Specialized interferon action in COVID-19.

The impacts of interferon (IFN) signaling on COVID-19 pathology are multiple, with both protective and harmful effects being documented. We report here a multiomics investigation of systemic IFN signaling in hospitalized COVID-19 patients, defining the multiomics biosignatures associated with varying levels of 12 different type I, II, and III IFNs. The antiviral transcriptional response in circulating immune cells is strongly associated with a specific subset of IFNs, most prominently IFNA2 and IFNG. In contrast, proteomics signatures indicative of endothelial damage and platelet activation associate with high levels of IFNB1 and IFNA6. Seroconversion and time since hospitalization associate with a significant decrease in a specific subset of IFNs. Additionally, differential IFN subtype production is linked to distinct constellations of circulating myeloid and lymphoid immune cell types. Each IFN has a unique metabolic signature, with IFNG being the most associated with activation of the kynurenine pathway. IFNs also show differential relationships with clinical markers of poor prognosis and disease severity. For example, whereas IFNG has the strongest association with C-reactive protein and other immune markers of poor prognosis, IFNB1 associates with increased neutrophil to lymphocyte ratio, a marker of late severe disease. Altogether, these results reveal specialized IFN action in COVID-19, with potential diagnostic and therapeutic implications.

FunSpace: A functional and spatial analytic approach to cell imaging data using entropy measures.

Spatial heterogeneity in the tumor microenvironment (TME) plays a critical role in gaining insights into tumor development and progression. Conventional metrics typically capture the spatial differential between TME cellular patterns by either exploring the cell distributions in a pairwise fashion or aggregating the heterogeneity across multiple cell distributions without considering the spatial contribution. As such, none of the existing approaches has fully accounted for the simultaneous heterogeneity caused by both cellular diversity and spatial configurations of multiple cell categories. In this article, we propose an approach to leverage spatial entropy measures at multiple distance ranges to account for the spatial heterogeneity across different cellular organizations. Functional principal component analysis (FPCA) is applied to estimate FPC scores which are then served as predictors in a Cox regression model to investigate the impact of spatial heterogeneity in the TME on survival outcome, potentially adjusting for other confounders. Using a non-small cell lung cancer dataset (n = 153) as a case study, we found that the spatial heterogeneity in the TME cellular composition of CD14+ cells, CD19+ B cells, CD4+ and CD8+ T cells, and CK+ tumor cells, had a significant non-zero effect on the overall survival (p = 0.027). Furthermore, using a publicly available multiplexed ion beam imaging (MIBI) triple-negative breast cancer dataset (n = 33), our proposed method identified a significant impact of cellular interactions between tumor and immune cells on the overall survival (p = 0.046). In simulation studies under different spatial configurations, the proposed method demonstrated a high predictive power by accounting for both clinical effect and the impact of spatial heterogeneity.

Dysregulated Lymphocyte Antigen Receptor Signaling in Common Variable Immunodeficiency with Granulomatous Lymphocytic Interstitial Lung Disease.

PURPOSE: A subset of common variable immunodeficiency (CVID) patients either presents with or develops autoimmune and lymphoproliferative complications, such as granulomatous lymphocytic interstitial lung disease (GLILD), a major cause of morbidity and mortality in CVID. While a myriad of phenotypic lymphocyte derangements has been associated with and described in GLILD, defects in T and B cell antigen receptor (TCR/BCR) signaling in CVID and CVID with GLILD (CVID/GLILD) remain undefined, hindering discovery of biomarkers for disease monitoring, prognostic prediction, and personalized medicine approaches. METHODS: To identify perturbations of immune cell subsets and TCR/BCR signal transduction, we applied mass cytometry analysis to peripheral blood mononuclear cells (PBMCs) from healthy control participants (HC), CVID, and CVID/GLILD patients. RESULTS: Patients with CVID, regardless of GLILD status, had increased frequency of HLADR+CD4+ T cells, CD57+CD8+ T cells, and CD21lo B cells when compared to healthy controls. Within these cellular populations in CVID/GLILD patients only, engagement of T or B cell antigen receptors resulted in discordant downstream signaling responses compared to CVID. In CVID/GLILD patients, CD21lo B cells showed perturbed BCR-mediated phospholipase C gamma and extracellular signal-regulated kinase activation, while HLADR+CD4+ T cells and CD57+CD8+ T cells displayed disrupted TCR-mediated activation of kinases most proximal to the receptor. CONCLUSION: Both CVID and CVID/GLILD patients demonstrate an activated T and B cell phenotype compared to HC. However, only CVID/GLILD patients exhibit altered TCR/BCR signaling in the activated lymphocyte subsets. These findings contribute to our understanding of the mechanisms of immune dysregulation in CVID with GLILD.

