De novo identification of CD4+ T cell epitopes.

CD4+ T cells recognize peptide antigens presented on class II major histocompatibility complex (MHC-II) molecules to carry out their function. The remarkable diversity of T cell receptor sequences and lack of antigen discovery approaches for MHC-II make profiling the specificities of CD4+ T cells challenging. We have expanded our platform of signaling and antigen-presenting bifunctional receptors to encode MHC-II molecules presenting covalently linked peptides (SABR-IIs) for CD4+ T cell antigen discovery. SABR-IIs can present epitopes to CD4+ T cells and induce signaling upon their recognition, allowing a readable output. Furthermore, the SABR-II design is modular in signaling and deployment to T cells and B cells. Here, we demonstrate that SABR-IIs libraries presenting endogenous and non-contiguous epitopes can be used for antigen discovery in the context of type 1 diabetes. SABR-II libraries provide a rapid, flexible, scalable and versatile approach for de novo identification of CD4+ T cell ligands from single-cell RNA sequencing data using experimental and computational approaches.

Optimization of the allergen classification of the International Classification Of Diseases, 11th Revision (ICD-11).

BACKGROUND: Accurate diagnosis of triggers or causative allergens is essential for appropriate risk assessment, providing correct advice to patients with allergy and their caregivers and personalized treatment. However, allergens have never been represented in the World Health Organization International Classification of Diseases (ICD). OBJECTIVE: In this article, we present the process of selection of allergens to better fit the ICD, 11th Revision (ICD-11) structure and the outcomes of this process. METHODS: The Logical Observation Identifiers Names and Codes database, containing 1444 allergens, was used as the basis for the selection process. Two independent experts were responsible for the first selection of the allergens according to specific technical criteria. The second step of the selection process was based on real-life relevance of the allergens according to the frequency of requests regarding each of them. RESULTS: We selected 1109 allergens (76.8%) from all 1444 present in the Logical Observation Identifiers Names and Codes database, with considerable agreement between experts (Cohen κ = 8.6). After assessment of real-life data, 297 additional relevant allergens worldwide were selected and grouped as plants (36.4%), drugs (32.6%), animal proteins (21%), mold and other microorganisms (1.5%), occupational allergens (0.4%), and miscellaneous allergens (0.5%). CONCLUSION: The stepwise approach allowed us to select the most relevant allergens in practice, which is the first step to building a classification of allergens for the WHO ICD-11. Aligned with the achievement in the construction of the pioneer section addressed to the allergic and hypersensitivity conditions in the ICD-11, the introduction of a classification for allergens can be considered timely and much needed in clinical practice.

B-cell-specific MhcII regulates microbiota composition in a primarily IgA-independent manner.

Background: The expression of major histocompatibility complex class II (MhcII) molecules on B cells is required for the development of germinal centers (GCs) in lymphoid follicles; the primary sites for the generation of T-cell-dependent (TD) antibody responses. Peyer's patches (PPs) are secondary lymphoid tissues (SLOs) in the small intestine (SI) that give rise to high-affinity, TD antibodies (mainly immunoglobulin A (IgA)) generated against the microbiota. While several studies have demonstrated that MhcII antigen presentation by other immune cells coordinate TD IgA responses and regulate microbiota composition, whether or not B-cell-specific MhcII influences gut microbial ecology is unknown. Methods: Here, we developed a novel Rag1 -/- adoptive co-transfer model to answer this question. In this model, Rag1 -/- mice were reconstituted with naïve CD4+ T cells and either MhcII-sufficient or MhcII-deficient naïve B cells. Subsequent to this, resulting shifts in microbiota composition was characterized via 16S rRNA gene sequencing of SI-resident and fecal bacterial communities. Results: Results from our experiments indicate that SLO development and reconstitution of an anti-commensal TD IgA response can be induced in Rag1 -/- mice receiving T cells and MhcII-sufficient B cells, but not in mice receiving T cells and MhcII-deficient B cells. Results from our 16S experiments confirmed that adaptive immunity is a relevant host factor shaping microbial ecology in the gut, and that its impact was most pronounced on SI-resident bacterial communities. Conclusion: Our data also clearly establishes that MhcII-mediated cognate interactions between B cells and T cells regulates this effect by maintaining species richness in the gut, which is a phenotype commonly associated with good health. Finally, contrary to expectations, our experimental results indicate that IgA was not responsible for driving any of the effects on the microbiota ascribed to the loss of B cell-specific MhcII. Collectively, results from our experiments support that MhcII-mediated antigen presentation by B cells regulates microbiota composition and promotes species richness through an IgA-independent mechanism.

