Comorbidities between tuberculosis and common mental disorders: A scoping review of epidemiological patterns and person-centred care interventions from low-to-middle income and BRICS countries

Background : There is increasing evidence that the substantial global burden of disease for tuberculosis unfolds in concert with dimensions of common mental disorders. Person-centred care holds much promise to ameliorate these comorbidities in low-tomiddle income countries and emerging economies. Towards this end, this paper aimed to review 1) the nature and extent of tuberculosis and common mental disorder comorbidity and 2) person-centred tuberculosis care in low-to-middle income countries and emerging economies. Main text : A scoping review was conducted of English-language studies published from 2000-2019 in peer-reviewed and grey literature, using established guidelines, for each of the study objectives. Four broad tuberculosis/mental disorder comorbidities were described in the literature, namely alcohol use and tuberculosis, depression and tuberculosis, anxiety and tuberculosis, and general mental health and tuberculosis. Rates of comorbidity varied widely across countries for depression, anxiety, alcohol use and general mental health. Alcohol use and tuberculosis were significantly related, especially in the context of poverty. The initial tuberculosis diagnostic episode had substantial socio-psychological effects on service users. While men tended to report higher rates of alcohol use and treatment default, women in general had worse mental health outcomes. Older age and a history of mental illness were also associated with pronounced tuberculosis and mental disorder comorbidity. Person-centred tuberculosis care interventions were almost absent, with only one study from Nepal identified. Conclusions : There is an emerging body of evidence describing the nature and extent of tuberculosis and mental disorders comorbidity in low-to-middle income countries. Despite the potential of person-centred interventions, evidence is limited. This review highlights a pronounced need to address psychosocial comorbidities with TB in LMICs, where models of person-centred TB care in routine care platforms may yield promising outcomes

Fast machine-learning online optimization of ultra-cold-atom experiments

We apply an online optimization process based on machine learning to the production of Bose-Einstein condensates (BEC). BEC is typically created with an exponential evaporation ramp that is optimal for ergodic dynamics with two-body s-wave interactions and no other loss rates, but likely sub-optimal for real experiments. Through repeated machine-controlled scientific experimentation and observations our ‘learner’ discovers an optimal evaporation ramp for BEC production. In contrast to previous work, our learner uses a Gaussian process to develop a statistical model of the relationship between the parameters it controls and the quality of the BEC produced. We demonstrate that the Gaussian process machine learner is able to discover a ramp that produces high quality BECs in 10 times fewer iterations than a previously used online optimization technique. Furthermore, we show the internal model developed can be used to determine which parameters are essential in BEC creation and which are unimportant, providing insight into the optimization process of the system

Current concepts on oxidative/carbonyl stress, inflammation and epigenetics in pathogenesis of chronic obstructive pulmonary disease

Chronic obstructive pulmonary disease (COPD) is a global health problem, and current therapy for COPD is poorly effective and the mainstays of pharmacotherapy are bronchodilators. A better understanding of the pathobiology of COPD is critical for the development of novel therapies. In the present review, we have discussed the roles of oxidative/aldehyde stress, inflammation/immunity, and chromatin remodeling in the pathogenesis of COPD. Imbalance of oxidant/antioxidant balance caused by cigarette smoke and other pollutants/biomass fuels plays an important role in the pathogenesis of COPD by regulating redox-sensitive transcription factors (e.g. NF-κB), autophagy and unfolded protein response leading to chronic lung inflammatory response. Cigarette smoke also activates canonical/alternative NF-κB pathways and their upstream kinases leading to sustained inflammatory response in lungs. Recently, epigenetic regulation has been shown to be critical for the development of COPD because the expression/activity of enzymes that regulate these epigenetic modifications have been reported to be abnormal in airways of COPD patients. Hence, the significant advances made in understanding the pathophysiology of COPD as described herein will identify novel therapeutic targets for intervening COPD

Implementation and scale-up of integrated depression care in South Africa: An observational implementation research protocol

Background: People with chronic general medical conditions who have comorbid depression experience poorer health outcomes. This problem has received scant attention in low- and middle-income countries. The aim of the ongoing study reported here is to refine and promote the scale-up of an evidence-based task-sharing collaborative care model, the Mental Health Integration (MhINT) program, to treat patients with comorbid depression and chronic disease in primary health care settings in South Africa. Methods: Adopting a learning-health-systems approach, this study uses an onsite, iterative observational implementation science design. Stage 1 comprises assessment of the original MhINT model under real-world conditions in an urban subdistrict in KwaZulu-Natal, South Africa, to inform refinement of the model and its implementation strategies. Stage 2 comprises assessment of the refined model across urban, semiurban, and rural contexts. In both stages, population-level effects are assessed by using the RE-AIM (Reach, Effectiveness, Adoption, Implementation, Maintenance) evaluation framework with various sources of data, including secondary data collection and a patient cohort study (N=550). The Consolidated Framework for Implementation Research is used to understand contextual determinants of implementation success involving quantitative and qualitative interviews (stage 1, N=78; stage 2, N=282). Results: The study results will help refine intervention components and implementation strategies to enable scale-up of the MhINT model for depression in South Africa. Next steps: Next steps include strengthening ongoing engagements with policy makers and managers, providing technical support for implementation, and building the capacity of policy makers and managers in implementation science to promote wider dissemination and sustainment of the intervention

53BP1 regulates DNA resection and the choice between classical and alternative end joining during class switch recombination

Class switch recombination (CSR) diversifies antibodies by joining highly repetitive DNA elements, which are separated by 60–200 kbp. CSR is initiated by activation-induced cytidine deaminase, an enzyme that produces multiple DNA double-strand breaks (DSBs) in switch regions. Switch regions are joined by a mechanism that requires an intact DNA damage response and classical or alternative nonhomologous end joining (A-NHEJ). Among the DNA damage response factors, 53BP1 has the most profound effect on CSR. We explore the role of 53BP1 in intrachromosomal DNA repair using I-SceI to introduce paired DSBs in the IgH locus. We find that the absence of 53BP1 results in an ataxia telangiectasia mutated–dependent increase in DNA end resection and that resected DNA is preferentially repaired by microhomology-mediated A-NHEJ. We propose that 53BP1 favors long-range CSR in part by protecting DNA ends against resection, which prevents A-NHEJ–dependent short-range rejoining of intra–switch region DSBs

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN