WorldWideScience

Sample records for svm-based gene finding

  1. SVM-based generalized multifactor dimensionality reduction approaches for detecting gene-gene interactions in family studies.

    Science.gov (United States)

    Fang, Yao-Hwei; Chiu, Yen-Feng

    2012-02-01

    Gene-gene interaction plays an important role in the etiology of complex diseases, which may exist without a genetic main effect. Most current statistical approaches, however, focus on assessing an interaction effect in the presence of the gene's main effects. It would be very helpful to develop methods that can detect not only the gene's main effects but also gene-gene interaction effects regardless of the existence of the gene's main effects while adjusting for confounding factors. In addition, when a disease variant is rare or when the sample size is quite limited, the statistical asymptotic properties are not applicable; therefore, approaches based on a reasonable and applicable computational framework would be practical and frequently applied. In this study, we have developed an extended support vector machine (SVM) method and an SVM-based pedigree-based generalized multifactor dimensionality reduction (PGMDR) method to study interactions in the presence or absence of main effects of genes with an adjustment for covariates using limited samples of families. A new test statistic is proposed for classifying the affected and the unaffected in the SVM-based PGMDR approach to improve performance in detecting gene-gene interactions. Simulation studies under various scenarios have been performed to compare the performances of the proposed and the original methods. The proposed and original approaches have been applied to a real data example for illustration and comparison. Both the simulation and real data studies show that the proposed SVM and SVM-based PGMDR methods have great prediction accuracies, consistencies, and power in detecting gene-gene interactions. © 2012 Wiley Periodicals, Inc.

  2. Multi-class clustering of cancer subtypes through SVM based ensemble of pareto-optimal solutions for gene marker identification.

    Science.gov (United States)

    Mukhopadhyay, Anirban; Bandyopadhyay, Sanghamitra; Maulik, Ujjwal

    2010-11-12

    With the advancement of microarray technology, it is now possible to study the expression profiles of thousands of genes across different experimental conditions or tissue samples simultaneously. Microarray cancer datasets, organized as samples versus genes fashion, are being used for classification of tissue samples into benign and malignant or their subtypes. They are also useful for identifying potential gene markers for each cancer subtype, which helps in successful diagnosis of particular cancer types. In this article, we have presented an unsupervised cancer classification technique based on multiobjective genetic clustering of the tissue samples. In this regard, a real-coded encoding of the cluster centers is used and cluster compactness and separation are simultaneously optimized. The resultant set of near-Pareto-optimal solutions contains a number of non-dominated solutions. A novel approach to combine the clustering information possessed by the non-dominated solutions through Support Vector Machine (SVM) classifier has been proposed. Final clustering is obtained by consensus among the clusterings yielded by different kernel functions. The performance of the proposed multiobjective clustering method has been compared with that of several other microarray clustering algorithms for three publicly available benchmark cancer datasets. Moreover, statistical significance tests have been conducted to establish the statistical superiority of the proposed clustering method. Furthermore, relevant gene markers have been identified using the clustering result produced by the proposed clustering method and demonstrated visually. Biological relationships among the gene markers are also studied based on gene ontology. The results obtained are found to be promising and can possibly have important impact in the area of unsupervised cancer classification as well as gene marker identification for multiple cancer subtypes.

  3. SVM-based glioma grading. Optimization by feature reduction analysis

    International Nuclear Information System (INIS)

    Zoellner, Frank G.; Schad, Lothar R.; Emblem, Kyrre E.; Harvard Medical School, Boston, MA; Oslo Univ. Hospital

    2012-01-01

    We investigated the predictive power of feature reduction analysis approaches in support vector machine (SVM)-based classification of glioma grade. In 101 untreated glioma patients, three analytic approaches were evaluated to derive an optimal reduction in features; (i) Pearson's correlation coefficients (PCC), (ii) principal component analysis (PCA) and (iii) independent component analysis (ICA). Tumor grading was performed using a previously reported SVM approach including whole-tumor cerebral blood volume (CBV) histograms and patient age. Best classification accuracy was found using PCA at 85% (sensitivity = 89%, specificity = 84%) when reducing the feature vector from 101 (100-bins rCBV histogram + age) to 3 principal components. In comparison, classification accuracy by PCC was 82% (89%, 77%, 2 dimensions) and 79% by ICA (87%, 75%, 9 dimensions). For improved speed (up to 30%) and simplicity, feature reduction by all three methods provided similar classification accuracy to literature values (∝87%) while reducing the number of features by up to 98%. (orig.)

  4. SVM-based glioma grading. Optimization by feature reduction analysis

    Energy Technology Data Exchange (ETDEWEB)

    Zoellner, Frank G.; Schad, Lothar R. [University Medical Center Mannheim, Heidelberg Univ., Mannheim (Germany). Computer Assisted Clinical Medicine; Emblem, Kyrre E. [Massachusetts General Hospital, Charlestown, A.A. Martinos Center for Biomedical Imaging, Boston MA (United States). Dept. of Radiology; Harvard Medical School, Boston, MA (United States); Oslo Univ. Hospital (Norway). The Intervention Center

    2012-11-01

    We investigated the predictive power of feature reduction analysis approaches in support vector machine (SVM)-based classification of glioma grade. In 101 untreated glioma patients, three analytic approaches were evaluated to derive an optimal reduction in features; (i) Pearson's correlation coefficients (PCC), (ii) principal component analysis (PCA) and (iii) independent component analysis (ICA). Tumor grading was performed using a previously reported SVM approach including whole-tumor cerebral blood volume (CBV) histograms and patient age. Best classification accuracy was found using PCA at 85% (sensitivity = 89%, specificity = 84%) when reducing the feature vector from 101 (100-bins rCBV histogram + age) to 3 principal components. In comparison, classification accuracy by PCC was 82% (89%, 77%, 2 dimensions) and 79% by ICA (87%, 75%, 9 dimensions). For improved speed (up to 30%) and simplicity, feature reduction by all three methods provided similar classification accuracy to literature values ({proportional_to}87%) while reducing the number of features by up to 98%. (orig.)

  5. Gene finding in novel genomes

    Directory of Open Access Journals (Sweden)

    Korf Ian

    2004-05-01

    Full Text Available Abstract Background Computational gene prediction continues to be an important problem, especially for genomes with little experimental data. Results I introduce the SNAP gene finder which has been designed to be easily adaptable to a variety of genomes. In novel genomes without an appropriate gene finder, I demonstrate that employing a foreign gene finder can produce highly inaccurate results, and that the most compatible parameters may not come from the nearest phylogenetic neighbor. I find that foreign gene finders are more usefully employed to bootstrap parameter estimation and that the resulting parameters can be highly accurate. Conclusion Since gene prediction is sensitive to species-specific parameters, every genome needs a dedicated gene finder.

  6. Dictionary-driven prokaryotic gene finding.

    Science.gov (United States)

    Shibuya, Tetsuo; Rigoutsos, Isidore

    2002-06-15

    Gene identification, also known as gene finding or gene recognition, is among the important problems of molecular biology that have been receiving increasing attention with the advent of large scale sequencing projects. Previous strategies for solving this problem can be categorized into essentially two schools of thought: one school employs sequence composition statistics, whereas the other relies on database similarity searches. In this paper, we propose a new gene identification scheme that combines the best characteristics from each of these two schools. In particular, our method determines gene candidates among the ORFs that can be identified in a given DNA strand through the use of the Bio-Dictionary, a database of patterns that covers essentially all of the currently available sample of the natural protein sequence space. Our approach relies entirely on the use of redundant patterns as the agents on which the presence or absence of genes is predicated and does not employ any additional evidence, e.g. ribosome-binding site signals. The Bio-Dictionary Gene Finder (BDGF), the algorithm's implementation, is a single computational engine able to handle the gene identification task across distinct archaeal and bacterial genomes. The engine exhibits performance that is characterized by simultaneous very high values of sensitivity and specificity, and a high percentage of correctly predicted start sites. Using a collection of patterns derived from an old (June 2000) release of the Swiss-Prot/TrEMBL database that contained 451 602 proteins and fragments, we demonstrate our method's generality and capabilities through an extensive analysis of 17 complete archaeal and bacterial genomes. Examples of previously unreported genes are also shown and discussed in detail.

