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Basophile:Accurate Fragment Charge State Prediction Improves Peptide Identification Rates

Genomics, Proteomics & Bioinformatics 2013年第2期11卷 86-95页

作者： Dong Wang Surendra Dasari Matthew C.Chambers Jerry D.Holman Kan Chen Daniel C.Liebler Daniel J.Orton Samuel O.Purvine Matthew E.Monroe chang y.chung Kristie L.Rose David L.Tabb Department of Biomedical Informatics Vanderbilt University Medical Center Division of Biomedical Statistics and Informatics Mayo Clinic Department of Biochemistry Vanderbilt University Medical Center Biological Sciences Division and Environmental Molecular Sciences Laboratory Pacific Northwest National Laboratory Department of Pharmacology Vanderbilt University Medical Center Vanderbilt-Ingram Cancer Center Vanderbilt University School of Medicine

In shotgun proteomics, database search algorithms rely on fragmentation models to pre- dict fragment ions that should be observed for a given peptide sequence. The most widely used strat- egy （Naive model） is oversimplified, cleaving all peptide bonds with equal probability to produce fragments of all charges below that of the precursor ion. More accurate models, based on fragmen- tation simulation, are too computationally intensive for on-the-fly use in database search algorithms. We have created an ordinal-regression-based model called Basophile that takes fragment size and basic residue distribution into account when determining the charge retention during CID/higher- energy collision induced dissociation （HCD） of charged peptides. This model improves the accuracy of predictions by reducing the number of unnecessary fragments that are routinely predicted for highly-charged precursors. Basophile increased the identification rates by 26% （on average） over the Naive model, when analyzing triply-charged precursors from ion trap data. Basophile achieves simplicity and speed by solving the prediction problem with an ordinal regression equation, which can be incorporated into any database search software for shotgun proteomic identification.

关键词： Fragmentation Basicity Fragment size Ordinal regression

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Hierarchical Control Strategy for Load Regulation Based on Stackelberg Game Theory Considering Randomness

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CSEE Journal of Power and Energy Systems 2024年第3期10卷 929-941页

作者： Tingyu Jiang Ping Ju C.y.chung yuzhong Gong College of Energy and Electrical Engineering Hohai UniversityNanjing 211100China Department of Electrical Engineering City University of Hong KongHong Kong CF624China Department of Electrical and Computer Engineering University of SaskatchewanSaskatoonSK S7N 5A9Canada CSEE IEEE

Demand response has been recognized as a valuable functionality of power systems for mitigating power *** paper proposes a hierarchical control strategy among the distribution system operator(DSO),load aggregators(LAs),and thermostatically controlled loads(TCLs);the strategy includes a scheduling layer and an executive layer to provide load *** the scheduling layer,the DSO(leader)offers compensation price(CP)strategies,and the LAs(followers)respond to CP strategies with available regulation power(ARP)*** of the DSO and LAs are modeled according to their behaviors during the load regulation *** game is adopted to capture interactions among the players and leader and to obtain the optimal strategy for each participant to achieve ***,considering inevitable random factors in practice,e.g.,renewable generation and behavior of users,two different stochastic models based on sample average approximation(SAA)and parameter modification are formulated with improved scheduling *** the executive layer,distributed TCLs are triggered based on strategies determined in the scheduling layer.A self-triggering method that does not violate user privacy is presented,where TCLs receive external signals from the LA and independently determine whether to alter their operation *** simulations are performed on the modified IEEE-24 bus system to verify effectiveness of the proposed strategy.

