Frame, metric and geodesic evolution in shape-changing nematic shells.

Non-uniform director fields in flat, responsive, glassy nematic sheets lead to the induction of shells with non-trivial topography on the application of light or heat. Contraction along the director causes metric change, with, in general, the induction of Gaussian curvature, that drives the topography change. We describe the metric change, the evolution of the director field, and the transformation of reference state material curves, e.g. spirals into radii, as curvature develops. The non-isometric deformations associated with heat or light change the geodesics of the surface, intriguingly even in regions where no Gaussian curvature results

Management and care of the herd boar (1995)

Reproductive performance of a herd boar depends upon proper care and management. Boars are frequently neglected, especially newly purchased boars en route and after they are brought home. There are essential steps in the care and management of a herd boar that will help eliminate sources of trouble and give you maximum service

Combining computer vision and standardised protocols for improved measurement of live sea urchins for research and industry

To allow sea urchin aquaculture to achieve its intended scale, efficient and precise methods for measuring large numbers of urchins in commercial-scale operations are needed. Current protocols for measuring urchin test (shell) dimensions and mass are time-consuming and prone to high measurement error, thus inconvenient in research and impractical in a commercial context. This study investigates and compares various measurement methods with a newly developed computer vision approach developed in this study, to establish a single protocol using precise, efficient and accessible methodology for measuring live urchins. We show that urchin wet mass can vary up to 8.73% depending on time out of water; this is significantly reduced to an average of 0.1% change by allowing urchins to drip-dry for at least 90 s prior to weighing. We found the conventional vernier calliper method used to measure urchin dimensions to be both time-consuming and imprecise (mean coefficient of variation (CV) of 2.41% for Tripneustes gratilla). Conversely, the computer vision programme we developed measures with higher precision (mean CV of 1.55% for T. gratilla) and is considerably faster. The software uses a series of hue saturation value filters, edge detection algorithms and distortions to measure the diameter of the test (excluding spines) of multiple urchins at once. The software is open-source, and the protocol does not require specialised equipment (can be performed with a mobile phone camera). When the computer vision application is combined with the simple procedures described in this paper, to reduce measurement inaccuracies, urchin wet mass and diameter can be more efficiently and precisely determined. For a larger scale context, this software could easily be incorporated into various tools, such as a grading machine, to completely automate various farm processes. As such, this study has potential to assist urchin data collection in both research and commercial contexts

The effect of fresh seaweed and a formulated diet supplemented with seaweed on the growth and gonad quality of the collector sea urchin, Tripneustes gratilla, under farm conditions

This gonad enhancement study investigates the effect of different fresh and formulated feeds and feeding regimes on the growth and gonad quality of wild-collected adult sea urchin, Tripneustes gratilla, under farm conditions for over 18 weeks. In the first 12 weeks (phase 1), urchins were fed fresh Ulva rigida (U); a 50:50 mixture of fresh U. rigida and Gracilaria gracilis (UG); fresh G. gracilis (G) and a formulated diet 20U (containing 20% U. rigida), and in the final 6 weeks (phase 2) of the study, diet was changed to a formulated feed (20U diet). By the end of phase 1, urchins fed the 20U diet produced gonads (50.72 ± 5.4 g) that were significantly heavier (p < .001) than the gonads of urchins fed the fresh seaweed diets (U, UG & G). By the end of phase 2, gonad weight of urchins in treatment groups UG-20U and G-20U were similar to those fed the 20U-20U diet. Gonad colour of urchins in the G-20U treatment became significantly lighter (ANOVA, p = .029) and poorer quality, compared with urchins in the U-20U group. This gonad enhancement study, conducted on wild collected adult T. gratilla, has shown that a formulated feed (20U diet) can enhance gonad growth and produce commercially acceptable gonads. This farm-based study supports previous findings from aquarium-based studies by our group and indicates that short-term sea urchin gonad enhancement can be carried out under farm conditions in South Africa

Evolution and implementation of radiographic response criteria in neuro-oncology

Radiographic response assessment in neuro-oncology is critical in clinical practice and trials. Conventional criteria, such as the MacDonald and response assessment in neuro-oncology (RANO) criteria, rely on bidimensional (2D) measurements of a single tumor cross-section. Although RANO criteria are established for response assessment in clinical trials, there is a critical need to address the complexity of brain tumor treatment response with multiple new approaches being proposed. These include volumetric analysis of tumor compartments, structured MRI reporting systems like the Brain Tumor Reporting and Data System, and standardized approaches to advanced imaging techniques to distinguish tumor response from treatment effects. In this review, we discuss the strengths and limitations of different neuro-oncology response criteria and summarize current research findings on the role of novel response methods in neuro-oncology clinical trials and practice

Custom Integrated Circuits

Contains reports on seven research projects.U.S. Air Force - Office of Scientific Research (Contract F49620-84-C-0004)National Science Foundation (Grant ECS81-18160)Defense Advanced Research Projects Agency (Contract NOO14-80-C-0622)National Science Foundation (Grant ECS83-10941

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

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

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