Performance of microbiological tests for tuberculosis diagnostic according to the type of respiratory specimen: A 10-year retrospective study.

Background: The microbial diagnosis of tuberculosis (TB) remains challenging and relies on multiple microbiological tests performed on different clinical specimens. Polymerase chain reactions (PCRs), introduced in the last decades has had a significant impact on the diagnosis of TB. However, questions remain about the use of PCRs in combination with conventional tests for TB, namely microscopy and culture. We aimed to determine the performance of microscopy, culture and PCR for the diagnosis of pulmonary tuberculosis according to the type of clinical specimen in order to improve the diagnostic yield and to avoid unnecessary, time and labor-intensive tests. Methods: We conducted a retrospective study (2008-2018) on analysis (34'429 specimens, 14'358 patients) performed in our diagnostic laboratory located in the Lausanne University Hospital to compare the performance of microbiological tests on sputum, induced sputum, bronchial aspirate and bronchoalveolar lavage (BAL). We analysed the performance using a classical "per specimen" approach and a "per patient" approach for paired specimens collected from the same patient. Results: The overall sensitivities of microscopy, PCR and culture were 0.523 (0.489, 0.557), 0.798 (0.755, 0.836) and 0.988 (0.978, 0.994) and the specificity were 0.994 (0.993, 0.995), 1 (0.999, 1) and 1 (1, 1). Microscopy displayed no significant differences in sensitivity according to the type of sample. The sensitivities of PCR for sputum, induced sputum, bronchial aspirate and BAL were, 0.821 (0.762, 0.871), 0.643 (0.480, 0.784), 0.837 (0.748, 0.904) and 0.759 (0.624, 0.865) respectively and the sensitivity of culture were, 0.993 (0.981, 0.998), 0.980 (0.931, 0.998), 0.965 (0.919, 0.988), and 1 (0.961, 1) respectively. Pairwise comparison of specimens collected from the same patient reported a significantly higher sensitivity of PCR on bronchial aspirate over BAL (p < 0.001) and sputum (p < 0.05) and a significantly higher sensitivity of culture on bronchial aspirate over BAL (p < 0.0001). Conclusions: PCR displayed a higher sensitivity and specificity than microscopy for all respiratory specimens, a rational for a smear-independent PCR-based approach to initiate tuberculosis microbial diagnostic. The diagnosis yield of bronchial aspirate was higher than BAL. Therefore, PCR should be systematically performed also on bronchial aspirates when available.

Contemporary self-reflective practices: A large-scale survey.

Although self-reflection is a topic that appears in Human-Computer Interaction, the empirical data on the subject can often be dated, fragmented and focused on particular use cases. Our work sought to capture data that would help us better understand the current use of technologies to support self-reflection in the broader population. We did this through a large-scale online survey with a representative sample of internet users in the United Kingdom (N = 998) and a smaller series of follow-up interviews (N = 20). We found that, regardless of recent stress, those with high scores on a scale that measured self-reflection maintained a wider variety of self-reflective activities in recent months. Men reported more access and use of technology for self-reflective activity than women, but women's self-reflection scores were usually higher. We noted that high self-reflectors appear more spontaneous and experimental, using heuristics to mitigate common barriers or adapt their practice to stressors. These individuals appear to favour analogue objects to facilitate reflective practice, utilising technology in more strategic and selective ways.

An Automated Dashboard to Improve Laboratory COVID-19 Diagnostics Management.

