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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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老子哲学与“道元”:人工智能token的语义与应用探索

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中国科技术语 2025年第1期27卷 57-63页

作者：张中鸿张庆瑞台湾大学哲学系中国台北市320314 中原大学物理系中国台湾中坜106319

自然语言处理建构在“道元(token)”之上,道元是AI算法处理和学习各种文字、图像与声音数据类型的基本元素。道元生成的过程与老子“道生一,一生二,二生三,三生万物”相似。大语言模型利用“间距”产生道元后,转换成位,透过大量数据的... 详细信息

自然语言处理建构在“道元(token)”之上,道元是AI算法处理和学习各种文字、图像与声音数据类型的基本元素。道元生成的过程与老子“道生一,一生二,二生三,三生万物”相似。大语言模型利用“间距”产生道元后,转换成位,透过大量数据的学习与计算,进行新的道元生成与意义重组。由于结合概率重组,人工智能出现类似于人类行为的不可预测性和独特性。未来借鉴老子哲学和汉字的多样性,人工智能可以发展出更全面和创新的框架。

关键词：道元位道元化间距人工智能老子之道

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A Modified Analytic Function Space Feynman Integral of Functionals on Function Space

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Chinese Annals of Mathematics,Series B 2020年第1期41卷 61-76页

作者： SeungJun chang HyunSoo chung Department of Mathematics Dankook UniversityCheonan 330-714Korea

In this paper, the authors introduce a class of functionals. This class forms a Banach algebra for the special cases. The main purpose of this paper is to investigate some properties of the modified analytic function space Feynman integral of functionals in the class. Those properties contain various results and formulas which were not obtained in previous papers. Also, the authors establish some relationships involving the first variation via the translation theorem on function space. In particular, the authors establish the Fubini theorem for the modified analytic function space Feynman integral which was not obtained in previous researches yet.

关键词： Generalized Brownian motion process Modified analytic Feynman integral First variation Cameron-Storvick type theorem Fubini theorem

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Is necrosectomy obsolete for infected necrotizing pancreatitis? Is a paradigm shift needed?

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World Journal of Gastroenterology 2014年第45期20卷 16925-16934页

作者： yu-chung chang Department of Surgery Chung Shan Medical University Hospital College of Medicine Chung Shan Medical University

In 1886,Senn stated that removing necrotic pancreatic and peripancreatic tissue would benefit patients with severe acute *** then,necrosectomy has been a mainstay of surgical procedures for infected necrotizing pancreatitis(NP).No published report has successfully questioned the role of ***,however,increasing evidence shows good outcomes when treating walled-off necrotizing pancreatitis without a *** literature concerning NP published primarily after 2000 was reviewed;it demonstrates the feasibility of a paradigm *** majority(75%)of minimally invasive necrosectomies show higher completion rates:between 80%and 100%.Transluminal endoscopic necrosectomy has shown remarkable results when combined with percutaneous drainage or a metallic *** morbidities range from 40%to 92%.Single-digit mortality rates have been achieved with transluminal endoscopic necrosectomy,but not with video-assisted retroperitoneal necrosectomy *** procedures without necrosectomy have evolved from percutaneous drainage to transluminal endoscopic drainage with or without percutaneous endoscopic gastrostomy access for laparoscopic *** series have reached higher success rates of 79%-93%,and even 100%,using transcystic multiple drainage *** is becoming evident that transluminal endoscopic drainage treatment of walledoff NP without a necrosectomy is *** further refinement of the drainage procedures,a paradigm shift from necrosectomy to drainage is inevitable.

关键词： Delay until liquefaction Infected necrotizing pancreatitis Minimally invasive treatment Transluminal endoscopic drainage/necrosectomy Walled-off pancreatic necrosis

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State-to-state Photoionization Dynamics of Vanadium Nitride by Two-color Laser Photoionization and Photoelectron Methods

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Chinese Journal of Chemical Physics 2013年第6期26卷 669-678,I0003页

作者： Huang Huang Zhi-hong Luo yih chung chang Kai-chung Lau C. y. Ng Department of Chemistry University of California Davis CA 95616 USA Department of Biology and Chemistry Oty University of Hone Kong Kowloon Hone Kong China

