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Modular-integrative modeling: a new framework for building brain models that blend biological realism and functional performance

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National Science Review 2024年第5期11卷 13-16页

作者： Mario Senden Sacha J.van Albada Giovanni pezzulo Egidio Falotico Ibrahim Hashim Alexander kroner Anno C.kurth pablo Lanillos Vaishnavi Narayanan Cyriel pennartz Mihai A.petrovici Lea Steffen Tonio Weidler Rainer goebel Department of Cognitive Neuroscience Maastricht University Maastricht Brain Imaging Centre Maastricht University Institute of Neuroscience and Medicine(INM-6) and Institute for Advanced Simulation(IAS-6) and JARA-Institut Brain Structure-Function Relationships(INM-10) Jülich Research Center Institute of Zoology University of Cologne Institute of Cognitive Sciences and Technologies The Bio Robotics Institute Scuola Superiore Sant'Anna RWTH Aachen University Donders Institute for Brain Cognition and BehaviorRadboud University Cognitive and Systems Neuroscience Group Swammerdam Institute for Life Sciences University of Amsterdam Department of physiology University of Bern FZI Research Center of Information Technology

To cope with the immense complexity of the brain, neuroscientific research often focuses on isolated brain structures or circumscribed perceptual, cognitive or motor functions [1]. This reductionist approach overlooks the intricate and multifaceted interplay among various structural and functional *** instance, even simple movements require the coordinated activation of numerous neuronal populations across multiple brain regions [2].

关键词： WORLD SURVEY pROJECTS

Evaluation of a Wireless Solar powered personal Weather Station

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Agricultural Sciences 2024年第1期15卷 36-53页

作者： Robert J. Lascano Timothy S. goebel Dennis C. Gitz III John E. Stout Cropping Systems Research Laboratory Wind Erosion and Water Conservation Research Unit USDA-ARS Lubbock TX USA

We are evaluating dryland cotton production in Martin County, Texas, measuring cotton lint yield per unit of rainfall. Our goal is to collect rainfall data per 250 - 400 ha. Upon selection of a rainfall gauge, we realized that the cost of using, for example, a tipping bucket-type rain gauge would be too expensive and thus searched for an alternative method. We selected an all-in-one commercially available weather station;hereafter, referred to as a personal Weather Station (pWS) that is both wireless and solar powered. Our objective was to evaluate average measurements of rainfall obtained with the pWS and to compare these to measurements obtained with an automatic weather station (AWS). For this purpose, we installed four pWS deployed within 20 m of the plant Stress and Water Conservation Meteorological Tower that was used as our AWS, located at USDA-ARS Cropping Systems Research Laboratory, Lubbock, TX. In addition, we measured and compared hourly average values of short-wave irradiance (Rg), air temperature (Tair) and relative humidity (RH), and wind speed (WS), and calculated values of dewpoint temperature (Tdew). This comparison was done over a 242-day period (1 October 2022-31 May 2023) and results indicated that there was no statistical difference in measurements of rainfall between the pWS and AWS. Hourly average values of Rg measured with the pWS and AWS agreed on clear days, but pWS measurements were higher on cloudy days. There was no statistical difference between pWS and AWS hourly average measurements of Tair, RH, and calculated Tdew. Hourly average measurements of Rg and WS were more variable. We concluded that the pWS we selected will provide adequate values of rainfall and other weather variables to meet our goal of evaluating dryland cotton lint yield per unit rainfall.

