We examined whether key sociodemographic and clinical risk factors for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection and mortality changed over time in a population-based ...cohort study.
In a cohort of 9,127,673 persons enrolled in the United States Veterans Affairs (VA) healthcare system, we evaluated the independent associations of sociodemographic and clinical characteristics with SARS-CoV-2 infection (n = 216,046), SARS-CoV-2-related mortality (n = 10,230), and case fatality at monthly intervals between February 1, 2020 and March 31, 2021. VA enrollees had a mean age of 61 years (SD 17.7) and were predominantly male (90.9%) and White (64.5%), with 14.6% of Black race and 6.3% of Hispanic ethnicity. Black (versus White) race was strongly associated with SARS-CoV-2 infection (adjusted odds ratio AOR 5.10, 95% CI 4.65 to 5.59, p-value <0.001), mortality (AOR 3.85 95% CI 3.30 to 4.50, p-value < 0.001), and case fatality (AOR 2.56, 95% CI 2.23 to 2.93, p-value < 0.001) in February to March 2020, but these associations were attenuated and not statistically significant by November 2020 for infection (AOR 1.03 95% CI 1.00 to 1.07 p-value = 0.05) and mortality (AOR 1.08 95% CI 0.96 to 1.20, p-value = 0.21) and were reversed for case fatality (AOR 0.86, 95% CI 0.78 to 0.95, p-value = 0.005). American Indian/Alaska Native (AI/AN versus White) race was associated with higher risk of SARS-CoV-2 infection in April and May 2020; this association declined over time and reversed by March 2021 (AOR 0.66 95% CI 0.51 to 0.85 p-value = 0.004). Hispanic (versus non-Hispanic) ethnicity was associated with higher risk of SARS-CoV-2 infection and mortality during almost every time period, with no evidence of attenuation over time. Urban (versus rural) residence was associated with higher risk of infection (AOR 2.02, 95% CI 1.83 to 2.22, p-value < 0.001), mortality (AOR 2.48 95% CI 2.08 to 2.96, p-value < 0.001), and case fatality (AOR 2.24, 95% CI 1.93 to 2.60, p-value < 0.001) in February to April 2020, but these associations attenuated over time and reversed by September 2020 (AOR 0.85, 95% CI 0.81 to 0.89, p-value < 0.001 for infection, AOR 0.72, 95% CI 0.62 to 0.83, p-value < 0.001 for mortality and AOR 0.81, 95% CI 0.71 to 0.93, p-value = 0.006 for case fatality). Throughout the observation period, high comorbidity burden, younger age, and obesity were consistently associated with infection, while high comorbidity burden, older age, and male sex were consistently associated with mortality. Limitations of the study include that changes over time in the associations of some risk factors may be affected by changes in the likelihood of testing for SARS-CoV-2 according to those risk factors; also, study results apply directly to VA enrollees who are predominantly male and have comprehensive healthcare and need to be confirmed in other populations.
In this study, we found that strongly positive associations of Black and AI/AN (versus White) race and urban (versus rural) residence with SARS-CoV-2 infection, mortality, and case fatality observed early in the pandemic were ameliorated or reversed by March 2021.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Ribosomal RNA profiling has become crucial to studying microbial communities, but meaningful taxonomic analysis and inter-comparison of such data are still hampered by technical limitations, ...between-study design variability and inconsistencies between taxonomies used.
Here we present MAPseq, a framework for reference-based rRNA sequence analysis that is up to 30% more accurate (F½ score) and up to one hundred times faster than existing solutions, providing in a single run multiple taxonomy classifications and hierarchical operational taxonomic unit mappings, for rRNA sequences in both amplicon and shotgun sequencing strategies, and for datasets of virtually any size.
Source code and binaries are freely available at https://github.com/jfmrod/mapseq.
mering@imls.uzh.ch.
Supplementary data are available at Bioinformatics online.
