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

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Genomics, Proteomics & Bioinformatics 2024年第2期22卷 171-187页

作者： Yiling Elaine Chen Xinzhou Ge kyla Woyshner MeiLu McDermott Antigoni Manousopoulou scott B.Ficarro Jarrod A.Marto kexin Li Leo David Wang Jingyi Jessica Li Department of Statistics and Data Science University of CaliforniaLos AngelesCA 90095USA Department of Immuno-Oncology Beckman Research InstituteCity of Hope National Medical CenterDuarteCA 91010USA Department of Quantitative and Computational Biology University of Southern CaliforniaLos AngelesCA 90089USA Department of Cancer Biology and Blais Proteomics Center Dana-Farber Cancer InstituteDepartment of PathologyBrigham and Women’s Hospital and Harvard Medical SchoolBostonMA 02215USA Department of Pediatrics City of Hope National Medical CenterDuarteCA 91010USA Bioinformatics Interdepartmental Program University of CaliforniaLos AngelesCA 90095USA Department of Human Genetics University of CaliforniaLos AngelesCA 90095USA Department of Computational Medicine University of CaliforniaLos AngelesCA 90095USA Department of Biostatistics University of CaliforniaLos AngelesCA 90095USA

Advances in mass spectrometry(MS)have enabled high-throughput analysis of proteomes in biological *** 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 *** database search algorithms use distinct search strategies and thus may identify unique ***,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 ***,under an FDR threshold,APIR is guaranteed to identify at least as many,if not more,peptides as individual database search algorithms *** of APIR on a complex proteomics standard dataset showed that APIR outpowers individual database search algorithms and empirically controls the *** data studies showed that APIR can identify disease-related proteins and post-translational modifications missed by some individual database search *** 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 *** APIR R package is available at https://***/yiling0210/APIR.

关键词： Shotgun proteomics Peptide–spectrum match Peptide identification Aggregation of lists FDR control

Excellent photoluminescence and electrochemical properties of Sm^(3+) doped Ca_(2)MgSi_(2)O_(7) nanophosphor:Display and electrochemical sensor applications

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Journal of Rare Earths 2024年第6期42卷 1046-1055,I0002页

作者： R.B.Basavaraj k.Sureshkumar D.P.Aarti M.B.Madhusudana Reddy G.Nagaraju T.Ramakrishnappa G.R.Navyashree k.R.Venkatesha Babu k.S.Hemalatha Department of Physics BMS Institute of Technology and ManagementBangalore560064India Department of Chemistry BMS Institute of Technology and ManagementBangalore560064India Department of Chemistry School of Applied SciencesREVA UniversityBangalore560064India Energy Materials ResearchLaboratory Department of ChemistrySiddaganga Institute of TechnologyTumakuru57203KarnatakaIndia School of Physical Sciences REVA UniversityBangalore560057Indi Department of Physics Govt.Science CollegeBengaluru560001India Department of Physics Maharani Science College for WomenMaharani Cluster UniversityBengaluru560001India

A series of orange-red light emitting Ca_(2)MgSi_(2)O_(7):Sm^(3+)nanopowders were fabricated via low-cost ecofriendly green combustion technique using Aloe vera gel as *** phase purity of the samples were confirmed by the powder X-ray diffraction(PXRD)*** single-phase tetragonal structure is observed from the PXRD results with no additional impurity *** band gap energy of the fabricated powders was estimated by diffuse reflectance spectra(DRS)and is found to be in the range of 4.01-5.98 eV.A high resolution scanning electron microscope(SEM)was used to study the morphological behaviour of the ***-like structures are observed from the SEM *** particle size was evaluated by transmission electron microscopy(TEM)and is found to be~50 *** interplanar distance is found to be 0.53 *** properties were systematically studied in *** phosphors are successfully excited at 403 nm NUV light,producing reddish-orange characteristic *** emission peaks are centered at 558(^(4)G_(5/2)→^(6)H_(5/2)),607(^(4)G_(5/2)→^(6)H_(7/2))and 645 nm(^(4)G_(5/2)→^(6)H_(9/2)),*** the observed peaks the red emanation(^(4)G_(5/2)→^(6)H_(7/2))is stronger than the orange emission(^(4)G_(5/2)→^(6)H_(5/2))in the current *** photoluminescent concentration quenching is noticed above 5 mol%Sm^(3+)ion doping *** dipole-dipole interaction resulting in cross relaxation is found to be the principal cause of concentration quenching *** color features such as Commission Internationale de I’Eclairage(CIE)and correlated color temperature(CCT)were studied in *** optimized chromaticity coordinates were estimated to be(0.6363,0.3632),which fall in the reddish-orange *** average CCT value obtained is 3362 *** average color purity is found to be~82%.Sm^(3+)incorporated Ca_(2)MgSi_(2)O_(7) samples are possible contender for single white light generation commercial candidates owing to

