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Enhancing 3D Reconstruction Accuracy of FIB Tomography Data Using Multi‑voltage Images and Multimodal Machine Learning

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Nanomanufacturing and Metrology 2024年第1期7卷 48-60页

作者： Trushal Sardhara Alexander Shkurmanov Yong Li Lukas Riedel Shan Shi Christian J.Cyron Roland C.Aydin Martin Ritter Institute for Continuum and Material Mechanics Hamburg University of TechnologyHamburgGermany Electron Microscopy Unit Hamburg University of TechnologyHamburgGermany Institute of Materials Physics and Technology Hamburg University of TechnologyHamburgGermany Institute of Materials Mechanics Helmholtz-Zentrum HereonGeesthachtGermany Research group of Integrated Metallic Nanomaterials systems Hamburg University of TechnologyHamburgGermany Institute of Material systems modeling Helmholtz-Zentrum HereonGeesthachtGermany

FIB-SEM tomography is a powerful technique that integrates a focused ion beam(FIB)and a scanning electron microscope(SEM)to capture high-resolution imaging data of *** approach involves collecting in-plane SEM imagesand using FIB to remove material layers for imaging subsequent planes,thereby producing image ***,theseimage stacks in FIB-SEM tomography are subject to the shine-through effect,which makes structures visible from theposterior regions of the current *** artifact introduces an ambiguity between image intensity and structures in thecurrent plane,making conventional segmentation methods such as thresholding or the k-means algorithm *** study,we propose a multimodal machine learning approach that combines intensity information obtained at differentelectron beam accelerating voltages to improve the three-dimensional(3D)reconstruction of *** treatingthe increased shine-through effect at higher accelerating voltages as a form of additional information,the proposed methodsignificantly improves segmentation accuracy and leads to more precise 3D reconstructions for real FIB tomography data.

关键词： Multimodal machine learning Multi-voltage images FIB-SEM Overdeterministic systems 3D reconstruction FIB tomography

Foraging valor linked with aggression:selection against completely abandoning aggression in the high-elevation ant Tetramorium alpestre?

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Insect Science 2024年第3期31卷 953-970页

作者： Marie-Luise Contala Patrick Krapf Florian M.Steiner Birgit C.Schlick-Steiner Molecular Ecology group Department of EcologyUniversitat InnsbruckInnsbruckAustria rganismal&Evolutionary biology Research Programme University of HelsinkiHelsinkiFinland

Aggression has multiple benefits and is often coupled with other behaviors("behavioral syndromes").The level of aggressiveness is influenced by an adaptive benefit-cost ratio suggesting that benefits should outweigh the costs of ***,we assess if several behaviors are coupled in two behaviorally different populations(aggressive,peaceful)of the high-elevation ant Tetramorium *** three weeks,we collected colony fragments and analyzed boldness,exploring,foraging,and risk-taking *** hypothesized that the aggressive population is bolder,more explorative and risk-prone,and forages more food than the peaceful *** test whether(a)the combination of experiments and parameters used yields a good setup,(b)populations differ behaviorally,and(c)populations display behavioral syndromes,we assessed(a)the frequency of repeatable behaviors of each experiment,(b)the behavioral means among populations,and(c)the behavioral repeatability,*** found that(a)boldness and exploring were most repeatable and represent a good experimental setup,(b)the aggressive population was bolder and more explorative and risk-prone than the peaceful population,(c)boldness and exploring behaviors were highly repeatable in both populations,thus corroborating our *** results suggest that boldness,exploring,and risk-taking but not foraging are presumably coupled with aggression and indicate the presence of behavioral syndromes in this *** specific ecological conditions,aggression may be coupled with other behaviors and important for finding *** is probably adaptive in ***,possibly indicating that selection favors aggression at least partially,which may counteract the complete loss of intraspecific aggression.

关键词： adaptive value behavioral syndromes boldness exploration repeatability trade-off

Identific tion of quantitative trait loci and associated candidate genes for pregnancy success in Angus–Brahman crossbred heifers

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Journal of Animal Science and Biotechnology 2024年第1期15卷 162-170页

作者： Quinn A.Hoorn Gabriel A.Zayas Eduardo E.Rodriguez Laura M.Jensen Raluca G.Mateescu Peter J.Hansen Department of Animal Sciences Donald Henry Barron Reproductive and Perinatal Biology Research Programand the Genetics InstituteUniversity of FloridaGainesvilleFLUSA School of Applied systems biology La Trobe UniversityBundooraVIC 3083Australia

