Inference for the dimension of a regression relationship using pseudo-covariates.

In data analysis using dimension reduction methods, the main goal is to summarize how the response is related to the covariates through a few linear combinations. One key issue is to determine the number of independent, relevant covariate combinations, which is the dimension of the sufficient dimension reduction (SDR) subspace. In this work, we propose an easily-applied approach to conduct inference for the dimension of the SDR subspace, based on augmentation of the covariate set with simulated pseudo-covariates. Applying the partitioning principal to the possible dimensions, we use rigorous sequential testing to select the dimensionality, by comparing the strength of the signal arising from the actual covariates to that appearing to arise from the pseudo-covariates. We show that under a "uniform direction" condition, our approach can be used in conjunction with several popular SDR methods, including sliced inverse regression. In these settings, the test statistic asymptotically follows a beta distribution and therefore is easily calibrated. Moreover, the family-wise type I error rate of our sequential testing is rigorously controlled. Simulation studies and an analysis of newborn anthropometric data demonstrate the robustness of the proposed approach, and indicate that the power is comparable to or greater than the alternatives.

Layilin Anchors Regulatory T Cells in Skin.

Regulatory T cells (Tregs) reside in nonlymphoid tissues where they carry out unique functions. The molecular mechanisms responsible for Treg accumulation and maintenance in these tissues are relatively unknown. Using an unbiased discovery approach, we identified LAYN (layilin), a C-type lectin-like receptor, to be preferentially and highly expressed on a subset of activated Tregs in healthy and diseased human skin. Expression of layilin on Tregs was induced by TCR-mediated activation in the presence of IL-2 or TGF-ß. Mice with a conditional deletion of layilin in Tregs had reduced accumulation of these cells in tumors. However, these animals somewhat paradoxically had enhanced immune regulation in the tumor microenvironment, resulting in increased tumor growth. Mechanistically, layilin expression on Tregs had a minimal effect on their activation and suppressive capacity in vitro. However, expression of this molecule resulted in a cumulative anchoring effect on Treg dynamic motility in vivo. Taken together, our results suggest a model whereby layilin facilitates Treg adhesion in skin and, in doing so, limits their suppressive capacity. These findings uncover a unique mechanism whereby reduced Treg motility acts to limit immune regulation in nonlymphoid organs and may help guide strategies to exploit this phenomenon for therapeutic benefit.

Single-cell RNA sequencing of psoriatic skin identifies pathogenic Tc17 cell subsets and reveals distinctions between CD8+ T cells in autoimmunity and cancer.

BACKGROUND: Psoriasis is an inflammatory, IL-17-driven skin disease in which autoantigen-induced CD8+ T cells have been identified as pathogenic drivers. OBJECTIVE: Our study focused on comprehensively characterizing the phenotypic variation of CD8+ T cells in psoriatic lesions. METHODS: We used single-cell RNA sequencing to compare CD8+ T-cell transcriptomic heterogeneity between psoriatic and healthy skin. RESULTS: We identified 11 transcriptionally diverse CD8+ T-cell subsets in psoriatic and healthy skin. Among several inflammatory subsets enriched in psoriatic skin, we observed 2 Tc17 cell subsets that were metabolically divergent, were developmentally related, and expressed CXCL13, which we found to be a biomarker of psoriasis severity and which achieved comparable or greater accuracy than IL17A in a support vector machine classifier of psoriasis and healthy transcriptomes. Despite high coinhibitory receptor expression in the Tc17 cell clusters, a comparison of these cells with melanoma-infiltrating CD8+ T cells revealed upregulated cytokine, cytolytic, and metabolic transcriptional activity in the psoriatic cells that differed from an exhaustion program. CONCLUSION: Using high-resolution single-cell profiling in tissue, we have uncovered the diverse landscape of CD8+ T cells in psoriatic and healthy skin, including 2 nonexhausted Tc17 cell subsets associated with disease severity.

NONPARAMETRIC TESTING FOR MULTIPLE SURVIVAL FUNCTIONS WITH NON-INFERIORITY MARGINS.

