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Regulation of the sQUAmOsA PROmOTER-BINDING PROTEIN-LIKE genes/microRNA 156 module by the Homeodomain Proteins PENNYWIsE and POUND-FOOLIsH in Arabidopsis

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molecular Plant 2011年第6期4卷 1123-1132页

作者： shruti Lal Leo bryan Pacis Harley m.s. smith Genetics Genomics and Bioinformatics Graduate Program University of California Riverside CA 92521 USA Center for Plant Cell Biology Institute of Integrative Genome Biology Department of Botany and Plant Sciences University of California Riverside CA 92521 USA

The morphology of inflorescences is regulated in part by the temporal and spatial events that regulate flower specification. In Arabidopsis, an endogenous flowering time pathway mediated by a subset of sQUAmOsA PROmOTER- BINDING PROTEIN-LIKE （sPL） transcription factors, including sPL3, sPL4, and sPL5, function to specify flowers by activating floral meristem identity genes. During shoot development, sPL3, sPL4, and sPL5 are post-transcriptionally regulated by microRNA156 （miR156）. The photoperiod regulated florigenic signal, FLOWERING LOCUs T （FT）, promotes floral induction, in part by activating sPL3, sPL4, and sPL5. In turn, these sPLs function in parallel with FT to specify flower meristems. Two related BELLl-like homeobox genes PENNYWIsE （PNY） and POUND-FOOLIsH （PNF） expressed in the shoot apical meristem are absolutely required for the specification of floral meristems. Genetic studies show that the floral specification function of FT depends upon PNYand PNF; however, the interplay between these homeodomain proteins and sPLs is not known. In this manuscript, we show that the photoperiodic floral induction of sPL3, sPL4, and sPL5 is dependent upon PNY and PNE Further, PNY and PNF also control sPL3, sPL4, and sPL5 expression by negatively regulating miR156. Lastly, ectopic expres- sion of sPL4 partially rescues the pny pnf non-flower-producing phenotype, while overexpression of sPL3 or sPL5 in pny pnf plants was unable to restore flower specification. These results suggest that：（1） sPL3, sPL4, and sPL5 function is dependent upon PNY and PNF, or （2） expression of multiple sPLs is required for floral specification in pny pnf plants.

关键词： Development meristem homeodomain flowering microRNA.

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microstructure segmentation with deep learning encoders pre-trained on a large microscopy dataset

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npj Computational materials 2022年第1期8卷 1905-1916页

作者： Joshua stuckner bryan Harder Timothy m.smith materials and structures Division NASA Glenn Research Center21000 Brookpark RdClevelandOH44135USA

This study examined the improvement of microscopy segmentation intersection over union accuracy by transfer learning from a large dataset of microscopy images called *** neural network encoder architectures were trained on over 100,000 labeled microscopy images from 54 material *** pre-trained encoders were then embedded into multiple segmentation architectures including UNet and DeepLabV3+to evaluate segmentation performance on created benchmark microscopy *** to ImageNet pre-training,models pre-trained on microNet generalized better to out-of-distribution micrographs taken under different imaging and sample conditions and were more accurate with less training *** training with only a single Ni-superalloy image,pre-training on microNet produced a 72.2%reduction in relative intersection over union *** results suggest that transfer learning from large in-domain datasets generate models with learned feature representations that are more useful for downstream tasks and will likely improve any microscopy image analysis technique that can leverage pre-trained encoders.

关键词： union intersection image

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Efficient predictions of formation energies and convex hulls from density functional tight binding calculations

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Journal of materials science & Technology 2023年第10期141卷 236-244页

作者： Anshuman Kumar Zulfikhar A.Ali bryan m.Wong materials science&Engineering Program University of California-RiversideRiverside92521CAUSA Department of Physics&Astronomy University of California-RiversideRiverside92521CAUSA materials science&Engineering Program Department of Chemical&Environmental EngineeringDepartment of Physics&Astronomyand Department of ChemistryUniversity of California-RiversideRiverside92521CAUSA

Defects in materials significantly alter their electronic and structural properties,which affect the per-formance of electronic devices,structural alloys,and functional ***,calculating all the possible defects in complex materials with conventional Density Functional Theory(DFT)can be compu-tationally *** enhance the efficiency of these calculations,we interfaced Density Functional Tight Binding(DFTB)with the Clusters Approach to statistical mechanics(CAsm)software package for the first *** siC and ZnO as representative examples,we show that DFTB gives accurate results and can be used as an efficient computational approach for calculating and pre-screening formation ener-gies/convex *** DFTB+CAsm implementation allows for an efficient exploration(up to an order of magnitude faster than DFT)of formation energies and convex hulls,which researchers can use to probe other complex systems.

