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Comparison of reduced point charge models of proteins: 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 Physique 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 point charge models of amino acids are used to model Ubiquitin （PDb： 1UbQ）. They are designed （i） from local ex- tremum positions in charge density （CD） distribution functions built from the Poisson equation applied to smoothed molecular electrostatic potential functions, or （ii） from local maximum positions in promolecular electron density distribution （ED） func- tions. Charge values are fitted versus all-atom Amber99 molecular electrostatic potentials. The program GROMACS is used to generate molecular dynamics trajectories of the protein, under various implementation schemes, solvation, and temperature conditions. Point 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 preserved with the CD-based model at low temperatures and in vacuum. This indi- cates that local potential energy wells are consistent with the all-atom model. However, at room temperature, the structure is best conserved when point charges are forced to be located on atoms, due to a better description of the Coulomb l-4 energy terms. The ED-based model, generated at a lower resolution, led to the largest discrepancies versus the all-atom case. The CD-based model allows the formation of protein-water H-bonds with geometrical properties similar to the all-atom ones. Con- trarily, intra-molecular H-bonds are not well described. Structural, thermodynamical, and dynamical properties of proteins modelled with reduced point charge models are also significantly affected by the choice of the solvent force field.

关键词： molecular electrostatic potential electron density smoothing of molecular fields critical points point charge model protein Ubiquitin

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F4ESS-a framework for interdisciplinary data-driven earth system science

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International Journal of Digital Earth 2023年第1期16卷 3973-3986页

作者： Doris Dransch daniel Eggert Mike Sips Remote sensing and Geoinformatics Helmholtz Center Potsdam–German Research Center for GeosciencePotsdamGermany Geography Department Humboldt-University at BerlinBerlinGermany

Earth system science is an interdisciplinary effort to understand the fundamentals and interactions of environmental *** research is challenging since it demands the integration of scientific schemes and practices from different research fields into a collaborative work *** paper introduces the framework F4ESS that supports this integration.F4ESS provides methods and technologies that facilitate the development of integrative work environments for Earth system science.F4ESS enables scientists a)to outline structured and summarized descriptions of scientific procedures to facilitate communication and synthesis,b)to combine a large variety of distributed data analysis software into seamless data analysis chains and workflows,c)to visually combine and interactively explore the manifold spatiotemporal data and results to support understanding and knowledge *** F4ESS methods and technologies are generic and can be applied in various scientific *** discuss F4EsS in the context of the interdisciplinary investigation of flood events.

关键词： Earth system science interdisciplinary research scientific workflows integration

Interactions of primary neuroepithelial progenitor and brain endothelial cells: distinct effect on neural progenitor maintenance and differentiation by soluble factors and direct contact

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Cell Research 2007年第7期17卷 619-626页

作者： Miguel A Gama Sosa Rita De Gasperi Anne b Rocher Gissel M Perez Keila Simons daniel E Cruz Patrick R Hof Gregory A Elder Departments of Psychiatry Research and Development Service James J. Peters Department of Veterans Affairs Medical Center 130 West Kingsbridge Road Bronx New York 10468 USA Neuroscience Mount Sinai School of Medicine of New York University New York NY Department of Research and Development Service James J. Peters Department of Veterans Affairs Medical Center 130 West Kingsbridge Road Bronx New York 10468 USA

Neurovascular interactions are crucial for the normal development of the central nervous system. To study suchinteractions in primary cultures, we developed a procedure to simultaneously isolate neural progenitor and endothelialcell fractions from embryonic mouse brains. Depending on the culture conditions endothelial cells were found to favormaintenance of the neuroprogenitor phenotype through the production of soluble factors, or to promote neuronal differ-entiation of neural progenitors through direct contact. These apparently opposing effects could reflect differential cellularinteractions needed for the proper development of the brain.

