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3D U-Net Segmentation Improves Root System Reconstruction from 3D MRI Images in Automated and Manual Virtual Reality Work Flows

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Plant Phenomics 2023年第3期5卷 598-611页

作者： Tobias Selzner jannis Horn Magdalena Landl Andreas Pohlmeier Dirk Helmrich Katrin Huber jan vanderborght Harry Vereecken Sven Behnke Andrea Schnepf Forschungszentrum Juelich GmbH Agrosphere(IBG-3)JuelichGermany Autonomous Intelligence Systems Group University of BonnBonnGermany Forschungszentrum Juelich GmbH Juelich Supercomputing CenterJuelichGermany

Magnetic resonance imaging(MRI)is used to image root systems grown in opaque soil.However,reconstruction of root system architecture(RSA)from 3-dimensional(3D)MRI images is challenging.Low resolution and poor contrast-to-noise ratios(CNRs)hinder automated reconstruction.Hence,manual reconstruction is still widely used.Here,we evaluate a novel 2-step work flow for automated RSA reconstruction.In the first step,a 3D U-Net segments MRI images into root and soil in super-resolution.In the second step,an automated tracing algorithm reconstructs the root systems from the segmented images.We evaluated the merits of both steps for an MRI dataset of 8 lupine root systems,by comparing the automated reconstructions to manual reconstructions of unaltered and segmented MRI images derived with a novel virtual reality system.We found that the U-Net segmentation offers profound benefits in manual reconstruction:reconstruction speed was doubled(+97%)for images with low CNR and increased by 27%for images with high CNR.Reconstructed root lengths were increased by 20%and 3%,respectively.Therefore,we propose to use U-Net segmentation as a principal image preprocessing step in manual work flows.The root length derived by the tracing algorithm was lower than in both manual reconstruction methods,but segmentation allowed automated processing of otherwise not readily usable MRI images.Nonetheless,model-based functional root traits revealed similar hydraulic behavior of automated and manual reconstructions.Future studies will aim to establish a hybrid work flow that utilizes automated reconstructions as scaffolds that can be manually corrected.

关键词： Root utilize otherwise

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Liver transplantation and liver resection as alternative treatments for primary hepatobiliary and secondary liver tumors: Competitors or allies?

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Hepatobiliary & Pancreatic Diseases International 2024年第2期23卷 111-116页

作者： jan Lerut Institute for Experimental and Clinical Research(IREC) Universitécatholique Louvain(UCL)Avenue Hippocrate 561200 Woluwe Saint PierreBrusselsBelgium

Although Starzl designed in the 1960’s liver transplantation(LT)to treat unresectable primary and also secondary liver tumors,transplantation still occupies a(too)small place in the respective therapeutic algorithms[1].Due to the lack of(any)selection criteria,the concept of transplantation became rapidly challenged because of the prohibitively high incidence of tumor recurrence[1–3].

关键词： liver tumors Liver

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Potential of molecular chaperones for treating Alzheimer’s disease

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Neural Regeneration Research 2024年第11期19卷 2343-2344页

作者： Gefei Chen jan Johansson Department of Biosciences and Nutrition Karolinska InstitutetHuddingeSweden Department of Cell and Molecular Biology Uppsala UniversityUppsalaSweden

Alzheimer’s disease(AD)is the most prevalent form of dementia,i.e.,progressive memory loss and profound cognitive dysfunction,resulting in a considerable societal burden.At the neuropathological level,the brains of AD patients exhibit amyloid-β(Aβ)plaques,neurofibrillary tangles,and neuroinflammation(Sala Frigerio and De Strooper,2016).

关键词： Alzheimer inflammation Aβ

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Development and Validation of a Deep Learning Based Automated Minirhizotron Image Analysis Pipeline

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Plant Phenomics 2022年第1期4卷 247-260页

作者： Felix Maximilian Bauer Lena Lärm Shehan Morandage Guillaume Lobet jan vanderborght Harry Vereecken Andrea Schnepf Institute of Bio-and Geosciences Agrosphere(IBG-3)Forschungszentrum Jülich GmbH52425 JülichGermany Institute of Soil Science and Land Evaluation University of Hohenheim7055978 StuttgartGermany

Root systems of crops play a significant role in agroecosystems.The root system is essential for water and nutrient uptake,plant stability,symbiosis with microbes,and a good soil structure.Minirhizotrons have shown to be effective to noninvasively investigate the root system.Root traits,like root length,can therefore be obtained throughout the crop growing season.

