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The impact of ancestral population size and incomplete lineage sorting on Bayesian estimation of species divergence times

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Current Zoology 2015年第5期61卷 874-885页

作者： Konstantinos ANGElIs Mario DOs reis Department of Genetics Evolution and Environment University College London Gower Street London WC 1E 6BT UK

Although the effects of the coalescent process on sequence divergence and genealogies are well understood, the vir- tual majority of studies that use molecular sequences to estimate times of divergence among species have failed to account for the coalescent process. Here we study the impact of ancestral population size and incomplete lineage sorting on Bayesian estimates of species divergence times under the molecular clock when the inference model ignores the coalescent process. Using a combination of mathematical analysis, computer simulations and analysis of real data, we find that the errors on estimates of times and the molecular rate can be substantial when ancestral populations are large and when there is substantial incomplete lineage sorting. For example, in a simple three-species case, we find that if the most precise fossil calibration is placed on the root of the phylogeny, the age of the internal node is overestimated, while if the most precise calibration is placed on the internal node, then the age of the root is underestimated. In both cases, the molecular rate is overestimated. Using simulations on a phylogeny of nine species, we show that substantial errors in time and rate estimates can be obtained even when dating ancient divergence events. We analyse the hominoid phylogeny and show that estimates of the neutral mutation rate obtained while ignoring the coalescent are too high. Using a coalescent-based technique to obtain geological times of divergence, we obtain estimates of the mutation rate that are within experimental estimates and we also obtain substantially older divergence times within the phylogeny [Current Zoology 61 （5）： 874-885, 2015].

关键词： Ancestral polymorphism Incomplete lineage sorting Divergence time estimation Gene tree species tree

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Properties of Collagen/sodium Alginate Hydrogels for Bioprinting of skin Models

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Journal of Bionic Engineering 2023年第1期20卷 105-118页

作者： Tian Jiao Qin lian Weilong lian Yonghui Wang Dichen li Rui l.reis Joaquim Miguel Oliveira state Key laboratory for Manufacturing system Engineering Xi’an Jiaotong UniversityXi’an710049China shaanxi Ketao-AM Technology Co. Ltd.Xi’an710100China B’s Research Group I3Bs—Research Institute on BiomaterialsBiodegradables and BiomimeticsHeadquarters of the European Institute of Excellence on Tissue Engineering and Regenerative MedicineUniversity of MinhoBarco4805-017GuimarãesPortugal ICVs/3B’s–PT Government Associate laboratory Barco4805-017GuimarãesPortugal

3D printing technology has great potential for the reconstruction of human ***,the reconstructed skin has some differences from natural skin,largely because the hydrogel used does not have the appropriate biological and physical properties to allow healing and *** study examines the swelling,degradability,microstructure and biological properties of Collagen/sodium Alginate(Col/sA)hydrogels of differing compositions for the purposes of skin *** the content of sodium alginate causes the hydrogel to exhibit stronger mechanical and swelling properties,a faster degradation ratio,smaller pore size,and less favorable biological *** optimal 1%collagen hydrogel was used to print bi-layer skin in which fibroblasts and keratinocytes showed improved spreading and proliferation as compared to other developed *** Col/sA hydrogels presented suitable tunability and properties to be used as a bioink for bioprinting of skin aiming at finding applications as 3D models for wound healing research.

关键词： Bioink Bioprinting-Collagen sodium alginate hydrogel-skin Wound healing Bionic

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Extracellular matrix-derived materials for tissue engineering and regenerative medicine:A journey from isolation to characterization and application

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Bioactive Materials 2024年第4期34卷 494-519页

作者： Helena Vilaça-Faria Jennifer Noro Rui l.reis Rogério P.Pirraco 3B’s Research Group I3Bs-Research Institute on BiomaterialsBiodegradables and BiomimeticsUniversity of MinhoHeadquarters of the European Institute of Excellence on Tissue Engineering and Regenerative MedicineAveParkParque de Ciência e TecnologiaZona Industrial da Gandra4805-017BarcoGuimarãesPortugal ICVs/3B’s-PT Government Associate laboratory BragaGuimarãesPortugal

Biomaterial choice is an essential step during the development tissue engineering and regenerative medicine(TERM)*** selected biomaterial must present properties allowing the physiological-like recapitulation of several processes that lead to the reestablishment of homeostatic tissue or organ *** derived from the extracellular matrix(ECM)present many such properties and their use in the field has been steadily *** this growing importance,it becomes imperative to provide a comprehensive overview of ECM biomaterials,encompassing their sourcing,processing,and integration into TERM *** review compiles the main strategies used to isolate and process ECM-derived biomaterials as well as different techniques used for its characterization,namely biochemical and chemical,physical,morphological,and ***,some of their applications in the TERM field are explored and discussed.

