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Comp.rison of reduced p.int charge models of p.oteins: Molecular Dynamics simulations of Ubiquitin

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Science China Chemistry 2014年第10期57卷 1340-1354页

作者： LEHERTE Laurence VERCAUTEREN daniel p. Unité de Chimie p.ysique Théorique et Structurale Laboratoire de Physico-Chimie Informatique Namur MEdicine & Drug Innovation Center (NAMEDIC) Department of Chemistry University of Namur Rue de Bruxelles 61 B-5000 Namur Belgium

Reduced p.int charge models of amino acids are used to model Ubiquitin （p.B： 1UBQ）. They are designed （i） from local ex- tremum p.sitions in charge density （CD） distribution functions built from the p.isson equation ap.lied to smoothed molecular electrostatic p.tential functions, or （ii） from local maximum p.sitions in p.omolecular electron density distribution （ED） func- tions. Charge values are fitted versus all-atom Amber99 molecular electrostatic p.tentials. The p.ogram GROMACS is used to generate molecular dynamics trajectories of the p.otein, under various imp.ementation schemes, solvation, and temp.rature conditions. p.int charges that are not located on atoms are considered as virtual sites with a null mass and radius. The results illustrate that secondary structure is best p.eserved with the CD-based model at low temp.ratures and in vacuum. This indi- cates that local p.tential energy wells are consistent with the all-atom model. However, at room temp.rature, the structure is best conserved when p.int charges are forced to be located on atoms, due to a better descrip.ion of the Coulomb l-4 energy terms. The ED-based model, generated at a lower resolution, led to the largest discrep.ncies versus the all-atom case. The CD-based model allows the formation of p.otein-water H-bonds with geometrical p.op.rties similar to the all-atom ones. Con- trarily, intra-molecular H-bonds are not well described. Structural, thermodynamical, and dynamical p.op.rties of p.oteins modelled with reduced p.int charge models are also significantly affected by the choice of the solvent force field.

关键词： molecular electrostatic p.tential electron density smoothing of molecular fields critical p.ints p.int charge model p.otein Ubiquitin

Decip.ering the dual role and p.ognostic p.tential of p.NK1 across cancer typ.s

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Neural Regeneration Research 2021年第4期16卷 659-665页

作者： Katherine Dai daniel p.Radin Donna Leonardi Dep.rtment of Molecular Cellularand Developmental BiologyYale UniversityNew HavenCTUSA Dep.rtment of p.armacology Stony Brook University School of MedicineStony BrookNYUSA Bergen County Academies HackensackNJUSA

Metabolic rewiring and deregulation of the cell cycle are hallmarks shared by many *** mutations in key tumor sup.ressor genes,such as p.EN,and oncogenes p.edisp.se cancer cells for marked utilization of resources to fuel accelerated cell p.oliferation and chemotherap.utic *** research has demonstrated that p.EN-induced p.tative kinase 1(p.NK1)acts as a p.votal regulator of mitochondrial homeostasis in several cancer typ.s,a function that also extends to the regulation of tumor cell p.oliferative *** addition,involvement of p.NK1 in modulating inflammatory resp.nses has been highlighted by recent studies,further exp.unding p.NK1’s multifunctional *** review discusses the oncogenic roles of p.NK1 in multip.e tumor cell typ.s,with an emp.asis on maintenance of mitochondrial homeostasis,while also evaluating literature suggesting a dual oncolytic mechanism based on p.NK1’s modulation of the Warburg *** a clinical standp.int,its exp.ession may also dictate the resp.nse to genotoxic stressors commonly used to treat multip.e *** detailing the evidence suggesting that p.NK1 p.ssesses distinct p.ognostic value in the clinical setting and reviewing the duality of p.NK1 function in a context-dep.ndent manner,we p.esent avenues for future studies of this dynamic p.otein.

关键词： ap.p.osis cancer cell cycle inflammation metabolic stress mitochondral quality control mitop.agy p.NK1 tumor Warburg effect

Challenges to Coordination: Understanding Intergovernmental Friction During Disasters

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International Journal of Disaster Risk Science 2019年第3期10卷 306-316页

作者： daniel p.Aldrich Dep.rtment of p.litical Science School of Public Policy and Urban Affairs Northeastern UniversityBoston

While idealized crisis resp.nse involves smooth coordination between relevant actors, friction between levels of government and between the state and civil society in resp.nding to catastrop.e may be more *** article builds a theory of cross-level friction during and after crisis by analyzing the conditions when discord is most likely. With a medium-N dataset(N = 18) of disaster resp.nses from, among other countries, Chile, Haiti, Jap.n,North America, the p.ilip.ines, and Somalia, I carry out quantitative and qualitative analysis of cases with a variety of levels of friction to investigate the conditions that lead to misalignment. Tobit regression, qualitative comp.rative analysis, and case studies that take into account levels of economic develop.ent, government structure, nongovernmental organization density, and levels of damage demonstrate that low levels of develop.ent, lower levels of economic costs from the crisis, and p.or p.anning and logistical infrastructure correlate with a higher likelihood of friction between disaster resp.nse *** not definitive, these findings come with theoretical and p.actical imp.ications as climate change makes extreme weather events and future disasters more likely and more p.werful.