关键词： structure crops soil

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Weak influence of natural vegetation in urban green spaces compared to agricultural ecosystems on House Martin populations:Insights from nationwide citizen science data in the Czech Republic

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Avian Research 2024年第2期15卷 139-146页

作者： Denisa Dvorakova jan Sipos Josef Suchomel Department of Zoology FisheriesHydrobiology and ApicultureMendel University in BrnoZemedelska 161300BrnoCzech Republic

The House Martin(Delichon urbicum)is a common farmland bird species in the European landscape,yet its population numbers are currently in decline.However,it is not yet sufficiently explained why this long-term decline occurs.To fill this gap in our knowledge,we investigated how land cover composition affects the abundance of House Martins on the landscape scale by using nationwide citizen science data.Utilizing a generalised linear mixed-effect model(GLMM),we evaluated 12,094 records from the Czech Republic spanning 2009-2017.Our analysis underscores the significance of land cover type in shaping House Martin abundance.More specifically,our results indicate that within agricultural land covers“naturally managed arable lands”exhibited significant positive effect,while forests,orchards,and vineyards were deemed less favourable for House Martin populations.Within urban land covers,we found a clear distinction in the impact on House Martin populations,with a positive effect observed in urban infrastructure,development areas,and post-industrial sites(i.e.,UrbanAreas),while an indifferent impact was noted within urban green spaces and landscaped areas(i.e.,GreenUrban).Notably,our findings suggest that the simple spatial,age,and species structure typical of forests in Europe,and similarly,the uniform structure of parks and gardens,may be responsible for the decline in the abundance of the House Martin.We advocate for the preservation or enhancement of urban greenery,expansion of natural vegetation in rural areas and adoption of ecological management practices in orchards and vineyards to mitigate further declines in House Martin populations.

关键词： Citizen science Habitat preferences House Martin Species distribution Urban and suburban landscape

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Solid Bi_(2)O_(3)-derived nanostructured metallic bismuth with high formate selectivity for the electrocatalytic reduction of CO_(2)

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International Journal of Minerals,Metallurgy and Materials 2024年第4期31卷 803-811页

作者： Xiaoyan Wang Safeer jan Zhiyong Wang Xianbo Jin College of Chemistry and Molecular Sciences Hubei Key Laboratory of Electrochemical Power SourcesWuhan UniversityWuhan 430072China Engineering Research Center of Organosilicon Compounds&Materials Ministry of EducationWuhan 430072China

CO_(2) electrochemical reduction(CO_(2)ER)is an important research area for carbon neutralization.However,available catalysts for CO_(2) reduction are still characterized by limited stability and activity.Recently,metallic bismuth(Bi)has emerged as a promising catalyst for CO_(2) ER.Herein,we report the solid cathode electroreduction of commercial micronized Bi2O3as a straightforward approach for the preparation of nanostructured Bi.At-1.1 V versus reversible hydrogen electrode in a KHCO3aqueous electrolyte,the resulting nanostructure Bi delivers a formate current density of~40 mA·cm^(-2) with a current efficiency of~86%,and the formate selectivity reaches97.6% at-0.78 V.Using nanosized Bi2O3as the precursor can further reduce the primary particle sizes of the resulting Bi,leading to a significantly increased formate selectivity at relatively low overpotentials.The high catalytic activity of nanostructured Bi is attributable to the ultrafine and interconnected Bi nanoparticles in the nanoporous structure,which exposes abundant active sites for CO_(2) electrocatalytic reduction.

