609 results on '"Kalina, T."'
Search Results
152. Pre-post synaptic alignment through neuroligin tunes synaptic transmission efficiency
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Haas, Kalina T., primary, Compans, Benjamin, additional, Letellier, Mathieu, additional, Bartol, Thomas M, additional, Grillo-Bosch, Dolors, additional, Sejnowski, Terrence J, additional, Sainlos, Matthieu, additional, Choquet, Daniel, additional, Thoumine, Olivier, additional, and Hosy, Eric, additional
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- 2017
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153. Assessment of executive functioning in binge-eating disorder independent of weight status
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Eneva, Kalina T., primary, Arlt, Jean M., additional, Yiu, Angelina, additional, Murray, Susan M., additional, and Chen, Eunice Y., additional
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- 2017
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154. Reward and punishment sensitivity and disordered eating behaviors in men and women
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Eneva, Kalina T., primary, Murray, Susan, additional, O’Garro-Moore, Jared, additional, Yiu, Angelina, additional, Alloy, Lauren B., additional, Avena, Nicole M., additional, and Chen, Eunice Y., additional
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- 2017
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155. Fast and simple spectral FLIM for biochemical and medical imaging
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Marina Popleteeva, Liam D. Cassidy, David Stoppa, Leonardo Gasparini, Kalina T. Haas, Lucio Pancheri, Ashok R. Venkitaraman, Alessandro Esposito, Clemens F. Kaminski, Kaminski, Clemens [0000-0002-5194-0962], Esposito, Alessandro [0000-0002-5051-091X], and Apollo - University of Cambridge Repository
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Fluorescence-lifetime imaging microscopy ,Computer science ,Image processing ,02 engineering and technology ,01 natural sciences ,Sensitivity and Specificity ,010309 optics ,Optics ,Optical imaging ,Atomic and Molecular Physics ,0103 physical sciences ,Microscopy ,Image Interpretation, Computer-Assisted ,Medical and biological imaging ,Confocal laser scanning microscopy ,Medical imaging ,Solid state detectors ,Spectral resolution ,Lenses ,Lifetime-based sensing ,Microscopy, Confocal ,business.industry ,Dynamic range ,Detector ,Optical Imaging ,Reproducibility of Results ,Equipment Design ,Multispectral and hyperspectral imaging ,021001 nanoscience & nanotechnology ,Image Enhancement ,Atomic and Molecular Physics, and Optics ,3. Good health ,Molecular Imaging ,Equipment Failure Analysis ,Spectrometry, Fluorescence ,Computer-Aided Design ,and Optics ,Molecular imaging ,0210 nano-technology ,business - Abstract
Spectrally resolved fluorescence lifetime imaging microscopy (λFLIM) has powerful potential for biochemical and medical imaging applications. However, long acquisition times, low spectral resolution and complexity of λFLIM often narrow its use to specialized laboratories. Therefore, we demonstrate here a simple spectral FLIM based on a solid-state detector array providing in-pixel histrogramming and delivering faster acquisition, larger dynamic range, and higher spectral elements than state-of-the-art λFLIM. We successfully apply this novel microscopy system to biochemical and medical imaging demonstrating that solid-state detectors are a key strategic technology to enable complex assays in biomedical laboratories and the clinic.
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- 2015
156. Molecular evolution of the hyaluronan synthase 2 gene in mammals: implications for adaptations to the subterranean niche and cancer resistance
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Nigel C. Bennett, Chris G. Faulkes, Kalina T. J. Davies, and Stephen J. Rossiter
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endocrine system ,Molecular Sequence Data ,Adaptation, Biological ,Rodentia ,Hyaluronan Synthase 2 ,Evolution, Molecular ,Rodent Diseases ,Negative selection ,Soil ,Molecular evolution ,Sequence Analysis, Protein ,Neoplasms ,Animals ,Glucuronosyltransferase ,Gene ,Naked mole-rat ,Disease Resistance ,Evolutionary Biology ,biology ,Ecology ,Eulipotyphla ,biology.organism_classification ,Agricultural and Biological Sciences (miscellaneous) ,Hyaluronan synthase ,Evolutionary biology ,biology.protein ,Adaptation ,General Agricultural and Biological Sciences ,Sequence Alignment ,Function (biology) - Abstract
The naked mole-rat (NMR) Heterocephalus glaber is a unique and fascinating mammal exhibiting many unusual adaptations to a subterranean lifestyle. The recent discovery of their resistance to cancer and exceptional longevity has opened up new and important avenues of research. Part of this resistance to cancer has been attributed to the fact that NMRs produce a modified form of hyaluronan—a key constituent of the extracellular matrix—that is thought to confer increased elasticity of the skin as an adaptation for living in narrow tunnels. This so-called high molecular mass hyaluronan (HMM-HA) stems from two apparently unique substitutions in the hyaluronan synthase 2 enzyme (HAS2). To test whether other subterranean mammals with similar selection pressures also show molecular adaptation in their HAS2 gene, we sequenced the HAS2 gene for 11 subterranean mammals and closely related species, and combined these with data from 57 other mammals. Comparative screening revealed that one of the two putatively important HAS2 substitutions in the NMR predicted to have a significant effect on hyaluronan synthase function was uniquely shared by all African mole-rats. Interestingly, we also identified multiple other amino acid substitutions in key domains of the HAS2 molecule, although the biological consequences of these for hyaluronan synthesis remain to be determined. Despite these results, we found evidence of strong purifying selection acting on the HAS2 gene across all mammals, and the NMR remains unique in its particular HAS2 sequence. Our results indicate that more work is needed to determine whether the apparent cancer resistance seen in NMR is shared by other members of the African mole-rat clade.
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- 2015
157. A phylogenomic analysis of the role and timing of molecular adaptation in the aquatic transition of cetartiodactyl mammals
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Stephen J. Rossiter, Mads F. Bertelsen, Georgia Tsagkogeorga, Michael R. McGowen, Simon N. Jarman, Kalina T. J. Davies, and Andrea M. Polanowski
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0106 biological sciences ,Zoology ,Biology ,010603 evolutionary biology ,01 natural sciences ,DNA sequencing ,Humpback whale ,03 medical and health sciences ,mammals ,14. Life underwater ,lcsh:Science ,Gene ,030304 developmental biology ,0303 health sciences ,Multidisciplinary ,Transition (genetics) ,Biology (Whole Organism) ,cetartiodactyla ,biology.organism_classification ,Taxon ,Sister group ,Hippopotamus ,rna-sequencing ,lcsh:Q ,Adaptation ,transcriptome ,Research Article - Abstract
Recent studies have reported multiple cases of molecular adaptation in cetaceans related to their aquatic abilities. However, none of these has included the hippopotamus, precluding an understanding of whether molecular adaptations in cetaceans occurred before or after they split from their semi-aquatic sister taxa. Here, we obtained new transcriptomes from the hippopotamus and humpback whale, and analysed these together with available data from eight other cetaceans. We identified more than 11 000 orthologous genes and compiled a genome-wide dataset of 6845 coding DNA sequences among 23 mammals, to our knowledge the largest phylogenomic dataset to date for cetaceans. We found positive selection in nine genes on the branch leading to the common ancestor of hippopotamus and whales, and 461 genes in cetaceans compared to 64 in hippopotamus. Functional annotation revealed adaptations in diverse processes, including lipid metabolism, hypoxia, muscle and brain function. By combining these findings with data on protein–protein interactions, we found evidence suggesting clustering among gene products relating to nervous and muscular systems in cetaceans. We found little support for shared ancestral adaptations in the two taxa; most molecular adaptations in extant cetaceans occurred after their split with hippopotamids.