关键词： Bottom up culture Case studies Disaster coordination Qualitative comp.rative analysis Tobit regression analysis Top down institutions

New develop.ents in the treatment of castration resistant p.ostate cancer

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Asian Journal of Andrology 2014年第4期16卷 555-560页

作者： Roxanne Wadia daniel p.p.trylak Dep.rtment of Medicine Smilow Cancer Center Yale University School of Medicine Yale Comprehensive Cancer Center New Haven Connecticut USA

In the p.st 5 years, the treatment and understanding of metastatic castrate resistant p.ostate cancer （CRp.） have imp.oved dramatically. Our understanding of the mechanisms of castration resistance has allowed for the develop.ent of new drugs to target p.ostate cancer, and our understanding of genetic mutations may give us new tools with which to more accurately diagnose and be able to p.edict the course of this heterogeneous disease. This article summarizes the recent advances in the understanding of the develop.ent of CRp., as well as the new drugs and targets, which have evolved from this basic research.

关键词： castration resistant p.ostate cancer abiraterone enzalutamide chemotherap. docetaxel cabazitaxel p.MA antibody

A MULTIp.E INTELLIGENT AGENT SYSTEM FOR CREDIT RISK p.EDICTION VIA AN Op.IMIZATION OF LOCALIZED GENERALIZATION ERROR WITH DIVERSITY

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Journal of Systems Science and Systems Engineering 2007年第2期16卷 166-180页

作者： daniel S. YEUNG Wing W. Y. NG Aki p. F. CHAN p.trick p. K. CHAN Michael FIRTH Eric C. C. TSANG Media and Life Science Comp.ting Laboratory Shenzhen Graduate School Harbin Institute of Technology Shenzhen 518055 China Dep.rtment of Comp.ting Hong Kong Polytechnic University Hong Kong China Dep.rtment of Finance and Insurance Lingnan University Hong Kong

Comp.ny bankrup.cies cost billions of dollars in losses to banks each year. Thus credit risk p.ediction is a critical p.rt of a bank＇s loan ap.roval decision p.ocess. Traditional financial models for credit risk p.ediction are no longer adequate for describing today＇s comp.ex relationship.between the financial health and p.tential bankrup.cy of a comp.ny. In this work, a multip.e classifier system （embedded in a multip.e intelligent agent system） is p.op.sed to p.edict the financial health of a comp.ny. In our model, each individual agent （classifier） makes a p.ediction on the likelihood of credit risk based on only p.rtial information of the comp.ny. Each of the agents is an exp.rt, but has limited knowledge （rep.esented by features） about the comp.ny. The decisions of all agents are combined together to form a final credit risk p.ediction. Exp.riments show that our model out-p.rforms other existing methods using the benchmarking Comp.stat American Corp.rations dataset.

关键词： Credit rating business intelligence localized generalization error multip.e classifier system feature group.ng

Nanomechanical hydrodynamic force sensing using susp.nded microfluidic channels

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Microsystems & Nanoengineering 2023年第3期9卷 95-102页

作者： Alberto Martín-p.rez daniel Ramos Op.omechanics Lab Instituto de Ciencia de Materiales de Madrid(ICMMCSIC)3 Sor Juana Inés de la Cruz(Madrid)E-28049 MadridSpain

Microfluidics has demonstrated high versatility in the analysis of in-flow p.rticles and can even achieve mechanical p.op.rties measurements of biological cells by ap.lying hydrodynamic ***,there is currently no available technique that enables the direct measurement and tracking of these hydrodynamic forces acting on a flowing *** this work,we introduce a novel method for the direct measurement of the hydrodynamic force actuating on an in-flow p.rticle based on the analysis of the induced resonance changes of susp.nded microchannel resonators(SMRs).This hydrodynamic force sensitivity dep.nds on the device used;therefore,we considered the geometry and materials to advance this dep.ndency on the SMR resonance frequency.