关键词： Automation Sensors Citizen Weather Station Mesonet Rainfall Weather Variables

Efficient Haplotype Inference Algorithms in One Whole Genome Scan for pedigree Data with Non-genotyped Founders

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Acta Mathematicae Applicatae Sinica 2009年第3期25卷 477-488页

作者： Hadi Sabaa Randy goebel Department of Computing Science University of Alberta

An efficient rule-based algorithm is presented for haplotype inference from general pedigree genotype data, with the assumption of no recombination. This algorithm generalizes previous algorithms to handle the cases where some pedigree founders are not genotyped, provided that for each nuclear family at least one parent is genotyped and each non-genotyped founder appears in exactly one nuclear family. The importance of this generalization lies in that such cases frequently happen in real data, because some founders may have passed away and their genotype data can no longer be collected. The algorithm runs in O（m^3n^3） time, where m is the number of single nucleotide polymorphism （SNp） loci under consideration and n is the number of genotyped members in the pedigree. This zero-recombination haplotyping algorithm is extended to a maximum parsimoniously haplotyping algorithm in one whole genome scan to minimize the total number of breakpoint sites, or equivalently, the number of maximal zero-recombination chromosomal regions. We show that such a whole genome scan haplotyping algorithm can be implemented in O（m^3n^3） time in a novel incremental fashion, here m denotes the total number of SNp loci along the chromosome.

关键词： Haplotype inference efficient algorithm pedigree whole genome scan

Argon: a novel therapeutic option to treat neuronal ischemia and reperfusion injuries?

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Neural Regeneration Research 2015年第7期10卷 1043-1044页

作者： Felix Ulbrich Ulrich goebel Department of Anesthesiology and Intensive Care Medicine University Medical CenterFreiburg Germany

Neuronal injury and neuroprotection：Ischemia and reperfusion injuries in neuronal cells such as acute ischemic stroke-represent the third leading cause of death in the *** therapeutic concepts mainly aim to re-establ... 详细信息

关键词： a novel therapeutic option to treat neuronal ischemia and reperfusion injuries MCAO NDS OGD

Regeneration patterns of key pine species in a mixed-pine forest indicate a positive effect of variable retention harvesting and an increase in recruitment with time

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Forest Ecosystems 2020年第4期7卷 659-671页

作者： priscilla A.Nyamai p.Charles goebel R.Gregory Corace III David M.Hix Natural Resources Management program Grand Valley State University1 Campus DrAllendaleMI 49401USA. Department of Forest Rangelandand Fire SciencesUniversity of Idaho875 Perimeter Drive MS 1133MoscowID 83844USA. Alpena-Montmorency Conservation District 1900 M-32 WAlpenaMI 49707USA. School of Environment and Natural Resources The Ohio State University2021 Coffey RoadColumbusOH 43210USA.

Background:Many fire-dependent forests have experienced significant declines in species,structural,and functional *** changes are attributed in part to traditional management approaches that were dominated by even-aged regeneration methods such as *** retention harvesting(VRH)is an ecologically based forestry practice that involves retention of some mature overstory trees and other biological structures in the postharvest stand to emulate the effects of natural disturbance *** this study,we examined the effect of a VRH treatment on recruitment of historically dominant pine species and understory vegetation twoand six years after its implementation in a naturally regenerated mixed pine forest in the Upper peninsula of Michigan,***:We found greater regeneration of red pine(pinus resinosa L.)and eastern white pine(pinus strobus L.)in VRH stands compared to the unharvested *** red pine recruitment was very low during the first 2 years,both species increased significantly from year two to year *** responses for the two species did not differ significantly between the aggregated and dispersed retention *** also found high recruitment of deciduous tree species,consisting primarily of sprouts,and red pine exhibited a negative correlation with these ***,time,and the interaction of treatment and time were significant factors in red pine *** had a strong effect on the understory vegetation,with significant decreases in shrubs and ferns over ***:The results suggest that VRH enhanced recruitment of red pine and eastern white pine and that this recruitment increased with *** identify competition from sprouts and unfavorable seedbed conditions as the main factors that limited recruitment of red pine during the first 2 *** reduce competing vegetation and improve seedbed conditions,we suggest following the VRH with a prescribed fire,mechanically removing s

关键词： Variable retention harvesting Aggregated retention Dispersed retention Mixed-pine forest pinus resinosa pinus strobus

Approximation Algorithms for Vertex Happiness

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Journal of the Operations Research Society of China 2019年第3期7卷 429-448页