关键词： CAsm DFTB DFT Formation energy Convex hull

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Environmental Exposure to Glyphosate and Reproductive Health Impacts in Agricultural Population of Argentina

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Journal of Environmental Protection 2018年第3期9卷 241-253页

作者： medardo Avila-Vazquez Flavia s. Difilippo bryan mac lean Eduardo maturano Agustina Etchegoyen Chair of Pediatric Clinic Faculty of Medical Sciences National University of Cordoba Cordoba Argentina Epidemiology Committee of Virology Institute Jose maria Vanella Faculty of Medical Sciences National University of Cordo-ba Cordoba Argentina Center for Environmental Research Faculty of Exact Sciences National University of La Plata La Plata Argentina

Argentina annually utilizes 240,000 tones of glyphosate in industrial agriculture and a change in the profile of morbidity is perceived for physicians of agricultural areas;now reproductive disorders seem to prevail. The objective of this study is to determine concurrence of glyphosate exposure and reproductive disorders in a typical argentine agricultural town (monte maíz). An ecological study was developed with an environmental analysis of pollution sources including measurements of glyphosate and other pesticides and a cross-sectional study of spontaneous abortions and congenital abnormalities prevalence. Glyphosate was detected in soil and grain dust and was found to be at an even higher concentration in the village soil than in the rural area;650 tonnes of glyphosate are used annually in the region and manipulated inner town contaminating the soil and dust in suspension of the town creating an burden of environmental exposure to glyphosate of 79 kg per person per year. We do not find other relevant sources of pollution. The spontaneous abortion and congenital abnormalities rates are three and two times higher than the national average reported by the national health (10% vs. 3% and 3% - 4.3% vs 1.4% respectively). Our study verified high environmental exposure to glyphosate in association with increased frequencies of reproductive disorders (spontaneous abortion and congenital abnormalities) in argentine agricultural village, but is unable to make assertions cause-effect. Further studies are required with designs for such purposes.

关键词： Glyphosate spontaneous Abortions Congenital Abnormalities Environmental Exposure Environmental Health

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Impacts of late Quaternary environmental change on the long-tailed ground squirrel(Urocitellus undulatus)in mongolia

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Zoological Research 2018年第5期39卷 364-372页

作者： bryan s.m.lean Batsaikhan Nyamsuren ANDrey Tchabovsky Joseph A.Cook University of Florida Florida Museum of Natural History Department of Biology School of Arts and Sciences National University of Mongolia Laboratory of Population Ecology A.N. Severtsov Institute of Ecology and Evolution University of New mexico Department of Biology and Museum of Southwestern Biology

Impacts of Quaternary environmental changes on mammal faunas of central Asia remain poorly understood due to a lack of comprehensive phylogeographic sampling for most *** help address this knowledge gap,we conducted the most extensive molecular analysis to date of the long-tailed ground squirrel （Urocitellus undulatus Pallas 1778） in mongolia,a country that comprises the southern core of this species＇ *** on material from recent collaborative field expeditions,we genotyped 128 individuals at two mitochondrial genes （cytochrome b and cytochrome oxidase Ⅰ;1797 bp total）.Phylogenetic inference supports the existence of two deeply divergent infraspecific lineages （corresponding to subspecies *** and ***）,a result in agreement with previous molecular investigations but discordant with patterns of range-wide craniometric and external phenotypic *** the widespread western eversmanni lineage,we recovered geographically-associated clades from the：（a） Khangai,（b） mongolian Altai,and （c） Govi Altai mountain *** structure in *** is consistent with an isolation-by-distance model;however,genetic distances are significantly lower than among subspecies,and intra-clade relationships are largely *** latter patterns,as well as the relatively higher nucleotide polymorphism of populations from the Great Lakes Depression of northwestern mongolia,suggest a history of range shifts into these lowland areas in response to Pleistocene glaciation and environmental change,followed by upslope movements and mitochondrial lineage sorting with Holocene *** study illuminates possible historical mechanisms responsible for *** genetic structure and contributes to a framework for ongoing exploration of mammalian response to past and present climate change in central Asia.