PaIRKAT: A pathway integrated regression-based kernel association test with applications to metabolomics and COPD phenotypes.

High-throughput data such as metabolomics, genomics, transcriptomics, and proteomics have become familiar data types within the "-omics" family. For this work, we focus on subsets that interact with one another and represent these "pathways" as graphs. Observed pathways often have disjoint components, i.e., nodes or sets of nodes (metabolites, etc.) not connected to any other within the pathway, which notably lessens testing power. In this paper we propose the Pathway Integrated Regression-based Kernel Association Test (PaIRKAT), a new kernel machine regression method for incorporating known pathway information into the semi-parametric kernel regression framework. This work extends previous kernel machine approaches. This paper also contributes an application of a graph kernel regularization method for overcoming disconnected pathways. By incorporating a regularized or "smoothed" graph into a score test, PaIRKAT can provide more powerful tests for associations between biological pathways and phenotypes of interest and will be helpful in identifying novel pathways for targeted clinical research. We evaluate this method through several simulation studies and an application to real metabolomics data from the COPDGene study. Our simulation studies illustrate the robustness of this method to incorrect and incomplete pathway knowledge, and the real data analysis shows meaningful improvements of testing power in pathways. PaIRKAT was developed for application to metabolomic pathway data, but the techniques are easily generalizable to other data sources with a graph-like structure.

Reproducibility of mass spectrometry based metabolomics data.

BACKGROUND: Assessing the reproducibility of measurements is an important first step for improving the reliability of downstream analyses of high-throughput metabolomics experiments. We define a metabolite to be reproducible when it demonstrates consistency across replicate experiments. Similarly, metabolites which are not consistent across replicates can be labeled as irreproducible. In this work, we introduce and evaluate the use (Ma)ximum (R)ank (R)eproducibility (MaRR) to examine reproducibility in mass spectrometry-based metabolomics experiments. We examine reproducibility across technical or biological samples in three different mass spectrometry metabolomics (MS-Metabolomics) data sets. RESULTS: We apply MaRR, a nonparametric approach that detects the change from reproducible to irreproducible signals using a maximal rank statistic. The advantage of using MaRR over model-based methods that it does not make parametric assumptions on the underlying distributions or dependence structures of reproducible metabolites. Using three MS Metabolomics data sets generated in the multi-center Genetic Epidemiology of Chronic Obstructive Pulmonary Disease (COPD) study, we applied the MaRR procedure after data processing to explore reproducibility across technical or biological samples. Under realistic settings of MS-Metabolomics data, the MaRR procedure effectively controls the False Discovery Rate (FDR) when there was a gradual reduction in correlation between replicate pairs for less highly ranked signals. Simulation studies also show that the MaRR procedure tends to have high power for detecting reproducible metabolites in most situations except for smaller values of proportion of reproducible metabolites. Bias (i.e., the difference between the estimated and the true value of reproducible signal proportions) values for simulations are also close to zero. The results reported from the real data show a higher level of reproducibility for technical replicates compared to biological replicates across all the three different datasets. In summary, we demonstrate that the MaRR procedure application can be adapted to various experimental designs, and that the nonparametric approach performs consistently well. CONCLUSIONS: This research was motivated by reproducibility, which has proven to be a major obstacle in the use of genomic findings to advance clinical practice. In this paper, we developed a data-driven approach to assess the reproducibility of MS-Metabolomics data sets. The methods described in this paper are implemented in the open-source R package marr, which is freely available from Bioconductor at http://bioconductor.org/packages/marr .

Subjects at-risk for future development of rheumatoid arthritis demonstrate a PAD4-and TLR-dependent enhanced histone H3 citrullination and proinflammatory cytokine production in CD14hi monocytes.