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- 2015
158. Dissection of the peripheral B-cell compartment and immunoglobulin subclass subsetting
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Perez-Andres, M, Blanco, E, de Arriba, S, Lopez-Granados, E, Torres-Canizales, J, van der Burg, Mirjam, Kalina, T, Kienzler, AK, Vlkova, M, Sobral, ES, Chapel, H, Lorente, F, van Zelm, Menno, Dongen, Jacques, Orfao, A, van Dongen, J.J.M., and Immunology
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- 2015
159. Divergent evolutionary rates in vertebrate and mammalian specific conserved non-coding elements (CNEs) in echolocating mammals
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Stephen J. Rossiter, Georgia Tsagkogeorga, and Kalina T. J. Davies
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0106 biological sciences ,Dolphins ,Human echolocation ,010603 evolutionary biology ,01 natural sciences ,Genome ,Conserved sequence ,Evolution, Molecular ,Hearing/deafness ,03 medical and health sciences ,Species Specificity ,Molecular evolution ,Phylogenetics ,Chiroptera ,biology.animal ,Bats ,Animals ,Conserved Sequence ,Phylogeny ,Ecology, Evolution, Behavior and Systematics ,030304 developmental biology ,Homeodomain Proteins ,Genetics ,0303 health sciences ,Base Sequence ,biology ,Phylogenetic tree ,Whales ,Vertebrate ,Ear ,Ear development ,Biological Evolution ,Gene Expression Regulation ,Echolocation ,Rate of evolution ,Conserved non-coding elements ,Research Article - Abstract
Background The majority of DNA contained within vertebrate genomes is non-coding, with a certain proportion of this thought to play regulatory roles during development. Conserved Non-coding Elements (CNEs) are an abundant group of putative regulatory sequences that are highly conserved across divergent groups and thus assumed to be under strong selective constraint. Many CNEs may contain regulatory factor binding sites, and their frequent spatial association with key developmental genes – such as those regulating sensory system development – suggests crucial roles in regulating gene expression and cellular patterning. Yet surprisingly little is known about the molecular evolution of CNEs across diverse mammalian taxa or their role in specific phenotypic adaptations. We examined 3,110 vertebrate-specific and ~82,000 mammalian-specific CNEs across 19 and 9 mammalian orders respectively, and tested for changes in the rate of evolution of CNEs located in the proximity of genes underlying the development or functioning of auditory systems. As we focused on CNEs putatively associated with genes underlying the development/functioning of auditory systems, we incorporated echolocating taxa in our dataset because of their highly specialised and derived auditory systems. Results Phylogenetic reconstructions of concatenated CNEs broadly recovered accepted mammal relationships despite high levels of sequence conservation. We found that CNE substitution rates were highest in rodents and lowest in primates, consistent with previous findings. Comparisons of CNE substitution rates from several genomic regions containing genes linked to auditory system development and hearing revealed differences between echolocating and non-echolocating taxa. Wider taxonomic sampling of four CNEs associated with the homeobox genes Hmx2 and Hmx3 – which are required for inner ear development – revealed family-wise variation across diverse bat species. Specifically within one family of echolocating bats that utilise frequency-modulated echolocation calls varying widely in frequency and intensity high levels of sequence divergence were found. Conclusions Levels of selective constraint acting on CNEs differed both across genomic locations and taxa, with observed variation in substitution rates of CNEs among bat species. More work is needed to determine whether this variation can be linked to echolocation, and wider taxonomic sampling is necessary to fully document levels of conservation in CNEs across diverse taxa. Electronic supplementary material The online version of this article (doi:10.1186/s12862-014-0261-5) contains supplementary material, which is available to authorized users.
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- 2014
160. Persistent heterogeneity in diabetes technology reimbursement for children with type 1 diabetes: The SWEET perspective.
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Sumnik, Zdenek, Szypowska, Agnieszka, Iotova, Violeta, Bratina, Natasa, Cherubini, Valentino, Forsander, Gun, Jali, Sujata, Raposo, Joao Felipe, Stipančic, Gordana, Vazeou, Andriani, Veeze, Henk, Lange, Karin, Papo, N., Kownatka, D., Lion, Silvia, Gerhardsson, P., Kalina, T., Rami‐Merhar, B., Svensson, J., and Hanas, R.
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MEDICAL technology equipment ,BLOOD sugar monitoring ,CONSORTIA ,PEOPLE with diabetes ,HEALTH services accessibility ,HEALTH status indicators ,INSULIN pumps ,TYPE 1 diabetes ,PEDIATRICS ,SURVEYS ,HEALTH insurance reimbursement ,EQUIPMENT & supplies ,CHILDREN - Abstract
Background: Frequent use of modern diabetes technologies increases the chance for optimal type 1 diabetes (T1D) control. Limited reimbursement influences the access of patients with T1D to these modalities and could worsen their prognosis. We aimed to describe the situation of reimbursement for insulins, glucometers, insulin pumps (CSII) and continuous glucose monitoring (CGM) for children with T1D in European countries participating in the SWEET Project and to compare data from EU countries with data from our previous study in 2009. Methods: The study was conducted between March 2017 and August 2017. First, we approached diabetes technology companies with a survey to map the reimbursement of insulins and diabetic devices. The data collected from these companies were then validated by members of the SWEET consortium. Results: We collected data from 29 European countries, whereas all types of insulins are mostly fully covered, heterogeneity was observed regarding the reimbursement of strips for glucometers (from 90 strips/month to no limit). CSII is readily available in 20 of 29 countries. Seven countries reported significant quota issues or obstacles for CSII prescription, and two countries had no CSII reimbursement. CGM is at least partially reimbursed in 17 of 29 countries. The comparison with the 2009 study showed an increasing availability of CSII and CGM across the EU. Conclusions: Although innovative diabetes technology is available, a large proportion of children with T1D still do not benefit from it due to its limited reimbursement. [ABSTRACT FROM AUTHOR]
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- 2019
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161. Genetic Variability and Molecular Evolution of the Human Respiratory Syncytial Virus Subgroup B Attachment G Protein
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Elien Moës, Marc Van Ranst, Kalina T. Zlateva, Anne-Mieke Vandamme, and Philippe Lemey
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Genetics ,Glycosylation ,biology ,Paramyxoviridae ,Molecular Sequence Data ,Immunology ,Genetic Variation ,biology.organism_classification ,Microbiology ,Virology ,Virus ,Evolution, Molecular ,Genetic Diversity and Evolution ,Viral Envelope Proteins ,Ectodomain ,Molecular evolution ,Respiratory Syncytial Virus, Human ,Insect Science ,Genetic variation ,Antigenic variation ,Amino Acid Sequence ,Genetic variability ,Mononegavirales ,Phylogeny - Abstract
Human respiratory syncytial virus (HRSV) is the most important cause of acute respiratory disease in infants. Two major subgroups (A and B) have been identified based on antigenic differences in the attachment G protein. Antigenic variation between and within the subgroups may contribute to reinfections with these viruses by evading the host immune responses. To investigate the circulation patterns and mechanisms by which HRSV-B viruses evolve, we analyzed the G protein genetic variability of subgroup B sequences isolated over a 45-year period, including 196 Belgian strains obtained over 22 epidemic seasons (1982 to 2004). Our study revealed that the HRSV-B evolutionary rate (1.95 × 10 −3 nucleotide substitutions/site/year) is similar to that previously estimated for HRSV-A (1.83 × 10 −3 nucleotide substitutions/site/year). However, natural HRSV-B isolates appear to accommodate more drastic changes in their attachment G proteins. The most recent common ancestor of the currently circulating subgroup B strains was estimated to date back to around the year 1949. The divergence between the two major subgroups was calculated to have occurred approximately 350 years ago. Furthermore, we have identified 12 positively selected sites in the G protein ectodomain, suggesting that immune-driven selective pressure operates in certain codon positions. HRSV-A and -B strains have similar phylodynamic patterns: both subgroups are characterized by global spatiotemporal strain dynamics, where the high infectiousness of HRSV permits the rapid geographic spread of novel strain variants.
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- 2005
162. Molecular Evolution and Circulation Patterns of Human Respiratory Syncytial Virus Subgroup A: Positively Selected Sites in the Attachment G Glycoprotein
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Philippe Lemey, Kalina T. Zlateva, Anne-Mieke Vandamme, and Marc Van Ranst
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Paramyxoviridae ,Molecular Sequence Data ,Immunology ,Population ,Respiratory Syncytial Virus Infections ,Microbiology ,Virus ,Evolution, Molecular ,Viral Proteins ,Belgium ,Molecular evolution ,Virology ,Humans ,Selection, Genetic ,Mononegavirales ,education ,Gene ,Phylogeny ,Genetics ,education.field_of_study ,biology ,Phylogenetic tree ,Infant, Newborn ,Infant ,Sequence Analysis, DNA ,biology.organism_classification ,Hypervariable region ,Child, Preschool ,Respiratory Syncytial Virus, Human ,Insect Science ,Recombination and Evolution - Abstract
Human respiratory syncytial virus (HRSV) is the most common etiological agent of acute lower respiratory tract disease in infants and can cause repeated infections throughout life. In this study, we have analyzed nucleotide sequences encompassing 629 bp at the carboxy terminus of the G glycoprotein gene for HRSV subgroup A strains isolated over 47 years, including 112 Belgian strains isolated over 19 consecutive years (1984 to 2002). By using a maximum likelihood method, we have tested the presence of diversifying selection and identified 13 positively selected sites with a posterior probability above 0.5. The sites under positive selection correspond to sites of O glycosylation or to amino acids that were previously described as monoclonal antibody-induced in vitro escape mutants. Our findings suggest that the evolution of subgroup A HRSV G glycoprotein is driven by immune pressure operating in certain codon positions located mainly in the second hypervariable region of the ectodomain. Phylogenetic analysis revealed the prolonged cocirculation of two subgroup A lineages among the Belgian population and the possible extinction of three other lineages. The evolutionary rate of HRSV subgroup A isolates was estimated to be 1.83 × 10 −3 nucleotide substitutions/site/year, projecting the most recent common ancestor back to the early 1940s.
