Does tiny-scale atomic structure exist in the interstellar medium ?

We report on preliminary results from the recent multi-epoch neutral hydrogen absorption measurements toward three pulsars, B0823+26, B1133+16 and B2016+28, using the Arecibo telescope. We do not find significant variations in optical depth profiles over periods of 0.3 and 9--10 yr, or on spatial scales of 10--20 and 70--85 AU. The large number of non detections of the tiny scale atomic structure suggests that the AU-sized structure is not ubiquitous in the interstellar medium and could be quite a rare phenomenon.Comment: Accepted by ApJ Letters, 5 pages, 2 figure

Multi-wavelength observations of the young binary system Haro 6-10: The case of misaligned discs

Context. We present a multi-wavelength, high-resolution observational survey of the young binary system Haro 6-10 (GV Tau, IRAS 04263+2426), which is harbouring one of the few known infrared companions. Aims. The primary goal of this project is to determine the physical and geometrical properties of the circumstellar and circumbinary material in the Haro 6-10 system. Methods. High-resolution optical (HST/WFPC2) and near-infrared (VLT/NACO) images in different bands were analysed to investigate the large-scale structures of the material around the binary.Mid-infrared interferometry (VLTI/MIDI) and spectroscopy (TIMMI2 at the 3.6m ESO telescope) were carried out to determine the structure and optical depth of the circumstellar material around the individual components. Results. The multi-wavelength observations suggest that both components of the binary system Haro 6-10 are embedded in a common envelope. The measured extinction indicates a dust composition of the envelope similar to that of the interstellar medium. Each component of the system has a circumstellar disc-like structure typical of young stars. The discs are highly misaligned: the northern component is seen almost edge-on and the southern component is an almost face-on disc. Conclusions. The two main formation scenarios of binary systems with misaligned discs are the gravitational capture of a passing object in a dense environment, and the fragmentation of the collapsing molecular cloud. Given the low-density environment of the Taurus-Aurigae star-forming region, the first scenario is unlikely for Haro 6-10. The binary system most probably formed via fragmentation of two different parts of the collapsing molecular cloud combined with other dynamical processes related to the cloud and/or the protostars. This can be the explanation also for other binary systems with an infrared companion.Comment: accepted for publication in A&A on July 15, 201

Evaluation of the impact of a school gardening intervention on children's fruit and vegetable intake: a randomised controlled trial.

Background: Current academic literature suggests that school gardening programmes can provide an interactive environment with the potential to change children’s fruit and vegetable intake. This is the first cluster randomised controlled trial (RCT) designed to evaluate whether a school gardening programme can have an effect on children’s fruit and vegetable intake. Methods: The trial included children from 23 schools; these schools were randomised into two groups, one to receive the Royal Horticultural Society (RHS)-led intervention and the other to receive the less involved Teacher-led intervention. A 24-hour food diary (CADET) was used to collect baseline and follow-up dietary intake 18 months apart. Questionnaires were also administered to evaluate the intervention implementation. Results: A total of 641 children completed the trial with a mean age of 8.1 years (95% CI: 8.0, 8.4). The unadjusted results from multilevel regression analysis revealed that for combined daily fruit and vegetable intake the Teacher-led group had a higher daily mean change of 8 g (95% CI: −19, 36) compared to the RHS-led group -32 g (95% CI: −60, −3). However, after adjusting for possible confounders this difference was not significant (intervention effect: −40 g, 95% CI: −88, 1; p = 0.06). The adjusted analysis of process measures identified that if schools improved their gardening score by 3 levels (a measure of school gardening involvement - the scale has 6 levels from 0 ‘no garden’ to 5 ‘community involvement’), irrespective of group allocation, children had, on average, a daily increase of 81 g of fruit and vegetable intake (95% CI: 0, 163; p = 0.05) compared to schools that had no change in gardening score. Conclusions: This study is the first cluster randomised controlled trial designed to evaluate a school gardening intervention. The results have found very little evidence to support the claims that school gardening alone can improve children’s daily fruit and vegetable intake. However, when a gardening intervention is implemented at a high level within the school it may improve children’s daily fruit and vegetable intake by a portion. Improving children’s fruit and vegetable intake remains a challenging task

Vulnerable people, vulnerable resources? Exploring the relationship between people's vulnerability and the sustainability of community-managed natural resources

Participatory approaches to the management of common-pool resources (CPRs) are built on the premise that resource-users are dependent on the productivity of the resource and therefore have the incentive to act as resource stewards if empowered to do so. Yet many CPR users have only temporary interest in using the resources. Moreover, they are vulnerable to a range of stressors and risks unrelated to resource access and sustainability concerns. Both of these may undermine such incentives. Furthermore, discounting theory posits that high vulnerability shortens time horizons so that vulnerable CPR users might be expected to heavily discount future benefits from resource conservation. We present an ethnographic study carried out in two communities on Lake Victoria, Uganda, where fisher folk face a range of elevated risks to health and security. These immediate risks undermine participatory fishery management but this does not necessarily indicate inherently short time-horizons; for many, fishing and fish-trading are not perceived as a life-long occupation but as a means to generate capital for investment in other businesses. Thus, whether they are vulnerable or not, it cannot simply be assumed that current CPR users will have a long-term interest in participating in resource management. Incentivizing participation in CPR management for long-term sustainability may have to address both people’s wider vulnerabilities and aspirations

New Herbig-Haro Objects and Giant Outflows in Orion

We present the results of a photographic and CCD imaging survey for Herbig-Haro (HH) objects in the L1630 and L1641 giant molecular clouds in Orion. The new HH flows were initially identified from a deep H-alpha film from the recently commissioned AAO/UKST H-alpha Survey of the southern sky. Our scanned H-alpha and broad band R images highlight both the improved resolution of the H-alpha survey and the excellent contrast of the H-alpha flux with respect to the broad band R. Comparative IVN survey images allow us to distinguish between emission and reflection nebulosity. Our CCD H-alpha, [SII], continuum and I band images confirm the presence of a parsec-scale HH flow associated with the Ori I-2 cometary globule and several parsec-scale strings of HH emission centred on the L1641-N infrared cluster. Several smaller outflows display one-sided jets. Our results indicate that for declinations south of -6 degrees in L1641, parsec-scale flows appear to be the major force in the large-scale movement of optical dust and molecular gas.Comment: 14 pages, Latex using MN style, 21 figures in JPEG format. Higher resolution figures available from S.L. Mader. Accepted by MNRAS. Email contact for higher resolution images: [email protected]

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

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

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

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