The presence of anti-citrullinated protein/peptide antibodies (ACPA) and epitope spreading across the target autoantigens is a unique feature of rheumatoid arthritis (RA). ACPA are present in the peripheral blood for several years prior to the onset of arthritis and clinical classification of RA. ACPA recognize multiple citrullinated proteins, including histone H3 (H3). Intracellular citrullination of H3 in neutrophils and T cells is known to regulate immune cell function by promoting neutrophil extracellular trap formation and citrullinated autoantigen release as well as regulating the Th2/Th17 T cell phenotypic balance. However, the roles of H3 citrullination in other immune cells are not fully elucidated. We aimed to explore H3 citrullination and cytokine/metabolomic signatures in peripheral blood immune cells from subjects prior to and after the onset of RA, at baseline and in response to ex vivo toll-like receptor (TLR) stimulation. Here, we analyzed 13 ACPA (+) subjects without arthritis but at-risk for future development of RA, 14 early RA patients, and 13 healthy controls. We found significantly elevated H3 citrullination in CD14hi monocytes, as well as CD1c+ dendritic cells and CD66+ granulocytes. Unsupervised analysis identified two distinct subsets in CD14hi monocytes characterized by H3 modification and unique cytokine/metabolomic signatures. CD14hi monocytes with elevated TLR-stimulated H3 citrullination were significantly increased in ACPA (+) at-risk subjects. These cells were skewed to produce TNFα, MIP1ß, IFNα, and partially IL-12. Additionally, they demonstrate peptidyl arginine deiminase 4 (PAD4) mediated upregulation of the glycolytic enzyme PFKFB3. These CD14hi monocytes with elevated H3 citrullination morphologically formed monocyte extracellular traps (METs). Taken together, dysregulated PAD4-driven cytokine production as well as MET formation in CD14hi monocytes in ACPA (+) at-risk subjects likely plays an important role in the development of RA via promoting and perpetuating inflammation and generation of citrullinated autoantigens.

Optimization of intracerebroventricular streptozotocin dose for the induction of neuroinflammation and memory impairments in rats.

Intracerebroventricular (ICV) injection of streptozotocin (STZ) is a well established procedure to induce neuroinflammation leading to dementia in experimental animals. However, the optimal dose of STZ has not been determined. In the present study, rats were ICV injected with 1.5, 3 and 6 mg of STZ per kg of body weight. After 21 days, neuroinflammatory markers i.e. TNF-α, IL-1ß, ROS and nitrite were quantified in the hippocampus. Memory function was assessed by the radial arm maze test after 9, 12, 15, 18, 21 days following STZ injection. STZ treatment significantly increased neuroinflammatory markers and decreased memory functions in a dose dependent manner showing optimum effects at the dose of 3 mg/kg.

Serum iron deficiency was associated with lower cognitive development in the children of the Santal tribe of West Bengal.

AIM: Poor cognitive scores and low serum iron have been reported among chronically undernourished children from the Santal tribe, West Bengal. Our aim was to investigate the association between iron status and non-verbal cognitive development. METHODS: We randomly selected 170 children (52.9% boys) aged 5-12 years from the Purulia district of West Bengal during 2007-2008 and assessed their iron status: haemoglobin concentration, serum concentration of iron, ferritin, transferrin, total iron-binding capacity and transferrin saturation. Their non-verbal cognitive development was assessed using the Raven's Coloured Progressive Matrices. RESULTS: The haemoglobin concentration, serum iron, serum ferritin and transferrin saturation levels of the 27 children with an intellectual deficit and the 32 who had a below average intelligence quotient (IQ) were significantly lower (P < .05) than the 65 children with an average IQ. A large number of boys (55.6%) and girls (41.7%) who have an intellectual deficit had stage III iron depletion. The cognitive scores of children with stage II and III iron depletion were significantly lower (P < .05) than those with a normal IQ. CONCLUSION: The iron depletion stage was associated with the severity of non-verbal cognitive impairment and serum ferritin appeared to be a sensitive biomarker for predicting non-verbal cognitive development.

Factors associated With the development of motor proficiency in school children of Kolkata: A cross-sectional study to assess the role of chronic nutritional and socio-economic status.

