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Identifying Novel Drug targets by iDtPnd:A Case Study of Kinase Inhibitors

Genomics, Proteomics & Bioinformatics 2021年第6期19卷 986-997页

作者： Hammad Naveed Corinna Reglin thomas Schubert Xin Gao stefan t.arold Michael L.Maitland toyota technological Institute at Chicago ChicagoIL 60637USA Department of Computer Science National University of Computer and Emerging SciencesIslamabad 44000Pakistan 2bind GmbH D-93053 RegensburgGermany King Abdullah University of Science and technology(KAUSt) Computational Bioscience Research Center(CBRC)ComputerElectrical and Mathematical Sciences and Engineering(CEMSE)DivisionThuwal 23955Saudi Arabia King Abdullah University of Science and technology(KAUSt) Computational Bioscience Research Center(CBRC)Biological and Environmental Sciences and Engineering(BESE)DivisionThuwal 23955Saudi Arabia Inova Center for Personalized Health and Schar Cancer Institute Falls ChurchVA 22042USA University of Virginia Cancer Center AnnandaleVA 22003USA

Current FDA-approved kinase inhibitors cause diverse adverse effects,some of which are due to the me-chanism-independent effects of these *** these mechanism-independent interactions could improve drug safety and support drug ***,we develop iDtPnd(integrated Drug target Predictor with negative dataset),a computational approach for large-scale discovery of novel targets for known *** a given drug,we construct a positive structural signature as well as a negative structural signature that captures the weakly conserved structural features of drug-binding *** facilitate assessment of unintended targets,iDtPnd also provides a docking-based interaction score and its statistical *** confirm the interactions of sorafenib,imatinib,dasatinib,sunitinib,and pazopanib with their known targets at a sensitivity of 52%and a specificity of 55%.We also validate 10 predicted novel targets by using in vitro *** results suggest that proteins other than kinases,such as nuclear receptors,cytochrome P450,and MHC class I molecules,can also be physiologically relevant targets of kinase *** method is general and broadly applicable for the identification of protein–small molecule interactions,when sufficient drug–target 3D data are *** code for constructing the structural signatures is available at https://***/Documents/***.

关键词： Protein-drug interaction iDtPnd Kinase inhibitor Drug-binding site signature Drug repurposing

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QAUSt:Protein Function Prediction Using Structure Similarity,Protein Interaction,and Functional Motifs

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Genomics, Proteomics & Bioinformatics 2021年第6期19卷 998-1011页

作者： Fatima Zohra Smaili Shuye tian Ambrish Roy Meshari Alazmi stefan t.arold Srayanta Mukherjee P.Scott Hefty Wei Chen Xin Gao Computational Bioscience Research Center(CBRC) ComputerElectrical and Mathematical Sciences and Engineering(CEMSE)DivisionKing Abdullah University of Science and Technology(KAUST)Thuwal 23955Saudi Arabia Department of Biology Southern University of Science and Technology of China(SUSTC)Shenzhen 518055China Department of Computational Medicine and Bioinformatics University of MichiganAnn ArborMI 48109USA College of Computer Science and Engineering University of Ha’ilHa'il 55476Saudi Arabia Biological and Environmental Sciences and Engineering(BESE)Division King Abdullah University of Science and Technology(KAUST)Thuwal 23955Saudi Arabia Department of Molecular Bioscience University of KansasLawrenceKS 66047USA

the number of available protein sequences in public databases is increasing ***,a sig-nificant percentage of these sequences lack functional annotation,which is essential for the understanding of how bio-logical systems ***,we propose a novel method,Quantitative Annotation of Unknown Structure(QAUSt),to infer protein functions,specifically Gene Ontology(GO)terms and Enzyme Commission(EC)*** uses three sources of information:structure information encoded by global and local structure similarity search,biological network information inferred by protein–protein interaction data,and sequence information extracted from functionally discriminative sequence *** three pieces of information are combined by consensus averaging to make the final *** approach has been tested on 500 protein targets from the Critical Assessment of Functional Annotation(CAFA)benchmark *** results show that our method provides accurate functional annotation and outperforms other prediction methods based on sequence similarity search or *** further demonstrate that a previously unknown function of human tripartite motif-containing 22(tRIM22)protein predicted by QAUSt can be experimentally validated.

