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Identification of a minimal microsatellite marker panel for the fingerprinting of peach and nectarine cultivars
Rojas,Gabriela; Méndez,Marco A; Mu?oz,Carlos; Lemus,Gamalier; Hinrichsen,Patricio;
Electronic Journal of Biotechnology , 2008,
Abstract: the genetic characterization of 117 peach and nectarine cultivars (prunus persica (l.) batsch) using microsatellite (ssr) markers is presented. analyzed genotypes include the complete list of cultivars under intellectual property (ip) protection in chile. one hundred and two out of the 117 cultivars under study could be identified using only 7 ssrs. other 5 cultivars were differentiated using 3 additional markers, but 5 pairs of genotypes were not differentiable. the average expected heterozygosity for the set of markers was 0.55, ranging from 0.28 in bppct-008 to 0.81 in cppct-022, with an f value of 0.37. a neighbor-joining dendrogram showed that, with few exceptions, peaches and nectarines clustered separately. these results are the basis for the development of a fingerprinting protocol for the unequivocal identification of most of the peach and nectarine cultivars officially registered in chile.
Medically Relevant Criteria used in EEG Compression for Improved Post-Compression Seizure Detection  [PDF]
Hoda Daou,Fabrice Labeau
Mathematics , 2014,
Abstract: Biomedical signals aid in the diagnosis of different disorders and abnormalities. When targeting lossy compression of such signals, the medically relevant information that lies within the data should maintain its accuracy and thus its reliability. In fact, signal models that are inspired by the bio-physical properties of the signals at hand allow for a compression that preserves more naturally the clinically significant features of these signals. In this paper, we illustrate this through the example of EEG signals; more specifically, we analyze three specific lossy EEG compression schemes. These schemes are based on signal models that have different degrees of reliance on signal production and physiological characteristics of EEG. The resilience of these schemes is illustrated through the performance of seizure detection post compression.
Human functional genetic studies are biased against the medically most relevant primate-specific genes
Lili Hao, Xiaomeng Ge, Haolei Wan, Songnian Hu, Martin J Lercher, Jun Yu, Wei-Hua Chen
BMC Evolutionary Biology , 2010, DOI: 10.1186/1471-2148-10-316
Abstract: Gene age and expression breadth are strongly correlated, but contribute independently to the variation of functional, structural and evolutionary features, even when we take account of variation in mRNA expression level. Human genes without orthologs in distant species ('young' genes) tend to be tissue-specific in their expression. As computational inference of gene function often relies on the existence of homologs in other species, and experimental characterization is facilitated by broad and high expression, young, tissue-specific human genes are often the least characterized. At the same time, young genes are most likely to be medically relevant.Our results indicate that functional characterization of human genes is biased against young, tissue-specific genes that are mostly medically relevant. The biases should not be taken lightly because they may pose serious obstacles to our understanding of the molecular basis of human diseases. Future studies should thus be designed to specifically explore the properties of primate-specific genes.Proteins and their encoding genes can be characterized by functional attributes, such as which pathways they act in or what molecular functions they have; structural attributes, such as lengths of their coding regions or UTRs and GC contents; and evolutionary attributes, such as substitution rates between species and estimates of selection pressures. With the increasing availability of functional genomic data and systems biology tools, correlations between some of these attributes have been observed. The two factors with the strongest associations with other data types in humans are expression breadth (the number of tissues one protein is expressed in) and phyletic age (defined by the evolutionarily most distant species where homologs can be found) [1,2]. For example, recent studies have shown that expression breadth correlated with promoter architecture, evolutionary rates (Ka and Ks) and gene length [2,3], while human proteins o
The in vitro leishmanicidal activity of hexadecylphosphocholine (miltefosine) against four medically relevant Leishmania species of Brazil
Morais-Teixeira, Eliane de;Damasceno, Quesia Souza;Galuppo, Mariana Kolos;Romanha, Alvaro José;Rabello, Ana;
Memórias do Instituto Oswaldo Cruz , 2011, DOI: 10.1590/S0074-02762011000400015
Abstract: the in vitro leishmanicidal activity of miltefosine? (zentaris gmbh) was assessed against four medically relevant leishmania species of brazil: leishmania (leishmania) amazonensis, leishmania (viannia) braziliensis, leishmania (viannia) guyanensis and leishmania (leishmania) chagasi. the activity of miltefosine against these new world species was compared to its activity against the old world strain, leishmania (leishmania) donovani, which is known to be sensitive to the effects of miltefosine. the ic50 and ic90 results suggested the new world species harboured similar in vitro susceptibilities to miltefosine; however, miltefosine was approximately 20 times more active against the old world l. (l.) donovani than against the new world l. (l.) chagasi species. the selectivity index varied from 17.2-28.9 for the new world leishmania species and up to 420.0 for l. (l.) donovani. the differences in susceptibility to miltefosine suggest that future clinical trials with this drug should include a laboratory pre-evaluation and a dose-defining step.