关键词： bismuth carbon dioxide electrocatalysis formate solid electroreduction

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Dieback of managed spruce stands in western Germany promotes beetle diversity

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Journal of Forestry Research 2024年第3期35卷 55-71页

作者： Eva Plath Chantal Trauth jan Gerhards Laura Griebel Klaus Fischer Department Biology Institute of Integrated Natural SciencesKoblenz-Landau University56070 KoblenzGermany

Biodiversity loss is a significant problem at a global scale and may be amplified by climate change.In recent years,coniferous forests have had substantial die-back across Europe due to drought and subsequent bark-beetle outbreaks.As many studies on the consequences of disturbance and subsequent management have focused on natural stands,management implications for managed spruce stands are not well understood,even though such stands are widespread throughout Europe.In this study,beetle taxonomy,conservation value,and community com-position are compared among spruce plantations and four post-disturbance management approaches:standing dead-wood,lying deadwood,clear cuts,and long-term succession.Diversity and community composition differed significantly among management categories,while different beetle fami-lies responded similarly.Intact spruce stands harbored the lowest beetle diversity while the highest taxonomic diver-sity and conservation value was on clear cuts and stands with lying or standing deadwood.The proportion of forest specialists was highest in successional forests.In summary,different forest management categories harbored distinct beetle communities at the family-,species-,and ecological guild levels.Therefore,post-disturbance management should consider the landscape scale and include different management types.This enhances landscape heterogeneity and thus overall biodiversity but could also mitigate negative impacts of natural disturbances on ecosystem services.

关键词： Bark-beetle outbreak Forest dieback Spruce Deadwood Nature conservation Beetle biodiversity-Coleoptera Coniferous forests

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Comparison of smoothness-constrained and geostatistically based cross-borehole electrical resistivity tomography for characterization of solute tracer plumes

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Water Science and Engineering 2016年第4期9卷 274-286页

作者： Andreas Englert Andreas Kemna Jun-feng Zhu jan vanderborght Harry Vereecken Tian-Chyi J.Yeh Institute of Geology Mineralogy and GeophysicsRuhr University Bochum Department of Geophysics Steinmann InstituteUniversity of Bonn Kentucky Geological Survey University of Kentucky Agrosphere Institute for Bio- and Geosciences(IBG-3)Forschungszentrum Jlich GmbH Department of Resources Engineering National Cheng Kung University Department of Hydrology and Water Resources The University of Arizona

Experiments using electrical resistivity tomography(ERT) have shown promising results in reducing the uncertainty of solute plume characteristics related to estimates based on the analysis of local point measurements only.To explore the similarities and differences between two cross-borehole ERT inversion approaches for characterizing salt tracer plumes,namely the classical smoothness-constrained inversion and a geostatistically based approach,we performed two-dimensional synthetic experiments.Simplifying assumptions about the solute transport model and the electrical forward and inverse model allowed us to study the sensitivity of the ERT inversion approaches towards a variety of basic conditions,including the number of boreholes,measurement schemes,contrast between the plume and background electrical conductivity,use of a priori knowledge,and point conditioning.The results show that geostatistically based and smoothness-constrained inversions of electrical resistance data yield plume characteristics of similar quality,which can be further improved when point measurements are incorporated and advantageous measurement schemes are chosen.As expected,an increased number of boreholes included in the ERT measurement layout can highly improve the quality of inferred plume characteristics,while in this case the benefits of point conditioning and advantageous measurement schemes diminish.Both ERT inversion approaches are similarly sensitive to the noise level of the data and the contrast between the solute plume and background electrical conductivity,and robust with regard to biased input parameters,such as mean concentration,variance,and correlation length of the plume.Although sophisticated inversion schemes have recently become available,in which flow and transport as well as electrical forward models are coupled,these schemes effectively rely on a relatively simple geometrical parameterization of the hydrogeological model.Therefore,we believe that standard uncoupled ERT inverse approaches,like the ones discussed and

关键词： Electrical resistivity tomography Inversion technique Solute tracer plume Synthetic experiment Plume characteristics

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Mechanistic insights toward identification and interaction of plant parasitic nematodes:A review

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Soil Ecology Letters 2024年第1期6卷 11-27页