  7. Dictionary-driven prokaryotic gene finding

    Science.gov (United States)

    Shibuya, Tetsuo; Rigoutsos, Isidore

    2002-01-01

    Gene identification, also known as gene finding or gene recognition, is among the important problems of molecular biology that have been receiving increasing attention with the advent of large scale sequencing projects. Previous strategies for solving this problem can be categorized into essentially two schools of thought: one school employs sequence composition statistics, whereas the other relies on database similarity searches. In this paper, we propose a new gene identification scheme that combines the best characteristics from each of these two schools. In particular, our method determines gene candidates among the ORFs that can be identified in a given DNA strand through the use of the Bio-Dictionary, a database of patterns that covers essentially all of the currently available sample of the natural protein sequence space. Our approach relies entirely on the use of redundant patterns as the agents on which the presence or absence of genes is predicated and does not employ any additional evidence, e.g. ribosome-binding site signals. The Bio-Dictionary Gene Finder (BDGF), the algorithm’s implementation, is a single computational engine able to handle the gene identification task across distinct archaeal and bacterial genomes. The engine exhibits performance that is characterized by simultaneous very high values of sensitivity and specificity, and a high percentage of correctly predicted start sites. Using a collection of patterns derived from an old (June 2000) release of the Swiss-Prot/TrEMBL database that contained 451 602 proteins and fragments, we demonstrate our method’s generality and capabilities through an extensive analysis of 17 complete archaeal and bacterial genomes. Examples of previously unreported genes are also shown and discussed in detail. PMID:12060689

  8. Gene recognition by combination of several gene-finding programs.

    Science.gov (United States)

    Murakami, K; Takagi, T

    1998-01-01

    A number of programs have been developed to predict the eukaryotic gene structures in DNA sequences. However, gene finding is still a challenging problem. We have explored the effectiveness when the results of several gene-finding programs were re-analyzed and combined. We studied several methods with four programs (FEXH, GeneParser3, GEN-SCAN and GRAIL2). By HIGHEST-policy combination method or BOUNDARY method, approximate correlation (AC) improved by 3-5% in comparison with the best single gene-finding program. From another viewpoint, OR-based combination of the four programs is the most reliable to know whether a candidate exon overlaps with the real exon or not, although it is less sensitive than GENSCAN for exon-intron boundaries. Our methods can easily be extended to combine other programs. We have developed a server program (Shirokane System) and a client program (GeneScope) to use the methods. GeneScope is available through a WWW site (http://gf.genome.ad.jp/). (katsu,takagi)@ims.u-tokyo.ac.jp

  9. DisArticle: a web server for SVM-based discrimination of articles on traditional medicine.

    Science.gov (United States)

    Kim, Sang-Kyun; Nam, SeJin; Kim, SangHyun

    2017-01-28

    Much research has been done in Northeast Asia to show the efficacy of traditional medicine. While MEDLINE contains many biomedical articles including those on traditional medicine, it does not categorize those articles by specific research area. The aim of this study was to provide a method that searches for articles only on traditional medicine in Northeast Asia, including traditional Chinese medicine, from among the articles in MEDLINE. This research established an SVM-based classifier model to identify articles on traditional medicine. The TAK + HM classifier, trained with the features of title, abstract, keywords, herbal data, and MeSH, has a precision of 0.954 and a recall of 0.902. In particular, the feature of herbal data significantly increased the performance of the classifier. By using the TAK + HM classifier, a total of about 108,000 articles were discriminated as articles on traditional medicine from among all articles in MEDLINE. We also built a web server called DisArticle ( http://informatics.kiom.re.kr/disarticle ), in which users can search for the articles and obtain statistical data. Because much evidence-based research on traditional medicine has been published in recent years, it has become necessary to search for articles on traditional medicine exclusively in literature databases. DisArticle can help users to search for and analyze the research trends in traditional medicine.

  10. CyclinPred: a SVM-based method for predicting cyclin protein sequences.

    Directory of Open Access Journals (Sweden)

    Mridul K Kalita

    Full Text Available Functional annotation of protein sequences with low similarity to well characterized protein sequences is a major challenge of computational biology in the post genomic era. The cyclin protein family is once such important family of proteins which consists of sequences with low sequence similarity making discovery of novel cyclins and establishing orthologous relationships amongst the cyclins, a difficult task. The currently identified cyclin motifs and cyclin associated domains do not represent all of the identified and characterized cyclin sequences. We describe a Support Vector Machine (SVM based classifier, CyclinPred, which can predict cyclin sequences with high efficiency. The SVM classifier was trained with features of selected cyclin and non cyclin protein sequences. The training features of the protein sequences include amino acid composition, dipeptide composition, secondary structure composition and PSI-BLAST generated Position Specific Scoring Matrix (PSSM profiles. Results obtained from Leave-One-Out cross validation or jackknife test, self consistency and holdout tests prove that the SVM classifier trained with features of PSSM profile was more accurate than the classifiers based on either of the other features alone or hybrids of these features. A cyclin prediction server--CyclinPred has been setup based on SVM model trained with PSSM profiles. CyclinPred prediction results prove that the method may be used as a cyclin prediction tool, complementing conventional cyclin prediction methods.

  11. SVM-Based Spectral Analysis for Heart Rate from Multi-Channel WPPG Sensor Signals

    Directory of Open Access Journals (Sweden)

    Jiping Xiong

    2017-03-01

    Full Text Available Although wrist-type photoplethysmographic (hereafter referred to as WPPG sensor signals can measure heart rate quite conveniently, the subjects’ hand movements can cause strong motion artifacts, and then the motion artifacts will heavily contaminate WPPG signals. Hence, it is challenging for us to accurately estimate heart rate from WPPG signals during intense physical activities. The WWPG method has attracted more attention thanks to the popularity of wrist-worn wearable devices. In this paper, a mixed approach called Mix-SVM is proposed, it can use multi-channel WPPG sensor signals and simultaneous acceleration signals to measurement heart rate. Firstly, we combine the principle component analysis and adaptive filter to remove a part of the motion artifacts. Due to the strong relativity between motion artifacts and acceleration signals, the further denoising problem is regarded as a sparse signals reconstruction problem. Then, we use a spectrum subtraction method to eliminate motion artifacts effectively. Finally, the spectral peak corresponding to heart rate is sought by an SVM-based spectral analysis method. Through the public PPG database in the 2015 IEEE Signal Processing Cup, we acquire the experimental results, i.e., the average absolute error was 1.01 beat per minute, and the Pearson correlation was 0.9972. These results also confirm that the proposed Mix-SVM approach has potential for multi-channel WPPG-based heart rate estimation in the presence of intense physical exercise.