Sitmate: an android mobile application for the prevention of musculoskeletal discomfort among a business process outsourcing company workforce management personnel / The Health Sciences Journal

INTRODUCTION@#Due to COVID-19 pandemic, many have shifted into working at home which led to physical inactivity. This may cause musculoskeletal discomfort, chronic disease, muscle atrophy and spinal imbalance due to improper and prolonged sitting posture. Since mobile devices are relatively available for most of the office workers, there were still a lack of evidence-based mobile applications that can counteract the inactivity through exercises, which led to the researchers to create an application called SitMate that consists of evidence-based exercises which aimed to prevent musculoskeletal discomfort among a business process outsourcing company Workforce Management Personnel (BPO-WMP).@*METHODS@#Eleven participants (18-40 years old) full-time, work-from-home BPO-WMP were randomized into Treatment Group(TG)(n=6) and Control Group (CG)(n=5). The TG received one month intervention with the use of SitMate Application containing relaxation exercises, range of motion exercises and stretching exercises, and notifications for postural correction while the CG continued their usual working schedule.@*RESULTS@#There were no significant differences between two groups on all body parts that were measured using the Cornell Musculoskeletal Discomfort Questionnaire, and no significant differences in the intragroup pre-test and post-test scores on all body parts between TG and CG. For the intra-group post-test of the TG, there were noted improvements on the hip/buttock, right shoulder, upper back (median = 0) and right wrist (median = 1.5). There was also a noted increase in discomfort on the neck (median = 1.5) and lower back (median = 3). For the post-test of the CG, there were noted improvements on the right shoulder, right wrist (median = 0) and lower back (median = 1.5).@*CONCLUSION@#This study has shown that the SitMate application does not effectively reduce the prolonged sitting-related discomfort among the personnel after 1 month of intervention.

Metapopulation ecology links antibiotic resistance, consumption, and patient transfers in a network of hospital wards.

Antimicrobial resistance (AMR) is a global threat. A better understanding of how antibiotic use and between-ward patient transfers (or connectivity) impact population-level AMR in hospital networks can help optimize antibiotic stewardship and infection control strategies. Here, we used a metapopulation framework to explain variations in the incidence of infections caused by seven major bacterial species and their drug-resistant variants in a network of 357 hospital wards. We found that ward-level antibiotic consumption volume had a stronger influence on the incidence of the more resistant pathogens, while connectivity had the most influence on hospital-endemic species and carbapenem-resistant pathogens. Piperacillin-tazobactam consumption was the strongest predictor of the cumulative incidence of infections resistant to empirical sepsis therapy. Our data provide evidence that both antibiotic use and connectivity measurably influence hospital AMR. Finally, we provide a ranking of key antibiotics by their estimated population-level impact on AMR that might help inform antimicrobial stewardship strategies.

Semantic data interoperability, digital medicine, and e-health in infectious disease management: a review.

Disease management requires the use of mixed languages when discussing etiology, diagnosis, treatment, and follow-up. All phases require data management, and, in the optimal case, such data are interdisciplinary and uniform and clear to all those involved. Such semantic data interoperability is one of the technical building blocks that support emerging digital medicine, e-health, and P4-medicine (predictive, preventive, personalized, and participatory). In a world where infectious diseases are on a trend to become hard-to-treat threats due to antimicrobial resistance, semantic data interoperability is part of the toolbox to fight more efficiently against those threats. In this review, we will introduce semantic data interoperability, summarize its added value, and analyze the technical foundation supporting the standardized healthcare system interoperability that will allow moving forward to e-health. We will also review current usage of those foundational standards and advocate for their uptake by all infectious disease-related actors.

