Optimization-Based Peptide Mass Fingerprinting for Protein Mixture Identification

*Motivation:* In current proteome research, peptide sequencing is probably the most widely used method for protein mixture identification. However, this peptide-centric method has its own disadvantages such as the immense volume of tandem Mass Spectrometry (MS) data for sequencing peptides. With the fast development of technology, it is possible to investigate other alternative techniques. Peptide Mass Fingerprinting (PMF) has been widely used to identify single purified proteins for more than 15 years. Unfortunately, this technique is less accurate than peptide sequencing method and cannot handle protein mixtures, which hampers the widespread use of PMF technique. If we can remove these limitations, PMF will become a useful tool in protein mixture identification. 
*Results:* We first formulate the problem of PMF protein mixture identification as an optimization problem. Then, we show that the use of some simple heuristics enables us to find good solutions. As a result, we obtain much better identification results than previous methods. Moreover, the result on real MS data can be comparable with that of the peptide sequencing method. Through a comprehensive simulation study, we identify a set of limiting factors that hinder the performance of PMF method in protein mixtures. We argue that it is feasible to remove these limitations and PMF can be a powerful tool in the analysis of protein mixtures

A Typical Medium Dynamical Cluster Approximation for the Study of Anderson Localization in Three Dimensions

We develop a systematic typical medium dynamical cluster approximation that provides a proper description of the Anderson localization transition in three dimensions (3D). Our method successfully captures the localization phenomenon both in the low and large disorder regimes, and allows us to study the localization in different momenta cells, which renders the discovery that the Anderson localization transition occurs in a cell-selective fashion. As a function of cluster size, our method systematically recovers the re-entrance behavior of the mobility edge and obtains the correct critical disorder strength for Anderson localization in 3D.Comment: 5 Pages, 4 Figures and Supplementary Material include

Correlates of Talkaholism in New Zealand: An Intracultural Analysis of the Compulsive Communication Construct

This study focused on correlates of the compulsive communication construct in New Zealand. Participants were 216 New Zealand university students who completed the Talkaholic Scale to measure their tendency to be compulsive communicators. Self-reports of communication apprehension, willingness to conununicate, argumentativeness, innovativeness, and self-monitoring were also completed. Results indicated a weak negative correlation with communication apprehension and weak positive correlations with argumentativeness and selfmonitoring. Differences in talkaholism between males and females were significant, but the amount of variance accounted for by biological sex was very small. This study provides further support for the distinctiveness of the compulsive communication construct and its measurement through the Talkaholic Scale

Developing an interactive game platform to promote learning and teamwork on mobile devices: an experience report

In the past few Years, many new development toolkits such as the Nebula2 and/or mobile technologies including the WiFi or mobileTV have opened up exciting learning opportunities on mobile devices. On top of it, new technologies continue to fuel the rapid growth of newly merged fields of research like the edutainment for educational entertainment. In a recent teaching development project, we have developed an interactive game platform to facilitate learning and more importantly the spirit of teamwork for collaborative problem-solving on desktop and pocket PCs. With the great challenges imposed by globalization, we strongly believe that learning to collaboratively analyze and then apply the "appropriate" knowledge to solve a specific problem is always the key to success. In this paper, we discuss about an on-going work, and share our relevant experience in system development. Furthermore, evaluation strategies will be thoroughly examined. After all, our work shed light on many interesting directions for future exploration. © 2008 IEEE.published_or_final_versio

Energy-efficient precoding in multicell networks with full-duplex base stations

© 2017, The Author(s). This paper considers multi-input multi-output (MIMO) multicell networks, where the base stations (BSs) are full-duplex transceivers, while uplink and downlink users are equipped with multiple antennas and operate in a half-duplex mode. The problem of interest is to design linear precoders for BSs and users to optimize the network’s energy efficiency. Given that the energy efficiency objective is not a ratio of concave and convex functions, the commonly used Dinkelbach-type algorithms are not applicable. We develop a low-complexity path-following algorithm that only invokes one simple convex quadratic program at each iteration, which converges at least to the local optimum. Numerical results demonstrate the performance advantage of our proposed algorithm in terms of energy efficiency