  12. PSO-SVM-Based Online Locomotion Mode Identification for Rehabilitation Robotic Exoskeletons.

    Science.gov (United States)

    Long, Yi; Du, Zhi-Jiang; Wang, Wei-Dong; Zhao, Guang-Yu; Xu, Guo-Qiang; He, Long; Mao, Xi-Wang; Dong, Wei

    2016-09-02

    Locomotion mode identification is essential for the control of a robotic rehabilitation exoskeletons. This paper proposes an online support vector machine (SVM) optimized by particle swarm optimization (PSO) to identify different locomotion modes to realize a smooth and automatic locomotion transition. A PSO algorithm is used to obtain the optimal parameters of SVM for a better overall performance. Signals measured by the foot pressure sensors integrated in the insoles of wearable shoes and the MEMS-based attitude and heading reference systems (AHRS) attached on the shoes and shanks of leg segments are fused together as the input information of SVM. Based on the chosen window whose size is 200 ms (with sampling frequency of 40 Hz), a three-layer wavelet packet analysis (WPA) is used for feature extraction, after which, the kernel principal component analysis (kPCA) is utilized to reduce the dimension of the feature set to reduce computation cost of the SVM. Since the signals are from two types of different sensors, the normalization is conducted to scale the input into the interval of [0, 1]. Five-fold cross validation is adapted to train the classifier, which prevents the classifier over-fitting. Based on the SVM model obtained offline in MATLAB, an online SVM algorithm is constructed for locomotion mode identification. Experiments are performed for different locomotion modes and experimental results show the effectiveness of the proposed algorithm with an accuracy of 96.00% ± 2.45%. To improve its accuracy, majority vote algorithm (MVA) is used for post-processing, with which the identification accuracy is better than 98.35% ± 1.65%. The proposed algorithm can be extended and employed in the field of robotic rehabilitation and assistance.

  13. Finding gene-environment interactions for Phobias

    OpenAIRE

    Gregory, Alice M.; Lau, Jennifer Y. F.; Eley, Thalia C.

    2008-01-01

    Phobias are common disorders causing a great deal of suffering. Studies of gene-environment interaction (G × E) have revealed much about the complex processes underlying the development of various psychiatric disorders but have told us little about phobias. This article describes what is already known about genetic and environmental influences upon phobias and suggests how this information can be used to optimise the chances of discovering G × Es for phobias. In addition to the careful concep...

  14. Hybrid PSO–SVM-based method for forecasting of the remaining useful life for aircraft engines and evaluation of its reliability

    International Nuclear Information System (INIS)

    García Nieto, P.J.; García-Gonzalo, E.; Sánchez Lasheras, F.; Cos Juez, F.J. de

    2015-01-01

    The present paper describes a hybrid PSO–SVM-based model for the prediction of the remaining useful life of aircraft engines. The proposed hybrid model combines support vector machines (SVMs), which have been successfully adopted for regression problems, with the particle swarm optimization (PSO) technique. This optimization technique involves kernel parameter setting in the SVM training procedure, which significantly influences the regression accuracy. However, its use in reliability applications has not been yet widely explored. Bearing this in mind, remaining useful life values have been predicted here by using the hybrid PSO–SVM-based model from the remaining measured parameters (input variables) for aircraft engines with success. A coefficient of determination equal to 0.9034 was obtained when this hybrid PSO–RBF–SVM-based model was applied to experimental data. The agreement of this model with experimental data confirmed its good performance. One of the main advantages of this predictive model is that it does not require information about the previous operation states of the engine. Finally, the main conclusions of this study are exposed. - Highlights: • A hybrid PSO–SVM-based model is built as a predictive model of the RUL values for aircraft engines. • The remaining physical–chemical variables in this process are studied in depth. • The obtained regression accuracy of our method is about 95%. • The results show that PSO–SVM-based model can assist in the diagnosis of the RUL values with accuracy

  15. Finding gene-environment interactions for phobias.

    Science.gov (United States)

    Gregory, Alice M; Lau, Jennifer Y F; Eley, Thalia C

    2008-03-01

    Phobias are common disorders causing a great deal of suffering. Studies of gene-environment interaction (G x E) have revealed much about the complex processes underlying the development of various psychiatric disorders but have told us little about phobias. This article describes what is already known about genetic and environmental influences upon phobias and suggests how this information can be used to optimise the chances of discovering G x Es for phobias. In addition to the careful conceptualisation of new studies, it is suggested that data already collected should be re-analysed in light of increased understanding of processes influencing phobias.

  16. In-Vivo Imaging of Cell Migration Using Contrast Enhanced MRI and SVM Based Post-Processing.

    Directory of Open Access Journals (Sweden)

    Christian Weis

    Full Text Available The migration of cells within a living organism can be observed with magnetic resonance imaging (MRI in combination with iron oxide nanoparticles as an intracellular contrast agent. This method, however, suffers from low sensitivity and specificty. Here, we developed a quantitative non-invasive in-vivo cell localization method using contrast enhanced multiparametric MRI and support vector machines (SVM based post-processing. Imaging phantoms consisting of agarose with compartments containing different concentrations of cancer cells labeled with iron oxide nanoparticles were used to train and evaluate the SVM for cell localization. From the magnitude and phase data acquired with a series of T2*-weighted gradient-echo scans at different echo-times, we extracted features that are characteristic for the presence of superparamagnetic nanoparticles, in particular hyper- and hypointensities, relaxation rates, short-range phase perturbations, and perturbation dynamics. High detection quality was achieved by SVM analysis of the multiparametric feature-space. The in-vivo applicability was validated in animal studies. The SVM detected the presence of iron oxide nanoparticles in the imaging phantoms with high specificity and sensitivity with a detection limit of 30 labeled cells per mm3, corresponding to 19 μM of iron oxide. As proof-of-concept, we applied the method to follow the migration of labeled cancer cells injected in rats. The combination of iron oxide labeled cells, multiparametric MRI and a SVM based post processing provides high spatial resolution, specificity, and sensitivity, and is therefore suitable for non-invasive in-vivo cell detection and cell migration studies over prolonged time periods.

  17. Detection of Alzheimer's disease using group lasso SVM-based region selection

    Science.gov (United States)

    Sun, Zhuo; Fan, Yong; Lelieveldt, Boudewijn P. F.; van de Giessen, Martijn

    2015-03-01

    Alzheimer's disease (AD) is one of the most frequent forms of dementia and an increasing challenging public health problem. In the last two decades, structural magnetic resonance imaging (MRI) has shown potential in distinguishing patients with Alzheimer's disease and elderly controls (CN). To obtain AD-specific biomarkers, previous research used either statistical testing to find statistically significant different regions between the two clinical groups, or l1 sparse learning to select isolated features in the image domain. In this paper, we propose a new framework that uses structural MRI to simultaneously distinguish the two clinical groups and find the bio-markers of AD, using a group lasso support vector machine (SVM). The group lasso term (mixed l1- l2 norm) introduces anatomical information from the image domain into the feature domain, such that the resulting set of selected voxels are more meaningful than the l1 sparse SVM. Because of large inter-structure size variation, we introduce a group specific normalization factor to deal with the structure size bias. Experiments have been performed on a well-designed AD vs. CN dataset1 to validate our method. Comparing to the l1 sparse SVM approach, our method achieved better classification performance and a more meaningful biomarker selection. When we vary the training set, the selected regions by our method were more stable than the l1 sparse SVM. Classification experiments showed that our group normalization lead to higher classification accuracy with fewer selected regions than the non-normalized method. Comparing to the state-of-art AD vs. CN classification methods, our approach not only obtains a high accuracy with the same dataset, but more importantly, we simultaneously find the brain anatomies that are closely related to the disease.

  18. A SVM-based method for sentiment analysis in Persian language

    Science.gov (United States)

    Hajmohammadi, Mohammad Sadegh; Ibrahim, Roliana

    2013-03-01

    Persian language is the official language of Iran, Tajikistan and Afghanistan. Local online users often represent their opinions and experiences on the web with written Persian. Although the information in those reviews is valuable to potential consumers and sellers, the huge amount of web reviews make it difficult to give an unbiased evaluation to a product. In this paper, standard machine learning techniques SVM and naive Bayes are incorporated into the domain of online Persian Movie reviews to automatically classify user reviews as positive or negative and performance of these two classifiers is compared with each other in this language. The effects of feature presentations on classification performance are discussed. We find that accuracy is influenced by interaction between the classification models and the feature options. The SVM classifier achieves as well as or better accuracy than naive Bayes in Persian movie. Unigrams are proved better features than bigrams and trigrams in capturing Persian sentiment orientation.