Brain and behavioral correlates of insulin resistance in youth with depression and obesity.

Depression, together with insulin resistance, is increasingly prevalent among youth. These conditions have traditionally been compartmentalized, but recent evidence suggests that a shared brain motivational network underlies their co-occurrence. We posit that, in the context of depressive symptoms, insulin resistance is associated with aberrant structure and functional connectivity in the Anterior Cingulate Cortex (ACC) and hippocampus. This motivational neural circuit underlies dysfunctional behavioral responses and increased sensitivity to rewarding aspects of ingesting high calorie food that lead to disinhibition of eating even when satiated. To investigate this shared mechanism, we evaluated a sample of forty-two depressed and overweight (BMI > 85th%) youth aged 9 to 17. Using ACC and hippocampus structural and seed-based regions of interest, we investigated associations between insulin resistance, depression, structure (ACC thickness, and ACC and hippocampal area), and resting-state functional connectivity (RSFC). We predicted that aberrant associations among these neural and behavioral characteristics would be stronger in insulin resistant compared to insulin sensitive youth. We found that youth with greater insulin resistance had higher levels of anhedonia and more food seeking behaviors, reduced hippocampal and ACC volumes, and greater levels of ACC and hippocampal dysconnectivity to fronto-limbic reward networks at rest. For youth with high levels of insulin resistance, thinner ACC and smaller hippocampal volumes were associated with more severe depressive symptoms, whereas the opposite was true for youth with low levels of insulin resistance. The ACC-hippocampal motivational network that subserves depression and insulin resistance separately, may represent a critical neural interaction that link these syndromes together.

Relationship between subjective and actigraphy-measured sleep in 237 patients with metastatic colorectal cancer.

OBJECTIVE: Patients with cancers frequently experience sleep and circadian dysfunction. To date, only a few studies have used both a questionnaire and actigraphy for concomitant evaluation of sleep and circadian function in patients with cancer. We sought to evaluate objective sleep and circadian parameters in metastatic colon cancer (MCC) patients and their associations with symptoms and quality of life (QOL). METHODS: Patients reported subjective sleep problems on the EORTC QLQ-C30. Sleep and circadian parameters were calculated using a wrist-actigraph that patients wore for 72 h. RESULTS: 237 Patients with MCC (mean age: 60.4 years; range: 20.7-77.6; Male/Female ratio: 1.66) participated in this cross-sectional study. Subjective sleep problems were reported by 63.4% of patients (S+). No differences in any sleep parameters (sleep efficiency, sleep latency, total sleep time, total time in bed, wake after sleep onset, activity bathyphase) were observed between S+ and S- patients. However, S+ patients displayed a significantly worse circadian function than S- patients (96.4 vs 98.1%; p = 0.005). The presence of poor subjective sleep and objective circadian dysfunction negatively affected symptoms and QOL domains (p = 0.038). CONCLUSIONS: Subjective report of sleep problems was not associated with worse objectively measured sleep parameters in patients with MCC although it was associated with disrupted circadian rest-activity rhythm and poorer QOL. These findings coincide with prior research in cancer patients in that an inconsistent relationship exists between subjective and objective sleep measurements on some sleep domains. This study supports the value of coupled evaluation of self-reported and objective measures of sleep and circadian function in cancer patients.

Φ-score: A cell-to-cell phenotypic scoring method for sensitive and selective hit discovery in cell-based assays.

Phenotypic screening monitors phenotypic changes induced by perturbations, including those generated by drugs or RNA interference. Currently-used methods for scoring screen hits have proven to be problematic, particularly when applied to physiologically relevant conditions such as low cell numbers or inefficient transfection. Here, we describe the Φ-score, which is a novel scoring method for the identification of phenotypic modifiers or hits in cell-based screens. Φ-score performance was assessed with simulations, a validation experiment and its application to gene identification in a large-scale RNAi screen. Using robust statistics and a variance model, we demonstrated that the Φ-score showed better sensitivity, selectivity and reproducibility compared to classical approaches. The improved performance of the Φ-score paves the way for cell-based screening of primary cells, which are often difficult to obtain from patients in sufficient numbers. We also describe a dedicated merging procedure to pool scores from small interfering RNAs targeting the same gene so as to provide improved visualization and hit selection.

