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Few-Shot Learning Enables Population-Scale Analysis of Leaf Traits in Populus trichocarpa

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Plant Phenomics 2023年第3期5卷 581-597页

作者： John Lagergren Mirko Pavicic Hari b.Chhetri Larry M.York Doug Hyatt David Kainer Erica M.Rutter Kevin Flores Jack bailey-bale Marie Klein Gail Taylor daniel Jacobson Jared Streich biosciences Division Oak Ridge National LaboratoryOak RidgeTNUSA Department of Applied Mathematics University of CaliforniaMercedCAUSA Department of Mathematics North Carolina State UniversityRaleighNCUSA Department of Plant Sciences University of CaliforniaDavisCAUSA

Plant phenotyping is typically a time-consuming and expensive endeavor,requiring large groups of researchers to meticulously measure biologically relevant plant traits,and is the main bottleneck in understanding plant adaptation and the genetic architecture underlying complex traits at population *** this work,we address these challenges by leveraging few-shot learning with convolutional neural networks to segment the leaf body and visible venation of 2,906 Populus trichocarpa leaf images obtained in the *** contrast to previous methods,our approach(a)does not require experimental or image preprocessing,(b)uses the raw RGb images at full resolution,and(c)requires very few samples for training(e.g.,just 8 images for vein segmentation).Traits relating to leaf morphology and vein topology are extracted from the resulting segmentations using traditional open-source image-processing tools,validated using real-world physical measurements,and used to conduct a genome-wide association study to identify genes controlling the *** this way,the current work is designed to provide the plant phenotyping community with(a)methods for fast and accurate image-based feature extraction that require minimal training data and(b)a new population-scale dataset,including 68 different leaf phenotypes,for domain scientists and machine learning *** of the few-shot learning code,data,and results are made publicly available.

关键词： networks neural image

CD34^(+ )progenitor cells as diagnostic and therapeutic targets in Alzheimer's disease

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Neural Regeneration Research 2023年第3期18卷 535-536页

作者： daniel Romaus-Sanjurjo Antía Custodia Alberto Ouro Tomás Sobrino NeuroAging Group(NEURAL) Clinical Neurosciences Research Laboratory(LINC)Health Research Institute of Santiago de Compostela(IDIS)Santiago de CompostelaSpain

Alzheimer’s disease(AD)is the main neurodegenerative disease leading to dementia and cognitive impairment in the *** AD to be an epidemic,an increase from the current 50 million to more than 150 million patients is e... 详细信息

关键词： Alzheimer progenitor impairment

Effects on physiologic measures of appetite from intragastric balloon and endoscopic sleeve gastroplasty: results of a prospective study

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Chinese Medical Journal 2022年第10期135卷 1234-1241页

作者： babusai Rapaka daniel b.Maselli Gontrand Lopez-Nava Inmaculada bautista-Castano Reem Matar Veeravich Jaruvongvanich Eric J.Vargas Andrew C.Storm Andres Acosta barham K.Abu Dayyeh Division of Gastroenterology and Hepatology Mayo ClinicRochesterMN 55905USA Madrid Sanchinarro University Hospital MadridSpain

background: Endoscopic bariatric therapies can help address widening management gaps in obesity. Their ability to facilitate weight loss is largely tied to influences on appetite through perturbations of gastric emptying and accommodation. As these tools gain traction in obesity therapy, their physiologic underpinnings require exploration, which may enhance efficacy, tolerance, and patient-tailored ***: We prospectively assessed consecutive subjects with fluid-filled intragastric balloons (IGbs) (n = 18) placed between October 2016 and June 2017 or underwent endoscopic sleeve gastroplasty (ESG) (n = 23) from March 2018 to June 2018. Patients underwent physiologic appraisal at 3 months with13C-spirulina-based gastric emptying breath test to determine time to half emptying (T50), as well as maximum tolerated volume (MTV) of a standard nutrient drink test. Changes in T50 and MTV at 3 months were compared with percent total body weight loss (%TbWL) at 3 and 6 months using best-fit linear ***: The change in T50 at 3 months correlated with %TbWL at 3 months for IGb (P = 0.01) and ESG (P = 0.01) but with greater impact on %TbWL in IGb compared to ESG (R2 = 0.42vs. 0.26). Change in T50 at 3 months was predictive of weight loss at 6 months for IGb (P = 0.01) but not ESG (P = 0.11). ESG was associated with greater decrease in MTV compared to IGb (340.25 ± 297.97 mLvs. 183.00 ± 217.13 mL,P = 0.08), indicting an enhanced effect on satiation through decreased gastric accommodation. Changes in MTV at 3 months did not correlate with %TbWL for either IGb (P = 0.26) or ESG (P = 0.49) but trended toward significance for predicting %TbWL at 6 months for ESG (P = 0.06) but not IGb (P = 0.19).Conclusion: IGb and ESG both induce weight loss but likely through distinct gastric motor function phenotypes, and gastric emptying may predict future weight loss in patients with IGb.

