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Using Folding Ensemble and Stem Probability Maximization Methods to Predict RNA H-type Pseudoknots

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tsinghua Science and technology 2012年第6期17卷 691-700页

作者： Junilda Spirollari Shawn Xiong Wang Jason t.l. Wang Bioinformatics Program Department of Computer Science New Jersey Institute of Technology University Heights Department of Computer Science California State University

We present in this paper an ab initio method, named KnotFold, for RNA H-type pseudoknot prediction. Our method employs an ensemble of RNA folding tools and a filtering heuristic to generate a set of pseudoknot-free stems, and then predicts pseudoknots by ut.l.zing a search technique with a pseudo-probability scoring scheme. Experiment.l.results show that KnotFold achieves higher sensitivity than existing methods. the KnotFold package with documentation is freely available at http：//***/KnotFold.

关键词： RNA structure pseudoknots tool ensemble

Identification of expected seismic activity areas by forecasting complex seismic-mode parameters in Uzbekistan

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Geodesy and Geodynamics 2018年第2期9卷 121-130页

作者： t.U.Artikov R.S.Ibragimov t.l.ibragimova M.A.Mirzaev Institute of Seismology

In this paper, the author proposed a methodology to reveal expected seismic activation places for coming years by a complex of forecasting parameters of a seismic mode. Areas in Uzbekistan where currently observed anomalies in various parameters of a seismic mode has been revealed. By number of displayed abnormal signs the areas has been ranked based on probability of occurrence of strong earthquakes there. It has prepared schemes of the synoptic forecast of expected seismic activation places in case of occurrence of strong earthquakes in the Central-Asian region.

关键词： long-term forecast of earthquakes Parameters of seismic mode Seismic activity Seismic gap

Study of modern seismic zoning maps'accuracy(case for Eastern Uzbekistan)

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Geodesy and Geodynamics 2016年第6期7卷 416-424页

作者： t.U.Artikov R.S.Ibragimov t.l.ibragimova M.A.Mirzaev Institute of Seismology Academy of Science of the Republic of UzbekistanTashkentUzbekistan

Influence of uncertainty factors of input parameters on results of the estimation of seismic hazard has been researched. It is found that the largest deviations, from seismic hazard maps designed on the basis of average values of distribution of seismic mode and seismic load parameters, may arise due to the imprecise depth of earthquake sources （H）, uncertain estimations of seismic potential and slope of recurrence curve （v）. the contribution of such uncertainty factors, like imprecise definition of seismic activity Alo, incorrect choice of prevailing type of a motion in the source, using regional laws of attenuation of seismic load intensity in distance instead of local once are substantially small. For Eastern Uzbekistan, it was designed the seismic hazard map with the highest value which takes into account every possible factors of uncertainty in parameters of seismic mode and seismic load.

关键词： Seismic hazardSeismic potentialSeismic activitySeismic intensitySeismic zoningSeismic sources

Searching for Non-coding RNAs in Genomic Sequences Using ncRNAscout

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Genomics, Proteomics & Bioinformatics 2012年第2期10卷 114-121页

作者： Michael Bao Miguel Cervantes Cervantes ling Zhong Jason t.l. Wang Bioinformatics Center New Jersey Institute of Technology Newark NJ 07102 USA Department of Biological Sciences Rutgers University Newark NJ 07102 USA Computer Science Department New Jersey Institute of Technology Newark NJ 07102 USA

Recently non-coding RNA （ncRNA） genes have been found to serve many important functions in the cell such as regulation of gene expression at the transcriptional level. Potentially there are more ncRNA molecules yet to be found and their possible functions are to be revealed. the discovery of ncRNAs is a difficult task because they lack sequence indicators such as the start and stop codons dis- played by protein-coding RNAs. Current methods ut.l.ze either sequence motifs or structural parameters to detect novel ncRNAs within genomes. Here, we present an ab initio ncRNA finder, named ncRNAscout, by ut.l.zing both sequence motifs and structural parameters. Specifically, our method has three components：（i） a measure of the frequency of a sequence, （ii） a measure of the structural stability of a sequence contained in a t-score, and （iii） a measure of the frequency of certain patterns within a sequence that may indicate the presence of ncRNA. Experiment.l.results show that, given a genome and a set of known ncRNAs, our method is able to accurat.l. identify and locate a significant number of ncRNA sequences in the genome. the ncRNAscout tool is available for downloading at http：/]bioinfor- ***/ncRNAscout.

关键词： Genome-wide ncRNA discovery Sequence motifs Structural parameters

Isotopic Shifts of the infrared Spectra of Cholic Acid and Sodium Cholate

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Chemical Research in Chinese Universities 1994年第1期10卷 59-62页

作者： tian, Wen Weng, Shi-fu Wu, Jin-guang Zhang, Qing-lian Chang, t.l.

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ＩｓｏｔｏｐｉｃＳｈｉｆｔｓｏｆｔｈｅｉｎｆｒａｒｅｄＳｐｅｃｔｒａｏｆＣｈｏｌｉｃＡｃｉｄａｎｄＳｏｄｉｕｍＣｈｏｌａｔｅＴＩＡＮＷｅｎ；ＷＥＮＧＳｈｉ－ｆｕ；ＷＵＪｉｎ－ｇｕａｎｇａｎｄＺＨＡＮＧＱｉｎｇ－ｌｉａｎ（Ｔ．Ｌ－ＣＨＡＮＧ）（Ｄｅｐａ...

