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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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Prediction of future capacity and internal resistance of Li-ion cells from one cycle of input data

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Energy and AI 2021年第3期5卷 209-216页

作者： Calum Strange Gonçalo dos reis School of Mathematics University of EdinburghThe King’s BuildingsEdinburghEH93FDUK Centro de Matemática e Aplicações(CMA) FCTUNLQuinta da Torre2829-516 CaparicaPortugal

There is a large demand for models able to predict the future capacity retention and internal resistance(IR)of Lithium-ion battery cells with as little testing as *** provide a data-centric model accurately predicting a cell’s entire capacity and IR trajectory from one single cycle of input *** represents a significant reduction in the amount of input data needed over previous *** approach characterises the capacity and IR curve through a small number of key points,which,once predicted and interpolated,describe the full *** this approach the remaining useful life is predicted with an 8.6%mean absolute percentage error when the input-cycle is within the first 100 cycles.

关键词： Capacity degradation Internal resistance degradation Prediction of full degradation curve Knee and elbow-points Lithium-ion cells Machine learning Remaining useful life

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Genetic diversity and structure of Drimys brasiliensis in southern Brazil:insights for conservation

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Journal of Forestry Research 2020年第4期31卷 1325-1332页

作者： Alexandre mariot Tiago Montagna Maurício Sedrez dos reis Núcleo de Pesquisas Em Florestas Tropicais Pós-Graduacāo Em Recursos Genéticos VegetaisCentro de Ciências AgráriasUniversidade Federal de Santa CatarinaRodovia Admar Gonzaga1346FlorianópolisSC 88034-000Brazil

Population genetics studies are widely recognized for generating useful knowledge for biodiversity *** date,however,little is known about the levels and distribution of genetic diversity of Drymis brasiliensis(Miers LC),a tree species from the Atlantic ***,in this study,we investigated how genetic diversity is distributed within and among populations of *** from southern Brazil using allozyme markers to genotype reproductive trees(8 populations)and seedlings(3 populations).Furthermore,in two populations,we established two permanent plots(5.1 and 1 ha)to analyze fine-scale genetic structure(FSGS).Studied populations presented low levels of genetic diversity(reproductive=0.085;seedlings=0.054)and high fixation indexes(reproductive=0.396;seedlings=0.231).Genetic divergence among populations was equal to 0.05,which is significant,signaling that few populations can conserve large portions of the species total genetic *** was only detected for one population,when reproductive individuals were separated by less than40 *** genetic diversity combined with high fixation indexes clearly signal a risk of losing ***,conservation efforts should be aimed at enhancing gene flow within the studied populations.

关键词： Atlantic Rainforest Effective population size Fine-scale genetic structure Seed collection

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Effects of bioactive compounds from Pleurotus mushrooms on COVID-19 risk factors associated with the cardiovascular system

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Journal of Integrative Medicine 2022年第5期20卷 385-395页

作者： Eduardo Echer dos reis Paulo Cavalheiro Schenkel Marli Camassola Department of Physiology Federal University of Rio Grande do SulCampus Centro 90050-170 Porto AlegreBrazil Enzymes and Biomass Laboratory Institute of BiotechnologyUniversity of Caxias do Sul95070-560 Caxias do SulBrazil Department of Physiology and Pharmacology Federal University of PelotasCampus Capão do Leão96900-010 PelotasBrazil

Mushrooms are a group of fungi with great diversity and ultra-accelerated *** a consequence,mushrooms have developed a protective mechanism consisting of high concentrations of antioxidants such as selenium,polyphenols,β-glucans,ergothioneine,various vitamins and other bioactive *** mushrooms of the Pleurotus genus have generated scientific interest due to their therapeutic properties,especially related to risk factors connected to the severity of coronavirus disease 2019(COVID-19).In this report,we highlight the therapeutic properties of Pleurotus mushrooms that may be associated with a reduction in the severity of COVID-19:antihypertensive,antihyperlipidemic,antiatherogenic,anticholesterolemic,antioxidant,anti-inflammatory and antihyperglycemic *** properties may interact significantly with risk factors for COVID-19 severity,and the therapeutic potential of these mushrooms for the treatment or prevention of this disease is *** this,studies show that regular consumption of Pleurotus species mushrooms or components isolated from their tissues is beneficial for immune *** species mushrooms may have a role in the prevention or treatment of infectious diseases either as food supplements or as sources for pharmacological agents.