关键词： Demand response hierarchical control load regulation self-triggering method Stackelberg game

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Data-driven Static Equivalence with Physics-informed Koopman Operators

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CSEE Journal of Power and Energy Systems 2024年第1期10卷 432-438页

作者： Wei Lin changhong Zhao Maosheng Gao C.y.chung Department of Electrical Engineering The Hong Kong Polytechnic UniversityHong Kong SARChina Department of Information Engineering The Chinese University of Hong KongHong Kong SARChina School of Electrical Engineering Chongqing UniversityChongqing 400044China

With deployment of measurement units,fitting static equivalent models of distribution networks(DNs)by linear regression has been recognized as an effective method in power flow analysis of a transmission *** volatility of measurements caused by variable distributed renewable energy sources makes it more difficult to accurately fit such equivalent *** tackle this challenge,this letter proposes a novel data-driven method to improve equivalency accuracy of DNs with distributed energy *** letter provides a new perspective that an equivalent model can be regarded as a mapping from internal conditions and border voltages to border power *** mapping can be established through 1)Koopman operator theory,and 2)physical features of power flow equations at the root node of a *** of the proposed method is demonstrated on the IEEE 33-bus and IEEE 136-bus test systems connected to a 661-bus utility system.

关键词： Data-driven distribution network Koopman operator theory static equivalent model

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Optimal Shape Factor and Fictitious Radius in the MQ-RBF:Solving Ill-Posed Laplacian Problems

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Computer Modeling in Engineering & Sciences 2024年第6期139卷 3189-3208页

作者： Chein-Shan Liu chung-Lun Kuo Chih-Wen chang Center of Excellence for Ocean Engineering Taiwan Ocean UniversityKeelung202301TaiwanChina Department of Mechanical Engineering National United UniversityMiaoli36063TaiwanChina

To solve the Laplacian problems,we adopt a meshless method with the multiquadric radial basis function(MQRBF)as a basis whose center is distributed inside a circle with a fictitious radius.A maximal projection technique is developed to identify the optimal shape factor and fictitious radius by minimizing a merit function.A sample function is interpolated by theMQ-RBF to provide a trial coefficient vector to compute the merit *** can quickly determine the optimal values of the parameters within a preferred rage using the golden section search *** novel method provides the optimal values of parameters and,hence,an optimal MQ-RBF;the performance of the method is validated in numerical ***,nonharmonic problems are transformed to the Poisson equation endowed with a homogeneous boundary condition;this can overcome the problem of these problems being *** optimal MQ-RBF is extremely *** further propose a novel optimal polynomial method to solve the nonharmonic problems,which achieves high precision up to an order of 10^(−11).

关键词： Laplace equation nonharmonic boundary value problem Ill-posed problem maximal projection optimal shape factor and fictitious radius optimal MQ-RBF optimal polynomial method

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Challenges and opportunities for battery health estimation:Bridging laboratory research and real-world applications

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Journal of Energy Chemistry 2024年第2期89卷 434-436,I0011页

作者： Te Han Jinpeng Tian C.y.chung yi-Ming Wei Center for Energy and Environmental Policy Research Beijing Institute of TechnologyBeijing 100081China School of Management and Economics Beijing Institute of TechnologyBeijing 100081China Department of Electrical and Electronic Engineering and Research Centre for Grid Modernization The Hong Kong Polytechnic UniversityKowloon 999077Hong KongChina

Addressing climate change demands a significant shift away from fossil fuels,with sectors like electricity and transportation relying heavily on renewable *** to this transition are energy storage systems,notably lithium-ion *** time,these batteries degrade,affecting their efficiency and posing safety *** and predicting battery aging is essential,especially estimating its state of health(SOH).Various SOH estimation methods exist,from traditional model-based approaches to machine learning approaches.

关键词： Energy storage systems State of health Multi-source data Scientific AI Data-sharing mechanism

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Ten- year follow- up investigation of stroke risk in systemic lupus erythematosus

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Stroke & Vascular Neurology 2024年第1期9卷 1-7页