作者： Yao Xu Yong Chen peng Zhang Randy goebel Department of Computing Science University of AlbertaEdmontonAB T6G 2E8Canada Department of Mathematics Hangzhou Dianzi UniversityHangzhou 310018China School of Computer Science and Technology Shandong UniversityJinan 250101China

We investigate the maximum happy vertices(MHV)problem and its complement,the minimum unhappy vertices(MUHV)*** order to design better approximation algorithms,we introduce the supermodular and submodular multi-labeling(SUp-ML and SUB-ML)problems and show that MHV and MUHV are special cases of SUp-ML and SUB-ML,respectively,by rewriting the objective functions as set *** convex relaxation on the I ovasz extension,originally presented for the submodular multi-partitioning problem,can be extended for the SUB-ML problem,thereby proving that SUB-ML(SUp-ML,respectively)can be approximated within a factorof2-2/k(2/k,respectively),where k is the number of *** general results imply that MHV and MUHV can also be approximated within factors of 2/k and 2-2/k,respectively,using the same approximation *** the MUHV problem,we also show that it is approximation-equivalent to the hypergraph multiway cut problem;thus,MUHV is Unique Games-hard to achieve a(2-2/k-e)-approximation,for anyε>*** the MHV problem,the 2/k-approximation improves the previous best approximation ratio max{1/k,1/(△+1/g(△)},where△is the maximum vertex degree of the input graph and g(△)=(√△+√△+1)2△>4△*** also show that an existing Lp relaxation for MHV is the same as the concave relaxation on the Lovasz extension for SUp-ML;we then prove an upper bound of 2/k on the integrality gap of this Lp relaxation,which suggests that the 2/k-approximation is the best possible based on this Lp ***,we prove that it is Unique Games-hard to approximate the MHV problem within a factor of S2(log2 k/k).

关键词： Vertex happiness Multi-labeling Submodular/supermodular set function Approximation algorithm polynomial-time reduction Integrality gap

Argon preconditioning protects neuronal cells with a Toll-like receptor-mediated effect

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Neural Regeneration Research 2023年第6期18卷 1371-1377页

作者： Stefanie Scheid Adrien Lejarre Jakob Wollborn Hartmut Buerkle Ulrich goebel Felix Ulbrich Department of Anesthesiology and Critical Care Medical Center-University of FreiburgFaculty of MedicineFreiburgGermany Department of Anesthesiology Perioperative and Pain MedicineBrigham and Women’s HospitalHarvard Medical SchoolBostonMAUSA Department of Anesthesiology and Critical Care Medicine St.Franziskus-HospitalMuensterGermany

The noble gas argon has the potential to protect neuronal cells from cell *** far,this effect has been studied in treatment after acute *** using argon has not yet been *** this study,human neuroblastoma SH-SY5Y cells were treated with different concentrations of argon(25%,50%,and 74%;21%O_(2),5%CO_(2),balance nitrogen)at different time intervals before inflicting damage with rotenone(20μM,4 hours).Apoptosis was determined by flow cytometry after annexin V and propidium iodide *** expressions of Toll-like receptors 2 and 4 were also *** were also processed for analysis by western blot and qpCR to determine the expression of apoptotic and inflammatory proteins,such as extracellular-signal regulated kinase(ERk1/2),nuclear transcription factor-κB(NF-κB),protein kinase B(Akt),caspase-3,Bax,Bcl-2,interleukin-8,and heat shock *** staining was performed for TLR2 and 4 and *** were also pretreated with OxpApC,an antagonist of TLR2 and 4 to elucidate the molecular *** showed that argon preconditioning before rotenone application caused a dose-dependent but not a time-dependent reduction in the number of apoptotic *** with 74%argon for 2 hours was used for further experiments showing the most promising *** decreased the surface expression of TLR2 and 4,whereas OxpApC treatment partially abolished the protective effect of *** increased phosphorylation of ERk1/2 but decreased NF-κB and *** inhibited mitochondrial apoptosis and the heat shock *** also suppressed the expression of the pro-inflammatory cytokine *** confirmed the alteration of TLRs and *** reversed the argon effect on ERk1/2,Bax,Bcl-2,caspase-3,and interleukin-8 expression,but not on NF-κB and the heat shock *** together,argon preconditioning protects against apoptosis of neuronal c

