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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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Hard life for sons in the nest?Sex-dependent offspring mortality in Great Tits in urban and forest areas

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Avian Research 2024年第1期15卷 91-97页

作者： nora Agh Henriett Anna Dalvári Krisztián Szabó Ivett Pipoly andrás Liker HUn-REn-PE Evolutionary Ecology Research Group University of PannoniaH-8200VeszpremPf.1158.Hungary Behavioral Ecology Research Group Center for Natural SciencesUniversity of PannoniaH-8200Pf.1158.VeszpremHungary molecular Ecology Research Group Department of EcologyUniversity of Veterinary Medicine BudapestH-1400Pf.2.BudapestHungary Synlab Hungary Ltd. H-1211Weiss Manfr´ed Str.5-7BudapestHungary

Sex-biased mortality can occur in birds during development,for example due to sexual differences in energy requirement and/or environmental sensitivity,or the effects of sex hormones or sex differences in the expression of mutations linked to sex *** extent of sex-bias in mortality may also be related to environmental conditions that influence offspring development and *** areas often provide poorer conditions for nestling development resulting in higher offspring mortality compared to natural areas,which may accelerate sex differences in offspring mortality in *** test this hypothesis,we examined the sex ratio of dead offspring in Great Tits(Parus major),using 427 samples of unhatched eggs and dead nestlings collected in two urban and two forest sites between 2013 and *** ratio of males in the whole sample of dead offspring(56.9%)was significantly higher than expected by an 1:1 ratio,and the strongest sex biases were detected in urban areas(57.6%males)and in young nestlings(males).However,the sex ratios of dead offspring did not differ significantly among study sites and between offspring developmental stages.29.3%of unhatched eggs contained a visible embryo,and the proportion of embryo-containing unhatched eggs did not differ significantly between urban and forest study *** results suggest male-biased offspring mortality in Great Tits,and highlight the need of large datasets to detect subtle differences between habitats and developmental stages.

关键词： Great Tit Urbanization nestling mortality Sex related differences

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Is it possible to run after positive affective experiences instead of health benefits without tackling social inequalities?

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Journal of Sport and Health Science 2024年第6期13卷 756-758页

作者： Raphael H.O.Araujo andre O.Werneck Gilmar m.de Jesus Danilo R.P.silva Graduation Program in Health Sciences Londrina State UniversityLondrina 86057-970Brazil School of Public Health The University of QueenslandBrisbane QLD 4006Australia Center for Epidemiological Research in nutrition and Health Department of NutritionSchool of Public HealthUniversidade de S~ao Paulo(USP)Sao Paulo 01246-904Brazil Department of Psychological medicine Institute of PsychiatryPsychology and NeuroscienceKing’s College LondonLondon SE58AFUK Public Health Post-Graduate Program State University of Feira de SantanaFeira de Santana 44036-900Brazil Department of Physical Education Federal University of SergipeSao Cristov~ao 490100-000Brazil

We recently read the opinion piece titled“Why people should run after positive affective experiences instead of health benefits”,which was carried out by maltagliati et al.^(1)and published in the Journal of Sport and Health *** article started an important discussion about a physical activity(PA)promotion approach that encourages the use of affective experience to PA *** we agree with the authors’point of view and believe that its message can generate an important insight for PA promotion,the authors presented a scenario where behavior change seems to be exclusively dependent on the *** the existence of other barriers to an active lifestyle(e.g.,social inequalities)could enhance the authors’suggested approach because many people live in conditions that reduce their opportunities to engage in affective experiences related to PA;furthermore,affective experiences can vary depending on individual context.

关键词： promotion inequalities furthermore

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Plant growth and metabolism of exotic and native Crotalaria species for mine land rehabilitation in the Amazon

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Journal of Forestry Research 2024年第1期35卷 143-154页

作者： Hemelyn Soares das Chagas Rafael silva Guedes markus Gastauer Paula Godinho Ribeiro Allan Klynger da silva Lobato Cecílio Frois Caldeira Fabrício William deÁvila andréRodrigues dos Reis Silvio Junio Ramos Instituto Tecnológico Vale Rua Boaventura da Silva955BelémPA 66055-090Brazil Universidade Federal do Sul e Sudeste do Pará XinguaraPABrazil núcleo de Pesquisa Vegetal Básica e Aplicada Universidade Federal Rural da AmazôniaParagominasPABrazil Departamento de Engenharia Florestal Universidade Estadual do Centro-Oeste/UNICENTROIratiPRBrazil School of Sciences and Engineering São Paulo State University(UNESP)TupãSP.CEP 17602-496Brazil

