Molecular Transducers of Physical Activity Consortium (MoTrPAC): Mapping the Dynamic Responses to Exercise.

Exercise provides a robust physiological stimulus that evokes cross-talk among multiple tissues that when repeated regularly (i.e., training) improves physiological capacity, benefits numerous organ systems, and decreases the risk for premature mortality. However, a gap remains in identifying the detailed molecular signals induced by exercise that benefits health and prevents disease. The Molecular Transducers of Physical Activity Consortium (MoTrPAC) was established to address this gap and generate a molecular map of exercise. Preclinical and clinical studies will examine the systemic effects of endurance and resistance exercise across a range of ages and fitness levels by molecular probing of multiple tissues before and after acute and chronic exercise. From this multi-omic and bioinformatic analysis, a molecular map of exercise will be established. Altogether, MoTrPAC will provide a public database that is expected to enhance our understanding of the health benefits of exercise and to provide insight into how physical activity mitigates disease.

A Bayesian network meta-analysis of 14 molecules inhibiting UV daylight-induced pigmentation.

INTRODUCTION: Hyperpigmentation disorders are very frequent, affect the quality of life and may become a psychological burden for afflicted patients. Many anti-pigmenting or depigmenting agents are available with various efficacy and almost no comparative data. 2-mercaptonicotinoyl glycine (2-MNG) was recently proposed as a viable candidate showing safe and effective results on hyperpigmentation control in vitro and in vivo. OBJECTIVES: A Bayesian network meta-analysis (BNMA) was conducted to map and rank the anti-pigmenting and depigmenting efficacy of 2-MNG 0.5% on UV daylight (UVDL)-induced pigmentation together with 13 other reference molecules. A comparison in the kinetics of 2-MNG 0.5% was also performed. METHODOLOGY: Fourteen studies were conducted, for each, on 15-30 women of skin phototype III in Shanghai, China and Paris, France. The products were applied on mini zone, in randomized and blinded protocol, on the back, 5 days a week during 6 weeks, at a dose of 4 mg/cm2 . During the second week, volunteers were exposed under to varying minimum erythemal dose of UVDL during 4 consecutive days-adapted to obtain a similar induction of skin pigmentation regardless of the population. Assessments were performed instrumentally using Chromameter®. Ascorbic acid 7% was used as a positive control for all experiments. A Bayesian network meta-analysis was then established to map and follow the kinetics of 2-MNG 0.5% performance with 13 reference molecules (glutathione 2%, kojic acid 1%, hydroquinone 4%, ascorbyl glucoside 2%, niacinamide 4%, etc.). RESULTS: 2-MNG 0.5% dominated the ranking at all time points with a significant high probability of strong efficacy against UVDL-induced pigmentation. Ascorbic acid 7% ranks second after 4 days of irradiations (D12 ) whereas hydroquinone 4% ranks second 1 month after irradiations (D40 ). In the kinetics, 2-MNG at 0.5% was effective as from the end of irradiations (D12 ) to the study endpoint (D40 ). This suggested an immediate and persistent efficacy across all timepoints evaluated. CONCLUSION: The BNMA revealed a rapid and lasting efficacy of 2-MNG 0.5% on the anti-pigmenting and depigmenting phases of the clinical protocol. 2-MNG 0.5% ranked first, with immediate and lasting effect compared to 13 other references. This study is the first allowing comparison between reference anti-pigmenting and depigmenting agents and will help clinicians for proposing the most effective approach for their patients.

Objective and automatic grading system of facial signs from smartphones' pictures in South African men: Validation versus dermatologists and characterization of changes with age.

OBJECTIVE: To evaluate the capacity of the automatic detection system to accurately grade, from selfie pictures, the severity of eight facial signs in South African men. METHODS: Selfie pictures (obtained from frontal and back cameras) of 281 South African men differently aged (20-70 years) were obtained and analyzed by an automatic artificial intelligence (AI)-based automatic grading system. Data were compared with the clinical gradings made by experts and dermatologists. RESULTS: In all facial signs, both series of gradings were found highly correlated with, however, different coefficients (0.59-0.95), those of marionette lines and cheek pores being of lower values. No differences were observed between data obtained by frontal and back cameras. With age, in most cases, gradings show up to the 50-59 year age-class, linear-like changes. When compared to men of other ancestries, South African men present lower wrinkles/texture, pigmentation, and ptosis/sagging scores till 50-59 years, albeit not much different in the cheek pores sign. The early onset (mean age) of visibility of wrinkles/texture for South African men were (i.e., reaching grade >1) 39 and 45 years for ptosis/sagging. CONCLUSION: This study completes and enlarges the previous works conducted on men of other ancestries by showing some South African specificities and slight differences with men of comparable phototypes (Afro American).

