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GranatumX:A Community-engaging, Modularized, and Flexible Webtool for Single-cell Data Analysis

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Genomics, Proteomics & Bioinformatics 2021年第3期19卷 452-460页

作者： David G.Garmire Xun Zhu Aravind Mantravadi Qianhui Huang Breck Yunits Yu Liu Thomas Wolfgruber Olivier Poirion Tianying Zhao Cédric Arisdakessian stefan stanojevic Lana X.Garmire Department of Electrical Engineering&Computer Science University of MichiganAnn ArborMI 48109USA Epidemiology Program University of Hawaii Cancer CenterHonoluluHI 96813USA Department of Biostatistics University of MichiganAnn ArborMI 48109USA Department of Computational Medicine and Bioinformatics University of MichiganAnn ArborMI 48105USA Molecular Biosciences and Bioengineering Graduate Program University of Hawaii at ManoaHonoluluHI 96822USA

We present GranatumX,a next-generation software environment for single-cell RNA sequencing(scRNA-seq)data *** is inspired by the interactive webtool *** enables biologists to access the latest scRNA-seq bioinformatics methods in a web-based graphical *** also offers software developers the opportunity to rapidly promote their own tools with others in customizable *** architecture of GranatumX allows for easy inclusion of plugin modules,named Gboxes,which wrap around bioinformatics tools written in various programming languages and on various *** can be run on the cloud or private servers and generate reproducible *** is a community-engaging,flexible,and evolving software ecosystem for scRNA-seq analysis,connecting developers with bench *** is freely accessible at http://***/granatumx/app.

关键词： Single-cell RNA sequencing Analysis Pipeline Webtool Module

Modulation of the Nogo signaling pathway to overcome amyloid-β-mediated neurite inhibition in human pluripotent stem cell-derived neurites

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Neural Regeneration Research 2025年第9期20卷 2645-2654页

作者： Kirsty Goncalves stefan Przyborski Department of Biosciences Durham UniversityDurhamUK Reprocell Europe Ltd. GlasgowUK

Neuronal cell death and the loss of connectivity are two of the primary pathological mechanisms underlying Alzheimer's *** accumulation of amyloid-βpeptides,a key hallmark of Alzheimer's disease,is believed to induce neuritic abnormalities,including reduced growth,extension,and abnormal growth cone morphology,all of which contribute to decreased ***,the precise cellular and molecular mechanisms governing this response remain *** this study,we used an innovative approach to demonstrate the effect of amyloid-βon neurite dynamics in both two-dimensional and three-dimensional cultu re systems,in order to provide more physiologically relevant culture *** utilized various methodologies,including the addition of exogenous amyloid-βpeptides to the culture medium,growth substrate coating,and the utilization of human-induced pluripotent stem cell technology,to investigate the effect of endogenous amyloid-βsecretion on neurite outgrowth,thus paving the way for potential future applications in personalized ***,we also explore the involvement of the Nogo signaling cascade in amyloid-β-induced neurite *** demonstrate that inhibition of downstream ROCK and RhoA components of the Nogo signaling pathway,achieved through modulation with Y-27632(a ROCK inhibitor)and Ibuprofen(a Rho A inhibitor),respectively,can restore and even enhance neuronal connectivity in the presence of amyloid-β.In summary,this study not only presents a novel culture approach that offers insights into the biological process of neurite growth and inhibition,but also proposes a specific mechanism for reduced neural connectivity in the presence of amyloid-βpeptides,along with potential intervention points to restore neurite ***,we aim to establish a culture system that has the potential to serve as an assay for measuring preclinical,predictive outcomes of drugs and their ability to promote neurite outgrowth,both generally and in a patie

关键词： Alzheimer's disease induced pluripotent stem cell neurite outgrowth neuron Nogo Rho A ROCK stem cell three-dimensional culture

BEV-Locator:an end-to-end visual semantic localization network using multi-view images

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Science China(Information Sciences) 2025年第2期68卷 134-150页