关键词： Protein function prediction GO term EC number Protein structure similarity Functionally discriminative motif

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In situ characterization of particle formation in spray flame synthesis using wide-angle light scattering

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Particuology 2024年第3期86卷 304-312页

作者： Simon Aβmann Franz J.t.Huber stefan Will Lehrstuhl für technische thermodynamik(Ltt) Friedrich-Alexander-Universitat Erlangen-Nürnberg(FAU)Erlangen91058Germany Erlangen Graduate Schoolin Advanced Optical technologies(SAOt) Friedrich-Alexander-Universitat Erlangen-Nurnberg(FAU)Erlangen91052Germany Competence Unit Engineering of Advanced Materials(EAM) Friedrich-Alexander-Universitat Erlangen-Nürnberg(FAU)Erlangen91052Germany

Wide-angle light scattering(WALS)was used for in situ measurements of droplet and nanoparticle size distributions during the synthesis of titania and iron oxide particles from liquid precursor solutions in the standardized SpraySyn burner for spray flame *** was synthesized from titanium tetraisopropoxide(ttIP)and iron oxide from iron(II)nitrate nonahydrate(INN)using ethanol(EtOH)as *** images were taken at heights up to 120 mm above the burner surface and classified into droplet and particle *** size distributions were derived from a sequential analysis of scattering data containing the oscillating Mie pattern,the lognormal size distribution parameters for spherical and fractal particle fractions from a multivariate approach on averaged particle scattering *** results show that the precursor addition leads to altered evaporation behavior and even droplet disruption probably induced by puffing or micro-explosions compared to pure *** the case of ttIP(a hygroscopic alkoxide),the synthesis of a large fraction of spheres was observed,while the nitrate INN leads to the formation of mostly fractal aggregates.

关键词： Spray flame synthesis Metal oxide particles Elastic light scattering Droplet size distribution Nanoparticle morphology Particle size distribution

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Getting the Most Out of Every training Day: the Influence of Instructors on Self-Regulated Learning During Firefighter Leadership Courses

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International Journal of Disaster Risk Science 2024年第3期15卷 332-345页

作者： stefan R?seler Micha Hilbert Guido Hertel Meinald t.thielsch Department of Psychology University of Münster

Leadership courses in the fire services are highly challenging, and they can seriously exhaust trainees and hamper their selfregulated learning efforts(for example, setting goals, focusing attention, seeking feedback). We theorize that experiences of failure or overload can curtail trainees' available energy resources on subsequent training days, which, in turn, should affect trainees' learning efforts. Given instructors' central role in leadership courses, we hypothesize that supportive and humble instructor behaviors decrease experiences of failure and overload and, thus, increase self-regulated learning. Moreover, we argue that supportive instructor behavior may amplify the positive effects of high energy resources, while humble behavior may alleviate the negative impact of low resource levels. We tested preregistered hypotheses with 118 firefighters participating in two-week leadership courses at a German fire academy. the participants completed short web-based questionnaires before and after classes each day. Multilevel analyses confirmed that perceived daily supportive and humble instructor behavior predicted trainees' reports of daily self-regulated learning activity. Notably, this effect was independent from positive effects of trainees' reported energy resources in the morning. Supportive and humble behavior did not moderate the eff ect of energy resources. Our findings suggest that instructors play a crucial role in facilitating effective learning under challenging training conditions. Furthermore, we offer implications for leaders in fire services, who often conduct trainings with their subordinates.