关键词： Pleurotus Food supplements COVID-19 SARS-Cov-2 Coronavirus Antiviral agents

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Lithium-ion battery data and where to find it

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Energy and AI 2021年第3期5卷 255-269页

作者： Gonçalo dos reis Calum Strange Mohit Yadav Shawn Li School of Mathematics University of EdinburghThe King’s BuildingsEdinburgh EH93FDUK Centro de Matemática e Aplicações(CMA) FCTUNLQuinta da Torre2829-516 CaparicaPortugal Indian Institute of Technology KanpurIndia

Lithium-ion batteries are fuelling the advancing renewable-energy based *** the core of transformational developments in battery design,modelling and management is *** this work,the datasets associated with lithium batteries in the public domain are *** review the data by mode of experimental testing,giving particular attention to test variables and data *** highlighted tools and platforms,over 30 datasets are reviewed.

关键词： Lithium battery Public data Battery data Battery tests Machine learning

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Automatic method for the estimation of li-ion degradation test sample sizesrequired to understand cell-to-cell variability

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Energy and AI 2022年第3期9卷 139-147页

作者： Calum Strange Michael Allerhand Philipp Dechent Gonçalo dos reis School of Mathematics University of EdinburghThe Kings buildingsEdinburghEH93JFScotlandUnited Kingdom Institute for Power Electronics and Electrical Drives(ISEA) RWTH Aachen UniversityAachenGermany Centro de Matematica e Aplicacoes(CMA) Faculdade de Ciencias e TecnologiaCampus da CaparicaCaparica2829-516Portugal

The testing of battery cells is a long and expensive process, and hence understanding how large a test set needsto be is very useful. This work proposes an automated methodology to estimate the smallest sample size ofcells required to capture the cell-to-cell variability seen in a larger population. We define cell-to-cell variationbased on the slopes of a linear regression model applied to capacity fade curves. Our methodology determinesa sample size which estimates this variability within user specified requirements on precision and *** sample size is found using the distributional properties of the slopes under a normality assumption, andan implementation of the approach is available on *** the five datasets in the study, we find that a sample size of 8–10 cells (at a prespecified precision andconfidence) captures the cell-to-cell variability of the larger datasets. We show that prior testing knowledge canbe leveraged with machine learning models to operationally optimise the design of new cell-testing, leadingup to a 75% reduction in experimental costs.

关键词： Battery Testing Lithium-ion Degradation Statistics Manufacturing Machine learning

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Agronomic evaluation of Herbaspirillum seropedicae strain ZAE94 as an inoculant to improve maize yield in Brazil

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Pedosphere 2021年第4期31卷 583-595页

作者： Gabriela C.ALVES Carlos L.R.dos SANTOS Jerri E.ZILLI Fabio B.dos reis JUNIOR Ivanildo E.MARRIEL Farley A.da F.BREDA Robert M.BODDEY Veronica M.reis Federal Rural University of Rio de Janeiro Department of Soilskm 7 BR 465Seropédica RJ 23900-000(Brazil) Federal University of Mato Grosso 2367 Fernando Corrêa Costa AvenueBoa Esperança M 78060-900(Brazil) Embrapa Agrobiology km 07 BR 465Seropédica RJ 23891-000(Brazil) Embrapa Cerrados BR-020 km 18Planaltina DF 73310-970(Brazil) Embrapa Maize and Sorghum MG 424 km 45Sete Lagoas MG 35701-970(Brazil)