关键词： Green combustion Photoluminescence Orange-red emission Color purity Sensors Rare earths

Supergravity effects on flame propagation and structure in hydrogen/air mixtures

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Acta Mechanica Sinica 2024年第6期40卷 31-38页

作者： Wenkai Liang Chung k.Law Center for Combustion Energy Department of Energy and Power EngineeringTsinghua UniversityBeijing100080China Department of Mechanical and Aerospace Engineering Princeton UniversityPrinceton08544USA

In the current work,we investigated hydrogen/air flame propagation under supergravity *** show that when gravity is in the same/opposite direction as flame propagation,it leads to acceleration/deceleration of the flame,and that such an effect could substantially modify the flame propagation and structure at high gravity ***,for the absolute and relative flame propagation speeds,the gravity-affected flame speed shows opposite trends as the absolute flame speed is more affected by the local induced flow field,while the relative flame speeds are controlled by the super-adiabatic or sub-adiabatic flame *** gravity-affected thermal and chemical flame structures are also examined through the influence of the mixture equivalence ratio,pressure,and flame stretch.

关键词： Supergravity Flame acceleration Laminar flame speed Flame stretch Hydrogen

Dynamical system analysis of Dirac-Born-Infeld scalar field cosmology in coincident f(Q)gravity

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Chinese Physics C 2024年第9期48卷 199-209页

作者： Sayantan Ghosh Raja Solanki P.k.Sahoo Department of Mathematics Birla Institute of Technology and Science-PilaniHyderabad CampusHyderabad-500078India

In this article,we present a dynamical system analysis of a Dirac-Born-Infeld scalar field in a modified f(Q)gravity *** considered a polynomial form of modified gravity,used two different types of scalar potential,polynomial and exponential,and found a closed autonomous dynamical system of *** analyzed the fixed points of such a system and evaluated the conditions under which deceleration to late-time acceleration occurs in this *** note the similarity of the two models and show that our result is consistent with a previous study on Einstein s *** also investigated the phenomenological implications of our models by plotting EoS(ω),energy density(Ω),and deceleration parameter(q)*** e-fold time and comparing to the present *** conclude the paper by observing how the dynamical system analysis differs in the modified f(Q)gravity,and present the future scope of our research.

关键词： Dirac-Born-Infeld field f(Q)gravity dark energy dynamical system analysis

Covalent Bond Based Android Malware Detection Using Permission and System Call Pairs

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Computers, Materials & Continua 2024年第3期78卷 4283-4301页

作者： Rahul Gupta kapil Sharma R.k.Garg Department of Information Technology Delhi Technological UniversityNew Delhi110042India Department of Mechanical Engineering Deenbandhu Chhotu Ram University of Science and TechnologyMurthal131039India