作者： Bisma jan Ali Haider Shah Mudasir Ahmad Bhat Arif Tasleem jan Ishfaq Ahmad Wani Ali Asghar Shah Section of Microbiology Baba Ghulam Shah Badshah UniversityRajouriJ&K185234India Department of Biotechnology Baba Ghulam Shah Badshah University RajouriJ&K185234India Department of Botany Baba Ghulam Shah Badshah University RajouriJ&K185234India Department of Zoology School of Biosciences and BiotechnologyBaba Ghulam Shah Badshah University RajouriJ&K185234India

Nematode identification serves as an important param-eter to study their behaviour,importance and pathogenic-ity.Application of classical morphometric based identifica-tion methods prove to be lacking due to insufficient knowledge on morphological variations among closely related taxa.Molecular approaches such as DNA and protein-based information,microarray,probing,sequence-based methods and others have been used to supplement morphology-based methods for nematode identification.Ascarosides and certain protein-based nematode-associated molecular patterns(NAMPs),can be perceived by the host plants,and can initiate a signalling cascade.This review primarily emphasizes on an updated account of different classical and modern tools used for the identification of nematodes.Besides we also summa-rize the mechanism of some important signalling pathways which are involved in the different plant nematode interactions.Nematodes constitute most diverse and least studied group of soil inhabiting invertebrates.They are ecologically and physiologically important,however,wide range of nematodes show harmful impact on the individuals that live within their vicinity.Plant parasitic nematodes(PPNs)are transparent,pseudocoelomate,free living or parasitic microorganisms.PPNs lack morphometric identification methods due to insufficient knowl-edge on morphological variations among closely related taxa.As such,molecular approaches such as DNA and protein-based information,microarray,probing,sequence-based methods and others have been used to supplement morphology-based methods for their identification.To invade the defense response of different plant species,parasitic nematodes have evolved different molecular strategies.Ascarosides and certain protein-based nematode-associated molecular patterns(NAMPs),can be perceived by the host plants,and can initiate a signaling cascade.To overcome the host confrontation and develop certain nematode feeding sites,some members can inject effectors into the cells of susceptible hosts to reprogram the

关键词： nematode identification plant nematode interaction DNA fingerprinting nematode-associated molecular patterns signaling path-ways

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Portable dielectrophoresis for biology:ADEPT facilitates cell trapping,separation,and interactions

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Microsystems & Nanoengineering 2024年第2期10卷 193-205页

作者： Lourdes Albina Nirupa Julius Dora Akgül Gowri Krishnan Fabian Falk jan Korvink Vlad Badilita Department Institute of Microstructure TechnologyKarlsruhe Institute of TechnologyHermann-von-Helmholtz-Platz 1Eggenstein-Leopoldshafen76344Baden-WürttembergGermany

Dielectrophoresis is a powerful and well-established technique that allows label-free,non-invasive manipulation of cells and particles by leveraging their electrical properties.The practical implementation of the associated electronics and user interface in a biology laboratory,however,requires an engineering background,thus hindering the broader adoption of the technique.In order to address these challenges and to bridge the gap between biologists and the engineering skills required for the implementation of DEP platforms,we report here a custom-built,compact,universal electronic platform termed ADEPT(adaptable dielectrophoresis embedded platform tool)for use with a simple microfluidic chip containing six microelectrodes.The versatility of the open-source platform is ensured by a custom-developed graphical user interface that permits simple reconfiguration of the control signals to address a wide-range of specific applications:(i)precision positioning of the single bacterium/cell/particle in the micrometer range;(ii)viability-based separation by achieving a 94%efficiency in separating live and dead yeast;(iii)phenotype-based separation by achieving a 96%efficiency in separating yeast and Bacillus subtilis;(iv)cell–cell interactions by steering a phagocytosis process where a granulocyte engulfs E.coli RGB-S bacterium.Together,the set of experiments and the platform form a complete basis for a wide range of possible applications addressing various biological questions exploiting the plug-and-play design and the intuitive GUI of ADEPT.

关键词： Together separation separating

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