Uncertainty is a crucial issue in statistics which can be considered from different points of view. One type of uncertainty, typically referred to as sampling uncertainty, arises through the ...variability of results obtained when the same analysis strategy is applied to different samples. Another type of uncertainty arises through the variability of results obtained when using the same sample but different analysis strategies addressing the same research question. We denote this latter type of uncertainty as method uncertainty. It results from all the choices to be made for an analysis, for example, decisions related to data preparation, method choice, or model selection. In medical sciences, a large part of omics research is focused on the identification of molecular biomarkers, which can either be performed through ranking or by selection from among a large number of candidates. In this paper, we introduce a general resampling‐based framework to quantify and compare sampling and method uncertainty. For illustration, we apply this framework to different scenarios related to the selection and ranking of omics biomarkers in the context of acute myeloid leukemia: variable selection in multivariable regression using different types of omics markers, the ranking of biomarkers according to their predictive performance, and the identification of differentially expressed genes from RNA‐seq data. For all three scenarios, our findings suggest highly unstable results when the same analysis strategy is applied to two independent samples, indicating high sampling uncertainty and a comparatively smaller, but non‐negligible method uncertainty, which strongly depends on the methods being compared.
Anti-CD20 monoclonal antibodies are widely used for the treatment of hematological malignancies or autoimmune disease but may be responsible for a secondary humoral deficiency. In the context of ...COVID-19 infection, this may prevent the elicitation of a specific SARS-CoV-2 antibody response. We report a series of 17 consecutive patients with profound B-cell lymphopenia and prolonged COVID-19 symptoms, negative immunoglobulin G (IgG)-IgM SARS-CoV-2 serology, and positive RNAemia measured by digital polymerase chain reaction who were treated with 4 units of COVID-19 convalescent plasma. Within 48 hours of transfusion, all but 1 patient experienced an improvement of clinical symptoms. The inflammatory syndrome abated within a week. Only 1 patient who needed mechanical ventilation for severe COVID-19 disease died of bacterial pneumonia. SARS-CoV-2 RNAemia decreased to below the sensitivity threshold in all 9 evaluated patients. In 3 patients, virus-specific T-cell responses were analyzed using T-cell enzyme-linked immunospot assay before convalescent plasma transfusion. All showed a maintained SARS-CoV-2 T-cell response and poor cross-response to other coronaviruses. No adverse event was reported. Convalescent plasma with anti-SARS-CoV-2 antibodies appears to be a very promising approach in the context of protracted COVID-19 symptoms in patients unable to mount a specific humoral response to SARS-CoV-2.
Atypical hemolytic uremic syndrome (aHUS) emerged during the last decade as a disease largely of complement dysregulation. This advance facilitated the development of novel, rational treatment ...options targeting terminal complement activation, e.g., using an anti-C5 antibody (eculizumab). We review treatment and patient management issues related to this therapeutic approach. We present consensus clinical practice recommendations generated by HUS International, an international expert group of clinicians and basic scientists with a focused interest in HUS. We aim to address the following questions of high relevance to daily clinical practice: Which complement investigations should be done and when? What is the importance of anti-factor H antibody detection? Who should be treated with eculizumab? Is plasma exchange therapy still needed? When should eculizumab therapy be initiated? How and when should complement blockade be monitored? Can the approved treatment schedule be modified? What approach should be taken to kidney and/or combined liver–kidney transplantation? How should we limit the risk of meningococcal infection under complement blockade therapy? A pressing question today regards the treatment duration. We discuss the need for prospective studies to establish evidence-based criteria for the continuation or cessation of anticomplement therapy in patients with and without identified complement mutations.
Previous studies have highlighted the increased risk of contracting the COVID-19 for health-care workers and suggest that oral health-care workers may carry the greatest risk. Considering the ...transmission route of the SARS-CoV-2 infection, a similar increased risk can be hypothesized for other respiratory infections. However, no study has specifically assessed the risk of contracting COVID-19 within the dental profession.
An online survey was conducted within a population of French dental professionals between April 1 and April 29, 2020. Univariable and multivariable logistic regression analyses were performed to explore risk indicators associated with laboratory-confirmed COVID-19 and COVID-19-related clinical phenotypes (i.e. phenotypes present in 15% or more of SARS-CoV-2-positive cases).
4172 dentists and 1868 dental assistants responded to the survey, representing approximately 10% of French oral health-care workers. The prevalence of laboratory-confirmed COVID-19 was 1.9% for dentists and 0.8% for dental assistants. Higher prevalence was found for COVID-19-related clinical phenotypes both in dentists (15.0%) and dental assistants (11.8%). Chronic kidney disease and obesity were associated with increased odds of laboratory-confirmed COVID-19, whereas working in a practice limited to endodontics was associated with decreased odds. Chronic obstructive pulmonary disease, use of public transportation and having a practice limited to periodontology were associated with increased odds of presenting a COVID-19-related clinical phenotype. Moreover, changes in work rhythm or clinical practice were associated with decreased odds of both outcomes.
