Singularity analysis: a tool for extracting lithologic and stratigraphic content from seismic data

In this work, we test an amplitude-independent method of seisimic data analysis designed to extract lithologic information about stratigraphic horizons. We apply the method of singularity characterization in an attempt to determine the sharpness of lithologic boundaries. We infer the sharpness of the boundary based upon a fractional integration of the seismic trace. The order of fractional integration is taken to represent the abruptness of the lithologic transition responsible for a given reflector. We find that the method output behaves in a geologically reasonable manner which suggests that our method is responding to lithologic variations along boundaries responsible for prominent reflectors in the data

Genetic alterations and cancer formation in a European flatfish at sites of different contamination burdens

Fish diseases are an indicator for marine ecosystem health since they provide a biological end-point of historical exposure to stressors. Liver cancer has been used to monitor the effects of exposure to anthropogenic pollution in flatfish for many years. The prevalence of liver cancer can exceed 20%. Despite the high prevalence and the opportunity of using flatfish to study environmentally induced cancer, the genetic and environmental factors driving tumor prevalence across sites are poorly understood. This study aims to define the link between genetic deterioration, liver disease progression, and anthropogenic contaminant exposures in the flatfish dab (Limanda limanda). We assessed genetic changes in a conserved cancer gene, Retinoblastoma (Rb), in association with histological diagnosis of normal, pretumor, and tumor pathologies in the livers of 165 fish from six sites in the North Sea and English Channel. The highest concentrations of metals (especially cadmium) and organic chemicals correlated with the presence of tumor pathology and with defined genetic profiles of the Rb gene, from these sites. Different Rb genetic profiles were found in liver tissue near each tumor phenotype, giving insight into the mechanistic molecular-level cause of the liver pathologies. Different Rb profiles were also found at sampling sites of differing contaminant burdens. Additionally, profiles indicated that histological “normal” fish from Dogger sampling locations possessed Rb profiles associated with pretumor disease. This study highlights an association between Rb and specific contaminants (especially cadmium) in the molecular etiology of dab liver tumorigenesis

Hepatocellular adenoma in a European flatfish (Limanda limanda) : genetic alterations in laser-capture microdissected tissue and global transcriptomic approach

Liver tumours in flatfish have been diagnosed using histopathology for decades to monitor the impacts of marine pollution. Here we describe the application of specific gene (retinoblastoma, Rb) profiling in laser capture micro-dissected samples, and a suppression subtractive hybridization (SSH) approach to isolate differentially expressed genes in hepatocellular adenoma (HCA) samples from dab, Limanda limanda. The Rb profiles from apparently normal and HCA micro-dissected samples of fish from the North Sea showed no significant difference, and genotypic heterogeneity within defined histological phenotypes was observed. In the SSH, sequences associated with cell signalling, cell cycle, gene expression regulation, protein transport and protein degradation were isolated. These included up-regulation of arrestin domain containing 3 (arrdc3), Rac-1 and tribbles, and down-regulation of ankyrin repeat/sterile alpha-motif domain-containing protein 1B-like (ANKS1B-like), c-fos, CDKN1B and RhoA-like sequences, previously implicated in mammalian HCA. This study offers new candidates involved in fish liver tumour development

Spectral binning as an approach to post-acquisition processing of high resolution FIE-MS metabolome fingerprinting data