New nonparametric tests for the ordering of multiple survival functions are developed with the possibility of right censorship taken into account. The motivation comes from non-inferiority trials with multiple treatments. The proposed tests are based on nonparametric likelihood ratio statistics, which are known to provide more powerful tests than Wald-type procedures, but in this setting have only been studied for pairs of survival functions or in the absence of censoring. We introduce a novel type of pool adjacent violator algorithm that leads to a complete solution of the problem. The limit distributions can be expressed as weighted sums of squares involving projections of certain Gaussian processes onto the given ordered alternative. A simulation study shows that the new procedures have superior power to a competing combined-pairwise Cox model approach. We illustrate the proposed methods using data from a three-arm non-inferiority trial.

Influence of diet on the gut microbiome and implications for human health.

Recent studies have suggested that the intestinal microbiome plays an important role in modulating risk of several chronic diseases, including inflammatory bowel disease, obesity, type 2 diabetes, cardiovascular disease, and cancer. At the same time, it is now understood that diet plays a significant role in shaping the microbiome, with experiments showing that dietary alterations can induce large, temporary microbial shifts within 24 h. Given this association, there may be significant therapeutic utility in altering microbial composition through diet. This review systematically evaluates current data regarding the effects of several common dietary components on intestinal microbiota. We show that consumption of particular types of food produces predictable shifts in existing host bacterial genera. Furthermore, the identity of these bacteria affects host immune and metabolic parameters, with broad implications for human health. Familiarity with these associations will be of tremendous use to the practitioner as well as the patient.

Feedback regulation via AMPK and HIF-1 mediates ROS-dependent longevity in Caenorhabditis elegans.

Mild inhibition of mitochondrial respiration extends the lifespan of many species. In Caenorhabditis elegans, reactive oxygen species (ROS) promote longevity by activating hypoxia-inducible factor 1 (HIF-1) in response to reduced mitochondrial respiration. However, the physiological role and mechanism of ROS-induced longevity are poorly understood. Here, we show that a modest increase in ROS increases the immunity and lifespan of C. elegans through feedback regulation by HIF-1 and AMP-activated protein kinase (AMPK). We found that activation of AMPK as well as HIF-1 mediates the longevity response to ROS. We further showed that AMPK reduces internal levels of ROS, whereas HIF-1 amplifies the levels of internal ROS under conditions that increase ROS. Moreover, mitochondrial ROS increase resistance to various pathogenic bacteria, suggesting a possible association between immunity and long lifespan. Thus, AMPK and HIF-1 may control immunity and longevity tightly by acting as feedback regulators of ROS.

Tests for stochastic ordering under biased sampling.

In two-sample comparison problems it is often of interest to examine whether one distribution function majorizes the other, i.e., for the presence of stochastic ordering. This paper develops a nonparametric test for stochastic ordering from size-biased data, allowing the pattern of the size bias to differ between the two samples. The test is formulated in terms of a maximally-selected local empirical likelihood statistic. A Gaussian multiplier bootstrap is devised to calibrate the test. Simulation results show that the proposed test outperforms an analogous Wald-type test, and that it provides substantially greater power over ignoring the size bias. The approach is illustrated using data on blood alcohol concentration of drivers involved in car accidents, where the size bias is due to drunker drivers being more likely to be involved in accidents. Further, younger drivers tend to be more affected by alcohol, so in making comparisons with older drivers the analysis is adjusted for differences in the patterns of size bias.

Three-dimensional computer-assisted orthognathic surgery: experience of 37 patients.

PURPOSE: Three-dimensional computer-assisted orthognathic surgery has been applied to improve planning and outcome. This study presents our experience with this promising modality for simulation of surgery, prefabrication of positioning guides, and navigation of the surgery. METHODS: Thirty-seven patients who received surgical simulation and intraoperative navigation for 2-jaw orthognathic surgery were recruited. Preoperative 3-dimensional cone-beam computed tomographic images were used for surgical simulation and design of intraoperative guidance. An initial surgical plan was developed and transferred for 3-dimensional virtual surgery. Modification of the surgical plan was made if facial symmetry and skeletal harmony or collision of ramus segments were concerned. The result of virtual surgery was used to design and manufacture positioning guides and perform preoperative navigation planning. During the operation, the positioning guides were used to transfer the virtual planning to actual surgery, and a real-time navigation system was used to confirm the predetermined position of the maxillomandibular complex. For assessment of the computer-assisted surgical system, the simulation image was superimposed to the postoperative image for comparison. RESULTS: The computer-assisted orthognathic surgery was successfully carried out in all patients. The initial surgical plan was modified in 17 patients in whom the position of maxillomandibular complex was changed. The positioning guides were helpful in controlling the spatial position of the maxillomandibular complex. The BrainLabTR navigation system was useful to further confirm the position of the facial bone. Superimposition of the simulation and postoperative images revealed satisfactory result with acceptable errors. The difference ranged from 0.05 to 1.46 mm, with a mean value of 0.66 mm, for patients using the positioning guides; and the difference ranged from 0.07 to 2.30 mm, with a mean value of 1.20 mm, for patients using the navigation system. Overall, patient and doctor satisfaction was high. CONCLUSION: This computer-assisted orthognathic surgery system helps to improve surgical planning, reduce surgical difficulty, facilitate positioning and fixation of the maxillomandibular complex, and improve outcome.

