Distractor-aware Event-based Tracking

Event cameras, or dynamic vision sensors, have recently achieved success from fundamental vision tasks to high-level vision researches. Due to its ability to asynchronously capture light intensity changes, event camera has an inherent advantage to capture moving objects in challenging scenarios including objects under low light, high dynamic range, or fast moving objects. Thus event camera are natural for visual object tracking. However, the current event-based trackers derived from RGB trackers simply modify the input images to event frames and still follow conventional tracking pipeline that mainly focus on object texture for target distinction. As a result, the trackers may not be robust dealing with challenging scenarios such as moving cameras and cluttered foreground. In this paper, we propose a distractor-aware event-based tracker that introduces transformer modules into Siamese network architecture (named DANet). Specifically, our model is mainly composed of a motion-aware network and a target-aware network, which simultaneously exploits both motion cues and object contours from event data, so as to discover motion objects and identify the target object by removing dynamic distractors. Our DANet can be trained in an end-to-end manner without any post-processing and can run at over 80 FPS on a single V100. We conduct comprehensive experiments on two large event tracking datasets to validate the proposed model. We demonstrate that our tracker has superior performance against the state-of-the-art trackers in terms of both accuracy and efficiency

Automated Raman based cell sorting with 3D microfluidics

Raman activated cell sorting has emerged as a label-free technology that can link phenotypic function with genotypic properties of cells. However, its broad implementation is limited by challenges associated with throughput and the complexity of biological systems. Here, we describe a three-dimensional hydrodynamic focusing microfluidic system for a fully automated, continuous Raman activated cell sorting (3D-RACS). The system consists of a 3D printed detection chamber (1 mm3) that is integrated with a PDMS based sorting unit, optical sensors and an in-line collection module. It has the ability to precisely position cells in the detection chamber for Raman measurements, effectively eliminating spectroscopic interference from the device materials. This enables the sorting of a range of cell sizes (from 1 μm bacteria to 10's μm mammalian cells) with stable operation over >8 hours and high throughput. As a proof-of-concept demonstration, Raman-activated sorting of mixtures of Chlorella vulgaris and E. coli has demonstrated a purity level of 92.0% at a throughput of 310 cells per min. The platform employed in this demonstration features a simple “Raman window” detection system, enabling it to be built on a standard, inverted microscope. Together with its facile and robust operation, it provides a versatile tool for function-based flow cytometry and sorting applications in the fields of microbiology, biotechnology, life science and diagnostics

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Impacts of cross-phase modulation on modulation instability of Airy pulses

<p>The modulation instability (MI) of Airy pulses with the influence of cross-phase modulation is studied based on the coupled nonlinear Schrödinger equations in nonlinear media. The main lobe of Airy pulses can be manifested as breakup of MI under interaction with higher power pumped solitons, although the power of Airy pulses is small. By comparing the main lobe’s gain spectrum of MI, the gain spectrum has gradually improved with the increase of power of pumped solitons. The gain spectrum of MI of the main lobe is inversely proportional to the truncation coefficient, and then it gradually approaches to that of Gauss pulses with the truncation coefficient increasing to 1. For the side lobes of Airy pulses, there are similar MI but smaller gain spectrum than the main lobe when the pumped solitons is overlapping with corresponding ones of Airy pulses.</p

Nucleosome Histone Tail Conformation and Dynamics: Impacts of Lysine Acetylation and a Nearby Minor Groove Benzo[<i>a</i>]pyrene-Derived Lesion

Histone tails in nucleosomes play critical roles in regulation of many biological processes, including chromatin compaction, transcription, and DNA repair. Moreover, post-translational modifications, notably lysine acetylation, are crucial to these functions. While the tails have been intensively studied, how the structures and dynamics of tails are impacted by the presence of a nearby bulky DNA lesion is a frontier research area, and how these properties are impacted by tail lysine acetylation remains unexplored. To obtain molecular insight, we have utilized all atom 3 μs molecular dynamics simulations of nucleosome core particles (NCPs) to determine the impact of a nearby DNA lesion, 10<i>S</i> (+)-<i>trans-anti</i>-B­[<i>a</i>]­P-<i>N</i>²-dGthe major adduct derived from the procarcinogen benzo­[<i>a</i>]­pyreneon H2B tail behavior in unacetylated and acetylated states. We similarly studied lesion-free NCPs to investigate the normal properties of the H2B tail in both states. In the lesion-free NCPs, charge neutralization upon lysine acetylation causes release of the tail from the DNA. When the lesion is present, it stably engulfs part of the nearby tail, impairing the interactions between DNA and tail. With the tail in an acetylated state, the lesion still interacts with part of it, although unstably. The lesion’s partial entrapment of the tail should hinder the tail from interacting with other nucleosomes, and other proteins such as acetylases, deacetylases, and acetyl-lysine binding proteins, and thus disrupt critical tail-governed processes. Hence, the lesion would impede tail functions modulated by acetylation or deacetylation, causing aberrant chromatin structures and impaired biological transactions such as transcription and DNA repair

Entrapment of a Histone Tail by a DNA Lesion in a Nucleosome Suggests the Lesion Impacts Epigenetic Marking: A Molecular Dynamics Study

Errors in epigenetic markings are associated with human diseases, including cancer. We have used molecular dynamics simulations of a nucleosome containing the 10<i>S</i> (+)-<i>trans-anti</i>-B­[<i>a</i>]­P-<i>N</i>²-dG lesion, derived from the environmental pro-carcinogen benzo­[<i>a</i>]­pyrene, to elucidate the impact of the lesion on the structure and dynamics of a nearby histone N-terminal tail. Our results show that a lysine-containing part of this H2B tail that is subject to post-translational modification is engulfed by the enlarged DNA minor groove imposed by the lesion. The tail entrapment suggests that epigenetic markings could be hampered by this lesion, thereby impacting critical cellular functions, including transcription and repair

Molecular basis for receptor tyrosine kinase A-loop tyrosine transphosphorylation

A long-standing mystery shrouds the mechanism by which catalytically repressed receptor tyrosine kinase domains accomplish transphosphorylation of activation loop (A-loop) tyrosines. Here we show that this reaction proceeds via an asymmetric complex that is thermodynamically disadvantaged because of an electrostatic repulsion between enzyme and substrate kinases. Under physiological conditions, the energetic gain resulting from ligand-induced dimerization of extracellular domains overcomes this opposing clash, stabilizing the A-loop-transphosphorylating dimer. A unique pathogenic fibroblast growth factor receptor gain-of-function mutation promotes formation of the complex responsible for phosphorylation of A-loop tyrosines by eliminating this repulsive force. We show that asymmetric complex formation induces a more phosphorylatable A-loop conformation in the substrate kinase, which in turn promotes the active state of the enzyme kinase. This explains how quantitative differences in the stability of ligand-induced extracellular dimerization promotes formation of the intracellular A-loop-transphosphorylating asymmetric complex to varying extents, thereby modulating intracellular kinase activity and signaling intensity