Despite its enormous benefits,mining is respon-sible for intense changes to vegetation and soil ***,after extraction,it is necessary to rehabilitate the mined areas,creating better conditions for the establishment of plant species which is *** study evaluated mineral and organic fertilization on the growth,and carbon and nitrogen(n)metabolism of two Crotalaria species[Cro-talaria spectabilis(exotic species)and Crotalaria maypu-rensis(native species from Carajás mineral Province(CmP)]established on a waste pile from an iron mine in CmP.A control(without fertilizer application)and six fertilization mixtures were tested(i=nPK;ii=nPK+micronutrients;iii=nPK+micronutrients+organic compost;iv=PK;v=PK+micronutrients;vi=PK+micronutrients+organic compost).Fertilization contributed to increased growth of both species,and treatments with nPK and micronutrients had the best results(up to 257%***),while organic fertilization did not show *** Crotalaria had a greater number of nodules,higher nodule dry mass,chlorophyll a and b contents and showed free ammonium as the predominant n form,reflecting greater increments in biomass compared to native *** having lower growth,the use of this native species in the rehabilitation of mining areas should be considered,mainly because it has good development and meets current government legislation as an opportunity to restore local biodiversity.

关键词： Biological nitrogen fixation mining nitrogen metabolism Plant nutrition

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Elevation transition of aquatic insects closely matches a thermal feature in the Yungas of northwestern Argentina

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Journal of mountain Science 2024年第2期21卷 433-448页

作者： Alexandra BUITRAGO-GUACAnAmE Carlos mOLInERI andrés LIRA-nORIEGA Daniel andrés DOS SAnTOS neotropical Biodiversity Institute(COnICET-UnT) UNT-DomesHorco Molle S/N4107 TucumánArgentina COnACYT Research Fellow Network of Advanced Molecular StudiesInstitute of Ecology A.COld Road to Coatepec 351El HayaCP 91073XalapaVeracruzMexico Biostatistics Chair Faculty of Natural Sciences and IMLNational University of TucumánSan Miguel de TucumánMiguel Lillo 2054000 TucumánArgentina

Temperature is a key factor that shapes the distribution of *** knowledge about how species respond to temperature is relevant to devise strategies for addressing the impacts of climate *** insects are particularly vulnerable to climate change,yet there is still much to learn about their ecology and *** the Yungas ecoregion of northwestern Argentina,cold-and warm-adapted species of the orders Ephemeroptera,Plecoptera,and Trichoptera(EPT)are segregated by *** modeled the ecological niche of South American EPT species in this region using available data and projected their potential distribution in geographic *** were grouped based on their ecogeographic similarity,and we analyzed their replacement pattern along elevation gradients,focusing on the ecotone where opposing thermal preferences *** this interface,we identified critical points where the combined incidence of cold and warm assemblages maximizes,indicating a significant transition *** found that the montane Cloud Forest holds the interface,with a particularly greater suitability at its lower *** main axis of the interface runs in a n-S direction and falls between 14°C-16°C mean annual *** probability of a particular location within a basin being classified as part of the interface increases as Kira’s warmth index approaches a score around *** the interface is critical for defining the thermal limits of species distribution and designing biomonitoring *** in the location of thermal constants related to mountainous ecotones may cause vertical displacement of aquatic insects and vegetation *** have recognized significant temperature thresholds that serve as indicators of suitability for the *** global warming is anticipated to shift these indicators,we suggest using them to monitor the imprints of climate change on mountain ecosystems.