Liver steatosis is the most frequent liver disorder and its advanced stage, non-alcoholic steatohepatitis (NASH), will soon become the main reason for liver fibrosis and cirrhosis. The "multiple hits ...hypothesis" suggests that progression from simple steatosis to NASH is triggered by multiple factors including the gut microbiota composition. The Epstein Barr virus induced gene 2 (EBI2) is a receptor for the oxysterol 7a, 25-dihydroxycholesterol synthesized by the enzymes CH25H and CYP7B1. EBI2 and its ligand control activation of immune cells in secondary lymphoid organs and the gut. Here we show a concurrent study of the microbial dysregulation and perturbation of the EBI2 axis in a mice model of NASH.We used mice with wildtype, or littermates with CH25H
, EBI2
, or CYP7B1
genotypes fed with a high-fat diet (HFD) containing high amounts of fat, cholesterol, and fructose for 20 weeks to induce liver steatosis and NASH. Fecal and small intestinal microbiota samples were collected, and microbiota signatures were compared according to genotype and NASH disease state.We found pronounced differences in microbiota composition of mice with HFD developing NASH compared to mice did not developing NASH. In mice with NASH, we identified significantly increased 33 taxa mainly belonging to the Clostridiales order and/ or the family, and significantly decreased 17 taxa. Using an Elastic Net algorithm, we suggest a microbiota signature that predicts NASH in animals with a HFD from the microbiota composition with moderate accuracy (area under the receiver operator characteristics curve = 0.64). In contrast, no microbiota differences regarding the studied genotypes (wildtype vs knock-out CH25H
, EBI2
, or CYP7B1
) were observed.In conclusion, our data confirm previous studies identifying the intestinal microbiota composition as a relevant marker for NASH pathogenesis. Further, no link of the EBI2 - oxysterol axis to the intestinal microbiota was detectable in the current study.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The gastrointestinal tract is abundantly colonized by microbes, yet the translocation of oral species to the intestine is considered a rare aberrant event, and a hallmark of disease. By studying ...salivary and fecal microbial strain populations of 310 species in 470 individuals from five countries, we found that transmission to, and subsequent colonization of, the large intestine by oral microbes is common and extensive among healthy individuals. We found evidence for a vast majority of oral species to be transferable, with increased levels of transmission in colorectal cancer and rheumatoid arthritis patients and, more generally, for species described as opportunistic pathogens. This establishes the oral cavity as an endogenous reservoir for gut microbial strains, and oral-fecal transmission as an important process that shapes the gastrointestinal microbiome in health and disease.
We report the results of ultraviolet (UV) and optical photometric and spectroscopic analysis of the tidal disruption event (TDE) AT 2019qiz. Our follow-up observations started <10 days after the ...source began to brighten in the optical and lasted for a period of six months. Our late-time host-dominated spectrum indicates that the host galaxy likely harbors a weak active galactic nucleus. The initial Hubble Space Telescope (HST) spectrum of AT 2019qiz exhibits an iron and low-ionization broad absorption line (FeLoBAL) system that is seen for the first time in a TDE. This spectrum also bears a striking resemblance to that of Gaia16apd, a superluminous supernova. Our observations provide insights into the outflow properties in TDEs and show evidence for a connection between TDEs and engine-powered supernovae at early phases, as originally suggested by Metzger & Stone (2016). In a time frame of 50 days, the UV spectra of AT 2019qiz started to resemble those of previous TDEs with only high-ionization BALs. The change in UV spectral signatures is accompanied by a decrease in the outflow velocity, which began at 15,000 km/s and decelerated to ~ 10,000 km/s. A similar evolution in the Ha emission-line width further supports the speculation that the broad Balmer emission lines are formed in TDE outflows. In addition, we detect narrow absorption features on top of the FeLoBAL signatures in the early HST UV spectrum of AT 2019qiz. The measured H I column density corresponds to a Lyman-limit system, whereas the metal absorption lines (such as N V, C IV, Fe II, and Mg II) are likely probing the circumnuclear gas and interstellar medium in the host galaxy.
To identify gut and oral metagenomic signatures that accurately predict pancreatic ductal carcinoma (PDAC) and to validate these signatures in independent cohorts.
We conducted a multinational study ...and performed shotgun metagenomic analysis of fecal and salivary samples collected from patients with treatment-naïve PDAC and non-PDAC controls in Japan, Spain, and Germany. Taxonomic and functional profiles of the microbiomes were characterized, and metagenomic classifiers to predict PDAC were constructed and validated in external datasets.