关键词： differentiation culture endothelial cells neuroepithelial cells

Potential of roots and shoots of Napier grass for arresting soil erosion and runoff of mollisols soils of Himalayas

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International Soil and Water Conservation Research 2023年第3期11卷 538-548页

作者： Sushma Tamta Akhilesh Kumar daniel Prakash Kushwaha Krishi Vigyan Kendra Khodawandpur848202BegusaraiBiharIndia Department of Soiland Water Conservation Engineering G.B.Pant University of Agriculture and TechnologyPantnagar263145India

In this study, a soil filled Hydraulic Tilting Flume (HTF) was used as a test plot under simulated rainfallconditions. This flume was flled with mollisols soils (sandy loam in texture) collected from tarai regionof Himalayas. The effects of root and shoot characteristics of Napier grass in terms of leaf area index (LAI),shoot length (SL), number of leaves (NL), number of tillers (NT), shoot biomass (Sb), root density (RD),root length (RL), root biomass (Rb), and total biomass (Tb) were investigated on runoff and sedimentoutflow at 90, 120 and 150 days after planting (DAP). Four simulated rainfall intensities namely 4.0, 6.5,8.3 and 9.4 cm/h over three land slopes of 1, 2 and 3% were selected. Runoff samples collected fromwhole plant plot and only root plot were analyzed for runoff and sediment outflow. Findings revealedthat Napier grasses were very effective to reduce runoff and sediment outflow and its efficacy increasedwith the extended growth stages. The reduction in runoff and sediment outflow at 90, 120 and 150 DAPwas obtained as 56% and 85%, 68% and 90%, and 74% and 96%, respectively, as compared to bare plotconditions. It was observed that the comparative contribution of shoots in runoff rate reduction washigher than the roots. On the contrary, the root part of the plant showed more contribution in sedimentrate reduction as compared to the shoot part. Step wise regression was attempted for the selection ofeffective input parameters to establish authentic runoff and sediment outflow models. Power form ofmultiple non-linear regression (MNLR) showed very satisfactory results for predicting runoff and sedimentoutflow with coefficient of determination (R^(2)) as 97.4% and 99.0%, respectively, root mean squareerror (RMSE) as 38.8 cc/m^(2)/min and 0.126 g/m^(2)/min, respectively, and coefficient of efficiency (CE) as93.9% and 96.7%, respectively, during testing period.

关键词： Rootand shoot characteristics Runoff and sedimentreduction Simulated rainfall conditions Hydraulic tilting flume Step wise regression analysis

Identification of novel small-molecule inhibitors of SARS-CoV-2 by chemical genetics

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Acta Pharmaceutica Sinica b 2024年第9期14卷 4028-4044页

作者： Chris Chun-Yiu Chan Qian Guo Jasper Fuk-Woo Chan Kaiming Tang Jian-Piao Cai Kenn Ka-Heng Chik Yixin Huang Mei Dai bo Qin Chon Phin Ong Allen Wing-Ho Chu Wan-Mui Chan Jonathan daniel Ip Lei Wen Jessica Oi-Ling Tsang Tong-Yun Wang Yubin Xie Zhenzhi Qin Jianli Cao Zi-Wei Ye Hin Chu Kelvin Kai-Wang To Xing-Yi Ge Tao Ni Dong-Yan Jin Sheng Cui Kwok-Yung Yuen Shuofeng Yuan State Key Laboratory of Emerging Infectious Diseases Carol Yu Centre for InfectionDepartment of MicrobiologySchool of Clinical MedicineLi Ka Shing Faculty of Medicinethe University of Hong KongPokfulamHong Kong SAR 999077China Department of Infectious Diseases and Microbiology the University of Hong Kong-Shenzhen HospitalShenzhen 518000China Centre for Virology Vaccinology and TherapeuticsHong Kong Science and Technology ParkHong Kong SAR 999077China Academician Workstation of Hainan Province Hainan Medical University-the University of Hong Kong Joint Laboratory of Tropical Infectious DiseasesHaikou 571100China School of biomedical Sciences Li Ka Shing Faculty of Medicinethe University of Hong KongPokfulamHong Kong SAR 999077China NHC Key Laboratory of Systems biology of Pathogens Institute of Pathogen Biology Chinese Academy of Medical Sciences&Peking Union Medical CollegeBeijing 100730China College of biology Hunan Provincial Key Laboratory of Medical VirologyHunan UniversityChangsha 410082China

