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Basophile:Accurate Fragment charge State Prediction Improves Peptide Identification Rates

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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

High-throughput discovery of fluoride-ion conductors via a decoupled,dynamic,and iterative(ddI)framework

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npj computational Materials 2022年第1期8卷 983-991页

作者： Jack d.Sundberg daniel L.druffel Lauren M.McRae Matthew G.Lanetti Jacob T.Pawlik Scott c.Warren department of chemistry The University of North Carolina at Chapel HillChapel HillNC27599United States

Fluoride–ion batteries are a promising alternative to lithium–ion batteries with higher theoretical capacities and working voltages,but they have experienced limited success due to the poor ionic conductivities of known electrolytes and ***,we report a high-throughput computational screening of 9747 fluoride-containing materials in search of fluoride-ion *** a combination of empirical,lightweight dFT,and nudged elastic band(NEB)calculations,we identified>10 crystal systems with high fluoride *** applied a search strategy where calculations are performed in any order(decoupled),computational resources are reassigned based on need(dynamic),and predictive models are repeatedly updated(iterative).Unlike hierarchical searches,our decoupled,dynamic,and iterative framework(ddI)began by calculating high-quality barrier heights for fluoride-ion mobility in a large and diverse group of *** high-quality dataset provided a benchmark against which a rapid calculation method could be *** accurate method was then used to measure the barrier heights for 6797 fluoride–ion *** final dataset has allowed us to discover many fascinating,high-performance conductors and to derive the design rules that govern their *** materials will accelerate experimental research into fluoride–ion batteries,while the design rules will provide an improved foundation for understanding ionic conduction.

关键词： fluoride dynamic repeatedly

pde2path – A Matlab Package for continuation and Bifurcation in 2d Elliptic Systems

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Numerical Mathematics(Theory,Methods and Applications) 2014年第1期7卷 58-106页

作者： Hannes Uecker daniel Wetzel Jens d.M.Rademacher Institut für Mathematik Universität Oldenburg26111 OldenburgGermany Universität Bremen Fachbereich MathematikPostfach 33044028359 BremenGermany

pde2path is a free and easy to use Matlab continuation/bifurcation package for elliptic systems of PdEs with arbitrary many components,on general two dimensional domains,and with rather general boundary *** package is based on the FEM of the Matlab pdetoolbox,and is explained by a number of examples,including Bratu’s problem,the Schnakenberg model,Rayleigh-Bénard convection,and von Karman plate *** serve as templates to study new problems,for which the user has to provide,via Matlab function files,a description of the geometry,the boundary conditions,the coefficients of the PdE,and a rough initial guess of a *** basic algorithm is a one parameter arclength-continuation with optional bifurcation detection and *** calculations,error control and mesh-handling,and some elementary timeintegration for the associated parabolic problem are also *** continuation,branch-switching,plotting etc are performed via Matlab command-line function calls guided by the AUTO *** software can be downloaded from ***/*** ker/pde2path,where also an online documentation of the software is provided such that in this paper we focus more on the mathematics and the example systems.

关键词： Elliptic systems continuation and bifurcation finite element method

Functional responses of cougars(Puma concolor)in a multiple prey-species system

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Integrative Zoology 2018年第1期13卷 84-93页

作者： Leroy SORIA-dÍAZ Mike SFOWLER Octavio MONROy-VILcHIS daniel ORO Institute of Applied Ecology Autonomous University of TamaulipasVictoria city TamaulipasMexico department of Biosciences Swansea UniversitySwanseaUK center for Research in Applied Biological Sciences Autonomous University of the State of MexicoCentro TolucaMexico Population Ecology Group Mediterranean Institute for Advanced Studies IMEDEA(CSIC-UIB)EsporlesMallorcaSpain