Comparative metagenomics revealed dysbiosis of both the gut and oral microbiomes and identified 30 gut and 18 oral species significantly associated with PDAC in the Japanese cohort. These microbial signatures achieved high area under the curve values of 0.78 to 0.82. The prediction model trained on the Japanese gut microbiome also had high predictive ability in Spanish and German cohorts, with respective area under the curve values of 0.74 and 0.83, validating its high confidence and versatility for PDAC prediction. Significant enrichments of Streptococcus and Veillonella spp and a depletion of Faecalibacterium prausnitzii were common gut signatures for PDAC in all the 3 cohorts. Prospective follow-up data revealed that patients with certain gut and oral microbial species were at higher risk of PDAC-related mortality. Finally, 58 bacteriophages that could infect microbial species consistently enriched in patients with PDAC across the 3 countries were identified.
Metagenomics targeting the gut and oral microbiomes can provide a powerful source of biomarkers for identifying individuals with PDAC and their prognoses. The identification of shared gut microbial signatures for PDAC in Asian and European cohorts indicates the presence of robust and global gut microbial biomarkers.
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This study analyzed the gut and oral microbiomes of patients with pancreatic cancer and showed the potential of the microbial species to be used as a biomarker for the disease and its prognosis.
Energy intake (EI) and physical activity energy expenditure (PAEE) are key modifiable determinants of energy balance, traditionally assessed by self-report despite its repeated demonstration of ...considerable inaccuracies. We argue here that it is time to move from the common view that self-reports of EI and PAEE are imperfect, but nevertheless deserving of use, to a view commensurate with the evidence that self-reports of EI and PAEE are so poor that they are wholly unacceptable for scientific research on EI and PAEE. While new strategies for objectively determining energy balance are in their infancy, it is unacceptable to use decidedly inaccurate instruments, which may misguide health-care policies, future research and clinical judgment. The scientific and medical communities should discontinue reliance on self-reported EI and PAEE. Researchers and sponsors should develop objective measures of energy balance.
Microorganisms play a role in the progression of various cancers. In this issue of Cancer Cell, Ghaddar et al. traced bacteria in pancreatic tumors at single-cell resolution and associated their ...intracellular presence with cell-type-specific transcriptional shifts, with links to clinical prognosis.
Microorganisms play a role in the progression of various cancers. In this issue of Cancer Cell, Ghaddar et al. traced bacteria in pancreatic tumors at single-cell resolution and associated their intracellular presence with cell-type-specific transcriptional shifts, with links to clinical prognosis.
Recent advances in thermal infrared remote sensing include the increased availability of airborne hyperspectral imagers (such as the Hyperspectral Thermal Emission Spectrometer, HyTES, or the Telops ...HyperCam and the Specim aisaOWL), and it is planned that an increased number spectral bands in the long-wave infrared (LWIR) region will soon be measured from space at reasonably high spatial resolution (by imagers such as HyspIRI). Detailed LWIR emissivity spectra are required to best interpret the observations from such systems. This includes the highly heterogeneous urban environment, whose construction materials are not yet particularly well represented in spectral libraries. Here, we present a new online spectral library of urban construction materials including LWIR emissivity spectra of 74 samples of impervious surfaces derived using measurements made by a portable Fourier Transform InfraRed (FTIR) spectrometer. FTIR emissivity measurements need to be carefully made, else they are prone to a series of errors relating to instrumental setup and radiometric calibration, which here relies on external blackbody sources. The performance of the laboratory-based emissivity measurement approach applied here, that in future can also be deployed in the field (e.g. to examine urban materials in situ), is evaluated herein. Our spectral library also contains matching short-wave (VIS–SWIR) reflectance spectra observed for each urban sample. This allows us to examine which characteristic (LWIR and) spectral signatures may in future best allow for the identification and discrimination of the various urban construction materials, that often overlap with respect to their chemical/mineralogical constituents. Hyperspectral or even strongly multi-spectral LWIR information appears especially useful, given that many urban materials are composed of minerals exhibiting notable reststrahlen/absorption effects in this spectral region. The final spectra and interpretations are included in the London Urban Micromet data Archive (LUMA; http://LondonClimate.info/LUMA/SLUM.html).
Benzotetramisole promotes the catalytic asymmetric 2,3-rearrangement of allylic quaternary ammonium salts (either isolated or prepared in situ from p-nitrophenyl bromoacetate and the corresponding ...allylic amine), generating syn-α-amino acid derivatives with excellent diastereo- and enantioselectivity (up to >95:5 dr; up to >99% ee).
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