Although oral health-care professionals were surprisingly not at higher risk of COVID-19 than the general population, specific risk indicators could exist, notably among high aerosol-generating dental subspecialties such as periodontology. Considering the similarities between COVID-19-related clinical phenotypes other viral respiratory infections, lessons can be learned from the COVID-19 pandemic regarding the usefulness of equipping and protecting oral health-care workers, notably during seasonal viral outbreaks, to limit infection spread.
Results from this study may provide important insights for relevant health authorities regarding the overall infection status of oral health-care workers in the current pandemic and draw attention to particular at-risk groups, as illustrated in the present study. Protecting oral health-care workers could be an interesting public health strategy to prevent the resurgence of COVID-19 and/or the emergence of new pandemics.
Abstract
We present a detailed description of the wavelength, astrometric and photometric calibration plan for SITELLE, the imaging Fourier transform spectrometer attached to the Canada–France–Hawaii ...telescope, based on observations of a red (647–685 nm) data cube of the central region (11 arcmin × 11 arcmin) of M 31. The first application, presented in this paper is a radial-velocity catalogue (with uncertainties of ∼2–6 km s−1) of nearly 800 emission-line point-like sources, including ∼450 new discoveries. Most of the sources are likely planetary nebulae, although we also detect five novae (having erupted in the first eight months of 2016) and one new supernova remnant candidate.
Abstract
Across a species range, multiple sources of environmental heterogeneity, at both small and large scales, create complex landscapes of selection, which may challenge adaptation, particularly ...when gene flow is high. One key to multidimensional adaptation may reside in the heterogeneity of recombination along the genome. Structural variants, like chromosomal inversions, reduce recombination, increasing linkage disequilibrium among loci at a potentially massive scale. In this study, we examined how chromosomal inversions shape genetic variation across a species range and ask how their contribution to adaptation in the face of gene flow varies across geographic scales. We sampled the seaweed fly Coelopa frigida along a bioclimatic gradient stretching across 10° of latitude, a salinity gradient, and a range of heterogeneous, patchy habitats. We generated a chromosome-level genome assembly to analyze 1,446 low-coverage whole genomes collected along those gradients. We found several large nonrecombining genomic regions, including putative inversions. In contrast to the collinear regions, inversions and low-recombining regions differentiated populations more strongly, either along an ecogeographic cline or at a fine-grained scale. These genomic regions were associated with environmental factors and adaptive phenotypes, albeit with contrasting patterns. Altogether, our results highlight the importance of recombination in shaping adaptation to environmental heterogeneity at local and large scales.
Mus musculus is the classic mammalian model for biomedical research. Despite global efforts to standardize breeding and experimental procedures, the undefined composition and interindividual ...diversity of the microbiota of laboratory mice remains a limitation. In an attempt to standardize the gut microbiome in preclinical mouse studies, here we report the development of a simplified mouse microbiota composed of 15 strains from 7 of the 20 most prevalent bacterial families representative of the fecal microbiota of C57BL/6J Specific (and Opportunistic) Pathogen-Free (SPF/SOPF) animals and the derivation of a standardized gnotobiotic mouse model called GM15. GM15 recapitulates extensively the functionalities found in the C57BL/6J SOPF microbiota metagenome, and GM15 animals are phenotypically similar to SOPF or SPF animals in two different facilities. They are also less sensitive to the deleterious effects of post-weaning malnutrition. In this work, we show that the GM15 model provides increased reproducibility and robustness of preclinical studies by limiting the confounding effect of fluctuation in microbiota composition, and offers opportunities for research focused on how the microbiota shapes host physiology in health and disease.
Background
This study assessed the prevalence and risk factors of unhealthy behaviors among survivors of early‐stage breast cancer.
Methods
Women (n = 9556) from the CANcer TOxicity cohort ...(NCT01993498) were included. Physical activity (PA), tobacco and alcohol consumption, and body mass index were assessed at diagnosis and at years 1 and 2 after diagnosis. A behavior was defined as unhealthy if patients failed to meet PA recommendations (≥10 metabolic equivalent task hours per week), reduce/quit tobacco, or decrease alcohol consumption to less than daily, or if they gained substantial weight over time. Multivariable‐adjusted generalized estimating equations explored associations with unhealthy behaviors.