作者： Jin-An Huang Ching-Heng Lin Ming-Ju Wu yi-Hsing Chen Kuo-Cheng chang chung-Wei Hou Division of Neurology Neurological InstituteTaichung Veterans General HospitalTaichungTaiwan Department of Health Business Administration Hungkuang UniversityTaichungTaiwan Department of Medical Research Taichung Veterans General HospitalTaichungTaiwan Division of Nephrology Department of Internal MedicineTaichung Veterans General HospitalTaichungTaiwan School of Medicine Chung Shan Medical UniversityTaichungTaiwan College of Medicine National Chung Hsing UniversityTaichungTaiwan Division of Allergy Immunology and RheumatologyDepartment of Internal MedicineTaichung Veterans General HospitalTaichungTaiwan School of Medicine National Yang-Ming Chiao Tung UniversityTaichungTaiwan

Background and purpose To analyse the long-term risk of ischaemic stroke and the clinical effects of antithrombotics on the risk of haemorrhagic stroke in patients with systemic lupus erythematosus(SLE).Methods A retrospective cohort study was conducted using a population-based database taken from Taiwan National Health Insurance Research *** with SLE between 2000 and 2008 were registered and matched with two controls by the index date,age,gender and Charlson Comorbidity Index(CCI).These subjects were followed until either stroke event or 31 December *** HRs(aHRs)for strokes were estimated with Cox regression models,and the cumulative incidence of ischaemic stroke was analysed by log-rank test and Kaplan-Meier survival *** In total,8310 patients with SLE and 16620 patients without SLE were *** general,patients with SLE had higher rates of ischaemic stroke(5.4%vs 3.3%)and haemorrhagic stroke(1.5%vs 0.6%)than in *** multivariate analysis adjusted to age,gender,CCI,urbanisation level and antithrombotics uses,aHRs of all strokes,ischaemic stroke and haemorrhagic stroke were 1.73(95%CI:1.54 to 1.94),1.65(95%CI:1.45 to 1.87)and 2.24(95%CI:1.71 to 2.95),respectively,in patients with *** with SLE were significantly more likely to suffer ischaemic stroke than patients without SLE,even 10 years after SLE diagnosis(6.12%vs 3.50%,py administered to prevent cardiovascular events in patients with SLE due to the risk of haemorrhagic stroke.

关键词： erythematosus diagnosis likely

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Linking Perceived Risk of Public Health Emergency to Psychological Distress among Chinese College Students: The Chain Mediation Role of Balanced Time Perspective and Negative Coping Styles

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International Journal of Mental Health Promotion 2024年第8期26卷 599-610页

作者： chang B. Zhu S. Xie Q. Dai y. School of Education Science Nanjing Normal University Nanjing 210024 China Center of Clinical Psychology The Third People’s Hospital of Heze City Heze 274031 China School of Education Science Northwest Normal University Lanzhou 730070 China Mental Health Center Hubei Polytechnic University Huangshi 435003 China College of Teacher Education Zhejiang Normal University Jinhua 321004 China

Background: With public health emergencies (PHE) worldwide increasing, the perceived risk of PHE has been one of the critical factors influencing college students’ psychological distress. However, the mechanisms by which the perceived risk of PHE affects college students’ psychological distress are not clear. The study’s purpose was to investigate the mediation roles of deviation from a balanced time perspective (DBTP) and negative coping styles between the perceived risk of PHE and psychological distress. Methods: A convenience sampling method was used to survey 1054 Chinese college students with self-reporting. Data was collected using the Public Risk Perception Scale (PRPS), the Zimbardo Time Perspective Inventory (ZTPI), the Simplified Coping Style Questionnaire (SCSQ), the PHE Anxiety Scale, and the Chinese version of the Patient Health Questionnaire (PHQ). The associations between the perceived risk of PHE, DBTP, negative coping styles, and psychological distress were clarified using the correlation analysis. Additionally, the mediating roles of DBTP and negative coping styles between the perceived risk of PHE and psychological distress were investigated using a structural equation model. Results: The findings revealed low to moderate correlations between the variables studied. Students’ perceived risk of PHE was a positive predictor of their psychological distress (b = 0.219, p yles played chain mediation roles between them with the effect being 0.009 and a 95% Boot CI of [0.003, 0.023]. This chain mediation model had an excellent fit index (χ2/df = 4.732, CFI = 0.973, TLI = 0.930, RMSEA = 0.048, SRMR = 0.047). Conclusion: These findings showed how the perceived risk of PHE affected college students’ psychological distress. Specifically, these results suggested that improving students’ mental ability to switch effectively among different time perspectives depending on task features and situational considerations and reducin