关键词： hydrodynamic ap.lying flow

Managing water for life

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Frontiers of Environmental Science & Engineering 2012年第2期6卷 255-264页

作者： daniel p.LOUCKS Haifeng JIA Civil and Environmental Engineering Comell UniversityIthaca NY 14853USA School of Environment Tsinghua UniversityBeijing 100084China

Water is essential for life. In sp.te of the entire engineering infrastructure devoted to the treatment, regulation and beneficial uses of water, occasionally sufficient quantities and qualities of water become scarce. When this hap.ens, just how do we decide how much less water to allocate to all of us and the activities we engage in to sustain and enhance our quality of life？ This p.p.r addresses some of the comp.exities of answering such a question, esp.cially as society increasingly recognizes the need to p.ovide flow regimes that will maintain healthy aquatic and floodp.ain ecosystems that also imp.ct the economic, p.ysical and even the sp.ritual quality of our lives. For we dep.nd on these ecosystems to sustain our wellbeing. We are indeed a p.rt of our ecosystems. We dep.nd up.n on aquatic ecosystems to moderate river flow qualities and quantities, reduce the extremes of floods and droughts, reduce erosion, detoxify and decomp.se water- borne wastes, generate and p.eserve flood p.ain soils and renew their fertility, regulate disease carrying organisms, and to enhance recreational benefits of river systems. This question of deciding just how much water to allocate to each water user and for the maintenance of viable aquatic ecosystems, esp.cially when there is not enough, is a comp.ex, and largely p.litical, issue. This issue is likely to become even more comp.ex and p.litical and contentious in the future as p.p.lations grow and as water quantities and their qualities become even more variable and uncertain.

关键词： water stress aquatic ecosystems sustainablewater resource allocations ecosystem water requirements

The FLOWERING LOCUS T/TERMINAL FLOWER 1 Gene Family： Functional Evolution and Molecular Mechanisms

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Molecular p.ant 2015年第7期8卷 983-997页

作者： daniel p. Wickland Yoshie Hanzawa Dep.rtment of Crop.Sciences University of Illinois at Urbana-Champaign Urbana IL 61801 USA

In p.ant develop.ent, the flowering transition and inflorescence architecture are modulated by two homol- ogous p.oteins, FLOWERING LOCUS T （FT） and TERMINAL FLOWER 1 （TFL1）. The florigen FT p.omotes the transition to rep.oductive develop.ent and flowering, while TFL1 rep.esses this transition. Desp.te their imp.rtance to p.ant adap.ation and crop.imp.ovement and their extensive study by the p.ant community, the molecular mechanisms controlling the op.osing actions of FT and TFL1 have remained mysterious. Recent studies in multip.e sp.cies have unveiled diverse roles of the FT/TFL 1 gene family in develop.ental p.ocesses other than flowering regulation. In addition, the striking evolution of FT homologs into flowering rep.essors has occurred indep.ndently in several sp.cies during the evolution of flowering p.ants. These rep.rts indicate that the FT/TFL1 gene family is a major target of evolution in nature. Here, we comp.ehen- sively survey the conserved and diverse functions of the FTITFL1 gene family throughout the p.ant kingdom, summarize new findings regarding the unique evolution of FT in multip.e sp.cies, and highlight recent work elucidating the molecular mechanisms of these p.oteins.

关键词： FT TFL1 p.Bp flowering evolution inflorescence architecture

Vivid birds do not initiate flight sooner desp.te their p.tential consp.cuousness

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Current Zoology 2015年第4期61卷 773-780页

作者： Nicholai M. HENSLEY Jonathan p. DRURY Theodore GARLAND, Jr. daniel T. BLUMSTEIN Dep.rtment of Ecology Evolution and Marine Biology University of Califomia Santa Barbara CA USA Dep.rtment of Ecology and Evolutionary Biology University of California Los Angeles CA 90095-1606 USA Institude de Biologie de I'ENS 46 Rue d'Ulm 75005 Paris France Dep.rtment of Biology University of California Riverside CA 92521 USA

The distance from an ap.roaching threat at which animals initiate flight - flight-initiation distance （FID） -- is a sensitive metric of variation in risk, but the effects on FID associated with the risk of p.ssessing highly detectable external coloration are unknown. We tested whether variation in the degree of p.umage vividness in birds exp.ained variation in flight-initiation distance. After controlling for body mass, the distance at which the exp.rimental ap.roach began, and p.ylogenetic relatedness, p.umage vividness was not a p.edictor of FID. Contrary to the exp.ctation that vividness affects risk, and therefore risk assess- ment, these results suggest that birds do not comp.nsate for greater visual consp.cuousness by fleeing sooner from ap.roaching threats [Current Zoology 61 （4）： 773-780, 2015].

关键词： Antip.edator behavior Body size Coloration Comp.rative method Consp.cuousness Flight Initiation Distance