Salvinorin B derivatives, EOM-Sal B and MOM-Sal B, produce stimulus generalization in male Sprague-Dawley rats trained to discriminate salvinorin A.

Salvinorin A, the main active component of Salvia divinorum, is a potent and selective κ opioid receptor agonist. Synthetic derivatives of this substance may be useful in the development of medicinal treatments for pain, mood disorders, and drug dependence. Such developments require extensive preclinical screening of these compounds. The drug discrimination assay is a valuable method for exploring potential similarities between novel compounds and known drugs of abuse with respect to their interoceptive stimulus properties, and can be used to investigate the potency of salvinorin A and its derivatives in vivo. This study used drug discrimination methods to compare two synthetic derivatives of salvinorin B, the ethoxymethyl ether (EOM-Sal B) and methoxymethyl ether (MOM-Sal B) with salvinorin A. Male Sprague-Dawley rats were trained to discriminate 2.0 mg/kg of salvinorin A from its vehicle (75% dimethylsulfoxide/25% water) in a fixed ratio 20 food-reinforced drug discrimination procedure, and were tested for stimulus generalization with EOM-Sal B and MOM-Sal B. For comparison, substitution tests were also conducted with a µ agonist, morphine, a dissociative hallucinogen, ketamine, and two serotonergic hallucinogens, D-lysergic diethylamide (LSD) and 1-(2,5-dimethoxy-4-methylphenyl)-2-aminopropane. Time-course tests were also conducted with salvinorin A and EOM-Sal B. Both EOM-Sal B and MOM-Sal B substituted fully for salvinorin A and displayed greater potency than salvinorin A. EOM-Sal B was discriminated at longer postinjection intervals than salvinorin A. Morphine and 1-(2,5-dimethoxy-4-methylphenyl)-2-aminopropane failed to substitute for salvinorin A, although ketamine and LSD produced significant drug-appropriate responding. The current findings are consistent with previous reports that salvinorin A produces detectable stimulus effects that are distinct from those of other drug classes and, for the first time, establish that synthetic derivatives of this substance produce similar discriminative stimulus effects. The unexpected partial substitution with LSD and ketamine indicate that further preclinical studies of these novel κ opioid receptor agonists may be warranted.

Fos-Tau-LacZ mice reveal sex differences in brainstem c-fos activation in response to mild carbon dioxide exposure.

There are sex differences in the neurochemistry of brainstem nuclei that participate in the control of breathing as well as sex differences in respiratory responses to hypoxia. Central chemoreception refers to the detection within the brain of minute changes in carbon dioxide (CO(2)) levels and the subsequent modulation of breathing. Putative central chemoreceptor sites are widespread and include cells located near the ventral surface of the brainstem in the retrotrapezoid nucleus (RTN), in the medullary midline raphe nuclei, and, more dorsally in the medulla, in the nucleus of the solitary tract and in the locus caeruleus at the pontomedullary junction as well as in the fastigial nucleus of the cerebellum. In this study, we ask if the cells that respond to CO(2) differ between the sexes. We used a transgenic mouse with a c-fos promoter driven tau-lacZ reporter construct (FTL) to map the locations of cells in the mouse brainstem and cerebellum that responded to exposure of mice of both sexes to 5% CO(2) or room air (control). X-gal (5-bromo-4-chloro-3-indolyl-beta-d-galactopyranoside) histochemical staining to detect the beta-galactosidase enzyme produced staining in the brains of mice of both sexes in all of the previously identified putative chemoreceptor sites, with the exception of the fastigial nucleus. Notably, the male RTN region contained significantly more x-gal-labeled cells than the female RTN region. In addition to new observations regarding potential sex differences in the retrotrapezoid region, we found the FTL mouse to be a useful tool for identifying cells that respond to the exposure of the whole animal to relatively low concentrations of CO(2).