关键词： Intragastric balloon Endoscopic sleeve gastroplasty Gastric emptying Gastric accommodation Obesity

Lovastatin as a supplement to mitigate rumen methanogenesis:an overview

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Journal of Animal Science and biotechnology 2022年第2期13卷 353-364页

作者： Amaury Ábrego-Gacía Héctor M.Poggi-Varaldo Vania Robles-González Teresa Ponce-Noyola Graciano Calva-Calva Elvira Ríos-Leal daniel Estrada-bárcenas Alfredo Mendoza-Vargas Department of biotechnology and bioengineering CINVESTAV-IPNP.O.Box 17-74007000 Mexico CityMexico Environmental biotechnology and Renewable Energies Group CINVESTAV-IPNP.O.Box 17-74007000 Mexico CityMexico Instituto de Hidrología Universidad Tecnológica de la MixtecaOaxaca 69000 Huajuapan de LeónMexico National Collection of Microbial and Cellular Cultures CINVESTAV-IPNP.O.Box17-74007000 Mexico CityMexico Unidad de Secuenciación e Identificación de Polimorfismos Instituto Nacional de Medicina Genómica14610 Mexico CityMexico

Methane from enteric fermentation is the gas with the greatest environmental impact emitted by ***(Lv)addition to feedstocks could be a strategy to mitigate rumen methane emissions via decreasing the population of methanogenic archaea(MA).Thus,this paper provides the first overview of the effects of Lv supplementation,focusing on the inhibition of methane production,rumen microbiota,and ruminal *** indicated that Lv treatment had a strong anti-methanogenic effect on pure strains of ***,there are uncertainties from in vitro rumen fermentation trials with complex substrates and rumen ***-state fermentation(SSF)has emerged as a cost-effective option to produce *** this way,SSF of agricultural residues as an Lv-carrier supplement in sheep and goats demonstrated a consistent decrease in ruminal methane *** experimental evidence for in vitro conditions showed that Lv did not affect the volatile fatty acids(VFA).However,in vivo experiments demonstrated that the production of VFA was *** did not negatively affect the digestibility of dry matter during in vitro and in vivo methods,and there is even evidence that it can induce an increase in *** the rumen microbiota,populations of MA were reduced,and no differences were detected in alpha and beta diversity associated with Lv ***,some changes in the relative abundance of the microbiota were *** studies are recommended on:(i)Lv biodegradation products and stability,as well as its adsorption onto the solid matter in the rumen,to gain more insight on the“available”or effective Lv concentration;and(ii)to determine whether the effect of Lv on ruminal fermentation also depends on the feed composition and different ruminants.

关键词： Fermentation Lovastatin Methanogenesis Microbiota Rumen

Targeted delivery of RNAi to cancer cells using RNA-ligand displaying exosome

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Acta Pharmaceutica Sinica b 2023年第4期13卷 1383-1399页

作者： Nasir Uddin daniel Wbinzel Dan Shu Tian-Min Fu Peixuan Guo Center for RNA Nanobiotechnology and Nanomedicine Division of Pharmaceutics and PharmacologyCollege of Pharmacythe Ohio State UniversityColumbusOH 43210USA Dorothy M.Davis Heart and Lung Research Institute the Ohio State UniversityColumbusOH 43210USA James Comprehensive Cancer Center College of Medicinethe Ohio State UniversityColumbusOH 43210USA Department of biological Chemistry&Pharmacology College of Medicinethe Ohio State UniversityColumbusOH 43210USA

