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More precise model of.<i>α</i>-helix and transmembrane <i>α</i>-helical peptide backbone structure

Journal of.Biophysical Chemistry 2012年第4期3卷 295-303页

作者： walter f. schmidt Clayton G. Thomas Agricultural Research Service USA Department of Agriculture Beltsville USA Department of.Engineering Morgan State University Baltimore USA

The 3-D structure of.the β-adrenergic receptor with a molecular weight of.55,000 daltons is available f.om crystallographic data. Within one of.the seven transmembrane ion channel helices in the β2-receptor, one loop of.a helix ACADL has previously been proposed as the site that explains β2 activity (f.ghts acute bronchitis) whereas ASADL in the β1-receptor at the corresponding site explains β1-activity (cardiac stimulation). The α-agonist responsible f.r this selective reaction is only 0.5% of.the receptor molecular weight, and only 1.5% of.the weight of.the trans-membrane portion of.the receptor. The understanding of.the mechanism by which a small molecule on binding to a site on one single loop of.a helix produces a specif.c agonist activity on an entire transmembrane ion channel is uncertain. A model of.an α-helix is presented in which of.pitch occurs at angles both smaller and larger than 180° n. Consequently, atomic coordinates in a peptide backbone α-helix match the data points of.individual atom (and atom types) in the backbone. More precisely, eleven atoms in peptide backbone routinely equal one loop of.a helix, instead of.eleven amino acid residues equaling three loops of.a helix;theref.re, an α-helix can begin (or end) at any specif.c atom in a peptide backbone, not just at any specif.c amino acid. Wavef.ont Topology System and f.nite Element Methods calculate this specif.c helical shape based only upon circumf.rence, pitch, and phase. Only external f.rces which specif.cally af.ect circumf.rence, pitch and/or phase (e.g. f.om agonist binding) can/will alter the shape of.an α-helix.

关键词： Helix Alpha-Helix Circumf.rence Pitch phase peptide backbone Wavef.ont Topology System f.nite Element Method

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Consequences of.Non-Unif.rmity in the Stoichiometry of.Component f.actions within One and Two Loops Models of.α-Helical Peptides

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Journal of.Biophysical Chemistry 2014年第4期5卷 125-133页

作者： walter f. schmidt Cathleen J. Hapeman James Wachira Clayton G. Thomas United State Department of.Agriculture Agricultural Research Service Beltsville Maryland USA Department of.Biology School of Computer Mathematical and Natural Sciences Morgan State University Baltimore Maryland USA Clarence M. Mitchell Jr. School of.Engineering Morgan State University Baltimore Maryland USA

A 3-D electrostatic density map generated using the Wavef.ont Topology System and f.nite Element Method clearly demonstrates the non-unif.rmity and periodicity present in even a single loop of.an α-helix. The f.ur dihedral angles (N-C*-C-N, C*-C-N-C*, and C-N-C*-C) f.lly def.ne a helical shape independent of.its length: the three dihedral angles, φ = -33.5°, ω = 177.3°, and Ψ = -69.4°, generate the precise (and identical) redundancy in a one loop (or longer) α-helical shape (pitch = 1.59 /residue;r = 2.25 ). Nevertheless the pattern of.dihedral angles within an 11 and a 22-peptide backbone atom sequence cannot be distributed evenly because the stoichiometry in f.action of.f.ur atoms never divides evenly into 11 or 22 backbone atoms. Thus, three sequential sets of.11 backbone atoms in an α-helix will have a discretely dif.erent chemical f.rmula and correspondingly dif.erent combinations of.molecular f.rces depending upon the assigned starting atom in an 11-step sequence. We propose that the unit cell of.one loop of.an α-helix occurs in the peptide backbone sequence C-(N-C*-C)3-N which contains an odd number of.C* plus even number of.amide groups. A two-loop pattern (C*-C-N)7-C* contains an even number of.C* atoms plus an odd number of.amide groups. Dividing the two-loop pattern into two equal lengths, one f.action will have an extra half.amide (N-H) and the other f.action will have an extra half.amide C=O, i.e., the stoichiometry of.each half.will be dif.erent. Also, since the length of.N-C*-C-N, C*-C-N-C*, and C-N-C*-C are unequal, the summation of.the number of.each in any f.action of.n loops of.an α-helix in sequence will always have unequal length, depending upon the starting atom (N, C*, or C).