Fitting birth-death processes to panel data with applications to bacterial DNA fingerprinting  [PDF]
Charles R. Doss,Marc A. Suchard,Ian Holmes,Midori Kato-Maeda,Vladimir N. Minin
Quantitative Biology , 2010, DOI: 10.1214/13-AOAS673
Abstract: Continuous-time linear birth-death-immigration (BDI) processes are frequently used in ecology and epidemiology to model stochastic dynamics of the population of interest. In clinical settings, multiple birth-death processes can describe disease trajectories of individual patients, allowing for estimation of the effects of individual covariates on the birth and death rates of the process. Such estimation is usually accomplished by analyzing patient data collected at unevenly spaced time points, referred to as panel data in the biostatistics literature. Fitting linear BDI processes to panel data is a nontrivial optimization problem because birth and death rates can be functions of many parameters related to the covariates of interest. We propose a novel expectation--maximization (EM) algorithm for fitting linear BDI models with covariates to panel data. We derive a closed-form expression for the joint generating function of some of the BDI process statistics and use this generating function to reduce the E-step of the EM algorithm, as well as calculation of the Fisher information, to one-dimensional integration. This analytical technique yields a computationally efficient and robust optimization algorithm that we implemented in an open-source R package. We apply our method to DNA fingerprinting of Mycobacterium tuberculosis, the causative agent of tuberculosis, to study intrapatient time evolution of IS6110 copy number, a genetic marker frequently used during estimation of epidemiological clusters of Mycobacterium tuberculosis infections. Our analysis reveals previously undocumented differences in IS6110 birth-death rates among three major lineages of Mycobacterium tuberculosis, which has important implications for epidemiologists that use IS6110 for DNA fingerprinting of Mycobacterium tuberculosis.
Two-dimensional low resolution raman spectroscopy applied to fast discrimination of clinically relevant microorganisms: a whole-organism fingerprinting approach
Mello, Cesar;Ciuffi, Katia J.;Nassar, Eduardo;Ribeiro, Diórginis;Poppi, Ronei Jesus;
Journal of the Brazilian Chemical Society , 2006, DOI: 10.1590/S0103-50532006000100011
Abstract: the discrimination of the bacteria that cause gastroenteritis through classical microbiological methods is very efficient in the great majority of the cases. however, the high cost of chemicals and the time spent for such identifications, about four days, could generate serious consequences for the patients. thus, the search for low cost spectroscopic methods which would allow a fast and reagentless discrimination of these microorganisms is extremely relevant. in this work the main microorganisms that cause gastroenteritis: e. coli, s. chroleraesuis, s. flexneri were studied. for each of the microorganisms sixty different dispersions were prepared using physiological solution as solvent and its raman spectra recorded. the 1d spectra obtained were similar, making it very difficult to differentiate the microorganisms. however, applying the 2d correlation method, it was possible to identify the microorganisms evaluated using the synchronous spectrum as "whole-organism fingerprinting" in a reduced time interval (~10 h).
Two-dimensional low resolution raman spectroscopy applied to fast discrimination of clinically relevant microorganisms: a whole-organism fingerprinting approach  [cached]
Mello Cesar,Ciuffi Katia J.,Nassar Eduardo,Ribeiro Diórginis
Journal of the Brazilian Chemical Society , 2006,
Abstract: The discrimination of the bacteria that cause gastroenteritis through classical microbiological methods is very efficient in the great majority of the cases. However, the high cost of chemicals and the time spent for such identifications, about four days, could generate serious consequences for the patients. Thus, the search for low cost spectroscopic methods which would allow a fast and reagentless discrimination of these microorganisms is extremely relevant. In this work the main microorganisms that cause gastroenteritis: E. coli, S. chroleraesuis, S. flexneri were studied. For each of the microorganisms sixty different dispersions were prepared using physiological solution as solvent and its Raman spectra recorded. The 1D spectra obtained were similar, making it very difficult to differentiate the microorganisms. However, applying the 2D correlation method, it was possible to identify the microorganisms evaluated using the synchronous spectrum as "whole-organism fingerprinting" in a reduced time interval (~10 h).