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- 2004
163. Molecular evolution of growth hormone and insulin-like growth factor 1 receptors in long-lived, small-bodied mammals
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Chris G. Faulkes, Kalina T. J. Davies, Nigel C. Bennett, Stephen J. Rossiter, Georgia Tsagkogeorga, and Liliana M. Dávalos
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medicine.medical_specialty ,Genetic Speciation ,media_common.quotation_subject ,Longevity ,Molecular Sequence Data ,Growth hormone receptor ,Biology ,Receptor, IGF Type 1 ,Evolution, Molecular ,Molecular evolution ,Chiroptera ,Internal medicine ,Genetics ,medicine ,Animals ,Body Size ,Amino Acid Sequence ,Gene ,Phylogeny ,Insulin-like growth factor 1 receptor ,media_common ,chemistry.chemical_classification ,Phylogenetic tree ,Mole Rats ,Genetic Variation ,Receptors, Somatotropin ,General Medicine ,Amino acid ,Transmembrane domain ,Endocrinology ,chemistry ,Evolutionary biology - Abstract
Mammals typically display a robust positive relationship between lifespan and body size. Two groups that deviate markedly from this pattern are bats and African mole-rats, with members of both groups being extremely long-lived given their body size, with the maximum documented lifespan for many species exceeding 20 years. A recent genomics study of the exceptionally long-lived Brandt's bat, Myotis brandtii (41 years), suggested that its longevity and small body size may be at least partly attributed to key amino acid substitutions in the transmembrane domains of the receptors of growth hormone (GH) and insulin-like growth factor 1 (IGF1). However, whereas elevated longevity is likely to be common across all 19 bat families, the reported amino acid substitutions were only observed in two closely related bat families. To test the hypothesis that an altered GH/IGF1 axis relates to the longevity of African mole-rats and bats, we compared and analysed the homologous coding gene sequences in genomic and transcriptomic data from 26 bat species, five mole-rats and 38 outgroup species. Phylogenetic analyses of both genes recovered the majority of nodes in the currently accepted species tree with high support. Compared to other clades, such as primates and carnivores, the bats and rodents had longer branch lengths. The single 24 amino acid transmembrane domain of IGF1R was found to be more conserved across mammals compared to that of GHR. Within bats, considerable variation in the transmembrane domain of GHR was found, including a previously unreported deletion in Emballonuridae. The transmembrane domains of rodents were found to be more conserved, with mole-rats lacking uniquely conserved amino acid substitutions. Molecular evolutionary analyses showed that both genes were under purifying selection in bats and mole-rats. Our findings suggest that while the previously documented mutations may confer some additional lifespan to Myotis bats, other, as yet unknown, genetic differences are likely to account for the long lifespans observed in many bat and mole-rat species.
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- 2014
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164. Flow diagnostics essential code: a simple and brief format for the summary of leukemia phenotyping
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Hrušák, O, Basso, Giuseppe, Ratei, R, Gaipa, G, Luria, D, Mejstříková, E, Karawajew, L, Buldini, Barbara, Rozenthal, E, Bourquin, Jp, Kalina, T, Sartor, M, Dworzak, Mn, and AIEOP BFM Flow Network
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Humans ,Precursor Cell Lymphoblastic Leukemia-Lymphoma ,Flow Cytometry ,Immunophenotyping - Abstract
Flow cytometry is a valuable part in the routine diagnostics of acute leukemia (AL). Although internationally recognized definitions of main AL subsets are available, there is currently no consensus format for the short summary of clinical flow cytometry reports. Since clinical reports are too long for most database purposes, there is a need for a standardized format of their short summaries.The Associazione Italiana Ematologia Oncologia Pediatrica--Berlin Frankfurt Muenster (AIEOP-BFM) Flow Network that encompasses reference diagnostics laboratories in Australia, Austria, Czechia, Germany, Israel, Italy, and Switzerland have designed a pro-forma for the summary of flow cytometry results in the diagnosis of leukemia. The process involved several meetings and other communications, during which the group established a consensus on the essentials that lead to the diagnostic conclusions in childhood AL.The "Flow Diagnostics Essential (FDE) Code" is a result from an agreement within the AIEOP-BFM Flow Network. In a standardized format, it reports the extent of the infiltration by a malignant clone, followed by description antigen expression as strong, weak or negative, and a diagnostic conclusion.A consensus brief format (the "FDE Code") has been designed as a brief summary of the diagnostic immunophenotype of childhood AL. It is also applicable for the diagnostic investigation of other malignancies by flow cytometry. The FDE code may be included in the final clinical report and/or used in the setting of a multicenter clinical trial database.
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- 2014
165. Quality assessment program for EuroFlow protocols: summary results of four-year (2010-2013) quality assurance rounds
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Kalina, T, Flores-Montero, J, Lecrevisse, Q, Pedreira, CE, van der Velden, Vincent, Novakova, M, Mejstrikova, E, Hrusak, O, Bottcher, S, Karsch, D, Sedek, L, Trinquand, A, Boeckx, N, Caetano, J, Asnafi, V, Lucio, P, Lima, M, Santos, AH, Bonaccorso, P, van der Sluijs-Gelling, AJ, Langerak, Ton, Martin-Ayuso, M, Szczepanski, T, Dongen, Jacques, Orfao, A, and Immunology
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Europe ,Quality Control ,Leukemia ,Lymphoma ,Reference Values ,Reference Standards ,Flow Cytometry ,Healthy Volunteers ,Lymphocyte Subsets ,Immunophenotyping - Abstract
Flow cytometric immunophenotyping has become essential for accurate diagnosis, classification, and disease monitoring in hemato-oncology. The EuroFlow Consortium has established a fully standardized "all-in-one" pipeline consisting of standardized instrument settings, reagent panels, and sample preparation protocols and software for data analysis and disease classification. For its reproducible implementation, parallel development of a quality assurance (QA) program was required. Here, we report on the results of four consecutive annual rounds of the novel external QA EuroFlow program. The novel QA scheme aimed at monitoring the whole flow cytometric analysis process (cytometer setting, sample preparation, acquisition and analysis) by reading the median fluorescence intensities (MedFI) of defined lymphocytes' subsets. Each QA participant applied the predefined reagents' panel on blood cells of local healthy donors. A uniform gating strategy was applied to define lymphocyte subsets and to read MedFI values per marker. The MedFI values were compared with reference data and deviations from reference values were quantified using performance score metrics. In four annual QA rounds, we analyzed 123 blood samples from local healthy donors on 14 different instruments in 11 laboratories from nine European countries. The immunophenotype of defined cellular subsets appeared sufficiently standardized to permit unified (software) data analysis. The coefficient of variation of MedFI for 7 of 11 markers performed repeatedly below 30%, average MedFI in each QA round ranged from 86 to 125% from overall median. Calculation of performance scores was instrumental to pinpoint standardization failures and their causes. Overall, the new EuroFlow QA system for the first time allowed to quantify the technical variation that is introduced in the measurement of fluorescence intensities in a multicentric setting over an extended period of time. EuroFlow QA is a proficiency test specific for laboratories that use standardized EuroFlow protocols. It may be used to complement, but not replace, established proficiency tests. © 2014 International Society for Advancement of Cytometry.
