mine spoil, etc. or it can be used for the comparative analysis of a set of data pertaining to groups of chemicals and plants.

Databases, Bibliographic↗
PubMed1987

[Evaluation of the effectiveness of medical prevention of pneumoconiosis based on studies of its incidence in selected coal mines].

In a group of 3,938 persons--pit miners of 3 coal mines--employed over 8 years, full-size X-ray pictures of the chest have been taken and through a special questionnaire information has been collected on the length of employment, workstation, risk of dustiness, exposure to fibrogenic dusts outside the mine. Basing on the studies, the mean annual incidence of pneumoconiosis in particular mines has been calculated. The data has been compared with the mean annual incidence rate of pneumoconiosis calculated for 10 years prior to epidemiological studies and based on the primary selection by means of small-size pictures. This comparison indicated that the full-size pictures revealed 3-7 times more pneumoconioses as compared to the hitherto applied system. The comparison of full-size and small-size X-ray pictures demonstrated that the lesions visible in full-size pictures have not been registered in small-size pictures in as many as half of the cases. The obtained results indicate that the effectiveness of the hitherto applied system of medical prevention of pneumoconiosis is insufficient. A change in this system is indispensable; miniature roentgenography should be replaced by full-size X-ray pictures.

Adult↗
PubMed1986

Pre-operational survey of a U mine near Val Vedello, Italy.

Results obtained from radiometric research carried out from 1980-81 in the region of U mines in the Val Vedello are provided. Data are presented on 222Rn, 226Ra and natural U concentrations in spring and surface waters. Concentrations were found to be relatively low. There is some increase in the vicinity of the exploratory U mine but this is, at least up to the present, only of a local character. Data are presented on external gamma exposure, 210Pb and 210Po in foodstuffs and in the urine of normal and exposed population as well as 226Ra in milk and vegetable samples. The aim of this study is to outline a preliminary map of natural radioactivity on the site before starting the mining activity. This will enable us later to detect changes caused by the U mining, milling and mill-tailing disposal operations.

Air Pollutants, Radioactive↗
PubMed1988

[Reaction time to single and double stimuli in operators of mining equipment].

The study was aimed at a comparison of the results of the reaction time for single (light or sound) and double stimuli (simultaneous emission of light and sound) in machine operators. The studies were carried out under laboratory conditions and in the working environment. The obtained data proved that underground, under specific copper mine conditions, similar to laboratory conditions, the theory of "intersensory facilitation" should be applied. The results of our studies can be useful for ergonomic practice.

Adult↗
PubMed1991

Risk assessment using exposure intensity: an application to vermiculite mining.

Estimation of exposure-response relations from epidemiological data is complicated by the fact that exposures usually vary in intensity over time. Cumulative exposure indices, which do not separate the effects of intensity and duration, are commonly used to circumvent this problem. In this paper the estimation of relative risk for specific ranges of exposure intensity from such data is considered using existing statistical methods for fitting multivariate relative risk models. This has the advantage that it does not assume that exposure intensity and duration have equivalent effects on risk. It also throws light on the possible existence of a threshold. The procedure was applied to data from a cohort of 406 vermiculite miners to examine the lung cancer risk associated with exposure to fibrous tremolite, which contaminated the vermiculite. The pattern of exposure-response differed substantially from that obtained using a cumulative exposure index to assess risk.

Aluminum Silicates↗
PubMed1983

[Risk of lung cancer in workers belonging to the occupational group of mining and stone processing].

Out of 1580 male lung cancer patients and 3160 controls (data collected in a nationwide study) 177 patients and 197 controls belonged to the occupation "mining and processing of stone" (asbestos, metals and coal excluded). 164 (92.6%) patients had a Kreyberg I tumor, 13 patients a Kreyberg II tumor. There are significant more smokers among patients (98.9%a), all patients with a K I tumor were smokers, compared to the controls (82.2%). Patients had a significant longer smoking career (40.9 yearsa) and a higher tar exposure (TE = 2544)b compared to the controls (36.2 years, TE = 2223). Lung cancer risk (adj. for age, years of occupation, TE) of smokers belonging to occupation "stone" compared to smokers belonging to group "white collar" (no occupational exposure in their anamnesis) was R = 2.0a. Significantly higher risks (adj. for age, TE) were in relation to years of occupation: less than 10 years: R = 2.2a, 11-20 years: R = 2.7a, 21-30 years: R = 2.6a. a P less than 1%; b P less than 5%.

Aged↗
PubMed1985

Leukemia risk among U.S. white male coal miners. A case-control study.