关键词： Pattern Recognition α-Helix Dihedral Angle Patterns Peptide Backbone Sequence Molecular Orbital Theory Electrostatic Density Gradient Wavef.ont Topology System f.nite Element Method

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Gradient Temperature Raman Spectroscopy of.f.tty Acids with One to Six Double Bonds Identif.es Specif.c Carbons and Provides Systematic Three Dimensional Structures

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Journal of.Biophysical Chemistry 2018年第1期9卷 1-14页

作者： C. Leigh Broadhurst walter f. schmidt Julie K. Nguyen Jianwei Qin Kuanglin Chao Moon S. Kim Environmental Microbiology and f.od Saf.ty Laboratory US Department of Agriculture Agricultural Research Service Beltsville MD USA Department of.Mechanical Engineering University of Maryland Baltimore County Baltimore MD USA

Specialized pro-resolving mediators provide promising targets f.r new drugs and natural products. Much work has been accomplished on the structure/ f.nction of.the lipoxygenase and cyclooxygenase enzymes but not on the substrates. A better visualization of.three-dimensional lipid structures will allow increased ref.nement of.the interactions that produce the pro-resolving mediators, and lead to improvements in synthetic pathways. We present systematic analysis of.oleic (18:1n-9), linoleic (18:2n-6), alpha-linolenic (18:3n-3), arachidonic (20:4n-6), docosapentaenoic (22:5n-3), and docosahexaenoic (22:6n-3) acids. Continuous gradient temperature Raman spectroscopy (GTRS) applies the temperature gradients utilized in dif.erential scanning calorimetry to Raman spectroscopy. GTRS can identif. and dif.erentiate specif.c carbon chain sites, f.nally allowing Raman analysis to explain why the long-chain polyunsaturated f.tty acids (LC-PUf.) exhibit such extreme f.nctional dif.erences despite minimal changes in chemical structure. Detailed vibrational analysis of.the important f.equency ranges 1450 - 1200 cm-1 (includes CH2 bending and twisting) and 1750 - 1425 cm-1 (includes C=C stretching and C-C stretching plus H-C in-plane rocking) shows f.r the f.rst time that each molecule has its own characteristic set of.modes with only some redundancy/commonality. The number and f.equency of.modes correlates with three-dimensional molecular structure, not the degree of.unsaturation. The high degree of.specif.city of.lipoxygenase and cyclooxygenase enzymes should be reconsidered in light of.the f.ct that individual sites on the polyunsaturated f.tty acid chain are nonequivalent, and each LC-PUf. molecule has an individual, specif.c three dimensional structure incorporating torsion.

关键词： Gradient Temperature Raman Spectroscopy Raman Spectroscopy Arachidonic Acid Docosapentaenoic Acid Docosahexaenoic Acid Alpha-Linolenic Acid N-3DPA DHA GTRS

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Quantif.cation of.Inositol Hexa-Kis Phosphate in Environmental Samples

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Open Journal of.Soil Science 2012年第1期2卷 55-63页

作者： Lynne P. Heighton Merle Zimmerman Clif.ord P. Rice Eton E. Codling John A. Tossell walter f. schmidt Department of.Chemistry and Biochemistry University of Maryland College Park United States EMBUL ARS USDA Beltsville United States

Phosphorous (P) is a major contributor to eutrophication of.surf.ce waters, yet a complete understanding of.the P cycle remains elusive. Inositol hexa-kis phosphate (IHP) is the primary f.rm of.organic (PO) in the environment and has been implicated as an important sink in aquatic and terrestrial samples. IHP readily f.rms complexes in the environment due to the 12 acidic sites on the molecule. Quantif.cation of.IHP in environmental samples has typically relied on harsh extraction methods that limit understanding of.IHP interactions with potential soil and aquatic complexation partners. The ability to quantif. IHP in-situ at the pH of.existing soils provides direct access to the role of.IHP in the P cycle. Since it is itself.a buf.er, adjusting the pH correspondingly alters charged species of.IHP present in soil. Density f.nctional Theory (Df.) calculations support the charged species assignments made based pKas associated with the IHP molecule. Raman spectroscopy was used to generate pH dependent spectra of.inorganic (PI) and IHP as well as (PO) f.om IHP and (PI) in soil samples. Electro-spray ionization mass spectroscopy (ESI-MS) was used to quantif. IHP-Iron complexes in two soil samples using a neutral aqueous extraction.

