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Advances in single‐cell level analytical techniques, especially cytometric approaches, have led to profound innovation in biomedical research, particularly in the field of clinical immunology. This has resulted in an expansion of high‐dimensional data, posing great challenges for comprehensive and unbiased analysis. Conventional manual analysis is thus becoming untenable to handle these challenges. Furthermore, most newly developed computational methods lack flexibility and interoperability, hampering their accessibility and usability. Here, we adapted Seurat, an R package originally developed for single‐cell RNA sequencing (scRNA‐seq) analysis, for high‐dimensional flow cytometric data analysis. Based on a 20‐marker antibody panel and analyses of T‐cell profiles in both adult blood and cord blood (CB), we showcased the robust capacity of Seurat in flow cytometric data analysis, which was further validated by Spectre, another high‐dimensional cytometric data analysis package, and conventional manual analysis. Importantly, we identified a unique CD8+ T‐cell population defined as CD8+CD45RA+CD27+CD161+ T cell that was predominantly present in CB. We characterised its IFN‐γ‐producing and potential cytotoxic properties using flow cytometry experiments and scRNA‐seq analysis from a published dataset. Collectively, we identified a unique human CB CD8+CD45RA+CD27+CD161+ T‐cell subset and demonstrated that Seurat, a widely used package for scRNA‐seq analysis, possesses great potential to be repurposed for cytometric data analysis. This facilitates an unbiased and thorough interpretation of complicated high‐dimensional data using a single analytical pipeline and opens a novel avenue for data‐driven investigation in clinical immunology. [ABSTRACT FROM AUTHOR]

Previous reports have shown that IL‐6 and IFN‐⍺ induce distinct transcriptomic and morphological changes in microglia. Here, we demonstrate that IL‐6 increases tissue surveillance, migration and phagocytosis in primary murine microglia, whereas IFN‐⍺ inhibits these functions. Our results provide a crucial link between transcriptome and function. It holds the potential to serve as the foundation for future studies aimed at identifying therapeutic targets for cytokine‐mediated neuroinflammatory diseases. [ABSTRACT FROM AUTHOR]

BackgroundThe impact of heat waves on mortality and health inequalities is well documented. Very few studies have assessed the effectiveness of heat action plans (HAPs) on health, and none has used quasi-experimental methods to estimate causal effects of such programs.ObjectivesWe developed a quasi-experimental method to estimate the causal effects associated with HAPs that allows the identification of heterogeneity across subpopulations, and to apply this method specifically to the case of the Montreal (Quebec, Canada) HAP.MethodsA difference-in-differences approach was undertaken using Montreal death registry data for the summers of 2000-2007 to assess the effectiveness of the Montreal HAP, implemented in 2004, on mortality. To study equity in the effect of HAP implementation, we assessed whether the program effects were heterogeneous across sex (male vs. female), age (≥ 65 years vs. < 65 years), and neighborhood education levels (first vs. third tertile). We conducted sensitivity analyses to assess the validity of the estimated causal effect of the HAP program.ResultsWe found evidence that the HAP contributed to reducing mortality on hot days, and that the mortality reduction attributable to the program was greater for elderly people and people living in low-education neighborhoods.ConclusionThese findings show promise for programs aimed at reducing the impact of extreme temperatures and health inequities. We propose a new quasi-experimental approach that can be easily applied to evaluate the impact of any program or intervention triggered when daily thresholds are reached. Citation: Benmarhnia T, Bailey Z, Kaiser D, Auger N, King N, Kaufman J. 2016. A difference-in-differences approach to assess the effect of a heat action plan on heat-related mortality, and differences in effectiveness according to sex, age, and socioeconomic status (Montreal, Quebec). Environ Health Perspect 124:1694-1699; http://dx.doi.org/10.1289/EHP203.

Nicholas B. King looks back at the dialectics of confidence and paranoia in the Ebola outbreaks of 1995 and 2014.

