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Mako:A Graph-based Pattern Growth Approach to Detect Complex Structural Variants

Genomics, Proteomics & Bioinformatics 2022年第1期20卷 205-218页

作者： Jiadong Lin Xiaofei Yang Walter Kosters Tun Xu Yanyan Jia Songbo Wang Qihui Zhu Mallory Ryan Li Guo Chengsheng Zhang The Human Genome Structural Variation Consortium Charles Lee scott e.devine evan e.eichler Kai Ye School of Automation Science and engineering Faculty of Electronic and Information EngineeringXi’an Jiaotong UniversityXi’an 710049China MOe Key Lab for Intelligent Networks&Networks Security Faculty of Electronic and Information EngineeringXi’an Jiaotong UniversityXi’an 710049China Genome Institute the First Affiliated Hospital of Xi’an Jiaotong UniversityXi’an 710061China Leiden Institute of Advanced Computer Science Faculty of ScienceLeiden UniversityLeiden 2311EZNetherland School of Computer Science and Technology Faculty of Electronic and Information EngineeringXi’an Jiaotong UniversityXi’an 710049China The Jackson Laboratory for Genomic Medicine FarmingtonCT 06032USA Precision Medicine Center the First Affiliated Hospital of Xi’an Jiaotong UniversityXi’an 710061China Institute for Genome Sciences University of Maryland School of MedicineBaltimoreMD 21201USA Department of Genome Sciences University of Washington School of MedicineSeattleWA 98119USA Howard Hughes Medical Institute University of WashingtonSeattleWA 98195USA The School of Life Science and Technology Xi’an Jiaotong UniversityXi’an 710049China 不详

Complex structural variants(CSVs) are genomic alterations that have more than two breakpoints and are considered as the simultaneous occurrence of simple structural ***,detecting the compounded mutational signals of CSVs is challenging through a commonly used model-match *** a result,there has been limited progress for CSV discovery compared with simple structural ***,we systematically analyzed the multi-breakpoint connection feature of CSVs,and proposed Mako,utilizing a bottom-up guided model-free strategy,to detect CSVs from paired-end short-read ***,we implemented a graph-based pattern growth approach,where the graph depicts potential breakpoint connections,and pattern growth enables CSV detection without pre-defined *** evaluations on both simulated and real datasets revealed that Mako outperformed other ***,validation rates of CSVs on real data based on experimental and computational validations as well as manual inspections are around 70%,where the medians of experimental and computational breakpoint shift are 13 bp and 26 bp,***,the Mako CSV subgraph effectively characterized the breakpoint connections of a CSV event and uncovered a total of 15 CSV types,including two novel types of adjacent segment swap and tandem dispersed *** analysis of these CSVs also revealed the impact of sequence homology on the formation of *** is publicly available at https://***/xjtu-omics/Mako.

关键词： Next-generation sequencing Complex structural variant Pattern growth Graph mining Formation mechanism

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extract Rules by Using Rough Set and Knowledge-Based NN

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Journal of Computer Science & Technology 1998年第3期13卷 279-284页

作者：王士同 e.scott 等 DepartmentofComputer EastChinaShipbuildingInstituteZhenjiang212003PR.China DepartmentofComputer Ro

In this paper, rough set theory is used to extract roughly-correct inference rules from information systems. Based on this idea, the learning algorithm eRCR is presented. In order to refine the learned roughly-correct inference rules, the knowledge-based neural network is used. The method presented here sufficiently combines the advanages of rough set theory and neural network.

关键词： Rough set theory ,knowledge-based NN (neural network) knowledge discovery machine learning

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Purinergic signaling systems across comparative models of spinal cord injury

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Neural Regeneration Research 2022年第3期17卷 2391-2398页

作者： eva e.Stefanova Angela L.scott Department of Pathology and Molecular Medicine McMaster UniversityHamiltonONCanada

Within the last several decades,the scientific community has made substantial progress in elucidating the complex pathophysiology underlying spinal cord ***,despite the many advances using conventional mammalian models,both cellular and axonal regeneration following spinal cord injury have remained out of *** this sense,turning to non-mammalian,regenerative species presents a unique opportunity to identify pro-regenerative cues and chara cterize a spinal cord microenvironment permissive to *** the signaling pathways hypothesized to be dysregulated during spinal cord injury is the purinergic signaling *** addition to its well-known role as energy currency in cells,ATP and its metabolites are small molecule neurotransmitte rs that mediate many diverse cellular processes within the central nervous *** our unde rstanding of the roles of the purinergic system following spinal cord injury is limited,this signaling pathway has been implicated in all injury-induced secondary processes,including cellular death,inflammation,reactive gliosis,and neural *** that the purinergic system is also evolutionarily conserved between mammalian and non-mammalian species,comparisons of these roles may provide important insights into conditions responsible for recovery ***,we compare the secondary processes between key model species and the influence of purinergic signaling in each *** our understanding of this signaling system and pro-regenerative conditions continues to evolve,so does the potential for the development of novel therapeutic interventions for spinal cord injury.

