The work of Jaroslav Pelikan on Insects of the order Thysanoptera.

Diese Arbeit ist eine kleine Ehrung für Doc. Ing. Dr. Jaroslav Pelikán, DrSc, einen bekannten Wissenschaftler auf den Gebieten der Entomologie, Theriologie und Ökologie. Er beschrieb rund 80 neue Arten und sieben neue Gattungen von Fransenflüglern (Thysanoptera). Seine Arbeiten auf nationaler Ebene schliessen neben detaillierteren Beiträgen zur Fauna der Tschechoslowakei einige Checklisten ein. Am 22. April 2006 feierte Jaroslav Pelikán seinen 80. Geburtstag.The paper is a small tribute to Doc. Ing. Dr. Jaroslav Pelikán, DrSc, who has been a reputable scientist in the fields of entomology, theriology and ecology. He described about 80 new species of thrips as well as seven new genera of Thysanoptera. His national contributions included several checklists, together with his more complex contribution within the Fauna of Czechoslovakia. On the 22nd of April 2006 Jaroslav Pelikán celebrated his 80th birthday

Progressor: Social navigation support through open social student modeling

The increased volumes of online learning content have produced two problems: how to help students to find the most appropriate resources and how to engage them in using these resources. Personalized and social learning have been suggested as potential ways to address these problems. Our work presented in this paper combines the ideas of personalized and social learning in the context of educational hypermedia. We introduce Progressor, an innovative Web-based tool based on the concepts of social navigation and open student modeling that helps students to find the most relevant resources in a large collection of parameterized self-assessment questions on Java programming. We have evaluated Progressor in a semester-long classroom study, the results of which are presented in this paper. The study confirmed the impact of personalized social navigation support provided by the system in the target context. The interface encouraged students to explore more topics attempting more questions and achieving higher success rates in answering them. A deeper analysis of the social navigation support mechanism revealed that the top students successfully led the way to discovering most relevant resources by creating clear pathways for weaker students. © 2013 Taylor and Francis Group, LLC

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

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

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

mRNA Secondary Structures Fold Sequentially But Exchange Rapidly In Vivo

Self-cleavage assays of RNA folding reveal that mRNA structures fold sequentially in vitro and in vivo, but exchange between adjacent structures is much faster in vivo than it is in vitro

Guidelines and Recommendations on Yeast Cell Death Nomenclature

Elucidating the biology of yeast in its full complexity has major implications for science, medicine and industry. One of the most critical processes determining yeast life and physiology is cellular demise. However, the investigation of yeast cell death is a relatively young field, and a widely accepted set of concepts and terms is still missing. Here, we propose unified criteria for the definition of accidental, regulated, and programmed forms of cell death in yeast based on a series of morphological and biochemical criteria. Specifically, we provide consensus guidelines on the differential definition of terms including apoptosis, regulated necrosis, and autophagic cell death, as we refer to additional cell death routines that are relevant for the biology of (at least some species of) yeast. As this area of investigation advances rapidly, changes and extensions to this set of recommendations will be implemented in the years to come. Nonetheless, we strongly encourage the authors, reviewers and editors of scientific articles to adopt these collective standards in order to establish an accurate framework for yeast cell death research and, ultimately, to accelerate the progress of this vibrant field of research

The third data release of the Kilo-Degree Survey and associated data products

The Kilo-Degree Survey (KiDS) is an ongoing optical wide-field imaging survey with the OmegaCAM camera at the VLT Survey Telescope. It aims to image 1500 square degrees in four filters (ugri). The core science driver is mapping the large-scale matter distribution in the Universe, using weak lensing shear and photometric redshift measurements. Further science cases include galaxy evolution, Milky Way structure, detection of high-redshift clusters, and finding rare sources such as strong lenses and quasars. Here we present the third public data release (DR3) and several associated data products, adding further area, homogenized photometric calibration, photometric redshifts and weak lensing shear measurements to the first two releases. A dedicated pipeline embedded in the Astro-WISE information system is used for the production of the main release. Modifications with respect to earlier releases are described in detail. Photometric redshifts have been derived using both Bayesian template fitting, and machine-learning techniques. For the weak lensing measurements, optimized procedures based on the THELI data reduction and lensfit shear measurement packages are used. In DR3 stacked ugri images, weight maps, masks, and source lists for 292 new survey tiles (~300 sq.deg) are made available. The multi-band catalogue, including homogenized photometry and photometric redshifts, covers the combined DR1, DR2 and DR3 footprint of 440 survey tiles (447 sq.deg). Limiting magnitudes are typically 24.3, 25.1, 24.9, 23.8 (5 sigma in a 2 arcsec aperture) in ugri, respectively, and the typical r-band PSF size is less than 0.7 arcsec. The photometric homogenization scheme ensures accurate colors and an absolute calibration stable to ~2% for gri and ~3% in u. Separately released are a weak lensing shear catalogue and photometric redshifts based on two different machine-learning techniques.Comment: small modifications; 27 pages, 12 figures, accepted for publication in Astronomy & Astrophysic