关键词： Austral Yungas Ecological niche model Ephemeroptera Kira’s warmth index Plecoptera Trichoptera

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Seasonal variation and host sex affect bat–bat fly interaction networks in the Amazonian savannahs

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Integrative Zoology 2024年第3期19卷 400-416页

作者： Paulo mEJIA Gustavo Lima URBIETA Bruna da silva XAVIER IsaíJorge de CASTRO JoséJúlio DE TOLEDO Gustavo GRACIOLLI Lucio andréVIAnA DIAS William Douglas CARVALHO Programa de Pós-Graduação em Biodiversidade Tropical Universidade Federal do Amapá(UNIFAP)MacapáAPBrazil Programa de Pós-Graduação em Ecologia Instituto de BiologiaCentro de Ciências da SaúdeUniversidade Federal do Rio de Janeiro(UFRJ)Rio de JaneiroRJBrazil Laboratório de mamíferos Instituto de Pesquisas Científicas e Tecnológicas do Estado do Amapá(IEPA)MacapáAPBrazil Programa de Pós-Graduação em Biologia Animal Laboratório de SistemáticaEcologia e Evolução(LSEE)Instituto de BiociênciasUniversidade Federal de Mato Grosso do Sul(UFMS)Campo GrandeMTBrazil Terrestrial Ecology Group(TEG-UAm) Departamento de EcologíaFacultad de CienciasUniversidad Autónoma de MadridMadridSpain Centro de Investigación en Biodiversidad y Cambio Global(CIBC-UAm) Universidad Autónoma de MadridMadridSpain

Bats are the second-most diverse group of mammals in the world,and bat flies are their main ***,significant knowledge gaps remain regarding these antagonistic interactions,especially since diverse factors such as seasonality and host sex can affect their network ***,we explore the influence of such factors by comparing species richness and composition of bat flies on host bats,as well as specialization and modularity of bat–bat fly interaction networks between seasons and adult host *** captured bats and collected their ectoparasitic flies at 10 sampling sites in the savannahs of AmapáState,northeastern region of the Brazilian *** female bats being more parasitized and recording greater bat fly species richness in the wet season,neither relationship was statistically *** pooled network could be divided into 15 compartments with 54 links,and all subnetworks comprised>12 *** total number of links ranged from 27 to 48(for the dry and wet seasons,respectively),and female and male subnetworks had 44 and 41 links,*** values were very low for the pooled network and for all *** results revealed higher bat fly species richness and abundance in the wet season,whereas specialization and modularity were higher in the dry ***,the subnetwork for female bats displayed higher specialization and modularity than the male ***,both seasonality and host sex contribute in different ways to bat–bat fly network *** studies should consider these factors when evaluating bat–bat fly interaction networks.

关键词： Amapá Amazon biome bat flies bats interaction networks

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Developing biophilic intermediate spaces for Arctic housing:Optimizing the thermal,visual,and energy performance

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Building Simulation 2024年第6期17卷 857-875页

作者： Tarlan Abazari andréPotvin Louis Gosselin Claude mH Demers GRAP(Groupe de recherche en ambiance physiques) School of ArchitectureLaval UniversityQuébecCanada Department of mechanical Engineering Faculty of Science and EngineeringLaval UniversityQuébecCanada

Connecting occupants to the outdoor environment and incorporating biophilic design principles are challenging in extreme Arctic climatic *** Arctic housing models do not provide efficient thermal and daylight transitions which are essential for the well-being and cultural needs of their *** address these challenges,this research develops free-running biophilic intermediate spaces,integrated into an existing Arctic housing *** simulation methods are employed to optimize the primary and secondary architectural design variables for 26 case studies of intermediate *** variables include volume,transparency ratio,and *** variables include materials and physical ***,Daylight Factor/Autonomy,and Energy Use are evaluated as performance *** reveal that free-running intermediate spaces with 6 meters depth and a transparency ratio above 50%provide efficient indoor–outdoor transitions regarding thermal,visual,and energy *** architectural configurations contribute to an approximately 5%reduction in energy consumption within the housing unit compared to the *** side windows prevents the risk of overheating during the summer by reducing the average indoor temperature of intermediate spaces by 7°C but increases the overall energy *** a potential alternative to double-glazing,polycarbonate sheets enable efficient thermal performance by increasing the average indoor temperature of intermediate spaces by approximately 15°C during the cold Arctic *** polycarbonate sheets results in a 16.6%reduction in energy consumption compared to using double-glazing material in intermediate space,and a 26%reduction from the *** outcomes contribute to efficient indoor–outdoor connections and energy efficiency in Arctic housing.

