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

Special Libraries, July 1978

Volume 69, Issue 7https://scholarworks.sjsu.edu/sla_sl_1978/1005/thumbnail.jp

Inferring the Origin Locations of Tweets with Quantitative Confidence

Social Internet content plays an increasingly critical role in many domains, including public health, disaster management, and politics. However, its utility is limited by missing geographic information; for example, fewer than 1.6% of Twitter messages (tweets) contain a geotag. We propose a scalable, content-based approach to estimate the location of tweets using a novel yet simple variant of gaussian mixture models. Further, because real-world applications depend on quantified uncertainty for such estimates, we propose novel metrics of accuracy, precision, and calibration, and we evaluate our approach accordingly. Experiments on 13 million global, comprehensively multi-lingual tweets show that our approach yields reliable, well-calibrated results competitive with previous computationally intensive methods. We also show that a relatively small number of training data are required for good estimates (roughly 30,000 tweets) and models are quite time-invariant (effective on tweets many weeks newer than the training set). Finally, we show that toponyms and languages with small geographic footprint provide the most useful location signals.Comment: 14 pages, 6 figures. Version 2: Move mathematics to appendix, 2 new references, various other presentation improvements. Version 3: Various presentation improvements, accepted at ACM CSCW 201

Generative Mixture of Networks

A generative model based on training deep architectures is proposed. The model consists of K networks that are trained together to learn the underlying distribution of a given data set. The process starts with dividing the input data into K clusters and feeding each of them into a separate network. After few iterations of training networks separately, we use an EM-like algorithm to train the networks together and update the clusters of the data. We call this model Mixture of Networks. The provided model is a platform that can be used for any deep structure and be trained by any conventional objective function for distribution modeling. As the components of the model are neural networks, it has high capability in characterizing complicated data distributions as well as clustering data. We apply the algorithm on MNIST hand-written digits and Yale face datasets. We also demonstrate the clustering ability of the model using some real-world and toy examples.Comment: 9 page

English as a foreign language (EFL) review: final report

The Further Education Funding Council (the Council) has undertaken a review of the position of English as foreign language (EFL) qualifications for the college year 2000-01 and beyond. This final report presents the findings of the review and its recommendations for the funding of EFL

Organic Upland Beef and Sheep Production

The technical guide addresses the issues relevant to the organic beef and sheep sector, acknowledging the questions that are frequently directed to the technical ‘Helpline’ of Organic Centre Wales. It draws on the experience of the ADAS Research Farm at Pwllpeiran and is intended as a guide for those with an interest in organic beef and sheep production production. This guide is in three interrelated parts. The first part deals primarily with technical issues of grassland and beef and sheep management, and provides practical information for farmers on key factors influencing the performance of the system. The upland organic unit at ADAS Pwllpeiran in mid-Wales was set up in 1993 to examine the feasibility of organic beef and sheep production in the hill situation. The organic unit at Pwllpeiran ADAS research farm located in the Cambrian Mountains Environmentally Sensitive Area (ESA) of mid-Wales has 237.5 ha, of which 111 ha achieved full organic status in 1995 and a further 126 ha was added in 2004. There is a suckler herd of Welsh Black cows and a breeding flock of Hardy Speckled Face ewes and Texel crosses. Annual average rainfal at 300 metres was 1765 mm, compared to over 2500 mm at 550 metres. Between 1993 and 2001, work focused on the feasibility of organic livestock production in the hills. With EAGGF Objective 5b funding, the unit was compared with the rest of the farm in terms of grassland productivity, livestock and financial per formance. Since 2001, the focus has been on key problems for organic upland farmers, particularly livestock health and welfare. Methods of internal and ectoparasite control, feeding to organic standards and maintaining the quality of forage by reseeding upland pastures have been investigated. Part 2 is a review of the financial performance of organic beef and sheep farming in Wales, provided by Andrew Jackson, of the Institute of Rural Sciences, University of Wales Aberystwyth. It is based mainly on two DEFRA funded studies: • Data for organic farms extracted from the main Farm Business Survey in Wales • A four year project focusing specifically on organic farms, drawing on all Farm Business Survey data collected for organic farms across England and Wales as well as independently collected data. From these data, it is possible to derive whole farm income data, gross margin and cost of production data to give an overview of the economics of organic dairy farming in Wales for the latest recorded financial periods (2004/05) The third and final part consists of 2 farmer case studies, which put many of the issues discussed in parts 1 and 2 in the context of individual farm businesses. We are grateful for the co-operation of Blaen y Nant and Cannon Farm

Phylogenetic relationships of Indian caecilians (Amphibia: Gymnophiona) inferred from mitochondrial rRNA gene sequences

India has a diverse caecilian fauna, including representatives of three of the six currently recognized families, the Caeciliidae, Ichthyophiidae, the endemic Uraeotyphlidae, but previous molecular phylogenetic studies of caecilians have not included sequences for any Indian caecilians. Partial 12S and 16S mitochondrial gene sequences were obtained for a single representative of each of the caecilian families found in India and aligned against previously reported sequences for 13 caecilian species. The resulting alignment (16 taxa, 1200 sites, of which 288 cannot be aligned unambiguously) was analyzed using parsimony, maximum-likelihood, and distance methods. As judged by bootstrap proportions, decay indices, and leaf stabilities, well-supported relationships of the Indian caecilians are recovered from the alignment. The data (1) corroborate the hypothesis, based on morphology, that the Uraeotyphlidae and Ichthyophiidae are sister taxa, (2) recover a monophyletic Ichthyophiidae, including Indian and South East Asian representatives, and (3) place the Indian caeciliid Gegeneophis ramaswamii as the sister group of the caeciliid caecilians of the Seychelles. Rough estimates of divergence times suggest an origin of the Uraeotyphlidae and Ichthyophiidae while India was isolated from Laurasia and Africa and are most consistent with an Indian origin of these families and subsequent dispersal of ichthyophiids into South East Asia

College Rankings Reformed: The Case for a New Order in Higher Education

Every year, students and parents eagerly scour the new college rankings. But those rankings may be misleading them about the "best" colleges and universities. New data and technology offer an opportunity to really measure how well colleges and universities are preparing their undergraduate students