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Benchmark Computations of the Phase Field Crystal and Functionalized Cahn-Hilliard Equations via Fully Implicit,Nesterov Accelerated Schemes

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Communications in Computational Physics 2023年第2期33卷 367-398页

作者： jea-Hyun Park abner j.salgado Steven M.Wise Department of Mathematics University of California Santa BarbaraCA 93106USA Department of Mathematics University of Tennessee KnoxvilleTN 37996USA.

We introduce a fast solver for the phase field crystal(PFC)and functionalized Cahn-Hilliard(FCH)equations with periodic boundary conditions on a rectangular domain that features the preconditioned Nesterov’s accelerated gradient descent(PAGD)*** discretize these problems with a Fourier collocation method in space,and employ various second-order schemes in *** observe a significant speedup with this solver when compared to the preconditioned gradient descent(PGD)*** the PAGD solver,fully implicit,second-order-in-time schemes are not only feasible to solve the PFC and FCH equations,but also do so more efficiently than some semi-implicit schemes in some cases where accuracy issues are taken into *** computations of four different schemes for the PFC and FCH equations are conducted and the results indicate that,for the FCH experiments,the fully implicit schemes(midpoint rule and BDF2 equipped with the PAGD as a nonlinear time marching solver)perform better than their IMEX versions in terms of computational cost needed to achieve a certain *** the PFC,the results are not as conclusive as in the FCH experiments,which,we believe,is due to the fact that the nonlinearity in the PFC is milder nature compared to the FCH *** also discuss some practical matters in applying the *** introduce an averaged Newton preconditioner and a sweeping-friction strategy as heuristic ways to choose good preconditioner *** sweeping-friction strategy exhibits almost as good a performance as the case of the best manually tuned parameters.

关键词： Phase field crystal functionalized Cahn-Hilliard preconditioning Nesterov acceleration nonlinear solver.

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Combinatorial therapies for spinal cord injury repair

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Neural Regeneration Research 2025年第5期20卷 1293-1308页

作者： Carla S.Sousa Andreia Monteiro António j.salgado Nuno A.Silva Life and Health Sciences Research Institute(ICVS) School of MedicineUniversity of MinhoCampus de Gualtar-gualtarBragaPortugal ICVS/3B’s Associate Lab PT Government Associated LabCampus de Gualtar-gualtarBragaPortugal

Spinal cord injuries have profound detrimental effects on individuals, regardless of whether they are caused by trauma or non-traumatic events. The compromised regeneration of the spinal cord is primarily attributed to damaged neurons, inhibitory molecules, dysfunctional immune response, and glial scarring. Unfortunately, currently, there are no effective treatments available that can fully repair the spinal cord and improve functional outcomes. Nevertheless, numerous pre-clinical approaches have been studied for spinal cord injury recovery, including using biomaterials, cells, drugs, or technological-based strategies. Combinatorial treatments, which target various aspects of spinal cord injury pathophysiology, have been extensively tested in the last decade. These approaches aim to synergistically enhance repair processes by addressing various obstacles faced during spinal cord regeneration. Thus, this review intends to provide scientists and clinicians with an overview of pre-clinical combinatorial approaches that have been developed toward the solution of spinal cord regeneration as well as update the current knowledge about spinal cord injury pathophysiology with an emphasis on the current clinical management.

关键词： electric stimulation neural tissue regeneration neuroprotection polytherapy spinal cord injury

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Mesenchymal stem cells secretome:current trends and future challenges

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Neural Regeneration Research 2020年第1期15卷 75-77页

作者： Fabio G.Teixeira Antonio j.salgado Life and Health Sciences Research Institute(ICVS) School of MedicineUniversity of MinhoBragaPortugalICVS/3B’s Associate LabPT Government Associated LabBraga/GuimaraesPortugal

Mesenchymal stem cells(MSCs)secretome:a good candidate for medical biotechnology?Medical biotechnology is currently defined as the application of biotechnological tools for producing multiple technologies and products to health care,becoming an important bridge between different fields,namely neuroscience,regenerative medicine,pharmacology and bio-engineering(Pham,2018).The use and manipulation of stem cells can potentially represent a medical biotechnology breakthrough that brings regenerative medicine to a new ***,over the last decade,the use of stem cells has remarkably been proposed as a regenerative tool,and within it,MSCs have emerged as a promising therapeutic option.

