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Glycoproteogenomics: Setting the Course for next-generation Cancer neoantigen Discovery for Cancer Vaccines

Genomics, Proteomics & Bioinformatics 2021年第1期19卷 25-43页

作者： José Alexandre Ferreira Marta Relvas-Santos andreia Peixoto andréM.n.Silva Lúcio Lara Santos Experimental Pathology and Therapeutics Group Portuguese Institute of OncologyPorto 4200-072Portugal Institute of Biomedical Sciences Abel Salazar University of PortoPorto 4050-313Portugal Porto Comprehensive Cancer Center(P.ccc) Porto 4200-072Portugal REQUIMTE-LAQV Department of Chemistry and BiochemistryFaculty of Sciences of the University of PortoPorto 4169-007Portugal

Molecular-assisted precision oncology gained tremendous ground with high-throughput next-generation sequencing(nGS),supported by robust *** quest for genomicsbased cancer medicine set the foundations for improved patient stratification,while unveiling a wide array of neoantigens for *** pre-clinical and clinical studies have successfully used tumor-specific peptides in vaccines with minimal off-target ***,the low mutational burden presented by many lesions challenges the generalization of these solutions,requiring the diversification of neoantigen *** utilizing customized databases for protein annotation by mass spectrometry(MS)is a powerful tool toward this *** the concept toward exploring proteoforms originated from post-translational modifications(PTMs)will be decisive to improve molecular subtyping and provide potentially targetable functional nodes with increased cancer *** through the path of systems biology,we highlight that alterations in protein glycosylation at the cell surface not only have functional impact on cancer progression and dissemination but also originate unique molecular fingerprints for targeted ***,we discuss the outstanding challenges required to accommodate glycoproteomics in oncoproteogenomics *** envisage that such rationale may flag a rather neglected research field,generating novel paradigms for precision oncology and immunotherapy.

关键词： Glycoproteogenomics Oncoproteogenomics Cancer neoantigens Glycosylation Precision oncology

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Cyano-containing ionic liquids for the extraction of aromatic hydrocarbons from an aromatic/aliphatic mixture

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Science China Chemistry 2012年第8期55卷 1488-1499页

作者： MEInDERSMA G. Wytze DE HAAn andré B. Department of Chemical Engineering & Chemistry Eindhoven University of Technology

Ionic liquids can replace conventional solvents in aromatic/aliphatic extractions, if they have higher aromatic distribution coef- ficients and higher or similar aromatic/aliphatic selectivities. Also physical properties, such as density and viscosity, must be taken into account if a solvent is applied in an industrial extraction process. Cyano-containing ionic liquids have a lower den- sity than the benchmark solvent sulfolane and a higher viscosity. Sulfolane is from a hydrodynamic point of view a better sol- vent than ionic liquids for the aromatic/aliphatic extraction. The most suitable ionic liquids for the extraction of aromatic hy- drocarbons from a mixture of aromatic and aliphatic hydrocarbons are [bmim]C(Cn)3, [3-mebupy]n(Cn)2, [3-mebupy]C(Cn)3, [3-mebupy]B(Cn)4 and [mebupyrr]B(Cn)4. They have factors of 1.2-2.3 higher mass-based distribution coefficients than sul- folane and a similar or higher, up to a factor of 1.9 higher, aromatic/aliphatic selectivity than sulfolane. The IL [3-mebupy]n(Cn)2 is a better extractant for the separation of toluene from a mixture of toluene/n-heptane in a pilot plant Ro- tating Disc Contactor (RDC) than sulfolane.

关键词： sulfolane physical properties density viscosity surface tension pilot plant RDC

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Engineering of immunoinstructive extracellular matrices for enhanced osteoinductivity

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Bioactive Materials 2023年第6期24卷 174-184页

作者： andrés García-García Sébastien Pigeot Ivan Martin Department of Biomedicine University Hospital BaselUniversity of Basel4031BaselSwitzerland Department of Biomedical Engineering University of Basel4123AllschwillSwitzerland