- Published
- 2014
166. Cell response to herpes simplex virus type 1 infection mediated by biphasic calcium-phosphate ceramics:In vitro approach
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E. Dyulgerova, T. Varadinova, and Kalina T. Zlateva
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Growth medium ,Cell ,Biomedical Engineering ,chemistry.chemical_element ,Calcium ,Biology ,medicine.disease_cause ,In vitro ,Herpesviridae ,Virus ,Microbiology ,Biomaterials ,chemistry.chemical_compound ,medicine.anatomical_structure ,Herpes simplex virus ,chemistry ,Cell culture ,medicine - Abstract
Based on well-documented data showing that bioactive ions (such as Ca2+, PO4-, etc.) released by BCPC induce various cell responses and on the significance of herpes outbreaks in human pathology, we investigated whether BCPC can modify cell response to HSV-1 infection. The roles of some physical and chemical properties of ceramics were evaluated using three BCPC samples--French commercial macro-microporous (FR) and two Bulgarian microporous laboratory samples--one of which was modified with magnesium (BG and BG + Mg). Samples only washed in 0.9% NaCl were designated as nonconditioned while those resuspended in cell growth medium for 10 days after washing were designated as conditioned. Experiments were done on cells from the continuous MDBK line precultured on BCPC surfaces for different time intervals and thereafter HSV-1 infected. The yield of infectious virus progeny, measured as virus titers, was the parameter used to determine the cell response to HSV-1 infection mediated by BCPC as compared to that of the virus control, that is, virus yield in cells cultured without BCPC. The data obtained show that all three nonconditioned BCPC samples were able to modify cells to resist HSV-1 infection. The prolongation of the resistant state depended on the specific physical and chemical properties of the particular BCPC sample: as the data show that the conditioning procedure (1) increased the ability of BG + Mg to promote cell resistance, and (2) reduced the ability of FR samples to modify cells to resist HSV-1 infection. The data obtained show that apart from Ca2+ and PO4-, ions of biometals such as Mg2+ also are responsible for the induction and maintenance of cell resistance to HSV-1 infection.
- Published
- 2001
167. Danon Disease: Clinical Presentation and Diagnostic Workup in a Case of a Male Patient with a Novel Mutation in the LAMP2 Gene
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Dieckmann, A., primary, Majer, F., additional, Hulkova, H., additional, Farr, M., additional, Kalina, T., additional, Romeike, B., additional, Vlaskova, H., additional, Brandl, U., additional, Sikora, J., additional, and Husain, R., additional
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- 2016
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168. Family-based therapy for young adults with Anorexia Nervosa restores weight
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Chen, Eunice Y., primary, Weissman, Jessica A., additional, Zeffiro, Thomas A., additional, Yiu, Angelina, additional, Eneva, Kalina T., additional, Arlt, Jean M., additional, and Swantek, Michael J., additional
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- 2016
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169. Quantitative expression of regulatory and differentiation-related genes in the key steps of human hematopoiesis: The LeukoStage Database
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Polgárová, K., primary, Vášková, M., additional, Froňková, E., additional, Slámová, L., additional, Kalina, T., additional, Mejstříková, E., additional, Dobiášová, A., additional, Fišer, K., additional, and Hrušák, O., additional
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- 2016
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170. Bookreviews
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Kalina, T., Jeník, Jan, Křísa, Bohdan, Šašek, Václav, Slavík, Bohumil, and Moravec, Jaroslav
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- 1989
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171. A phylomedicine approach to understanding the evolution of auditory sensory perception and disease in mammals
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Emma C. Teeling, Kalina T. J. Davies, Michaël Bekaert, Stephen J. Rossiter, John D. Kirwan, and Jennifer M. Commins
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media_common.quotation_subject ,Human echolocation ,Disease ,Biology ,Conserved sequence ,03 medical and health sciences ,Negative selection ,0302 clinical medicine ,positive selection ,Perception ,Genetics ,phylomedicine ,TECTA ,Ecology, Evolution, Behavior and Systematics ,030304 developmental biology ,media_common ,Neurosciences ,0303 health sciences ,Otorhinolaryngology ,hearing ,purifying selection ,General Agricultural and Biological Sciences ,030217 neurology & neurosurgery ,KCNQ4 ,STRC - Abstract
Hereditary deafness affects 0.1% of individuals globally and is considered as one of the most debilitating diseases of man. Despite recent advances, the molecular basis of normal auditory function is not fully understood and little is known about the contribution of single-nucleotide variations to the disease. Using cross-species comparisons of 11 'deafness' genes (Myo15, Ush1g, Strc, Tecta, Tectb, Otog, Col11a2, Gjb2, Cldn14, Kcnq4, Pou3f4) across 69 evolutionary and ecologically divergent mammals, we elucidated whether there was evidence for: (i) adaptive evolution acting on these genes across mammals with similar hearing capabilities; and, (ii) regions of long-term evolutionary conservation within which we predict disease-associated mutations should occur. We find evidence of adaptive evolution acting on the eutherian mammals in Myo15, Otog and Tecta. Examination of selection pressures in Tecta and Pou3f4 across a taxonomic sample that included a wide representation of auditory specialists, the bats, did not uncover any evidence for a role in echolocation. We generated ‘conservation indices' based on selection estimates at nucleotide sites and found that known disease mutations fall within sites of high evolutionary conservation. We suggest that methods such as this, derived from estimates of evolutionary conservation using phylogenetically divergent taxa, will help to differentiate between deleterious and benign mutations.
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- 2013
172. No novel coronaviruses identified in a large collection of human nasopharyngeal specimens using family-wide CODEHOP-based primers
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Kalina T. Zlateva, Marco C. Viveen, Margareta Ieven, Eric C. J. Claas, Alexander E. Gorbalenya, F.R. Leus, Frank E. J. Coenjaerts, Kelly M. Crusio, Willy J. M. Spaan, and Christine Lammens
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medicine.medical_specialty ,Pcr assay ,RT-PCR ,Torovirus ,Respiratory tract infections ,medicine.disease_cause ,Medical microbiology ,Nasopharynx ,Virology ,medicine ,Humans ,Virus discovery ,DNA Primers ,Coronavirus ,biology ,Reverse Transcriptase Polymerase Chain Reaction ,Brief Report ,virus diseases ,General Medicine ,biology.organism_classification ,Reverse transcriptase ,CODEHOP ,Real-time polymerase chain reaction ,Healthy individuals ,Human medicine ,Real-time PCR - Abstract
Novel viruses might be responsible for numerous disease cases with unknown etiology. In this study, we screened 1800 nasopharyngeal samples from adult outpatients with respiratory disease symptoms and healthy individuals. We employed a reverse transcription (RT)-PCR assay and CODEHOP-based primers (CT12-mCODEHOP) previously developed to recognize known and unknown corona- and toroviruses. The CT12-mCODEHOP assay detected 42.0 % (29/69) of samples positive for human coronaviruses (HCoV), including HCoV-229 (1/16), HCoV-NL63 (9/17), and HCoV-OC43 (19/36), and additionally HCoV-HKU1 (3), which was not targeted by the diagnostic real-time PCR assays. No other coronaviruses were identified in the analyzed samples.
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- 2013
173. Parallel signatures of sequence evolution among hearing genes in echolocating mammals: an emerging model of genetic convergence
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Kalina T. J. Davies, John D. Kirwan, James Cotton, Emma C. Teeling, and Stephen J. Rossiter
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Hearing loss ,Molecular Sequence Data ,Zoology ,Human echolocation ,Biology ,Evolution, Molecular ,Monophyly ,Negative selection ,Hearing ,Phylogenetics ,Genetics ,medicine ,Animals ,Humans ,Selection, Genetic ,Clade ,Genetics (clinical) ,Phylogeny ,Mammals ,Phylogenetic tree ,Proteins ,News and Commentary ,Evolutionary biology ,Echolocation ,Original Article ,medicine.symptom ,Adaptation - Abstract
Recent findings of sequence convergence in the Prestin gene among some bats and cetaceans suggest that parallel adaptations for high-frequency hearing have taken place during the evolution of echolocation. To determine if this gene is an exception, or instead similar processes have occurred in other hearing genes, we have examined Tmc1 and Pjvk, both of which are associated with non-syndromic hearing loss in mammals. These genes were amplified and sequenced from a number of mammalian species, including echolocating and non-echolocating bats and whales, and were analysed together with published sequences. Sections of both genes showed phylogenetic signals that conflicted with accepted species relationships, with coding regions uniting laryngeal echolocating bats in a monophyletic clade. Bayesian estimates of posterior probabilities of convergent and divergent substitutions provided more direct evidence of sequence convergence between the two groups of laryngeal echolocating bats as well as between echolocating bats and dolphins. We found strong evidence of positive selection acting on some echolocating bat species and echolocating cetaceans, contrasting with purifying selection on non-echolocating bats. Signatures of sequence convergence and molecular adaptation in two additional hearing genes suggest that the acquisition of high-frequency hearing has involved multiple loci.
