Effects of Anthropogenic Noise on Body Mass in Gryllodes sigillatus

Insects use vibrational structures to produce and sense airborne sounds in intraspecific communication. These signals are important in courtship as well as defensive behavior against predators. For example, insects can detect the presence of nearby predators using vibrations. With an increase in anthropogenic activity, processing these signals and the constant threat they represent may increase stress on insects, subsequently affecting their behavior and physiology. Our experiment was designed to determine whether anthropogenic noise, possibly perceived as a stressor, will decrease the body mass of banded crickets, Gryllodes sigillatus. We predicted that the anthropogenic noise would stress the crickets, leading to a decrease in body mass and increase in mortality rate. In this study, we subjected crickets to three different levels of anthropogenic activity for three days: high, low, and negligible. We found no significant difference in body mass or mortality throughout the duration of the experiment

How to collect high quality segmentations: use human or computer drawn object boundaries?

High quality segmentations must be captured consistently for applications such as biomedical image analysis. While human drawn segmentations are often collected because they provide a consistent level of quality, computer drawn segmentations can be collected efficiently and inexpensively. In this paper, we examine how to leverage available human and computer resources to consistently create high quality segmentations. We propose a quality control methodology. We demonstrate how to apply this approach using crowdsourced and domain expert votes for the "best" segmentation from a collection of human and computer drawn segmentations for 70 objects from a public dataset and 274 objects from biomedical images. We publicly share the library of biomedical images which includes 1,879 manual annotations of the boundaries of 274 objects. We found for the 344 objects that no single segmentation source was preferred and that human annotations are not always preferred over computer annotations. These results motivated us to examine the traditional approach to evaluate segmentation algorithms, which involves comparing the segmentations produced by the algorithms to manual annotations on benchmark datasets. We found that algorithm benchmarking results change when the comparison is made to consensus-voted segmentations. Our results led us to suggest a new segmentation approach that uses machine learning to predict the optimal segmentation source and a modified segmentation evaluation approach.National Science Foundation (IIS-0910908

Dynamic Position Encoding for Transformers

Recurrent models have been dominating the field of neural machine translation (NMT) for the past few years. Transformers \citep{vaswani2017attention}, have radically changed it by proposing a novel architecture that relies on a feed-forward backbone and self-attention mechanism. Although Transformers are powerful, they could fail to properly encode sequential/positional information due to their non-recurrent nature. To solve this problem, position embeddings are defined exclusively for each time step to enrich word information. However, such embeddings are fixed after training regardless of the task and the word ordering system of the source or target language. In this paper, we propose a novel architecture with new position embeddings depending on the input text to address this shortcoming by taking the order of target words into consideration. Instead of using predefined position embeddings, our solution \textit{generates} new embeddings to refine each word's position information. Since we do not dictate the position of source tokens and learn them in an end-to-end fashion, we refer to our method as \textit{dynamic} position encoding (DPE). We evaluated the impact of our model on multiple datasets to translate from English into German, French, and Italian and observed meaningful improvements in comparison to the original Transformer

Quantitative profiling of selective Sox/POU pairing on hundreds of sequences in parallel by Coop-seq

© The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research. Cooperative binding of transcription factors is known to be important in the regulation of gene expression programs conferring cellular identities. However, current methods to measure cooperativity parameters have been laborious and therefore limited to studying only a few sequence variants at a time. We developed Coop-seq (cooperativity by sequencing) that is capable of efficiently and accurately determining the cooperativity parameters for hundreds of different DNA sequences in a single experiment. We apply Coop-seq to 12 dimer pairs from the Sox and POU families of transcription factors using 324 unique sequences with changed half-site orientation, altered spacing and discrete randomization within the binding elements. The study reveals specific dimerization profiles of different Sox factors with Oct4. By contrast, Oct4 and the three neural class III POU factors Brn2, Brn4 and Oct6 assemble with Sox2 in a surprisingly indistinguishable manner. Two novel half-site configurations can support functional Sox/Oct dimerization in addition to known composite motifs. Moreover, Coop-seq uncovers a nucleotide switch within the POU half-site when spacing is altered, which is mirrored in genomic loci bound by Sox2/Oct4 complexes.Link_to_subscribed_fulltex

Consistency of the Disposition Index in the Face of Diet Induced Insulin Resistance: Potential Role of FFA