The increasing recognition of the contribution of the immune system to activate and prime regeneration implies that tissue engineering strategies and biomaterials design should target regulation of early immunological *** previously proposed the cell-based engineering and devitalization of extracellular matrices(ECMs)as a strategy to generate implant materials delivering custom-defined ***,in the context of bone regeneration,we aimed at enhancing the osteoinductivity of such ECMs by enriching their immunomodulatory factors *** with IL1βa cell line overexpressing BMP-2 enabled engineering of ECMs preserving osteoinductive signals and containing larger amounts of angiogenic(VEGF)and pro-inflammatory molecules(IL6,IL8 and MCP1).Upon implantation,these IL1β-induced materials enhanced processes typical of the inflammatory phase(e.g.,vascular invasion,osteoclast recruitment and differentiation),leading to‘regenerative’events(e.g.,M2 macrophage polarization)and ultimately resulting in faster and more efficient bone *** results bear relevance towards the manufacturing of potent off-the-shelf osteoinductive materials and outline the broader paradigm of engineering immunoinstructive implants to enhance tissue regeneration.

关键词： Immunomodulation Bone tissue engineering Inflammation Hypertrophic cartilage matrices Osteoinduction

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Laser Measurements in High Speed Compressors for Rotor-Stator Interaction Analysis

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Journal of Thermal Science 2003年第4期12卷 310-317,309页

作者： Xavier Ottavy Isabelle Trébinjac andré Vouillarmet David Arnaud Laboratoire de Mecanique des Fluides et d'Acoustique UMR CNRS 5509/ECL/UCB Lyon I Ecole Centrale de Lyon 36 Avenue Guy de Collongue 69134 ECULLY Cedex France

This paper deals with the experimental quantification of the unsteady effects of the interactions between rotor and stator rows in high speed compressors. Due to the fact that the levels of the periodic fluctuations arising from the unsteady interaction may be low compared with the random fluctuations arising from the measurement uncertainties, it is crucial to minimize the errors inherent to the used technique. The first part of the paper concentrates on technical details relative to the experimental process. The second part is devoted to the data post-processing. Two tools for analysing the rotor-stator interactions are presented. The first tool is based on a decomposition of the flow field which was initially introduced to solve numerical problems when attempting to calculate the flow field in a multi-row configuration. The second tool is based on a spectral analysis of the signal, that qualifies the interaction in a sense of circumferential spinning lobes. Experimental results obtained within both an axial and a centrifugal high speed compressors are used to illustrate the data processing. In both cases, the effects of the unsteady interaction are quantified.

关键词： laser anemometry high speed compressor rotor-stator interaction.

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Trends in lactose-derived bioactives:synthesis and purification

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Systems Microbiology and Biomanufacturing 2022年第3期2卷 393-412页

作者： Carlos Vera Cecilia Guerrero andrés Illanes Department of Biology Faculty of Chemistry and BiologyUniversidad de Santiago de Chile(USACH)SantiagoChile School of Biochemical Engineering Pontificia Universidad Católica de Valparaíso(PUCV)ValparaisoChile

Lactose obtained from cheese whey is a low value commodity despite its great potential as raw material for the production of bioactive *** them,prebiotics stand out as valuable ingredients to be added to food matrices to build up functional foods,which currently represent the most active sector within the food *** foods market has been growing steadily in the recent decades along with the increasing awareness of the World population about healthy nutrition,and this is having a strong impact on lactose-derived *** of them are produced by enzyme biocatalysis because of molecular precision and environmental sustainability *** current status and outlook of the production of lactose-derived bioactive compounds is presented with special emphasis on downstream operations which are critical because of the rather modest lactose conversion and product yields that are *** though some of these products have already an established market,there are still several challenges referring to the need of developing better catalysts and more cost-effective downstream operations for delivering high quality products at affordable *** technological push is expected to broaden the spectrum of lactose-derived bioactive compounds to be produced at industrial scale in the near future.

关键词： Prebiotic Lactose β-Galactosidase Oligosaccharide purification

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Anthropomorphism Indexes of the Kinematic Chain for Artificial Hands

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Journal of Bionic Engineering 2020年第3期17卷 501-511页

作者： Immaculada Llop-Harillo Antonio Pérez-González Javier andrés-Esperanza Grupo de Biomecdnicay Ergonomia Departamento de Ingenieria Mecdnicay Construccidny Universitat Jaume I(UJI)Castelldn 12071Spain

Anthropomorphic hands have received increasing research interest in the fields of robotics and *** it is not yet clear how to evaluate their *** in the kinematic chain is essential to achieve both functionality and cosmesis.A few previous works have addressed the definition of anthropomorphism indexes,although they have some limitations in its *** this study,three different anthropomorphism indexes have been defined to compare the kinematic chain of artificial hands with that of the human *** indexes are based on the comparison of:(I)the parameters of the kinematic chain(dimensions,type of joints,orientations and ranges of motion),(2)the reachable workspace,and(3)common grasping *** artificial hands with different degrees of anthropomorphism have been compared using the three Anthropomorphism Indexes of the Kinematic Chain(AIKC).The results show a high correlation between the first and third AIKC for the hands *** second AIKC presents much lower values than the other two,although they are higher for hands that combine abduction/adduction and flexion/extension movements in the kinematic chain of each *** indexes can be useful during the initial stage of designing artificial hands or evaluating their anthropomorphism.