关键词： Arctic housing intermediate spaces biophilic design positive thermal transitions daylight availability energy efficiency

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Global prevalence and gender inequalities in at least 60 min of self-reported moderate-to-vigorous physical activity 1 or more days per week:An analysis with 707,616 adolescents

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Journal of Sport and Health Science 2024年第5期13卷 709-716页

作者： Raphael H.O.Araujo andrúO.Werneck Clarice L.martins Luciana L.Barboza Rafael m.Tassitano nicolas Aguilar-Farias Gilmar m.Jesus Robinson Ramírez-Véelez Riki Tesler Adewale L.Oyeyemi Ellen C.m.silva Robert G.Weaver mark S.Tremblay Javier Brazo-Sayavera Grégore I.mielke Danilo R.P.silva Graduation Program in Health Sciences Londrina State University(UEL)Londrina 86057-970Brazil Center for Epidemiological Research in nutrition and Health Department of NutritionSchool of Public HealthUniversidade de Sao Paulo(USP)Sao Paulo 01246-904Brazil Department of Physical Education Federal University of ParaıbaParaıba 58051-900Brazil Research Centre of Physical Activity Health and LeisureFaculty of SportsLaboratory for Integrative and Translational Research in Population Health(ITR)University of PortoPorto 4500Portugal Postgraduate Program in Physical Education University of BrasıliaBrasılia 70910-900Brazil Department of Kinesiology and Community Health University of Illinois at Urbana-ChampaignChampaignIL 61801-3841USA Department of Physical Education Sports and RecreationUniversidad de La FronteraTemuco 4680000Chile Department of Health State University of Feira de SantanaFeira de Santana 44036-900Brazil navarrabiomed Hospital Universitario de Navarra(HUN)Navarra Institute for Health Research(IdiSNA)Universidad Publica de Navarra(UPNA)Pamplona 31006Spain Facultad de Ciencias de la Educacion Unidad Central del Valle del Cauca(UCEVA)TuluaValle del Cauca 763022Colombia Health management Department Faculty of Heath sciencesAriel UniversityAriel 40700Israel College of Health Solutions Arizona State UniversityPhoenixAZ 85004USA Arnold School of Public Health University of South CarolinaColumbiaSC 29208USA Healthy Active Living and Obesity Research Group Children’s Hospital of Eastern Ontario Research InstituteOttawaON K1H 8L1Canada Department of Pediatrics University of OttawaOttawaON K1H 8L1Canada Department of Health Sciences Carleton UniversityOttawaON K1S 5B6Canada Department of Sports and Computer Science Universidad Pablo de Olavide(UPO)Seville 41013Spain Centro Universitario Regional noreste Universidad de la RepublicaRivera 40000Uruguay School of Public Health The University of QueenslandBrisbaneQLD 4006Australia Department of Physical Education

Background:Guidelines recommend that adolescents should accumulate an average of 60 min per day of moderate-to-vigorous physical activity(mVPA).However,using only this cut-off could hide important *** instance,from a population-level point of view,increasing physical activity for those with no or low physical activity could provide more health benefits than increasing physical activity for those with intermediate ***,including a more sensitive cut-point of≥1 days per week could be an additional strategy for identifying those with low access/opportunities for physical activity ***,the current study aims to estimate the prevalence of≥60 min of mVPA≥1 days per week among adolescents globally,and to describe any relevant gender ***:We used representative datasets from 146 countries/territories collected between 2003 and *** was *** were grouped into younger(≤14 years old)and older(>14 years old)*** Poisson regression models were used to identify the relative differences in≥60 min of mVPA≥1 days per week between boys and girls,and random-effects meta-analysis models were used to identify the pooled *** were stratified by country and ***:Approximately 80%of both younger and older adolescents reported≥60 min of mVPA≥1 days per *** prevalence was≥94%in Europe and Central Asia and north America,while the estimates for the other regions werence of≥60 min of mVPA≥1 days per week was higher among boys than girls,with the largest differences occurring among the oldest adolescents(Prevalence ratio_(≤14y)=1.04(95%confidence interval(95%CI)):1.03-1.04)*** ratio_(>14y)=1.09(95%CI:1.08-1.10)).Conclusion:Approximately 8 out of 10 adolescents reported accumulating≥60 min of mVPA≥1 days per week,with notable differences between *** differences were observed in several countries,especially among the oldest *** fo