INTRODUCTION: Flow infusion electrospray high resolution mass spectrometry (FIE-HRMS) fingerprinting produces complex, high dimensional data sets which require specialist in-silico software tools to process the data prior to analysis. OBJECTIVES: Present spectral binning as a pragmatic approach to post-acquisition procession of FIE-HRMS metabolome fingerprinting data. METHODS: A spectral binning approach was developed that included the elimination of single scan m/z events, the binning of spectra and the averaging of spectra across the infusion profile. The modal accurate m/z was then extracted for each bin. This approach was assessed using four different biological matrices and a mix of 31 known chemical standards analysed by FIE-HRMS using an Exactive Orbitrap. Bin purity and centrality metrics were developed to objectively assess the distribution and position of accurate m/z within an individual bin respectively. RESULTS: The optimal spectral binning width was found to be 0.01 amu. 80.8% of the extracted accurate m/z matched to predicted ionisation products of the chemical standards mix were found to have an error of below 3 ppm. The open-source R package binneR was developed as a user friendly implementation of the approach. This was able to process 100 data files using 4 Central Processing Units (CPU) workers in only 55 seconds with a maximum memory usage of 1.36 GB. CONCLUSION: Spectral binning is a fast and robust method for the post-acquisition processing of FIE-HRMS data. The open-source R package binneR allows users to efficiently process data from FIE-HRMS experiments with the resources available on a standard desktop computer. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11306-022-01923-6

De novo transcriptome assembly of the Qatari pearl oyster Pinctada imbricata radiata

© 2019 The pearl oyster Pinctada imbricata radiata is an iconic species in Qatar, representing an integral part of the nation's cultural heritage and one of the main economic foundations upon which the nation developed. During the early part of the 20th century, nearly half the Qatar population was involved in the pearl oyster industry. However, the fishery has undergone steady decline since the 1930s, and the species is now under threat due to multiple confounding pressures. This manuscript presents the first de novo transcriptome of the Qatari pearl oyster assembled into 30,739 non-redundant coding sequences and with a BUSCO completeness score of 98.4%. Analysis of the transcriptome reveals the close evolutionary distance to the conspecific animal Pinctada imbricata fucata but also highlights differences in immune genes and the presence of distinctive transposon families, suggesting recent adaptive divergence. This data is made available for all to utilise in future studies on the species.This publication was made possible by the NPRP award [NPRP9-394-1-090 “The Pearl Oyster: from national icon to guardian of Qatar's marine environment”] from the Qatar National Research Fund (a member of Qatar Foundation). The findings herein reflect the work, and are solely the responsibility, of the authors. In addition, the authors would like to thank Prof. Eduarda Santos for advice regarding sequencing requirements and Mr. Mark Chatting and Mr. Reyniel Gasang for their support in the collection of the samples

Effects of glycerol and creatine hyperhydration on doping-relevant blood parameters

Glycerol is prohibited as an ergogenic aid by the World Anti-Doping Agency (WADA) due to the potential for its plasma expansion properties to have masking effects. However, the scientific basis of the inclusion of Gly as a “masking agent” remains inconclusive. The purpose of this study was to determine the effects of a hyperhydrating supplement containing Gly on doping-relevant blood parameters. Nine trained males ingested a hyperhydrating mixture twice per day for 7 days containing 1.0 g•kg<sup>−1</sup> body mass (BM) of Gly, 10.0 g of creatine and 75.0 g of glucose. Blood samples were collected and total hemoglobin (Hb) mass determined using the optimized carbon monoxide (CO) rebreathing method pre- and post-supplementation. BM and total body water (TBW) increased significantly following supplementation by 1.1 ± 1.2 and 1.0 ± 1.2 L (BM, P < 0.01; TBW, P < 0.01), respectively. This hyperhydration did not significantly alter plasma volume or any of the doping-relevant blood parameters (e.g., hematocrit, Hb, reticulocytes and total Hb-mass) even when Gly was clearly detectable in urine samples. In conclusion, this study shows that supplementation with hyperhydrating solution containing Gly for 7 days does not significantly alter doping-relevant blood parameters

Observational Limit on Gravitational Waves from Binary Neutron Stars in the Galaxy

Using optimal matched filtering, we search 25 hours of data from the LIGO 40-meter prototype laser interferometric gravitational-wave detector for gravitational-wave chirps emitted by coalescing binary systems within our Galaxy. This is the first test of this filtering technique on real interferometric data. An upper limit on the rate R of neutron star binary inspirals in our Galaxy is obtained: with 90% confidence, R< 0.5/hour. Similar experiments with LIGO interferometers will provide constraints on the population of tight binary neutron star systems in the Universe.Comment: RevTeX, minor revisions, exactly as published in PRL 83 (1999) p1498, 4 pages, 2 figures include