关键词： cell death differenriation glia inflammation neurogenesis proliferation purinergic signaling reactive gliosis regeneration spinal cord injury teleost

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Climate refugia along Lake Superior’s shores:disjunct arctic-alpine plants rely on cool shoreline temperatures but are restricted to highly exposed habitat under climate warming

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Journal of Plant ecology 2024年第4期17卷 23-41页

作者： Ashley Hillman scott e.Nielsen Department of Renewable Resources University of AlbertaEdmontonAB T6G 2R3Canada

Climate refugia can serve as a remnant habitat or stepping stones for species dispersal under climate *** largest freshwater lake by surface area,Lake Superior,USA and Canada,serves as a model system for understanding cooling-mediated local refugia,as its cool water temperatures and wave action have maintained shoreline habitats suitable for southern disjunct populations of arctic-alpine plants since ***,we seek to explain spatial patterns and environmental drivers of arctic-alpine plant refugia along Lake Superior’s shores,and assess future risk to refugia under moderate(+3.5℃)and warmest(+5.7℃)climate warming ***,we examined how the interactive effects of summer surface water temperatures and wind affected onshore temperatures,resulting in areas of cooler ***,we developed an ecological niche model for the presence of disjunct arctic-alpine refugia(pooling 1253 occurrences from 58 species)along the lake’s ***,we fit species distribution models for 20 of the most common arctic-alpine disjunct species and predicted presence to identify refugia ***,we used the two climate warming scenarios to predict changes in the presence of refugia and disjunct *** type,elevation above water,inland distance,July land surface temperature from MODIS/Terra satellite and near-shore depth of water were the best predictors of disjunct ***,we predicted 2236 km of the shoreline(51%)as disjunct refugia habitat for at least one species under current conditions,but this was reduced to 20% and 7% with moderate(894 km)and warmest(313 km)climate change projections.

关键词： climate refugia disjunct populations lake effect Lake Superior species distribution models

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A modified intron of VRT2 drives glume and grain elongation in wheat

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Molecular Plant 2021年第9期14卷 1421-1423页

作者： Laura e.Dixon scott A.Boden Faculty of Biological Sciences University of LeedsLeeds LS29JTUK School of Agriculture Food and WineWaite Research InstituteUniversity of AdelaideGlen OsmondSA 5064Australia

Yield is a complex trait that is determined predominantly by the number,size,and weight of grain produced by a plant,which are all in fluenced by multiple genes and environ mental *** cereals,grain size is in flue need by envir on mental signals including nutrient availability and temperature,and by variation for genes that control the dimensions of a grain or the size of floral organs(e.g.,Heang and Sassa,2012;Brinton et al.,2017;Adamski et al.,2021;Liu et al.,2021;Xiao et al.,2021).Three recent studies have investigated subspecies of tetrapioid and hexapioid wheat that produce Ion ger grains,which form in florets that contain elongated floral structures(Adamski et al.,2021;Liu et al.,2021;Xiao et al.,2021);their findings provide new understanding of the genes controlling floret architecture,which could be used by breeders to enhance grain size and yield.

关键词： grain organs wheat

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Forge AHeAD with stricter criteria in future trials of embolic stroke of undetermined source

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Neural Regeneration Research 2022年第5期17卷 1009-1010页

作者： David Z.Rose scott e.Kasner Department of Neurology Morsani College of MedicineUniversity of South FloridaTampaFLUSA Department of Neurology Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA

What lurks within the crypt?With more than 200 known causes of is chemic stroke(Saver,2016),what should be the minimum work up?Many centers offer high-resolution brain imaging and vessel studies,telemetry monitoring f... 详细信息

关键词： strict thoracic centers

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Hybrid Predictive ensembles:Synergies Between Human and Computational Forecasts

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Journal of Social Computing 2021年第2期2卷 89-102页

作者： Lu Hong PJ Lamberson scott e Page Department of Finance Loyola University ChicagoChicagoIL 606002USA Department of Communication University of California at Los Angeles(UCLA)Los AngelesCA 90095USA School University of MichiganAnn ArborMI 48104USA

An increasing proportion of decisions,design choices,and predictions are being made by hybrid groups consisting of humans and artificial intelligence(AI).In this paper,we provide analytic foundations that explain the potential benefits of hybrid groups on predictive tasks,the primary use of *** analysis relies on interpretive and generative signal frameworks as well as a distinction between the big data used by AI and the thick,often narrative data used by *** derive several conditions on accuracy and correlation necessary for humans to remain in the *** conclude that human adaptability along with the potential for atypical cases that mislead AI will likely mean that humans always add value on predictive tasks.