The prevalence of smartphones is deeply embedded in modern society,impacting various aspects of our *** versatility and functionalities have fundamentally changed how we communicate,work,seek entertainment,and access *** the many smartphones available,those operating on the Android platform dominate,being the most widely used *** widespread adoption of the Android OS has significantly contributed to increased malware attacks targeting the Android ecosystem in recent ***,there is an urgent need to develop new methods for detecting Android *** literature contains numerous works related to Android malware *** far as our understanding extends,we are the first ones to identify dangerous combinations of permissions and system calls to uncover malicious behavior in Android *** introduce a novel methodology that pairs permissions and system calls to distinguish between benign and malicious *** approach combines the advantages of static and dynamic analysis,offering a more comprehensive understanding of an application’s *** establish covalent bonds between permissions and system calls to assess their combined *** introduce a novel technique to determine these pairs’Covalent Bond Strength *** pair is assigned two scores,one for malicious behavior and another for benign *** scores serve as the basis for classifying applications as benign or *** correlating permissions with system calls,the study enables a detailed examination of how an app utilizes its requested permissions,aiding in differentiating legitimate and potentially harmful *** comprehensive analysis provides a robust framework for Android malware detection,marking a significant contribution to the *** results of our experiments demonstrate a remarkable overall accuracy of 97.5%,surpassing various state-of-the-art detection techniques proposed in the current literature.

关键词： Android malware android security hybrid analysis permission and system call pairs

Improving Channel Estimation in a NOMA Modulation Environment Based on Ensemble Learning

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Computer Modeling in Engineering & Sciences 2024年第8期140卷 1315-1337页

作者： Lassaad k.Smirani Leila Jamel Latifah Almuqren Elearning Deanship and Distance Education Umm Al-Qura UniversityP.O.Box 715MekkahSaudi Arabia Department of Information Systems College of Computer and Information SciencesPrincess Nourah bint Abdulrahman UniversityP.O.Box 84428Riyadh11671Saudi Arabia

This study presents a layered generalization ensemble model for next generation radio mobiles,focusing on supervised channel estimation *** estimation typically involves the insertion of pilot symbols with a well-balanced rhythm and suitable *** model,called Stacked Generalization for Channel Estimation(SGCE),aims to enhance channel estimation performance by eliminating pilot insertion and improving *** SGCE model incorporates six machine learning methods:random forest(RF),gradient boosting machine(GB),light gradient boosting machine(LGBM),support vector regression(SVR),extremely randomized tree(ERT),and extreme gradient boosting(XGB).By generating meta-data from five models(RF,GB,LGBM,SVR,and ERT),we ensure accurate channel coefficient predictions using the XGB *** validate themodeling performance,we employ the leave-one-out cross-validation(LOOCV)approach,where each observation serves as the validation set while the remaining observations act as the training *** performances’results demonstrate higher mean andmedian accuracy compared to the *** achieves an average accuracy of 98.4%,precision of 98.1%,and the highest F1-score of 98.5%,accurately predicting channel ***,our proposedmethod outperforms prior traditional and intelligent techniques in terms of throughput and bit error ***’s superior performance highlights its efficacy in optimizing channel *** can effectively predict channel coefficients and contribute to enhancing the overall efficiency of radio mobile *** extensive experimentation and evaluation,we demonstrate that SGCE improved performance in channel estimation,surpassing previous ***,SGCE’s capabilities have significant implications for optimizing channel estimation in modern communication systems.

关键词： Stacked generalization ensemble learning Non-Orthogonal Multiple Access(NOMA) channel estimation 5G

Multiple sclerosis drug repurposing for neuroregeneration

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Neural Regeneration Research 2024年第3期19卷 507-508页

作者： Peter Göttle Michael Dietrich Patrick küry Department of Neurology Medical FacultyHeinrich-Heine UniversityDüsseldorfGermany

Multiple sclerosis(MS)is an autoimmune disorder of the central nervous system(CNS)and is primarily characterized by immune cell infiltration leading to relapses followed by remission phases and a disease course turning progressive over time with neurodegenerative processes taking over(Amin and Hersh,2023).Of note,beyond relapse-associated worsening early in disease progression independent of relapse activity may arise independently of relapse activity and can occur in all ***-mediated damage of myelin sheaths and the subsequent loss of mature oligodendrocytes are resulting in impaired axonal integrity,neurodegeneration and accounts for irreversible neuronal damage(kuhlmann et al.,2023).The current landscape of available disease-modifying therapies comprises mainly immunomodulatory drugs that effectively diminish relapses and slow down progression at the onset form of the disease,namely relapsing MS(RMS).In this regard,a number of drugs have been approved as disease-modifying therapies for MS by US Food and Drug Administration and European Medicines Agencies(Box 1).