Background In beef cattle, more than 50% of the energy input to produce a unit of beef is consumed by the female that produced the calf. Development of genomic tools to identify females with high genetic merit for reproductive function could increase the profitability and sustainability of beef *** Genome-wide association studies(GWAS) were performed using a single-step genomic best linear unbiased prediction approach on pregnancy outcome traits from a population of Angus–Brahman crossbred heifers. Furthermore, a validation GWAS was performed using data from another farm. Heifers were genotyped with the Bovine GGP F250 array that contains 221,077 SNPs. In the discovery population, heifers were bred in winter breeding seasons involving a single round of timed artificial insemination(AI) followed by natural mating for 3 months. Two phenotypes were analyzed: pregnancy outcome to first-service AI(PAI;n = 1,481) and pregnancy status at the end of the breeding season(PEBS;n = 1,725). The heritability was estimated as 0.149 and 0.122 for PAI and PEBS, respectively. In the PAI model, one quantitative trait locus(QTL), located between 52.3 and 52.5 Mb on BTA7, explained about 3% of the genetic variation, in a region containing a cluster of γ-protocadherin genes and SLC25A2. Other QTLs explaining between 0.5% and 1% of the genetic variation were found on BTA12 and 25. In the PEBS model, a large QTL on BTA7 was synonymous with the QTL for PAI, with minor QTLs located on BTA5, 9, 10, 11, 19, and 20. The validation population for pregnancy status at the end of the breeding season were Angus–Brahman crossbred heifers bred by natural mating. In concordance with the discovery population, the large QTL on BTA7 and QTLs on BTA10 and 12 were *** In summary, QTLs and candidate SNPs identified were associated with pregnancy outcomes in beef heifers, including a large QTL associated with a group of protocadherin genes. Confirmation of these associations

关键词： Beef cattle Fertility GWAS QTL

Characterization of the infectivity of an Indonesian Zika virus strain in mammalian cell lines

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Asian Pacific Journal of Tropical Biomedicine 2024年第5期14卷 215-224页

作者： Justus Thomas Obiajulu Sievers Anom Bowolaksono R.Tedjo Sasmono Graduate School of biology Department of BiologyFaculty of Mathematics and Natural SciencesUniversitas IndonesiaDepok 16424Indonesia Eijkman Research Center for Molecular biology National Research and Innovation AgencyCibinong 16911Indonesia Cellular and Molecular Mechanisms in Biological System Research group Department of BiologyFaculty of Mathematics and Natural SciencesUniversitas IndonesiaDepok 16424Indonesia

Objective:To characterize the infection patterns and growth characteristics of the Zika virus(ZIKV)strain JMB-185 from Indonesia in various mammalian cell ***:ZIKV was grown in human(A549,HEK293,HepG2,Huh7,Jurkat,and THP-1)and non-human mammalian(RAW264.7,Vero,and Vero76)cell *** replication kinetics were measured using plaque assay,while intra-and extracellular viral RNA concentrations were assessed using *** cytometry was used to quantify the infected cells and cell viability was measured using an MTT *** ability of ZIKV to infect cell lines was visualized using a fluorescence immunostaining ***:This ZIKV strain preferentially infected the lung,kidney,and liver cell lines A549,HEK293,Huh7,Vero,and Vero76,but not the immune cells Jurkat,RAW264.7,and *** contrast,the ZIKV showed no sign of infection in HepG2 cells,while maintaining viral titer over 3 days post-infection,with no infection recorded in immunostaining,no increase in viral RNA,and no indication of cell ***:The Indonesian ZIKV strain has a similar infection profile as other strains,except for its poor infectivity on HepG2 *** on the growth characteristics of Indonesia ZIKV will help expand our understanding of the biology of ZIKV which will be useful for various applications including antiviral discovery.

关键词： Zika virus Infectivity Replication Cell lines In vitro

G protein-mediated signal transduction: a molecular choreography of G protein activation after GTP binding

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Signal Transduction and Targeted Therapy 2024年第8期9卷 3155-3157页

作者： Evi Kostenis Lars Jurgenliemke Judith Alenfelder Department of Molecular- Cellular-and PharmacobiologyInstitute of Pharmaceutical BiologyUniversity of BonnBonnGermany Graduate Training group RTG2873 University of BonnBonnGermany

A recent report from the Skiniotis group,'published in Nature,provides fascinating insight into the molecular choreography underlying a quintessential cellular signaling mechanism:G protein-mediated signal *** time-resolved cryo-EM,the authors pieced together many sequential structural snapshots to visualize how a trimeric aβy G protein-after being convinced by its activated G protein-coupled receptor(GPCR)to release GDP-picks up GTP,to set in motion finely tuned conformational transitions that lead to the conversion into the active state and,finally,subunit dissociation as well as disengagement from the receptor.