关键词： Extracted ECM Extraction methods Characterization ECM-derived applications

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Analyzing the economic viability of a large-scale integrated model of municipal solid waste:a study case for the most important Brazilian economic region

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Waste Disposal and sustainable Energy 2020年第3期2卷 231-247页

作者： Octavio Pimenta reis Neto Mechanical Engineering Faculty at state University of Campinas(PDsE/FEM/UNICAMP) Av.Mofarrej275-Apto 212 B1São PauloSP CEP 05311-000Brazil

Despite the National Policy for solid Waste(PNRs)in 2010,nothing has changed to waste disposal in *** to reach 100%of all Municipal solid Waste(MsW)collected and treated in landfills by Aug.2nd,2014,until nowadays,42%of this total remains in *** the most important national economic region treating its urban waste in landfills,what it has is no more than 4%of recycling and its landfills reaching the *** other ones is getting harder year by year,due to water reservoirs around the region,high freight costs,waste disposal and the severe control of emissions associated with its *** article comes to break the paradigm of investment and profitability proposing an alternative to the land-use,achieving higher rates of *** economic viability,carried out through well-known financial variables and Monte Carlo analysis,has taken into account proven local waste characteristics and market prices for recyclables and energy without *** considered a proposal highly intensive in capital and people,the revenues from the sales would be enough to guarantee the viability of 100%equity with IRR of 33.7%and ROI of 24.5%per year within the confidence of 99%.

关键词： solid waste sorting Recycling Waste-to-energy Metropolitan Region of são Paulo Energy recovering

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Glucagon-like peptide-1 and impaired counterregulatory responses to hypoglycemia in type 1 diabetes

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World Journal of Diabetes 2025年第2期16卷 297-304页

作者： Gabriel reis Rocha Fabrício Freire de Melo Instituto Multidisciplinar em saúde Universidade Federal da BahiaVitória da Conquista 45065-430BahiaBrazil

This letter comments on a study by Jin et al,published recently in the World Journal of *** is a significant complication of diabetes,with primary defense mechanisms involving the stimulation of glucagon secretion inα-cells and the inhibition of insulin secretion in pancreaticβ-cells,which are often compromised in type 1 diabetes mellitus(T1DM)and advanced type 2 diabetes *** hypoglycemia predisposes the development of impaired hypoglycemia awareness,a condition underpinned by complex pathophysiological processes,encompassing central nervous system adaptations and several hormonal interactions,including a potential role for glucagon-like peptide-1(GlP-1)in paracrine and endocrine *** evidence indicates that GlP-1 may impair hypoglycemic counterregulation by disrupting the sympathoadrenal system and promoting somatostatin release in pancreaticδ-cells,which inhibits glucagon secretion from neighboringα-***,current trials evaluating GlP-1 receptor agonists(GlP-1 RAs)in T1DM patients have shown promising benefits in reducing insulin requirements and body weight,without increasing the risk of *** research is essential to elucidate the specific roles of GlP-1 and GlP-1 RAs in modulating glucagon secretion and the sympathetic-adrenal reflex,and their impact on hypoglycemia unawareness in T1DM patients.

关键词： Glucagon-like peptide 1 Type 1 diabetes mellitus Counterregulatory hypoglycemic dysfunction Hypoglycemia unawareness Glucagon sympathoadrenal system

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An Outlook on Implantable Biosensors for Personalized Medicine

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Engineering 2021年第12期7卷 1696-1699页

作者： Rita Rebelo Ana Isabel Barbosa Vitor M.Correlo Rui l.reis Research Institute on Biomaterials Biodegradablesand BiomimeticsUniversity of MinhoHeadquarters of the European Institute of Excellence on Tissue Engineering and Regenerative MedicineBarcoGuimarães 4805-017Portugal ICVs/3B’s-PT Government-Associated laboratory BragaGuimarães 4710-057Portugal

Biosensors are a fast-growing field,as they have been shown to be very helpful in our daily life,playing roles in industries such as agriculture,food safety,homeland security,bioprocessing,environmental monitoring,and industrial *** these,the application of biosensing in medicine and biomedical engineering may have the highest potential for growth and for affecting human quality of life in the near *** potential is driven by the need for new and improved devices and technologies with improved sensitivity,specificity,reliability,and biocompatibility.

关键词： Outlook specificity playing

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Replication of natural surface topographies to generate advanced cell culture substrates

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Bioactive Materials 2023年第10期28卷 337-347页

