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Flu pandemic emergence, genesis of thalamic oscillations, making sense of tumor heterogeneity, ten simple rules for responding to reviewers and structuring papers

Check out our highlights from the PLOS Computational Biology October issue:



Seasonality in risk of pandemic influenza emergence

Influenza pandemics emerge via genomic reassortment between circulating human and animal strains. The risk of pandemic emergence should therefore be high during the flu season, when viruses are abundant and conditions favor transmission. However, the six pandemics on record since 1889 all emerged in the Northern Hemisphere following the flu season, suggesting that other forces may predictably constrain pandemic risk. Spencer J. Fox and colleagues find that seasonal influenza epidemics leave a wake of immunity that impedes pandemic emergence. This transient refractory period is consistent with the spring-summer emergence, multiple wave dynamics of recent pandemics, and may cause initial underestimation of the viral transmission rate. These findings may improve pre-pandemic risk assessments and real-time situational awareness, particularly as we gain greater insight into the extent of immunity.


Oscillatory state transition as a function of ACh/NE modulation and afferent input. Image Credit: Fröhlich et al.

Unified thalamic model generates multiple distinct oscillations with state-dependent entrainment by stimulation

Computational modeling has served as an important tool to understand the cellular and circuit mechanisms of thalamocortical oscillations. However, most of the existing thalamic models focus on only one particular oscillatory pattern such as alpha or spindle oscillations. Thus, it remains unclear whether the same thalamic circuitry on its own could generate all major oscillatory patterns and if so what mechanisms underlie the transition among these distinct states. Here Flavio Fröhlich and colleagues present a unified model of the thalamus that is capable of independently generating multiple distinct oscillations corresponding to different physiological conditions. They then mapped out the different thalamic oscillations by varying the acetylcholine/norepinephrine modulatory level and input level systematically. Their simulation results offer a mechanistic understanding of thalamic oscillations and support the long-standing notion of a thalamic “pacemaker”. It also suggests that pathological oscillations associated with neurological and psychiatric disorders may stem from malfunction of the thalamic circuitry.


Automated deconvolution of structured mixtures from heterogeneous tumor genomic

October Issue Image: An area with heightened sensitivity to spatial detail, known as the fovea in mammals is oriented through eye and head movements to scrutinize regions of interest in the visual environment. Akbas and Eckstein showed using a computer vision object detection model, that the foveated version of the model can attain similar search performance to its non-foveated version while bringing significant computational savings. The image shows the spatial pooling regions of the foveated model.
Image Credit: Emre Akbas


One of the major challenges in making sense of cancer genomics is high heterogeneity cell-to-cell, as a tumor is typically made up of multiple cell populations with distinct genomes and gene expression patterns. The difficulty of working with such data has led to interest in computationally inferring the components of genomic mixtures. Russell Schwartz and colleagues develop a new approach to this problem, designed to take better advantage of the fact that mixtures of cells across tumors (or tumor regions) can be expected to be highly non-uniform; samples that share greater common ancestry or progression mechanisms are likely to have more similar mixtures of cell types. They present new work on reconstructing mixtures from multiple genomic samples where the samples can be presumed to share such a pattern of similarity. Their methods automate the process of reconstructing these mixtures and the relationships between samples. They demonstrate their effectiveness on tumor genomic data in comparison to alternative methods in the literature.



Ten Simple Rules


Ten simple rules for writing a response to reviewers

A well-crafted “response to reviewers” document is a critical part of your re-submission. This document is submitted alongside your revised manuscript, summarizing the changes that you made in response to the critiques. Too frequently, authors focus on revising the manuscript itself and spend too little time making the response document clear and compelling. The result can be misunderstandings between the reviewers and the authors and—ultimately—the possible rejection of a high-quality manuscript.

By William Stafford Noble


Ten simple rules for structuring papers

Good scientific writing is essential to career development and to the progress of science. A well-structured manuscript allows readers and reviewers to get excited about the subject matter, to understand and verify the paper’s contributions, and to integrate these contributions into a broader context. However, many scientists struggle with producing high-quality manuscripts and are typically untrained in paper writing. Focusing on how readers consume information, we present a set of ten simple rules to help you communicate the main idea of your paper. These rules are designed to make your paper more influential and the process of writing more efficient and pleasurable.

By Konrad Kording and Brett Mensh

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