Nasal changes after orthognathic surgery for patients with prognathism and Class III malocclusion: analysis using three-dimensional photogrammetry.

BACKGROUND/PURPOSE: Orthognathic surgery alters the position of maxilla and mandible, and consequently changes the nasal shape. The nasal change remains a concern to Asian patients. The aim of this study was to measure the nasal changes using a novel three-dimensional photographic imaging method. METHODS: A total of 38 patients with Class III malocclusion and prognathism were enrolled. All patients underwent two-jaw surgery with the standard technique. A nasal alar cinching suture was included at the end of procedure. Facial landmarks and nasal morphology were defined and measured from pre- and postoperative three-dimensional photographic images. Intra-rater errors on landmark identification were controlled. Patient's reports of perceptual nasal changes were recorded. RESULTS: The average width of the alar base and subalare remained similar after surgery. Alar width was increased by 0.74 mm. Nasal height and length remained the same. Nasolabial angle increased significantly. The area of nostril show revealed a significant increase and was correlated with a decrease of columella inclination. Nasal tip projection decreased significantly, by 1.99 mm. Preoperative nasal morphology was different between patients with and without cleft lip/palate, but most nasal changes were concordant. In the self-perception, 37% of patients reported improved nasal appearance, 58% reported no change, and 5% were not satisfied with the nasal changes. CONCLUSION: After the surgery, characteristic nasal changes occurred with an increase of nasolabial angle and nostril show, but a preserved nasal width. The majority of patients did not perceive adverse nasal changes.

The homeobox protein CEH-23 mediates prolonged longevity in response to impaired mitochondrial electron transport chain in C. elegans.

Recent findings indicate that perturbations of the mitochondrial electron transport chain (METC) can cause extended longevity in evolutionarily diverse organisms. To uncover the molecular basis of how altered METC increases lifespan in C. elegans, we performed an RNAi screen and revealed that three predicted transcription factors are specifically required for the extended longevity of mitochondrial mutants. In particular, we demonstrated that the nuclear homeobox protein CEH-23 uniquely mediates the longevity but not the slow development, reduced brood size, or resistance to oxidative stress associated with mitochondrial mutations. Furthermore, we showed that ceh-23 expression levels are responsive to altered METC, and enforced overexpression of ceh-23 is sufficient to extend lifespan in wild-type background. Our data point to mitochondria-to-nucleus communications to be key for longevity determination and highlight CEH-23 as a novel longevity factor capable of responding to mitochondrial perturbations. These findings provide a new paradigm for how mitochondria impact aging and age-dependent diseases.

Molecular modeling of p38α mitogen-activated protein kinase inhibitors through 3D-QSAR and molecular dynamics simulations.

The p38 mitogen-activated protein kinase (MAPK) signaling pathway plays an essential role in inflammation and other physiological processes. Because specific inhibitors of p38α and p38ß MAPK block the production of the major inflammatory cytokines and other proteins, p38α and p38ß MAPK represent promising targets for the treatment of inflammation. In this work, a series of p38α inhibitors based on the structural scaffold of 4-benzoyl-5-aminopyrazole were analyzed using a combination of molecular modeling techniques. We generated three-dimensional quantitative structure-activity relationship (3D-QSAR) models for both comparative molecular field analysis (CoMFA) and comparative molecular similarity index analysis (CoMSIA) to highlight the structural requirements for p38 MAPK inhibition. Furthermore, we employed molecular dynamics (MD) simulations and the MM/GBSA method to compare the binding modes and binding free energies of a potent and selective compound interacting with p38α, p38ß, p38γ, and p38δ MAPK in detail. Contour maps generated via 3D-QSAR analysis identified several key interactions that were also indicated through MD simulations. The binding free energies calculated via the MM/GBSA method were strongly correlated with experimentally observed biological activities and explained the selective inhibition of p38α and p38ß, but not p38γ and p38δ detected here. On the basis of the obtained results, we provide insights regarding the development of novel potent p38α MAPK inhibitors.