- Published
- 2011
174. A phylogenomic analysis of the role and timing of molecular adaptation in the aquatic transition of cetartiodactyl mammals
- Author
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Tsagkogeorga, Georgia, primary, McGowen, Michael R., additional, Davies, Kalina T. J., additional, Jarman, Simon, additional, Polanowski, Andrea, additional, Bertelsen, Mads F., additional, and Rossiter, Stephen J., additional
- Published
- 2015
- Full Text
- View/download PDF
175. Fast and simple spectral FLIM for biochemical and medical imaging
- Author
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Popleteeva, Marina, primary, Haas, Kalina T., additional, Stoppa, David, additional, Pancheri, Lucio, additional, Gasparini, Leonardo, additional, Kaminski, Clemens F., additional, Cassidy, Liam D., additional, Venkitaraman, Ashok R., additional, and Esposito, Alessandro, additional
- Published
- 2015
- Full Text
- View/download PDF
176. Molecular evolution of the hyaluronan synthase 2 gene in mammals: implications for adaptations to the subterranean niche and cancer resistance
- Author
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Faulkes, Christopher G., primary, Davies, Kalina T. J., additional, Rossiter, Stephen J., additional, and Bennett, Nigel C., additional
- Published
- 2015
- Full Text
- View/download PDF
177. Flowcytometrische immunofenotypering van acute myeloïde leukemieën en myelodysplastisch syndroom
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van der Velden, Vincent, te Marvelde, Jeroen, Cullen, M, Mejstrikova, E, Flores-Montero, J, Sedek, L, Richards, S, Hrusek, O, Szczepanski, Tomek, Evans, P, Kalina, T, Wind, Henk, Orfao, A, Dongen, Jacques, van Dongen, JJM, Dik, WA, Langerak, AW, van der Velden, VHJ, Hooijkaas, H, and Immunology
- Published
- 2010
178. Diagnosis and classification of acute lymphoblastic leukemia
- Author
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Lhermitte, L, Asnafi, V, Flores-Montero, J, Lecrevisse, Q, Sedek, L, Szczepanski, Tomek, Bottcher, S, Bruggemann, M, Mejstrikova, E, Kalina, T, De Mendonca, A, Lucio, P, Cullen, M, Richards, S, te Marvelde, Jeroen, Wind, Henk, van der Velden, Vincent, van der Sluijs, AJ, Vidriales, MB, Hernandez, J, Costa, ES, Macintyre, E, Dongen, Jacques, Orfao, A, van Dongen, JJM, Dik, WA, Langerak, AW, van der Velden, VHJ, Hooijkaas, H, and Immunology
- Published
- 2010
179. Aantonen van fusiegenen op eiwitniveau bij leukemiepatiënten met behulp van de flowcytometrische immunobead assay
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Dekking, E, van der Velden, Vincent, Bottcher, S, Bruggemann, M, Sonneveld, E (Edwin), van der Sluijs, AJ, Boeckx, N, Lucio, P, Sedek, L, Szczepanski, Tomek, Kalina, T, Kovac, M, Evans, P, Hoogeveen, Patricia, Flores-Montero, J, Orfao, A, Bitter, Marieke, Staal, Frank, Dongen, Jacques, Immunology, and Molecular Genetics
- Published
- 2010
180. Subgroup prevalence and genotype circulation patterns of human respiratory syncytial virus in Belgium during ten successive epidemic seasons
- Author
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Kalina T. Zlateva, Marc Van Ranst, Leen Vijgen, Cecilia Naranjo, and Nathalie Dekeersmaeker
- Subjects
Microbiology (medical) ,Serotype ,Adult ,Paramyxoviridae ,Adolescent ,Genotype ,Molecular Sequence Data ,Respiratory Syncytial Virus Infections ,Biology ,Virus ,Pneumovirinae ,Belgium ,Virology ,Prevalence ,Humans ,Serotyping ,Mononegavirales ,Child ,Phylogeny ,Aged ,Molecular epidemiology ,Age Factors ,Infant, Newborn ,Genetic Variation ,Infant ,Pneumovirus ,Sequence Analysis, DNA ,Middle Aged ,biology.organism_classification ,Child, Preschool ,Respiratory Syncytial Virus, Human ,Immunology ,RNA, Viral ,Seasons - Abstract
Human respiratory syncytial virus (HRSV) is the leading viral cause of severe respiratory illness for infants and young children worldwide. Two major antigenic groups (A and B) of HRSV exist, and viruses from both subgroups can cocirculate during epidemics; however, their frequencies might differ between seasons. The subgroup prevalence and genotype distribution patterns of HRSV strains were investigated in a community in Belgium during 10 successive epidemic seasons (1996 to 2006). A regular 3-year cyclic pattern of subgroup dominance was observed, consisting of two predominant HRSV-A seasons, followed by a single HRSV-B-dominant year. HRSV infections with both subgroups were more prevalent among children younger than 6 months and had a peak incidence in December. The most frequently detected genotypes were GA5 and GB13, the latter including strains with the 60-nucleotide duplication in the G gene. Furthermore, GA5 remained the dominant HRSV genotype in two consecutive epidemic seasons twice during the study period. Additional variability was detected among the GB13 isolates, due to the usage of a novel termination codon in the G gene. Dual infections with both HRSV subgroups were detected for 9 patients, and subsequent infections with the heterologous HRSV subgroup were documented for 15 patients. Among five patients with homologous reinfections, only one was caused by HRSV-B. Our results support the hypothesis that the overall prevalence of HRSV-A over HRSV-B could be due to a more-transient subgroup A-specific immune protection.
- Published
- 2007
181. Women in Low-Skill Work
- Author
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8. Weinkopf, C., Grimshaw, D., Stupnytskyy, O., Hieming, B., Jaehrling, K., Kalina, T., Shimron, N.
- Published
- 2007
182. Family Wide Molecular Adaptations to Underground Life in African Mole-Rats Revealed by Phylogenomic Analysis
- Author
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Nigel C. Bennett, Stephen J. Rossiter, Kalina T. J. Davies, Chris G. Faulkes, and Georgia Tsagkogeorga
- Subjects
Acclimatization ,Niche ,subterranean ,Genomics ,Biology ,Evolution, Molecular ,03 medical and health sciences ,0302 clinical medicine ,positive selection ,mole-rats ,Molecular evolution ,Phylogenetics ,Genetics ,Animals ,Selection, Genetic ,Clade ,Molecular Biology ,Africa South of the Sahara ,Ecosystem ,Phylogeny ,Discoveries ,Ecology, Evolution, Behavior and Systematics ,030304 developmental biology ,0303 health sciences ,adaptive evolution ,Ecology ,Mole Rats ,Sequence Analysis, DNA ,Phenotypic trait ,15. Life on land ,Adaptation, Physiological ,Biological Evolution ,Evolutionary radiation ,Rats ,Taxon ,Evolutionary biology ,Transcriptome ,030217 neurology & neurosurgery - Abstract
During their evolutionary radiation, mammals have colonized diverse habitats. Arguably the subterranean niche is the most inhospitable of these, characterized by reduced oxygen, elevated carbon dioxide, absence of light, scarcity of food, and a substrate that is energetically costly to burrow through. Of all lineages to have transitioned to a subterranean niche, African mole-rats are one of the most successful. Much of their ecological success can be attributed to a diet of plant storage organs, which has allowed them to colonize climatically varied habitats across sub-Saharan Africa, and has probably contributed to the evolution of their diverse social systems. Yet despite their many remarkable phenotypic specializations, little is known about molecular adaptations underlying these traits. To address this, we sequenced the transcriptomes of seven mole-rat taxa, including three solitary species, and combined new sequences with existing genomic data sets. Alignments of more than 13,000 protein-coding genes encompassed, for the first time, all six genera and the full spectrum of ecological and social variation in the clade. We detected positive selection within the mole-rat clade and along ancestral branches in approximately 700 genes including loci associated with tumorigenesis, aging, morphological development, and sociality. By combining these results with gene ontology annotation and protein–protein networks, we identified several clusters of functionally related genes. This family wide analysis of molecular evolution in mole-rats has identified a suite of positively selected genes, deepening our understanding of the extreme phenotypic traits exhibited by this group.