There are only eight approved small molecule antiviral drugs for treating *** them,four are nucleotide analogues(remdesivir,JT001,molnupiravir,and azvudine),while the other four are protease inhibitors(nirmatrelvir,ensitrelvir,leritrelvir,and simnotrelvir-ritonavir).Antiviral resistance,unfavourable drug‒drug interaction,and toxicity have been reported in previous *** there is a dearth of new treatment options for *** this work,a three-tier cell-based screening was employed to identify novel compounds with anti-SARS-CoV-2 *** compound,designated 172,demonstrated broad-spectrum antiviral activity against multiple human pathogenic coronaviruses and different SARS-CoV-2 variants of *** studies validated by reverse genetics showed that compound 172 inhibits the 3-chymotrypsin-like protease(3CLpro)by binding to an allosteric site and reduces 3CLpro dimerization.A drug synergistic checkerboard assay demonstrated that compound 172 can achieve drug synergy with nirmatrelvir in *** vivo studies confirmed the antiviral activity of compound 172 in both Golden Syrian Hamsters and K18 humanized ACE2 ***,this study identified an alternative druggable site on the SARS-CoV-23CLpro,proposed a potential combination therapy with nirmatrelvir to reduce the risk of antiviral resistance and shed light on the development of allosteric protease inhibitors for treating a range of coronavirus diseases.

关键词： SARS-CoV-2 High throughput screening broad-spectrum antiviral treatment 3CLpro inhibitor Allosteric-site inhibitor Animal models Chemical genetics Reverse genetics

Optical parameters induced by phase transformation in RF magnetron sputtered TiO2 nanostructured thin films

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Progress in Natural Science:Materials International 2014年第3期24卷 218-225页

作者： Prabitha b.Nair V.b.Justinvictor Georgi P.daniel K.Joy K.C.James Raju David Devraj Kumar P.V.Thomas Thin Film Lab Post Graduate and Research Department of Physics Mar Ivanios College 2. School of Physics University of Hyderabad Central University P. O. 3. College of Education Florida Atlantic University

Pure TiO2 thin films were deposited onto quartz substrates using a ceramic TiO2 target at an elevated substrate temperature of 573 K by RF magnetron sputtering, and an analysis of structural, optical and photoluminescence characteristics of the films upon phase transformation is reported in this paper. Structural investigations using X-ray diffraction revealed that the as-deposited film was amorphous in nature. Thermal annealing for 2 h at 873 K in air resulted in the formation of anatase phase, and a phase transformation to rutile was observed at 1073 *** increase in grain size and an improvement in crystallinity were also observed on annealing. Rod- like rutile crystallites were observed in the SEM images of the film annealed at 1273 K. As-deposited films and films annealed up to 1073 K were highly transparent in the visible region with a transparency 480%. Optical band gap of the films decreased upon thermal annealing which is attributed to phase transformation from amorphous to anatase and then to rutile. Optical parameters such as refractive index, optical conductivity and optical dielectric constant increased with increase in annealing temperature. Since rutile is the optically active phase, the superior refractive index of the film annealed at 1073 K along with its high transparency in visible region suggests the application of this film in antireflective coatings. Photoluminescence emission of maximum intensity was observed for the film annealed at 873 K, which exhibits anatase phase. Intense blue emission observed in this film makes it suitable for use in optoelectronic display devices.

关键词： RF magnetron sputtering TiO2thin films Dislocation density Optical conductivity Photoluminescence

Hepatotropic growth factors protect hepatocytes during inflammation by upregulation of antioxidative systems

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World Journal of Gastroenterology 2011年第17期17卷 2199-2205页

作者： Matthias Glanemann daniel Knobeloch Sabrina Ehnert Mihaela Culmes Claudine Seeliger daniel Seehofer Andreas K Nussler Department of General- Visceral-and Transplantation SurgeryCharitéCampus Virchow KlinikumUniversittsmedizin Berlin13353 BerlinGermany Department of Traumatology Klinikum rechts der IsarTechnische Universitt München81675 MunichGermany

AIM:To investigate effects of hepatotropic growth factors on radical production in rat hepatocytes during ***:Rat hepatocytes,isolated by collagenase perfusion,were incubated with a lipopolysaccharide(LPS)-containing cytokine mixture of interleukin-1β,tumor necrosis factor-α and interferon-γ to simulate sepsis and either co-incubated or pre-incubated with hepatotropic growth factors,*** growth factor,epidermal growth factor and/or transforming growth factor-α.Cells were analyzed for glutathione *** supernatants were assayed for produc-tion of reactive oxygen intermediates(ROIs) as well as NO2-,NO3-and *** determine cellular damage,release of aspartate aminotransferase(AST) into the culture medium was *** of nuclear factor(NF)-κb was measured by electrophoretic mobility shift ***:Rat hepatocytes treated with the LPS-containing cytokine mixture showed a significant increase in ROI and nitrogen oxide intermediate *** leakage was not significantly increased in cells treated with the LPS-containing cytokine mixture,independent of growth-factor ***,pretreatment with growth factors significantly reduced AST leakage and ROI formation while increasing cellular *** of growth factors did not result in increased NF-κb *** with growth factors further increased formation of NO2-,NO3-and S-nitrosothiols in hepatocytes stimulated with LPS-containing cytokine ***,we propose that,together with an increase in glutathione increased NO2-,NO3-formation might shift their metabolism towards non-toxic ***:Our data suggest that hepatotropic growth factors positively influence sepsis-induced hepatocellular injury by reducing cytotoxic ROI formation via induction of the cellular protective antioxidative systems.