The study of predator-prey interactions is commonly analyzed using functional responses to gain an understanding of predation patterns and the impact they have on prey *** this,little is known about predator-prey systems with multiple prey species in sites near the *** we studied the functional response of cougars(Puma concolor)in relation to their main prey,armadillo(dasypus novemcinctus),coati(Nasua narica)and white-tailed deer(Odocoileus virginianus).Between 2004 and 2010,cougar scats were collected along 5 transects to estimate the consumption of different prey species.A relative abundance index(RAI)was calculated for each prey species and cougar using 18 camera *** compared Holling type I,II and III functional response models to determine patterns in prey consumption based on the relative abundance and biomass of each prey species *** 3 main prey species comprised 55%(armadillo),17%(coati)and 8%(white-tailed deer)of the *** I and II functional responses described consumption of the 2 most common prey species armadillos and coati similarly well,while a type I response best characterized consumption of white-tailed deer.A negative correlation between the proportions of armadillo versus coati and white-tailed deer biomass in cougar scats suggests switching to consume alternative prey,confirming high foraging plasticity of this *** work represents one of the few studies to compare functional responses across multiple prey species,combined with evidence for prey-switching at low densities of preferred prey.

关键词： cougar functional responses Holling model comparison multiple prey

Gastric polyps are not created equal: Know your enemy

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World Journal of Gastroenterology 2025年第2期31卷 144-146页

作者： Fady daniel department of Gastroenterology and Hepatology American University of Beirut Medical CenterBeirut 11072020Lebanon

Gastric polyps are commonly detected during upper gastrointestinal *** are most often benign and rarely become ***,adequate knowledge,diagnostic modalities,and management strategies should be the endoscopist’s readily available“weapons”to defeat the potentially malignant“enemies”.This article sheds light on the valuable effort by costa et al to generate a new classification system of gastric polyps as“good”,“bad”,and“ugly”.This comprehensive overview provides clinicians with a simplified decision-making process.

关键词： Gastric polyps Polypoid subepithelial lesions Early gastric cancer Endoscopic ultrasonography Electronic chromoendoscopy

Polyhydroxyurethanes from Biobased Monomers and cO_(2):A Bridge between Sustainable chemistry and cO_(2) Utilization

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chinese Journal of chemistry 2024年第6期42卷 652-685页

作者： Tharinee Theerathanagorn Tanika Kessaratikoon Hafeez Ur Rehman Valerio d'Elia daniel crespy VISTEc Advanced Laboratory for Environment-Related Inorganic and Organic Syntheses Department of Materials Science and EngineeringVidyasirimedhi Institute of Science and Technology21210Wang ChanRayongThailand department of Materials Science and Engineering Vidyasirimedhi Institute of Science and Technology21210Wang ChanRayongThailand

Polyhydroxyurethanes(PHUs)have received considerable attention in the last decade as potential alternatives to traditional phosgene-based polyurethanes(PUs).The development of suitable 5cc(five membered-ring cyclic carbonate)precursors bearing multiple carbonate moieties(multi-5ccs)is a key requisite for preparing PHUs by polyaddition reaction with bis-or *** sustainable PHUs from cO_(2)-based five-membered cyclic carbonates(5ccs)obtained from biobased epoxides is a valuable strategy to bridge cO_(2) utilization and the upcycling of renewable *** this context,while many multi-5cc monomers reported in the literature are oil-based,recent efforts have led to the development of a large variety of multifunctional 5ccs that are produced by the combination of cO_(2) and renewable resources such as fatty acids and vegetable oils,lignin,terpenes,and *** this work,recent crucial advances(2019—2023)on PHUs prepared from bis-and multi-5ccs produced from cO_(2) and(partially/potentially)biobased substrates are reviewed with respect to their synthesis,thermal and mechanical properties,and their recent,emerging applications.

