AVAILABILITY The method described in this paper has been incorporated into R package mpMap2. It is available from CRAN and also from https//github.com/rohan-shah/mpMap2. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online. © The Author(s) (2020). Published by Oxford University Press. All rights reserved. For Permissions, please email journals.permissions@oup.com.In population-based cancer studies, net survival is a crucial measure for population comparison purposes. However, alternative measures, namely the crude probability of death (CPr) and the number of life years lost (LYL) due to death according to different causes, are useful as complementary measures for reflecting different dimensions in terms of prognosis, treatment choice, or development of a control strategy. When the cause of death (COD) information is available, both measures can be estimated in competing risks setting using either cause-specific or subdistribution hazard regression models or with the pseudo-observation approach through direct modeling. We extended the pseudo-observation approach in order to model the CPr and the LYL due to different causes when information on COD is unavailable or unreliable (i.e., in relative survival setting). In a simulation study, we assessed the performance of the proposed approach in estimating regression parameters and examined models with different link functions that can provide an easier interpretation of the parameters. We showed that the pseudo-observation approach performs well for both measures and we illustrated their use on cervical cancer data from the England population-based cancer registry. A tutorial showing how to implement the method in R software is also provided. © The Author 2020. Published by Oxford University Press. All rights reserved. For permissions, please e-mail journals.permissions@oup.com.MOTIVATION Oxford Nanopore MinION is a portable DNA sequencer that is marketed as a device that can be deployed anywhere. Current base callers, however, require a powerful GPU to analyze data produced by MinION in real time, which hampers field applications. RESULTS We have developed a fast base caller DeepNano-blitz that can analyze stream from up to two MinION runs in real time using a common laptop CPU (i7-7700HQ), with no GPU requirements. The base caller settings allow trading accuracy for speed and the results can be used for real time run monitoring (i.e. sample composition, barcode balance, species identification, etc.) or pre-filtering of results for more detailed analysis (i.e. filtering out human DNA from human-pathogen runs). AVAILABILITY DeepNano-blitz has been developed and tested on Linux and Intel processors and is available under MIT license at https//github.com/fmfi-compbio/deepnano-blitz. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online. © The Author(s) (2020). Published by Oxford University Press. All rights reserved. Lonafarnib ic50 For Permissions, please email journals.permissions@oup.com.Background The new coronavirus, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has caused more than 210 000 deaths worldwide. However, little is known about the causes of death and the virus's pathologic features. Objective To validate and compare clinical findings with data from medical autopsy, virtual autopsy, and virologic tests. Design Prospective cohort study. Setting Autopsies performed at a single academic medical center, as mandated by the German federal state of Hamburg for patients dying with a polymerase chain reaction-confirmed diagnosis of COVID-19. Patients The first 12 consecutive COVID-19-positive deaths. Measurements Complete autopsy, including postmortem computed tomography and histopathologic and virologic analysis, was performed. Clinical data and medical course were evaluated. Results Median patient age was 73 years (range, 52 to 87 years), 75% of patients were male, and death occurred in the hospital (n = 10) or outpatient sector (n = 2). Coronary heart disease and asthmaimary Funding Source University Medical Center Hamburg-Eppendorf.[This corrects the article doi 10.1590/0004-282X20190139].To compare the shaping ability of different single-file systems in the preparation of mesial curved canals of mandibular molars using micro-CT technology. Fifteen mesial roots of mandibular molars with two independent and curved canals (n = 30) were selected, scanned at a resolution of 26.7 μm anatomically matched, and distributed into three groups (n = 10), according to the preparation system WaveOne 25.08, Reciproc 25.08, and OneShape 25.06. A final micro-CT scanning was performed, data sets were registered with their respective counterparts, and compared regarding the three-dimensional (volume, surface area, and structure model index - SMI) and two-dimensional (perimeter, area, roundness, major and minor diameters) parameters, as well as, canal transportation, using ANOVA and post hoc Tukey tests (α = 5%). Overall, no difference was observed between groups regarding area, perimeter, volume, surface area, and canal transportation (p > 0.05). Within group, no canal transportation was significantly higherobserved in the apical third (0.10 ± 0.05 mm) compared to coronal (0.08±0.040 mm) and middle (0.07 ± 0.03 mm) thirds (p less then 0.05). Structure model index (SMI) was statistically higher after preparation with OneShape instrument (0.36 ± 0.26) compared to other systems (p less then 0.05). Within the parameters of this study, similar shaping ability was observed in the preparation of mesial curved root canals of mandibular molars with Reciproc, OneShape and WaveOne systems.The possible role of B-cell growth and differentiation-related cytokines on the pathogenesis of diabetes-related periodontitis has not been addressed so far. The aim of this study was to evaluate the effects of diabetes mellitus (DM) on the gene expression of proliferation-inducing ligand (APRIL) and B-lymphocyte stimulator (BLyS), two major cytokines associated to survival, differentiation and maturation of B cells in biopsies from gingival tissue with periodontitis. Gingival biopsies were obtained from subjects with periodontitis (n = 17), with periodontitis and DM (n = 19) as well as from periodontally and systemically healthy controls (n = 10). Gene expressions for APRIL, BLyS, RANKL, OPG, TRAP and DC-STAMP were evaluated using qPCR. The expressions APRIL, BLyS, RANKL, OPG, TRAP and DC-STAMP were all higher in both periodontitis groups when compared to the control group (p less then 0.05). Furthermore, the expressions of BLyS, TRAP and RANKL were significantly higher in the subjects with periodontitis and DM when compared to those with periodontitis alone (p less then 0.