We have conducted a two-color visible-ultraviolet （VIS-UV） resonance-enhanced laser pho- toionization and pulsed field ionization-photoelectron （PFI-PE） study of gaseous vana- dium mononitride （VN） in the total energy range of 56900-59020 cm-1. The VN molecules were selectively excited to single rotational levels of the intermediate VN（D3H0, v＇=0） state by using a VIS dye laser prior to photoionization by employing a UV laser. This two-color scheme allows the measurements of rovibronically selected and re- solved PFI-PE spectra for the VN＋（X2A; v＋=0, 1, and 2） ion vibrational bands. By simulating the rotationally resolved PFI-PE spectra, J＋=3/2 is determined to be the lowest rotational level of the ground electronic state, indicating that the symmetry of the ground VN＋ electronic state is 2A3/2. The analysis of the PFI-PE spectra for VN＋ also yields accurate values for the adiabatic ionization energy for the formation of VN＋（X2A3/2）, IE（VN）=56909.5＋0.8 cm-1 （7.05588±0.00010 eV）, the vibrational fre- quency wc＋=1068.0±0.8 cm-1, the anharmonicity constant wc＋Xe＋=5.8±0.8 cm-1, the rotational constants Be＋=0.6563±0.0005 cm-1 and ae＋=0.0069±0.0004 cm-1, and the equi-librium bond length, re＋=1.529A, for VN＋（X2A3/2）; along with the rotational constants Bc＋=0.6578i0.0028 cm-1 and a＋=0.0085±0.0028 cm-1, and the equilibrium bond length re＋=1.527A for VN＋（X2As/2）, and the spin-orbit coupling constant A=153.3±0.8 cm-1 for VN＋（X2/k5/2,3/2）. The highly precise energetic and spectroscopic data obtained in the present study are valuable for benchmarking the predictions based on state-of-the-art ab initio quantum calculations.

关键词： Vanadium nitride Vanadium nitride cation Photoionization dynamics Two- color photoionization Pulsed field ionization-photoelectron Ionization energy Bond disso- ciation energy

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Bayesian-inspired minimum contamination designs under a double-pair conditional effect model

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Statistical Theory and Related Fields 2023年第4期7卷 336-349页

作者： Ming-chung chang Institute of Statistical Science Academia SinicaTaipeiTaiwanChina

In two-level fractional factorial designs,conditional main effects can provide insights by which to analyze factorial effects and facilitate the de-aliasing of fully aliased two-factor ***-ditional main effects are of particular interest in situations where some factors are nested within *** of the relevant literature has focused on the development of data analysis tools that use conditional main effects,while the issue of optimal factorial design for a given linear model involving conditional main effects has been largely ***,Wu and chang[*** 27(2017)997-1016]established a framework by which to optimize designs under a con-ditional effect *** theoretically sound,their results were limited to a single pair of conditional and conditioning *** this paper,we extend the applicability of their frame-work to double pairs of conditional and conditioning factors by providing the corresponding parameterization and effect *** propose a minimum contamination-based criterion by which to evaluate designs and develop a complementary set theory to facilitate the search of minimum contamination *** catalogues of 16-and 32-run minimum contamination designs are *** five to twelve factors,we show that all 16-run minimum contamination designs under the conditional effect model are also minimum aberration according to Fries and Hunter[Technometrics 22(1980)601-608].

关键词： Minimum aberration two-level factorials effect hierarchy functional prior

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Benefits of the Seattle biopsy protocol in the diagnosis of Barrett's esophagus in a Chinese population

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World Journal of Clinical Cases 2018年第14期6卷 753-758页

作者： Shou-Wu Lee Han-chung Lien Chi-Sen chang Ming-Xian Lin chung-Hsin chang chung-Wang Ko Division of Gastroenterology Department of Internal Medicine Taichung Veterans General Hospital Taichung 40705 Taiwan Department of Internal Medicine Chung Shan Medical University Taichung 40201 Taiwan Department of Internal Medicine National Yang-Ming University Taipei 11221 Taiwan

AIMTo investigate the benefits of the Seattle protocol in the diagnosis of Chinese individuals with Barrett’s *** enrolled were patients from one center with endoscopically-suspected esophageal metaplasia. These patients first received narrow-band imaging-targeted biopsy, and later, the Seattle protocol-guided biopsy, within a period from October 2012 to December 2014. Those cases without initial pathologic patterns of intestinal metaplasia （IM） and then appearance or loss of IM tissue were designated as Group A or B, respectively. Those with initial pathologic patterns ofIM, which then persisted or were lost were designated as Group C or D, *** number of cases for each group was as follows： A： 20, B： 78, C： 31 and D： 14. The distribution of the Prague criteria M levels of Group A was significantly higher than Group B （ P = 0.174）. Among these groups, Group C had the highest proportions of hiatus hernia （54.8%）, long segment Barrett’s esophagus （29%）, and also the highest Prague criteria M levels. The sensitivity of IM detection was 69.2% for the narrow-band imaging-targeted biopsy and 78.5% for the Lee SW et al . Seattle protocol for Barrett’s esophagusSeattle protocol-guided biopsy. The difference was not signifcant （P = 0.231）. The number of detectable dysplasias increased from one case via the NBI-target biopsy to five cases via the Seattle protocol-guided biopsy, including one case of *** Seattle protocol improved the IM detection in our subjects with higher Prague criteria M levels and disclosed more cases with dysplastic tissues.