作者： Zhihuang ZHANG Meng XU Wenqiang ZHOU Tao PENG Liang LI stefan POSLAD School of Vehicle and Mobility Tsinghua University School of Information Technology & Management University of International Business and Economics Qcraft Inc. School of Electronic Engineering and Computer Science Queen Mary University of London

Accurate localization ability is fundamental in autonomous driving. Traditional visual localization frameworks approach the semantic map-matching problem with geometric models, which rely on complex parameter tuning and thus hinder large-scale deployment. In this paper, we propose BEV-Locator: an end-to-end visual semantic localization neural network using multi-view camera images. Specifically, a visual BEV(bird-eye-view) encoder extracts and flattens the multi-view images into BEV space. While the semantic map features are structurally embedded as map query sequences. Then a cross-model transformer associates the BEV features and semantic map queries. The localization information of ego-car is recursively queried out by cross-attention modules. Finally, the ego pose can be inferred by decoding the transformer outputs. This end-to-end model speaks to its broad applicability across different driving environments, including high-speed scenarios. We evaluate the proposed method in large-scale nuScenes and Qcraft datasets. The experimental results show that the BEV-Locator is capable of estimating the vehicle poses under versatile scenarios, which effectively associates the cross-model information from multi-view images and global semantic maps. The experiments report satisfactory accuracy with mean absolute errors of 0.052 m, 0.135 m and 0.251° in lateral, longitudinal translation and heading angle degree.

关键词： visual localization semantic map bird-eye-view transformer pose estimation

Influence of symmetric and asymmetric rolling on texture evolution of work-hardened AA 5xxx aluminium alloy

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Transactions of Nonferrous Metals Society of China 2025年第1期35卷 30-44页

作者： MatjažGODEC stefan ZAEFFERER Jakob KRANER Črtomir DONIK Irena PAULIN Institute of Metals and Technology Lepi pot 111000LjubljanaSlovenia Max-Planck-Institut für Eisenforschung Max-Planck-Strasse 140237 DüsseldorfGermany Impol 2000 d.d. Partizanska cesta 382310 Slovenska BistricaSlovenia

The textures and microstructures of hot-and cold-rolled sheets of an AA 5454 aluminium alloy were studied,with special attention paid to comparing the texture development for the symmetric and asymmetric cold *** electron microscopy with electron-backscatter diffraction was used to monitor the development of the microstructure in the differently deformed and additionally annealed *** of the formations and transformations of individual texture components occurring during the rolling processes were observed and *** average grain sizes,textures and mechanical properties were correlated and explained for the symmetric and asymmetric cold-rolled *** asymmetric rolling is beneficial in terms of deep drawability because it reduces the planar anisotropy of the annealed material due to the decrease of the Cube,Goss,rotated-Cube and η-fibre texture components and at the same time strengthens X1-and X2-fibre texture components which are shear texture components and improve deep *** the asymmetric cold rolling,the temperature increases due to friction,triggering recrystallisation processes and leading to larger *** is also confirmed that asymmetric cold rolling uses less rolling force and consequently less energy to produce a final material with better formability,particularly earing.

关键词： crystallographic texture EBSD aluminium alloy symmetric/asymmetric rolling anisotropy

Advanced hepatocellular carcinoma treatment strategies:Are transarterial approaches leading the way?

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World Journal of Gastrointestinal Oncology 2025年第1期17卷 22-27页

作者： stefan Patauner Giovanni Scotton Francesca Notte Antonio Frena Department of General and Pediatric Surgery Bolzano Central Hospital-SABESBolzano 39100Trentino-Alto AdigeItaly