BACKGROUND: Development of coordinated movements is determined among others by individual growth and environmental factors, but the dynamic relationship between motor proficiency and potential contributing factors such as chronic nutritional status and socio-economic status (SES) is not known in school children of Kolkata. AIM: To characterize the motor proficiency in school children of Kolkata and to investigate association of chronic nutritional and SES on motor proficiency. METHODS: Motor proficiency in 843 school children of Kolkata aged 5-12 years was assessed by the Bruininks-Oseretsky Test of Motor-Proficiency-Second Edition-Short Form (BOT-2 SF). Chronic nutritional status was determined from height-for-age Z-scores (HAZ) using WHO reference and SES was measured using the updated Kuppuswamy's scale. RESULTS: Children's motor proficiency was poor compared with the reference values. Children classified as severely undernourished and children of lower SES were found to be "below average" and "well-below average" in motor proficiency categories compared with normal nourished groups and children of upper SES. Children's BOT-2 SF standardized scores decreased incrementally with the severity of chronic undernutrition and lower grades of SES. CONCLUSION: Chronic undernutrition and lower SES are associated with poorer motor proficiency in children. Understanding the complex interrelationships that shape childen's motor skills can help inform the development of health promotion programs and tailored interventions to help children reach their full potential. © 2016 Wiley Periodicals, Inc. Dev Psychobiol 58:734-744, 2016.

Grades of undernutrition and socioeconomic status influence cognitive development in school children of Kolkata.

Cognitive development of children is influenced by different environmental factors like nutritional and socio-economic status. The objectives of the present study were to determine the influence of grades of undernutrition and socio-economic status (SES) on the cognitive development of school children of Kolkata. Five hundred sixty six (566) school children having 5-12 years of age were selected from different schools of Kolkata. The cognitive development was measured by the scores of Raven's colored progressive matrices (RCPM). The chronic and acute nutritional statuses were measured from height-for-age (HAZ) and weight-for-age (WAZ) Z scores respectively with reference to the values of WHO. SES was determined by updated Kuppuswamy scale. The prevalences of undernutrition in the observed children were 57.95% (according to HAZ) and 52.82% (according to WAZ). The age dependent growth curve of RCPM scores of the observed children remains in between the 10th and 25th centile of British children. The children belonging to superior and intellectual deficit IQ classes were 21.55 and 36.40%, respectively of the total subjects. Most of the subjects belong to lower middle (39.93%) and upper middle (36.40%) class of SES. RCPM scores of school children were gradually decreased with the grades of undernutrition and SES. RCPM scores were significantly correlated with HAZ, WAZ, SES, age, and sex (P < 0.001) and strongly associated with HAZ, SES, age, and sex (P < 0.001, P < 0.05). Present study indicates that cognitive development of school children of Kolkata is influenced by the grade of undernutrition and SES.

Effects of naproxen on immune responses in a colchicine-induced rat model of Alzheimer's disease.

BACKGROUND: The components of the immune system have been indicated to be linked with the neurotoxicity in Alzheimer's disease (AD). The participation of the immune system in the neurodegeneration in a rat model of colchicine-induced AD has not been explored. METHODS: In the present study, hippocampal neurodegeneration along with reactive oxygen species (ROS), nitrite and TNF-α in the hippocampus and some systemic immune responses were measured after 15 and 21 days of intracerebroventricular colchicine injection in rats and again after oral administration of different doses of the anti-inflammatory drug naproxen in AD rats. RESULTS: Chromatolysis and amyloid plaques were found along with higher ROS, nitrite and TNF-α levels in the hippocampus of colchicine-induced AD rats, and these changes were prevented by naproxen in a dose-dependent manner. Alterations in immunological parameters [increased phagocytic activity of white blood cells and splenic polymorphonuclear cells (PMN), increased cytotoxicity and decreased leucocyte adhesive inhibition index (LAI) of splenic mononuclear cells (MNC)] were also observed in colchicine-injected rats, which showed a dose-dependent recovery after oral administration of naproxen in AD rats. The number of plaques, chromatolysis of Nissl granules, TNF-α, nitrite and ROS levels in the hippocampus, phagocytic activity of splenic PMN and LAI of splenic MNC in AD rats showed greater changes in the 21- than in the 15-day study, and the recovery of these parameters after administration of naproxen differed between the two study durations. CONCLUSION: The present study shows that colchicine-induced neurodegeneration is time dependent and mediated by cyclooxygenase-induced neuroinflammation, which is reflected in the systemic immunological responses.