Diazotrophic bacteria applied as a seed inoculant can improve the grain yield of several crops including maize. The current study aimed to test the agronomic efficiency and contribution of biological nitrogen fixation(BNF) of the endophytic diazotroph Herbaspirillum seropedicae strain ZAE94 to maize under field conditions. Eighteen field assays were conducted in four different locations during consecutive years on two hybrids and two varieties of maize in a random block design with four replicates using a peat-based inoculant. The inoculant containing the ZAE94 strain was applied without nitrogen(N)fertilization or with 40 kg N ha^(-1) and was compared to the application of 40 and 80 kg N ha^(-1) without inoculation. Crop productivity and N accumulation in the grain were evaluated in addition to ^(15)N natural abundance(δ^(15)N) to evaluate BNF in the treatments without N fertilization. Fertilization at 40 kg N ha^(-1) plus bacterial inoculation produced crop yields similar to the treatment with 80 kg N ha^(-1) and increased grain N content, especially in the off-season with 40 kg N ha^(-1). The inoculation treatments showed lower δ^(15)N values than the non-inoculated treatments, which was most evident in the off-season. The BNF contributed about 30% of N accumulated in plants inoculated with ZAE94. On average, 64% of the N fertilized plots showed an increase of the parameters evaluated in the inoculated treatments, compared with the control. Inoculation also increased root length, root volume, and leaf area, and these parameters were positively correlated with plant weight using a hydroponic assay. This study revealed that the application of H. seropedicae inoculant increased the amount of N in plants owing to BNF, and there is a better chance of yield response to inoculation under low N fertilizer application in the off-season.

关键词： agronomic efficiency biological nitrogen fixation endophytic diazotroph inoculation 15N natural abundance plant growth-promoting bacteria

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Omics analyses in citrus reveal a possible role of RNA translation pathways and Unfolded Protein Response regulators in the tolerance to combined drought, high irradiance, and heat stress

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Horticulture Research 2023年第7期10卷 165-175页

作者： Damián Balfagón Sara IZandalinas Tadeu dos reis de Oliveira Claudete Santa-Catarina Aurelio Gómez-Cadenas Departamento de Biología Bioquímica y Ciencias NaturalesAv.Sos Baynat s/n.Universitat Jaume I46520 Castellóde la PlanaSpain Laboratório de Biologia Celular e Tecidual(LBCT) Centro de Biociências E Biotecnologia(CBB)Universidade Estadual Do Norte Fluminense Darcy Ribeiro(UENF)Av.Alberto Lamego 2000Campos Dos GoytacazesRJ28013-602Brazil

Environmental changes derived from global warming and human activities increase the intensity and frequency of stressful conditions for *** abiotic factors acting simultaneously enhance stress pressure and drastically reduce plant growth,yield,and *** combination causes a specific stress situation that induces a particular plant response different to the sum of responses to the individual ***,by comparing transcriptomic and proteomic profiles to different abiotic stress combinations in two citrus genotypes,Carrizo citrange(Citrus sinensis×Poncirus trifoliata)and Cleopatra mandarin(Citrus reshni),with contrasting tolerance to different abiotic stresses,we revealed key responses to the triple combination of heat stress,high irradiance and *** specific transcriptomic response to this stress combination in Carrizo was directed to regulate RNA metabolic pathways and translation processes,potentially conferring an advantage with respect to *** addition,we found endoplasmic reticulum stress response as common to all individual and combined stress conditions in both genotypes and identified the accumulation of specific groups of heat shock proteins(HSPs),such as small HSPs and HSP70s,and regulators of the unfolded protein response,BiP2 and PDIL2-2,as possible factors involved in citrus tolerance to triple stress *** together,our findings provide new insights into the acclimation process of citrus plants to multiple stress combination,necessary for increasing crop tolerance to the changing climatic conditions.