关键词： drugs impaired irreversible

Microstructure transformations and improving wear resistance of austenitic stainless steel additively fabricated by arc-based DED process

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Defence Technology（防务技术） 2024年第8期38卷 194-204页

作者： Ashish Yadav Manu Srivastava Prashant k.Jain Sandeep Rathee Hybrid Additive Manufacturing Laboratory Mechanical Engineering DepartmentPDPM Indian Institute of Information TechnologyDesign&ManufacturingJabalpur482005Madhya PradeshIndia FFF Laboratory Mechanical Engineering DepartmentPDPM Indian Institute of Information TechnologyDesign&ManufacturingJabalpur482005Madhya PradeshIndia Department of Mechanical Engineering National Institute of TechnologySrinagarIndia

In this study, austenitic stainless steel(ASS) was additively fabricated by an arc-based direct energy deposition(DED) technique. Macrostructure, microstructure, mechanical characteristics at different spatial orientations(0°, 90°, and 45°), and wear characteristics were evaluated at the deposited structure top, middle, and bottom regions. Results show that austenite(γ) and delta-ferrite(δ) phases make up most of the microstructure of additively fabricated SS316LSi steel. Within γ matrix, δ phase is dispersed both(within and along) grain boundaries, exhibiting a fine vermicular morphology. The bottom, middle,and top regions of WAAM deposited ASS exhibit similar values to those of wrought SS316L in the tensile and impact test findings. Notably, a drop in hardness values is observed as build height increases. During SEM examinations of fractured surfaces from tensile specimen, closed dimples were observed, indicating good ductility of as-built structure. Wear test findings show signs of mild oxidation and usual adhesive wear. By depositing a mechanically mixed composite layer, an increase in the oxidation percentage was discovered to facilitate healing of worn surfaces. The findings of this study will help in design, production and renovation of products/components that are prone to wear. WAAM-deposited ASS has remarkable strength and ability to withstand impacts;it can be used in the production of armour plates for defence applications, mainly military vehicles and aircraft.

关键词： Metal additive deposition Defence applications Arc-based DED Characterization Wear behaviour Fractography

Evaluation of slope stability through rock mass classification and kinematic analysis of some major slopes along NH-1A from Ramban to Banihal, North Western Himalayas

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Journal of Rock Mechanics and Geotechnical Engineering 2024年第1期16卷 167-182页

作者： Amit Jaiswal A.k.Verma T.N.Singh Department of Civil and Environmental Engineering Indian Institute of Technology PatnaPatna801106India

The network of Himalayan roadways and highways connects some remote regions of valleys or hill slopes,which is vital for India’s socio-economic *** to natural and artificial factors,frequency of slope instabilities along the networks has been increasing over last few *** of stability of natural and artificial slopes due to construction of these connecting road networks is significant in safely executing these roads throughout the *** rock mass classification methods are generally used to assess the strength and deformability of rock *** study assesses slope stability along the NH-1A of Ramban district of North Western *** structurally and non-structurally controlled rock mass classification systems have been applied to assess the stability conditions of 14 *** evaluating the stability of these slopes,kinematic analysis was performed along with geological strength index(GSI),rock mass rating(RMR),continuous slope mass rating(CoSMR),slope mass rating(SMR),and Q-slope in the present *** SMR gives three slopes as completely unstable while CoSMR suggests four slopes as completely *** stability of all slopes was also analyzed using a design chart under dynamic and static conditions by slope stability rating(SSR)for the factor of safety(FoS)of 1.2 and 1 respectively.Q-slope with probability of failure(PoF)1%gives two slopes as stable *** slope angle has been determined based on the Q-slope safe angle equation and SSR design chart based on the *** value ranges given by different empirical classifications were RMR(37-74),GSI(27.3-58.5),SMR(11-59),and CoSMR(3.39-74.56).Good relationship was found among RMR&SSR and RMR&GSI with correlation coefficient(R 2)value of 0.815 and 0.6866,***,a comparative stability of all these slopes based on the above classification has been performed to identify the most critical slope along this road.

关键词： Rock mass classification kinematic analysis Slope stability Himalayan road Static and dynamic conditions