Amiodarone with or without N-Acetylcysteine for the Prevention of Atrial Fibrillation after Thoracic Surgery: A Double-blind, Randomized Trial.

BACKGROUND: Postoperative atrial fibrillation may identify patients at risk of subsequent atrial fibrillation, with its greater risk of stroke. This study hypothesized that N-acetylcysteine mitigates inflammation and oxidative stress to reduce the incidence of postoperative atrial fibrillation. METHODS: In this double-blind, placebo-controlled trial, patients at high risk of postoperative atrial fibrillation scheduled to undergo major thoracic surgery were randomized to N-acetylcysteine plus amiodarone or placebo plus amiodarone. On arrival to the postanesthesia care unit, N-acetylcysteine or placebo intravenous bolus (50 mg/kg) and then continuous infusion (100 mg/kg over the course of 48 h) was administered plus intravenous amiodarone (bolus of 150 mg and then continuous infusion of 2 g over the course of 48 h). The primary outcome was sustained atrial fibrillation longer than 30 s by telemetry (first 72 h) or symptoms requiring intervention and confirmed by electrocardiography within 7 days of surgery. Systemic markers of inflammation (interleukin-6, interleukin-8, tumor necrosis factor α, C-reactive protein) and oxidative stress (F2-isoprostane prostaglandin F2α; isofuran) were assessed immediately after surgery and on postoperative day 2. Patients were telephoned monthly to assess the occurrence of atrial fibrillation in the first year. RESULTS: Among 154 patients included, postoperative atrial fibrillation occurred in 15 of 78 who received N-acetylcysteine (19%) and 13 of 76 who received placebo (17%; odds ratio, 1.24; 95.1% CI, 0.53 to 2.88; P = 0.615). The trial was stopped at the interim analysis because of futility. Of the 28 patients with postoperative atrial fibrillation, 3 (11%) were discharged in atrial fibrillation. Regardless of treatment at 1 yr, 7 of 28 patients with postoperative atrial fibrillation (25%) had recurrent episodes of atrial fibrillation. Inflammatory and oxidative stress markers were similar between groups. CONCLUSIONS: Dual therapy comprising N-acetylcysteine plus amiodarone did not reduce the incidence of postoperative atrial fibrillation or markers of inflammation and oxidative stress early after major thoracic surgery, compared with amiodarone alone. Recurrent atrial fibrillation episodes are common among patients with postoperative atrial fibrillation within 1 yr of major thoracic surgery.

Outcomes After Multidisciplinary Management of Primary Mediastinal Germ Cell Tumors.

OBJECTIVE: We examined management strategies, overall survival (OS), and progression-free survival (PFS) among patients with PMNSGCTs undergoing resection and multidisciplinary management at a high-volume institution. SUMMARY OF BACKGROUND DATA: Outcomes after resection of PMNSGCTs are not well-characterized, with limited data on factors associated with survival. METHODS: We reviewed patients with PMNSGCT who underwent resection between 1980 and 2019. Median follow-up was 3.4 years. Preoperative therapy (including use of bleomycin), surgical management, recurrence, and survival were examined. Factors associated with survival were analyzed using Cox regression. RESULTS: In total, 113 patients were included [median age, 28 years (range, 16-65)]. Preoperative serum tumor markers (STMs) normalized/decreased in 74% of patients. Pathology included necrosis only (25%), teratoma +/- necrosis (20%), viable nonteratomatous germ cell tumor +/- teratoma (41%), and secondary somatic-type malignancy +/- teratoma (20%). Bleomycin chemotherapy was not associated with pulmonary complications or 90-day mortality. Patients receiving second-line chemotherapy followed by resection had significantly worse OS and PFS than patients receiving first-line chemotherapy followed by resection. On multivariable analysis, R1/R2 resection (HR, 3.92; P < 0.001) and increasing postoperative STMs (HR, 4.98; P < 0.001) were associated with shorter PFS; necrosis on pathology (HR, 0.42, P = 0.043) was associated with longer PFS. CONCLUSIONS: In patients with PMNSGCT undergoing resection, completeness of resection, postoperative pathology, and postoperative STMs were associated with PFS. Induction bleomycin was not associated with pulmonary complications or mortality in patients undergoing resection. Patients undergoing second-line chemotherapy followed by resection have a poor prognosis, with long-term survival of 22%.