关键词： Skin activation finally

Pollen analysis reveals the effects of uncovered interactions,pollen-carrying structures,and pollinator sex on the structure of wild bee-plant networks

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Insect Science 2024年第3期31卷 971-988页

作者： Clément Tourbez Carmelo Gómez-Martínez MiguelÁngel Gonzalez-Estévez Amparo Lazaro Mediterranean Institute for Advanced Studies(UIB-CSIC) Global Change Research GroupEsporlesBalearic IslandsSpain Department of biology Ecology AreaUniversity of the Balearic/slandsPalmaSpain

Pollination networks are increasingly used to model the complexity of interactions between pollinators and flowering plants in *** methods exist to sample these interactions,with direct observations of plant-pollinator contacts in the field being by far the most *** the identification of pollen carried by pollinators allows uncovering interactions and increasing sample sizes,the methods used to build pollen-transport networks are variable and their effect on network structure remains *** understand how interaction sampling influences the structure of networks,we analyzed the pollen found on wild bees from eight communities across Mallorca Island and investigated the differences in pollen loads between bee body parts(scopa ***)and *** then assessed how these differences,as well as the uncovered interactions not detected in the field,influenced the structure of wild bee-plant *** identified a higher quantity and diversity of pollen in the scopa than in the rest of the female body,but these differences did not lead to differences in structure between plant-pollination(excluding scopa pollen)and bee-feeding interaction(including scopa pollen)***,networks built with pollen data were richer in plant species and interactions and showed lower modularity and specialization(H2'),and higher nestedness than visitation networks based on field *** interactions with plants were stronger compared to those of males,although not ***,females were more generalist(low d')and tended to be more central in interaction networks,indicating their more key role structuring pollination networks in comparison to *** study highlights the importance of palynological data to increase the resolution of networks,as well as to understand important ecological questions such as the differences between plant-pollination and bee-feeding interaction networks,and the role of sexes in pollination.

关键词： palynology pollen-transport networks pollination role of bee sexes sampling methodology visitation networks

A Neural-network-based Alternative Scheme to Include Nonhydrostatic Processes in an Atmospheric Dynamical Core

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Advances in Atmospheric Sciences 2024年第6期41卷 1083-1099,I0002,I0003页

作者： Yang XIA Bin WANG Lijuan LI Li LIU Jianghao LI Li DONG Shiming XU Yiyuan LI Wenwen XIA Wenyu HUANG Juanjuan LIU Yong WANG Hongbo LIU Ye PU Yujun HE Kun XIA Ministry of Education Key Laboratory for Earth System modeling and Department of Earth System ScienceTsinghua UniversityBeijing 100084China State Key Laboratory of Numerical modeling for Atmospheric Sciences and Geophysical Fluid Dynamics Institute of Atmospheric PhysicsChinese Academy of SciencesBeijing 100029China Innovation group 311020008 Southern Marine Science and Engineering Guangdong LaboratoryZhuhai 519000China Shanghai Ecological Forecasting and Remote Sensing Center Shanghai 200030China Key Laboratory of Earth System modeling and Prediction China Meteorological AdministrationBeijing 100081China College of Ocean Sciences University of Chinese Academy of SciencesBeijing 100049China

Here,a nonhydrostatic alternative scheme(NAS)is proposed for the grey zone where the nonhydrostatic impact on the atmosphere is evident but not large enough to justify the necessity to include an implicit nonhydrostatic solver in an atmospheric dynamical *** NAS is designed to replace this solver,which can be incorporated into any hydrostatic models so that existing well-developed hydrostatic models can effectively serve for a longer *** advances in machine learning(ML)provide a potential tool for capturing the main complicated nonlinear-nonhydrostatic *** this study,an ML approach called a neural network(NN)was adopted to select leading input features and develop the *** NNs were trained and evaluated with 12-day simulation results of dry baroclinic-wave tests by the Weather Research and Forecasting(WRF)*** forward time difference of the nonhydrostatic tendency was used as the target variable,and the five selected features were the nonhydrostatic tendency at the last time step,and four hydrostatic variables at the current step including geopotential height,pressure in two different forms,and potential temperature,***,a practical NAS was developed with these features and trained layer by layer at a 20-km horizontal resolution,which can accurately reproduce the temporal variation and vertical distribution of the nonhydrostatic *** by the NN-based NAS,the improved hydrostatic solver at different horizontal resolutions can run stably for at least one month and effectively reduce most of the nonhydrostatic errors in terms of system bias,anomaly root-mean-square error,and the error of the wave spatial pattern,which proves the feasibility and superiority of this scheme.

