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New real-time-PCR method to identify single point mutations in hepatitis C virus

World Journal of Gastroenterology 2016年第43期22卷 9604-9612页

作者： Qian Chen Irene Belmonte Maria Buti Leonardo Nieto damir garcia-cehic Josep Gregori Celia Perales Laura Ordeig Meritxell Llorens Maria Eugenia Soria Rafael Esteban Juan Ignacio Esteban Francisco Rodriguez-Frias Josep Quer Liver Unit Internal Medicine Lab. Malalties Hepàtiques Vall d’Hebron Institut Recerca-Hospital Universitari Vall d’ Hebron08035 Barcelona Spain Centro de Investigación Biomédica en Red Enfermedades Hepáticas y Digestivas Instituto de Salud Carlos Ⅲ28029 madrid Spain Liver Pathology Unit Departments of Biochemistry and Microbiology Hospital Universitari Vall d’Hebron Autonomous University of Barcelona 08035 Bareelona Spain Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas del Instituto de Salud Carlos Ⅲ 28029 Madrid Spain Universitat Autònoma de Barcelona 08193 Bareelona Spain

AIM To develop a fast, low-cost diagnostic strategy to identify single point mutations in highly variable genomes such as hepatitis C virus(HCV).METHODS In patients with HCV infection, resistance-associated amino acid substitutions within the viral quasispecies prior to therapy can confer decreased susceptibility to direct-acting antiviral agents and lead to treatment failure and virological relapse. One such naturally occurring mutation is the Q80 K substitution in the HCV-NS3 protease gene, which confers resistance to PI inhibitors, particularly simeprevir. Low-cost, highly sensitive techniques enabling routine detection of these single point mutations would be useful to identify patients at a risk of treatment failure. Light Cycler methods, based on real-time PCR with sequencespecific probe hybridization, have been implemented in most diagnostic laboratories. However, this technique cannot identify single point mutations in highly variable genetic environments, such as the HCV genome. To circumvent this problem, we developed a new method to homogenize all nucleotides present in a region except the point mutation of interest. RESULTS Using nucleotide-specific probes Q, K, and R substitutions at position 80 were clearly identified at a sensitivity of 10%(mutations present at a frequency of at least 10% were detected). The technique was successfully applied to identify the Q80 K substitution in 240 HCV G1 serum samples, with performance comparable to that of direct Sanger sequencing, the current standard procedure for this purpose. The new method was then validated in a Catalonian population of 202 HCV G1-infected individuals. Q80 K was detected in 14.6% of G1 a patients and 0% of G1 b in our setting. CONCLUSION A fast, low-cost diagnostic strategy based on real-time PCR and fluorescence resonance energy transfer probe melting curve analysis has been successfully developed to identify single point mutations in highly variable genomes such as hepatitis C virus. This

关键词： Hepatitis C virus Resistance-associated amino acid substitutions Low-cost test Single-point mutations Q80K

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Single molecule fluorescence fluctuations of the cyanine dyes linked covalently to DNA

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Science China Chemistry 2009年第8期52卷 1148-1153页

作者： AUMILER damir State Key Laboratory of Molecular Reaction Dynamics and Beijing National Laboratory for Molecular Sciences(BNLMS)Institute of ChemistryChinese Academy of Sciences Institute of Physics

The intersystem crossing and isomerization dynamics of free-Cy3,Cy3-ssDNA,free-Cy5 and Cy5-ssDNA are obtained through simple analysis of rapid on/off blinking from single molecule fluorescence intensity time-traces and the fluorescence correlation spectroscopy(FCS).The on-and off-times observed in fluorescence time traces of single cyanine dyes are due to the formation of the triplet state and isomerization,where both the interaction with DNA and long central polymethine chain of cyanine dyes increase the barriers of isomerization,leading to long *** results indicate that the single molecule fluorescence fluctuation together with the resulting second autocorrelation analysis are powerful methods for determining the triplet state and isomerization dynamics,which could be the simple techniques and complementary to other spectroscopic techniques,such as fluorescence decay measurement and laser flash photolysis to study the photophysical processes of complex molecules.