Activator-independent transcription of Snf1-dependent genes in mutants lacking histone tails.

Transcriptional regulation of Snf1-dependent genes occurs in part by histone-acetylation-dependent binding of the transcription factor Adr1. Analysis of previously published microarray data indicated unscheduled transcription of a large number of Snf1- and Adr1-dependent genes when either the histone H3 or H4 tail was deleted. Quantitative real-time PCR confirmed that the tails were important to preserve stringent transcriptional repression of Snf1-dependent genes when glucose was present. The absence of the tails allowed Adr1 and RNA Polymerase II to bind promoters in normally inhibitory conditions. The promoters escaped glucose repression to a limited extent and the weak constitutive ADH2 transcription induced by deletion of the histone tails was transcription factor- and Snf1-independent. These effects were apparently due to a permissive chromatin structure that allowed transcription in the absence of repression mediated by the histone tails. Deleting REG1, and thus activating Snf1 in the H3 tail mutant enhanced transcription in repressing conditions, indicating that Snf1 and the H3 tail influence transcription independently. Deleting REG1 in the histone H4 tail mutant appeared to be lethal, even in the absence of Snf1, suggesting that Reg1 and the H4 tail have redundant functions that are important for cell viability.

Assessment of the Association of Vitamin D and the Risk of Tuberculosis among End-Stage Kidney Disease Population.

We investigated the role of vitamin D in the risk of tuberculosis (TB) among patients with end-stage kidney disease (ESKD). The retrospective cohort was conducted with data of 20,985 patients with kidney disease and 20,985 controls without kidney disease (1:1 matching on age of cohort entry and sex) in the duration of 1997−2010 from the Taiwan National Health insurance database. Then, by a case−cohort study, among 20,985 kidney disease, 3194 ESKD patients were identified with matched 3194 non-ESKD patients. Multivariate analyses revealed a significant association between kidney disease and tuberculosis (adjusted incidence rate ratio (IRR) 1.57 (1.33−1.86)), and the risk increased after 3 years of follow-up the (adjusted IRR 3.79 (2.55−5.62)), but after more years of follow-up no significance was observed. We also found that ESKD increases the risk of tuberculosis (adjusted IRR 3.67 (2.27−5.93)). However, vitamin D usage was not related with the tuberculosis risk in ESKD patients (p > 0.1783). Our study showed increased risk of tuberculosis in kidney disease and ESKD patients, and vitamin D was not beneficial in ESKD.

Multiomic Analysis of the Gut Microbiome in Psoriasis Reveals Distinct Host‒Microbe Associations.

Psoriasis is a chronic, inflammatory skin disease that affects 2‒3% of the global population. Besides skin manifestations, patients with psoriasis have increased susceptibility to a number of comorbidities, including psoriatic arthritis, cardiovascular disease, and inflammatory bowel disease. To understand the systemic component of psoriasis pathogenesis, we performed a pilot study to examine the fecal metagenome, host colonic transcriptome, and host peripheral blood immune profiles of patients with psoriasis and healthy controls. Our study showed increased functional diversity in the gut microbiome of patients with psoriasis. In addition, we identified microbial species that preferentially associate with patients with psoriasis and which have been previously found to associate with other autoimmune diseases. Intriguingly, our data revealed three psoriasis subgroups that have distinct microbial and host features. Integrating these features revealed host‒microbe associations that are specific to psoriasis or particular psoriasis subgroups. Our findings provide insight into the factors that may affect the development of comorbidities in patients with psoriasis and may hold diagnostic potential for early identification of patients with psoriasis at risk for these comorbidities.

Single Cell Transcriptome and Surface Epitope Analysis of Ankylosing Spondylitis Facilitates Disease Classification by Machine Learning.