  19. Automatic epileptic seizure detection in EEGs using MF-DFA, SVM based on cloud computing.

    Science.gov (United States)

    Zhang, Zhongnan; Wen, Tingxi; Huang, Wei; Wang, Meihong; Li, Chunfeng

    2017-01-01

    Epilepsy is a chronic disease with transient brain dysfunction that results from the sudden abnormal discharge of neurons in the brain. Since electroencephalogram (EEG) is a harmless and noninvasive detection method, it plays an important role in the detection of neurological diseases. However, the process of analyzing EEG to detect neurological diseases is often difficult because the brain electrical signals are random, non-stationary and nonlinear. In order to overcome such difficulty, this study aims to develop a new computer-aided scheme for automatic epileptic seizure detection in EEGs based on multi-fractal detrended fluctuation analysis (MF-DFA) and support vector machine (SVM). New scheme first extracts features from EEG by MF-DFA during the first stage. Then, the scheme applies a genetic algorithm (GA) to calculate parameters used in SVM and classify the training data according to the selected features using SVM. Finally, the trained SVM classifier is exploited to detect neurological diseases. The algorithm utilizes MLlib from library of SPARK and runs on cloud platform. Applying to a public dataset for experiment, the study results show that the new feature extraction method and scheme can detect signals with less features and the accuracy of the classification reached up to 99%. MF-DFA is a promising approach to extract features for analyzing EEG, because of its simple algorithm procedure and less parameters. The features obtained by MF-DFA can represent samples as well as traditional wavelet transform and Lyapunov exponents. GA can always find useful parameters for SVM with enough execution time. The results illustrate that the classification model can achieve comparable accuracy, which means that it is effective in epileptic seizure detection.

  20. Finding protein-coding genes through human polymorphisms.

    Directory of Open Access Journals (Sweden)

    Edward Wijaya

    Full Text Available Human gene catalogs are fundamental to the study of human biology and medicine. But they are all based on open reading frames (ORFs in a reference genome sequence (with allowance for introns. Individual genomes, however, are polymorphic: their sequences are not identical. There has been much research on how polymorphism affects previously-identified genes, but no research has been done on how it affects gene identification itself. We computationally predict protein-coding genes in a straightforward manner, by finding long ORFs in mRNA sequences aligned to the reference genome. We systematically test the effect of known polymorphisms with this procedure. Polymorphisms can not only disrupt ORFs, they can also create long ORFs that do not exist in the reference sequence. We found 5,737 putative protein-coding genes that do not exist in the reference, whose protein-coding status is supported by homology to known proteins. On average 10% of these genes are located in the genomic regions devoid of annotated genes in 12 other catalogs. Our statistical analysis showed that these ORFs are unlikely to occur by chance.

  1. GeneWaltz--A new method for reducing the false positives of gene finding

    Directory of Open Access Journals (Sweden)

    Misawa Kazuharu

    2010-09-01

    Full Text Available Abstract Background Identifying protein-coding regions in genomic sequences is an essential step in genome analysis. It is well known that the proportion of false positives among genes predicted by current methods is high, especially when the exons are short. These false positives are problematic because they waste time and resources of experimental studies. Methods We developed GeneWaltz, a new filtering method that reduces the risk of false positives in gene finding. GeneWaltz utilizes a codon-to-codon substitution matrix that was constructed by comparing protein-coding regions from orthologous gene pairs between mouse and human genomes. Using this matrix, a scoring scheme was developed; it assigned higher scores to coding regions and lower scores to non-coding regions. The regions with high scores were considered candidate coding regions. One-dimensional Karlin-Altschul statistics was used to test the significance of the coding regions identified by GeneWaltz. Results The proportion of false positives among genes predicted by GENSCAN and Twinscan were high, especially when the exons were short. GeneWaltz significantly reduced the ratio of false positives to all positives predicted by GENSCAN and Twinscan, especially when the exons were short. Conclusions GeneWaltz will be helpful in experimental genomic studies. GeneWaltz binaries and the matrix are available online at http://en.sourceforge.jp/projects/genewaltz/.

  2. Robust LS-SVM-based adaptive constrained control for a class of uncertain nonlinear systems with time-varying predefined performance

    Science.gov (United States)

    Luo, Jianjun; Wei, Caisheng; Dai, Honghua; Yuan, Jianping

    2018-03-01

    This paper focuses on robust adaptive control for a class of uncertain nonlinear systems subject to input saturation and external disturbance with guaranteed predefined tracking performance. To reduce the limitations of classical predefined performance control method in the presence of unknown initial tracking errors, a novel predefined performance function with time-varying design parameters is first proposed. Then, aiming at reducing the complexity of nonlinear approximations, only two least-square-support-vector-machine-based (LS-SVM-based) approximators with two design parameters are required through norm form transformation of the original system. Further, a novel LS-SVM-based adaptive constrained control scheme is developed under the time-vary predefined performance using backstepping technique. Wherein, to avoid the tedious analysis and repeated differentiations of virtual control laws in the backstepping technique, a simple and robust finite-time-convergent differentiator is devised to only extract its first-order derivative at each step in the presence of external disturbance. In this sense, the inherent demerit of backstepping technique-;explosion of terms; brought by the recursive virtual controller design is conquered. Moreover, an auxiliary system is designed to compensate the control saturation. Finally, three groups of numerical simulations are employed to validate the effectiveness of the newly developed differentiator and the proposed adaptive constrained control scheme.

  3. An integrated approach for finding overlooked genes in Shigella.

    Directory of Open Access Journals (Sweden)

    Junping Peng

    Full Text Available BACKGROUND: The completion of numerous genome sequences introduced an era of whole-genome study. However, many genes are missed during genome annotation, including small RNAs (sRNAs and small open reading frames (sORFs. In order to improve genome annotation, we aimed to identify novel sRNAs and sORFs in Shigella, the principal etiologic agents of bacillary dysentery. METHODOLOGY/PRINCIPAL FINDINGS: We identified 64 sRNAs in Shigella, which were experimentally validated in other bacteria based on sequence conservation. We employed computer-based and tiling array-based methods to search for sRNAs, followed by RT-PCR and northern blots, to identify nine sRNAs in Shigella flexneri strain 301 (Sf301 and 256 regions containing possible sRNA genes. We found 29 candidate sORFs using bioinformatic prediction, array hybridization and RT-PCR verification. We experimentally validated 557 (57.9% DOOR operon predictions in the chromosomes of Sf301 and 46 (76.7% in virulence plasmid.We found 40 additional co-expressed gene pairs that were not predicted by DOOR. CONCLUSIONS/SIGNIFICANCE: We provide an updated and comprehensive annotation of the Shigella genome. Our study increased the expected numbers of sORFs and sRNAs, which will impact on future functional genomics and proteomics studies. Our method can be used for large scale reannotation of sRNAs and sORFs in any microbe with a known genome sequence.

  4. Finding gene regulatory network candidates using the gene expression knowledge base.

    Science.gov (United States)

    Venkatesan, Aravind; Tripathi, Sushil; Sanz de Galdeano, Alejandro; Blondé, Ward; Lægreid, Astrid; Mironov, Vladimir; Kuiper, Martin

    2014-12-10

    Network-based approaches for the analysis of large-scale genomics data have become well established. Biological networks provide a knowledge scaffold against which the patterns and dynamics of 'omics' data can be interpreted. The background information required for the construction of such networks is often dispersed across a multitude of knowledge bases in a variety of formats. The seamless integration of this information is one of the main challenges in bioinformatics. The Semantic Web offers powerful technologies for the assembly of integrated knowledge bases that are computationally comprehensible, thereby providing a potentially powerful resource for constructing biological networks and network-based analysis. We have developed the Gene eXpression Knowledge Base (GeXKB), a semantic web technology based resource that contains integrated knowledge about gene expression regulation. To affirm the utility of GeXKB we demonstrate how this resource can be exploited for the identification of candidate regulatory network proteins. We present four use cases that were designed from a biological perspective in order to find candidate members relevant for the gastrin hormone signaling network model. We show how a combination of specific query definitions and additional selection criteria derived from gene expression data and prior knowledge concerning candidate proteins can be used to retrieve a set of proteins that constitute valid candidates for regulatory network extensions. Semantic web technologies provide the means for processing and integrating various heterogeneous information sources. The GeXKB offers biologists such an integrated knowledge resource, allowing them to address complex biological questions pertaining to gene expression. This work illustrates how GeXKB can be used in combination with gene expression results and literature information to identify new potential candidates that may be considered for extending a gene regulatory network.