Liposomal Bupivacaine Versus Bupivacaine Hydrochloride for Intercostal Nerve Blockade in Minimally Invasive Thoracic Surgery.

OBJECTIVES: The objective of this study was to compare the effects of liposomal bupivacaine (Lipo-B) and bupivacaine hydrochloride (B-HCl), in the presence of multimodal analgesia, on postoperative analgesia and opioid consumption in minimally invasive thoracic surgery (MITS) lobectomy. DESIGN: Retrospective observational cohort study. SETTING: Tertiary care cancer center. PARTICIPANTS: A total of 60 patients who underwent MITS lobectomy and received intercostal nerve blockade (ICNB) with either 0.66% Lipo-B (n = 29) or 0.5% B-HCl (n = 31). INTERVENTIONS: All patients received intravenous patient-controlled analgesia for the first 12 hours postoperatively, followed by opioids and nonsteroidal anti-inflammatory drugs as needed. MEASUREMENTS AND MAIN RESULTS: Perioperative opioid and nonopioid consumption and pain scores were compared between groups at 12-hour intervals for the first 72 hours. Between the two groups, there were no statistically significant differences in demographic characteristics, intraoperative (p = 0.46) and postoperative opioid consumption, Richmond Agitation-Sedation Scale scores and pain scores upon postanesthesia care unit arrival and after four hours, length of postanesthesia care unit stay (p = 0.84), or length of hospital stay (p = 0.55). Both groups received intra- and postoperative multimodal analgesia. CONCLUSIONS: In this cohort, no differences in opioid consumption or pain scores were observed in the immediate postoperative period following MITS lobectomy between patients given ICNB with Lipo-B and those given ICNB with B-HCl in the presence of multimodal analgesia.

Use of vasopressors during esophagectomy is not associated with increased risk of anastomotic leak.

Vasopressor use during esophagectomy has been reported to increase the risk of postoperative anastomotic leak and associated morbidity. We sought to assess the association between vasopressor use and fluid (crystalloid and colloid) administration and anastomotic leak following open esophagectomy. Patients who underwent open Ivor Lewis esophagectomy were identified from a prospective institutional database. The primary outcome was postoperative anastomotic leak (any grade) and analyzed using logistic regression models. Postoperative anastomotic leak developed in 52 of 327 consecutive patients (16%) and was not significantly associated with vasopressor use or fluid administered in either univariable or multivariable analyses. Increasing body mass index was the only significant characteristic of both univariable (P = 0.004) and multivariable analyses associated with anastomotic leak (odds ratio, 1.05; 95% confidence interval, 1.01-1.09; P = 0.007). Of the 52 patients that developed an anastomotic leak, 12 (23%) were grade 1, 21 (40%) were grade 2 and 19 (37%) were grade 3. In our cohort, only body mass index, and not intraoperative vasopressor use and fluid administration, was significantly associated with increased odds of postoperative anastomotic leak following open Ivor Lewis esophagectomy.

Gender-related differences in the facial aging of Chinese subjects and their relations with perceived ages.