Background: In response to the COVID-19 pandemic, our microbial diagnostic laboratory located in a university hospital has implemented several distinct SARS-CoV-2 RT-PCR systems in a very short time. More than 148,000 tests have been performed over 12 months, which represents about 405 tests per day, with peaks to more than 1,500 tests per days during the second wave. This was only possible thanks to automation and digitalization, to allow high throughput, acceptable time to results and to maintain test reliability. An automated dashboard was developed to give access to Key Performance Indicators (KPIs) to improve laboratory operational management. Methods: RT-PCR data extraction of four respiratory viruses-SARS-CoV-2, influenza A and B and RSV-from our laboratory information system (LIS), was automated. This included age, gender, test result, RT-PCR instrument, sample type, reception time, requester, and hospitalization status etc. Important KPIs were identified and the visualization was achieved using an in-house dashboard based on the open-source language R (Shiny). Results: The dashboard is organized into three main parts. The "Filter" page presents all the KPIs, divided into five sections: (i) general and gender-related indicators, (ii) number of tests and positivity rate, (iii) cycle threshold and viral load, (iv) test durations, and (v) not valid results. Filtering allows to select a given period, a dedicated instrument, a given specimen, an age range or a requester. The "Comparison" page allows a custom charting of all the available variables, which represents more than 182 combination. The "Data" page, gives the user an access to the raw data in tables format, with possibility of filtering, allowing for a deeper analysis and data download. Informations are updated every 4 h. Conclusions: By giving a rapid access to a huge number of up-to-date information, represented using the most relevant visualization types, without the burden of timely data extraction and analysis, the dashboard represents a reliable and user-friendly tool for operational laboratory management. The dashboard represents a reliable and user-friendly tool improving the decision-making process, resource planning and quality management.

Statistical inference in ensemble modeling of cellular metabolism.

Kinetic models of metabolism can be constructed to predict cellular regulation and devise metabolic engineering strategies, and various promising computational workflows have been developed in recent years for this. Due to the uncertainty in the kinetic parameter values required to build kinetic models, these workflows rely on ensemble modeling (EM) principles for sampling and building populations of models describing observed physiologies. Sensitivity coefficients from metabolic control analysis (MCA) of kinetic models can provide important insight about cellular control around a given physiological steady state. However, despite considering populations of kinetic models and their model outputs, current approaches do not provide adequate tools for statistical inference. To derive conclusions from model outputs, such as MCA sensitivity coefficients, it is necessary to rank/compare populations of variables with each other. Currently existing workflows consider confidence intervals (CIs) that are derived independently for each comparable variable. Hence, it is important to derive simultaneous CIs for the variables that we wish to rank/compare. Herein, we used an existing large-scale kinetic model of Escherichia Coli metabolism to present how univariate CIs can lead to incorrect conclusions, and we present a new workflow that applies three different multivariate statistical approaches. We use the Bonferroni and the exact normal methods to build symmetric CIs using the normality assumptions. We then suggest how bootstrapping can compute asymmetric CIs whilst relaxing this normality assumption. We conclude that the Bonferroni and the exact normal methods can provide simple and efficient ways for constructing reliable CIs, with the exact normal method favored over the Bonferroni when the compared variables present dependencies. Bootstrapping, despite its significantly higher computational cost, is recommended when comparing non-normal distributions of variables. Additionally, we show how the Bonferroni method can readily be used to estimate required sample numbers to attain a certain CI size.

Propagation of respiratory viruses in human airway epithelia reveals persistent virus-specific signatures.

BACKGROUND: The leading cause of acute illnesses, respiratory viruses, typically cause self-limited diseases, although severe complications can occur in fragile patients. Rhinoviruses (RVs), respiratory enteroviruses (EVs), influenza virus, respiratory syncytial viruses (RSVs), and coronaviruses are highly prevalent respiratory pathogens, but because of the lack of reliable animal models, their differential pathogenesis remains poorly characterized. OBJECTIVE: We sought to compare infections by respiratory viruses isolated from clinical specimens using reconstituted human airway epithelia. METHODS: Tissues were infected with RV-A55, RV-A49, RV-B48, RV-C8, and RV-C15; respiratory EV-D68; influenza virus H3N2; RSV-B; and human coronavirus (HCoV)-OC43. Replication kinetics, cell tropism, effect on tissue integrity, and cytokine secretion were compared. Viral adaptation and tissue response were assessed through RNA sequencing. RESULTS: RVs, RSV-B, and HCoV-OC43 infected ciliated cells and caused no major cell death, whereas H3N2 and EV-D68 induced ciliated cell loss and tissue integrity disruption. H3N2 was also detected in rare goblet and basal cells. All viruses, except RV-B48 and HCoV-OC43, altered cilia beating and mucociliary clearance. H3N2 was the strongest cytokine inducer, and HCoV-OC43 was the weakest. Persistent infection was observed in all cases. RNA sequencing highlighted perturbation of tissue metabolism and induction of a transient but important immune response at 4 days after infection. No majority mutations emerged in the viral population. CONCLUSION: Our results highlight the differential in vitro pathogenesis of respiratory viruses during the acute infection phase and their ability to persist under immune tolerance. These data help to appreciate the range of disease severity observed in vivo and the occurrence of chronic respiratory tract infections in immunocompromised hosts.

