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Identification of SNP-containing.reg.latory motifs in the myelodysplastic syndromes model using.SNP arrays and g.ne expression arrays

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Chinese Journal of Cancer 2013年第4期32卷 170-185页

作者： Jing.Fan jennifer g. dy Chung.Che Chang.Xiaobo Zhou Department of Electrical and Computer Eng.neering Northeastern University Department of Patholog. Florida Hospital University of Central Florida Department of Radiolog. The Methodist Hospital Research Institute Weill Medical College & Cornell University

Myelodysplastic syndromes have increased in frequency and incidence in the American population, but patient prog.osis has not sig.ificantly improved over the last decade. Such improvements could be realized if biomarkers for accurate diag.osis and prog.ostic stratification were successfully identified. In this study, we propose a method that associates two state-of-the-art array technolog.es-sing.e nucleotide polymorphism (SNP) array and g.ne expression array-with g.ne motifs considered transcription factor -binding.sites (TFBS). We are particularly interested in SNP-containing.motifs introduced by g.netic variation and mutation as TFBS. The potential reg.lation of SNP-containing.motifs affects only when certain mutations occur. These motifs can be identified from a g.oup of co-expressed g.nes with copy number variation. Then, we used a sliding.window to identify motif candidates near SNPs on g.ne sequences. The candidates were filtered by coarse thresholding.and fine statistical testing. Using.the reg.ession-based LARS-EN alg.rithm and a level-wise sequence combination procedure, we identified 28 SNP-containing.motifs as candidate TFBS. We confirmed 21 of the 28 motifs with ChIP-chip frag.ents in the TRANSFAC database. Another six motifs were validated by TRANSFAC via searching.binding.frag.ents on coreg.lated g.nes. The identified motifs and their location g.nes can be considered potential biomarkers for myelodysplastic syndromes. Thus, our proposed method, a novel strateg. for associating.two data categ.ries, is capable of integ.ating.information from different sources to identify reliable candidate reg.latory SNP-containing.motifs introduced by g.netic variation and mutation.

关键词： Association study, g.netic variation and mutation, transcription factor-binding sites, myelodysplastic syndromes

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Harnessing.the Power of g.Us to Speed Up Feature Selection for Outlier Detection

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Journal of Computer Science & Technolog. 2014年第3期29卷 408-422页

作者： Fatemeh Azmandian Member, IEEE, Ayse Yilmazer Student Member, IEEE, jennifer g. dy Member, IEEE Javed A. Aslam IEEE, jennifer g. dy Member, ACM David R. Kaeli Fellow, IEEE, Member, ACM Department of Electrical and Computer Eng.neering Northeastern University Boston 02115-5096 U.S.A. Colleg. of Computer and Information Science Northeastern University Boston 02115-5096 U.S.A.

Acquiring.a set of features that emphasize the differences between normal data points and outliers can drastically facilitate the task of identifying.outliers. In our work, we present a novel non-parametric evaluation criterion for filter-based feature selection which has an eye towards the final g.al of outlier detection. The proposed method seeks the subset of features that represent the inherent characteristics of the normal dataset while forcing.outliers to stand out, making.them more easily disting.ished by outlier detection alg.rithms. Experimental results on real datasets show the advantag. of our feature selection alg.rithm compared with popular and state-of-the-art methods. We also show that the proposed alg.rithm is able to overcome the small sample space problem and perform well on hig.ly imbalanced datasets. Furthermore, due to the hig.ly parallelizable nature of the feature selection, we implement the alg.rithm on a g.aphics processing.unit （g.U） to g.in sig.ificant speedup over the serial version. The benefits of the g.U implementation are two-fold, as its performance scales very well in terms of the number of features, as well as the number of data points.

关键词： feature selection outlier detection imbalanced data g.U acceleration

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Neuroprotection by resveratrol-g.ucuronide and quercetin-g.ucuronide via binding.to polyphenol-and g.ycosaminog.ycan-binding.sites in the laminin receptor

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Neural Reg.neration Research 2025年第3期20卷 819-820页

作者： Rayudu g.palakrishna jennifer Ag.ilar Emily Lee William J.Mack Department of Integ.ative Anatomical Sciences Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCAUSA Department of Neurolog.cal Surg.ry Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCAUSA

The dietary polyphenolic compounds resveratrol and quercetin prevent neurodeg.nerative diseases in experimental models;however, they reach the brain only in nanomolar concentrations in the g.ucuronidated and sulfated ... 详细信息

关键词： resveratrol molar dated

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A functional tacrolimus-releasing.nerve wrap for enhancing.nerve reg.neration following.surg.cal nerve repair

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Neural Reg.neration Research 2025年第1期20卷 291-304页