关键词： balanced time perspective China college students negative coping styles Perceived risk of public health emergency psychological distress

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Recent innovations in laser additive manufacturing of titanium alloys

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International Journal of Extreme Manufacturing 2024年第3期6卷 2-37页

作者： Jinlong Su Fulin Jiang Jie Teng Lequn Chen Ming yan Guillermo Requena Lai-chang Zhang y Morris Wang Ilya V Okulov Hongmei Zhu Chaolin Tan College of Materials Science and Engineering Hunan UniversityChangsha 410082People’s Republic of China Singapore Institute of Manufacturing Technology(SIM Tech) Agency for ScienceTechnology and Research(A∗STAR)5 Cleantech LoopSingapore 636732Singapore Department of Materials Science and Engineering Southern University of Science and TechnologyShenzhen 518055People’s Republic of China Institute of Materials Research German Aerospace Center(DLR)Linder Höhe51147 CologneGermany Centre for Advanced Materials and Manufacturing Edith Cowan University270 Joondalup DriveJoondalupPerthWestern Australia 6027Australia Department of Materials Science and Engineering University of CaliforniaLos AngelesCA 900095United States of America Leibniz Institute for Materials Engineering-IWT Badgasteiner Str.328359 BremenGermany Faculty of Production Engineering University of BremenBadgasteiner Str.128359 BremenGermany Key Laboratory of Hunan Province of Equipment Safety Service Technology under Extreme Environment University of South ChinaHengyangPeople’s Republic of China RWTH Aachen University Metallic Structures and Materials Systems for Aerospace EngineeringD-52062 AachenGermany

Titanium(Ti)alloys are widely used in high-tech fields like aerospace and biomedical *** additive manufacturing(LAM),as an innovative technology,is the key driver for the development of Ti *** the significant advancements in LAM of Ti alloys,there remain challenges that need further research and development *** recap the potential of LAM high-performance Ti alloy,this article systematically reviews LAM Ti alloys with up-to-date information on process,materials,and *** feasible solutions to advance LAM Ti alloys are reviewed,including intelligent process parameters optimization,LAM process innovation with auxiliary fields and novel Ti alloys customization for *** auxiliary energy fields(***,acoustic,mechanical deformation and magnetic fields)can affect the melt pool dynamics and solidification behaviour during LAM of Ti alloys,altering microstructures and mechanical *** kinds of novel Ti alloys customized for LAM,like peritecticα-Ti,eutectoid(α+β)-Ti,hybrid(α+β)-Ti,isomorphousβ-Ti and eutecticβ-Ti alloys are reviewed in ***,machine learning in accelerating the LAM process optimization and new materials development is also *** review summarizes the material properties and performance envelops and benchmarks the research achievements in LAM of Ti *** addition,the perspectives and further trends in LAM of Ti alloys are also highlighted.

关键词： additive manufacturing titanium alloys auxiliary field machine learning aerospace materials lightweight materials novel alloys

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Optimal sequential therapy using tyrosine kinase inhibitors as the first-line treatment in patients with metastatic renal cell carcinoma: A nationwide multicenter study

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Asian Journal of Urology 2024年第3期11卷 450-459页

