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

Amphiphilic Anionic Pt(II) Complexes: from spectroscopic to morphological changes

A new class of amphiphilic anionic platinum(II) bzimpy complexes has been demonstrated to show aggregation in water through PtfflfflfflPt and π–π stacking interactions. An interesting aggregation–partial deaggregation–aggregation process and a morphological transformation from vesicles to nanofibers have been demonstrated. These changes can be systematically controlled by the variation of solvent composition and could readily be probed by UV-vis absorption, emission, NMR, transmission electron microscopy and even with our naked eyes ...postprin

Fuzzy rule based multiwavelet ECG signal denoising

Since different multiwavelets, pre- and post-filters have different impulse responses and frequency responses, different multiwavelets, pre- and post-filters should be selected and applied at different noise levels for signal denoising if signals are corrupted by additive white Gaussian noises. In this paper, some fuzzy rules are formulated for integrating different multiwavelets, pre- and post-filters together so that expert knowledge on employing different multiwavelets, pre- and post-filters at different noise levels on denoising performances is exploited. When an ECG signal is received, the noise level is first estimated. Then, based on the estimated noise level and our proposed fuzzy rules, different multiwavelets, pre- and post-filters are integrated together. A hard thresholding is applied on the multiwavelet coefficients. According to extensive numerical computer simulations, our proposed fuzzy rule based multiwavelet denoising algorithm outperforms traditional multiwavelet denoising algorithms by 30%

Autonomous response of a third-order digital filter with two’s complement arithmetic realized in parallel form

This paper investigates the output and state trajectories of a third-order digital filter with two’s complement arithmetic realized in parallel form. Although the output of the third-order digital filter seems to behave randomly, some regular patterns can be displayed on the plot of versus , where those regular patterns are similar to the second-order case. When the first-order subsystem is operated at the marginally stable points, the output of the third-order system is still mainly dependent on the behaviors of the corresponding second-order digital filter, even though overflow occurs. Explicit equations relating the trajectories of the system to the filter parameters and the initial conditions provide further insights into the behaviors of the system

Fuzzy multiwavelet denoising on an ECG signal

Since different multiwavelets, pre- and post-filters have different impulse and frequency responses characteristics, different multiwavelets, pre- and post-filters should be selected, integrated and applied at different noise levels if a signal is corrupted by an additive white Gaussian noise (AWGN). In this letter, some fuzzy rules on selecting and integrating different multiwavelets, pre- and post-filters together are proposed. These fuzzy rules are setup based on the training results of the denoising performances of applying different multiwavelets, pre- and post-filters at different noise levels. When a new electrocardiogram (ECG) signal is applied, the appropriate multiwavelets, pre- and post-filters are selected and integrated based on fuzzy rules and the noise level of the signal. A hard thresholding is applied on the multiwavelet coefficients. According to an extensive simulation, we found that our proposed fuzzy rule-based multiwavelet denoising algorithm achieves 30% improvement compared to the traditional multiwavelet denoising algorithms

Control over the Self-Assembly Modes of Pt^II Complexes by Alkyl Chain Variation: From Slipped to Parallel π-Stacks

We report the self-assembly of a new family of hydrophobic, bis(pyridyl) PtII complexes featuring an extended oligophenyleneethynylene-derived π-surface appended with six long (dodecyloxy (2)) or short (methoxy (3)) side groups. Complex 2, containing dodecyloxy chains, forms fibrous assemblies with a slipped arrangement of the monomer units (dPt⋯Pt≈14 Å) in both nonpolar solvents and the solid state. Dispersion-corrected PM6 calculations suggest that this organization is driven by cooperative π-π, C-H⋯Cl and π-Pt interactions, which is supported by EXAFS and 2D NMR spectroscopic analysis. In contrast, nearly parallel π-stacks (dPt⋯Pt≈4.4 Å) stabilized by multiple π-π and C-H⋯Cl contacts are obtained in the crystalline state for 3 lacking long side chains, as shown by X-ray analysis and PM6 calculations. Our results reveal not only the key role of alkyl chain length in controlling self-assembly modes but also show the relevance of Pt-bound chlorine ligands as new supramolecular synthons. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

