The Experts below are selected from a list of 41664 Experts worldwide ranked by ideXlab platform
Hongyuan Zha - One of the best experts on this subject based on the ideXlab platform.
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a dirichlet mixture model of hawkes processes for event Sequence Clustering
arXiv: Learning, 2017Co-Authors: Hongyuan ZhaAbstract:We propose an effective method to solve the event Sequence Clustering problems based on a novel Dirichlet mixture model of a special but significant type of point processes --- Hawkes process. In this model, each event Sequence belonging to a cluster is generated via the same Hawkes process with specific parameters, and different clusters correspond to different Hawkes processes. The prior distribution of the Hawkes processes is controlled via a Dirichlet distribution. We learn the model via a maximum likelihood estimator (MLE) and propose an effective variational Bayesian inference algorithm. We specifically analyze the resulting EM-type algorithm in the context of inner-outer iterations and discuss several inner iteration allocation strategies. The identifiability of our model, the convergence of our learning method, and its sample complexity are analyzed in both theoretical and empirical ways, which demonstrate the superiority of our method to other competitors. The proposed method learns the number of clusters automatically and is robust to model misspecification. Experiments on both synthetic and real-world data show that our method can learn diverse triggering patterns hidden in asynchronous event Sequences and achieve encouraging performance on Clustering purity and consistency.
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a dirichlet mixture model of hawkes processes for event Sequence Clustering
Neural Information Processing Systems, 2017Co-Authors: Hongyuan ZhaAbstract:How to cluster event Sequences generated via different point processes is an interesting and important problem in statistical machine learning. To solve this problem, we propose and discuss an effective model-based Clustering method based on a novel Dirichlet mixture model of a special but significant type of point processes --- Hawkes process. The proposed model generates the event Sequences with different clusters from the Hawkes processes with different parameters, and uses a Dirichlet process as the prior distribution of the clusters. We prove the identifiability of our mixture model and propose an effective variational Bayesian inference algorithm to learn our model. An adaptive inner iteration allocation strategy is designed to accelerate the convergence of our algorithm. Moreover, we investigate the sample complexity and the computational complexity of our learning algorithm in depth. Experiments on both synthetic and real-world data show that the Clustering method based on our model can learn structural triggering patterns hidden in asynchronous event Sequences robustly and achieve superior performance on Clustering purity and consistency compared to existing methods.
Aykut Ozkul - One of the best experts on this subject based on the ideXlab platform.
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Novel Tick Phlebovirus Genotypes Lacking Evidence for Vertebrate Infections in Anatolia and Thrace, Turkey.
Viruses, 2019Co-Authors: Nergis Emanet, Ender Dinçer, Annika Brinkmann, Sabri Hacıoğlu, Pelin Fatoş Polat, Sırrı Kar, Touraj Aligholipour Farzani, Zeliha Kocak Tufan, Adem Şahan, Aykut OzkulAbstract:We screened ticks and human clinical specimens to detect and characterize tick phleboviruses and pathogenicity in vertebrates. Ticks were collected at locations in Istanbul (Northwest Anatolia, Thrace), Edirne, Kirklareli, and Tekirdag (Thrace), Mersin (Mediterranean Anatolia), Adiyaman and Şanliurfa (Southeastern Anatolia) provinces from 2013–2018 and were analyzed following morphological identification and pooling. Specimens from individuals with febrile disease or meningoencephalitic symptoms of an unknown etiology were also evaluated. The pools were screened via generic tick phlebovirus amplification assays and products were Sequenced. Selected pools were used for cell culture and suckling mice inoculations and next generation sequencing (NGS). A total of 7492 ticks were screened in 609 pools where 4.2% were positive. A phylogenetic Sequence Clustering according to tick species was observed. No human samples were positive. NGS provided near-complete viral replicase coding Sequences in three pools. A comprehensive analysis revealed three distinct, monophyletic virus genotypes, comprised of previously-described viruses from Anatolia and the Balkans, with unique fingerprints in conserved amino acid motifs in viral replicase. A novel tick phlebovirus group was discovered circulating in the Balkans and Turkey, with at least three genotypes or species. No evidence for replication in vertebrates or infections in clinical cases could be demonstrated.