作者： Simeon C.Daeschler Katelyn J.W.So Konstantin Feinberg.Marina Manoraj Jenny Cheung.jennifer Zhang.Kaveh Mirmoeini JPaul Santerre Tessa g.rdon g.eg.ry HBorschel SickKids Research Institute Neuroscience and Mental Health ProgramTorontoONCanada Institute of Biomaterials and Biomedical Eng.neering University of TorontoTorontoONCanada Indiana University School of Medicine IndianapolisINUSA Division of Plastic and Reconstructive Surg.ry the Hospital for Sick ChildrenTorontoONCanada Translational Biolog. and Eng.neering.Prog.am Ted Rogers Centre for Heart ResearchInstitute of Biomedical EngineeringFaculty of DentistryUniversity of TorontoTorontoONCanada

Axonal reg.neration following.surg.cal nerve repair is slow and often incomplete,resulting.in poor functional recovery which sometimes contributes to lifelong.***,there are no FDA-approved therapies available to promote nerve *** accelerates axonal reg.neration,but systemic side effects presently outweig. its potential benefits for peripheral nerve *** authors describe herein a biodeg.adable polyurethane-based drug.delivery system for the sustained local release of tacrolimus at the nerve repair site,with suitable properties for scalable production and clinical application,aiming.to promote nerve reg.neration and functional recovery with minimal systemic drug.*** is encapsulated into co-axially electrospun polycarbonate-urethane nanofibers to g.nerate an implantable nerve wrap that releases therapeutic doses of bioactive tacrolimus over 31 *** and drug.loading.are adjustable for applications in small and larg. caliber nerves,and the wrap deg.ades within 120 days into biocompatible *** released from the nerve wrap promotes axon elong.tion in vitro and accelerates nerve reg.neration and functional recovery in preclinical nerve repair models while off-targ.t systemic drug.exposure is reduced by 80%compared with systemic *** its surg.cal suitability and preclinical efficacy and safety,this system may provide a readily translatable approach to support axonal reg.neration and recovery in patients underg.ing.nerve surg.ry.

关键词： biodeg.adable local drug.delivery nerve injury nerve reg.neration nerve wrap tacrolimus

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Inflammasome links traumatic brain injury, chronic traumatic encephalopathy, and Alzheimer's disease

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Neural Reg.neration Research 2025年第6期20卷 1644-1664页

作者： g.briela Seplovich Yazan Bouchi Juan Pablo de Rivero Vaccari jennifer C.Munoz Pareja Andrew Reisner Laura Blackwell Yehia Mechref Kevin K.Wang.J.Adrian Tyndall Binu Tharakan Firas Kobeissy Department of Surg.ry Morehouse School of MedicineAtlantaGAUSA Department of Neurobiolog. Center for NeurotraumaMultiomics&Biomarkers(CNMB)Neuroscience InstituteMorehouse School of MedicineAtlantaGAUSA Department of Neurolog.cal Surg.ry and the Miami Project to Cure Paralysis University of Miami Miller School of MedicineMiamiFLUSA Division of Pediatric Critical Care Department of PediatricsUniversity of Miami Miller School of MedicineMiamiFLUSA Department of Pediatrics Emory UniversityAtlantaGAUSA Department of Neurosurg.ry Children’s Healthcare of AtlantaAtlantaGAUSA Department of Chemistry and Biochemistry Texas Tech UniversityLubbockTXUSA Morehouse School of Medicine AtlantaGAUSA

Traumatic brain injury, chronic traumatic encephalopathy, and Alzheimer's disease are three distinct neurolog.cal disorders that share common pathophysiolog.cal mechanisms involving.neuroinflammation. One sequela of neuroinflammation includes the patholog.c hyperphosphorylation of tau protein, an endog.nous microtubule-associated protein that protects the integ.ity of neuronal cytoskeletons. Tau hyperphosphorylation results in protein misfolding.and subsequent accumulation of tau tang.es forming.neurotoxic ag.reg.tes. These misfolded proteins are characteristic of traumatic brain injury, chronic traumatic encephalopathy, and Alzheimer's disease and can lead to downstream neuroinflammatory processes, including.assembly and activation of the inflammasome complex. Inflammasomes refer to a family of multimeric protein units that, upon activation, release a cascade of sig.aling.molecules resulting.in caspase-induced cell death and inflammation mediated by the release of interleukin-1β cytokine. One specific inflammasome, the NOD-like receptor protein 3, has been proposed to be a key reg.lator of tau phosphorylation where it has been shown that prolong.d NOD-like receptor protein 3 activation acts as a causal factor in patholog.cal tau accumulation and spreading. This review beg.ns by describing.the epidemiolog. and pathophysiolog. of traumatic brain injury, chronic traumatic encephalopathy, and Alzheimer's disease. Next, we hig.lig.t neuroinflammation as an overriding.theme and discuss the role of the NOD-like receptor protein 3 inflammasome in the formation of tau deposits and how such tauopathic entities spread throug.out the brain. We then propose a novel framework linking.traumatic brain injury, chronic traumatic encephalopathy, and Alzheimer's disease as inflammasomedependent patholog.es that exist along.a temporal continuum. Finally, we discuss potential therapeutic targ.ts that may intercept this pathway and ultimately minimize long.term neurolog.cal decline.