关键词： Primary human hepatocytes Hepatocyte proliferation Cytokines Hepatotropic growth factors Nitric oxide Glutathione

Tinker,tailor,soldier,cell:the role of C-type lectins in the defense and promotion of disease

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Protein & Cell 2023年第1期14卷 4-16页

作者： James N.Arnold daniel A.Mitchell School of Cancer and Pharmaceutical Sciences King's College LondonLondon SE11ULUK Warwick Medical School University of WarwickCoventry CV22DXUK

C-type lectins(CTLs)represent a large family of soluble and membrane-bound proteins which bind calcium dependently via carbohydrate recognition domains(CRDs)to glycan residues presented on the surface of a variety of *** deconvolution of a cell’s glycan code by CTLs underpins several important physiological processes in mammals such as pathogen neutralization and opsonization,leukocyte trafficking,and the inflammatory ***,as our knowledge of CTLs has developed it has become apparent that the role of this innate immune family of proteins can be double-edged,where some pathogens have developed approaches to subvert and exploit CTL interactions to promote infection and sustain the pathological ***,CTL interactions with host glycoproteins can contribute to inflammatory diseases such as arthritis and cancer whereby,in certain contexts,they exacerbate inflammation and drive malignant *** review discusses the‘dual agent’roles of some of the major mammalian CTLs in both resolving and promoting infection,inflammation and inflammatory disease and highlights opportunities and emerging approaches for their therapeutic modulation.

关键词： C-type lectins DC-SIGN MbL selectins infection arthritis cancer

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Factors Associated with Mortality in Diabetic Patients with End-Stage Renal Failure Starting Emergency Hemodialysis

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Open Journal of Nephrology 2024年第1期14卷 17-24页

作者： Gaël Honal Mahoungou daniel Tony Eyeni Sinomono Farel Elilié Mawa Ongoth Éric Ngandzali-Ngabé Nestor Andzouana Raissa Laure Mayanda Aymande Okoumou-Moko Francky Ambounou Précieux Ngoma berline Ndinga Héléna botokoto bothard Hardy Ibovi Richard Loumingou Department of Nephrology University Hospital of Brazzaville Brazzaville Congo Faculty of Health Sciences University Marien Ngouabi Brazzaville Congo Department of Metabolic Diseases University Hospital of Brazzaville Brazzaville Congo

background: Diabetic nephropathy is the leading cause of end-stage chronic kidney disease with poor prognosis in resource-limited settings. This study aimed to determine factors associated with mortality in patients starting dialysis treatment for end-stage chronic renal disease in an emergency context. Patients and Methods: This was a retrospective study from January 2020 to December 2022 at CHU-b. Data from 79 diabetic patients requiring emergency dialysis were compared with those of 79 non-diabetic patients with an end-stage renal disease requiring emergency dialysis. Data were collected from the Nephrology Department registry. We studied their initial clinical and biological profiles and factors related to mortality. Results: Out of 545 compiled records, 79 diabetic chronic kidney disease patients needing dialysis were included (group 1). A control group of 79 non-diabetic chronic kidney disease patients requiring emergency dialysis was also included (group 2). The average age of patients was 53.5 ± 17 years, and the duration of diabetes at dialysis initiation was 14.8 ± 4.3 years. Twenty-three percent were hypertensive. Fifty-two percent of patients experienced intra-dialytic hypotension. Death occurred in 22% of patients. Results show that age (adjusted OR 1.955;CI: 1.025 - 1.086;p-value: Conclusion: Emergency dialysis in diabetics is associated with unfavorable outcomes in terms of mortality. Despite follow-up, renal involvement remains poorly explored, emphasizing the need for physician awareness.

关键词： Diabetic Nephropathy Emergency Dialysis Republic of the Congo