- Published
- 2015
183. Sensitivity but not specificity of minimal residual disease by 4-color flow cytometry depends on the time point during the treatment of childhood B lineage ALL
- Author
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Mejstrikova, Ester, Fronkova, E, Pospisilova, K, Batinić, Drago, Dubravčić, Klara, Luria, D, Izraeli, S, Stark, B, Kappelmayer, J, Kiss, F, Ng, M, Leung, Y, Cheng, AS, Kalina, T, Vaskova, M, Stary, J, and Hrusak, O.
- Subjects
4-color flow cytometry ,MRD ,ALL - Abstract
Several studies showed a good correlation between minimal residual disease (MRD) obtained by flow cytometry (FC) and by PCR (Ig/TCR rearrangements). However, before FC is widely applied for therapeutic decisions we need exact, objective and standardized criteria. Therefore, we pre-defined B-lineage cell subsets using 4- and 3-color FC and we established background levels for each subset in pre-defined time-points on therapy. Investigators’ subjective bias was minimized. Values above the background are compared to PCR- based MRD. Patients and methods. Children with ALL were treated by ALL IC BFM2002 protocol. This international flow cytometric trial MiniMini contained 4 laboratories (Croatia 36 patients, Israel 48, Hong Kong 33 and Czech Republic 136). 442 samples were measured simultaneously by PCR and 4color FC. Pre-defined subsets (28 values) were measured in all patients at 5 time points (d0, d8, d15, d33 and week 12). Cut off for positivity and negativity of individual subpopulations were assessed as follows: 1) negative samples by PCR for respective time point were randomly divided into training and testing cohort 2) 98.5 percentile of individual subpopulation in training cohort was selected as a cut off for positivity and negativity. 3) cut off values were tested on testing cohort and PCR positive samples (total 337 samples), sample was considered positive when having at least one value above cut off (when more values were above cut off, highest value was considered as MRD) Results. When all time points were analyzed together, sensitivity of FC MRD was 82% and specificity 88% There are no negative patients at day 8 in bone marrow by FC or by PCR. 5 samples at day 15 were positive by PCR (
- Published
- 2006
184. Chromatography paper strip sampling of enteric adenoviruses type 40 and 41 positive stool specimens
- Author
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Zlateva, Kalina T, Maes, Piet, Rahman, Mustafizur, and Van Ranst, Marc
- Subjects
Diarrhea ,Paper ,Time Factors ,Chromatography, Paper ,Research ,Adenoviridae Infections ,Temperature ,enteric adenoviruses ,Polymerase Chain Reaction ,Adenoviridae ,lcsh:Infectious and parasitic diseases ,Feces ,DNA, Viral ,Humans ,lcsh:RC109-216 ,HeLa Cells - Abstract
Background The enteric subgroup F adenoviruses type 40 (Ad40) and 41 (Ad41) are the second most important cause of acute infantile gastroenteritis after rotaviruses. Repeated community outbreaks have been associated with antigenic changes among the Ad40 and Ad41 strains due to host immune pressure. Therefore large field epidemiological surveys and studies on the genetic variations in different isolates of Ad40 and Ad41 are important for disease control programs, the design of efficient diagnostic kits and vaccines against subgroup F adenoviruses. A novel method using sodium dodecyl sulphate SDS/EDTA-pretreated chromatography paper strips was evaluated for the collection, storage and shipping of Ad40/41 contaminated stool samples. Results This study shows that adenoviral DNA can be successfully detected in the filter strips by PCR after four months storage at -20°C, 4°C, room temperature (20–25°C) and 37°C. Furthermore no adenoviral infectivity was observed upon contact with the SDS/EDTA-pretreated strips. Conclusions Collecting, storing and transporting adenovirus type 40 and 41 positive stool samples on SDS/EDTA-pretreated chromatography filter strips is a convenient, biosafe and cost effective method for studying new genome variants and monitoring spread of enteric adenovirus strains during outbreaks.
- Published
- 2005
185. A novel pancoronavirus RT-PCR assay: frequent detection of human coronavirus NL63 in children hospitalized with respiratory tract infections in Belgium
- Author
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Sandra Li, Piet Maes, Kalina T. Zlateva, Leen Vijgen, Ben Berkhout, Els Keyaerts, Krzysztof Pyrc, Marc Van Ranst, Lia van der Hoek, Elien Moës, AII - Amsterdam institute for Infection and Immunity, Medical Microbiology and Infection Prevention, and Faculteit der Geneeskunde
- Subjects
Male ,Human coronavirus NL63 ,medicine.medical_specialty ,Adolescent ,viruses ,Molecular Sequence Data ,medicine.disease_cause ,lcsh:Infectious and parasitic diseases ,Medical microbiology ,Belgium ,stomatognathic system ,Consensus Sequence ,medicine ,Humans ,lcsh:RC109-216 ,Respiratory system ,Child ,Respiratory Tract Infections ,Phylogeny ,DNA Primers ,Coronavirus ,Base Sequence ,Respiratory tract infections ,biology ,Reverse Transcriptase Polymerase Chain Reaction ,Incidence ,Incidence (epidemiology) ,Infant ,virus diseases ,respiratory system ,biology.organism_classification ,Virology ,Infectious Diseases ,medicine.anatomical_structure ,Parasitology ,Child, Preschool ,RNA, Viral ,Female ,Seasons ,Coronavirus Infections ,Sequence Alignment ,Research Article ,Respiratory tract - Abstract
Background Four human coronaviruses are currently known to infect the respiratory tract: human coronaviruses OC43 (HCoV-OC43) and 229E (HCoV-229E), SARS associated coronavirus (SARS-CoV) and the recently identified human coronavirus NL63 (HCoV-NL63). In this study we explored the incidence of HCoV-NL63 infection in children diagnosed with respiratory tract infections in Belgium. Methods Samples from children hospitalized with respiratory diseases during the winter seasons of 2003 and 2004 were evaluated for the presence of HCoV-NL63 using a optimized pancoronavirus RT-PCR assay. Results Seven HCoV-NL63 positive samples were identified, six were collected during January/February 2003 and one at the end of February 2004. Conclusions Our results support the notation that HCoV-NL63 can cause serious respiratory symptoms in children. Sequence analysis of the S gene showed that our isolates could be classified into two subtypes corresponding to the two prototype HCoV-NL63 sequences isolated in The Netherlands in 1988 and 2003, indicating that these two subtypes may currently be cocirculating.
- Published
- 2005
186. Book reviews
- Author
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Krekule, J., Šatava, J., Zárubová, Helena, Kalina, T., and Slavík, B.
- Published
- 1983
- Full Text
- View/download PDF
187. A Paradox of Activation Strategies: Why Increasing Labour Market Participation among Single Mothers Failed to Bring Down Poverty Rates
- Author
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Jaehrling, K., primary, Kalina, T., additional, and Mesaros, L., additional
- Published
- 2014
- Full Text
- View/download PDF
188. Use of polymerase chain reaction for diagnosis of disseminated adenovirus infection
- Author
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Annabel Rector, Danielle Van Beers, Kalina T. Zlateva, Corinne Liesnard, Robert Snoeck, Marc Van Ranst, and Nadira Azzi
- Subjects
Microbiology (medical) ,Male ,viruses ,Adenoviridae Infections ,Multiple Organ Failure ,Polymerase Chain Reaction ,Sensitivity and Specificity ,Severity of Illness Index ,Virus ,Leukemia, Myelomonocytic, Acute ,law.invention ,Fulminant hepatic failure ,Fatal Outcome ,law ,Medicine ,Humans ,Viremia ,Respiratory system ,Adenovirus infection ,Polymerase chain reaction ,business.industry ,Adenoviruses, Human ,Hematopoietic Stem Cell Transplantation ,Infant ,Consensus primer ,medicine.disease ,Hexon gene ,Virology ,Infectious Diseases ,Pediatrics, Perinatology and Child Health ,DNA, Viral ,Peripheral Blood Stem Cell Transplantation ,Disease Progression ,business - Abstract
We report a fatal case of disseminated adenovirus infection with fulminant hepatic failure in an 8-month-old child after peripheral blood stem cell transplantation. The virus was identified in blood, urine, respiratory aspirate and stool samples and was typed as adenovirus type 2 through PCR and sequencing of part of the hexon gene, with the use of degenerated consensus primers.