Effects of vitamin C on the hypobaric hypoxia-induced immune changes in male rats.

Hypobaric hypoxia (HH) induces oxidative stress (OS) and is associated with the generation of reactive oxygen species (ROS). Vitamin C is an efficient antioxidant, and it is used in a high-altitude environment to reduce the OS. The present study explores the role of vitamin C on some HH-induced changes of immune parameters in rats which were exposed to HHc condition at 18,000 ft in a simulated chamber for 8 h/day for 6 days with and without vitamin C administration at three different doses (200, 400, and 600 mg/kg body wt). The phagocytic activity of circulating blood WBC was increased, and the cytotoxic activity of splenic mononuclear cell (MNC) and the delayed type of hypersensitivity (DTH) responses to bovine serum albumin (BSA) were decreased in rats exposed to HHc condition, but these immune changes were blocked after administration of vitamin C at 400 mg/kg body wt. The leukocyte adhesive inhibition index (LAI) was not altered either in HHc condition or after administration of vitamin C in HHc condition. The serum corticosterone (CORT) concentration was increased in rats exposed to HHc condition which was blocked after administration of vitamin C (400 mg/kg body wt). The immune parameters and serum CORT concentration, however, did not show any recovery after administration of vitamin C at the dose of 200 and 600 mg/kg body wt. The present study indicates that administration of vitamin C at a dose of 400 mg/kg body wt may prevent the HH-induced immunological changes but not at the lower dose (200 mg/kg body wt) or higher dose (600 mg/kg body wt) in rats.

SARS-CoV-2 Vaccine-Elicited Immunity after B Cell Depletion in Multiple Sclerosis.

The impact of B cell deficiency on the humoral and cellular responses to SARS-CoV2 mRNA vaccination remains a challenging and significant clinical management question. We evaluated vaccine-elicited serological and cellular responses in 1) healthy individuals who were pre-exposed to SARS-CoV-2 (n = 21), 2) healthy individuals who received a homologous booster (mRNA, n = 19; or Novavax, n = 19), and 3) persons with multiple sclerosis on B cell depletion therapy (MS-αCD20) receiving mRNA homologous boosting (n = 36). Pre-exposure increased humoral and CD4 T cellular responses in immunocompetent individuals. Novavax homologous boosting induced a significantly more robust serological response than mRNA boosting. MS-α CD20 had an intact IgA mucosal response and an enhanced CD8 T cell response to mRNA boosting compared with immunocompetent individuals. This enhanced cellular response was characterized by the expansion of only effector, not memory, T cells. The enhancement of CD8 T cells in the setting of B cell depletion suggests a regulatory mechanism between B and CD8 T cell vaccine responses.

Blood immunophenotyping identifies distinct kidney histopathology and outcomes in patients with lupus nephritis.

Lupus nephritis (LN) is a frequent manifestation of systemic lupus erythematosus, and fewer than half of patients achieve complete renal response with standard immunosuppressants. Identifying non-invasive, blood-based pathologic immune alterations associated with renal injury could aid therapeutic decisions. Here, we used mass cytometry immunophenotyping of peripheral blood mononuclear cells in 145 patients with biopsy-proven LN and 40 healthy controls to evaluate the heterogeneity of immune activation in patients with LN and to identify correlates of renal parameters and treatment response. Unbiased analysis identified 3 immunologically distinct groups of patients with LN that were associated with different patterns of histopathology, renal cell infiltrates, urine proteomic profiles, and treatment response at one year. Patients with enriched circulating granzyme B+ T cells at baseline showed more severe disease and increased numbers of activated CD8 T cells in the kidney, yet they had the highest likelihood of treatment response. A second group characterized primarily by a high type I interferon signature had a lower likelihood of response to therapy, while a third group appeared immunologically inactive by immunophenotyping at enrollment but with chronic renal injuries. Main immune profiles could be distilled down to 5 simple cytometric parameters that recapitulate several of the associations, highlighting the potential for blood immune profiling to translate to clinically useful non-invasive metrics to assess immune-mediated disease in LN.

A study on the physical fitness index, heart rate and blood pressure in different phases of lunar month on male human subjects.