关键词： manipulation breakthrough becoming

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From regenerative strategies to pharmacological approaches:can we fine-tune treatment for Parkinson's disease?

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Neural Regeneration Research 2022年第5期17卷 933-936页

作者： Rita Caridade Silva Helena Sofia Domingues António j.salgado Fábio G.Teixeira Life and Health Sciences Research Institute(ICVS) School of MedicineUniversity of MinhoBragaPortugal ICVS/3B’s Associate Lab PT Government Associated LabBraga/GuimarãesPortugal

Parkinson's disease is the second most prevalent neurodegenerative disorder ***,it is characterized by severe motor complications caused by progressive degeneration of dopaminergic *** treatment is focused on mitigating the symptoms through the administration of levodopa,rather than on preventing dopaminergic neuronal ***,the use and development of neuroprotective/disease-modifying strategies is an absolute need that can lead to promising gains on translational research of Parkinson's *** instance,N-acetylcysteine,a natural compound with strong antioxidant effects,has been shown to modulate oxidative stress,preventing dopamine-induced cell *** the evidence of neuroprotective and modulatory effects of this drug,as far as we know,it does not induce per se any regenerative ***,it would be of interest to combine the latter with innovative therapies that induce dopaminergic neurons repair or even differentiation,as stem cell-based *** cells secretome has been proposed as a promising therapeutic approach for Parkinson's disease,given its ability to modulate cell viability/preservation of dopaminergic *** approach represents a shift in the paradigm,showing that cell-transplantation free therapies based on the use of stem cells secretome may represent a potential alternative for regenerative medicine of Parkinson's ***,in this review,we address the current understanding of the potential combination of stem cell free-based strategies and neuroprotective/disease-modifying strategies as a new paradigm for the treatment of central nervous system neurodegenerative diseases,like Parkinson's disease.

关键词： disease-modifying strategies mesenchymal stem cells N-acetylcysteine neuroprotection Parkinson's disease stem cells secretome

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This work was supported by the European Research Council Advanced Grant(ETAP-742985 to *** j.F.)and by the Ministry of Science and Technology(grant 110-2636-B-005-001 to K.-j.L.).

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Plant Communications 2024年第1期5卷 130-147页

作者： Yu Zhang Yuan Fu Wenfei Xian Xiuli Li Yong Feng Fengjiao Bu Yan Shi Shiyu Chen Robin van Velzen Kai Battenberg Alison M.Berry Marco G.salgado Hui Liu Tingshuang Yi Pascale Fournier Nicole Alloisio Petar Pujic Hasna Boubakri M.Eric Schranz Pierre-Marc Delaux Gane Ka-Shu Wong Valerie Hocher Sergio Svistoonoff Hassen Gherbi Ertao Wang Wouter Kohlen Luis G.Wall Martin Parniske Katharina Pawlowski Philippe Normand jeffrey j.Doyle Shifeng Cheng Shenzhen Branch Guangdong Laboratory for Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518124China Biosystematics Group Department of Plant SciencesWageningen University6708PB Wageningenthe Netherlands Department of Plant Sciences University of CaliforniaDavisDavisCA 95616USA Department of Ecology Environment and Plant SciencesStockholm University10691 StockholmSweden Germplasm Bank of Wild Species Kunming Institute of BotanyChinese Academy of SciencesLanhei RoadKunming 650201China Universite´de Lyon Universite´Lyon 1CNRSUMR5557Ecologie MicrobienneINRAUMR 141843 bd du 11 novembre 191869622 VilleurbanneFrance Laboratoire de Recherche en Sciences Ve´ge´tales(LRSV) Universite´de ToulouseCNRSUPS24 chemin de Borde RougeAuzevilleBP4261731326 Castanet TolosanFrance Department of Biological Sciences University of AlbertaEdmontonAB T6G 2E9Canada French National Research Institute for Sustainable Development(IRD) UMR LSTM(IRD/CIRAD/INRAe/Montpellier University/Supagro)-Campus International BaillarguetTA A-82/J34398 Montpellier Cedex 5France National Key Laboratory of Plant Molecular Genetics CAS Center for Excellence in Molecular Plant SciencesInstitute of Plant Physiology and EcologySIBSChinese Academy of SciencesShanghaiChina Laboratory of Molecular Biology Department of Plant SciencesWageningen University6708PB Wageningenthe Netherlands Laboratory of Biochemistry Microbiology and Soil Biological InteractionsDepartment of Science and TechnologyNational University of QuilmesCONICETBernalArgentina Faculty of Biology GeneticsLMU MunichGroßhaderner Strasse 2-482152 MartinsriedGermany School of Integrative Plant Science Sections of Plant Biology and Plant Breeding&GeneticsCornell UniversityIthacaNY 14853USA State Key Laboratory of Systematic and Evolutionary Botany Institute of BotanyChinese Academy of SciencesBeijing 100093China Univer