Jane F. Turton - One of the best experts on this subject based on the ideXlab platform.
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prevalence of burkholderia species including members of burkholderia cepacia complex among uk cystic and non cystic fibrosis patients
Journal of Medical Microbiology, 2017Co-Authors: D Kenna, Amy Coward, Claire Perry, Kate Martin, Daniel Lilley, Rachel Pike, Robert Hill, Jane F. TurtonAbstract:Purpose. We aimed to establish the prevalence of different Burkholderia species among UK cystic fibrosis (CF) and non-CF patients over a 2 year period. Methodology. Matrix-assisted laser desorption/ionization-time of flight mass spectrometry was used to identify isolates to genus level, followed by recA/gyrB Sequence Clustering or species-specific PCR. In all, 1047 Burkholderia isolates were submitted for identification from 361 CF patients and 112 non-CF patients, 25 from the hospital environment and three from a commercial company. Potential cross-infection was assessed by pulsed-field gel electrophoresis (PFGE) and multi- locus-Sequence typing (MLST). MICs were determined for 161 Burkholderia cepacia complex (Bcc) isolates. CF Trust registry data were sought to examine clinical parameters relating to Bcc infection. Results. Burkholderia multivorans was the most prevalent species among CF patients affecting 56 % (192) patients, followed by Burkholderia cenocepacia IIIA (15 %; 52 patients). Five novel recA clusters were found. Among non-CF patients, Burkholderia cepacia was the most prevalent species (37/112; 34 %), with 18 of 40 isolates part of a UK-wide B. cepacia ‘cluster’. This and three other clusters were investigated by PFGE and MLST. Cable-pili positive isolates included two novel Sequence types and representatives of ET12. Antibiotic susceptibility varied between and within species and CF/non- CF isolates. CF Trust registry data suggested no significant difference in lung function between patients harbouring B. cenocepacia, B. multivorans and other Bcc species (P=0.81). Conclusion. The dominance of B. multivorans in CF, the presence of a B. cepacia cluster among non-CF patients and the existence of putative novel species all highlighted the continuing role of Burkholderia species as opportunistic pathogens.
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use of nrda gene Sequence Clustering to estimate the prevalence of different achromobacter species among cystic fibrosis patients in the uk
Journal of Cystic Fibrosis, 2016Co-Authors: Amy Coward, D Kenna, Claire Perry, Kate Martin, Michel Doumith, Jane F. TurtonAbstract:Abstract Background We aimed to estimate the prevalence of different Achromobacter species among UK Cystic Fibrosis (CF) patients. Methods nrdA Sequence Clustering was used to identify 147 Achromobacter isolates from 96 patients from 27 hospitals to species level. Potential cross-infection was investigated by MLST, pulsed-field gel electrophoresis and whole genome sequencing (WGS). Results Achromobacter xylosoxidans was the most prevalent species affecting 59 of 96 (61%) patients, followed by Achromobacter insuavis and Achromobacter dolens (12.4% and 8%, respectively). Three novel nrdA clusters were identified. One was further characterised by sequencing the intrinsic bla OXA gene, revealing novel variants. WGS of A. insuavis 2a isolates from four patients attending the same paediatric unit revealed that three were ST144, but differed from one another by a minimum of 385 SNPs, suggesting cross-infection was unlikely. Conclusions nrdA Sequence Clustering permitted an estimation of UK Achromobacter species prevalence, highlighted additional novel species, and aided cross-infection investigations.
Horst Aspock - One of the best experts on this subject based on the ideXlab platform.