- Published
- 2003
189. CD2-positive B-cell precursor acute lymphoblastic leukemia with an early switch to the monocytic lineage
- Author
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Slamova, L, primary, Starkova, J, additional, Fronkova, E, additional, Zaliova, M, additional, Reznickova, L, additional, van Delft, F W, additional, Vodickova, E, additional, Volejnikova, J, additional, Zemanova, Z, additional, Polgarova, K, additional, Cario, G, additional, Figueroa, M, additional, Kalina, T, additional, Fiser, K, additional, Bourquin, J P, additional, Bornhauser, B, additional, Dworzak, M, additional, Zuna, J, additional, Trka, J, additional, Stary, J, additional, Hrusak, O, additional, and Mejstrikova, E, additional
- Published
- 2013
- Full Text
- View/download PDF
190. Flow cytometric immunobead assay for fast and easy detection of PML-RARA fusion proteins for the diagnosis of acute promyelocytic leukemia
- Author
-
Dekking, E.H.A. (Liesbeth), Velden, V.H.J. (Vincent) van der, Varro, A. (Andras), Wai, H., Böttcher, S. (Stephan), Kneba, M. (Michael), Sonneveld, E. (Edwin), Koning, A., Boeckx, N. (Nancy), Van Poecke, N., Lucio, P. (Paulo), Mendonça, A., Sedek, L. (Lukasz), Szczepanski, T. (Tomasz), Kalina, T. (Tomas), Kanderová, V. (V.), Hoogeveen, P.G. (Patricia), Flores-Montero, J. (Juan), Chillón, C. (Carmen), Orfao, A. (Alberto), Almeida, J.M.M. (Julia), Evans, P.A.S., Cullen, C., Noordijk, A.L., Vermeulen, P.M. (P.), Man, M.T. (M.) de, Dixon, E.P. (Eric), Comans-Bitter, W.M., Dongen, J.J.M. (Jacques) van, Dekking, E.H.A. (Liesbeth), Velden, V.H.J. (Vincent) van der, Varro, A. (Andras), Wai, H., Böttcher, S. (Stephan), Kneba, M. (Michael), Sonneveld, E. (Edwin), Koning, A., Boeckx, N. (Nancy), Van Poecke, N., Lucio, P. (Paulo), Mendonça, A., Sedek, L. (Lukasz), Szczepanski, T. (Tomasz), Kalina, T. (Tomas), Kanderová, V. (V.), Hoogeveen, P.G. (Patricia), Flores-Montero, J. (Juan), Chillón, C. (Carmen), Orfao, A. (Alberto), Almeida, J.M.M. (Julia), Evans, P.A.S., Cullen, C., Noordijk, A.L., Vermeulen, P.M. (P.), Man, M.T. (M.) de, Dixon, E.P. (Eric), Comans-Bitter, W.M., and Dongen, J.J.M. (Jacques) van
- Abstract
The PML-RARA fusion protein is found in approximately 97% of patients with acute promyelocytic leukemia (APL). APL can be associated with life-threatening bleeding complications when undiagnosed and not treated expeditiously. The PML-RARA fusion protein arrests maturation of myeloid cells at the promyelocytic stage, leading to the accumulation of neoplastic promyelocytes. Complete remission can be obtained by treatment with all-trans-retinoic acid (ATRA) in combination with chemotherapy. Diagnosis of APL is based on the detection of t(15;17) by karyotyping, fluorescence in situ hybridization or PCR. These techniques are laborious and demand specialized laboratories. We developed a fast (performed within 4-5 h) and sensitive (detection of at least 10% malignant cells in normal background) flow cytometric immunobead assay for the detection of PML-RARA fusion proteins in cell lysates using a bead-bound anti-RARA capture antibody and a phycoerythrin-conjugated anti-PML detection antibody. Testing of 163 newly diagnosed patients (including 46 APL cases) with the PML-RARA immunobead assay showed full concordance with the PML-RARA PCR results. As the applied antibodies recognize outer domains of the fusion protein, the assay appeared to work independently of the PML gene break point region. Importantly, the assay can be used in parallel with routine immunophenotyping for fast and easy diagnosis of APL.
- Published
- 2012
- Full Text
- View/download PDF
191. EuroFlow antibody panels for standardized n-dimensional flow cytometric immunophenotyping of normal, reactive and malignant leukocytes
- Author
-
Dongen, J.J.M. (Jacques) van, Lhermitte, L., Böttcher, S. (Stephan), Almeida, J.M.M. (Julia), Velden, V.H.J. (Vincent) van der, Flores-Montero, J. (Juan), Rawstron, A.C., Asnafi, V. (Vahid), Lecrevisse, Q. (Quentin), Lucio, P. (Paulo), Mejstříková, E. (Ester), Szczepanski, T. (Tomasz), Kalina, T. (Tomas), Tute, R.M. (Ruth) de, Brüggemann, M. (Monika), Sedek, L. (Lukasz), Cullen, C., Langerak, A.W. (Anton), Mendonça, A., Macintyre, E.A. (Elizabeth), Martin-Ayuso, M. (M.), Hrusak, O., Vidriales, M.B. (M.), Orfao, A. (Alberto), Dongen, J.J.M. (Jacques) van, Lhermitte, L., Böttcher, S. (Stephan), Almeida, J.M.M. (Julia), Velden, V.H.J. (Vincent) van der, Flores-Montero, J. (Juan), Rawstron, A.C., Asnafi, V. (Vahid), Lecrevisse, Q. (Quentin), Lucio, P. (Paulo), Mejstříková, E. (Ester), Szczepanski, T. (Tomasz), Kalina, T. (Tomas), Tute, R.M. (Ruth) de, Brüggemann, M. (Monika), Sedek, L. (Lukasz), Cullen, C., Langerak, A.W. (Anton), Mendonça, A., Macintyre, E.A. (Elizabeth), Martin-Ayuso, M. (M.), Hrusak, O., Vidriales, M.B. (M.), and Orfao, A. (Alberto)
- Abstract
Most consensus leukemia lymphoma antibody panels consist of lists of markers based on expert opinions, but they have not been validated. Here we present the validated EuroFlow 8-color antibody panels for immunophenotyping of hematological malignancies. The single-tube screening panels and multi-tube classification panels fit into the EuroFlow diagnostic algorithm with entries defined by clinical and laboratory parameters. The panels were constructed in 2-7 sequential design-evaluation-redesign rounds, using novel Infinicyt software tools for multivariate data analysis. Two groups of markers are combined in each 8-color tube: (i) backbone markers to identify distinct cell populations in a sample, and (ii) markers for characterization of specific cell populations. In multi-tube panels, the backbone markers were optimally placed at the same fluorochrome position in every tube, to provide identical multidimensional localization of the target cell population(s). The characterization markers were positioned according to the diagnostic utility of the combined markers. Each proposed antibody combination was tested against reference databases of normal and malignant cells from healthy subjects and WHO-based disease entities, respectively. The EuroFlow studies resulted in validated and flexible 8-color antibody panels for multidimensional identification and characterization of normal and aberrant cells, optimally suited for immunophenotypic screening and classification of hematological malignancies.