Hepatocellular carcinoma(HCC)is a leading cause of cancer-related mortality worldwide,with advanced stages posing significant treatment ***-though hepatic arterial infusion chemotherapy(HAIC)has emerged as a promising modality for treating advanced HCC,particularly in Asian clinical practice,its adoption in Western medicine remains limited due to a lack of large-scale randomized controlled *** editorial reviews and comments on the meta-analysis conducted by Zhou et al,which evaluates the efficacy and safety of HAIC and its combination strategies for advanced *** authors performed a comprehensive meta-analysis of various clinical trials and cohort studies comparing HAIC and its combinations to other first-line treatments,such as sorafenib and transarterial chemoembolization(TACE).In this work,HAIC showed significantly better results regarding overall survival and progression-free survival compared to sorafenib or TACE alone and their *** in combination with lenvatinib,ablation,programmed cell death 1 inhibitors,and radiotherapy further enhanced patient outcomes,indicating a synergistic *** editorial focuses on the critical role of multimodal treatment strategies in managing advanced *** advocates for a paradigm shift towards integrated treatment approaches to enhance survival rates and improve the quality of life in patients with advanced HCC.

关键词： Hepatocellular carcinoma Hepatic arterial infusion chemotherapy Transarterial chemoembolization Sorafenib Combined therapy

The Influence of Major Climatic Elements on the Devastated Geo-Hydrological Disasters: A Case of Hanang Disaster of 3rd December 2023 in Tanzania

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Atmospheric and Climate Sciences 2025年第1期15卷 106-125页

作者： Asnath Alberto Malekela stefan Sieber Jafari Swalehe Chobo Joseph Ndunguru Department of Geography and History Mwalimu Nyerere Memorial Academy Dar es Salaam Tanzania Leibniz Centre for Agricultural Landscape Research (ZALF) Mncheberg Germany Department of Agricultural Economics Humboldt University of Berlin Berlin Germany Department of Climatology and Climate Change Tanzania Meteorological Authority Dar es Salaam Tanzania

Changes in major climatic elements such as temperature, precipitation and wind distribution have triggered weather-related and geophysical disasters. In recent years, the globe has experienced an increased number of floods and landslide events which are said to be the most common among other natural disasters. This study examines the influence of climatic elements on the geo-hydrological disaster which occurred in Hanang district-Tanzania on 3rd December 2023. The study used the primary data collected from 182 respondents. Also, the trend analysis (1981-2023) was conducted using average rainfall from 7 meteorological stations in the study area. Annual and seasonal rainfall as well as a number of rainy days were analyzed. The calculated rainfall data were then used to compute the dimensions of the standardized precipitation anomalies (SPA) which is designated as SPA = (P − P*)/σp. Besides, the temperature was analysed to investigate its trend and trend anomaly. Also, the wind rose statistics for the annual, March to May (MAM) and October to December (OND) for the climatology period of 1991-2020 were analysed so as to examine its contribution to rainfall distribution in Hanang district. The examination of annual rainfall data indicates an upward trend in precipitation levels, accompanied by notable variability in rainfall patterns, including seasonal anomalies and deviations from historical averages. The combination of elevated rainfall, anomalies in rainfall patterns, and potentially unfavourable terrain characteristics may have contributed to devastated geo-hydrological disaster risk. However, future research is recommended that could focus on integrating rainfall and temperature data with comprehensive geo-hydrological susceptibility assessments, considering factors such as terrain stability, land cover and land use practices.

关键词： Climate Elements Climate Change Landslides Floods Geo-Hydrological Disasters

Light tuning CO/H_(2)composition on Ag:Unraveling CO_(2)mass transfer and electron-phonon coupling in plasmon-enhanced electrocatalysis

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Nano Research 2025年第1期18卷 173-185页

