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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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能源与人工智能(英文) 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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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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Plant growth and metabolism of exotic and native Crotalaria species for mine land rehabilitation in the Amazon

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林业研究（英文版） 2024年第1期 147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 de Ávila André Rodrigues dos reis Silvio Junio Ramos

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Lithium-ion battery data and where to find it

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能源与人工智能(英文) 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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Effect of Turbidity on Semi-Automatic Analysis of Copepod Size and Abundance Distribution in the Water Column

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Advances in Bioscience and Biotechnology（生命科学与技术进展） 2024年第6期 380页

作者： Thiago da Silva Matos Carolina Siqueira dos reis Laura de Andrade Moura Márcio Abreu Ricardo Coutinho Lohengrin Fernandes

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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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Gleason score and tumor laterality in radical prostatectomy and transrectal ultrasound-guided biopsy of the prostate： a comparative study

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Asian Journal of Andrology 2015年第5期17卷 815-820,I0009-I0010页

作者： Renan A Pereira Roberto S Costa Valdair F Muglia Fabio Franca Silva Joyce S Lajes Rodolfo B dos reis Gyl EB Silva Department of Pathology Ribeirao Preto School of Medicine University of Sao Paulo Sao Paulo Brazil Department of Internal Medicine (Center of Science of Image) Ribeirao Preto School of Medicine University of Sao Paulo Sao Paufo Brazil Pathology Service University Hospital of Federal University of Maranhao Sao Luis Maranhao Brazil University Hospital of Federal University of Maranhao Sao Luis Maranhao Brazil Department of Surgery and Anatomy Division of Urology Ribeirao Preto School of Medicine University of Sao Paulo Sao Paulo Brazil

We aimed to compare Gleason score and tumor laterality between transrectal ultrasound-guided biopsy of the prostate （TRUSBX） and radical prostatectomy （RP）. Some factors that could cause a discrepancy in results between these two procedures were also evaluated. Among the 318 cases reviewed, 191 cases were selected for inclusion in this comparative Study, We divided the patients into two groups using the Gleason score： an intermediate/high-grade group （≥7） and a low-grade group （〈6）. Exploratory analyses were conducted for comparisons between groups. We also performed comparisons between TRUSBX and RP for tumor laterality. TRUSBX overestimated 6% and underestimated 24% cases in comparison with RP for Gleason score, and overestimated 2.6% and underestimated 46% cases compared with RP for tumor laterality. Biopsy specimens were slightly smaller in TRUSBX cases with underestimated tumor laterality （P〈 0.05）, and no relationship between the biopsy specimen size and underestimated Gleason score in TRUSBX was found. Prostatic volume showed no statistical correlation with the likelihood of under or overestimation （P 〉 0.05）. Thus, our study showed that TRUSBX has a high likelihood of underestimating both the Gleason score and tumor laterality in prostate cancer （PCa）. The size of the fragment appears to be an important factor influencing the likelihood of laterality underestimation and Gleason score overestimation via TRUSBX. Due to the high likelihood of underestimation of the Gleason score and tumor laterality by 12-core prostate biopsy, we conclude that this type of biopsy should not be used alone to guide therapy in Pca.

关键词： Gleason score prostate biopsy prostate carcinoma prostatectomy tumor tumor laterality

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Risk Stratification in Obstetrics: An Integrated Approach to Maternal Health

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Open Journal of Obstetrics and Gynecology（妇产科期刊） 2024年第6期 903页

作者： Taina Crespo Mendonca Bianca Beatriz Soares dos reis Júlia Cruz Coelho Antônio de Oliveira Battistini Pestana Vitória Carolina Barreto Negri Alvaro Augusto Trigo

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J-A formulation: A finite element methodology for simulating superconducting devices

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Superconductivity 2023年第2期6卷 64-73页

作者： Gabriel dos Santos Bárbara Maria Oliveira Santos Felipe Sass Flávio Goulart dos reis Martins Guilherme Gonçalves Sotelo Rubens de Andrade Junior Federal Fluminense University Brazil State University of Rio de Janeiro Brazil Federal University of Rio de Janeiro Brazil

High‐temperature superconductors are a powerful technological option to be applied in the current scenario of energy *** applications include fault current limiters,power electrical cables,and electrical machines,for *** to the non‐linearities of superconductors,it is computationally costly to run real models of superconducting ***,it is of paramount importance to have a reliable and fast formulation to model superconducting *** paper proposes a new hybrid J‐A formulation to simulate superconducting *** new formulation is validated with 5 case studies,some of which are *** J‐A formulation agrees in all cases and has a smaller computation time when compared with the T‐A ***,due to the simple implementation,the proposed formulation allows the possibility of running the J and A formulations in the same order and presents itself as a potential feature to speed up and help the design of the superconducting devices.

关键词： High‐temperature superconductors Finite element method J‐A formulation

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