关键词： cyanine dyes single molecule spectroscopy on/off blinking fluorescence correlation spectroscopy(FCS)

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The roles of black phosphorus in performance enhancement of halide perovskite solar cells

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Journal of Energy Chemistry 2022年第4期31卷 672-683页

作者： damir Aidarkhanov Charles Surya Annie Ng Department of Electrical and Computer Engineering School of Engineering and Digital SciencesNazarbayev UniversityKabanbay Batyr Ave.53Nur-Sultan 010000Kazakhstan Innovation and Technology Commission Central Government Offices2 Tin Mei AvenueHong Kong 999077China

Hybrid organic-inorganic perovskite solar cells(PSCs) are considered to be the most promising thirdgeneration photovoltaic(PV) technology with the most rapid rate of increase in the power conversion efficiency(PCE). To date, their PCE values are comparable to the established photovoltaic technologies such as crystalline silicon. Intensive research activities associated with PSCs have been being performed,since 2009, aiming to further boost the device performance in terms of efficiency and stability via different strategies in order to accelerate the progress of commercialization. The emerging 2 D black phosphorus(BP) is a novel class of semiconducting material owing to its unique characteristics, allowing them to become attractive materials for applications in a variety of optical and electronic devices, which have been comprehensively reviewed in the literature. However, comprehensive reviews focusing on the application of BP in PSCs are scarce in the community. This review discusses the research works with the incorporation of BP as a functional material in PSCs. The methodology as well as the effects of employing BP in different regions of PSCs are summarized. Further challenges and potential research directions are also highlighted.

关键词： Perovskite solar cells Black phosphorus Power conversion efficiency Stability Low dimensional materials

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Multi-catenary isogeometric discretization with the sliding constraint

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Acta Mechanica Sinica 2021年第1期37卷 80-91,I0003页

作者： damir Sedlar Zeljan Lozina Andela Bartulovic Faculty of Electrical Engineering Mechanical Engineering and Naval Architecture University of Split21000SplitCroatia

The purpose of this paper is to present the formulation of isogeometric dynamic analysis with frictionless sliding constraint between two *** sliding condition at the constraint point is defined employing the augmented Lagrangian method,that specifies unique degree of freedom along sliding *** governing equations for the coupled system are derived in terms of Hamilton’s principle together with sliding constraint form differential algebraic equations of multi-catenary *** developed isogeometric approach is employed to discretize the catenaries what enables us to define the unique degree of freedom of sliding constraint along the whole catenary and thus avoid the process of searching for the sliding point as required in some other discretization techniques,*** element *** numerical examples are provided to validate the proposed method and the results are assessed against the results in the literature.

关键词： Isogeometric analysis Multi-catenary dynamics Large displacement Sliding constraint

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Acoustics of a viscoelastic medium with encapsulated bubbles

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Journal of Hydrodynamics 2021年第1期33卷 55-62页

作者： damir A.Gubaidullin Yuri V.Fedorov Laboratory of Continuum Mechanics Institute of Mechanics and EngineeringFRC Kazan Scientific CenterRussian Academy of SciencesKazanRussia

In this paper,a modified Rayleigh-Lamb equation is derived that takes into account the radial vibrations of a gas bubble coated with a viscoelastic shell and located in an elastic *** small oscillations of inclusion,the problem of heat exchange between a gas,a liquid phase,a viscoelastic shell,and an elastic medium is *** energy integral is *** the case of small disturbances,the dispersion relation is found from the Rayleigh-Lamb equations,energy,and the known wave equation for the bubbly *** analytical expression of the equilibrium speed of sound is written out and its dependence on the size of the viscoelastic shell and the disturbance frequency is *** example of a mixture of polydimethylsiloxane with air bubbles coated with a rubber shell illustrates the influence of the elasticity of the carrier medium and the shell of the bubbles on the dependence of the phase velocity and attenuation coefficient on the perturbation *** a mixture of water with air bubbles coated with a rubber shell,the influence of the dependences of the shear modulus and viscosity of butyl rubber on the frequency of disturbances at different temperature on the dispersion curves is shown.A comparison of the theory with experimental data is given.

关键词： Acoustic wave gas bubbles viscoelastic medium and shell shear modulus dispersion equation

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Molecular epidemiology and putative origin of hepatitis C virus in random volunteers from Argentina

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World Journal of Gastroenterology 2013年第35期19卷 5813-5827页

作者： Noemí del Pino José Raúl Oubia Francisco Rodríguez-Frías Juan Ignacio Esteban María Buti Teresa Otero Josep Gregori damir García-cehic Silvia Camos María Cubero Rosario Casillas Jaume Guàrdia Rafael Esteban Josep Quer Apunlab Laboratories Institute of Medical Microbiology and Parasitology (IMPAM) UBA-CONICET Department of MicrobiologyParasitology and Immunology Faculty of Medicine University of Buenos Aires CIBER de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos Ⅲ and Biochemistry Department Hospital Universitari Vall d’Hebrón (HUVH) CIBERehd del Instituto de Salud Carlos Ⅲ Autonomous University of Barcelona and Liver Unit Internal Medicine Lab. Malalties Hepatiques Vall d’Hebron Institut de Recerca (VHIR) Hospital Universitari Vall d’Hebrón (HUVH) Unitat de Diagnostic Molecular HUVH Liver Unit Internal Medicine Lab Malalties Hepatiques VHIR-HUVH Roche Diagnostics SL CIBERehd del Instituto de Salud Carlos Ⅲ Liver Unit Internal Medicine Lab MalaltiesHepatiques VHIR-HUVH Liver Unit and Biochemistry Department HUVH