关键词： Phytic Acid Inositol Hexkis Phosphate Electrospray Mass Spectroscopy (ESI-MS) Density f.nctional Theory (Df.) Raman Spectroscopy

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Application of.dynamic image analysis to the optical characterisation of.f.brous bulk material

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Particuology 2024年第7期90卷 51-60页

作者： Johannes Lunewski Eberhard schmidt Institute of.Particle Technology University of WuppertalGermany

Dynamic image analysis provides an automated evaluation method to determine the size and shape of.multiple particles. This method represents a common application f.r ordinary bulk material. The latest draf. of.ISO 13322–2:2021 describes the state of.the art, but lacks instructions f.r handling f.brous bulk material. Interlocking f.bres complicate the measurement conditions and require a disentanglement of.f.brous samples during a pre-dispersion step. A f.rther error source includes the f.bre orientation inside the measurement zone of.the device. If.the thresholding algorithm f.ils to dif.erentiate between the f.bre projection area and the background, a subsequent image optimisation solves the problem. This article addresses the mentioned problems by analysing cotton cellulose and polyacrylonitrile f.bres. Besides the execution of.a pre-dispersion step, the experiments compare the discrepancies between dry and wet dispersion. Here, the sof.ware packages PAQXOS and ImageJ perf.rm the image evaluation. In this case, the wet dispersion setup with a subsequent image evaluation by ImageJ provides comprehensible results.

关键词： Bootstrap method Dynamic image analysis f.bre diameter f.bre length distribution Natural f.bres Synthetic f.bres

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Mechanistic modeling of.copper corrosions in data center environments

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Building Simulation 2024年第3期17卷 483-492页

作者： Rui Zhang Jianshun Zhang Roger schmidt Jeremy L.Gilbert Department of.Mechanical and Aerospace Engineering College of Engineering and Computer ScienceSyracuse UniversitySyracuseNY13244USA Buildings and Transportation Science Division Oak Ridge National LaboratoryOak RidgeTN37830USA SyracuseCoE-New York Center of.Excellence in Environmental and Energy Systems Syracuse University727 E.Washington StreetSyracuseNY13244USA Department of.Bioengineering Clemson UniversityClemson-Medical University of South Carolina Bioengineering ProgramCharlestonSC29425USA

Air-side economizers are increasingly used to take advantage of.f.ee-cooling”in data centers with the intent of.reducing the carbon f.otprint of.***,they can introduce outdoor pollutants to indoor environment of.data centers and cause corrosion damage to the inf.rmation technology *** evaluate the reliability of.inf.rmation technology equipment under various thermal and air-pollution conditions,a mechanistic model based on multi-ion transport and chemical reactions was *** model was used to predict Cu corrosion caused by Cl_(2)-containing pollutant *** also accounted f.r the ef.ects of.temperature(25℃and 28℃),relative humidity(50%,75%,and 95%),and *** also identif.ed higher air temperature as a corrosion barrier and higher relative humidity as a corrosion accelerator,which agreed well with the experimental *** average root mean square error of.the prediction was 13.7Å.The model can be used to evaluate the thermal guideline f.r data centers design and operation when Cl_(2)is present based on pre-established acceptable risk of.corrosion in data centers’environment.

关键词： chloride pollutant mixture copper corrosion model data center temperature relative humidity synergistic ef.ect

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Transf.r learning f.om synthetic data f.r open-circuit voltage curve reconstruction and state of.health estimation of.lithium-ion batteries f.om partial charging segments

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Energy and AI 2024年第3期17卷 80-97页

作者： Tobias Hof.ann Jacob Hamar Bastian Mager Simon Erhard Jan Philipp schmidt Chair of.Systems Engineering f.r Electrical Energy Storage University of BayreuthWeiherstraße 26Bayreuth95448BavariaGermany BMW Group Petuelring 130Munich80809BavariaGermany

Data-driven models f.r battery state estimation require extensive experimental training data,which may not be available or suitable f.r specif.c tasks like open-circuit voltage(OCV)reconstruction and subsequent state of.health(SOH)*** study addresses this issue by developing a transf.r-learning-based OCV reconstruction model using a temporal convolutional long short-term memory(TCN-LSTM)network trained on synthetic data f.om an automotive nickel cobalt aluminium oxide(NCA)cell generated through a mechanistic model *** data consists of.voltage curves at constant temperature,C-rates between C/30 to 1C,and a SOH-range f.om 70%to 100%.The model is ref.ned via Bayesian optimization and then applied to f.ur use cases with reduced experimental nickel manganese cobalt oxide(NMC)cell training data f.r higher use *** TL models’perf.rmances are compared with models trained solely on experimental data,f.cusing on dif.erent C-rates and voltage *** results demonstrate that the OCV reconstruction mean absolute error(MAE)within the average battery electric vehicle(BEV)home charging window(30%to 85%state of.charge(SOC))is less than 22 mV f.r the f.rst three use cases across all *** SOH estimated f.om the reconstructed OCV exhibits an mean absolute percentage error(MAPE)below 2.2%f.r these *** study f.rther investigates the impact of.the source domain on TL by incorporating two additional synthetic datasets,a lithium iron phosphate(Lf.)cell and an entirely artif.cial,non-existing,cell,showing that solely the shif.ing and scaling of.gradient changes in the charging curve suf.ice to transf.r knowledge,even between dif.erent cell chemistries.A key limitation with respect to extrapolation capability is identif.ed and evidenced in our f.urth use case,where the absence of.such comprehensive data hindered the TL process.

