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APIR: Aggregating Universal Proteomics Database Search Algorithms for Peptide Identification with FDR Control

geNOMICS PROTEOMICS & BIOINFORMATICS 2024年第2期22卷 qzae042页

作者： Chen, Yiling Elaine ge, xinzhou Woyshner, Kyla McDermott, Meilu Manousopoulou, Antigoni Ficarro, Scott B. Marto, Jarrod A. Li, Kexin Wang, Leo David Li, Jingyi Jessica Univ Calif Los Angeles Dept Stat & Data Sci Los Angeles CA 90095 USA Univ Calif Los Angeles Bioinformat Interdept Program Los Angeles CA 90095 USA Univ Calif Los Angeles Dept Human Genet Los Angeles CA 90095 USA Univ Calif Los Angeles Dept Computat Med Los Angeles CA 90095 USA Univ Calif Los Angeles Dept Biostat Los Angeles CA 90095 USA City Hope Natl Med Ctr Beckman Res Inst Dept Immuno Oncol Duarte CA 91010 USA Univ Southern Calif Dept Quantitat & Computat Biol Los Angeles CA 90007 USA City Hope Natl Med Ctr Dept Pediat Duarte CA 91010 USA Brigham & Womens Hosp Dept Canc Biol Boston MA 02215 USA Brigham & Womens Hosp Dana Farber Canc Inst Blais Prote Ctr Dept Pathol Boston MA 02215 USA Harvard Med Sch Boston MA 02215 USA

Advances in mass spectrometry (MS) have enabled high-throughput analysis of proteomes in biological systems. The state-of-the-art MS data analysis relies on database search algorithms to quantify proteins by identifying peptide-spectrum matches (PSMs), which convert mass spectra to peptide sequences. Different database search algorithms use distinct search strategies and thus may identify unique PSMs. However, no existing approaches can aggregate all user-specified database search algorithms with a guaranteed increase in the number of identified peptides and a control on the false discovery rate (FDR). To fill in this gap, we proposed a statistical framework, Aggregation of Peptide Identification Results (APIR), that is universally compatible with all database search algorithms. Notably, under an FDR threshold, APIR is guaranteed to identify at least as many, if not more, peptides as individual database search algorithms do. Evaluation of APIR on a complex proteomics standard dataset showed that APIR outpowers individual database search algorithms and empirically controls the FDR. Real data studies showed that APIR can identify disease-related proteins and post-translational modifications missed by some individual database search algorithms. The APIR framework is easily extendable to aggregating discoveries made by multiple algorithms in other high-throughput biomedical data analysis, e.g., differential gene expression analysis on RNA sequencing data. The APIR R package is available at https://***/yiling0210/APIR.

关键词： Shotgun proteomics Peptide-spectrum match Peptide identification Aggregation of lists FDR control PROTEIN IDENTIFICATION BRCA2 MUTATIONS CELL-CYCLE TANDEM TARgeT CANCER PREVALENCE EXPRESSION geNE APOPTOSIS

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Recent Advances in Nickel Catalyzed Carbonylative Reactions via the Insertion of Carbon Monoxide

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Chinese Journal of Chemistry 2024年第2期42卷 177-189页

作者： xinzhou Chen Gang Chen Zhong Lian Department of Dermatology State Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan UniversityChengduSichuan 610041China

Carbonyl compounds have attracted considerable attention due to their extensive applications in drug ***,they are important synthetic intermediates for the construction of carbon-carbon and carbon-heteroatom ***-metal-catalyzed carbonylation via the insertion of co is one of the most efficient and straightforward strategies to access carbonyl ***,most of the transition-metal-catalyzed carbonylative reactions require expensive and toxic noble-metal ***,there is a growing demand for the exploration of nickel-catalyzed carbonylative reactions via the insertion of CO due to the earth abundance and low cost of *** with the well-established palladium-catalyzed carbonylative reactions,nickel-catalyzed analogous transformations have been relatively *** is primarily because CO strongly binds to nickel,often resulting in catalyst *** recent years,some research groups have focused on using CO surrogates or NN_(2) pincer nickel catalyst to circumvent the formation of Ni(CO)_(4).Nickel-catalyzed carbonylation has been applied in the construction of carbonyl-containing compounds,such as ketones,carboxylic acids,thioesters,acyl chloride and carboxamides.