Ankylosing spondylitis (AS) is an immune-mediated inflammatory disorder that primarily affects the axial skeleton, especially the sacroiliac joints and spine. This results in chronic back pain and, in extreme cases, ankylosis of the spine. Despite its debilitating effects, the pathogenesis of AS remains to be further elucidated. This study used single cell CITE-seq technology to analyze peripheral blood mononuclear cells (PBMCs) in AS and in healthy controls. We identified a number of molecular features associated with AS. CD52 was found to be overexpressed in both RNA and surface protein expression across several cell types in patients with AS. CD16+ monocytes overexpressed TNFSF10 and IL-18Rα in AS, while CD8+ TEM cells and natural killer cells overexpressed genes linked with cytotoxicity, including GZMH, GZMB, and NKG7. Tregs underexpressed CD39 in AS, suggesting reduced functionality. We identified an overrepresented NK cell subset in AS that overexpressed CD16, CD161, and CD38, as well as cytotoxic genes and pathways. Finally, we developed machine learning models derived from CITE-seq data for the classification of AS and achieved an Area Under the Receiver Operating Characteristic (AUROC) curve of > 0.95. In summary, CITE-seq identification of AS-associated genes and surface proteins in specific cell subsets informs our understanding of pathogenesis and potential new therapeutic targets, while providing new approaches for diagnosis via machine learning.

Combined Single Cell Transcriptome and Surface Epitope Profiling Identifies Potential Biomarkers of Psoriatic Arthritis and Facilitates Diagnosis via Machine Learning.

Early diagnosis of psoriatic arthritis (PSA) is important for successful therapeutic intervention but currently remains challenging due, in part, to the scarcity of non-invasive biomarkers. In this study, we performed single cell profiling of transcriptome and cell surface protein expression to compare the peripheral blood immunocyte populations of individuals with PSA, individuals with cutaneous psoriasis (PSO) alone, and healthy individuals. We identified genes and proteins differentially expressed between PSA, PSO, and healthy subjects across 30 immune cell types and observed that some cell types, as well as specific phenotypic subsets of cells, differed in abundance between these cohorts. Cell type-specific gene and protein expression differences between PSA, PSO, and healthy groups, along with 200 previously published genetic risk factors for PSA, were further used to perform machine learning classification, with the best models achieving AUROC ≥ 0.87 when either classifying subjects among the three groups or specifically distinguishing PSA from PSO. Our findings thus expand the repertoire of gene, protein, and cellular biomarkers relevant to PSA and demonstrate the utility of machine learning-based diagnostics for this disease.

Transcriptomic Profiling of Plaque Psoriasis and Cutaneous T-Cell Subsets during Treatment with Secukinumab.

The IL-17A inhibitor secukinumab is efficacious for the treatment of psoriasis. To better understand its mechanism of action, we investigated its impact on psoriatic lesions from 15 patients with moderate-to-severe plaque psoriasis undergoing secukinumab treatment. We characterized the longitudinal transcriptomic changes of whole lesional skin tissue as well as cutaneous CD4+ and CD8+ T effector cells and CD4+ T regulatory cells across 12 weeks of treatment. Secukinumab was clinically effective and reduced disease-associated overexpression of IL17A , IL17F, IL23A, IL23R, and IFNG in whole tissue as soon as 2 weeks after initiation of treatment. IL17A overexpression in T-cell subsets, primarily CD8+ T cells, was also reduced. Although secukinumab treatment resolved 89‒97% of psoriasis-associated expression differences in bulk tissue and T-cell subsets by week 12 of treatment, we observed expression differences involved in IFN signaling and metallothionein synthesis that remained unresolved at this time point as well as potential treatment-associated expression differences involved in IL-15 signaling. These changes were accompanied by shifts in broader immune cell composition on the basis of deconvolution of RNA-sequencing data. In conclusion, our study reveals several phenotypic and cellular changes within the lesion that underlie clinical improvement from secukinumab.

Associations among phthalate exposure, DNA methylation of TSLP, and childhood allergy.