作者： Jung Ki Jo Seong Il Seo Minyong Kang Jinsoo chung Cheol Kwak Sung-Hoo Hong Cheryn Song Jae young Park chang Wook Jeong Seok Hwan Choi Sung Han Kim Eu chang Hwang Chan Ho Lee Hakmin Lee Department of Urology Medical and Digital EngineeringCollege of MedicineHanyang UniversitySeoulRepublic of Korea Department of Urology Samsung Medical CenterSungkyunkwan University School of MedicineSeoulRepublic of Korea Department of Urology National Cancer CenterGoyangRepublic of Korea Department of Urology Seoul National University HospitalSeoulRepublic of Korea Department of Urology Kangnam St Mary’s HospitalSeoulRepublic of Korea Department of Urology Asan Medical CenterSeoulRepublic of Korea Department of Urology Korea University Ansan HospitalAnsanRepublic of Korea Department of Urology Kyungpook National University HospitalDaeguRepublic of Korea Department of Urology Chonnam National University Hwasun HospitalHwasunRepublic of Korea Department of Urology Inje University Busan Paik HospitalBusanRepublic of Korea Department of Urology Seoul National University Bundang HospitalSeongnamRepublic of Korea

Objective:The purpose of the study was to identify the best sequence of therapy beginning with a tyrosine kinase inhibitor(TKI)as the first-line therapy for patients with metastatic renal cell carcinoma(mRCC)in terms of overall survival(OS),progression-free survival(PFS),and rates of discontinuation and adverse effects during the treatment ***:This is a retrospective,nationwide multicenter study of patients with mRCC after diagnosis at 10 different tertiary medical centers in Korea from January 1992 to December *** focused on patients at either“favorable”or“intermediate”risk according to the International mRCC Database Consortium criteria,and they were followed up(median 335 days).Finally,a total of 1409 patients were selected as the study *** generated a Cox proportional hazard model adjusted for covariates,and the different therapy schemes were statistically tested in terms of OS as well as *** addition,frequencies of discontinuation and adverse events were compared among the therapy ***:Of the primary patterns of treatment sequences(24 sequences),“sunitinib epazopanib”and“sunitinibeeverolimuseimmunotherapy”showed the most beneficial results in both OS and PFS with significantly lower hazards than“sunitinib”,which is the most commonly treated agent in *** that the“TKIeTKI”structure showed relatively higher discontinuation rates with higher adverse effects,the overall beneficial sequence would be“sunitinibeeverolimuseimmunotherapy”.Conclusion:Among several sequential therapy starting with TKIs,“sunitinibeeverolimuse immunotherapy”was found to be the best scheme for mRCC patients with“favorable”or“intermediate”risks.

关键词： Tyrosinekinase inhibitor Metastaticrenalcell carcinoma Overall survival Progression-free survival

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Environmentally adaptive reshaping of plant photomorphogenesis by karrikin and strigolactone signaling

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Journal of Integrative Plant Biology 2024年第5期66卷 865-882页

作者： young-Joon Park Bo Eun Nam chung-Mo Park Department of Smart Farm Science Kyung Hee UniversityYongin 17104Korea Departmentof Biological Sciences Seoul National UniversitySeoul 08826Korea Department of Chemistry Seoul National UniversitySeoul 08826Korea

Coordinated morphogenic adaptation of growing plants is critical for their survival and propagation under fluctuating *** morphogenic responses to light and warm temperatures,termed photomorphogenesis and thermomorphogenesis,respectively,have been extensively studied in recent *** photomorphogenesis,plants actively reshape their growth and developmental patterns to cope with changes in light ***,photomorphogenesis is closely associated with diverse growth hormonal ***,accumulating evidence indicates that light-directed morphogenesis is profoundly affected by two recently identified phytochemicals,karrikins(KARs)and strigolactones(SLs).KARs and SLs are structurally related butenolides acting as signaling molecules during a variety of developmental steps,including seed *** receptors and signaling mediators have been identified,and associated working mechanisms have been explored using gene-deficient mutants in various plant *** particular interest is that the KAR and SL signaling pathways play important roles in environmental responses,among which their linkages with photomorphogenesis are most comprehensively studied during seedling *** this review,we focus on how the phytochemical and light signals converge on the optimization of morphogenic *** also discuss molecular mechanisms underlying the signaling crosstalks with an aim of developing potential ways to improve crop productivity under climate changes.

关键词： karrikins morphogenic adaptation photomorphogenesis seedling establishment strigolactones

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