Ferrocene-Decorated Hyperbranched Poly(aroxycarbonylphenylene)s: Synthesis, Light Refraction, Photopatterning and Precursor to Magnetic Ceramics

Ferrocene-decorated hyperbranched poly[1,3,5-tri(aroycarbonyl)phenylene]s (hb-PTACPs) are prepared in moderate yields with high molecular weights by one-pot polycyclotrimerization of 4,4'-isopropylidenediphenyl bipropiolate with 4-(ferrocenylmethyl)phenyl propiolate in reflux dimethylformamide. All the polymers are soluble and film-forming. They enjoy high thermal stability and lost little of their weight when heated to 300 °C under nitrogen. Thin solid films of the organometallic polymers shows high refractive indices (RI = 1.7038–1.6295) in the wavelength region of 400–1,700 nm. Ceramization of the organometallic hb-PTACPs at high temperature under inert atmosphere gives iron nanoparticles with high magnetizabilities. The organometallic polymers are readily cross-linked under UV irradiation and pyrolysis of the patterned polymer films produces magnetic ceramic patterns with good shape retention

The ENIGMA Stroke Recovery Working Group: Big data neuroimaging to study brain–behavior relationships after stroke

The goal of the Enhancing Neuroimaging Genetics through Meta‐Analysis (ENIGMA) Stroke Recovery working group is to understand brain and behavior relationships using well‐powered meta‐ and mega‐analytic approaches. ENIGMA Stroke Recovery has data from over 2,100 stroke patients collected across 39 research studies and 10 countries around the world, comprising the largest multisite retrospective stroke data collaboration to date. This article outlines the efforts taken by the ENIGMA Stroke Recovery working group to develop neuroinformatics protocols and methods to manage multisite stroke brain magnetic resonance imaging, behavioral and demographics data. Specifically, the processes for scalable data intake and preprocessing, multisite data harmonization, and large‐scale stroke lesion analysis are described, and challenges unique to this type of big data collaboration in stroke research are discussed. Finally, future directions and limitations, as well as recommendations for improved data harmonization through prospective data collection and data management, are provided

Pollinator monitoring more than pays for itself

1. Resilient pollination services depend on sufficient abundance of pollinating insects over time. Currently, however, most knowledge about the status and trends of pollinators is based on changes in pollinator species richness and distribution only. 2. Systematic, long‐term monitoring of pollinators is urgently needed to provide baseline information on their status, to identify the drivers of declines and to inform suitable response measures. 3. Power analysis was used to determine the number of sites required to detect a 30% change in pollinator populations over 10 years. We then evaluated the full economic costs of implementing four national monitoring schemes in the UK: (a) professional pollinator monitoring, (b) professional pollination service monitoring, (c) volunteer collected pan traps and (d) volunteer focal floral observations. These costs were compared to (a) the costs of implementing separate, expert‐designed research and monitoring networks and (b) the economic benefits of pollination services threatened by pollinator loss. 4. Estimated scheme costs ranged from £6,159/year for a 75‐site volunteer focal flower observation scheme to £2.7 M/year for an 800‐site professional pollination service monitoring network. The estimated research costs saved using the site network as research infrastructure range from £1.46–4.17 M/year. The economic value of UK crop yield lost following a 30% decline in pollinators was estimated at ~£188 M/year. 5. Synthesis and applications. We evaluated the full costs of running pollinator monitoring schemes against the economic benefits to research and society they provide. The annual costs of monitoring are <0.02% of the economic value of pollination services that would be lost after a 30% decline in pollination services. Furthermore, by providing high‐quality scientific data, monitoring schemes would save at least £1.5 on data collection per £1 spent. Our findings demonstrate that long‐term systematic monitoring can be a cost‐effective tool for both answering key research questions and setting action points for policymakers. Careful consideration must be given to scheme design, the logistics of national‐scale implementation and resulting data quality when selecting the most appropriate combination of surveyors, methods and site networks to deliver a successful scheme

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

Phylogenomic Analysis of Marine Roseobacters

Background: Members of the Roseobacter clade which play a key role in the biogeochemical cycles of the ocean are diverse and abundant, comprising 10–25 % of the bacterioplankton in most marine surface waters. The rapid accumulation of whole-genome sequence data for the Roseobacter clade allows us to obtain a clearer picture of its evolution. Methodology/Principal Findings: In this study about 1,200 likely orthologous protein families were identified from 17 Roseobacter bacteria genomes. Functional annotations for these genes are provided by iProClass. Phylogenetic trees were constructed for each gene using maximum likelihood (ML) and neighbor joining (NJ). Putative organismal phylogenetic trees were built with phylogenomic methods. These trees were compared and analyzed using principal coordinates analysis (PCoA), approximately unbiased (AU) and Shimodaira–Hasegawa (SH) tests. A core set of 694 genes with vertical descent signal that are resistant to horizontal gene transfer (HGT) is used to reconstruct a robust organismal phylogeny. In addition, we also discovered the most likely 109 HGT genes. The core set contains genes that encode ribosomal apparatus, ABC transporters and chaperones often found in the environmental metagenomic and metatranscriptomic data. These genes in the core set are spread out uniformly among the various functional classes and biological processes. Conclusions/Significance: Here we report a new multigene-derived phylogenetic tree of the Roseobacter clade. Of particular interest is the HGT of eleven genes involved in vitamin B12 synthesis as well as key enzynmes fo