  5. Finding Clocks in Genes: A Bayesian Approach to Estimate Periodicity

    Directory of Open Access Journals (Sweden)

    Yan Ren

    2016-01-01

    Full Text Available Identification of rhythmic gene expression from metabolic cycles to circadian rhythms is crucial for understanding the gene regulatory networks and functions of these biological processes. Recently, two algorithms, JTK_CYCLE and ARSER, have been developed to estimate periodicity of rhythmic gene expression. JTK_CYCLE performs well for long or less noisy time series, while ARSER performs well for detecting a single rhythmic category. However, observing gene expression at high temporal resolution is not always feasible, and many scientists are interested in exploring both ultradian and circadian rhythmic categories simultaneously. In this paper, a new algorithm, named autoregressive Bayesian spectral regression (ABSR, is proposed. It estimates the period of time-course experimental data and classifies gene expression profiles into multiple rhythmic categories simultaneously. Through the simulation studies, it is shown that ABSR substantially improves the accuracy of periodicity estimation and clustering of rhythmic categories as compared to JTK_CYCLE and ARSER for the data with low temporal resolution. Moreover, ABSR is insensitive to rhythmic patterns. This new scheme is applied to existing time-course mouse liver data to estimate period of rhythms and classify the genes into ultradian, circadian, and arrhythmic categories. It is observed that 49.2% of the circadian profiles detected by JTK_CYCLE with 1-hour resolution are also detected by ABSR with only 4-hour resolution.

  6. PlantRNA_Sniffer: A SVM-Based Workflow to Predict Long Intergenic Non-Coding RNAs in Plants

    Directory of Open Access Journals (Sweden)

    Lucas Maciel Vieira

    2017-03-01

    Full Text Available Non-coding RNAs (ncRNAs constitute an important set of transcripts produced in the cells of organisms. Among them, there is a large amount of a particular class of long ncRNAs that are difficult to predict, the so-called long intergenic ncRNAs (lincRNAs, which might play essential roles in gene regulation and other cellular processes. Despite the importance of these lincRNAs, there is still a lack of biological knowledge and, currently, the few computational methods considered are so specific that they cannot be successfully applied to other species different from those that they have been originally designed to. Prediction of lncRNAs have been performed with machine learning techniques. Particularly, for lincRNA prediction, supervised learning methods have been explored in recent literature. As far as we know, there are no methods nor workflows specially designed to predict lincRNAs in plants. In this context, this work proposes a workflow to predict lincRNAs on plants, considering a workflow that includes known bioinformatics tools together with machine learning techniques, here a support vector machine (SVM. We discuss two case studies that allowed to identify novel lincRNAs, in sugarcane (Saccharum spp. and in maize (Zea mays. From the results, we also could identify differentially-expressed lincRNAs in sugarcane and maize plants submitted to pathogenic and beneficial microorganisms.

  7. Gene finding with a hidden Markov model of genome structure and evolution

    DEFF Research Database (Denmark)

    Pedersen, Jakob Skou; Hein, Jotun

    2003-01-01

    the model are linear in alignment length and genome number. The model is applied to the problem of gene finding. The benefit of modelling sequence evolution is demonstrated both in a range of simulations and on a set of orthologous human/mouse gene pairs. AVAILABILITY: Free availability over the Internet...

  8. Gene finding with a hidden Markov model of genome structure and evolution

    DEFF Research Database (Denmark)

    Pedersen, Jakob Skou; Hein, Jotun

    2003-01-01

    the model are linear in alignment length and genome number. The model is applied to the problem of gene finding. The benefit of modelling sequence evolution is demonstrated both in a range of simulations and on a set of orthologous human/mouse gene pairs. AVAILABILITY: Free availability over the Internet...... annotation. The modelling of evolution by the existing comparative gene finders leaves room for improvement. Results: A probabilistic model of both genome structure and evolution is designed. This type of model is called an Evolutionary Hidden Markov Model (EHMM), being composed of an HMM and a set of region...

  9. An SVM-Based Classifier for Estimating the State of Various Rotating Components in Agro-Industrial Machinery with a Vibration Signal Acquired from a Single Point on the Machine Chassis

    Directory of Open Access Journals (Sweden)

    Ruben Ruiz-Gonzalez

    2014-11-01

    Full Text Available The goal of this article is to assess the feasibility of estimating the state of various rotating components in agro-industrial machinery by employing just one vibration signal acquired from a single point on the machine chassis. To do so, a Support Vector Machine (SVM-based system is employed. Experimental tests evaluated this system by acquiring vibration data from a single point of an agricultural harvester, while varying several of its working conditions. The whole process included two major steps. Initially, the vibration data were preprocessed through twelve feature extraction algorithms, after which the Exhaustive Search method selected the most suitable features. Secondly, the SVM-based system accuracy was evaluated by using Leave-One-Out cross-validation, with the selected features as the input data. The results of this study provide evidence that (i accurate estimation of the status of various rotating components in agro-industrial machinery is possible by processing the vibration signal acquired from a single point on the machine structure; (ii the vibration signal can be acquired with a uniaxial accelerometer, the orientation of which does not significantly affect the classification accuracy; and, (iii when using an SVM classifier, an 85% mean cross-validation accuracy can be reached, which only requires a maximum of seven features as its input, and no significant improvements are noted between the use of either nonlinear or linear kernels.

  10. Similarity-based gene detection: using COGs to find evolutionarily-conserved ORFs

    Directory of Open Access Journals (Sweden)

    Hutchison Clyde A

    2006-01-01

    Full Text Available Abstract Background Experimental verification of gene products has not kept pace with the rapid growth of microbial sequence information. However, existing annotations of gene locations contain sufficient information to screen for probable errors. Furthermore, comparisons among genomes become more informative as more genomes are examined. We studied all open reading frames (ORFs of at least 30 codons from the genomes of 27 sequenced bacterial strains. We grouped the potential peptide sequences encoded from the ORFs by forming Clusters of Orthologous Groups (COGs. We used this grouping in order to find homologous relationships that would not be distinguishable from noise when using simple BLAST searches. Although COG analysis was initially developed to group annotated genes, we applied it to the task of grouping anonymous DNA sequences that may encode proteins. Results "Mixed COGs" of ORFs (clusters in which some sequences correspond to annotated genes and some do not are attractive targets when seeking errors of gene predicion. Examination of mixed COGs reveals some situations in which genes appear to have been missed in current annotations and a smaller number of regions that appear to have been annotated as gene loci erroneously. This technique can also be used to detect potential pseudogenes or sequencing errors. Our method uses an adjustable parameter for degree of conservation among the studied genomes (stringency. We detail results for one level of stringency at which we found 83 potential genes which had not previously been identified, 60 potential pseudogenes, and 7 sequences with existing gene annotations that are probably incorrect. Conclusion Systematic study of sequence conservation offers a way to improve existing annotations by identifying potentially homologous regions where the annotation of the presence or absence of a gene is inconsistent among genomes.

  11. Principles and limitations of computational microRNA gene and target finding

    DEFF Research Database (Denmark)

    Lindow, Morten; Gorodkin, Jan

    2007-01-01

    of sequence data being generated, the need for analysis by computational approaches is obvious. Here, we review the general principles used in computational gene and target finding, and discuss the strengths and weaknesses of the methods. Several methods rely on detection of evolutionary conserved candidates...