关键词： cO_(2) conversion Polyhydroxyurethanes cyclic carbonates Biobased compounds Fatty acids Functional polymers Monomers Renewable resources

The role of extracorporeal life support and timing of repair in infants with congenital diaphragmatic hernia

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World Journal of Pediatric Surgery 2024年第2期7卷 90-99页

作者： daniel B Gehle Logan c Meyer Tim Jancelewicz Le Bonheur children's Hospital University of Tennessee Health Science CenterMemphisTennesseeUSA

Extracorporeal life support(EcLS)serves as a rescue therapy for patients with congenital diaphragmatic hernia(cdH)and severe cardiopulmonary failure,and only half of these patients survive to *** costly intervention has a significant complication risk and is reserved for patients with the most severe disease physiology refractory to maximal cardiopulmonary *** contraindications to EcLS do exist such as coagulopathy,lethal chromosomal or congenital anomaly,very preterm birth,or very low birth weight,but many of these limits are being evaluated through further *** guidelines from the past decade vary in recommendations for EcLS use in patients with cdH but this therapy appears to have a survival benefit in the most severe subset of *** outcomes have been observed for patients treated at high-volume *** review details the evolving literature surrounding management paradigms for timing of cdH repair for patients receiving preoperative *** recent data support early repair following cannulation to avoid non-repair which is uniformly fatal in this *** EcLS runs are associated with decreased survival,and patient physiology should guide EcLS weaning and eventual decannulation rather than limiting patients to arbitrary run *** of care across centers is a major focus to limit unnecessary costs and improve short-term and long-term outcomes for these complex patients.

关键词： congenital life repair

Network analysis to inform invasive species spread among lakes

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Journal of Oceanology and Limnology 2019年第3期37卷 1037-1041页

作者： EScOBAR Luis E. ROMERO-ALVAREZ daniel LARKIN daniel J. PHELPS Nicholas B. d. department of Fish and Wildlife conservation Virginia TechBlacksburgVirginiaUSA department of Ecology and Evolutionary Biology-Biodiversity Institute University of KansasLawrenceUSA department of Fisheries Wildlifeand Conservation BiologyUniversity of MinnesotaSt.PaulMinnesotaUSA Minnesota Aquatic Invasive Species Research center University of MinnesotaSt.PaulMinnesotaUSA

Often facilitated by human-mediated pathways,aquatic invasive species are a threat to the health and biodiversity of global *** present a novel approach incorporating survey data of watercraft movement in a social network analysis to reconstruct potential pathways of aquatic invasive species spread between *** an example,we use the green alga Nitellopsis obtusa,also known as starry stonewort,an aquatic invasive species affecting the Great Lakes region in the United States and *** movement of algal fragments via human-mediated pathways(i.e.,watercraft)has been hypothesized as the primary driver of starry stonewort *** used survey data collected at boat ramps during the 2013 and 2014 openwater seasons to describe the flow of watercraft from Lake Koronis,where *** was first detected in Minnesota,to other lakes in the *** results suggest that the risk of *** expansion is not highly constrained by geographic proximity and management efforts should consider highly connected *** human movement via network analysis may help to explain past and future routes of aquatic invasive species infestation between lakes and can improve evidence-based prevention and control efforts.

关键词： Nitellopsis obtusa starry stonewort lake network invasion

Prediction of pavement roughness using a hybrid gene expression programming-neural network technique

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Journal of Traffic and Transportation Engineering(English Edition) 2016年第5期3卷 448-455页

作者： Mehran Mazari daniel d.Rodriguez department of civil Engineering California State University Los Angeles department of civil Engineering The University of Texas at El Paso

Effective prediction of pavement performance is essential for transportation agencies to appropriately strategize maintenance, rehabilitation, and reconstruction of roads. One of the primary performance indicators is the international roughness index （IRI） which rep- resents the pavement roughness. correlating the pavement roughness to other perfor- mance measures has been under continuous development in the past decade. However, the drawback of existing correlations is that most of them are not practical yet reliable for prediction of roughness. In this study a novel approach was developed to predict the IRI, utilizing two data sets extracted from long term pavement performance （LTPP） database. The proposed methodology included the application of a hybrid technique which combines the gene expression programming （GEP） and artificial neural network （ANN）. The developed algorithm showed reasonable performance for prediction of IRI using traffic parameters and structural properties of pavement. Furthermore, estimation of present IRI from his- torical data was evaluated through another set of LTPP data. The second prediction model also depicted a reasonable performance power. Further extension of the proposed models including different pavement types, traffic and environmental conditions would be desir- ab]e in future studies.

关键词： International roughness index PavementGene expression programming Artificial neural network Long term pavement performance