Objective Insulin resistance induces hyperinsulinemic compensation, which in turn maintains almost a constant disposition index. However, the signal that gives rise to the hyperinsulinemic compensation for insulin resistance remains unknown. Methods In a dog model of obesity we examined the possibility that potential early-week changes in plasma FFA, glucose, or both could be part of a cascade of signals that lead to compensatory hyperinsulinemia induced by insulin resistance. Results Hypercaloric high fat feeding in dogs resulted in modest weight gain, and an increase in adipose tissue with no change in the non-adipose tissue size. To compensate for the drop in insulin sensitivity, there was a significant rise in plasma insulin, which can be attributed in part to a decrease in the metabolic clearance rate of insulin and increased insulin secretion. In this study we observed complete compensation for high fat diet induced insulin resistance as measured by the disposition index. The compensatory hyperinsulinemia was coupled with significant changes in plasma FFAs and no change in plasma glucose. Conclusions We postulate that early in the development of diet induced insulin resistance, a change in plasma FFAs may directly, through signaling at the level of β-cell, or indirectly, by decreasing hepatic insulin clearance, result in the observed hyperinsulinemic compensation

Challenging Official Propaganda? Public Opinion Leaders on Sina Weibo.

This article examines the prominence of various user categories as opinion leaders, defined as initiators, agenda setters or disseminators, in 29 corruption cases exposed on SinaWeibo. It finds that ordinary citizens made up the largest category of initiators but that their power of opinion leadership was limited as they had to rely on media organizations to spread news about the cases. News organizations and online media were the main opinion leaders. Government and Party bodies initiated a fair number of cases and, despite not being strong agenda setters or disseminators, were able to dominate public opinion owing to the fact that news organizations and online media mainly published official announcements about the cases. Media organizations also played a secondary role as the voice of the people. While individuals from some other user categories were able to become prominent opinion leaders, news workers are likely to be the most promising user category to challenge official propaganda.Faculty Research Support Scheme of the Faculty of Arts and Social Sciences, the University of Sydney. University of Hong Kong Seed Funding Program for Basic Research and the General Research Fund, Research Grants Council, Hong Kong (Project Code: 17402314)

Delayed Wound Closure in Fibromodulin-Deficient Mice Is Associated with Increased TGF-β3 Signaling

Fibromodulin (FMOD), a small leucine-rich proteoglycan, mediates scarless fetal skin wound repair through, in part, transforming growth factor-Β (TGF-Β) modulation. Using an adult fmod-null (fmod -/-) mouse model, this study further elucidates the interplay between FMOD and TGF-Β expression during cutaneous repair and scar formation. Full-thickness skin wounds on fmod -/- and wild-type (WT) mice were closed primarily and analyzed. Histomorphometry revealed delayed dermal cell migration leading to delayed wound closure and significantly increased scar size in fmod -/- mice relative to WT, which was partially rescued by exogenous FMOD administration. In addition, fmod -/- wounds exhibited early elevation (within 24 hours post-wounding) of type I and type II TGF-Β receptors as well as unexpectedly high fibroblast expression of TGF-Β3, a molecule with reported antifibrotic and antimigratory effects. Consistent with elevated fibroblastic TGF-Β3, fmod -/- fibroblasts were significantly less motile than WT fibroblasts. fmod -/- fibroblasts were also more susceptible to migration inhibition by TGF-Β3, leading to profound delays in dermal cell migration. Increased scarring in fmod -/- mice indicates that TGF-Β3\u27s antimotility effects predominate over its antifibrotic effects when high TGF-Β3 levels disrupt early fibroblastic wound ingress. These studies demonstrate that FMOD presence is critical for proper temporospatial coordination of wound healing events and normal TGF-Β bioactivity. © 2011 The Society for Investigative Dermatology

Characterization of genome-wide H3K27ac profiles reveals a distinct PM2.5-associated histone modification signature

Complete list of differentially modified H3K27ac loci. (XLSX 69 kb

DNA Polymerase Conformational Dynamics and the Role of Fidelity-Conferring Residues: Insights from Computational Simulations

Herein we investigate the molecular bases of DNA polymerase I conformational dynamics that underlie the replication fidelity of the enzyme. Such fidelity is determined by conformational changes that promote the rejection of incorrect nucleotides before the chemical ligation step. We report a comprehensive atomic resolution study of wild type and mutant enzymes in different bound states and starting from different crystal structures, using extensive molecular dynamics (MD) simulations that cover a total timespan of ~5 ms. The resulting trajectories are examined via a combination of novel methods of internal dynamics and energetics analysis, aimed to reveal the principal molecular determinants for the (de)stabilization of a certain conformational state. Our results show that the presence of fidelity-decreasing mutations or the binding of incorrect nucleotides in ternary complexes tend to favor transitions from closed toward open structures, passing through an ensemble of semi-closed intermediates. The latter ensemble includes the experimentally observed ajar conformation which, consistent with previous experimental observations, emerges as a molecular checkpoint for the selection of the correct nucleotide to incorporate. We discuss the implications of our results for the understanding of the relationships between the structure, dynamics, and function of DNA polymerase I at the atomistic level