Discovery of a Sub-Parsec Radio Counterjet in the Nucleus of Centaurus A

A sub-parsec scale radio counterjet has been detected in the nucleus of the closest radio galaxy, Centaurus A (NGC 5128), with VLBI imaging at 2.3 and 8.4 GHz. This is one of the first detections of a VLBI counterjet and provides new constraints on the kinematics of the radio jets emerging from the nucleus of Cen A. A bright, compact core is seen at 8.4 GHz, along with a jet extending along P.A. 51 degrees. The core is completely absorbed at 2.3 GHz. Our images show a much wider gap between the base of the main jet and the counterjet at 2.3 GHz than at 8.4 GHz and also that the core has an extraordinarily inverted spectrum. These observations provide evidence that the innermost 0.4-0.8 pc of the source is seen through a disk or torus of ionized gas which is opaque at low frequencies due to free-free absorption.Comment: 3 pages, 2 postscript figures, scheduled for publication in August 1, 1996 issue of Ap.J. Letter

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

Background The Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function. Results Here, we report on the results of the third CAFA challenge, CAFA3, that featured an expanded analysis over the previous CAFA rounds, both in terms of volume of data analyzed and the types of analysis performed. In a novel and major new development, computational predictions and assessment goals drove some of the experimental assays, resulting in new functional annotations for more than 1000 genes. Specifically, we performed experimental whole-genome mutation screening in Candida albicans and Pseudomonas aureginosa genomes, which provided us with genome-wide experimental data for genes associated with biofilm formation and motility. We further performed targeted assays on selected genes in Drosophila melanogaster, which we suspected of being involved in long-term memory. Conclusion We conclude that while predictions of the molecular function and biological process annotations have slightly improved over time, those of the cellular component have not. Term-centric prediction of experimental annotations remains equally challenging; although the performance of the top methods is significantly better than the expectations set by baseline methods in C. albicans and D. melanogaster, it leaves considerable room and need for improvement. Finally, we report that the CAFA community now involves a broad range of participants with expertise in bioinformatics, biological experimentation, biocuration, and bio-ontologies, working together to improve functional annotation, computational function prediction, and our ability to manage big data in the era of large experimental screens.Peer reviewe

From Sea to Sea: Canada's Three Oceans of Biodiversity

Evaluating and understanding biodiversity in marine ecosystems are both necessary and challenging for conservation. This paper compiles and summarizes current knowledge of the diversity of marine taxa in Canada's three oceans while recognizing that this compilation is incomplete and will change in the future. That Canada has the longest coastline in the world and incorporates distinctly different biogeographic provinces and ecoregions (e.g., temperate through ice-covered areas) constrains this analysis. The taxonomic groups presented here include microbes, phytoplankton, macroalgae, zooplankton, benthic infauna, fishes, and marine mammals. The minimum number of species or taxa compiled here is 15,988 for the three Canadian oceans. However, this number clearly underestimates in several ways the total number of taxa present. First, there are significant gaps in the published literature. Second, the diversity of many habitats has not been compiled for all taxonomic groups (e.g., intertidal rocky shores, deep sea), and data compilations are based on short-term, directed research programs or longer-term monitoring activities with limited spatial resolution. Third, the biodiversity of large organisms is well known, but this is not true of smaller organisms. Finally, the greatest constraint on this summary is the willingness and capacity of those who collected the data to make it available to those interested in biodiversity meta-analyses. Confirmation of identities and intercomparison of studies are also constrained by the disturbing rate of decline in the number of taxonomists and systematists specializing on marine taxa in Canada. This decline is mostly the result of retirements of current specialists and to a lack of training and employment opportunities for new ones. Considering the difficulties encountered in compiling an overview of biogeographic data and the diversity of species or taxa in Canada's three oceans, this synthesis is intended to serve as a biodiversity baseline for a new program on marine biodiversity, the Canadian Healthy Ocean Network. A major effort needs to be undertaken to establish a complete baseline of Canadian marine biodiversity of all taxonomic groups, especially if we are to understand and conserve this part of Canada's natural heritage

Comment letters to the National Commission on Commission on Fraudulent Financial Reporting, 1987 (Treadway Commission) Vol. 1

https://egrove.olemiss.edu/aicpa_sop/1661/thumbnail.jp

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

BackgroundThe Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function.ResultsHere, we report on the results of the third CAFA challenge, CAFA3, that featured an expanded analysis over the previous CAFA rounds, both in terms of volume of data analyzed and the types of analysis performed. In a novel and major new development, computational predictions and assessment goals drove some of the experimental assays, resulting in new functional annotations for more than 1000 genes. Specifically, we performed experimental whole-genome mutation screening in Candida albicans and Pseudomonas aureginosa genomes, which provided us with genome-wide experimental data for genes associated with biofilm formation and motility. We further performed targeted assays on selected genes in Drosophila melanogaster, which we suspected of being involved in long-term memory.ConclusionWe conclude that while predictions of the molecular function and biological process annotations have slightly improved over time, those of the cellular component have not. Term-centric prediction of experimental annotations remains equally challenging; although the performance of the top methods is significantly better than the expectations set by baseline methods in C. albicans and D. melanogaster, it leaves considerable room and need for improvement. Finally, we report that the CAFA community now involves a broad range of participants with expertise in bioinformatics, biological experimentation, biocuration, and bio-ontologies, working together to improve functional annotation, computational function prediction, and our ability to manage big data in the era of large experimental screens.</p

Classifying cancer genome aberrations by their mutually exclusive effects on transcription

Abstract Background Malignant tumors are typically caused by a conglomeration of genomic aberrations—including point mutations, small insertions, small deletions, and large copy-number variations. In some cases, specific chemotherapies and targeted drug treatments are effective against tumors that harbor certain genomic aberrations. However, predictive aberrations (biomarkers) have not been identified for many tumor types and treatments. One way to address this problem is to examine the downstream, transcriptional effects of genomic aberrations and to identify characteristic patterns. Even though two tumors harbor different genomic aberrations, the transcriptional effects of those aberrations may be similar. These patterns could be used to inform treatment choices. Methods We used data from 9300 tumors across 25 cancer types from The Cancer Genome Atlas. We used supervised machine learning to evaluate our ability to distinguish between tumors that had mutually exclusive genomic aberrations in specific genes. An ability to accurately distinguish between tumors with aberrations in these genes suggested that the genes have a relatively different downstream effect on transcription, and vice versa. We compared these findings against prior knowledge about signaling networks and drug responses. Results Our analysis recapitulates known relationships in cancer pathways and identifies gene pairs known to predict responses to the same treatments. For example, in lung adenocarcinomas, gene-expression profiles from tumors with somatic aberrations in EGFR or MET were negatively correlated with each other, in line with prior knowledge that MET amplification causes resistance to EGFR inhibition. In breast carcinomas, we observed high similarity between PTEN and PIK3CA, which play complementary roles in regulating cellular proliferation. In a pan-cancer analysis, we found that genomic aberrations in BRAF and VHL exhibit downstream effects that are clearly distinct from other genes. Conclusion We show that transcriptional data offer promise as a way to group genomic aberrations according to their downstream effects, and these groupings recapitulate known relationships. Our approach shows potential to help pharmacologists and clinical trialists narrow the search space for candidate gene/drug associations, including for rare mutations, and for identifying potential drug-repurposing opportunities