关键词： Carbonylation Nickel catalysis Carbon monoxide C1 chemistry Carbonyl-containing compounds

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Versatile strategies for adult neurogenesis:avenues to repair the injured brain

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Neural Regeneration Research 2024年第4期19卷 774-780页

作者： Junyi Zhao Siyu Liu Xianyuan Xiang xinzhou Zhu The Brain Cognition and Brain Disease Institute(BCBDI) Shenzhen Institute of Advanced TechnologyChinese Academy of Sciences Faculty of Life and Health Sciences Shenzhen Institutes of Advanced TechnologyChinese Academy of Sciences Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions

Brain injuries due to trauma or stroke are major causes of adult death and ***,few interventions are effective for post-injury repair of brain *** a long debate on whether endogenous neurogenesis actually happens in the adult human brain,there is now substantial evidence to support its *** neurogenesis is usually significantly stimulated by injury,the reparative potential of endogenous differentiation from neural stem/progenitor cells is usually ***,exogenous stem cell transplantation has shown promising results in animal models,but limitations such as poor long-term survival and inefficient neuronal differentiation make it still challenging for clinical ***,a high focus was placed on glia-to-neuron conversion under single-factor *** some inspiring results,the validity of this strategy is still *** this review,we summarize historical findings and recent advances on neurogenesis strategies for neurorepair after brain *** also discuss their advantages and drawbacks,as to provide a comprehensive account of their potentials for further studies.

关键词： adult neurogenesis glia-to-neuron conversion ischemic stroke neurogenic niche neuroinflammation stem cell transplantation traumatic brain injury

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Reactive molecular dynamics insight into the thermal decomposition mechanism of 2,6-Bis(picrylamino)-3,5-dinitropyridine

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Defence Technology（防务技术） 2024年第3期33卷 134-146页

作者： Jianbo Fu Hui Ren xinzhou Wu Yongjin Chen Mi Zhang Yazhi Cheng State Key Laboratory of Explosion Science and Technology Beijing Institute of TechnologyBeijing 100081China

2,6-bis(picrylamino)-3,5-dinitropyridine(PYX)has excellent thermostability,which makes its thermal decomposition mechanism receive much *** this paper,the mechanism of PYX thermal decomposition was investigated thoroughly by the ReaxFF-lg force field combined with DFT-B3LYP(6-311++G)*** detailed decomposition mechanism,small-molecule product evolution,and cluster evolution of PYX were mainly *** the initial stage of decomposition,the intramolecular hydrogen transfer reaction and the formation of dimerized clusters are earlier than the denitration *** the progress of the reaction,one side of the bitter amino group is removed from the pyridine ring,and then the pyridine ring is *** final products produced in the thermal decomposition process are CO_(2),H_(2)O,N_(2),and H_(2).Among them,H_(2)O has the earliest generation time,and the reaction rate constant(k_(3))is the *** clusters are formed during the decomposition of PYX,and the formation,aggregation,and decomposition of these clusters are strongly affected by *** low temperatures(2500 K-2750 K),many clusters are *** high temperatures(2750 K-3250 K),the clusters aggregate to form larger *** 3500 K,the large clusters decompose and become *** the late stage of the reaction,H and N in the clusters escaped almost entirely,but more O was trapped in the clusters,which affected the auto-oxidation process of ***'s initial decomposition activation energy(E_(a))was calculated to be 126.58 kJ/*** work contributes to a theoretical understanding of PYX's entire thermal decomposition process.