The relevance of occupational exposure to electrical and magnetic fields (EMF) in the etiology of leukemia has been raised in several studies. Underground coal miners represent an occupational group with situationally determined EMF exposure, as high-voltage power distribution lines are strung overhead in the mines and converters and step-down transformers provide power to mining equipment. Risk in occupational exposure to EMF was examined in a case-control study of 40 leukemia decedents and 160 control subjects who died of causes other than cancer or accident and who were matched on age at death. The control subjects were selected from a group of 6,066 persons whose deaths were reported in four National Institute for Occupational Safety and Health cohort mortality follow-up studies. Based on these data, 25 or more years of underground mining, a surrogate of EMF exposure, was found to pose a statistically significant risk for leukemia (International Classification of Diseases [ICD] codes 204 through 207, eighth revision), myelogenous leukemia (ICD 205), and chronic lymphocytic leukemia (CLL) (ICD 204.1). Accumulative exposure to chemical agents probably poses a risk for acute myelogenous leukemia, although this relationship fell short of being statistically significant. Although CLL has not previously been attributed to environmental agents, these data suggest a possible CLL risk from prolonged exposure to EMF.

Adult↗
PubMed2026

Community-driven advances in computational mass spectrometry: The perspective of EuBIC-MS members.

Advances in data acquisition, artificial intelligence, and integrative bioinformatics are driving the rapid evolution of computational mass spectrometry, and in turn, transforming modern proteomics, metabolomics, and lipidomics. These developments have greatly increased the scale and complexity of mass spectrometry data, underscoring the importance of evolving accurate, transparent, efficient and reproducible data processing workflows. Addressing these challenges requires collaborative innovation that brings together expertise in software engineering, statistics, and biology. The European Bioinformatics Community for Mass Spectrometry (EuBIC-MS), an initiative of the European Proteomics Association (EuPA), fosters a culture of open, community-driven development through its biennial Developers Meetings and Winter Schools. This commentary summarizes the scientific background and outcomes of the EuBIC-MS Developers Meeting 2025, which took place in Novacella, Italy. Three keynote presentations highlighted major frontiers in the field: deep proteome and phosphoproteome profiling, text mining for protein-protein interaction extraction, and scalable proteomics for AI-driven drug discovery. Seven community-selected hackathons addressed emerging challenges such as single-cell proteomics data analysis, FAIR metadata extraction, deep learning frameworks, R-Python interoperability, and DIA validation. Together, these efforts demonstrate the potential for scientific and technical innovation to arise from open collaboration, and highlight how community-driven initiatives can accelerate progress in computational mass spectrometry. SIGNIFICANCE: Modern proteomics increasingly depends on computational advances to translate complex, high-dimensional data into biological knowledge. The EuBIC-MS Developers Meeting 2025 exemplifies how community-driven collaboration can directly accelerate this process by bringing together experts from bioinformatics, statistics, and experimental proteomics to co-develop open, interoperable, and reproducible analytical tools. By fostering shared software frameworks, transparent benchmarking, and collaborative problem solving, the EuBIC-MS community helps ensure that technological innovation translates into reliable biological insights. This collaborative model strengthens the foundation for quantitative, system-level understanding of proteomes and establishes a sustainable path for integrating artificial intelligence and next-generation data acquisition into routine biological discovery. This commentary shows some current highlights in the field of computational mass spectrometry and community-based approaches undertaken during the most recent Developers Meeting to solve these challenges. The approaches discussed and initiated during the meeting - ranging from deep proteome profiling and phosphosite mapping to text mining, single-cell data analysis, and FAIR metadata extraction - address key bottlenecks that currently limit the biological interpretability and comparability of proteomics data.

Mass Spectrometry↗
PubMed1992

Mutations of p53 and ras genes in radon-associated lung cancer from uranium miners.

Radon increases the risk of lung cancer in smoking and non-smoking underground miners. To investigate the mutational spectrum associated with exposure to high levels of radon, we sequenced exons 5-9 of the p53 tumour suppressor gene and codons 12-13 of the Ki-ras protooncogene in 19 lung cancers from uranium miners exposed to radon and tobacco smoke. Mutations were not found in Ki-ras, but 9 p53 mutations, including 2 deletions, were found in 7 patients by direct DNA sequencing after polymerase chain reaction amplification of DNA from formalin-fixed, paraffin-embedded tissue. In tumours from 5 patients, the mutation produced an aminoacid change and an increased nuclear content of p53 protein. The tumours with either a stop codon or frame-shift deletion in the p53 gene were negative by immunohistochemistry. None of the mutations were G:C to T:A transversions in the coding strand of the p53 gene, which are the most frequent base substitutions associated with tobacco smoking, and none were found at the hotspot codons described in lung cancer. The observed differences from the usual lung cancer mutational spectrum may reflect the genotoxic effects of radon.

Aged↗