Clustering and Symbolic Analysis of Cardiovascular Signals: Discovery and Visualization of Medically Relevant Patterns in Long-Term Data Using Limited Prior Knowledge  [cached]
Zeeshan Syed,John Guttag,Collin Stultz
EURASIP Journal on Advances in Signal Processing , 2007, DOI: 10.1155/2007/67938
Abstract: This paper describes novel fully automated techniques for analyzing large amounts of cardiovascular data. In contrast to traditional medical expert systems our techniques incorporate no a priori knowledge about disease states. This facilitates the discovery of unexpected events. We start by transforming continuous waveform signals into symbolic strings derived directly from the data. Morphological features are used to partition heart beats into clusters by maximizing the dynamic time-warped sequence-aligned separation of clusters. Each cluster is assigned a symbol, and the original signal is replaced by the corresponding sequence of symbols. The symbolization process allows us to shift from the analysis of raw signals to the analysis of sequences of symbols. This discrete representation reduces the amount of data by several orders of magnitude, making the search space for discovering interesting activity more manageable. We describe techniques that operate in this symbolic domain to discover rhythms, transient patterns, abnormal changes in entropy, and clinically significant relationships among multiple streams of physiological data. We tested our techniques on cardiologist-annotated ECG data from forty-eight patients. Our process for labeling heart beats produced results that were consistent with the cardiologist supplied labels 98.6% of the time, and often provided relevant finer-grained distinctions. Our higher level analysis techniques proved effective at identifying clinically relevant activity not only from symbolized ECG streams, but also from multimodal data obtained by symbolizing ECG and other physiological data streams. Using no prior knowledge, our analysis techniques uncovered examples of ventricular bigeminy and trigeminy, ectopic atrial rhythms with aberrant ventricular conduction, paroxysmal atrial tachyarrhythmias, atrial fibrillation, and pulsus paradoxus.
Clustering and Symbolic Analysis of Cardiovascular Signals: Discovery and Visualization of Medically Relevant Patterns in Long-Term Data Using Limited Prior Knowledge  [cached]
Syed Zeeshan,Guttag John,Stultz Collin
EURASIP Journal on Advances in Signal Processing , 2007,
Abstract: This paper describes novel fully automated techniques for analyzing large amounts of cardiovascular data. In contrast to traditional medical expert systems our techniques incorporate no a priori knowledge about disease states. This facilitates the discovery of unexpected events. We start by transforming continuous waveform signals into symbolic strings derived directly from the data. Morphological features are used to partition heart beats into clusters by maximizing the dynamic time-warped sequence-aligned separation of clusters. Each cluster is assigned a symbol, and the original signal is replaced by the corresponding sequence of symbols. The symbolization process allows us to shift from the analysis of raw signals to the analysis of sequences of symbols. This discrete representation reduces the amount of data by several orders of magnitude, making the search space for discovering interesting activity more manageable. We describe techniques that operate in this symbolic domain to discover rhythms, transient patterns, abnormal changes in entropy, and clinically significant relationships among multiple streams of physiological data. We tested our techniques on cardiologist-annotated ECG data from forty-eight patients. Our process for labeling heart beats produced results that were consistent with the cardiologist supplied labels 98.6 of the time, and often provided relevant finer-grained distinctions. Our higher level analysis techniques proved effective at identifying clinically relevant activity not only from symbolized ECG streams, but also from multimodal data obtained by symbolizing ECG and other physiological data streams. Using no prior knowledge, our analysis techniques uncovered examples of ventricular bigeminy and trigeminy, ectopic atrial rhythms with aberrant ventricular conduction, paroxysmal atrial tachyarrhythmias, atrial fibrillation, and pulsus paradoxus.
Compilation of a panel of informative single nucleotide polymorphisms for bovine identification in the Northern Irish cattle population
Adrian R Allen, Malcolm Taylor, Brian McKeown, April I Curry, John F Lavery, Andy Mitchell, David Hartshorne, Rüdi Fries, Robin A Skuce
BMC Genetics , 2010, DOI: 10.1186/1471-2156-11-5
Abstract: 6 SNPs exhibiting a minor allele frequency of less than 0.2 in more than 3 of the breed panels were excluded. 2 Further SNPs were found to reside in coding areas of the cattle genome and were excluded from the final panel. The remaining 43 SNPs exhibited genotype frequencies which were in Hardy Weinberg Equilibrium. SNPs on the same chromosome were observed to have no significant linkage disequilibrium/allelic association. Minimal probabilities of uniquely identifying individual animals from each of the breeds were obtained and were observed to be superior to those conferred by the industry standard STR assay.The 43 SNPs characterised herein may constitute a starting point for the development of a SNP based DNA identification test for European cattle.The identification and registration of livestock and monitoring of their movements is an essential part of agricultural policy for national governments. Such schemes underpin disease control, grant and subsidy management, food hygiene/safety assurance and facilitate product recalls if necessary.As a result of these benefits, and also in response to major animal health problems such as BSE (Bovine Spongiform Encephalopathy) and Foot and Mouth Disease that impact livestock, producers and consumers, many countries in the developed world have adopted national databases, based on numbered ear tags, to record cattle identity and movements [1,2].Trade globalisation has also strengthened the case for improved animal traceability. Modern consumers confronted with increased choice from multiple sources may also face elevated risks as a result of increased likelihood of chemical/pathogenic contamination in foodstuffs [3,4]. Such crises can compromise the economic well being of agri-food industries as well as affecting the health and confidence of the consumer. The BSE crisis of the 1990s aptly demonstrates both points and proves that the actions of one state can impact negatively on the public health of others [5].In light of the
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