关键词： Barrett’s esophagus Dysplasia Intestinal metaplasia Seattle protocol Chinese

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Self-sustained oscillation for compressible cylindrical cavity flows

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Chinese Journal of Aeronautics 2017年第4期30卷 1294-1299页

作者： Kung-Ming chung Kuan-Huang LEE Keh-Chin chang Aerospace Science and Technology Research Center National Cheng Kung University Tainan 711 China Department of Aeronautics and Astronautics National Cheng Kung University Tainan 701 China

The presence of a cavity changes the mean and fluctuating pressure distributions. Similarities are observed between a cylindrical cavity and a rectangular cavity for a compressible *** type of cavity flow field depends on the diameter-to-depth ratio and the length-to-depth *** feedback loop is responsible for the generation of discrete acoustic tones. In this study, the selfsustained oscillation for a compressible cylindrical cavity flow was investigated experimentally. For open-type cavities, the power spectra show that the strength of resonance depends on the diameterto-depth ratio（4.43–43.0） and the incoming boundary layer thickness-to-depth ratio（0.72–7.0）. The effective streamwise length is used as the characteristic length to estimate the Strouhal number. At higher modes, there is a large deviation from Rossiter＇s formula for rectangular cavities. The gradient-based searching method was used to evaluate the values of the empirical parameters. Less phase lag and a lower convection velocity are observed.

关键词： Cavity flow Compressible flow Convection velocity Open cavity Oscillation

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RF/wireless-interconnect: The next wave of connectivity

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Science China(Information Sciences) 2011年第5期54卷 1026-1038页

作者： TAM SaiWang chang Mau-chung Frank Electrical Engineering Department University of California Los Angeles Los Angeles CA 90095 USA

In the era of the nanometer CMOS technology, due to stringent system requirements in power, performance and other fundamental physical limitations (such as mechanical reliability, thermal constraints, overall system form factor, etc.), future VLSI systems are relying more on ultra-high data rates (up to 100 Gbps/pin or 20 Tbps aggregate), scalable, re-configurable, highly compact and reliable interconnect fabric. To overcome such challenges, we first explore the use of multiband RF/wireless-interconnects which can communicate simultaneously through multiple frequency bands with low power signal transmission, reconfigurable bandwidth and excellent mechanical flexibility and reliability. We then review recent advances in RF/wireless-interconnect in four different potential application domains, which include network-on-chips (NoCs), 3-dimensional integrated circuit (3DIC), advanced memory interface and ultra-high speed contactless connectors. Based on those developments, we further propose the future research direction on future inter- and intra-VLSI interconnect system through the comparison of performance and the proper communication range for all three types of interconnects, including communication data throughput, range and power consumption (pJ/bit) among the RF/wireless-interconnects, the optical interconnects and traditional parallel repeated bus.

关键词： RF-interconnect wireless RF-interconnect network-on-chips multi-band 3-dimensional integrated circuit advanced memory interface wireless contactless connector

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Optimal design theories of tuned mass dampers with nonlinear viscous damping

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Earthquake Engineering and Engineering Vibration 2009年第4期8卷 547-560页

作者： Lap-Loi chung Lai-yun Wu Hsu-Hui Huang chung-Hsin chang Kuan-Hua Lien Center for Research on Earthquake Engineering （NCREE） Chinese Taipei Department of Civil Engineering Taiwan University. Chinese Taipei

Optimal design theory for linear tuned mass dampers （TMD） has been thoroughly investigated, but is still under development for nonlinear TMDs. In this paper, optimization procedures in the time domain are proposed for design of a TMD with nonlinear viscous damping. A dynamic analysis of a structure implemented with a nonlinear TMD is conducted first. Optimum design parameters for the nonlinear TMD are searched using an optimization method to minimize the performance index. The feasibility of the proposed optimization method is illustrated numerically by using the Taipei 101 structure implemented with TMD. The sensitivity analysis shows that the performance index is less sensitive to the damping coefficient than to the frequency ratio. Time history analysis is conducted using the Taipei 101 structure implemented with different TMDs under wind excitation. For both linear and nonlinear TMDs, the comfort requirements for building occupants are satisfied as long as the TMD is properly designed. It was found that as the damping exponent increases, the relative displacement of the TMD decreases but the damping force increases.

关键词： optimal design theory tuned mass damper (TMD) nonlinear performance index sensitivity analysis Taipei 101

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