Exosome is an excellent vesicle for in vivo delivery of therapeutics,including RNAi and chemical *** extremely high efficiency in cancer regression can partly be attributed to its fusion mechanism in delivering therapeutics to cytosol without endosome ***,being composed of a lipidbilayer membrane without specific recognition capacity for aimed-cells,the entry into nonspecific cells can lead to potential side-effects and *** engineering approaches for targeting-capacity to deliver therapeutics to specific cells is *** with chemical modification in vitro and genetic engineering in cells have been reported to decorate exosomes with targeting *** nanoparticles have been used to harbor tumor-specific ligands displayed on exosome *** negative charge reduces nonspecific binding to vital cells with negatively charged lipid-membrane due to the electrostatic repulsion,thus lowering the side-effect and *** this review,we focus on the uniqueness of RNA nanoparticles for exosome surface display of chemical ligands,small peptides or RNA aptamers,for specific cancer targeting to deliver anticancer therapeutics,highlighting recent advances in targeted delivery of siRNA and miRNA that overcomes the previous RNAi delivery *** understanding of exosome engineering with RNA nanotechnology promises efficient therapies for a wide range of cancer subtypes.

关键词： RNA interference RNA nanotechnology Endolysosome trapping Exosome engineering Targeted delivery Chemical drug delivery

A Meshless Regularization Method for a Two-Dimensional Two-Phase Linear Inverse Stefan Problem

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Advances in Applied Mathematics and Mechanics 2013年第6期5卷 825-845页

作者： b.Tomas Johansson daniel Lesnic Thomas Reeve Department of Science and Technology Campus Norrk¨opingLink¨oping UniversitySweden Department of AppliedMathematics University of LeedsLeeds LS29JTUK School of Mathematics University of BirminghamBirmingham B152TTUK

In this paper,a meshless regularization method of fundamental solutions is proposed for a two-dimensional,two-phase linear inverse Stefan *** numerical implementation and analysis are challenging since one needs to handle composite materials in higher ***,the inverse Stefan problem is ill-posed since small errors in the input data cause large errors in the desired output ***,regularization is necessary in order to obtain a stable *** results for several benchmark test examples are presented and discussed.

关键词： Heat conduction method of fundamental solutions(MFS) inverse Stefan problem two-phase change

Identification of KASP markers and putative genes for pre-harvest sprouting resistance in common wheat(Triticum aestivum L.)

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The Crop Journal 2023年第2期11卷 549-557页

作者： Guannan Liu daniel Mullan Aimin Zhang Hui Liu Dongcheng Liu Guijun Yan UWA School of Agriculture and Environment and The UWA Institute of AgricultureThe University of Western AustraliaPerthWA 6009Australia InterGrain Pty.Ltd. 19 Ambitious Link Bibra LakeWA 6163Australia State Key Laboratory of North China Crop Improvement and Regulation College of AgronomyHebei Agriculture UniversityBaoding 071000HebeiChina

Common wheat(Triticum aestivum L.)is the most important crop in the world and a typical allopolyploid with a large and complex ***-harvest sprouting(PHS)leads to a significant reduction in grain quality *** is a complex trait with related QTL located on different ***,the study of markers and genes related to PHS resistance is limited especially for whitegrained *** pairs of near isogenic lines(NILs)from a white-grained wheat cross of CharaDM5637b*8 targeting a major QTL for PHS resistance(***-3A.1)on wheat chromosme 3AL were genotyped using the 90K SNP Illumina iSelect *** SNPs were identified,with a 75%-100%consistency between genotype and phenotype in the resistant or susceptible *** 10 SNPs were converted to cost-effective kompetitive allele-specific PCR(KASP)*** of 48 wheat cultivars with different phenotypes of PHS identified four KASP markers with 81.3%-85.4%conformity between genotype and *** investigation revealed that the four SNPs(bS00022245_51,Kukri_c49927_151,bS00022884_51 and bS00110550_51)corresponding to the four validated KASP markers are residing in three independent genes(TraesCS3A03G1072800,TraesCS3A03G1072400,TraesCS3A03G1071800)close to each other with a distance of 4.28-4.48 Mb to the targeted *** three annotated genes have potential functions related to PHS *** study revealed that combined use of NILs and the 90K SNP chip is a powerful approach for developing KASP markers and mining functional genes in *** KASP markers for PHS resistance on chromosome 3AL are useful for high-throughput evaluation and marker-assisted selection,and the three identified genes could lead to a better understanding of the genetic pathways controlling PHS.