OBJECTIVE: To describe the progressing severity of facial signs and their links with perceived age, of Chinese men and women. METHODS: Full-face photographs of 438 Chinese subjects (220 men, 218 women) differently aged (18-80 years) were taken. These photographs afforded a zoom on 5 facial signs of aging: forehead and crow's feet wrinkles, nasolabial fold, marionette lines and ptosis of the lower face. A panel of 15 experts graded each sign, using the Asian skin aging atlas reference. A naïve panel of 80 Chinese women (20-60 years) was asked to attribute an apparent age. RESULTS: Despite slight differences in severity between genders, men and women share in common a rather regular progression rate, correlated with perceived ages. 15% of men were judged older by more than 10 years, and all 5 signs were found more severe than the means of the other 85%. Forehead and Crow's feet wrinkles appear more pronounced in men. Ptosis is slightly more pronounced in women. Nasolabial fold does not differ. Marionette lines show distinct changes: those of men show a lessened severity and a slower rate of progression. In contrast with changes in facial signs with real ages, the upper face seems privileged in the perception of ages in women whereas the latter seems more focusing on its lower part in men. CONCLUSION: The facial skin aging process in Chinese subjects presents an almost linear progression with perceived ages, common to both genders, at the exception of marionette lines that are more marked and more rapidly progressing in women.

Enhancer methylation dynamics contribute to cancer plasticity and patient mortality.

During development, enhancers play pivotal roles in regulating gene expression programs; however, their involvement in cancer progression has not been fully characterized. We performed an integrative analysis of DNA methylation, RNA-seq, and small RNA-seq profiles from thousands of patients, including 25 diverse primary malignances and seven body sites of metastatic melanoma. We found that enhancers are consistently the most differentially methylated regions (DMR) as cancer progresses from normal to primary tumors and then to metastases, compared to other genomic features. Remarkably, identification of enhancer DMRs (eDMRs) enabled classification of primary tumors according to physiological organ systems, and in metastasis eDMRs are the most correlated with patient outcome. To further understand the eDMR role in cancer progression, we developed a model to predict genes and microRNAs that are regulated by enhancer and not promotor methylation, which shows high accuracy with chromatin architecture methods and was experimentally validated. Interestingly, among all metastatic melanoma eDMRs, the most correlated with patient survival were eDMRs that "switched" their methylation patterns back and forth between normal, primary, and metastases and target cancer drivers, e.g., KIT We further demonstrated that eDMR target genes were modulated in melanoma by the bone metastasis microenvironment, suggesting that eDMRs respond to microenvironmental cues in metastatic niches. Our findings that aberrant methylation in cancer cells mostly affects enhancers, which contribute to tumor progression and cancer cell plasticity, will facilitate development of epigenetic anticancer approaches.

ADEPTUS: a discovery tool for disease prediction, enrichment and network analysis based on profiles from many diseases.

Motivation: Large-scale publicly available genomic data on many disease phenotypes could improve our understanding of the molecular basis of disease. Tools that undertake this challenge by jointly analyzing multiple phenotypes are needed. Results: ADEPTUS is a web-tool that enables various functional genomics analyses based on a high-quality curated database spanning >38, 000 gene expression profiles and >100 diseases. It offers four types of analysis. (i) For a gene list provided by the user it computes disease ontology (DO), pathway, and gene ontology (GO) enrichment and displays the genes as a network. (ii) For a given disease, it enables exploration of drug repurposing by creating a gene network summarizing the genomic events in it. (iii) For a gene of interest, it generates a report summarizing its behavior across several studies. (iv) It can predict the tissue of origin and the disease of a sample based on its gene expression or its somatic mutation profile. Such analyses open novel ways to understand new datasets and to predict primary site of cancer. Availability and implementation: Data and tool: http://adeptus.cs.tau.ac.il/home Analyses: Supplementary Material. Contact: rshamir@tau.ac.il. Supplementary information: Supplementary data are available at Bioinformatics online.

Extracting replicable associations across multiple studies: Empirical Bayes algorithms for controlling the false discovery rate.

In almost every field in genomics, large-scale biomedical datasets are used to report associations. Extracting associations that recur across multiple studies while controlling the false discovery rate is a fundamental challenge. Here, we propose a new method to allow joint analysis of multiple studies. Given a set of p-values obtained from each study, the goal is to identify associations that recur in at least k > 1 studies while controlling the false discovery rate. We propose several new algorithms that differ in how the study dependencies are modeled, and compare them and extant methods under various simulated scenarios. The top algorithm, SCREEN (Scalable Cluster-based REplicability ENhancement), is our new algorithm that works in three stages: (1) clustering an estimated correlation network of the studies, (2) learning replicability (e.g., of genes) within clusters, and (3) merging the results across the clusters. When we applied SCREEN to two real datasets it greatly outperformed the results obtained via standard meta-analysis. First, on a collection of 29 case-control gene expression cancer studies, we detected a large set of consistently up-regulated genes related to proliferation and cell cycle regulation. These genes are both consistently up-regulated across many cancer studies, and are well connected in known gene networks. Second, on a recent pan-cancer study that examined the expression profiles of patients with and without mutations in the HLA complex, we detected a large active module of up-regulated genes that are both related to immune responses and are well connected in known gene networks. This module covers thrice more genes as compared to the original study at a similar false discovery rate, demonstrating the high power of SCREEN. An implementation of SCREEN is available in the supplement.