关键词： PYX Thermal decomposition ReaxFF-lg MD simulations Excellent thermostable explosives

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Characteristics of Controlled Bridge Circuit and Its Application in Magnetic Field Induction Measurement

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Tsinghua Science and Technology 2024年第4期29卷 1105-1117页

作者： Yanchu Li Qingqing Ding Mingchen Yan Jiyao Wang Jun Xu xinzhou Dong Department of Electrical Engineering Tsinghua UniversityBeijing 100084China State Key Laboratory of Control and Simulation of Power System and generation Equipments Tsinghua UniversityBeijing 100084China School of Electrical and Electronic Engineering North China Electric Power UniversityBeijing 100096China

The article designs a new type of bridge circuit with a controlled source—when the resistance on the bridge arm of the controlled source bridge circuit meets the bridge balance condition, and the bridge branch contains only one Current-Controlled Current Source (CCCS), a Voltage-Controlled Current Source (VCCS), a Current-Controlled Voltage Source (CCVS), or a Voltage-Controlled Voltage Source (VCVS), the circuit is called a controlled bridge circuit, which has the characteristics of bridge balance. Due to the relationship between the controlled source and the bridge arm, the sensitivity of the components on the bridge is higher mathematically and logically. When applied to measurement, engineering, automatic control, and other fields, the controlled bridge circuit has higher control ac-curacy. Mathematical derivation and simulation results prove the correctness of the bridge balance conclusion and the special properties of this bridge when applied to the measurement field.

关键词： bridge bircuit bridge circuit applications bridge balanced condition controlled bridge circuit magnetic field induction measurement

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Controllability of Semilinear Integrodifferential Degenerate Sobolev Equations

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Journal of Systems Science & Complexity 2024年第5期37卷 1923-1936页

作者： ge Zhaoqiang School of Mathematics and Statistics Xi’an Jiaotong University

In this paper, the approximate controllability of semilinear integrodifferential degenerate Sobolev equations with nonlocal conditions is investigated in the sense of integral solution in Hilbert spaces. Some sufficient and necessary conditions are obtained. Firstly, the existence and uniqueness of integral solutions of semilinear integrodifferential degenerate Sobolev equations with nonlocal conditions are considered by ge-evolution operator theory and Sadovskii's fixed point theorem, the existence and uniqueness theorem of solutions is given. Secondly, the approximate controllability of semilinear integrodifferential degenerate Sobolev equations with nonlocal conditions is studied in the sense of integral solution. The criterion for approximate controllability is provided. The obtained results have important theoretical and practical value for the study of controllability of semilinear integrodifferential degenerate Sobolev equations with nonlocal conditions.

关键词： Approximate controllability ge-evolution operator integral solution Sadovskii’s fixed point theorem semilinear integrodifferential degenerate Sobolev equations

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Polymeric piezoelectric accelerometers with high sensitivity,broad bandwidth,and low noise density for organic electronics and wearable microsystems

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Microsystems & Nanoengineering 2024年第3期10卷 63-74页

作者： Chang ge Edmond Cretu The Department of Electrical and Computer Engineering The University of British ColumbiaVancouverBCCanada

Piezoelectric accelerometers excel in vibration *** the emerging trend of fully organic electronic microsystems,polymeric piezoelectric accelerometers can be used as vital front-end components to capture dynamic signals,such as vocal vibrations in wearable speaking assistants for those with speaking ***,high-performance polymeric piezoelectric accelerometers suitable for such applications are *** organic compounds such as PVDF have inferior properties to their inorganic counterparts such as ***,most existing polymeric piezoelectric accelerometers have very unbalanced performance *** often sacrifice resonance frequency and bandwidth for a flat-band sensitivity comparable to those of PZT-based accelerometers,leading to increased noise density and limited application *** this study,a new polymeric piezoelectric accelerometer design to overcome the material limitations of PVDF is *** new design aims to simultaneously achieve high sensitivity,broad bandwidth,and low *** samples were manufactured and characterized,demonstrating an average sensitivity of 29.45 pC/g within a±10 g input range,a 5%flat band of 160 Hz,and an in-band noise density of 1.4μg/√*** results surpass those of many PZT-based piezoelectric accelerometers,showing the feasibility of achieving comprehensively high performance in polymeric piezoelectric accelerometers to increase their potential in novel applications such as organic microsystems.