关键词： collective intelligence predictive models hybrid groups big data thick data

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Region-specific microRNA signatures in the human epididymis

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Asian Journal of Andrology 2018年第6期20卷 539-544页

作者： James A Browne Shih-Hsing Leir scott e eggener Ann Harris Department of Genetics and Genome Sciences Case Western Reserve UniversityClevelandOH 44106USA Human Molecular Genetics Program Lurie Children＇s Research CenterChicagoIL 60614USA Department of Pediatrics Northwestern University Feinberg School of MedicineChicagoIL 60611USA Section of Urology University of Chicago Medical CenterChicagoIL 60611USA.

The epithelium of the human epididymis maintains an appropriate luminal environment for sperm maturation that is essential for male fertility. Regional expression of small noncoding RNAs such as microRNAs contributes to segment-specific gene expression and differentiated functions. MicroRNA profiles were reported in human epididymal tissues but not specifically in the epithelial cells derived from those regions. Here, we reveal miRNA signatures of primary cultures of caput, corpus, and cauda epididymis epithelial cells and of the tissues from which they were derived. We identify 324 epithelial cell-derived microRNAs and 259 tissue-derived microRNAs in the epididymis, some of which displayed regionalized expression patterns in cells and/or tissues. Caput cell-enriched miRNAs included miR-573 and miR-155. Cauda cell-enriched miRNAs included miR-1204 and miR-770. Next, we determined the gene ontology pathways associated with in silico predicted target genes of the differentially expressed miRNAs. The effect of androgen receptor stimulation on miRNA expression was also investigated. These data show novel epithelial cell-derived miRNAs that may regulate the expression of important gene networks that are responsible for the regionalized gene expression and function of the epididymis.

关键词： caput cauda corpus human epididymis microRNA

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Numerical modeling of the effects of roughness on flow and eddy formation in fractures

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Journal of Rock Mechanics and Geotechnical engineering 2017年第1期9卷 105-115页

作者： scott Briggs Bryan W. Karney Brent e. Sleep University of Toronto Toronto M5S 1A4 Canada

The effect of roughness on flow in fractures was investigated using lattice Boltzmann method(LBM).Simulations were conducted for both statistically generated hypothetical fractures and a natural dolomite fracture. The effect of increasing roughness on effective hydraulic aperture, Izbash and Forchheimer parameters with increasing Reynolds number(Re) ranging from 0.01 to 500 was examined. The growth of complex flow features, such as eddies arising near the fracture surface, was directly associated with changes in surface roughness. Rapid eddy growth above Re values of 1, followed by less rapid growth at higher Re values, suggested a three-zone nonlinear model for flow in rough fractures. This three-zone model, relating effective hydraulic conductivity to Re, was also found to be appropriate for the simulation of water flow in the natural dolomite fracture. Increasing fracture roughness led to greater eddy volumes and lower effective hydraulic conductivities for the same Re values.

关键词： Hydrogeology Fracture flow Fracture roughness Computational fluid dynamics Lattice Boltzmann method(LBM)

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Tumor necrosis factor alpha inhibits in vitro bovine embryo development through a prostaglandin mediated mechanism

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Journal of Animal Science and Biotechnology 2012年第1期3卷 21-24页

作者： Lauren R Jackson Char e Farin scott Whisnant Department of Animal Science North Carolina State University PO Box 7621 Raleigh NC 27695-7621 USA

Mastitis or other infectious diseases have been related to reduced fertility in cattle. Inflammatory cytokines such as tumor necrosis factor α （TNFα are released in response to infection and may have negative effects on embryo development, in the current study the effect of exposure to TNFα on the development of in vitro fertilized bovine embryos was examined. Indomethacin, a prostaglandin synthesis inhibitor, was used to determine if blockade of prostaglandin synthesis would alter the effects of TNFα Ovaries were obtained from a local abattoir and immature COC were isolated from 2-10 mm follicles, in vitro matured and fertilized. After fertilization, groups of presumptive zygotes were randomly placed into either control development medium, medium containing 25 ng/mL TNFα or medium containing 25 ng/mL TNFα plus 1 μg/mL indomethacin. The proportion of blastocysts formed was assessed at day 7 of culture. Fewer embryos exposed to TNFα alone reached the blastocyst stage （17.5 ± 2.4%, P 〈 0.01） compared with controls （30.5 ± 2.4%） or embryos developed in TNFα plus indomethacin （25.8 ± 2.8%）. There was no difference between control embryos and embryos developed in TNFα plus indomethacin. These results indicate that TNFα is inhibitory to the in vitro development of bovine embryos and that this inhibition may be mediated by prostaglandins because it can be blocked by indomethacin.

关键词： tumor necrosis factor o bovine embryo indomethacin

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