关键词： Pre-harvest sprouting(PHS) KASP marker Functional genes Chromosome 3AL 90K SNP assay Near-isogenic lines

Sediment transport simulation and design optimization of a novel marsh shoreline protection technology using computational fluid dynamics (CFD) modeling

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International Journal of Sediment Research 2022年第1期37卷 14-25页

作者： Salman Saki Grant besse Peng Yin daniel Gang Donald Hayes Department of Civil Engineering University of Louisiana at Lafayette University of Texas at San Antonio U.S.Army Engineer Research and Development Center (ERDC)

Coastal Louisiana has the nation’s most fragile and valuable wetlands,whose loss represents 80% of the total losses in the United *** severely restricted mobility of conventional shoreline protection structures makes them impossible to be *** Wave Suppression and Sediment Collection(WSSC) system is a novel technology of high mobility and compatible with existing shoreline protection *** laboratory studies on WSSC showed great potential for wave reduction and sediment *** current study aimed to optimize the design parameters of WSSC using a validated computational model.A computational fluid dynamics (CFD) model was developed and validated using experimental data from the previous laboratory ***,a parametric analysis was conducted with a focus on the performance optimization of wave reduction and sediment collection with respect to pipe diameter and face *** results showed that the wave reduction efficiency decreased with increasing pipe diameter and face *** contrast,the sediment transport efficiency was enhanced by increasing pipe diameter but was not affected significantly by varying face slopes.

关键词： breakwaters Computational fluid dynamics Sediment transport Shoreline protection Coastal engineering ANSYS FLUENT

Assessment of ERA5 and ERA-Interim in Reproducing Mean and Extreme Climates over West Africa

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Advances in Atmospheric Sciences 2023年第4期40卷 570-586页

作者： Imoleayo Ezekiel GbODE Toju Esther bAbALOLA Gulilat Tefera DIRO Joseph daniel INTSIFUL Department of Meteorology and Climate Science Federal University of Technology AkureP.M.B.704 Ilesa-Owo ExpresswayAkureOndo State 340420Nigeria Department of Water Resources Management and Agro-Meteorology Federal University Oye-Ekiti371104Nigeria Canadian Network for Regional Climate and Weather Processes University of Quebec at Montreal201 President-Kennedy AvenueMontrealQC H2X 3Y7Canada Division of Mitigation and Adaptation Green Climate FundIncheon 22004South Korea

In situ data in West Africa are scarce,and reanalysis datasets could be an alternative source to alleviate the problem of data ***,because of uncertainties in numerical prediction models and assimilation methods,among other things,existing reanalysis datasets can perform with various degrees of quality and ***,a proper assessment of their shortcomings and strengths should be performed prior to their *** this study,we examine the performance of ERA5 and ERA-interim(ERAI)products in representing the mean and extreme climates over West Africa for the period 1981-2018 using observations from CRU and *** major conclusion is that ERA5 showed a considerable decrease in precipitation and temperature biases and an improved representation of inter-annual variability in much of western ***,the annual cycle is better captured by ERA5 in three of the region’s climatic zones;specifically,precipitation is well-reproduced in the Savannah and Guinea Coast,and temperature in the *** terms of extremes,the ERA5 performance is ***,both reanalyses underestimate the intensity and frequency of heavy precipitations and overestimate the number of wet days,as the numerical models used in reanalyses tend to produce drizzle more *** ERA5 performs better than ERAI,both datasets are less successful in capturing the observed long-term *** ERA5 has achieved considerable progress compared to its predecessor,improved datasets with better resolution and accuracy continue to be needed in sectors like agriculture and water resources to enable climate impact assessment.

关键词： West Africa ERAI ERA5 reanalysis precipitation temperature extremes