关键词： Diary study Fire services Instructor behavior Leadership training Resource investment

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Experimental investigation on slip conditions during thread rolling with flat dies

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Friction 2024年第1期12卷 136-143页

作者： stefan VOLZ Peter GROCHE Institute for Production Engineering and Forming Machines Technical University DarmstadtOtto-Berndt Straße 2Darmstadt 64287Germany

the process design of flat die rolling operations can be a tedious and costly process due to the challenges posed by small process *** this work,an effort is made to closely investigate and understand the process limits caused by excessive slippage of the *** measurements are carried out to capture the characteristics of excessive slippage and the influence of the stroke rate and the tribological system on this process *** differences in slippage were observed,depending on the tribological *** systems with polymer based lubricants showed excessive slippage at low stroke rates,systems using oil or no lubricant endured higher stroke rates before process limits were *** optical measurements revealed three major forms of slippage:successful rolling without slippage,failure due to excessive slippage at process start,and failure due to excessive slippage at around one workpiece rotation.

关键词： rolling incremental forming thread rolling slippage profile rolling

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the big data challenge-and how polypharmacology supports the translation from pre-clinical research into clinical use against neurodegenerative diseases and beyond

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Neural Regeneration Research 2024年第8期19卷 1647-1648页

作者： Sven Marcel stefan Muhammad Rafehi Drug Development and Chemical Biology Lübeck Institute of Experimental Dermatology(LIED)University of Lübeck and University Medical Center Schleswig-HolsteinLübeckGermany Department of Pathology Section of NeuropathologyTranslational Neurodegeneration Research and Neuropathology LabUniversity of Oslo and Oslo University HospitalOsloNorway School of Medical Sciences Faculty of Medicine and HealthUniversity of SydneySydneyNSWAustralia Institute of Clinical Pharmacology University Medical Center GöttingenGöttingenGermany Department of Medical Education Augsburg University MedicineAugsburgGermany

Introductory comments:the identification and validation of disease-modifying proteins are fundamental aspects in drug ***,the m ultifactority of n eurodegen era tive diseases poses a real challenge for targeted ***,the behavior of individually(over-)expressed to rget proteins in vitro is likely to differ from their actual functional behavior when embedded in cascades and pathways in vivo.

关键词： translation beyond likely

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Implementation and validation of a bonded particle model to predict rheological properties of viscoelastic materials

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Particuology 2024年第6期89卷 198-210页

作者： Michael Mascara Arno Mayrhofer stefan Radl Christoph Kloss Institute of Process and Particle Engineering Graz University of TechnologyInffeldgasse 13Graz8010Austria DCS Computing GmbH Industriezeile 35Linz4020Austria

this work focuses on implementing a particle-based method able to characterize viscoelastic materials whose rheological properties,such as storage modulus G′and loss modulus G″,are *** is based on the bonded particle model,with the elastic constitutive relation here substituted with a viscoelastic one to capture time-scale *** Burgers model,vastly used in literature to model viscoelastic systems,is discretized and *** test case used for calibration comprises of a cubic lattice,sheared with a periodic motion,to mimic the effect of a shear *** appropriate filtering of the stress response,the rheological properties are obtained,highlighting the effect of the lattice geometry,as well as the particle size,on the accuracy of the ***,the Burgers parameters are calibrated by analytically fitting the experimental dataset,showing the limitation of the Burgers *** micro-contact parameters are obtained from the macro parameters through appropriate *** completing a frequency sweep,the simulated G′and G″show a relatively large error,around 25%for G’for *** this reason,a more robust model,namely the generalized Maxwell model,has been *** calibration procedure is performed in the same fashion as for the Burgers ***,the tangential micro-contact parameters are scaled *** normal *** scaling parameter,calledα,is calibrated by minimizing the root mean square error between simulation and experimental data,giving errors below 10%in both G′and G″for a large ***,a full ring plate-plate rheometer setup is simulated,and the simulation is compared with the given experimental dataset,again finding a good agreement.

