Journal Articles

Implicit Value Updating Explains Transitive Inference Performance: The Betasort Model

PLoS Computational Biology - Fri, 09/25/2015 - 16:00

by Greg Jensen, Fabian Muñoz, Yelda Alkan, Vincent P. Ferrera, Herbert S. Terrace

Transitive inference (the ability to infer that B > D given that B > C and C > D) is a widespread characteristic of serial learning, observed in dozens of species. Despite these robust behavioral effects, reinforcement learning models reliant on reward prediction error or associative strength routinely fail to perform these inferences. We propose an algorithm called betasort, inspired by cognitive processes, which performs transitive inference at low computational cost. This is accomplished by (1) representing stimulus positions along a unit span using beta distributions, (2) treating positive and negative feedback asymmetrically, and (3) updating the position of every stimulus during every trial, whether that stimulus was visible or not. Performance was compared for rhesus macaques, humans, and the betasort algorithm, as well as Q-learning, an established reward-prediction error (RPE) model. Of these, only Q-learning failed to respond above chance during critical test trials. Betasort’s success (when compared to RPE models) and its computational efficiency (when compared to full Markov decision process implementations) suggests that the study of reinforcement learning in organisms will be best served by a feature-driven approach to comparing formal models.
Categories: Journal Articles

miRTex: A Text Mining System for miRNA-Gene Relation Extraction

PLoS Computational Biology - Fri, 09/25/2015 - 16:00

by Gang Li, Karen E. Ross, Cecilia N. Arighi, Yifan Peng, Cathy H. Wu, K. Vijay-Shanker

MicroRNAs (miRNAs) regulate a wide range of cellular and developmental processes through gene expression suppression or mRNA degradation. Experimentally validated miRNA gene targets are often reported in the literature. In this paper, we describe miRTex, a text mining system that extracts miRNA-target relations, as well as miRNA-gene and gene-miRNA regulation relations. The system achieves good precision and recall when evaluated on a literature corpus of 150 abstracts with F-scores close to 0.90 on the three different types of relations. We conducted full-scale text mining using miRTex to process all the Medline abstracts and all the full-length articles in the PubMed Central Open Access Subset. The results for all the Medline abstracts are stored in a database for interactive query and file download via the website at http://proteininformationresource.org/mirtex. Using miRTex, we identified genes potentially regulated by miRNAs in Triple Negative Breast Cancer, as well as miRNA-gene relations that, in conjunction with kinase-substrate relations, regulate the response to abiotic stress in Arabidopsis thaliana. These two use cases demonstrate the usefulness of miRTex text mining in the analysis of miRNA-regulated biological processes.
Categories: Journal Articles

Ni-Catalyzed Borylation of Aryl Fluorides via C–F Cleavage

Journal of American Chemical Society - Fri, 09/25/2015 - 15:24

Journal of the American Chemical SocietyDOI: 10.1021/jacs.5b08103
Categories: Journal Articles

Self-Assembly of Russian Doll Concentric Porphyrin Nanorings

Journal of American Chemical Society - Fri, 09/25/2015 - 15:19

Journal of the American Chemical SocietyDOI: 10.1021/jacs.5b07956
Categories: Journal Articles

Li-Filled, B-Substituted Carbon Clathrates

Journal of American Chemical Society - Fri, 09/25/2015 - 15:02

Journal of the American Chemical SocietyDOI: 10.1021/jacs.5b07883
Categories: Journal Articles

Confinement, Desolvation, And Electrosorption Effects on the Diffusion of Ions in Nanoporous Carbon Electrodes

Journal of American Chemical Society - Fri, 09/25/2015 - 14:50

Journal of the American Chemical SocietyDOI: 10.1021/jacs.5b07416
Categories: Journal Articles

Colloidal Hybrid Nanoparticle Insertion Reaction for Transforming Heterodimers into Heterotrimers

Journal of American Chemical Society - Fri, 09/25/2015 - 13:04

Journal of the American Chemical SocietyDOI: 10.1021/jacs.5b08850
Categories: Journal Articles

Palladium-Catalyzed Formal Insertion of Carbenoids into Aminals via C–N Bond Activation

Journal of American Chemical Society - Fri, 09/25/2015 - 13:00

Journal of the American Chemical SocietyDOI: 10.1021/jacs.5b08476
Categories: Journal Articles

Peptide Recognition of Cholesterol in Fluid Phospholipid Bilayers

Journal of American Chemical Society - Fri, 09/25/2015 - 12:58

Journal of the American Chemical SocietyDOI: 10.1021/jacs.5b08132
Categories: Journal Articles

Melting of Pb Charge Glass and Simultaneous Pb–Cr Charge Transfer in PbCrO3 as the Origin of Volume Collapse

Journal of American Chemical Society - Fri, 09/25/2015 - 06:18

Journal of the American Chemical SocietyDOI: 10.1021/jacs.5b08216
Categories: Journal Articles

[Editorial] Preimplantation genetic screens

Science - Thu, 09/24/2015 - 23:00
Although our knowledge of genetic abnormalities that cause health disorders is expanding, the pace of discovering cures for genetic diseases is not nearly as fast. However, technologies applicable to preventing heritable genetic diseases have been developing, among them so-called “next-generation sequencing.” This efficient and inexpensive means to sequence DNA has revolutionized the study of genomics and could play a major role in future preimplantation genetic screening approaches. It may even improve screening during early pregnancy. Author: Arthur L. Beaudet
Categories: Journal Articles

[In Brief] This week's section

Science - Thu, 09/24/2015 - 23:00
In science news around the world, the U.S. government decides against declaring the greater sage grouse an endangered species, a European Space Agency committee endorses the FLuorescence EXplorer as the agency's next mission, a U.K. researcher applies to edit the genes of human embryos, a U.S. National Academies panel wants Congress to create a new entity to oversee federal policies that affect academic research, the 2015 Ig Nobel Prizes are awarded, and more. Also, President Barack Obama nominates veteran heart researcher Robert Califf to be head of the U.S. Food and Drug Administration, Pope Francis selects Jesuit brother Guy Consolmagno to lead the Vatican Observatory, and lawyer Christopher Pyne is sworn in as Australia's science minister. And artist Kindra Crick, granddaughter of molecular biologist Francis Crick, talks with Science about the DNA sculpture she created for an upcoming auction to raise money for the London-based Francis Crick Institute.
Categories: Journal Articles
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