Background Photochemical tissue bonding (PTB) is a technique for peripheral nerve repair in which a collagenous membrane is bonded around approximated nerve ends. Studies using PTB with cryopreserved human amnion have shown promising results in a rat sciatic nerve transection model including a more rapid and complete return of function, larger axon size, and thicker myelination than suture repair. Commercial collagen membranes, such as dehydrated amnion allograft, are readily available, offer ease of storage, and have no risk of disease transmission or tissue rejection. However, the biomechanical properties of these membranes using PTB are currently unknown in comparison to PTB of cryopreserved human amnion and suture neurorrhaphy. Methods Rat sciatic nerves (n = 10 per group) were transected and repaired using either suture neurorrhaphy or PTB with one of the following membranes: cryopreserved human amnion, monolayer human amnion allograft (crosslinked and noncrosslinked), trilayer human amnion/chorion allograft (crosslinked and noncrosslinked), or swine submucosa. Repaired nerves were subjected to mechanical testing. Results During ultimate stress testing, the repair groups that withstood the greatest strain increases were suture neurorrhaphy (69 ± 14%), PTB with crosslinked trilayer amnion (52 ± 10%), and PTB with cryopreserved human amnion (46 ± 20%), although the differences between these groups were not statistically significant. Neurorrhaphy repairs had a maximum load (0.98 ± 0.30 N) significantly greater than all other repair groups except for noncrosslinked trilayer amnion (0.51 ± 0.27 N). During fatigue testing, all samples repaired with suture, or PTBs with either crosslinked or noncrosslinked trilayer amnion were able to withstand strain increases of at least 50%. Conclusion PTB repairs with commercial noncrosslinked amnion allograft membranes can withstand physiological strain and have comparable performance to repairs with human amnion, which has demonstrated efficacy in vivo. These results indicate the need for further testing of these membranes using in vivo animal model repairs. [ABSTRACT FROM AUTHOR]

Introduction: There are inconsistencies in outcome reporting for patients with necrotising soft tissue infections (NSTI). The aim of this study was to evaluate reported outcome measures in NSTI literature that could inform a core outcome set (COS) such as could be used in a study of hyperbaric oxygen in this indication. Methods: A systematic review of all NSTI literature identified from Cochrane, Ovid MEDLINE and Scopus databases as well as grey literature sources OpenGrey and the New York Academy of Medicine databases which met inclusion criteria and were published between 2010 and 2020 was performed. Studies were included if they reported on > 5 cases and presented clinical endpoints, patient related outcomes, or resource utilisation in NSTI patients. Studies did not have to include intervention. Two independent researchers then extracted reported outcome measures. Similar outcomes were grouped and classified into domains to produce a structured inventory. An attempt was made to identify trends in outcome measures over time and by study design. Results: Three hundred and seventy-five studies were identified and included a total of 311 outcome measures. Forty eight percent (150/311) of outcome measures were reported by two or more studies. The four most frequently reported outcome measures were mortality without time specified, length of hospital stay, amputation performed, and number of debridements, reported in 298 (79.5%), 260 (69.3%), 156 (41.6%) and 151 (40.3%) studies respectively. Mortality outcomes were reported in 23 different ways. Randomised controlled trials (RCTs) were more likely to report 28-day mortality or 90-day mortality. The second most frequent amputation related outcome was level of amputation, reported in 7.5% (28/375) of studies. The most commonly reported patient-centred outcome was the SF-36 which was reported in 1.6% (6/375) of all studies and in 2/10 RCTs. Conclusions: There was wide variance in outcome measures in NSTI studies, further highlighting the need for a COS. [ABSTRACT FROM AUTHOR]

CD8+ T cells are critical to the adaptive immune response against viral pathogens. However, overwhelming antigen exposure can result in their exhaustion, characterised by reduced effector function, failure to clear virus, and the upregulation of inhibitory receptors, including programmed cell death 1 (PD-1). However, exhausted T cell responses can be "re-invigorated" by inhibiting PD-1 or the primary ligand of PD-1: PD-L1. Further, the absence of the type I interferon receptor IFNAR1 also results in T cell exhaustion and virus persistence in lymphocytic choriomeningitis virus Armstrong (LCMV-Arm)-infected mice. In this study, utilizing single- and double-knockout mice, we aimed to determine whether ablation of PD-1 could restore T cell functionality in the absence of IFNAR1 signalling in LCMV-Arm-infected mice. Surprisingly, this did not re-invigorate the T cell response and instead, it converted chronic LCMV-Arm infection into a lethal disease characterized by severe lung inflammation with an infiltration of neutrophils and T cells. Depletion of CD8+ T cells, but not neutrophils, rescued mice from lethal disease, demonstrating that IFNAR1 is required to prevent T cell exhaustion and virus persistence in LCMV-Arm infection, and in the absence of IFNAR1, PD-L1 is required for survival. This reveals an important interplay between IFNAR1 and PD-L1 with implications for therapeutics targeting these pathways. [ABSTRACT FROM AUTHOR]