  12. A unified framework for finding differentially expressed genes from microarray experiments

    Directory of Open Access Journals (Sweden)

    Yeasin Mohammed

    2007-09-01

    Full Text Available Abstract Background This paper presents a unified framework for finding differentially expressed genes (DEGs from the microarray data. The proposed framework has three interrelated modules: (i gene ranking, ii significance analysis of genes and (iii validation. The first module uses two gene selection algorithms, namely, a two-way clustering and b combined adaptive ranking to rank the genes. The second module converts the gene ranks into p-values using an R-test and fuses the two sets of p-values using the Fisher's omnibus criterion. The DEGs are selected using the FDR analysis. The third module performs three fold validations of the obtained DEGs. The robustness of the proposed unified framework in gene selection is first illustrated using false discovery rate analysis. In addition, the clustering-based validation of the DEGs is performed by employing an adaptive subspace-based clustering algorithm on the training and the test datasets. Finally, a projection-based visualization is performed to validate the DEGs obtained using the unified framework. Results The performance of the unified framework is compared with well-known ranking algorithms such as t-statistics, Significance Analysis of Microarrays (SAM, Adaptive Ranking, Combined Adaptive Ranking and Two-way Clustering. The performance curves obtained using 50 simulated microarray datasets each following two different distributions indicate the superiority of the unified framework over the other reported algorithms. Further analyses on 3 real cancer datasets and 3 Parkinson's datasets show the similar improvement in performance. First, a 3 fold validation process is provided for the two-sample cancer datasets. In addition, the analysis on 3 sets of Parkinson's data is performed to demonstrate the scalability of the proposed method to multi-sample microarray datasets. Conclusion This paper presents a unified framework for the robust selection of genes from the two-sample as well as multi

  13. A polynomial time biclustering algorithm for finding approximate expression patterns in gene expression time series

    Directory of Open Access Journals (Sweden)

    Madeira Sara C

    2009-06-01

    Full Text Available Abstract Background The ability to monitor the change in expression patterns over time, and to observe the emergence of coherent temporal responses using gene expression time series, obtained from microarray experiments, is critical to advance our understanding of complex biological processes. In this context, biclustering algorithms have been recognized as an important tool for the discovery of local expression patterns, which are crucial to unravel potential regulatory mechanisms. Although most formulations of the biclustering problem are NP-hard, when working with time series expression data the interesting biclusters can be restricted to those with contiguous columns. This restriction leads to a tractable problem and enables the design of efficient biclustering algorithms able to identify all maximal contiguous column coherent biclusters. Methods In this work, we propose e-CCC-Biclustering, a biclustering algorithm that finds and reports all maximal contiguous column coherent biclusters with approximate expression patterns in time polynomial in the size of the time series gene expression matrix. This polynomial time complexity is achieved by manipulating a discretized version of the original matrix using efficient string processing techniques. We also propose extensions to deal with missing values, discover anticorrelated and scaled expression patterns, and different ways to compute the errors allowed in the expression patterns. We propose a scoring criterion combining the statistical significance of expression patterns with a similarity measure between overlapping biclusters. Results We present results in real data showing the effectiveness of e-CCC-Biclustering and its relevance in the discovery of regulatory modules describing the transcriptomic expression patterns occurring in Saccharomyces cerevisiae in response to heat stress. In particular, the results show the advantage of considering approximate patterns when compared to state of

  14. HIGEDA: a hierarchical gene-set genetics based algorithm for finding subtle motifs in biological sequences.

    Science.gov (United States)

    Le, Thanh; Altman, Tom; Gardiner, Katheleen

    2010-02-01

    Identification of motifs in biological sequences is a challenging problem because such motifs are often short, degenerate, and may contain gaps. Most algorithms that have been developed for motif-finding use the expectation-maximization (EM) algorithm iteratively. Although EM algorithms can converge quickly, they depend strongly on initialization parameters and can converge to local sub-optimal solutions. In addition, they cannot generate gapped motifs. The effectiveness of EM algorithms in motif finding can be improved by incorporating methods that choose different sets of initial parameters to enable escape from local optima, and that allow gapped alignments within motif models. We have developed HIGEDA, an algorithm that uses the hierarchical gene-set genetic algorithm (HGA) with EM to initiate and search for the best parameters for the motif model. In addition, HIGEDA can identify gapped motifs using a position weight matrix and dynamic programming to generate an optimal gapped alignment of the motif model with sequences from the dataset. We show that HIGEDA outperforms MEME and other motif-finding algorithms on both DNA and protein sequences. Source code and test datasets are available for download at http://ouray.cudenver.edu/~tnle/, implemented in C++ and supported on Linux and MS Windows.

  15. Cross-pollination of research findings, although uncommon, may accelerate discovery of human disease genes

    Directory of Open Access Journals (Sweden)

    Duda Marlena

    2012-11-01

    Full Text Available Abstract Background Technological leaps in genome sequencing have resulted in a surge in discovery of human disease genes. These discoveries have led to increased clarity on the molecular pathology of disease and have also demonstrated considerable overlap in the genetic roots of human diseases. In light of this large genetic overlap, we tested whether cross-disease research approaches lead to faster, more impactful discoveries. Methods We leveraged several gene-disease association databases to calculate a Mutual Citation Score (MCS for 10,853 pairs of genetically related diseases to measure the frequency of cross-citation between research fields. To assess the importance of cooperative research, we computed an Individual Disease Cooperation Score (ICS and the average publication rate for each disease. Results For all disease pairs with one gene in common, we found that the degree of genetic overlap was a poor predictor of cooperation (r2=0.3198 and that the vast majority of disease pairs (89.56% never cited previous discoveries of the same gene in a different disease, irrespective of the level of genetic similarity between the diseases. A fraction (0.25% of the pairs demonstrated cross-citation in greater than 5% of their published genetic discoveries and 0.037% cross-referenced discoveries more than 10% of the time. We found strong positive correlations between ICS and publication rate (r2=0.7931, and an even stronger correlation between the publication rate and the number of cross-referenced diseases (r2=0.8585. These results suggested that cross-disease research may have the potential to yield novel discoveries at a faster pace than singular disease research. Conclusions Our findings suggest that the frequency of cross-disease study is low despite the high level of genetic similarity among many human diseases, and that collaborative methods may accelerate and increase the impact of new genetic discoveries. Until we have a better

  16. Finding candidate genes under positive selection in Non-model species: examples of genes involved in host specialization in pathogens.

    Science.gov (United States)

    Aguileta, G; Lengelle, J; Marthey, S; Chiapello, H; Rodolphe, F; Gendrault, A; Yockteng, R; Vercken, E; Devier, B; Fontaine, M C; Wincker, P; Dossat, C; Cruaud, C; Couloux, A; Giraud, T

    2010-01-01

    Numerous genes in diverse organisms have been shown to be under positive selection, especially genes involved in reproduction, adaptation to contrasting environments, hybrid inviability, and host-pathogen interactions. Looking for genes under positive selection in pathogens has been a priority in efforts to investigate coevolution dynamics and to develop vaccines or drugs. To elucidate the functions involved in host specialization, here we aimed at identifying candidate sequences that could have evolved under positive selection among closely related pathogens specialized on different hosts. For this goal, we sequenced c. 17,000-32,000 ESTs from each of four Microbotryum species, which are fungal pathogens responsible for anther smut disease on host plants in the Caryophyllaceae. Forty-two of the 372 predicted orthologous genes showed significant signal of positive selection, which represents a good number of candidate genes for further investigation. Sequencing 16 of these genes in 9 additional Microbotryum species confirmed that they have indeed been rapidly evolving in the pathogen species specialized on different hosts. The genes showing significant signals of positive selection were putatively involved in nutrient uptake from the host, secondary metabolite synthesis and secretion, respiration under stressful conditions and stress response, hyphal growth and differentiation, and regulation of expression by other genes. Many of these genes had transmembrane domains and may therefore also be involved in pathogen recognition by the host. Our approach thus revealed fruitful and should be feasible for many non-model organisms for which candidate genes for diversifying selection are needed.