A machine learning approach for predicting CRISPR-Cas9 cleavage efficiencies and patterns underlying its mechanism of action.

The adaptation of the CRISPR-Cas9 system as a genome editing technique has generated much excitement in recent years owing to its ability to manipulate targeted genes and genomic regions that are complementary to a programmed single guide RNA (sgRNA). However, the efficacy of a specific sgRNA is not uniquely defined by exact sequence homology to the target site, thus unintended off-targets might additionally be cleaved. Current methods for sgRNA design are mainly concerned with predicting off-targets for a given sgRNA using basic sequence features and employ elementary rules for ranking possible sgRNAs. Here, we introduce CRISTA (CRISPR Target Assessment), a novel algorithm within the machine learning framework that determines the propensity of a genomic site to be cleaved by a given sgRNA. We show that the predictions made with CRISTA are more accurate than other available methodologies. We further demonstrate that the occurrence of bulges is not a rare phenomenon and should be accounted for in the prediction process. Beyond predicting cleavage efficiencies, the learning process provides inferences regarding patterns that underlie the mechanism of action of the CRISPR-Cas9 system. We discover that attributes that describe the spatial structure and rigidity of the entire genomic site as well as those surrounding the PAM region are a major component of the prediction capabilities.

Protective Lung Ventilation and Morbidity After Pulmonary Resection: A Propensity Score-Matched Analysis.

BACKGROUND: Protective lung ventilation (PLV) during one-lung ventilation (OLV) for thoracic surgery is frequently recommended to reduce pulmonary complications. However, limited outcome data exist on whether PLV use during OLV is associated with less clinically relevant pulmonary morbidity after lung resection. METHODS: Intraoperative data were prospectively collected in 1080 patients undergoing pulmonary resection with OLV, intentional crystalloid restriction, and mechanical ventilation to maintain inspiratory peak airway pressure <30 cm H2O. Other ventilator settings and all aspects of anesthetic management were at the discretion of the anesthesia care team. We defined PLV and non-PLV as <8 or ≥8 mL/kg (predicted body weight) mean tidal volume. The primary outcome was the occurrence of pneumonia and/or acute respiratory distress syndrome (ARDS). Propensity score matching was used to generate PLV and non-PLV groups with comparable characteristics. Associations between outcomes and PLV status were analyzed by exact logistic regression, with matching as cluster in the anatomic and nonanatomic lung resection cohorts. RESULTS: In the propensity score-matched analysis, the incidence of pneumonia and/or ARDS among patients who had an anatomic lung resection was 9/172 (5.2%) in the non-PLV compared to the PLV group 7/172 (4.1%; odds ratio, 1.29; 95% confidence interval, 0.48-3.45, P= .62). The incidence of pneumonia and/or ARDS in patients who underwent nonanatomic resection was 3/118 (2.5%) in the non-PLV compared to the PLV group, 1/118 (0.9%; odds ratio, 3.00; 95% confidence interval, 0.31-28.84, P= .34). CONCLUSIONS: In this prospective observational study, we found no differences in the incidence of pneumonia and/or ARDS between patients undergoing lung resection with tidal volumes <8 or ≥8 mL/kg. Our data suggest that when fluid restriction and peak airway pressures are limited, the clinical impact of PLV in this patient population is small. Future randomized trials are needed to better understand the benefits of a small tidal volume strategy during OLV on clinically important outcomes.

Preoperative Echocardiographic Indices of Diastolic Dysfunction and Brain Natriuretic Peptide in Predicting Postoperative Atrial Fibrillation After Noncardiac Surgery.