AIM:To study the subtype prevalence and the phylogenetic relatedness of hepatitis C virus(HCV)sequences obtained from the Argentine general population,a large cohort of individuals was ***:Healthy Argentinian volunteers(n=6251)from 12 provinces representing all geographical regions of the country were *** parents or legal guardians of individuals younger than 18 years provided informed written consent for *** corresponding written permission from all municipal authorities was obtained from each city or town where subjects were to be *** RNA reverse transcription-polymerase chain reaction products were sequenced and phylogenetically *** 5’untranslated region(5’UTR)was used for RNA detection and initial genotype *** NS5B polymerase region,encompassing nt 8262-8610,was used for ***:An unexpectedly low prevalence of HCV infection in the general population(0.32%)was *** data contrasted with previous studies that reported rates ranging from 1.5%to 2.5%,mainly performed in selected populations of blood donors or vulnerable *** latter values are in keeping with the prevalence reported by the 2007 Argentinian HCV Consensus(approximately 2%).HCV subtypes weredistributed as follows:1a(25%),1b(25%),2c(25%),3a(5%),and 2j(5%).Two isolates ascribed either to genotype 1(5%)or to genotype 3(5%)by 5’UTR phylogenetic analysis could not be *** 1a sequences comprised a highly homogeneous population and clustered with United States ***1b sequences represented a heterogeneous population,suggesting that this genotype might have been introduced from different *** subtype 2c sequences clustered close to the 2c reported from Italy and Southern ***:HCV has a low prevalence of 0.32%in the studied general population of *** pattern of HCV introduction and transmission in Argentina appears to be a consequence of multiple events and different

关键词： Hepatitis C virus NS5B subtyping Molecular epidemiology Hepatitis C virus Argentina Hepatitis C virus 5’ untranslated region

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Transcranial photobiomodulation with near-infrared light:a promising therapeutic modality for Alzheimer's disease

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Neural Regeneration Research 2023年第9期18卷 1944-1945页

作者： Hanli Liu damir Nizamutdinov Jason H.Huang Bioengineering Department the University of Texas at ArlingtonArlingtonTXUSA Neurosurgery Neuroscience InstituteBaylor Scott and White HealthTempleTXUSA Neurosurgery College of MedicineTexas A&M UniversityTempleTXUSA

Transcranial photobiomodulation(tPBM) is a noninvasive neuromodulation technique that delivers near-infrared(NIR) light with low irradiance(i.e.,power density in mW/cm2) in the wavelength range of 800-1070 *** recently published books or collected literature(Hamblin,2019;GonzalezLima,2021) and papers(Nizamutdinov et al. 2022)offer comprehensive reviews of the mechanism of action and potential clinical translations of tPBM for the treatment of a variety of diseases,including neurodegenerative diseases(Alzheimer’s disease(AD),and Parkinson’s disease),traumatic brain injury.

关键词： Alzheimer diseases

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Flooding as a cause of ungulate mortality in floodplain forests in Croatia

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Journal of Forestry Research 2020年第3期31卷 1045-1052页

作者： damir Ugarkovic Nikica Sprem Nikolina Kelava Ugarkovic Milan Orsanic Department of Ecology and Silviculture Faculty of ForestryUniversity of ZagrebSvetosimunska 2510002 ZagrebCroatia Department of Fisheries BeekeepingGame Management and Special ZoologyFaculty of AgricultureUniversity of ZagrebSvetosimunska cesta 2510002 ZagrebCroatia Department of Animal Science and Technology Faculty of AgricultureUniversity of ZagrebSvetosimunska cesta 2510002 ZagrebCroatia

Floodplain forests with regular flooding regimes are the largest natural retentions areas in Croatia and are important as natural habitats for *** aim of this study was to determine the scale of mortality caused by flooding within these *** a 10-year period,data on ungulate mortality(red deer,roe deer and wild boar),flood duration and flooded surface area were *** study was conducted in primary(Posavske Sume—RET I)and secondary(Opeke II—RET II)retention areas within Lonjsko Polje Nature Park(Sava River region,Croatia).The longest flood period and the largest flooded surface area were recorded in RET *** ungulate mortality was749 individuals,with 482 individuals in RET I and 267 individuals in RET II,predominantly wild *** mortality did not differ by *** highest mortality of wild boar was recorded for the juvenile and yearling *** mortality of red and roe deer can be attributed to their body size and ecological *** in mortality between the primary and secondary retention areas corresponded to differences in flood regimes,flood column heights and micro relief *** both retention areas,wild boar mortality and flood duration,*** surface area,were positively *** the growth rate of the analysed ungulate populations was higher than the recorded mortality,no long-term effect of floods is expected on species abundance in these areas.