关键词： Cholic acid Sodium cholate Deuteration Infrared spectra Isotopic shift

Performance of GPS slant tot.l.electron content and IRI-Plas-StEC for days with ionospheric disturbance

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Geodesy and Geodynamics 2016年第1期7卷 1-10页

作者： Feza Arikan Seymur Shukurov Hakan tuna Orhan Arikan t.l. Gulyaeva Department of Electrical and Electronics Engineering Hacettepe University Beytepe Ankara 06800 Turkey Department of Electrical and Electronics Engineering Bilkent Uniuersity Bilkent Ankara 06800 Turkey IZMIRAN Moscow 142190 Troitsk Russian Federation

tot.l.Electron Content （tEC） is an important observable parameter of the ionosphere which forms the main source of error for space based navigation and positioning systems. Since the deployment of Global Navigation Sat.l.ite Systems （GNSS）, cost-effective esti- mation of tEC between the earth based receiver and Global Positioning System （GPS） sat- ellites became the major means of investigation of local and regional disturbance for earthquake precursor and augmentation system studies. International Reference Iono- sphere （IRI） extended to plasmasphere （IRI-Plas） is the most developed ionospheric and plasmaspheric climatic model that provides hourly, mont.l. median of electron density distribution globally. Recently, IONOlAB group {***） has presented a new online space weather service that can compute slant tEC （StEC） on a desired ray path for a given date and time using IRI-Plas model （IRI-Plas-StEC）. In this study, the performance of the model based StEC is compared with GPS-StEC computed according to the estimation method developed by the IONOlAB group and includes the receiver bias as IONOlAB-BIAS （IONOlAB-StEC）. Using Symmetric Kullback-leibler Distance （SKlD）, Cross Correlation （CC） coefficient and the metric norm （l2N） to compare IRI-Plas-StEC and IONOlAB-StEC for the month of October 2011 over the turkish National Permanent GPS Network （tNPGN- Active）, it has been observed that SKlD provides a good indicator of disturbance for both earthquakes and geomagnetic storms.

关键词： Ionospheretot.l.Electron Content (tEC)GPSIRI-Plas

Beginning from the end:the presynaptic terminal as a pathomechanism hub in frontotemporal dementia and amyotrophic lateral sclerosis

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Neural Regeneration Research 2025年第11期20卷 3217-3218页

作者： laura Huggon Emma l.Clayton UK Dementia Research Institute at King’s College london LondonUK Department of Basic and Clinical Neuroscience Institute of Psychiatry Psychology&NeuroscienceKing’s College LondonLondonUK

Frontotemporal dementia and amyotrophic lateral sclerosis:Frontotemporal dementia(F t D)and amyo t rophic lateral sclerosis(AlS)are neurodegenerative diseases with significant overlapping *** these neurodegenerative diseases affect different neuronal populations(with FtD affecting neurons of the front.l.and temporal lobes,and AlS affecting upper and lower motor neurons),these two diseases are complexly *** and AlS exist on a disease spectrum,with shared genetic causes,clinical presentations,and pathologies.

关键词： diseases amyotrophic sclerosis

Generation of brain vascular heterogeneity:recent advances from the perspective of angiogenesis

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Neural Regeneration Research 2025年第7期20卷 2013-2014页

作者： Nathanael J.lee Ryota l.Matsuoka Department of Neurosciences Lerner Research InstituteCleveland ClinicClevelandOHUSA Department of Molecular Medicine Cleveland Clinic Lerner College of MedicineCase Western Reserve UniversityClevelandOHUSA

Heterogeneous proper t i es of vascular endothelial cells in the brain:the brain displays large energy dynamics and consumption,and this high level of metabolic demands is fulfilled by a continuous supply of glucose and oxygen through its vascular *** vasculature consists of highly divergent blood vessel branches,giving rise to a dense network of capillaries that supply blood to all cells across the *** elaborated vascular network is thought to develop via angiogenesis,a process in which new blood vessels grow from pre-existing *** capillaries exhibit organotypic features distinct from other tissues and are formed primarily by two major endothelial cell(EC)types:those that form the semi-permeable blood-brain barrier(BBB)and those that develop highly permeable pores known as fenestrae(Matsuoka et al.,2022).the structural and functional differences between BBB and fenestrated vascular ECs represent a fundament.l.feature of brain vasculature and form the foundation for both brain function and homeostasis.

关键词： angiogenesis homeostasis network

Compositional change of seismic event sequences in focal zones during preparation of strong earthquakes

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Geodesy and Geodynamics 2014年第2期5卷 1-8页

作者： Artikov t U Ibragimov R S ibragimova t.l.Mirzayev M A Artikov M t Institute of Seismology Academy of Science of Uzbekistan

the change of the structure of seismic event sequences in focal area in preparation period of strong earthquakes has been studied. Findings show that weak earthquake clustering in time increases in earlier stage of fo... 详细信息

关键词： seismicity structure focus of earthquake seismic regime earthquake forecast