BACKGROUND: We have shown previously that either echocardiographic indices of diastolic dysfunction or increased preoperative brain natriuretic peptide (BNP) predict postoperative atrial fibrillation (POAF). Because these 2 predictors of POAF have not been evaluated together, our goal was to further elucidate their concurrent role in patients undergoing noncardiac thoracic surgery. METHODS: We retrospectively identified 191 patients who had a preoperative transthoracic echocardiogram and serum BNP level collected as part of routine care before major lung or esophageal resection. Clinical and echocardiographic data were compared between patients who did or did not develop POAF (>5 minutes), and prognostic factors for POAF were identified. RESULTS: Univariate associations with POAF (41 of 191; 22% patients) included older age (P = .04), male sex (P = .01), hypertension (P = .03), increased body mass index (P = .01), and prolonged transmitral flow deceleration time (P < .0001), whereas BNP was not statistically significant (P = .07). Stepwise logistic regression analysis showed that both increasing transmitral flow deceleration time (continuous data log base 2 transformed; odds ratio, 16.05; 95% confidence interval, 3.74-68.96; P = .0002) and left atrial diastolic volume index (continuous data log base 2 transformed; odds ratio, 3.29; 95% confidence interval, 1.22-8.91; P = .02) were independent risk factors of POAF (area under the receiver operating characteristic curve = 0.73). There was no significant interaction between BNP and the 2 independent variables (P = .60, and P = .90), respectively. CONCLUSIONS: In a cohort of patients who had echocardiography and BNP measurements before undergoing major thoracic surgery, this study showed that when evaluated together greater preoperative left atrial diastolic volume index and transmitral flow deceleration time but not BNP levels were independent predictors for POAF.

Evidence of TAF1 dysfunction in peripheral models of X-linked dystonia-parkinsonism.

The molecular dysfunction in X-linked dystonia-parkinsonism is not completely understood. Thus far, only noncoding alterations have been found in genetic analyses, located in or nearby the TATA-box binding protein-associated factor 1 (TAF1) gene. Given that this gene is ubiquitously expressed and is a critical component of the cellular transcription machinery, we sought to study differential gene expression in peripheral models by performing microarray-based expression profiling in blood and fibroblasts, and comparing gene expression in affected individuals vs. ethnically matched controls. Validation was performed via quantitative polymerase chain reaction in discovery and independent replication sets. We observed consistent downregulation of common TAF1 transcripts in samples from affected individuals in gene-level and high-throughput experiments. This signal was accompanied by a downstream effect in the microarray, reflected by the dysregulation of 307 genes in the disease group. Gene Ontology and network analyses revealed enrichment of genes involved in RNA polymerase II-dependent transcription, a pathway relevant to TAF1 function. Thus, the results converge on TAF1 dysfunction in peripheral models of X-linked dystonia-parkinsonism, and provide evidence of altered expression of a canonical gene in this disease. Furthermore, our study illustrates a link between the previously described genetic alterations and TAF1 dysfunction at the transcriptome level.

Integrated analysis of numerous heterogeneous gene expression profiles for detecting robust disease-specific biomarkers and proposing drug targets.

Genome-wide expression profiling has revolutionized biomedical research; vast amounts of expression data from numerous studies of many diseases are now available. Making the best use of this resource in order to better understand disease processes and treatment remains an open challenge. In particular, disease biomarkers detected in case-control studies suffer from low reliability and are only weakly reproducible. Here, we present a systematic integrative analysis methodology to overcome these shortcomings. We assembled and manually curated more than 14,000 expression profiles spanning 48 diseases and 18 expression platforms. We show that when studying a particular disease, judicious utilization of profiles from other diseases and information on disease hierarchy improves classification quality, avoids overoptimistic evaluation of that quality, and enhances disease-specific biomarker discovery. This approach yielded specific biomarkers for 24 of the analyzed diseases. We demonstrate how to combine these biomarkers with large-scale interaction, mutation and drug target data, forming a highly valuable disease summary that suggests novel directions in disease understanding and drug repurposing. Our analysis also estimates the number of samples required to reach a desired level of biomarker stability. This methodology can greatly improve the exploitation of the mountain of expression profiles for better disease analysis.