BACKGROUND: Dysregulation of thymic stromal lymphopoietin (TSLP) expressions is linked to asthma and allergic disease. Exposure to phthalate esters, a widely used plasticizer, is associated with respiratory and allergic morbidity. Dibutyl phthalate (DBP) causes TSLP upregulation in the skin. In addition, phthalate exposure is associated with changes in environmentally induced DNA methylation, which might cause phenotypic heterogeneity. This study examined the DNA methylation of the TSLP gene to determine the potential mechanism between phthalate exposure and allergic diseases. RESULTS: Among all evaluated, only benzyl butyl phthalate (BBzP) in the settled dusts were negatively correlated with the methylation levels of TSLP and positively associated with children's respiratory symptoms. The results revealed that every unit increase in BBzP concentration in the settled dust was associated with a 1.75% decrease in the methylation level on upstream 775 bp from the transcription start site (TSS) of TSLP (ß = - 1.75, p = 0.015) after adjustment for child's sex, age, BMI, parents' smoking status, allergic history, and education levels, PM2.5, formaldehyde, temperature; and relative humidity. Moreover, every percentage increase in the methylation level was associated with a 20% decrease in the risk of morning respiratory symptoms in the children (OR 0.80, 95% CI 0.65-0.99). CONCLUSIONS: Exposure to BBzP in settled dust might increase children's respiratory symptoms in the morning through decreasing TSLP methylation. Therefore, the exposure to BBzP should be reduced especially for the children already having allergic diseases.

Sleep and the gut microbiome in psoriasis: clinical implications for disease progression and the development of cardiometabolic comorbidities.

Background: Sleep dysfunction and sleep disorders are important comorbidities of psoriasis. Not only do these sleep comorbidities contribute to reduced quality of life, but they may also lead to worsening psoriasis and increased susceptibility to cardiometabolic diseases. While psoriasis and sleep dysfunction are thought to be linked by itch, depression, and immune system dysregulation, the relationship between psoriasis and sleep dysfunction is not yet fully understood. Objective: We sought to compare previous studies characterizing the gut microbiome in psoriasis and sleep dysfunction and examine the potential relevance of shared findings on cardiometabolic and overall health. Methods: We performed literature searches of PubMed and Embase databases to find studies evaluating the gut microbiome in psoriasis, sleep dysfunction, and cardiometabolic diseases. Results: Studies characterizing the gut microbiome in psoriasis and sleep dysfunction reveal shared findings, specifically an increased Firmicutes to Bacteroidetes ratio and reduced abundance of short chain fatty acid-producing bacteria. These dysbiotic features have also been shown to promote systemic inflammation and cardiometabolic disease. Conclusion: In favoring an increased Firmicutes to Bacteroidetes ratio and reduced abundance of short chain fatty acid-producing bacteria, sleep dysfunction could be contributing to worsening psoriasis and cardiometabolic comorbidities through intestinal dysbiosis. Future studies are needed to determine whether gut- and sleep-targeting interventions could be therapeutic in psoriasis patients with poor sleep.

Precision therapeutic opioid dosing implications from genetic biomarkers and craving score.

Determining the clinically optimal dose in methadone maintenance therapy (MMT) is a time-consuming procedure, which considers clinical signs and symptoms.To perform a quantitative trait locus association for identifying genetic variants for MMT dosage that underlie heroin addiction and methadone metabolism and then integrate several genotypic and phenotypic factors are potential predictors for clinically optimal MMT dose for personalized prescription.In total, 316 heroin-dependent patients undergoing MMT were recruited at the Addiction Center of the China Medical University Hospital. A multinomial logistic regression model was used to assess associations between genetic polymorphisms and MMT dosing. The data were randomly separated into training and testing sets. In order to enhance the prediction accuracy and the reliability of the prediction model, we used areas under the receiver operating characteristic curves to evaluate optimal MMT dose in both training and testing sets.Four single nucleotide polymorphisms, namely rs806368 in CNR1, s1386493 in TPH2, s16974799 in CYP2B6, and rs2229205 in OPRL1, were significantly associated with the maximum MMT dose (P < .05). The genetic risk score (GRS) was associated with maximum MMT dose, and after adjustments for age, sex, and body mass index, the GRS remained independently associated with the maximum MMT dose. The area under the receiver operating characteristic curve of the combined GRS and craving score was 0.77 for maximum MMT dose, with 75% sensitivity and 60% specificity.Integrating the GRS and craving scores may be useful in the evaluation of individual MMT dose requirements at treatment initiation. Optimal dose prediction allows clinicians to tailor MMT to each patient's needs.