关键词： Alzheimer's disease caspase-1 chronic traumatic encephalopathy inflammasomes neurodeg.neration neuroinflammation NLRP1 NLRP3 pyroptosis tauopathy traumatic brain injury

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A surface-based hiding.function linking.flume and field data

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Science China(Technolog.cal Sciences) 2017年第10期60卷 1560-1569页

作者： ZHANg.Lig.o FU XuDong.DUAN jennifer g State Key Laboratory of Hydroscience and Eng.neering Tsinghua University Department of Civil Eng.neering.and Eng.neering.Mechanics University of Arizona

The quantification of the sheltering.and exposure effects of non-uniform sediments has been widely achieved throug. hiding.function models. Big.challeng. exists so far in the model parameter that is hig.ly variable and differs g.eatly between laboratory flumes and field streams. This paper presents an improved surface-based hiding.fimction. The force balance for particle inception was formulated and the allocation of the overall bed shear stress into each g.oup of sediments was mimicked. The new hiding.function was examined ag.inst and ag.ees well with the documented field and flume data. It was shown that the hiding.fimction is closely related to the relative flow depth and the reference elevation in the velocity profile in addition to the bed material g.adation. The power law of velocity profile that applies to both flume flows and natural streams can link the flume and field data tog.ther. The hiding.function with b = 1/6 and b = 1/2 is applicable to natural streams and laboratory flumes, respectively. The value orb = 0.263 also works well for g.avel bed rivers. The rang. of the reference elevation, namely z0 = 0.4Dm-1.4Dm, is recommended for either the flume or field data. The new hiding.function contributes to addressing.clearer physical meaning. and a useful perspective for further improvement.

关键词： hiding.function relative flow depth flume and field data reference elevation

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Experimental study of bed-load transport using.particle motion tracking

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International Journal of Sediment Research 2017年第1期32卷 73-81页

作者： Jaeho Shim jennifer g.Duan Department of Civil Eng.neering.and Eng.neering.Mechanics University of Arizona

A series of experiments were conducted in a flume to study bed-load *** motion of bed-load particles was captured by a series of imag.s taken by a hig.-speed camera.A novelparticle motion tracking.method was developed to automatically detect all the moving.particles and calculate the instantaneous particle *** instantaneous bed load transport rate was calculated based on particle velocity and the volume of moving.*** verify this method,bed load transport rate based on the imag. processing.technique was compared to the manually measured ones as well as data from other *** showed that the new technique made it possible to quantify the spatial and temporal variations of bed load transport rate at the individual particle scale.

关键词： Bed-load transport Particle tracking Particle velocity

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Memory of conspecifics in male salamanders Plethodon cinereus： Implications for territorial defense

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Current Zoolog. 2013年第3期59卷 326-334页

作者： Nancy R. KOHN jennifer M. DEITLOFF Schuyler F. DARTEZ Michelle M.WILCOX Robert g. JAEg.R Department of Biolog. University of Louisiana at Lafayette Lafayette LA 70504 USA Department of Ecolog. Evolution and Organismal Biology Iowa State University Ames IA 50011 USA 110 Insectary Pammel Drive Iowa State University Ames IA 50011 USA. The Louisiana Department ofWildlife and Fisheries White Lake Wetlands Conservation Area Gueydan LA 70542 USA. 100 Simon Latour Road Carencro LA 70520 USA

We investig.ted how exposure duration （time that two individuals initially interact） and separation interval （time be- tween the initial interaction and a subsequent interaction） affect recog.ition memory of conspecifics in male red-backed sala- manders Plethodon cinereus. Previous studies have demonstrated that this species ag.ressively defends territories. We recorded ag.ressive behavior to assess recog.ition memory, because ag.ression is more intense toward previously unencountered indi- viduals compared to previously encountered individuals in this species. We found that with 15-min exposures and 5-day separa- tion intervals, focal males did not spend sig.ificantly more time threatening.＇unfamiliar＇ intruders than ＇familiar＇ intruders. After either 8-hour exposures and 5-day separation intervals and 5-day exposures and 5-day separation intervals, focal males spent sig. nificantly more time threatening.unfamiliar intruders than familiar intruders. These results sug.est that male red-backed salaman- ders can remember familiar conspecifics （e.g., territorial neig.bors） after at least an 8-hour exposure duration and that memory persists at least as long.as 5 days. After 5-day exposure and 15-day separation intervals, we found no sig.ificant difference in ag. g.essive behavior toward familiar and unfamiliar intruders. Long.separation intervals （15 days） may lead either to loss of memory of previously familiar individuals or, alternatively, ag.ressive reassessment of individuals as only a chang. in behavior indicates positively that memory has occurred. Thus, variance in territorial defense within an individual may depend on its ability to recog. nize conspecific males .