关键词： citrus Citrus stress

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The use of Vis-NIR-SWIR spectroscopy in the prediction of soil available ions after application of rock powder

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Information Processing in Agriculture 2024年第1期11卷 26-44页

作者： Marlon Rodrigues Josiane Carla Argenta Everson Cezar Glaucio Leboso Alemparte Abrantes dos Santos ÖnderÖzal Amanda Silveira reis Marcos Rafael Nanni Department of Agronomy State University of MaringáColombo AvenueMaringá87020900Brazil Department of Plant and Soil Sciences Mississippi State UniversityMS 39762USA International Agricultural Research and Training Center Izmir 35660Turkey

Some of the problems attributed to traditional laboratory analyses that limit the correct assessment of the nutrient contents in the soil are time requirements and high cost of the soil nutrient *** solve these problems,a study was carried out to evaluate the use of visible,near-infrared,and short-wave infrared(Vis-NIR-SWIR)spectroscopy in the prediction of soil available ions submitted to the application of rock *** study was carried out on an Arenosol in ParanavaíCity/***(rock powders)were arranged within a split-plot system designed in randomized blocks with four *** was cultivated for 14 months after the application of rock ***,96 soil samples were collected for measuring the pH and available ions P,K^(+),Ca^(2+),Mg^(2+),S-SO_(4)^(2-),Si,Cu^(2+),Fe^(2+),Mn^(2+),and Zn^(2+)as well as spectral reading through a Vis-NIR-SWIR spectroradiometer to predict the soil chemical attributes through the partial least square regression(PLS)*** results showed that the elements K^(+),Ca^(2+),Mg^(2+),Cu^(2+),and Fe^(2+)could be predicted with a reasonable rightness degree(R^(2)_(p)>0.50,RPDp>1.40)from spectral ***,for the attributes pH,P,S-SO_(4)^(2-),Si,Mn^(2+),and Zn^(2+),there were no satisfactory models(R^(2)_(p)<0.50,RPDp<1.40).Thus,the application of rock powder changed the spectral curves and,because of that,allows the building of PLS models to predict the elements K^(+),Ca^(2+),Mg^(2+),Cu^(2+),and Fe^(2+).Therefore,Vis-NIR-SWIR spectroscopy is a promising alternative to the routine analyses of soil fertility since it has advantages such as fast analytical speed,low cost,easy to operate,non-destructive,and environmentally friendly,because it does not use harmful chemicals.

关键词： Alternative inputs Available Ions Multivariate analysis Soil Spectroscopy

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Metabolic disease and the liver: A review

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World Journal of Hepatology 2024年第1期16卷 33-40页

作者： Márcia Vargas Sheila de Castro Cardoso Toniasso Patricia G Riedel Camila Pereira Baldin Francielle Lopes dos reis Robson Martins Pereira Maria Carlota Borba Brum Dvora Joveleviths mario reis Alvares-da-Silva Program of Graduate Science in Gastroenterology and Hepatology Federal University of Rio Grande do SulPorto Alegre 90040-060Rio Grande do SulBrazil School of Medicine Federal University of Rio Grande do SulPorto Alegre 90040-060Brazil Program of Graduate Science in Gastroenterology and Hepatology Clinicas Hospital of Porto AlegrePorto Alegre 90410000Brazil Medicine Faculty Federal University of Rio Grande do Sul Federal University of Rio Grande do SulPorto Alegre 90040-060Brazil Division of Gastroenterology and Hepatology Clinicas Hospital of Porto AlegrePorto Alegre 90035007Brazil

Metabolic dysfunction-associated steatotic liver disease(MASLD)is the most common liver disease worldwide,with an estimated prevalence of 31%in Latin *** presence of metabolic comorbidities coexisting with liver disease varies substantially among *** is acknowledged that obesity is boosting the type 2 diabetes mellitus“epidemic,”and both conditions are significant contributors to the increasing number of patients with *** steatohepatitis represents a condition of chronic liver inflammation and is considered the most severe form of *** diagnosis is based on the presence of steatosis,noninvasive scores and altered liver *** scores of liver fibrosis,such as serum biomarkers,which should be used in primary care to rule out advanced fibrosis,are simple,inexpensive,and widely ***,guidelines from international hepatology societies recommend using noninvasive strategies to simplify case finding and management of high-risk patients with MASLD in clinical ***,there is no definite pharmacological treatment for the *** public health policies to treat patients with risk factors for MASLD prevention is essential.

关键词： Nonalcoholic fatty liver disease Primary care Metabolic risk Liver Metabolism

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