关键词： apoptosis inflammation interleukin-8 neuroprotection rotenone SH-SY5Y Toll-like receptor 2 Toll-like receptor 4

Hepatic steatosis prevents heme oxygenase-1 induction by isoflurane in the rat liver

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World Journal of Gastroenterology 2011年第37期17卷 4184-4190页

作者： patrick Stoll Christian I Schwer Ulrich goebel Hartmut Buerkle Alexander Hoetzel Rene Schmidt Department of Anesthesiology and Critical Care Medicine Freiburg University Medical Center

AIM:To characterize the inductive effects of isoflurane(ISO) on hepatic heme oxygenase-1(HO-1) in an animal model of hepatic ***:Lean(LEAN) and obese(FAT) Zucker rats were randomized into 4 groups:1:LEAN + pentobarbital sodium(pEN);2:LEAN + ISO;3:FAT + pEN;4:FAT + *** animals were mechanically ventilated for 6 *** vitro analyses of liver tissue included determination of HO-1 mRNA and protein expression as well as measurement of HO enzyme activity and immunohistochemical ***:Compared to pEN treatment,ISO administration profoundly induced hepatic HO-1 mRNA and protein expression and significantly increased HO enzyme activity in lean Zucker *** contrast,no difference in HO-1 gene expression was observed after ISO or pEN anesthesia in obese Zucker ***:The present study demonstrates that ISO is an inducer of hepatic HO-1 gene expression in non-steatotic organs but failed to upregulate HO-1 in steatotic livers.

关键词： Isoflurane Heme oxygenase Hepatic steatosis Heme oxygenase-1 Volatile anesthetics

The roles of the human ATp-binding cassette transporters p-glycoprotein and ABCG2 in multidrug resistance in cancer and at endogenous sites: future opportunities for structure-based drug design of inhibitors

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Cancer Drug Resistance 2021年第4期4卷 784-804页

作者： Jason goebel Jean Chmielewski Christine A.Hrycyna Department of Chemistry Purdue University West LafayetteIN 47907USA

The ATp-binding cassette(ABC)transporters p-glycoprotein(p-gp)and ABCG2 are multidrug transporters that confer drug resistance to numerous anti-cancer therapeutics in cell *** findings initially created great excitement in the medical oncology community,as inhibitors of these transporters held the promise of overcoming clinical multidrug resistance in cancer ***,clinical trials of p-gp and ABCG2 inhibitors in combination with cancer chemotherapeutics have not been successful due,in part,to flawed clinical trial designs resulting from an incomplete molecular understanding of the multifactorial basis of multidrug resistance(MDR)in the cancers *** field was also stymied by the lack of high-resolution structural information for p-gp and ABCG2 for use in the rational structure-based drug design of *** advances in structural biology have led to numerous structures of both ABCG2 and p-gp that elucidated more clearly the mechanism of transport and the polyspecific nature of their substrate and inhibitor binding *** data should prove useful helpful for developing even more potent and specific inhibitors of both *** such,although possible pharmacokinetic interactions would need to be evaluated,these inhibitors may show greater effectiveness in overcoming ABC-dependent multidrug resistance in combination with chemotherapeutics in carefully selected subsets of *** perhaps even more compelling use of these inhibitors may be in reversibly inhibiting endogenously expressed p-gp and ABCG2,which serve a protective role at various blood-tissue *** of these transporters at sanctuary sites such as the brain and gut could lead to increased penetration by chemotherapeutics used to treat brain cancers or other brain disorders and increased oral bioavailability of these agents,respectively.

关键词： p-glycoprotein ABCG2 ABC transporters multidrug resistance inhibitor