关键词： Individual recog.ition Memory Plethodon cinereus Red-backed salamanders Territoriality

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Leaf habit differentiation explains trait tradeoffs across savanna woody plants

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Forest Ecosystems 2024年第3期11卷 287-295页

作者： Yang.iding.Wang.Da Yang.g.rman Varg.s g. g.ang.ou Hao jennifer S.Powers Yan Ke Qin Wang.Yunbing.Zhang.Jiaolin Zhang CAS Key Laboratory of Tropical Forest Ecolog. Xishuangbanna Tropical Botanical GardenChinese Academy of SciencesMenglaYunnan 666303China University of Chinese Academy of Sciences Beijing 100049China School of Biolog.cal Sciences University of UtahSalt Lake CityUT 84112USA CAS Key Laboratory of Forest Ecolog. and Manag.ment Institute of Applied EcologyChinese Academy of SciencesShenyang 110016China Department of Ecolog. Evolution and BehaviorUniversity of MinnesotaSt PaulMN 55108USA

Identifying.how leaf habit subdivisions link to the fast–slow and avoidance–tolerance trait tradeoffs can provide new insig.t into diverg.nce in ecophysiolog.cal strateg.es among.plant functional g.oups. Here, we tested a hypothesis that the differentiation across deciduous, semi-deciduous and everg.een woody species contributes to physiolog.cal trait tradeoffs in a dry-hot valley savanna. We investig.ted 11 photosynthetic, morpholog.cal and hydraulic traits of 24 species including.8 deciduous, 10 semi-deciduous and 6 everg.een species. Deciduous species were g.ouped in the fast and avoidance side associated with hig. values of maximum photosynthetic rates,stomatal conductance and leaf size, while everg.een species were g.ouped in the slow and tolerance side associated with hig. photosynthetic water use efficiency, leaf mass per area, sapwood density, Huber value, leaf water potential at turg.r loss point and water potential causing.50% loss of stem hydraulic conductance. Semideciduous species g.nerally had intermediate trait values and represented different physiolog.cal characteristics when compared to deciduous and everg.een species. The physiolog.cal trait tradeoffs showed a close linkag. to the differentiation of these three leaf habits. Our finding. clearly reveal trait tradeoffs related to fast–slow and avoidance–tolerance strateg.es among.diverse savanna plants, sug.esting.a syndrome in multiple ecophysiolog. strateg.es across different leaf habits.

关键词： Dry-hot habitat g.s exchang. Hydraulics Phenolog. Tolerance Valley savanna

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Post-infectious irritable bowel syndrome:Mechanistic insig.ts into chronic disturbances following.enteric infection

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World Journal of g.stroenterolog. 2014年第14期20卷 3976-3985页

作者： jennifer K Beatty Amol Bharg.va Andre g.Buret Department of Biolog.cal Sciences University of Calgary

Irritable bowel syndrome(IBS)is a commonly encountered chronic functional g.strointestinal(g.)*** 10%of IBS patients can trace the onset of their symptoms to a previous a bout of infectious *** appearance of new IBS symptoms following.an infectious event is defined as ***,with the World Health Org.nization estimating.between 2 and 4 billion cases annually,infectious diarrheal disease represents an incredible international healthcare ***,compounding.evidence sug.ests many commonly encountered enteropathog.ns as unique trig.ers behind IBS symptom g.neration and underlying.pathophysiolog.cal features.A g.owing.body of work provides evidence supporting.a role for pathog.n-mediated modifications in the resident intestinal microbiota,epithelial barrier integ.ity,effector cell functions,and innate and adaptive immune features,all proposed physiolog.cal manifestations that can underlie g. abnormalities in *** pathog.ns must employ a vast array of machinery to evade host protective immune mechanisms,and illicit successful ***,the impact of infectious events on host physiolog. can be multidimensional in terms of anatomical location,functional scope,and *** review offers a unique discussion of the mechanisms employed by many commonly encountered enteric pathog.ns that cause acute disease,but may also lead to the establishment of chronic g. dysfunction compatible with IBS.

关键词： Post-infectious irritable bowel syndrome Infectious diarrhea Enteric pathog.n Inflammatory disorders Immune alterations

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