关键词： neural network nonhydrostatic alternative scheme atmospheric model dynamical core

Isotopic insights on quantitative assessments of interaction of eco-hydrological processes in multi-scale karst watersheds

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International Soil and Water Conservation Research 2024年第1期12卷 156-170页

作者： Zhuo Hao Yang Gao Qingwen Zhang Wen Wen Agricultural Clean Watershed Research group Institute of Environment and Sustainable Development in AgricultureCAASBeijing100081China Key Laboratory of Ecosystem Network Observation and modeling Institute of Geographic Sciences and Natural Resources ResearchCASBeijing100101China School of Humanities and Social Sciences Beijing Institute of TechnologyBeijing100081China

The dynamics of hydrological processes and the storage mechanisms of karst water resources are the most important issues in karst *** impact of environmental changes on water quantity,and the evaluation and quantification of eco-hydrological processes remain poorly *** this study,high-frequency continuous monitoring in multi-scale karst watersheds in Southwest China combined the approaches of water isotopes and the hybrid single-particle lagrangian integrated trajectory(HYSPLIT)model to identify the recharge mechanisms between atmospheric vapor,rainfall,surface water,and groundwater,and to reveal the interaction of eco-hydrological *** dominant moisture sources in Puding(PD)County were the Indian Ocean(43-69%)and local moisture(24-33%).Theδ^(18)O and deuterium excess(d-excess)values showed a positive correlation indicating that secondary or sub-cloud evaporation was prominent in the wet *** water line-conditioned excess(lc-excess)indicated that karst water interacted with recent precipitation,groundwater,and evaporation across *** to its specific hydrogeological structure,surface water and rainwater have a higher contribution rate to groundwater *** Chenqi stream replenished the Houzhai River mainly in the form of groundwater,with percentages ranging from 38.1 to 93.5%in the wet season,and 47.8-80.1%in the dry *** the Houzhai outlet,surface water and groundwater interconverted frequently with a percentage of 45.6-49.1%.We believe this is the first systematic study to quantify the supply relationship between water vapor transport,rainfall,surface water and groundwater in the Chinese karst zone,making a significant move forward in the field of karst hydrological processes and improving the efficiency of water resource evaluation and management.

关键词： Stable isotope Moisture sources Water cycle Karst watersheds

Applications of cnoidal and snoidal wave solutions via optimal system of subalgebras for a generalized extended (2+1)-D quantum Zakharov-Kuznetsov equation with power-law nonlinearity in oceanography and ocean engineering

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Journal of Ocean Engineering and Science 2024年第2期9卷 126-153页

作者： Oke Davies Adeyemo International Institute for Symmetry Analysis and mathematical Modelling Department of Mathematical SciencesNorth-West UniversityMafikeng CampusPrivate Bag X 2046Mmabatho 2735Republic of South Africa

The nonlinear evolution equations have a wide range of applications,more precisely in physics,biology,chemistry and engineering *** domain serves as a point of interest to a large extent in the world’s mathematical ***,this paper purveys an analytical study of a generalized extended(2+1)-dimensional quantum Zakharov-Kuznetsov equation with power-law nonlinearity in oceanography and ocean *** Lie group theory of differential equations is utilized to compute an optimal system of one dimension for the Lie algebra of the *** further reduce the equation using the subalgebras ***,more general solutions of the underlying equation are secured for some special cases of n with the use of extended Jacobi function expansion ***,we secure new bounded and unbounded solutions of interest for the equation in various solitonic structures including bright,dark,periodic(cnoidal and snoidal),compact-type as well as singular *** applications of cnoidal and snoidal waves of the model in oceanography and ocean engineering for the first time,are outlined with suitable *** can be of interest to oceanographers and ocean engineers for future ***,to visualize the dynamics of the results found,we present the graphic display of each of the ***,we construct conservation laws of the understudy equation via the application of Noether’s theorem.

关键词： A generalized extended(2+1)-dimensional quantum Zakharov-Kuznetsov equation Lie point symmetries Optimal system of subalgebras Cnoidal and snoidal waves Extended Jacobi function expansion technique Conservation laws