关键词： Central Asia Gobi Desert Great LakesDepression mongolia Phylogeography

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Characterization and evolutionary dynamics of complex regions in eukaryotic genomes

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science China(Life sciences) 2019年第4期62卷 467-488页

作者： José Ranz bryan Clifton Department of Ecology and Evolutionary Biology University of California Irvine

Complex regions in eukaryotic genomes are typically characterized by duplications of chromosomal stretches that often include one or more genes repeated in a tandem array or in relatively close proximity. Nevertheless, the repetitive nature of these regions,together with the often high sequence identity among repeats, have made complex regions particularly recalcitrant to proper molecular characterization, often being misassembled or completely absent in genome assemblies. This limitation has prevented accurate functional and evolutionary analyses of these regions. This is becoming increasingly relevant as evidence continues to support a central role for complex genomic regions in explaining human disease, developmental innovations, and ecological adaptations across phyla. With the advent of long-read sequencing technologies and suitable assemblers, the development of algorithms that can accommodate sample heterozygosity, and the adoption of a pangenomic-like view of these regions, accurate reconstructions of complex regions are now within reach. These reconstructions will finally allow for accurate functional and evolutionary studies of complex genomic regions, underlying the generation of genotype-phenotype maps of unprecedented resolution.

关键词： complex genomic regions sequencing technologies genome assembly structural variation tandem gene duplicates,evolutionary novelty

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Development of an in vitro protein digestibility assay mimicking the chicken digestive tract

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Animal Nutrition 2018年第4期4卷 401-409页

作者： Dervan D.s.L.bryan Dawn A.Abbott Henry L.Classen Department of Animal and Poultry science University of Saskatchewan

It is difficult to obtain in vivo digestion kinetics data of high protein ingredients using chickens. Collecting kinetics data requires repeated sampling of digesta from the small intestine during the digestion process,which is not easily accomplished due to the anatomical structure of chicken digestive tract. An in vitro technique is proposed for measuring the digestion kinetics of protein sources fed to chickens. The method has a 30 min gastric and 3 h intestinal phase. Five hundred milligram crude protein(CP)equivalent of each meal sample(CP = % N × 6.25) was digested with pepsin(28,260 units) in 50 m L polyethylene centrifuge tubes for 30 min in a shaking water bath(150 strokes/min; 30 mm stroke length)at 41C. The 6.5 mL pancreatin was selected as the enzyme concentration for the intestinal phase, during which time 500 m L aliquots were collected at 0, 15, 30, 45, 60, 90, 120, 150, 180 and 240 min. samples were diluted 1:820 with HCl and sodium acetate buffer, and then mixed with ninhydrin reagent(2:1) at100 ± 2C for 15 min and spectrometric readings taken at 568 nm. To validate the assay, 5 replications of soybean meal(sBm), corn gluten meal(CGm), corn distillers dried grains with solubles(CDDGs), porcine meal(PCm), fish meal(Fm) and casein(CA) were digested. The digestion data were modeled with PROC NLIN procedure, and the intra coefficient of variation(CV) assessed using PROC mEANs of sAs 9.4. The digestion values at 180 min were sBm 95 ± 4, Fm 93 ± 3, PCm 68 ± 4, CGm 82 ± 3 and CDDGs 70 ± *** CV for sBm, CGm, CDDGs, PCm and Fm were 5%, 5%, 12%, 10% and 2%, respectively. The estimated fractional digestion rates for sBm, CGm, CDDGs, Fm and PCm were 0.023, 0.013, 0.009, 0.024 and 0.013,respectively. In conclusion, the proposed in vitro technique estimated the rate and extent of the digestion of CP for the meals with low intra CV.

关键词： Protein digestion rate soybean meal Corn gluten meal Corn distillers dried grains with solubles Fish meal Porcine meal

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Option Pricing under the Double Exponential Jump-Diffusion model with stochastic Volatility and Interest Rate

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Journal of management science and Engineering 2017年第4期2卷 252-289页

作者： Rongda Chen Zexi Li Liyuan Zeng lean Yu Qi Lin Jia Liu school of Finance Zhejiang University of Finance and EconomicsHangzhou 310018China Collaborative Innovation Center for Wealth management and Quantitative Investment Zhejiang University of Finance and EconomicsHangzhou 310018China school of Economics and management University of Chinese Academy of SciencesBeijing 100190China PricewaterhouseCoopers Zhong Tian LLP Beijing BranchBeijing 100020China school of Economics and management Beijing University of Chemical TechnologyBeijing 100029China salford Business school Salford UniversitySalford M54WTUUK

This paper proposes an efficient option pricing model that incorporates stochastic interest rate(sIR),stochastic volatility(sV),and double exponential jump into the jump-diffusion *** model comprehensively considers the leptokurtosis and heteroscedasticity of the underlying asset’s returns,rare events,and an *** the model,we deduce the pricing characteristic function and pricing formula of a European ***,we develop the markov chain monte Carlo method with latent variable to solve the problem of parameter estimation under the double exponential jump-diffusion model with sIR and *** verification purposes,we conduct time efficiency analysis,goodness of fit analysis,and jump/drift term analysis of the proposed *** addition,we compare the pricing accuracy of the proposed model with those of the Black-scholes and the Kou(2002)*** empirical results show that the proposed option pricing model has high time efficiency,and the goodness of fit and pricing accuracy are significantly higher than those of the other two models.