  17. Evaluating bacterial gene-finding HMM structures as probabilistic logic programs

    DEFF Research Database (Denmark)

    Mørk, Søren; Holmes, Ian

    2012-01-01

    , a probabilistic dialect of Prolog. Results: We evaluate Hidden Markov Model structures for bacterial protein-coding gene potential, including a simple null model structure, three structures based on existing bacterial gene finders and two novel model structures. We test standard versions as well as ADPH length...

  18. Finding cancer genes in copy number data and insertional mutagenesis data

    NARCIS (Netherlands)

    Klijn, C.N.

    2011-01-01

    Cancer is a genetic disease. Step-wise alteration of genes that have a normal function in the cell can lead to the transformation of a healthy cell into a malignant cancer cell. Cancer genes provide several traits to the cell that allow it to become malignant. These traits have been researched for

  19. Finding the missing honey bee genes: Lessons learned from a genome upgrade

    KAUST Repository

    Elsik, Christine G

    2014-01-30

    Background: The first generation of genome sequence assemblies and annotations have had a significant impact upon our understanding of the biology of the sequenced species, the phylogenetic relationships among species, the study of populations within and across species, and have informed the biology of humans. As only a few Metazoan genomes are approaching finished quality (human, mouse, fly and worm), there is room for improvement of most genome assemblies. The honey bee (Apis mellifera) genome, published in 2006, was noted for its bimodal GC content distribution that affected the quality of the assembly in some regions and for fewer genes in the initial gene set (OGSv1.0) compared to what would be expected based on other sequenced insect genomes. Results: Here, we report an improved honey bee genome assembly (Amel_4.5) with a new gene annotation set (OGSv3.2), and show that the honey bee genome contains a number of genes similar to that of other insect genomes, contrary to what was suggested in OGSv1.0. The new genome assembly is more contiguous and complete and the new gene set includes ~5000 more protein-coding genes, 50% more than previously reported. About 1/6 of the additional genes were due to improvements to the assembly, and the remaining were inferred based on new RNAseq and protein data. Conclusions: Lessons learned from this genome upgrade have important implications for future genome sequencing projects. Furthermore, the improvements significantly enhance genomic resources for the honey bee, a key model for social behavior and essential to global ecology through pollination. 2014 Elsik et al.; licensee BioMed Central Ltd.

  20. An efficient approach to finding Siraitia grosvenorii triterpene biosynthetic genes by RNA-seq and digital gene expression analysis.

    Science.gov (United States)

    Tang, Qi; Ma, Xiaojun; Mo, Changming; Wilson, Iain W; Song, Cai; Zhao, Huan; Yang, Yanfang; Fu, Wei; Qiu, Deyou

    2011-07-05

    Siraitia grosvenorii (Luohanguo) is an herbaceous perennial plant native to southern China and most prevalent in Guilin city. Its fruit contains a sweet, fleshy, edible pulp that is widely used in traditional Chinese medicine. The major bioactive constituents in the fruit extract are the cucurbitane-type triterpene saponins known as mogrosides. Among them, mogroside V is nearly 300 times sweeter than sucrose. However, little is known about mogrosides biosynthesis in S. grosvenorii, especially the late steps of the pathway. In this study, a cDNA library generated from of equal amount of RNA taken from S. grosvenorii fruit at 50 days after flowering (DAF) and 70 DAF were sequenced using Illumina/Solexa platform. More than 48,755,516 high-quality reads from a cDNA library were generated that was assembled into 43,891 unigenes. De novo assembly and gap-filling generated 43,891 unigenes with an average sequence length of 668 base pairs. A total of 26,308 (59.9%) unique sequences were annotated and 11,476 of the unique sequences were assigned to specific metabolic pathways by the Kyoto Encyclopedia of Genes and Genomes. cDNA sequences for all of the known enzymes involved in mogrosides backbone synthesis were identified from our library. Additionally, a total of eighty-five cytochrome P450 (CYP450) and ninety UDP-glucosyltransferase (UDPG) unigenes were identified, some of which appear to encode enzymes responsible for the conversion of the mogroside backbone into the various mogrosides. Digital gene expression profile (DGE) analysis using Solexa sequencing was performed on three important stages of fruit development, and based on their expression pattern, seven CYP450s and five UDPGs were selected as the candidates most likely to be involved in mogrosides biosynthesis. A combination of RNA-seq and DGE analysis based on the next generation sequencing technology was shown to be a powerful method for identifying candidate genes encoding enzymes responsible for the

  1. Finding high yield genes in weedy red rice to improve new cultivars

    Science.gov (United States)

    Red rice (Oryza rufipogon) is a weedy, wild relative of cultivated rice (Oryza sativa) that is considered a major pest in rice production fields. However, researchers have found that it can be a valuable source of disease and insect resistance genes. Researchers with USDA ARS and Cornell University ...

  2. Gene-Environment Interplay in Internalizing Disorders: Consistent Findings across Six Environmental Risk Factors

    Science.gov (United States)

    Hicks, Brian M.; Dirago, Ana C.; Iacono, William G.; McGue, Matt

    2009-01-01

    Background: Behavior genetic methods can help to elucidate gene-environment (G-E) interplay in the development of internalizing (INT) disorders (i.e., major depression and anxiety disorders). To date, however, no study has conducted a comprehensive analysis examining multiple environmental risk factors with the purpose of delineating general…

  3. Wnt target genes and where to find them [version 1; referees: 3 approved

    Directory of Open Access Journals (Sweden)

    Aravinda-Bharathi Ramakrishnan

    2017-05-01

    Full Text Available Wnt/β-catenin signaling is highly conserved throughout metazoans, is required for numerous essential events in development, and serves as a stem cell niche signal in many contexts. Misregulation of the pathway is linked to several human pathologies, most notably cancer. Wnt stimulation results in stabilization and nuclear import of β-catenin, which then acts as a transcriptional co-activator. Transcription factors of the T-cell family (TCF are the best-characterized nuclear binding partners of β-catenin and mediators of Wnt gene regulation. This review provides an update on what is known about the transcriptional activation of Wnt target genes, highlighting recent work that modifies the conventional model. Wnt/β-catenin signaling regulates genes in a highly context-dependent manner, and the role of other signaling pathways and TCF co-factors in this process will be discussed. Understanding Wnt gene regulation has served to elucidate many biological roles of the pathway, and we will use examples from stem cell biology, metabolism, and evolution to illustrate some of the rich Wnt biology that has been uncovered.

  4. Molecular basis of albinism in India: evaluation of seven potential candidate genes and some new findings.

    Science.gov (United States)

    Mondal, M; Sengupta, M; Samanta, S; Sil, A; Ray, K

    2012-12-15

    Albinism represents a group of genetic disorders with a broad spectrum of hypopigmentary phenotypes dependent on the genetic background of the patients. Oculocutaneous albinism (OCA) patients have little or no pigment in their eyes, skin and hair, whereas ocular albinism (OA) primarily presents the ocular symptoms, and the skin and hair color may vary from near normal to very fair. Mutations in genes directly or indirectly regulating melanin production are responsible for different forms of albinism with overlapping clinical features. In this study, 27 albinistic individuals from 24 families were screened for causal variants by a PCR-sequencing based approach. TYR, OCA2, TYRP1, SLC45A2, SLC24A5, TYRP2 and SILV were selected as candidate genes. We identified 5 TYR and 3 OCA2 mutations, majority in homozygous state, in 8 unrelated patients including a case of autosomal recessive ocular albinism (AROA). A homozygous 4-nucleotide novel insertion in SLC24A5 was detected in a person showing with extreme cutaneous hypopigmentation. A potential causal variant was identified in the TYRP2 gene in a single patient. Haplotype analyses in the patients carrying homozygous mutations in the classical OCA genes suggested founder effect. This is the first report of an Indian AROA patient harboring a mutation in OCA2. Our results also reveal for the first time that mutations in SLC24A5 could contribute to extreme hypopigmentation in humans. Copyright © 2012 Elsevier B.V. All rights reserved.