VHE Gamma-ray Afterglow Emission from Nearby GRBs

Gamma-ray Bursts (GRBs) are among the potential extragalactic sources of very-high-energy (VHE) gamma-rays. We discuss the prospects of detecting VHE gamma-rays with current ground-based Cherenkov instruments during the afterglow phase. Using the fireball model, we calculate the synchrotron self-Compton (SSC) emission from forward-shock electrons. The modeled results are compared with the observational afterglow data taken with and/or the sensitivity level of ground-based VHE instruments (e.g. STACEE, H.E.S.S., MAGIC, VERITAS, and Whipple). We find that modeled SSC emission from bright and nearby bursts such as GRB 030329 are detectable by these instruments even with a delayed observation time of ~10 hours.Comment: Proceeding of "Heidelberg International Symposium on High Energy Gamma-Ray Astronomy", held in Heidelberg, 7-11 July 2008, submitted to AIP Conference Proceedings. 4 pages, 3 figures, 1 tabl

Electrical Characteristics And Thermal Stability Of Ti Contact To p-Gan.

Wide band gap GaN semiconductor has a variety of applications in optoelectronic devices such as lightemitting diodes and laser diodes

FinEntity: Entity-level Sentiment Classification for Financial Texts

In the financial domain, conducting entity-level sentiment analysis is crucial for accurately assessing the sentiment directed toward a specific financial entity. To our knowledge, no publicly available dataset currently exists for this purpose. In this work, we introduce an entity-level sentiment classification dataset, called \textbf{FinEntity}, that annotates financial entity spans and their sentiment (positive, neutral, and negative) in financial news. We document the dataset construction process in the paper. Additionally, we benchmark several pre-trained models (BERT, FinBERT, etc.) and ChatGPT on entity-level sentiment classification. In a case study, we demonstrate the practical utility of using FinEntity in monitoring cryptocurrency markets. The data and code of FinEntity is available at \url{https://github.com/yixuantt/FinEntity}Comment: EMNLP'23 Main Conference Short Pape

Novel 3D Reciprocal Space Visualization of Strain Relaxation in InSb on GaAs Substrates

This study introduces the Reciprocal Space Polar Visualization (RSPV) method, a novel approach for visualizing X-ray diffraction-based reciprocal space data. RSPV allows for the precise separation of tilt and strain, facilitating their individual analysis. InSb was grown by molecular beam epitaxy (MBE) on two (001) GaAs substrates \unicode{x2014} one with no misorientation (Sample A) \unicode{x2014} one with 2{\deg} surface misorientation from the (001) planes (Sample B). There is a substantial lattice mismatch with the substrate and this results in the generation of defects within the InSb layer during growth. To demonstrate RSPV's effectiveness, a comprehensive comparison of surface morphology, dislocation density, strain, and tilt was conducted. RSPV revealed previously unobserved features of the (004) InSb Bragg peak, partially explained by the presence of threading dislocations and oriented abrupt steps (OASs). Surface morphologies examined by an atomic force microscope (AFM) revealed that Sample B had significantly lower root mean square (RMS) roughness. Independent estimates of threading dislocation density (TDD) using X-ray diffraction (XRD) and electron channelling contrast imaging (ECCI) confirmed that Sample B exhibited a significantly lower TDD than Sample A. XRD methods further revealed unequal amounts of $\alpha$ and $\beta$ type threading dislocations in both samples, contributing to an anisotropic Bragg peak. RSPV is shown to be a robust method for exploring 3D reciprocal space in any crystal, demonstrating that growing InSb on misoriented GaAs produced a higher-quality crystal compared to an on-orientation substrate.Comment: 11 pages, 7 figures. This paper will be submitted to Journal of Vacuum Science and Technology