关键词： Lithium-ion battery State of.health estimation Transf.r learning OCV curve Partial charging Synthetic data

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A complete ref.rence genome f.r the soybean ***

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Plant Communications 2024年第2期5卷 19-22页

作者： Yicheng Huang Dal-Hoe Koo Yizhou Mao Eliot M.Herman Jianwei Zhang Monica A.schmidt National Key Laboratory of.Crop Genetic Improvement Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhan 430070China Wheat Genetics Resource Center Department of Plant PathologyKansas State UniversityManhattanKS 66506USA BIO5 Institute School of Plant SciencesUniversity of ArizonaTucsonAZ 85721USA

Dear Editors,Soybeans are a global commodity f.r their edible protein and vegetable *** global population is predicted to be 9.7 billion by 2050(UN,2022),with a concomitant drastic increase in protein *** already 2.4 billion people suf.ering f.om f.od insecurity(f.O et al.,2023),there is an urgent need to meet f.ture production demands f.r plant-based proteins.

关键词： commodity soybean urgent

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Temporally Preserving Latent Variable Models:Of.line and Online Training f.r Reconstruction and Interpretation of.f.ult Data f.r Gearbox Condition Monitoring

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Journal of.Dynamics, Monitoring and Diagnostics 2024年第2期3卷 156-177页

作者： Ryan Balshaw P.Stephan Heyns Daniel N.Wilke Stephan schmidt Center f.r Asset Integrity Management Department of Mechanical and Aeronautical EngineeringUniversity of PretoriaPretoriaSouth Africa

Latent variable models can ef.ectively determine the condition of.essential rotating machinery without needing labeled *** models analyze vibration data via an unsupervised learning *** preservation is necessary to obtain an inf.rmative latent manif.ld f.r the f.ult diagnosis *** a temporalpreserving context,two approaches exist to develop a condition-monitoring methodology:of.line and *** latent variable models,the available training modes are not *** many traditional methods use of.line training,online training can dynamically adjust the latent manif.ld,possibly leading to better f.ult signature extraction f.om the vibration *** study explores online training using temporal-preserving latent variable *** online training,there are two main methods:one f.cuses on reconstructing data and the other on interpreting the data *** are considered to evaluate how they diagnose f.ults over *** two experimental datasets,the study conf.rms that models f.om both training modes can detect changes in machinery health and identif. f.ults even under varying ***,the complementarity of.of.line and online models is emphasized,reassuring their versatility in f.ult *** the implications of.the training approach and the available model f.rmulations is crucial f.r f.rther research in latent variable modelbased f.ult diagnostics.

关键词： Condition monitoring unsupervised learning latent variable models temporal preservation training approaches

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Advancing Evaluation of.Microplastics Thresholds to Inf.rm Water Treatment Needs and Risks

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Environment & Health 2024年第7期2卷 441-452页

作者： Omar S.Chowdhury Philip J.schmidt William B.Anderson Monica B.Emelko Department of.Civil and Environmental Engineering University of Waterloo200 University Avenue WestWaterlooON N2L 3G1Canada

Although human health impacts of.microplastics are not well understood,concern regarding chemical contaminants retained on or within them is *** water providers are increasingly asked about these risks,but strategies f.r evaluating them and the extent of.treatment needed to manage them are currently *** can potentially induce health ef.ects if.the concentration of.contaminants adsorbed to them exceeds predetermined drinking water guidelines(e.g.,Maximum Contaminant Levels).The risk posed by microplastics due to adsorbed contaminants is dif.icult to determine,but a worst-case scenario can be evaluated by using adsorption ***,a“Threshold Microplastics Concentration”(TMC)f.amework is developed to evaluate whether waterborne microplastic concentrations can potentially result in the intake of.regulated contaminants on/in microplastics at levels of.human health concern and identif. treatment targets f.r managing associated health *** the TMC does not indicate an immediate health risk;it inf.rms the need f.r detailed risk assessment or f.rther treatment evaluation to ensure particle removal targets are ***,the TMC concept and f.amework provide an updateable,science-based screening tool to determine if.there is a need f.r detailed risk assessment or treatment modif.cation due to waterborne microplastics in supplies used f.r potable water production.

关键词： drinking water treatment chemical contaminants adsorption capacity risk management maximum contaminant level

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