Healthcare-associated infections (HAIs) during the coronavirus disease 2019 (COVID-19) pandemic: A time-series analysis

OBJECTIVE: To use interrupted time-series analyses to investigate the impact of the coronavirus disease 2019 (COVID-19) pandemic on healthcare-associated infections (HAIs). We hypothesized that the pandemic would be associated with higher rates of HAIs after adjustment for confounders. DESIGN: We conducted a cross-sectional study of HAIs in 3 hospitals in Missouri from January 1, 2017, through August 31, 2020, using interrupted time-series analysis with 2 counterfactual scenarios. SETTING: The study was conducted at 1 large quaternary-care referral hospital and 2 community hospitals. PARTICIPANTS: All adults ≥18 years of age hospitalized at a study hospital for ≥48 hours were included in the study. RESULTS: In total, 254,792 admissions for ≥48 hours occurred during the study period. The average age of these patients was 57.6 (±19.0) years, and 141,107 (55.6%) were female. At hospital 1, 78 CLABSIs, 33 CAUTIs, and 88 VAEs were documented during the pandemic period. Hospital 2 had 13 CLABSIs, 6 CAUTIs, and 17 VAEs. Hospital 3 recorded 11 CLABSIs, 8 CAUTIs, and 11 VAEs. Point estimates for hypothetical excess HAIs suggested an increase in all infection types across facilities, except for CLABSIs and CAUTIs at hospital 1 under the no pandemic scenario. CONCLUSIONS: The COVID-19 era was associated with increases in CLABSIs, CAUTIs, and VAEs at 3 hospitals in Missouri, with variations in significance by hospital and infection type. Continued vigilance in maintaining optimal infection prevention practices to minimize HAIs is warranted

Body Mass of Late Quaternary Mammals (Data Set)

The purpose of this data set was to compile body mass information for all mammals on Earth so that we could investigate the patterns of body mass seen across geographic and taxonomic space and evolutionary time. We were interested in the heritability of body size across taxonomic groups (How conserved is body mass within a genus, family, and order?), in the overall pattern of body mass across continents (Do the moments and other descriptive statistics remain the same across geographic space?), and over evolutionary time (How quickly did body mass patterns iterate on the patterns seen today? Were the Pleistocene extinctions size specific on each continent, and did these events coincide with the arrival of man?). These data are also part of a larger project that seeks to integrate body mass patterns across very diverse taxa (NCEAS Working Group on Body Size in Ecology and Paleoecology: linking pattern and process across space, time, and taxonomic scales). We began with the updated version of D. E. Wilson and D. M. Reeder’s taxonomic list of all known Recent mammals of the world (N 5 4629 species) to which we added status, distribution, and body mass estimates compiled from the primary and secondary literature. Whenever possible, we used an average of male and female body mass, which was in turn averaged over multiple localities to arrive at our species body mass values. The sources are line referenced in the main data set, with the actual references appearing in a table within the metadata. Mammals have individual records for each continent they occur on. Note that our data set is more than an amalgamation of smaller compilations. Although we relied heavily on a data set for Chiroptera by K. E. Jones (N 5 905), the CRC handbook of Mammalian Body Mass (N 5 688), and a data set compiled for South America by P. Marquet (N 5 505), these represent less than half the records in the current database. The remainder are derived from more than 150 other sources. Furthermore, we include a comprehensive late Pleistocene species assemblage for Africa, North and South America, and Australia (an additional 230 species). ‘‘Late Pleistocene’’ is defined as approximately 11 ka for Africa, North and South America, and as 50 ka for Australia, because these times predate anthropogenic impacts on mammalian fauna. Estimates contained within this data set represent a generalized species value, averaged across sexes and geographic space. Consequently, these data are not appropriate for asking population-level questions where the integration of body mass with specific environmental conditions is important. All extant orders of mammals are included, as well as several archaic groups (N 5 4859 species). Because some species are found on more than one continent (particularly Chiroptera), there are 5731 entries. We have body masses for the following: Artiodactyla (280 records), Bibymalagasia (2 records), Carnivora (393 records), Cetacea (75 records), Chiroptera (1071 records), Dasyuromorphia (67 records), Dermoptera (3 records), Didelphimorphia (68 records), Diprotodontia (127 records), Hydracoidea (5 records), Insectivora (234 records), Lagomorpha (53 records), Litopterna (2 records), Macroscelidea (14 records), Microbiotheria (1 record), Monotremata (7 records), Notoryctemorphia (1 record), Notoungulata (5 records), Paucituberculata (5 records), Peramelemorphia (24 records), Perissodactyla (47 records), Pholidota (8 records), Primates (276 records), Proboscidea (14 records), Rodentia (1425 records), Scandentia (15 records), Sirenia (6 records), Tubulidentata (1 record), and Xenarthra (75 records)