作者： N.O.Monteiro J.F.Fangueiro R.l.reis N.M.Neves 3B’s Research Group I3Bs-Research Institute on BiomaterialsBiodegradables and BiomimeticsUniversity of MinhoHeadquarters of the European Institute of Excellence on Tissue Engineering and Regenerative MedicineAveParkParque de Ciencia e Tecnologi1Zona Industrial da Gandr14805-017BarcoGuimaraesPortugal ICVs/3B’s-PT Government Associate laboratory Brag1Guimar˜aesPortugal

surface topographies of cell culture substrates can be used to generate in vitro cell culture environments similar to the in vivo cell niches. In vivo, the physical properties of the extracellular matrix (ECM), such as its topography, provide physical cues that play an important role in modulating cell function. Mimicking these properties remains a challenge to provide in vitro realistic environments for cells. Artificially generated substrates’ topographies were used extensively to explore this important surface cue. More recently, the replication of natural surface topographies has been enabling to exploration of characteristics such as hierarchy and size scales relevant for cells as advanced biomimetic substrates. These substrates offer more realistic and mimetic environments regarding the topographies found in vivo. This review will highlight the use of natural surface topographies as a template to generate substrates for in-vitro cell culture. This review starts with an analysis of the main cell functions that can be regulated by the substrate’s surface topography through cell-substrate interactions. Then, we will discuss research works wherein substrates for cell biology decorated with natural surface topographies were used and investigated regarding their influence on cellular performance. At the end of this review, we will highlight the advantages and challenges of the use of natural surface topographies as a template for the generation of advanced substrates for cell culture.

关键词： Biomimetic topography Cell culture substrates Natural surface topographies

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Functionally graded additive manufacturing to achieve functionality specifications of osteochondral scaffolds

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Bio-Design and Manufacturing 2018年第1期1卷 69-75页

作者： Mario Monzon Chaozong liu sara Ajami Miguel Oliveira Ricardo Donate Viviana Ribeiro Rui l. reis Departamento de Ingenieria Mecanica Universidad de Las Palmas de Gran Canaria Edificio de fabricacion integrada 35017 Las Palmas de GC Spain Division of surgery and Interventional science University College London Stanmore London HA7 4LP UK 3Bs Biomaterials Biodegradables and Biomimetics Universidade Do Minho Parque de Ciencia e Tecnologia Zona Industrial da Gandra 4805-17 Barco GMR Portugal Integrated and Advanced Manufacturing Processes Research Group Universidad de Las PaJmas de Gran Canaria Edificio de fabricacion integrada 35017 Las Palmas de GC Spain

Introduction Osteoarthritis （OA） is a degenerative joint disease, characterized by cartilage loss and changes in bone at the interface of a joint resulting in pain, stiffness and reduced mobility. OA is one of the most prevalent chronic conditions as identified in Bone and Joint Decade. According to the World Health Organization, 40% of people over the age of 70 have OA. This joint disease affects around 0.4 billion people with patients in Europe accounting for up to 30%. The figure is set to increase with the ageing problem.

关键词：骨性关节炎疾病治疗方法生物技术

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Exploring spatial relationships between stream channel features,water depths and flow velocities during flash floods using HEC-GeoRAs and Geographic Information systems

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Journal of Geographical sciences 2022年第4期32卷 757-782页

作者： Miguel lEAl Eusébio reis Pedro Pinto sANTOs Centre of Geographical studies and Associated laboratory TERRA Institute of Geography and Spatial PlanningUniversidade de Lisboa1600-276 LisbonPortugal Forest Research Centre and Associated laboratory TERRA School of AgricultureUniversidade de LisboaTapada da Ajuda1349-017 LisbonPortugal

Water depths and flow velocities decisively influence the damage caused by flash *** Information system(GIs)is a powerful and useful tool,allowing the spatial analysis of results obtained by hydraulic modelling,namely from the HEC-RAs/HEC-GeoRAs *** GIs spatial analysis performed in this study seeks to explain and quantify the spatial relationships between the stream channel features and flow components during flash flood *** these relationships are generically known,there are few studies exploring this subject in different geographic contexts.A 1D hydraulic model was applied in a small watershed in Portugal,providing good results in the definition of floodable areas,water depths and longitudinal *** direct relationship was found between water depths and velocities in the floodable areas;however,negative strong correlations were found between the two flow components along the stream *** slope,channel and flood width,and roughness prove to be highly relevant on the longitudinal variations of water depths and velocities and on the location of maximum *** peak discharges and return periods(R;)can change the relationships between water depths and velocities at the same *** can be improved with more accurate elevation data for stream channels and floodplains.

关键词： flash floods water depth flow velocity geographic information systems(GIs) spatial analysis

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Neurochemical plasticity of Müller cells after retinal injury: overexpression of GAT-3 may potentiate excitotoxicity

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Neural Regeneration Research 2015年第9期10卷 1376-1378页

作者： Clarissa s.schitine Fernando G.de Mello Ricardo A.M.reis laboratório de Neuroquímica Instituto de Biofísica Carlos Chagas Filho Universidade Federal do Rio de Janeiro laboratório de Neuroanatomia Celular Instituto de Biofísica Carlos Chagas Filho Universidade Federal do Rio de Janeiro

The retina is a multilayered tissue that develops following a central-to-peripheral gradient. Its structure derives from multipotent precursors, as shown through clonal analysis of retinal cell lineage. These progenitors generate diverse cell types, controlled by complex influences of intrinsic and extrinsic factors （Hatakevama and Kagevama, 2004）.

关键词： GAT Neurochemical plasticity of M ller cells after retinal injury overexpression of GAT-3 may potentiate excitotoxicity RGCs

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