Time Dependence of Few-Body Forster Interactions Among Ultracold Rydberg Atoms

Rubidium Rydberg atoms in either |mj| sublevel of the 36p3/2 state can exchange energy via Stark-tuned Förster resonances, including two-, three-, and four-body dipole-dipole interactions. Three-body interactions of this type were first reported and categorized by Faoro et al. [Nat. Commun. 6, 8173 (2015)] and their Borromean nature was confirmed by Tretyakov et al. [Phys. Rev. Lett. 119, 173402 (2017)]. We report the time dependence of the N-body Förster resonance N×36p3/2,|mj|=1/2→36s1/2+37s1/2+(N−2)×36p3/2,|mj|=3/2, for N=2, 3, and 4, by measuring the fraction of initially excited atoms that end up in the 37s1/2 state as a function of time. The essential features of these interactions are captured in an analytical model that includes only the many-body matrix elements and neighboring atom distribution. A more sophisticated simulation reveals the importance of beyond-nearest-neighbor interactions and of always-resonant interactions

Ret receptor tyrosine kinase sustains proliferation and tissue maturation in intestinal epithelia

Expression of the Ret receptor tyrosine kinase is a defining feature of enteric neurons. Its importance is underscored by the effects of its mutation in Hirschsprung disease, leading to absence of gut innervation and severe gastrointestinal symptoms. We report a new and physiologically significant site of Ret expression in the intestine: the intestinal epithelium. Experiments in Drosophila indicate that Ret is expressed both by enteric neurons and adult intestinal epithelial progenitors, which require Ret to sustain their proliferation. Mechanistically, Ret is engaged in a positive feedback loop with Wnt/Wingless signalling, modulated by Src and Fak kinases. We find that Ret is also expressed by the developing intestinal epithelium of mice, where its expression is maintained into the adult stage in a subset of enteroendocrine/enterochromaffin cells. Mouse organoid experiments point to an intrinsic role for Ret in promoting epithelial maturation and regulating Wnt signalling. Our findings reveal evolutionary conservation of the positive Ret/Wnt signalling feedback in both developmental and homeostatic contexts. They also suggest an epithelial contribution to Ret loss-of-function disorders such as Hirschsprung disease.Peer reviewe

Computational toxicology using the OpenTox application programming interface and Bioclipse

BACKGROUND: Toxicity is a complex phenomenon involving the potential adverse effect on a range of biological functions. Predicting toxicity involves using a combination of experimental data (endpoints) and computational methods to generate a set of predictive models. Such models rely strongly on being able to integrate information from many sources. The required integration of biological and chemical information sources requires, however, a common language to express our knowledge ontologically, and interoperating services to build reliable predictive toxicology applications. FINDINGS: This article describes progress in extending the integrative bio- and cheminformatics platform Bioclipse to interoperate with OpenTox, a semantic web framework which supports open data exchange and toxicology model building. The Bioclipse workbench environment enables functionality from OpenTox web services and easy access to OpenTox resources for evaluating toxicity properties of query molecules. Relevant cases and interfaces based on ten neurotoxins are described to demonstrate the capabilities provided to the user. The integration takes advantage of semantic web technologies, thereby providing an open and simplifying communication standard. Additionally, the use of ontologies ensures proper interoperation and reliable integration of toxicity information from both experimental and computational sources. CONCLUSIONS: A novel computational toxicity assessment platform was generated from integration of two open science platforms related to toxicology: Bioclipse, that combines a rich scriptable and graphical workbench environment for integration of diverse sets of information sources, and OpenTox, a platform for interoperable toxicology data and computational services. The combination provides improved reliability and operability for handling large data sets by the use of the Open Standards from the OpenTox Application Programming Interface. This enables simultaneous access to a variety of distributed predictive toxicology databases, and algorithm and model resources, taking advantage of the Bioclipse workbench handling the technical layers

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

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

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

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

Treatment and outcomes of crisis resolution teams: a prospective multicentre study

<p>Abstract</p> <p>Background</p> <p>Crisis resolution teams (CRTs) aim to help patients in acute mental health crises without admitting them to hospital. The aims of this study were to investigate content of treatment, service practice, and outcomes of crises of CRTs in Norway.</p> <p>Methods</p> <p>The study had a multicentre prospective design, examining routine data for 680 patients and 62 staff members of eight CRTs. The clinical staff collected data on the demographic, clinical, and content of treatment variables. The service practices of the staff were assessed on the Community Program Practice Scale. Information on each CRT was recorded by the team leaders. The outcomes of crises were measured by the changes in Global Assessment of Functioning scale scores and the total scores on the Health of the Nation Outcome Scales between admission and discharge. Regression analysis was used to predict favourable outcomes.</p> <p>Results</p> <p>The mean length of treatment was 19 days for the total sample (N = 680) and 29 days for the 455 patients with more than one consultation; 7.4% of the patients had had more than twice-weekly consultations with any member of the clinical staff of the CRTs. A doctor or psychologist participated in 55.5% of the treatment episodes. The CRTs collaborated with other mental health services in 71.5% of cases and with families/networks in 51.5% of cases. The overall outcomes of the crises were positive, with a small to medium effect size. Patients with depression received the longest treatments and showed most improvement of crisis. Patients with psychotic symptoms and substance abuse problems received the shortest treatments, showed least improvement, and were most often referred to other parts of the mental health services. Length of treatment, being male and single, and a team focus on out-of-office contact were predictors of favourable outcomes of crises in the adjusted model.</p> <p>Conclusions</p> <p>Our study indicates that, compared with the UK, the Norwegian CRTs provided less intensive and less out-of-office care. The Norwegian CRTs worked more with depression and suicidal crises than with psychoses. To be an alternative to hospital admission, the Norwegian CRTs need to intensify their treatment and meet more patients outside the office.</p