Trajectories in chronic disease accrual and mortality across the lifespan in Wales, UK (2005-2019), by area deprivation profile : linked electronic health records cohort study on 965,905 individuals

Funding: This work was supported by Health Data Research UK (HDRUK) Measuring and Understanding Multimorbidity using Routine Data in the UK (MUrMuRUK, HDR-9006; CFC0110). Health Data Research UK (HDR-9006) is funded by: UK Medical Research Council, Engineering and Physical Sciences Research Council, Economic and Social Research Council, the National Institute for Health Research (England), Chief Scientist Office of the Scottish Government Health and Social Care Directorates, Health and Social Care Research and Development Division (Welsh Government), Public Health Agency (Northern Ireland), British Heart Foundation, and Wellcome Trust. This work also was co-funded by the Medical Research Council (MRC) and the National Institute for Health Research (NIHR) through grant number MR/S027750/1. The work was supported by the ADR Wales programme of work, part of the Economic and Social Research Council (part of UK Research and Innovation) funded ADR UK (grant ES/S007393/1).Background  Understanding and quantifying the differences in disease development in different socioeconomic groups of people across the lifespan is important for planning healthcare and preventive services. The study aimed to measure chronic disease accrual, and examine the differences in time to individual morbidities, multimorbidity, and mortality between socioeconomic groups in Wales, UK. Methods  Population-wide electronic linked cohort study, following Welsh residents for up to 20 years (2000-2019). Chronic disease diagnoses were obtained from general practice and hospitalisation records using the CALIBER disease phenotype register. Multi-state models were used to examine trajectories of accrual of 132 diseases and mortality, adjusted for sex, age and area-level deprivation. Restricted mean survival time was calculated to measure time spent free of chronic disease(s) or mortality between socioeconomic groups. Findings  In total, 965,905 individuals aged 5-104 were included, from a possible 2·9m individuals following a 5-year clearance period, with an average follow-up of 13·2 years (12·7 million person-years). Some 673,189 (69·7 %) individuals developed at least one chronic disease or died within the study period. From ages 10 years upwards, the individuals living in the most deprived areas consistently experienced reduced time between health states, demonstrating accelerated transitions to first and subsequent morbidities and death compared to their demographic equivalent living in the least deprived areas. The largest difference were observed in 10 and 20 year old males developing multimorbidity (-0·45 years (99%CI:-0·45,-0·44)) and in 70 year old males dying after developing multimorbidity (-1·98 years (99%CI:-2·01,-1·95)). Interpretation  This study adds to the existing literature on health inequalities by demonstrating that individuals living in more deprived areas consistently experience accelerated time to diagnosis of chronic disease and death across all ages, accounting for competing risks.Publisher PDFPeer reviewe