Plant root-nodule symbiosis(RNS)with mutualistic nitrogen-fixing bacteria is restricted to a single clade of angiosperms,the Nitrogen-Fixing Nodulation Clade(NFNC),and is best understood in the legume *** species share many commonalities,explained either by divergence from a common ancestor over 100 million years ago or by convergence following independent origins over that same time ***,comparative analyses of diverse nodulation syndromes can provide insights into constraints on nodulation—what must be acquired or cannot be lost for a functional symbiosis—and the latitude for Plant Communications Genomic landscape of nodulation variation in the ***,much remains to be learned about nodulation,especially outside of ***,we employed a large-scale phylogenomic analysis across 88 species,complemented by 151 RNA-seq libraries,to elucidate the evolution of *** phylogenomic analyses further emphasize the uniqueness of the transcription factor NIN as a master regulator of nodulation and identify key muta-tions that affect its function across the *** transcriptomic assessment revealed nodule-specific upregulated genes across diverse nodulating plants,while also identifying nodule-specific and nitrogen-response *** 70%of symbiosis-related genes are highly conserved in the four representative species,whereas defense-related and host-range restriction genes tend to be lineage *** study also identified over 900000 conserved non-coding elements(CNEs),over 300000 of which are unique to sampled NFNC ***-specific CNEs are enriched with the active H3K9ac mark and are correlated with accessible chromatin regions,thus representing a pool of candidate regula-tory elements for genes involved in ***,our results provide novel insights into the evolution of nodulation and lay a foundation for engineering of RNS traits in agriculturally important crops.

关键词： nitrogen-fixing root-nodule symbiosis two competing hypotheses phylogenomics phylotranscrip-tomics conserved non-coding elements convergence deep homology

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Immunomodulation as a neuroprotective strategy after spinal cord injury

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Neural Regeneration Research 2018年第3期13卷 423-424页

作者： Susana Monteiro António j. salgado Nuno A. Silva Life and Health Sciences Research Institute(ICVS) School of MedicineUniversity of MinhoCampus de GualtarBragaPortugal ICVS/3B's-PT Government Associate Laboratory Braga/GuimaraesPortugal

The initial trauma to the spinal cord is just the starting point for a cascade of endogenous events that will collectively determine the injury extension. These secondary events include, but are not limited to： glutamate excitoxicity, induction of apoptotic pathways, ionic imbalances and the development of a strong and dysfunctional inflammatory response. The secondary injury is associated to an aggravation of neuronal damage increasing the extent of neurological deficits （Ek et al., 2010）.

关键词： Immunomodulation as a neuroprotective strategy after spinal cord injury SCI

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Combinatorial therapies for spinal cord injury: strategies to induce regeneration

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Neural Regeneration Research 2019年第1期14卷 69-71页

作者： Eduardo D.Gomes Nuno A.Silva António j. salgado Life and Health Sciences Research Institute (ICVS) School of Medicine University of Minho Campus de Gualtar ICVS/3B’s–PT Government Associate Laboratory

Spinal cord injury(SCI)is a condition without treatment,mainly characterized by the loss of motor and sensory function below the level of *** is accompanied by several complications such as cardiac and respiratory compromise,and often patients present psychological ailments associated with the drastic alteration of their normal *** pathophysiology derives from a massive damage to the spinal cord tissue,which is propagated

关键词：损害绳索新生治疗感觉功能生活方式星形细胞并发症

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Automated classification of big X-ray diffraction data using deep learning models

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npj Computational Materials 2023年第1期9卷 169-180页

作者： jerardo E.salgado Samuel Lerman Zhaotong Du Chenliang Xu Niaz Abdolrahim Materials Science program University of RochesterRochesterNew York 14627USA Department of Computer Science University of RochesterRochesterNew York 14627USA Department of Mechanical Engineering University of RochesterRochesterNew York 14627USA Laboratory for Laser Energetics University of RochesterRochesterNew York 14627USA