关键词： Floods Floodplain forests Mortality Red deer Roe deer Wild boar

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Magnetostructural Transition and Magnetocaloric Effect in Co-and Ga-doped MnNiSi Alloys

Magnetostructural Transition and Magnetocaloric Effect in Co...

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作者： Kasimov damir 南京理工大学

学位级别：硕士

The MnM'X-based(M' = Ni or Co,X = Ge or Si)intermetallic compounds have received considerable attention in recent years thanks to their tunable magnetostructural transitions and the associated large magnetocaloric *** a member of MnM'X family,stoichiometric MnNiSi alloy has some interesting structural and magnetic properties,which can result in sufficient flexibility for the design of magnetocaloric ***,MnNiSi-based systems cannot achieve stable magnetostructural coupling through the traditional methods,such as single element doping or applying *** the method of isostructural alloying,magnetostructural coupling has been successfully realized in some MnNiSi-based systems by binary element *** now are mainly focused on obtaining a wide temperature interval where magnetostructural coupling can take place and achieving a large associated magnetocaloric effect,which both are desired in practical *** this work,we decided to introduce Co and Ga atoms into MnNiSi matrix and analyze the structural and magnetic properties of several Mn-Co-Ni-Si-Ga polycrystalline alloys through the use of X-ray diffraction,differential scanning calorimetry and vibrating sample *** work includes study of structural properties,structural phase transition temperatures,annealing treatment,magnetic properties and magnetocaloric *** research has shown that the structural transition temperature of Mn1-yCoyNiSi1-xGax(y1 = 0.4,y2 = 0.5),Mno.7Coo.6Nio.7Si1-xGax,Mno.7Coo.7Nio.6Si1-xGax and Mn1-yCo2yNi1-ySi1-xGax(y1 = 0.25,y1 = 0.20,y3 = 0.15)alloys can be efficiently reduced from 1200 K to below room temperature with increasing the Ga content(x).In all studied systems increased substitution level of Co resulted in a stronger stabilization of high-temperature hexagonal *** studying Mn1-yCoyNiSi1-xGax(y1 = 0.4,0.030 ≤x1≤ 0.100;y2 = 0.5,0≤x2≤0.11)alloys,we found that introducing Co only at Mn sites is insufficient t

关键词： MnNiSi-based alloys phase structural transformation magnetostructural transition magnetocaloric effect Curie-temperature window

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Astrocytic calcium waves:unveiling their roles in sleep and arousal modulation

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Neural Regeneration Research 2024年第5期19卷 984-987页

作者： Erxi Wu Dan Qi damir Nizamutdinov Jason H.Huang Department of Neurosurgery and Neuroscience Institute Baylor Scott&White HealthTempleTXUSA Texas A&M University School of Medicine TempleTXUSA Texas A&M University School of Pharmacy College StationTXUSA LIVESTRONG Cancer Institutes and Department of Oncology Dell Medical Schoolthe University of Texas at AustinAustinTXUSA Department of Neurosurgery Baylor College of MedicineTempleTXUSA

Neuron-astrocyte interactions are vital for the brain’s *** astrocyte activities is crucial for comprehending the complex neural network,particularly the population-level functions of neurons in different cortical states and associated behaviors in *** on animal sleep and wakefulness have revealed distinct cortical synchrony patterns between ***,outnumbering neurons by nearly fivefold,support and regulate neuronal and synaptic *** research on astrocyte activation during cortical state transitions has emphasized the influence of norepinephrine as a neurotransmitter and calcium waves as key components of ion channel *** summary focuses on a few recent studies investigating astrocyte-neuron interactions in mouse models during sleep,wakefulness,and arousal levels,exploring the involvement of noradrenaline signaling,ion channels,and glutamatergic signaling in different cortical *** findings highlight the significant impact of astrocytes on large-scale neuronal networks,influencing brain activity and *** astrocytic signaling pathways shows promise for treating sleep disorders and arousal *** research is needed to understand astrocytic calcium signaling in different brain regions and its implications for dysregulated brain states,requiring future human studies to comprehensively investigate neuron-astrocyte interactions and pave the way for therapeutic interventions in sleep-and arousal-related disorders.

关键词： arousal astrocyte calcium waves locus coeruleus neuron-astrocyte interaction norepinephrine sleep wakefulness

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