关键词： DEM Rheology Numerical modeling Viscoelasticity

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Artificial intelligence analysis of videos to augment clinical assessment:an overview

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Neural Regeneration Research 2024年第4期19卷 717-718页

作者： David C.Wong stefan Williams University of Leeds Leeds teaching Hospitals trust LeedsUK

Observation is a fundamental part of the practice of clinical *** of movement is particularly important for the *** such as Parkinson’s disease,multiple sclerosis,stroke,epilepsy,and many others affect a person’s movement in characteristic *** some conditions,changes in the patient’s voice can be included in this-changes in sound caused by changes in the movements of *** clinician’s detection of a characteristic abnormality,and their judgment of its severity,plays a central role in both diagnosis and the assessment of prognosis or response to ***,that practice depends upon a limited resource of experienced *** addition,these experts are limited by human visual judgment,which cannot reliably or precisely detect and measure small or subtle changes in movement(Williams et al.,2023).

关键词： clinical epilepsy diagnosis

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theoretical investigation on axial cyclic performance of monopile in sands using interface constitutive models

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Journal of Rock Mechanics and Geotechnical Engineering 2024年第7期16卷 2645-2662页

作者： Pan Zhou Jingpei Li Kaoshan Dai stefan Vogt Seyedmohsen Miraei Department of Geotechnical Engineering Tongji UniversityShanghai200092China Department of Civil Geo and Environmental EngineeringTechnical University of MunichFranz-Langinger-Str.10München81245Germany Department of Civil Engineering Sichuan UniversityChengdu610065China

Cyclic loads generated by environmental factors,such as winds,waves,and trains,will likely lead to performance degradation in pile foundations,resulting in issues like permanent displacement accumulation and bearing capacity *** paper presents a semi-analytical solution for predicting the axial cyclic behavior of piles in *** solution relies on two enhanced nonlinear load-transfer models considering stress-strain hysteresis and cyclic degradation in the pile-soil *** parameters are calibrated through cyclic shear tests of the sand-steel interface and laboratory geotechnical testing of sands.A novel aspect involves the meticulous formulation of the shaft loadtransfer function using an interface constitutive model,which inherently inherits the interface model’s advantages,such as capturing hysteresis,hardening,degradation,and particle *** semi-analytical solution is computed numerically using the matrix displacement method,and the calculated values are validated through model tests performed on non-displacement and displacement piles in *** results demonstrate that the predicted values show excellent agreement with the measured values for both the static and cyclic responses of piles in *** displacement pile response,including factors such as bearing capacity,mobilized shaft resistance,and convergence rate of permanent settlement,exhibit improvements compared to non-displacement piles attributed to the soil squeezing *** methodology presents an innovative analytical framework,allowing for integrating cyclic interface models into the theoretical investigation of pile responses.

关键词： Piles Cyclic degradation Load-transfer models Interface constitutive model Semi-analytical solution Model tests

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Quality assessment of surgery for colorectal cancer:Where do we stand?

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World Journal of Gastrointestinal Surgery 2024年第4期16卷 982-987页

作者： stefan Morarasu Cristian Livadaru Gabriel-Mihail Dimofte the Second Department of Surgical Oncology Regional Institute of OncologyIasi 707483Romania

Quality assurance in surgery has been one of the most important topics of debate among colorectal surgeons in the past *** has produced new surgical standards that led in part to the impressive oncological outcomes we see in many units *** mesorectal excision,complete mesocolic excision(CME),and the Japanese D3 lymphadenectomy are now benchmark techniques embraced by many surgeons and widely recommended by surgical ***,there are still ongoing discrepancies in outcomes largely based on surgeon *** is one of the main reasons why many countries have shifted colorectal cancer surgery only to high volume *** markers of surgical quality is thus a perquisite to ensure that standards and oncological outcomes are met at an institutional *** the evolution of CME surgery,various quality markers have been described,mostly based on measurements on the surgical specimen and lymph node yield,while others have proposed radiological markers(*** stumps)measured on postoperative scans as part of the routine cancer *** is no ideal marker;however,taken together and assembled into a new score or set of criteria may become a future point of reference for reporting outcomes of colorectal cancer surgery in research studies and defining subspecialization requirements both at an individual and hospital level.

关键词： Colorectal cancer Colon surgery Arterial stump Complete mesocolic excision Surgical quality

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