关键词： Option pricing model stochastic interest rate stochastic volatility Double exponential jump markov Chain monte Carlo with Latent Variable

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Association of Congenital Heart Defects (CHD) with Factors Related to maternal Health and Pregnancy in Newborns in Puerto Rico

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Congenital Heart Disease 2024年第1期19卷 19-31页

作者： Yamixa Delgado Caliani Gaytan Naydi Perez Eric miranda bryan Colón morales mónica santos Biochemistry&Pharmacology Department San Juan Bautista School of MedicineCaguas00726Puerto Rico Hispanic Alliance for Clinical and Translational Research University of Puerto Rico Medical Sciences CampusSan Juan00936Puerto Rico Department of Internal medicine University of Puerto Rico Medical Sciences CampusSan Juan00936Puerto Rico

Background:Given the pervasive issues of obesity and diabetes both in Puerto Rico and the broader United states,there is a compelling need to investigate the intricate interplay among body mass index(BmI),pregesta-tional,and gestational maternal diabetes,and their potential impact on the occurrence of congenital heart defects(CHD)during neonatal ***:Using the comprehensive system of Vigilance and surveillance of Congenital Defects in Puerto Rico,we conducted a focused analysis on neonates diagnosed with CHD between 2016 and *** assessment encompassed a range of variables,including maternal age,gestational age,BmI,pregestational diabetes,gestational diabetes,hypertension,history of abortion,and presence of ***:A cohort of 673 patients was included in our *** average maternal age was 26 years,within a range of 22 to 32 *** mean gestational age measured 39 weeks,with a median span of 38 to 39 *** the 673 patients,274(41%)mothers gave birth to neonates diagnosed with *** this group,22 cases were linked to pre-gestational diabetes,while 202 were not;20 instances were associated with gestational diabetes,compared to 200 without;and 148 cases exhibited an overweight or obese BmI,whereas 126 displayed a normal ***:We identiﬁed a statistically signiﬁcant correlation between pre-gestational diabetes mellitus and the occurrence of ***,our analysis did not show a statistically signiﬁcant association between maternal BmI and the likelihood of *** results may aid in developing effective strategies to prevent and manage CHD in neonates.

关键词： Congenital heart defects(CHD) obesisty maternal health diabetes body mass index(BmI)

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Antibiotic residues from aquaculture farms and their ecological risks in southeast Asia:a case study from malaysia

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Ecosystem Health and sustainability 2021年第1期7卷 300-317页

作者： Ee lean Thiang Choon Weng Lee Hideshige Takada Kanako seki Ayaka Takei satoru suzuki Aijun Wang Chui Wei Bong Institute of Ocean and Earth sciences University MalayaKuala LumpurMalaysia Institute for Advanced studies University MalayaKuala LumpurMalaysia Institute of Biological sciences University MalayaKuala LumpurMalaysia Laboratory of Organic Geochemistry Tokyo University of Agriculture and TechnologyFuchuTokyoJapan Center for marine Environmental studies Ehime UniversityMatsuyamaEhimeJapan Third Institute of Oceanography State Oceanic AdministrationXiamenChina

Background and Objectives:One major source of antibiotic contamination in the sea is from *** monitored the concentration of commonly used antibiotic classes and antibiotic resistance genes(tet(m),sul1,sul2 and sul3)in aquaculture farms in Peninsular ***:Antibiotic residues and resistance genes were quantified using high-performance liquid chromatography and real-time PCR *** quotients in European technical guidance document on risk assessment was used to assess the potential environmental ***:We detected 23 antibiotics with tetracyclines,sulfonamides and quinolones were the most frequently detected classes,indicating a wide distribution of antibiotics in malaysian aquaculture *** dendrogram and heatmap revealed three groups of antibiotic concentration patterns but with no differences in the types of antibiotics usage among aquaculture *** ARGs(10^(−3)copies/16s)were detected in>90%of the sites except for ***,enrofloxacin,norfloxacin and lincomycin posed risks to cyanobacteria and algae in Kelantan,Perak and ***:Relative to Asian aquaculture farms,the residues detected here were at low or moderate levels except for *** study will be useful to develop effective management of aquaculture wastewater in order to mitigate antibiotic pollution and transmission of ARGs to humans through the food chain.

关键词： Antibiotic residues resistance genes risk assessment aquaculture

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