关键词： anthropomorphism grasping indexes kinematics multifingered hands

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Groundwater uptake of different surface cover and its consequences in great Hungarian plain

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Ecological Processes 2017年第1期6卷 408-416页

作者： Zoltán Gribovszki Péter Kalicz Kitti Balog andrás Szabó Tibor Tóth Péter Csáfordi Mohamed Metwaly Sándor Szalai Institute of Geomatics and Civil Engineering University of SopronSopronHungary Institute for Soil Sciences and Agricultural Chemistry Centre for Agricultural ResearchHungarian Academy of SciencesBudapestHungary Forest Research Institute National Agricultural Research and Innovation CentreBudapestHungary Archaeology Department College of Tourism and ArchaeologyKing Saud UniversityRiyadhSaudi Arabia national Research Institute of Astronomy and Geophysics(nRIAG) CairoEgypt MTA CSFK GGI SopronHungary

Introduction:Forest cover in Hungary has increased from 1.1 to 2.0 million hectares during the last *** EU(European Union)promotes further afforestation;thus,15,000–18,000 ha are being forested each year,mainly in the Hungarian Great *** terms of species used for afforestation,poplar plantations are preferred over native oak *** groundwater uptake of trees can be a significant water balance element of forested areas in shallow groundwater environments within the Hungarian Great *** can cause water table depressions and subsurface salt accumulation in areas with negative water *** study examined the hydrological impact of forest cover in the Hungarian Great *** the framework of this research,climatic water balance,water table depth and salinity,subsoil layering,tree species and stand age were analysed as influencing *** paper compares the effect which an oak forest,a poplar plantation and a pasture have on groundwater uptake and salt ***:The water table level was roughly 0.4–0.5 m lower beneath the oak forest and the poplar plantation than it was beneath the *** groundwater use was 1.5–2 times higher than that of *** uptake of oak forest was greater than that of poplar plantation during the monitoring *** accumulation,which shows water use in the longer run,was slightly higher for poplar in deeper ***:The greater amount of groundwater used by trees does not lead to a higher salt uptake as only a slight accumulation of salt was measured beneath the ***,hybrid poplar was slightly less favourable than native oak when considering salinization ***,even greater groundwater uptake by trees over longer timescales could cause more significant salt accumulation under pronounced drought conditions due to climate change.

关键词： Groundwater recharge/water budget Evapotranspiration Diurnal fluctuation Forest cover Salinization

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Sticky-MARTInI as a reactive coarse-grained model for molecular dynamics simulations of silica polymerization

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npj Computational Materials 2022年第1期8卷 467-479页

作者： andréP.Carvalho Sérgio M.Santos Germán Pérez-Sánchez JoséD.Gouveia JoséR.B.Gomes Miguel Jorge CICECO-Aveiro Institute of Materials Department of ChemistryUniversity of AveiroCampus Universitário de Santiago3810-193AveiroPortugal Department of Chemical and Process Engineering University of Strathclyde75 Montrose StreetGlasgowG11XJUK

We report a molecular modeling paradigm to describe silica polymerization reactions in aqueous solutions at conditions that are representative of realistic experimental processes like biosilicification or porous silica synthesis–*** close to ambient temperatures and over a wide range of *** key point is to describe the Si-O-Si chemical bond formation and breakage processes through a continuous potential with a balance between attractive and repulsive interactions between suitably placed virtual sites and sticky *** simplicity of the model,its applicability in standard parallelized molecular dynamics codes,and its compatibility with the widely used MARTInI coarse-grained force-field allows for the study of systems containing millions of atoms over microsecond time *** model is calibrated to match experimental results for the temporal evolution of silica polymerization in aqueous solution close to the isoelectric point,and can describe silica polymerization and self-assembly processes during encapsulation of a surfactant micelle.