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correlations between morphological molecular biological and physiological characteristics in clinical and nonclinical isolates of acanthamoeba spp
Applied and Environmental Microbiology, 2000Co-Authors: Julia Walochnik, Andreas Obwaller, Horst AspockAbstract:Eleven Acanthamoeba isolates, obtained from Acanthamoeba keratitis patients, from contact lens cases of non-Acanthamoeba keratitis patients, from asymptomatic individuals, from necrotic tissue, and from tap water and two reference strains were investigated by morphological, molecular biological, and physiological means in order to discriminate clinically relevant and nonrelevant isolates. All clinically relevant isolates showed Acanthamoeba sp. group II morphology. 18S ribosomal DNA sequencing revealed Sequence type T4 to be the most prevalent group among the isolates and also the group recruiting most of the pathogenic strains. Interestingly, within T4 the strains of no clinical relevance clustered together. Moreover, physiological properties appeared to be highly consistent with initial pathogenicity and with Sequence Clustering. Altogether, the results of our study indicate a correlation between the phylogenetic relationship and pathogenicity.
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correlations between morphological molecular biological and physiological characteristics in clinical and nonclinical isolates of acanthamoeba spp
Applied and Environmental Microbiology, 2000Co-Authors: Julia Walochnik, Andreas Obwaller, Horst AspockAbstract:Eleven Acanthamoeba isolates, obtained from Acanthamoeba keratitis patients, from contact lens cases of non-Acanthamoeba keratitis patients, from asymptomatic individuals, from necrotic tissue, and from tap water and two reference strains were investigated by morphological, molecular biological, and physiological means in order to discriminate clinically relevant and nonrelevant isolates. All clinically relevant isolates showed Acanthamoeba sp. group II morphology. 18S ribosomal DNA sequencing revealed Sequence type T4 to be the most prevalent group among the isolates and also the group recruiting most of the pathogenic strains. Interestingly, within T4 the strains of no clinical relevance clustered together. Moreover, physiological properties appeared to be highly consistent with initial pathogenicity and with Sequence Clustering. Altogether, the results of our study indicate a correlation between the phylogenetic relationship and pathogenicity.
Nergis Emanet - One of the best experts on this subject based on the ideXlab platform.
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Novel Tick Phlebovirus Genotypes Lacking Evidence for Vertebrate Infections in Anatolia and Thrace, Turkey.
Viruses, 2019Co-Authors: Nergis Emanet, Ender Dinçer, Annika Brinkmann, Sabri Hacıoğlu, Pelin Fatoş Polat, Sırrı Kar, Touraj Aligholipour Farzani, Zeliha Kocak Tufan, Adem Şahan, Aykut OzkulAbstract:We screened ticks and human clinical specimens to detect and characterize tick phleboviruses and pathogenicity in vertebrates. Ticks were collected at locations in Istanbul (Northwest Anatolia, Thrace), Edirne, Kirklareli, and Tekirdag (Thrace), Mersin (Mediterranean Anatolia), Adiyaman and Şanliurfa (Southeastern Anatolia) provinces from 2013–2018 and were analyzed following morphological identification and pooling. Specimens from individuals with febrile disease or meningoencephalitic symptoms of an unknown etiology were also evaluated. The pools were screened via generic tick phlebovirus amplification assays and products were Sequenced. Selected pools were used for cell culture and suckling mice inoculations and next generation sequencing (NGS). A total of 7492 ticks were screened in 609 pools where 4.2% were positive. A phylogenetic Sequence Clustering according to tick species was observed. No human samples were positive. NGS provided near-complete viral replicase coding Sequences in three pools. A comprehensive analysis revealed three distinct, monophyletic virus genotypes, comprised of previously-described viruses from Anatolia and the Balkans, with unique fingerprints in conserved amino acid motifs in viral replicase. A novel tick phlebovirus group was discovered circulating in the Balkans and Turkey, with at least three genotypes or species. No evidence for replication in vertebrates or infections in clinical cases could be demonstrated.
