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Table of Contents: August 2012

COVER

Harvester ant foragers waiting inside the nest.

Image Credit: Katherine N. Dektar, Stanford University.
Issue Image

Whether an outgoing forager leaves the nest depends on its rate of interaction with foragers returning with seeds. This simple positive feedback links foraging activity to food availability: the more food is available, the more quickly foragers find it and return to the nest. See Prabhakar et al., doi:10.1371/journal.pcbi.1002670.

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Education

Review

Research Articles

On Genetic Specificity in Symbiont-Mediated Host-Parasite Coevolution

Marek Kwiatkowski, Jan Engelstädter, Christoph Vorburger

Teasing Apart Translational and Transcriptional Components of Stochastic Variations in Eukaryotic Gene Expression

Raheleh Salari, Damian Wojtowicz, Jie Zheng, David Levens, Yitzhak Pilpel, Teresa M. Przytycka

Mutual Repression Enhances the Steepness and Precision of Gene Expression Boundaries

Thomas R. Sokolowski, Thorsten Erdmann, Pieter Rein ten Wolde

Weighted Frequent Gene Co-expression Network Mining to Identify Genes Involved in Genome Stability

Jie Zhang, Kewei Lu, Yang Xiang, Muhtadi Islam, Shweta Kotian, Zeina Kais, Cindy Lee, Mansi Arora, Hui-wen Liu, Jeffrey D. Parvin, Kun Huang

Quantitative Predictions of Binding Free Energy Changes in Drug-Resistant Influenza Neuraminidase

Daniel R. Ripoll, Ilja V. Khavrutskii, Sidhartha Chaudhury, Jin Liu, Robert A. Kuschner, Anders Wallqvist, Jaques Reifman

External Drive to Inhibitory Cells Induces Alternating Episodes of High- and Low-Amplitude Oscillations

Oscar J. Avella Gonzalez, Karlijn I. van Aerde, Ronald A. J. van Elburg, Simon-Shlomo Poil, Huibert D. Mansvelder, Klaus Linkenkaer-Hansen, Jaap van Pelt, Arjen van Ooyen

Coupling Mechanical Deformations and Planar Cell Polarity to Create Regular Patterns in the Zebrafish Retina

Guillaume Salbreux, Linda K. Barthel, Pamela A. Raymond, David K. Lubensky

Modeling of Gap Gene Expression in Drosophila Kruppel Mutants

Konstantin Kozlov, Svetlana Surkova, Ekaterina Myasnikova, John Reinitz, Maria Samsonova

Prediction of Mutational Tolerance in HIV-1 Protease and Reverse Transcriptase Using Flexible Backbone Protein Design

Elisabeth Humphris-Narayanan, Eyal Akiva, Rocco Varela, Shane Ó Conchúir, Tanja Kortemme

Defining the Nature of Thermal Intermediate in 3 State Folding Proteins: Apoflavodoxin, a Study Case

Rebeca García-Fandiño, Pau Bernadó, Sara Ayuso-Tejedor, Javier Sancho, Modesto Orozco

Diversity and Noise Effects in a Model of Homeostatic Regulation of the Sleep-Wake Cycle

Marco Patriarca, Svetlana Postnova, Hans A. Braun, Emilio Hernández-García, Raúl Toral

Artificial Neural Networks Trained to Detect Viral and Phage Structural Proteins

Victor Seguritan, Nelson Alves Jr., Michael Arnoult, Amy Raymond, Don Lorimer, Alex B. Burgin Jr., Peter Salamon, Anca M. Segall

The Regulation of Ant Colony Foraging Activity without Spatial Information

Balaji Prabhakar, Katherine N. Dektar, Deborah M. Gordon

Activity Dependent Degeneration Explains Hub Vulnerability in Alzheimer's Disease

Willem de Haan, Katherine Mott, Elisabeth C. W. van Straaten, Philip Scheltens, Cornelis J. Stam

Evolution of Stress Response in the Face of Unreliable Environmental Signals

Markus Arnoldini, Rafal Mostowy, Sebastian Bonhoeffer, Martin Ackermann

A Network-based Approach for Predicting Missing Pathway Interactions

Saket Navlakha, Anthony Gitter, Ziv Bar-Joseph

Locust Dynamics: Behavioral Phase Change and Swarming

Chad M. Topaz, Maria R. D'Orsogna, Leah Edelstein-Keshet, Andrew J. Bernoff

Assessing the Relative Stability of Dimer Interfaces in G Protein-Coupled Receptors

Jennifer M. Johnston, Hao Wang, Davide Provasi, Marta Filizola

Maintaining a Cognitive Map in Darkness: The Need to Fuse Boundary Knowledge with Path Integration

Allen Cheung, David Ball, Michael Milford, Gordon Wyeth, Janet Wiles

Literature Based Drug Interaction Prediction with Clinical Assessment Using Electronic Medical Records: Novel Myopathy Associated Drug Interactions

Jon D. Duke, Xu Han, Zhiping Wang, Abhinita Subhadarshini, Shreyas D. Karnik, Xiaochun Li, Stephen D. Hall, Yan Jin, J. Thomas Callaghan, Marcus J. Overhage, David A. Flockhart, R. Matthew Strother, Sara K. Quinney, Lang Li

Performance Limitations of Relay Neurons

Rahul Agarwal, Sridevi V. Sarma

A Canonical Model of Multistability and Scale-Invariance in Biological Systems

Frank Freyer, James A. Roberts, Petra Ritter, Michael Breakspear

Decorrelation of Neural-Network Activity by Inhibitory Feedback

Tom Tetzlaff, Moritz Helias, Gaute T. Einevoll, Markus Diesmann

Inferring Dynamic Signatures of Microbes in Complex Host Ecosystems

Georg K. Gerber, Andrew B. Onderdonk, Lynn Bry

The Role of Local Backrub Motions in Evolved and Designed Mutations

Daniel A. Keedy, Ivelin Georgiev, Edward B. Triplett, Bruce R. Donald, David C. Richardson, Jane S. Richardson