关键词： piezoelectric polymeric overcome

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Meridional deflection of global eddy propagation derived from tandem altimetry: Mechanism and implication

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Science China Earth Sciences 2024年第3期67卷 811-825页

作者： ge CHEN Xiaoyan CHEN Frontiers Science Center for Deep Ocean Multispheres and Earth System School of Marine TechnologyOcean University of ChinaQindao 266100China Laboratory for Regional Oceanography and Numerical Modeling Laoshan LaboratoryQindao 266237China

A common view on meridional deflection of eddy propagation is poleward for cyclones and equatorward for anticyclones. This widely accepted polarity-sensitive pattern has been increasingly undermined given that it is systematically violated on both zonal and regional scales as recently reported. Here, we approach the problem by exploring these violations in terms of eddy effects of spatiotemporal geostrophy, thermal fading, and flow dragging, yielding the following main conclusions.(1) The polarity-dependent deflection discrepancy is a pseudo feature resulting from a biased fit to the normalized eddy tracks which are spatially asymmetric(though azimuthally symmetric) between the two signs;Instead, the primary pattern of eddy deflection appears to be geographically correlated and polarity independent.(2) geostrophic adjustment plays a critical role in defining the meridional movement of an eddy. Specifically, a consistent poleward(equatorward) trajectory bending of spatially(temporally) ageostrophic eddies is observed irrespective of their polarity.(3) The mechanism of eddy deflection is also determined by its zonal propagation direction. Westward propagating eddies are substantially affected by thermal fading, while opposite ones by flow dragging. A realistic and comprehensive understanding of eddy deflection mechanisms serves as a significant contribution to the prediction of eddy trajectory, and the protection of ocean environment.

关键词： Mesoscale eddies Eddy propagation Eddy meridional deflection Satellite observation geostrophic adjustment

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Solid Desiccant Heat Pump Fresh Air Unit using Composite Silica gel

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Journal of Thermal Science 2024年第4期33卷 1286-1300页

作者： YANG Tianyu GUO Defang ge Tianshu Institute of Refrigeration and Cryogenics Shanghai Jiao Tong UniversityKey Laboratory of Power Mechanical EngineeringMOE ChinaShanghai200240China Qingdao Haier A/C Electronic Co. LtdQingdao266101China

The introduction of fresh air into the indoor space leads to a significant increase in cooling or heating *** desiccant heat pump fresh air unit which can handle the latent and sensible load of fresh air efficiently have been proposed *** improve the performance of the solid desiccant heat pump fresh air unit in the fresh air handling process,in this paper,the application of composite silica gel in a heat pump fresh air unit was *** comparison between silica gel coating(SGC)and composite silica gel coating(CSGC)shows that the adsorption rate and water uptake capacity of CSGC are more than two times higher than those of *** experimental setup for the solid desiccant heat pump fresh air unit was *** performance of SGC and CSGC was tested in the setup *** show that under summer conditions,compared with the solid desiccant heat pump fresh air unit using silica gel(SGFU),the average moisture removal and COP of the one using composite silica gel(CSGFU)increased by 15%and 30%,*** winter conditions,compared with SGFU,the average humidification and COP of CSGFU increased by 42%and 17%.With optimal operation conditions of 3 min switchover time and 40 r/s compressor frequency,the COP of CSGFU under summer conditions can reach *** also show that the CSGFU and SGFU have higher COP and dehumidification rate under higher outdoor temperature and humidity ratio.

关键词： fresh air system desiccant coated heat exchanger humidification dehumidification experimental comparison

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Theoretical study on the stability of nanobubbles and its verification in molecular dynamics simulation

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Particuology 2024年第4期87卷 99-105页

作者： Sheng Mi Chaofeng Hou Wei ge School of Chemical Engineering and Technology Tianjin UniversityTianjin300072China State Key Laboratory of Multiphase Complex Systems Institute of Process EngineeringChinese Academy of SciencesBeijing.100190China School of Chemical Engineering University of Chinese Academy of SciencesBeijing100049China

The stability of vapor nanobubbles in bulk liquid was investigated theoretically and the critical bubble size was derived from macroscale thermodynamic equations,below which the system destabilizes with sharp drop in *** critical size was quantitatively verified in molecular dynamic simulation using the Lennard-Jones model of argon,where stronger attraction between the molecules at lower density is found to contribute most to the drop of system pressure and,as the Laplace pressure on the curved bubble interface fails to balance the pressure difference across the interface,the bubbles become *** theoretical model could be extended to other systems where reliable equations of state and interfacial tension are available.

关键词： Nanobubble Stability Phase diagram Critical size

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