关键词： silica polymerization dynamics

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Integration of high-rate filtration using waste-derived biochar as a potential sustainable technology for drinking water supply

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Biochar 2023年第1期5卷 1075-1097页

作者： Fernando García-Ávila andrés Galarza-Guamán Mónica Barros-Bermeo Emigdio Antonio Alfaro-Paredes Alex Avilés-Añazco Sergio lglesias-Abad Carrera de Ingeniería Ambiental Facultad de Ciencias QuímicasUniversidad de CuencaCuencaEcuador Departamento de Química Aplicada y Sistemas de Producción Grupo de Evaluación de Riesgos Ambientales en Sistemas de Producción y Servicios(RISKEN)CuencaEcuador Professional School of Systems Engineering Research Institute of Science and TechnologyUniversidad César VallejoLimaPeru Carrera de Ingeniería Ambiental Universidad Católica de CuencaCuencaEcuador

This research aimed to evaluate the efficiency of eucalyptus(E)and bamboo(B)residual biomass biochars as filter materials for drinking water *** efficiencies of these two biochars in the rapid filtration process were evaluated using water(raw,flocculated and settled)at the rate of 120 m^(3)/m^(2)/*** that bamboo biochar manufactured under a slow pyrolysis process"b"(Bb)had the best ***,Bb was evaluated with three different granulometries,and it was found that the effective size with the best performance was the finest(0.6-1.18 mm).Subsequently,this biochar was compared with conventional filter materials such as gravel,sand and anthracite,using different types of water(raw,flocculated and settled)and at different filtration rates(120 and 240 m^(3)/m^(2)/d),and it was found that the filter material with the best performance was precisely biochar,with average removal efficiencies of 64.37%turbidity and 45.08%colour for raw water;93.9%turbidity and 90.75%colour for flocculated water,and 80.79%turbidity and 69.03%colour for settled *** efficiency using simple beds of sand,biochar,anthracite and gravel at the rate of 180 m^(3)/m^(2)/d was 75.9%copper,90.72%aluminium,95.7%iron,10.9%nitrates,94.3%total coliforms and 88.9%fecal *** efficiencies achieved by biochar were higher compared to those of conventional filter *** was also found that biochar contributes to improving the performance of sand and anthracite in mixed ***,it was possible to demonstrate that the volume of washing water required for the biochar is lower compared to the other filter ***,it is recommended to carry out more tests for the purification of water with biochars from rural areas affected by the mining and oil exploitation,as well as the purification of seawater with biochars from coastal areas with residues from dry forests and organic residues from municipalities.

关键词： Biochar Filter medium Rapid filtration Pyrolysis Eucalyptus Bamboo

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Variability of platelet aggregation in patients with clopidogrel treatment and hip fracture: A retrospective case-control study on 112 patients

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World Journal of Orthopedics 2015年第5期6卷 439-445页

作者： Anna Clareus Inga Fredriksson Hkan Wallén Max Gordon andré Stark Olof Skldenberg Division of Orthopaedics Department of Clinical Sciences at Danderyd Hospital Karolinska Institutet Division of Anesthesiology Department of Clinical Sciences at Danderyd Hospital Karolinska Institutet Division of Cardiology Department of Clinical Sciences at Danderyd Hospital Karolinska Institute

AIM: To identify the rate of non-responders to clopidogrel treatment in hip fracture patients and study how non-responders differ from ***: In a retrospective case-control study we included 28 cases of acute proximal femoral fracture with clopidogrel treatment 2011 to 2013. Eighty-four controls from the same time period were included. Data collected included response to clopidogrel measured with multiple electrode aggregometry(MEA), intraoperative bleeding, erythrocyte transfusion, time to surgery and the incidence of adverse events up to 3 mo after surgery. RESULTS: Eight(29%) of the 28 cases were nonresponders. The median intraoperative bleeding was 300 mL(range, 0-1500), and was lower for non-responders(50 m L) but did not reach statistical significance. Erythrocyte transfusions did not differ between responders, non-responders and controls. Forty-five(40%) of 112 patients had adverse events postoperatively but the rate did not differ between patients with and without clopidogrel ***: Almost one-third of patients withclopidogrel treatment and an acute proximal femoral fracture are non-responders to antiplatelet therapy and can be operated without delay.

关键词： Proximal femoral fracture Clopidogrel Variability Bleeding Adverse events

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