In current in situ X-ray diffraction(XRD)techniques,data generation surpasses human analytical capabilities,potentially leading to the loss of *** techniques require human intervention,and lack the performance and adaptability required for material *** the critical need for high-throughput automated XRD pattern analysis,we present a generalized deep learning model to classify a diverse set of materials’crystal systems and space *** our approach,we generate training data with a holistic representation of patterns that emerge from varying experimental conditions and crystal *** also employ an expedited learning technique to refine our model’s expertise to experimental *** addition,we optimize model architecture to elicit classification based on Bragg’s Law and use evaluation data to interpret our model’s *** evaluate our models using experimental data,materials unseen in training,and altered cubic crystals,where we observe state-of-the-art performance and even greater advances in space group classification.

关键词： Automate classify cubic

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Effects of estrogen receptor modulators on cytoskeletal proteins in the central nervous system

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Neural Regeneration Research 2017年第8期12卷 1231-1240页

作者： julia j.Segura-Uribe Rodolfo Pinto-Almazán Angélica Coyoy-salgado Claudia E.Fuentes-Venado Christian Guerra-Araiza Unidad de Investigacion Modica en Enfermedades Neurologicas Hospital de Especialidades Centro Medico Nacional Siglo XXI Instituto Mexicano del Seguro Social Mexico City Mexico Seccion de Estudios de Posgrado e Investigacion Escuela Superior de Medicina Instituto Politecnico Nacional Mexico City Mexico Unidad de Investigacion Hospital Regional de Alta Especialidad Ixtapaluca Ixtapaluca Mexico Institute for the Developing Mind Children's Hospital Los Angeles Los Angeles CA USA Department of Pediatrics Keck School of Medicine University of Southern California Los Angeles CA USA Consejo Nacional de Ciencia y Tecnologia Mexico City Mexico Clinica de Trastornos del Sueno Universidad Autonoma Metropolitana-Iztapalapa Mexico City Mexico Servicio de Medicina Fisica y Rehabilitacion Hospital General de Zona No. 197 Texcoco Mexico Unidad de Investigacion Modica en Farmacologla Hospital de Especialidades Centro Medico Nacional Siglo XXI Instituto Mexicano del Seguro Social Mexico City Mexico

Estrogen receptor modulators are compounds of interest because of their estrogenic agonistic/antagonistic effects and tissue specificity. These compounds have many clinical applications, particularly for breast cancer treatment and osteoporosis in postmenopausal women, as well as for the treatment of climacteric symptoms. Similar to estrogens, neuroprotective effects of estrogen receptor modulators have been described in different models. However, the mechanisms of action of these compounds in the central nervous system have not been fully described. We conducted a systematic search to investigate the effects of estrogen receptor modulators in the central nervous system, focusing on the modulation of cytoskeletal proteins. We found that raloxifene, tamoxifen, and tibolone modulate some cytoskeletal proteins such as tau, microtuble-associated protein 1（MAP1）, MAP2, neurofilament 38（NF38） by different mechanisms of action and at different levels： neuronal microfilaments, intermediate filaments, and microtubule-associated proteins. Finally, we emphasize the importance of the study of these compounds in the treatment of neurodegenerative diseases since they present the benefits of estrogens without their side effects.

关键词： estrogen receptor modulators selective estrogen receptor modulators microtubules neurofilaments tibolone tamoxifen raloxifene

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催化:古老却富有挑战性的石墨烯基材料(英文)

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催化学报 2014年第6期35卷 792-797页

作者： Ljubisa R.Radovic Camila Mora-Vilches Adolfo j.A.salgado-Casanova Department of Chemical Engineering University of Concepción Concepción Chile Department of Energy & Mineral Engineering Penn State University University Park PA USA

An assessment is offered regarding the progress made, and the remaining challenges, in the field of carbocatalysis. The fundamental principles that govern the preparation and performance of sp2-hybridized carbon materials in heterogeneous catalysis have been known for decades, and the level of understanding of key issues – especially the importance of textural and ion-exchange properties (i.e., surface area, pore size distribution, and proton transfer) – remains quite satisfactory. The opportunities for novel catalytic materials – especially graphene nanosheets and carbon nanotubes– are tremendous, especially when it comes to taking advantage of their structural order, such that electron transfer can be both better understood and controlled to enhance catalytic activity and selectivity.

关键词：碳材料石墨催化剂个旧基础碳纳米管多相催化离子交换

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