Surface passivation effect by fluorine plasma treatment on ZnO for efficiency and lifetime improvement of inverted polymer solar cells

Zinc oxide (ZnO) is an important material for polymer solar cells (PSCs) where the characteristics of the interface can dominate both the efficiency and lifetime of the device. In this work we study the effect of fluorine (SF6) plasma surface treatment of ZnO films on the performance of PSCs with an inverted structure. The interaction between fluorine species present in the SF6 plasma and the ZnO surface is also investigated in detail. We provide fundamental insights into the passivation effect of fluorine by analyzing our experimental results and theoretical calculations and we propose a mechanism according to which a fluorine atom substitutes an oxygen atom or occupies an oxygen vacancy site eliminating an electron trap while it may also attract hydrogen atoms thus favoring hydrogen doping. These multiple fluorine roles can reduce both the recombination losses and the electron extraction barrier at the ZnO/fullerene interface improving the selectivity of the cathode contact. Therefore, the fabricated devices using the fluorine plasma treated ZnO show high efficiency and stable characteristics, irrespective of the donor : acceptor combinations in the photoactive blend. Inverted polymer solar cells, consisting of the P3HT:PC71BM blend, exhibited increased lifetime and high power conversion efficiency (PCE) of 4.6%, while the ones with the PCDTBT:PC71BM blend exhibited a PCE of 6.9%. Our champion devices with the PTB7:PC71BM blends reached a high PCE of 8.0% and simultaneously showed exceptional environmental stability when using the fluorine passivated ZnO cathode interlayers

Suicide ideation in older people: a qualitative review and Meta-aggregation of Asian studies

AimsTo appraise and synthesize qualitative studies examining older Asian people’s experiences of suicidal ideation.DesignQualitative review and meta-aggregation.Data sourcesFour databases were accessed to retrieve papers published between 1990 and 2022 including the grey literature, hand-searching of reference lists of retrieved papers and key journals. The phenomenon of interest included participants older than 60 years old, must have experienced a form of suicidal ideation and/or an unsuccessful attempt, had actively thought about harming themselves and be of Asian ethnicity.Review methodsThis review was conducted according to Consolidated Criteria for Reporting Qualitative Research and the Joanna Briggs Institute’s System for the Unified Management of the Assessment and Review of Information.ResultsOf the 289 potential studies, seven papers met the inclusion criteria. Two synthesized findings resulted from this review–The Suffering Situation: A Life without Meaning in Older Age and The Healing Situation: A Life Worth Living. The experiences of older Asian people varied from feelings of loneliness, despair and isolation to wanting to live a fruitful life into old age.ConclusionSuicidal ideation in the older person is a growing concern especially with the rise in suicide in this age group. Rising health care costs and erosion of traditional family values means that the older person views themselves as a burden. However, because of the limited number of qualitative studies from an Asian perspective it is difficult to ascertain the full extent of the issues surrounding suicide in older people

Observation of associated near-side and away-side long-range correlations in √sNN=5.02 TeV proton-lead collisions with the ATLAS detector

Two-particle correlations in relative azimuthal angle (Δϕ) and pseudorapidity (Δη) are measured in √sNN=5.02  TeV p+Pb collisions using the ATLAS detector at the LHC. The measurements are performed using approximately 1  μb-1 of data as a function of transverse momentum (pT) and the transverse energy (ΣETPb) summed over 3.1<η<4.9 in the direction of the Pb beam. The correlation function, constructed from charged particles, exhibits a long-range (2<|Δη|<5) “near-side” (Δϕ∼0) correlation that grows rapidly with increasing ΣETPb. A long-range “away-side” (Δϕ∼π) correlation, obtained by subtracting the expected contributions from recoiling dijets and other sources estimated using events with small ΣETPb, is found to match the near-side correlation in magnitude, shape (in Δη and Δϕ) and ΣETPb dependence. The resultant Δϕ correlation is approximately symmetric about π/2, and is consistent with a dominant cos⁡2Δϕ modulation for all ΣETPb ranges and particle pT