The gravitational pull of the moon on the earth is not the same in all phases of the lunar month, i.e. new moon (NM), first quarter (FQ), full moon (FM) and third quarter (TQ), and as a result the amplitude of tide differs in different phases. The gravitational pull of the moon may have effects on the fluid compartments of the human body and hence the cardiovascular system may be affected differentially in the different phases of the lunar month. In the present study resting heart rate (HR) and blood pressure (BP), physical fitness index (PFI), peak HR and BP immediately after step test, and recovery HR and BP after step test were measured during different phases of the lunar month in 76 male university students (age 23.7 ± 1.7 years). At rest, both systolic and mean arterial BP were ∼5 mmHg lower in NM and FM compared to FQ and TQ, but resting HR was not significantly different between phases. Further, peak HR and peak systolic BP after step test were lower (∼4 beat/min and ∼5 mmHg, respectively) in NM and FM compared to FQ and TQ. PFI was also higher (∼5) in NM and FM compared to FQ and TQ. Recovery of HR after step test was quicker in NM and FM compared to that of FQ and TQ. It appears from this study that gravitational pull of the moon may affect the cardiovascular functions of the human body. Moreover, the physical efficiency of humans is increased in NM and FM due to these altered cardiovascular regulations.

Expansion of extrafollicular B and T cell subsets in childhood-onset systemic lupus erythematosus.

Introduction: Most childhood-onset SLE patients (cSLE) develop lupus nephritis (cLN), but only a small proportion achieve complete response to current therapies. The prognosis of children with LN and end-stage renal disease is particularly dire. Mortality rates within the first five years of renal replacement therapy may reach 22%. Thus, there is urgent need to decipher and target immune mechanisms that drive cLN. Despite the clear role of autoantibody production in SLE, targeted B cell therapies such as rituximab (anti-CD20) and belimumab (anti-BAFF) have shown only modest efficacy in cLN. While many studies have linked dysregulation of germinal center formation to SLE pathogenesis, other work supports a role for extrafollicular B cell activation in generation of pathogenic antibody secreting cells. However, whether extrafollicular B cell subsets and their T cell collaborators play a role in specific organ involvement in cLN and/or track with disease activity remains unknown. Methods: We analyzed high-dimensional mass cytometry and gene expression data from 24 treatment naïve cSLE patients at the time of diagnosis and longitudinally, applying novel computational tools to identify abnormalities associated with clinical manifestations (cLN) and disease activity (SLEDAI). Results: cSLE patients have an extrafollicular B cell expansion signature, with increased frequency of i) DN2, ii) Bnd2, iii) plasmablasts, and iv) peripheral T helper cells. Most importantly, we discovered that this extrafollicular signature correlates with disease activity in cLN, supporting extrafollicular T/B interactions as a mechanism underlying pediatric renal pathogenesis. Discussion: This study integrates established and emerging themes of extrafollicular B cell involvement in SLE by providing evidence for extrafollicular B and peripheral T helper cell expansion, along with elevated type 1 IFN activation, in a homogeneous cohort of treatment-naïve cSLE patients, a point at which they should display the most extreme state of their immune dysregulation.

Deep immunophenotyping reveals circulating activated lymphocytes in individuals at risk for rheumatoid arthritis.

Rheumatoid arthritis (RA) is a systemic autoimmune disease with currently no universally highly effective prevention strategies. Identifying pathogenic immune phenotypes in 'At-Risk' populations prior to clinical disease onset is crucial to establishing effective prevention strategies. Here, we applied mass cytometry to deeply characterize the immunophenotypes in blood from At-Risk individuals identified through the presence of serum antibodies to citrullinated protein antigens (ACPA) and/or first-degree relative (FDR) status (n=52), as compared to established RA (n=67), and healthy controls (n=48). We identified significant cell expansions in At-Risk individuals compared with controls, including CCR2+CD4+ T cells, T peripheral helper (Tph) cells, type 1 T helper cells, and CXCR5+CD8+ T cells. We also found that CD15+ classical monocytes were specifically expanded in ACPA-negative FDRs, and an activated PAX5 low naïve B cell population was expanded in ACPA-positive FDRs. Further, we developed an "RA immunophenotype score" classification method based on the degree of enrichment of cell states relevant to established RA patients. This score significantly distinguished At-Risk individuals from controls. In all, we systematically identified activated lymphocyte phenotypes in At-Risk individuals, along with immunophenotypic differences among both ACPA+ and ACPA-FDR At-Risk subpopulations. Our classification model provides a promising approach for understanding RA pathogenesis with the goal to further improve prevention strategies and identify novel therapeutic targets.