- Published
- 2012
- Full Text
- View/download PDF
192. Flow cytometric immunobead assay for fast and easy detection of PML-RARA fusion proteins for the diagnosis of acute promyelocytic leukemia
- Author
-
Dekking, Liesbeth, van der Velden, Vincent, Varro, R, Wai, H, Böttcher, S, Kneba, M, Sonneveld, E (Edwin), Koning, A, Boeckx, N, Van Poecke, N, Lucio, P, De Mendonca, A, Sedek, L, Szczepanski, Tomek, Kalina, T, Kanderova, V, Hoogeveen, Patricia, Flores-Montero, J, Chillon, MC, Orfao, A, Almeida, J, Evans, P, Cullen, M, Noordijk, Rianne, Vermeulen, PM, Man, Martijn, Dixon, EP, Bitter, Marieke, Dongen, Jacques, Dekking, Liesbeth, van der Velden, Vincent, Varro, R, Wai, H, Böttcher, S, Kneba, M, Sonneveld, E (Edwin), Koning, A, Boeckx, N, Van Poecke, N, Lucio, P, De Mendonca, A, Sedek, L, Szczepanski, Tomek, Kalina, T, Kanderova, V, Hoogeveen, Patricia, Flores-Montero, J, Chillon, MC, Orfao, A, Almeida, J, Evans, P, Cullen, M, Noordijk, Rianne, Vermeulen, PM, Man, Martijn, Dixon, EP, Bitter, Marieke, and Dongen, Jacques
- Abstract
The PML-RARA fusion protein is found in approximately 97% of patients with acute promyelocytic leukemia (APL). APL can be associated with life-threatening bleeding complications when undiagnosed and not treated expeditiously. The PML-RARA fusion protein arrests maturation of myeloid cells at the promyelocytic stage, leading to the accumulation of neoplastic promyelocytes. Complete remission can be obtained by treatment with all-trans-retinoic acid (ATRA) in combination with chemotherapy. Diagnosis of APL is based on the detection of t(15; 17) by karyotyping, fluorescence in situ hybridization or PCR. These techniques are laborious and demand specialized laboratories. We developed a fast (performed within 4-5 h) and sensitive (detection of at least 10% malignant cells in normal background) flow cytometric immunobead assay for the detection of PML-RARA fusion proteins in cell lysates using a bead-bound anti-RARA capture antibody and a phycoerythrin-conjugated anti-PML detection antibody. Testing of 163 newly diagnosed patients (including 46 APL cases) with the PML-RARA immunobead assay showed full concordance with the PML-RARA PCR results. As the applied antibodies recognize outer domains of the fusion protein, the assay appeared to work independently of the PML gene break point region. Importantly, the assay can be used in parallel with routine immunophenotyping for fast and easy diagnosis of APL.
- Published
- 2012
193. EuroFlow antibody panels for standardized n-dimensional flow cytometric immunophenotyping of normal, reactive and malignant leukocytes
- Author
-
Dongen, Jacques, Lhermitte, L, Bottcher, S, Almeida, J, van der Velden, Vincent, Flores-Montero, J, Rawstron, A, Asnafi, V, Lecrevisse, Q, Lucio, P, Mejstrikova, E, Szczepanski, Tomek, Kalina, T, de Tute, R, Bruggemann, M, Sedek, L, Cullen, M, Langerak, Ton, De Mendonca, A, Macintyre, E, Martin-Ayuso, M, Hrusak, O, Vidriales, MB, Orfao, A, Dongen, Jacques, Lhermitte, L, Bottcher, S, Almeida, J, van der Velden, Vincent, Flores-Montero, J, Rawstron, A, Asnafi, V, Lecrevisse, Q, Lucio, P, Mejstrikova, E, Szczepanski, Tomek, Kalina, T, de Tute, R, Bruggemann, M, Sedek, L, Cullen, M, Langerak, Ton, De Mendonca, A, Macintyre, E, Martin-Ayuso, M, Hrusak, O, Vidriales, MB, and Orfao, A
- Abstract
Most consensus leukemia & lymphoma antibody panels consist of lists of markers based on expert opinions, but they have not been validated. Here we present the validated EuroFlow 8-color antibody panels for immunophenotyping of hematological malignancies. The single-tube screening panels and multi-tube classification panels fit into the EuroFlow diagnostic algorithm with entries defined by clinical and laboratory parameters. The panels were constructed in 2-7 sequential design-evaluation-redesign rounds, using novel Infinicyt software tools for multivariate data analysis. Two groups of markers are combined in each 8-color tube: (i) backbone markers to identify distinct cell populations in a sample, and (ii) markers for characterization of specific cell populations. In multi-tube panels, the backbone markers were optimally placed at the same fluorochrome position in every tube, to provide identical multidimensional localization of the target cell population(s). The characterization markers were positioned according to the diagnostic utility of the combined markers. Each proposed antibody combination was tested against reference databases of normal and malignant cells from healthy subjects and WHO-based disease entities, respectively. The EuroFlow studies resulted in validated and flexible 8-color antibody panels for multidimensional identification and characterization of normal and aberrant cells, optimally suited for immunophenotypic screening and classification of hematological malignancies.
- Published
- 2012
194. The Evolution of Bat Vestibular Systems in the Face of Potential Antagonistic Selection Pressures for Flight and Echolocation
- Author
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Davies, Kalina T. J., primary, Bates, Paul J. J., additional, Maryanto, Ibnu, additional, Cotton, James A., additional, and Rossiter, Stephen J., additional
- Published
- 2013
- Full Text
- View/download PDF
195. A phylomedicine approach to understanding the evolution of auditory sensory perception and disease in mammals
- Author
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Kirwan, John D., primary, Bekaert, Michaël, additional, Commins, Jennifer M., additional, Davies, Kalina T. J., additional, Rossiter, Stephen J., additional, and Teeling, Emma C., additional
- Published
- 2013
- Full Text
- View/download PDF
196. Family Wide Molecular Adaptations to Underground Life in African Mole-Rats Revealed by Phylogenomic Analysis.
- Author
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Davies, Kalina T. J., Bennett, Nigel C., Tsagkogeorga, Georgia, Rossiter, Stephen J., and Faulkes, Christopher G.
- Abstract
During their evolutionary radiation, mammals have colonized diverse habitats. Arguably the subterranean niche is the most inhospitable of these, characterized by reduced oxygen, elevated carbon dioxide, absence of light, scarcity of food, and a substrate that is energetically costly to burrow through. Of all lineages to have transitioned to a subterranean niche, African mole-rats are one of the most successful. Much of their ecological success can be attributed to a diet of plant storage organs, which has allowed them to colonize climatically varied habitats across sub-Saharan Africa, and has probably contributed to the evolution of their diverse social systems. Yet despite their many remarkable phenotypic specializations, little is known about molecular adaptations underlying these traits. To address this, we sequenced the transcriptomes of seven mole-rat taxa, including three solitary species, and combined new sequences with existing genomic data sets. Alignments of more than 13,000 protein-coding genes encompassed, for the first time, all six genera and the full spectrum of ecological and social variation in the clade. We detected positive selection within the mole-rat clade and along ancestral branches in approximately 700 genes including loci associated with tumorigenesis, aging, morphological development, and sociality. By combining these results with gene ontology annotation and protein-protein networks, we identified several clusters of functionally related genes. This family wide analysis of molecular evolution in mole-rats has identified a suite of positively selected genes, deepening our understanding of the extreme phenotypic traits exhibited by this group. [ABSTRACT FROM AUTHOR]
- Published
- 2015
- Full Text
- View/download PDF
197. No novel coronaviruses identified in a large collection of human nasopharyngeal specimens using family-wide CODEHOP-based primers
- Author
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Zlateva, Kalina T., primary, Coenjaerts, Frank E. J., additional, Crusio, Kelly M., additional, Lammens, Christine, additional, Leus, Frank, additional, Viveen, Marco, additional, Ieven, Margareta, additional, Spaan, Willy J. M., additional, Claas, Eric C. J., additional, and Gorbalenya, Alexander E., additional
- Published
- 2012
- Full Text
- View/download PDF
198. Danon disease: A focus on processing of the novel LAMP2 mutation and comments on the beneficial use of peripheral white blood cells in the diagnosis of LAMP2 deficiency
- Author
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Majer, F., primary, Vlaskova, H., additional, Krol, L., additional, Kalina, T., additional, Kubanek, M., additional, Stolnaya, L., additional, Dvorakova, L., additional, Elleder, M., additional, and Sikora, J., additional
- Published
- 2012
- Full Text
- View/download PDF
199. Signature Profiles of CMV-Specific T-Cells in Pediatric Patients with CMV Reactivation After Hematopoietic Stem Cell Transplantation
- Author
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Krol, L., primary, Stuchly, J., additional, Hubacek, P., additional, Sedlacek, P., additional, and Kalina, T., additional
- Published
- 2011
- Full Text
- View/download PDF
200. Signature profiles of CMV-specific T-cells in patients with CMV reactivation after hematopoietic SCT
- Author
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Król, L, primary, Stuchlý, J, additional, Hubáček, P, additional, Keslová, P, additional, Sedláček, P, additional, Starý, J, additional, Hrušák, O, additional, and Kalina, T, additional
- Published
- 2010
- Full Text
- View/download PDF
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