作者： Rui Lin Dong Fan Luca MBerger Thomas Possmayer Yu Zhou Jiexin Zhu Xingbao Chen Wen Luo Lars Allmendinger Andreas Tittl Leonardo de Souza Menezes Guillaume Maurin Shihe Yang and stefan AMaier Nanoinstitute Munich Faculty of PhysicsLudwig-Maximilians-Universität München80539 MunichGermany Institut Charles Gerhardt Montpellier UMR 5253 CNRS ENSCM UniversitéMontpellierPlace E.Bataillon34090 MontpellierFrance Guangdong Provincial Key Lab of Nano-Micro Material Research School of Advanced MaterialsPeking University Shenzhen Graduate SchoolShenzhen 518055China State Key Laboratory of Advanced Technology for Materials Synthesis and Processing Wuhan University of TechnologyWuhan 430070China Faculty of Chemistry and Pharmacy Ludwig-Maximilians-Universität München81377 MunichGermany Departamento de Física Universidade Federal de Pernambuco50670-901 Recife-PEBrazil School of Physics and Astronomy Monash University Clayton CampusMelbourneVictoria 3800Australia Department of Physics Imperial College LondonSW72AZ LondonUK

Plasmon-enhanced electrocatalysis(PEEC)is an emerging approach to mitigate CO_(2)*** mechanisms behind CO_(2)adsorption and reduction at the catalyst-electrolyte interface in PEEC still need to be further ***,we employ a well-defined Ag nanostructure to elucidate these pivotal *** shining light with wavelengths of 625,525,405 nm on Ag,an adjustable CO/H_(2)ratio from 35 to 1 can be *** reaction pathway changing under plasmonic excitation does not originate from the lowered CO_(2)mass transfer in the vicinity of Ag,as the electrochemical quartz crystal microbalance results unravel that a slightly elevated temperature in bulk electrolyte caused by light irradiation cannot weaken the CO_(2)adsorption at the Ag catalyst-electrolyte *** calculations reveal that optical excitation towards shorter wavelengths leads to a progressive lowered energy barrier for H_(2)formation together with an enhanced energy barrier for^(*)COOH *** thermodynamically suppressed,CO_(2)reduction can still be improved kinetically by optimizing the excitation wavelength and intensity,being accompanied with the enhanced *** absorption spectroscopy results further correlate the higher photocurrent with a prolonged electron-phonon coupling time,verifying that the improvement of CO_(2)reduction kinetics in PEEC can be realized by hot electron harnessing.

关键词： plasmonic catalysis photoelectrochemical CO_(2)reduction CO/H_(2)ratio hot electron generation electronphonon coupling thermal effect

Generalized Sampling in Shift Invariant Spaces with Frames

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Acta Mathematica Sinica,English Series 2012年第9期28卷 1823-1844页

作者： stefan ERICSSON Department of Engineering Sciences and Mathematics Lule University of Technology

Generalized sampling in a shift invariant subspace V of L2（R） is considered. A function f in V is processed with different filters Lm and then one tries to reconstruct f from the samples L^mf（j＇k）. We develop a theory of how to do this in the case when V possesses a shift invariant frame. Special attention is paid to the question： How to obtain dual frames with compact support？

关键词： Generalized sampling frames Riesz basis reproducing kernel shift invariant spaces

Constitutive relations for the shear band evolution in granular matter under large strain

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Particuology 2008年第6期6卷 501-505页

作者： stefan Luding Multi Scale Mechanics TS CTW UTwente P.O. Box 217 7500 AE Enschede Netherlands

A so-called ＂split-bottom ring shear cell＂ leads to wide shear bands under slow, quasi-static deformation. Unlike normal cylindrical Couette shear cells or rheometers, the bottom plate is split such that the outer part of it can move with the outer wall, while the other part （inner disk） is immobile. From discrete element simulations （DEM）, several continuum fields like the density, velocity, deformation gradient and stress are computed and evaluated with the goal to formulate objective constitutive relations for the powder flow behavior. From a single simulation, by applying time- and （local） space-averaging, a non-linear yield surface is obtained with peculiar stress dependence. The anisotropy is always smaller than the macroscopic friction coefficient. However, the lower bound of anisotropy increases with the strain rate, approaching the maximum according to a stretched exponential with a specific rate that is consistent with a shear path of about one particle diameter.

关键词： Ring shear cell Shear bands DEM simulation Micro-macro transition Objective constitutive relations Yield stress fluid