Effects of naproxen on the hypobaric hypoxia-induced immune changes in male rats.

Some cell-mediated immune responses are altered in hypobaric hypoxic (HH) condition in rats. Prostaglandins (PGs) are increased in hypobaric hypoxia and non-steroidal anti-inflammatory drugs are used to facilitate acclimatization in high altitude by inhibiting PGs. The present study explores the role of PGs in hypobaric hypoxia-induced immune responses by inhibiting its synthesis with different doses of naproxen. The rats were exposed to HH condition at 18,000 ft in a simulated chamber for 8 h/day for 6 days. The phagocytic activity of circulating blood WBC, measured by fluorescein isothiocyanate-tagged bacterial cell, was increased in HH and this change was blocked after administration of naproxen. There was reduction of natural killer cell cytotoxicity of splenic mononuclear cell and delayed type of hypersensitivity responses to bovine serum albumin in rats exposed to HH condition but these immune responses were blocked after administration of naproxen in HH condition. The leukocytes adhesive inhibition index was not altered in HH condition and after administration of naproxen in HH condition. The serum corticosterone (CORT) concentration was increased in rats exposed to HH condition and this elevated CORT concentration was blocked after administration of naproxen in HH condition. The observed HH-induced immune changes are inhibited by naproxen in a dose-dependent manner. The study indicates that hypobaric hypoxia-induced immune changes are mediated by PGs.

Undernutrition in Nepalese children: a biochemical and haematological study.

AIM: This study was undertaken to assess the nutritional status of 6-10 years old Nepalese children by measuring some haematological and biochemical parameters. METHODS: Nutritional status was assessed by height-for-age z-score. Total count of red blood corpuscles (TC of RBC), packed cell volume, haemoglobin concentration, mean corpuscular volume (MCV), mean corpuscular haemoglobin (MCH) and mean corpuscular haemoglobin concentration were measured. Biochemical parameters such as serum iron, total iron-binding capacity (TIBC), serum ferritin, serum transferrin, transferrin saturation (TS) and serum albumin were also measured. Serum folate and vitamin B(12) were measured in well-nourished and undernourished children. RESULTS: TC of RBC, serum iron, serum ferritin, TS and serum albumin of stunted children were significantly lower (p < 0.05) than that of well-nourished children. MCV, MCH, TIBC and serum transferrin of stunted children were significantly higher (p < 0.05) than that of well-nourished children. Serum folate and vitamin B(12) values of stunted children were significantly lower (p < 0.001) than that of well-nourished children. CONCLUSION: A mild iron deficiency was found in stunted Nepalese children. The serum ferritin has been identified as a sensitive marker for measurement of iron status in surveyed children. A deficiency of serum protein, serum folate and vitamin B(12) was also found in the undernourished Nepalese children.

DenVar: density-based variation analysis of multiplex imaging data.

Summary: Multiplex imaging platforms have become popular for studying complex single-cell biology in the tumor microenvironment (TME) of cancer subjects. Studying the intensity of the proteins that regulate important cell-functions becomes extremely crucial for subject-specific assessment of risks. The conventional approach requires selection of two thresholds, one to define the cells of the TME as positive or negative for a particular protein, and the other to classify the subjects based on the proportion of the positive cells. We present a threshold-free approach in which distance between a pair of subjects is computed based on the probability density of the protein in their TMEs. The distance matrix can either be used to classify the subjects into meaningful groups or can directly be used in a kernel machine regression framework for testing association with clinical outcomes. The method gets rid of the subjectivity bias of the thresholding-based approach, enabling easier but interpretable analysis. We analyze a lung cancer dataset, finding the difference in the density of protein HLA-DR to be significantly associated with the overall survival and a triple-negative breast cancer dataset, analyzing the effects of multiple proteins on survival and recurrence. The reliability of our method is demonstrated through extensive simulation studies. Availability and implementation: The associated R package can be found here, https://github.com/sealx017/DenVar. Supplementary information: Supplementary data are available at Bioinformatics Advances online.