关键词： Global School-based Student Health Survey Health Behaviour Among School-aged Children survey Inequality Surveillance Youth

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Effect of thermo-mechanical conditions during constrained friction processing on the particle refinement of Am50 mg-alloy phases

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Journal of magnesium and Alloys 2024年第6期12卷 2298-2311页

作者： Camila Caroline de Castro andrémartins neves Benjamin Klusemann Helmholtz-Zentrum Hereon Institute of Material and Process DesignSolid-State Materials Processing21502 GeesthachtGermany Helmholtz-Zentrum Hereon Institute of Hydrogen TechnologySystem Design for Mobility21502 GeesthachtGermany Helmut Schmidt University/University of the German Federal Armed Forces Hamburg Department of Mechanical and Civil Engineering22043 HamburgGermany Leuphana University Lüneburg Institute for Production Technology and Systems21335 LüneburgGermany

Constrained Friction Processing(CFP)is a novel solid-state processing technique suitable for lightweight materials,such mg-and *** technique enables grain size refinement to fine or even ultrafine *** this study,the effect of CFP on the microstructural refinement of Am50 rods is investigated in terms of particle size and morphology of the eutectic and secondary phases originally present in the base material,in particular the eutecticβ-mg_(17)Al_(12)and Al-mn *** that purpose,as-cast and solution heat-treated base material and processed samples were *** Al8mn5 intermetallic phase was identified as the main secondary phase present in all samples before and after the processing.A notorious refinement of these particles was observed,starting from particles with an average equivalent length of a few micrometers to around 560 nm after the *** refinement of the secondary phase refinement is attributed to a mechanism analogous to the attrition comminution,where the combination of temperature increase and shearing of the material enables the continuous breaking of the brittle intermetallic particles into smaller *** for the eutectic phase,the results indicate the presence of the partially divorcedβ-mg_(17)Al_(12)particles exclusively in the as-cast base material,indicating that no further phase transformations regarding the eutectic phase,such as dynamic precipitation,occurred after the *** the case of the processed as-cast material analyzed after the CFP,the thermal energy generated during the processing led to temperature values above the solvus limit of the eutectic phase,which associated with the mechanical breakage of the particles,enabled the complete dissolution of this ***,CFP was successfully demonstrated to promote an extensive microstructure refinement in multiple aspects,in terms of grain sizes of theα-mg phase and presence and morphology of the Al-mn and eutecticβ-mg_(17)Al_(12).

关键词： Constrained friction processing Am50 Refill friction stir spot welding Extrusion β-mg_(17)Al_(12) Al-mn phases

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molecular and cellular mechanisms of neuroprotection by oligopeptides from snake venoms

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BIOCELL 2024年第6期48卷 897-904页

作者： CARLOS ALBERTO-silva BREnDA RUFInO DA silva natural and Humanities Sciences Center Experimental Morphophysiology LaboratoryFederal University of ABC(UFABC)São Bernardo do CampoSão PauloBrazil

Venom snake-derived peptides have multiple biochemical,pharmacological,and toxicological proﬁles,allowing for the discovery of new medicinal products and therapeutic *** review speciﬁcally examines the fundamental elements of neuroprotection offered by different oligopeptides derived from snake *** also includes a brief evaluation of short peptides that are being considered as potential therapeutic ***-rich peptides and tryptophyllin family peptides isolated from the crude venom of Viperidae family snakes,speciﬁcally Bothrops atrox,Bothrops jararaca,and Bothrops moojeni,have been shown to have pro-survival properties,the ability to reduce oxidative stress,and the ability to promote cell viability and mitochondrial *** signiﬁcant mechanisms are related to the neuroprotection mediated by snake venom oligopeptides:(1)Activation of the L-arginine metabolite pathway,such as polyamines from ornithine metabolism,which reduces n-methyl-D-aspartate(nmDA)-type glutamate receptor activity;(2)Enhancement of cell viability by activating the nerve growth factor-signaling pathway;and(3)Activation of the muscarinic acetylcholine receptor subtype m1(mAChR-m1).These small peptides show promise as neuroprotective agents against a variety of neurodegenerative disorders.

关键词： neuroprotective peptides neurodegenerative disease Oxidative stress Reactive oxygen species Biopeptides

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