Pregnancy-induced Changes in Corneal Biomechanics and Topography Are Thyroid Hormone Related.

PURPOSE: To identify biomechanical and topographic changes of the cornea during pregnancy and the postpartum period and its association to hormonal changes. DESIGN: Prospective single-center observational cohort study. METHODS: Participants were 24 pregnant women (48 eyes), monitored throughout pregnancy and after delivery. Biomechanical and topographic corneal properties were measured using the Ocular Response Analyzer (ORA) and a Scheimpflug imaging system (Pentacam HR) each trimester and 1 month after delivery. At the same consultations blood plasma levels of estradiol (E2) and thyroid hormones (TSH, T3t, T4t) were also determined. A factorial MANCOVA was used to detect interactions between hormonal plasma levels and ocular parameters. RESULTS: Significant differences in corneal biomechanical and topographic parameters were found during pregnancy in relation to T3t (p = .01), T4t (p < .001), T3t/T4t (P = .001), and TSH (p = .001) plasma levels. E2 plasma levels (p = .092) and time period of measurement (p = .975) did not significantly affect corneal parameters. TSH levels significantly affected the maximal keratometry reading (p = .036), the vertical keratometry reading (p = .04), and the index of height asymmetry (p = .014). Those results persist after excluding hypothyroidism patients from the statistical analysis. CONCLUSIONS: Hormonal changes affecting corneal biomechanics and topography during pregnancy could be thyroid related. Dysthyroidism may directly influence corneal biomechanics and represents a clinically relevant factor that needs further investigation.

Establishing Corneal Cross-Linking With Riboflavin and UV-A in the Mouse Cornea In Vivo: Biomechanical Analysis.

PURPOSE: To establish corneal cross-linking (CXL) with riboflavin and UV-A in in the mouse cornea in vivo and to develop tools to measure the biomechanical changes observed. METHODS: A total of 55 male C57BL/6 wild-type mice (aged 5 weeks) were divided into 14 groups. Standard CXL parameters were adapted to the anatomy of the mouse cornea, and riboflavin concentration (0.1%-0.5%) and fluence series (0.09-5.4 J/cm²) were performed on the assumption of the endothelial damage thresholds. Untreated and riboflavin only corneas were used as controls. Animals were killed at 30 minutes and at 1 month after CXL. Corneas were harvested. Two-dimensional (2D) biomechanical testing was performed using a customized corneal holder in a commercially available stress-strain extensometer/indenter. Both elastic and viscoelastic analyses were performed. Statistical inference was performed using t-tests and specific mathematical models fitted to the experimental stress-strain and stress-relaxation data. Adjusted P values by the method of Benjamini and Hochberg are reported. RESULTS: For all CXL treatment groups, stress-relaxation showed significant differences (P < 0.0001) after 120 seconds of constant strain application, with cross-linked corneas maintaining a higher stress (441 ± 40 kPa) when compared with controls (337 ± 39 kPa). Stress-strain analysis confirmed these findings but was less sensitive to CXL-induced changes: at 0.5% of strain, cross-linked corneas remained at higher stress (778 ± 111 kPa) when compared with controls (659 ± 121 kPa). CONCLUSIONS: Cross-linking was induced in the mouse cornea in vivo, and its biomechanical effect successfully measured. This could create opportunities to study molecular pathways of CXL in transgenic mice.

Door-in-the-face: is it really necessary that both requests be made by the same requester?

The door-in-the-face technique increases the likelihood of individuals accepting a target request by confronting them, beforehand, with an extreme request. The present research tests a new door-in-the-face technique in which the two requests are formulated by two different requesters during the same interaction. 160 participants were asked to help a charity organization following a door-in-the-face procedure. According to the experimental conditions, requests were formulated by one or two requesters during the same or a different interaction. As predicted, the door-in-the-face effect was observed even if two requests are formulated by two requesters, but only if both are present during the interaction. Results are discussed in terms of a reciprocal concessions interpretation and a motivational interpretation.