Results
At diagnosis, 41.7% of patients were inactive, 18.2% currently used tobacco, 14.6% consumed alcohol daily, and 48.9% were overweight or obese. At years 1 and 2, unhealthy PA behavior was reported among 37.0% and 35.6% of patients, respectively, unhealthy tobacco use behavior was reported among 11.4% and 9.5%, respectively, and unhealthy alcohol behavior was reported among 13.1% and 12.6%, respectively. In comparison with the previous assessment, 9.4% and 5.9% of underweight and normal‐weight patients had transitioned to the overweight or obese category at years 1 and 2, respectively, and 15.4% and 16.2% of overweight and obese patients had gained ≥5% of their weight at years 1 and 2, respectively. One in 3 current tobacco smokers and 1 in 10 daily alcohol users reported improved behaviors after diagnosis. Older women (5‐year increment) were more likely to be inactive (adjusted odds ratio aOR, 1.03; 95% confidence interval CI, 1.01‐1.05) and report unhealthy alcohol behavior (aOR, 1.28; 95% CI, 1.23‐1.33) but were less likely to engage in unhealthy tobacco use (aOR, 0.81; 95% CI, 0.78‐0.85). Being at risk for depression (vs not being at risk for depression) was associated with reduced odds of unhealthy tobacco use (aOR, 0.67; 95% CI, 0.46‐0.97) and with a higher likelihood of unhealthy alcohol behavior (aOR, 1.58; 95% CI, 1.14‐2.19). Women with a college education (vs a primary school education) less frequently reported an unhealthy PA behavior (aOR, 0.61; 95% CI, 0.51‐0.73) and were more likely to report unhealthy alcohol behavior (aOR, 1.85; 95% CI, 1.37‐2.49). Receipt of chemotherapy (vs not receiving chemotherapy) was associated with higher odds of gaining weight (aOR, 1.51; 95% CI, 1.23‐1.87) among those who were overweight or obese at diagnosis.
Conclusions
The majority of women were adherent to healthy lifestyle behaviors at the time of their breast cancer diagnosis, but a significant subset was nonadherent. Unhealthy behaviors tended to persist after the breast cancer diagnosis, having varying clinical, psychological, sociodemographic, and treatment‐related determinants. This study will inform more targeted interventions to promote optimal health.
Unhealthy behaviors are common at the diagnosis of breast cancer and tend to persist afterward with varying clinical, psychological, sociodemographic, and treatment‐related determinants. Targeted behavioral interventions are needed to promote optimal health for breast cancer survivors and capitalize on a teachable moment.
Complement pathway inhibition may provide benefit for severe acute respiratory illnesses caused by viral infections such as COVID-19. We present results from a nonrandomized proof-of-concept study of ...complement C5 inhibitor eculizumab for treatment of severe COVID-19.
All patients (N = 80) with confirmed SARS-CoV-2 infection and severe COVID-19 admitted to our intensive care unit between March 10 and May 5, 2020 were included. Forty-five patients were treated with standard care and 35 with standard care plus eculizumab through expanded-access emergency treatment. The prespecified primary outcome was day-15 survival. Clinical laboratory values and biomarkers, complement levels, and treatment-emergent serious adverse events (TESAEs) were also assessed.
At day 15, estimated survival was 82.9% (95% CI: 70.4%‒95.3%) with eculizumab and 62.2% (48.1%‒76.4%) without eculizumab (log-rank test, P = 0.04). Patients treated with eculizumab experienced a significantly more rapid decrease in lactate, blood urea nitrogen, total and conjugated bilirubin levels and a significantly more rapid increase in platelet count, prothrombin time, and in the ratio of arterial oxygen tension over fraction of inspired oxygen versus patients treated without eculizumab. Eculizumab-associated changes in complement levels, laboratory values, and biomarkers were consistent with terminal complement inhibition, reduced hypoxia, and decreased inflammation. TESAEs of special interest occurring in >5% of patients treated with/without eculizumab were ventilator-associated pneumonia (51%/24%), bacteremia (11%/2%), gastroduodenal hemorrhage (14%/16%), and hemolysis (3%/18%).
Findings from this proof-of-concept study suggest eculizumab may improve survival and reduce hypoxia in patients with severe COVID-19. Randomized studies evaluating the efficacy and safety of this treatment approach are needed.
Programme d'Investissements d'Avenir: ANR-18-RHUS60004.
It is currently accepted that cancer-associated fibroblasts (CAF) participate in T-cell exclusion from tumor nests. To unbiasedly test this, we used single-cell RNA sequencing coupled with multiplex ...imaging on a large cohort of lung tumors. We identified four main CAF populations, two of which are associated with T-cell exclusion: (i) MYH11+αSMA+ CAF, which are present in early-stage tumors and form a single cell layer lining cancer aggregates, and (ii) FAP+αSMA+ CAF, which appear in more advanced tumors and organize in patches within the stroma or in multiple layers around tumor nests. Both populations orchestrate a particular structural tissue organization through dense and aligned fiber deposition compared with T cell-permissive CAF. Yet they produce distinct matrix molecules, including collagen IV (MYH11+αSMA+ CAF) and collagen XI/XII (FAP+αSMA+ CAF). Hereby, we uncovered unique molecular programs of CAF driving T-cell marginalization, whose targeting should increase immunotherapy efficacy in patients bearing T cell-excluded tumors.
The cellular and molecular programs driving T-cell marginalization in solid tumors remain unclear. Here, we describe two CAF populations associated with T-cell exclusion in human lung tumors. We demonstrate the importance of pairing molecular and spatial analysis of the tumor microenvironment, a prerequisite to developing new strategies targeting T cell-excluding CAF. See related commentary by Sherman, p. 2501. This article is highlighted in the In This Issue feature, p. 2483.
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