  5. REVIEW: Genome-wide findings in schizophrenia and the role of gene-environment interplay.

    Science.gov (United States)

    Van Winkel, Ruud; Esquivel, Gabriel; Kenis, Gunter; Wichers, Marieke; Collip, Dina; Peerbooms, Odette; Rutten, Bart; Myin-Germeys, Inez; Van Os, Jim

    2010-10-01

    The recent advent of genome-wide mass-marker technology has resulted in renewed optimism to unravel the genetic architecture of psychotic disorders. Genome-wide association studies have identified a number of common polymorphisms robustly associated with schizophrenia, in ZNF804A, transcription factor 4, major histocompatibility complex, and neurogranin. In addition, copy number variants (CNVs) in 1q21.1, 2p16.3, 15q11.2, 15q13.3, 16p11.2, and 22q11.2 were convincingly implicated in schizophrenia risk. Furthermore, these studies have suggested considerable genetic overlap with bipolar disorder (particularly for common polymorphisms) and neurodevelopmental disorders such as autism (particularly for CNVs). The influence of these risk variants on relevant intermediate phenotypes needs further study. In addition, there is a need for etiological models of psychosis integrating genetic risk with environmental factors associated with the disorder, focusing specifically on environmental impact on gene expression (epigenetics) and convergence of genes and environment on common biological pathways bringing about larger effects than those of genes or environment in isolation (gene-environment interaction). Collaborative efforts that bring together expertise in statistics, genetics, epidemiology, experimental psychiatry, brain imaging, and clinical psychiatry will be required to succeed in this challenging task. © 2010 Blackwell Publishing Ltd.

  6. Finding genes on the X chromosome by which homo may have become sapiens

    Energy Technology Data Exchange (ETDEWEB)

    Turner, G. [Univ. of Newcastle, Waratah, New South Wales (Australia)

    1996-06-01

    The map of the X chromosome is now littered, from one telomere to the other, with genes for mental handicap, alone or in combination with other features. In this issue of the journal, report such an entity from the Scottish Highlands, which they give the catchy title of {open_quotes}PPM-X syndrome,{close_quotes} denoting the association of pyramidal tract signs, psychosis, and macroorchidism with mental handicap (XLMR). They have localized this to Xq28 and discuss other genes in the same area, which include L1CAM (associated with MASA [mental retardation, aphasia, shuffling gait, and adducted thumbs] and X-linked hydrocephalus) and two genes for nonspecific XLMR-MRX3 and MRX25. It is also the localization of the gene for G6PD deficiency, which, in earlier studies, had demonstrated linkage to bipolar affective disorders, although this has been questioned in more recent studies. There may well be other families with this pattern of abnormalities who have remained undescribed because depression is so often not diagnosed in those with moderate mental handicap. The occurrence, in this family, of mental handicap with a bipolar disorder may be the chance association of two common disorders, or it may a significant association; at this stage, one cannot judge. 8 refs.

  7. A quest to find good primers for gene expression analysis of Candida albicans from clinical samples.

    Science.gov (United States)

    Alonso, Gabriela C; Pavarina, Ana C; Sousa, Tábata V; Klein, Marlise I

    2018-04-01

    Biofilm production contributes to several human diseases, including oral candidiasis. Among the Candida species, Candida albicans is the most prevalent. The expression of virulence genes is implicated in the pathogenic potential of Candida biofilms. However, the evaluation of microbial gene expression from in vivo biofilm samples is not trivial, specifically, assessment via quantitative PCR (qPCR) can be a challenge because of several species present in clinical samples. Hence, the necessity of primers specificity. The aim of this study was to evaluate through in silico and in vitro analyses the specificity of published primers and newly designed primers for C. albicans virulence genes: ALS1, CAP1, CAT1, EFG1, HWP1, LIP3, PLB1, SAP1, SAP4, SOD1, SOD5 and ACT1 (normalizing gene). In silico analysis was performed through a PubMed search of articles with primer sequences that evaluated gene expression of C. albicans. Then, the sequence similarity of twenty-eight primers was checked through BLASTn and ClustalW2. The analysis of secondary structures was performed using mfold. When the primers did not present satisfactory characteristics (absence of secondary structures, not discrepant Tm of forward and reverse sequences and specificity) following in vitro analysis (i.e., end point PCR), new primers were designed using Beacon Designer™ and sequences obtained from the "Candida Genome Database". The selected primers were tested in vitro by end point PCR using a panel of genomic DNA from five different Candida species (C. albicans, Candida glabrata, Candida dubliniensis, Candida krusei, and Candida tropicalis). The resulting PCR products were visualized on agarose gel. qPCR reactions were performed to determine primers' optimal concentration and PCR efficiency. End point PCR demonstrated that published primers for the SAP1 and HWP1 were specific for C. albicans and the one for SOD1 reacted with C. albicans and C. dubliniensis. The sequence of primers designed for ACT1

  8. Genetic testing including targeted gene panel in a diverse clinical population of children with autism spectrum disorder: Findings and implications.

    Science.gov (United States)

    Kalsner, Louisa; Twachtman-Bassett, Jennifer; Tokarski, Kristin; Stanley, Christine; Dumont-Mathieu, Thyde; Cotney, Justin; Chamberlain, Stormy

    2017-12-21

    Genetic testing of children with autism spectrum disorder (ASD) is now standard in the clinical setting, with American College of Medical Genetics and Genomics (ACMGG) guidelines recommending microarray for all children, fragile X testing for boys and additional gene sequencing, including PTEN and MECP2, in appropriate patients. Increasingly, testing utilizing high throughput sequencing, including gene panels and whole exome sequencing, are offered as well. We performed genetic testing including microarray, fragile X testing and targeted gene panel, consistently sequencing 161 genes associated with ASD risk, in a clinical population of 100 well characterized children with ASD. Frequency of rare variants identified in individual genes was compared with that reported in the Exome Aggregation Consortium (ExAC) database. We did not diagnose any conditions with complete penetrance for ASD; however, copy number variants believed to contribute to ASD risk were identified in 12%. Eleven children were found to have likely pathogenic variants on gene panel, yet, after careful analysis, none was considered likely causative of disease. KIRREL3 variants were identified in 6.7% of children compared to 2% in ExAC, suggesting a potential role for KIRREL3 variants in ASD risk. Children with KIRREL3 variants more often had minor facial dysmorphism and intellectual disability. We also observed an increase in rare variants in TSC2. However, analysis of variant data from the Simons Simplex Collection indicated that rare variants in TSC2 occur more commonly in specific racial/ethnic groups, which are more prevalent in our population than in the ExAC database. The yield of genetic testing including microarray, fragile X (boys) and targeted gene panel was 12%. Gene panel did not increase diagnostic yield; however, we found an increase in rare variants in KIRREL3. Our findings reinforce the need for racial/ethnic diversity in large-scale genomic databases used to identify variants that

  9. Finding Combination of Features from Promoter Regions for Ovarian Cancer-related Gene Group Classification

    KAUST Repository

    Olayan, Rawan S.

    2012-12-01

    In classification problems, it is always important to use the suitable combination of features that will be employed by classifiers. Generating the right combination of features usually results in good classifiers. In the situation when the problem is not well understood, data items are usually described by many features in the hope that some of these may be the relevant or most relevant ones. In this study, we focus on one such problem related to genes implicated in ovarian cancer (OC). We try to recognize two important OC-related gene groups: oncogenes, which support the development and progression of OC, and oncosuppressors, which oppose such tendencies. For this, we use the properties of promoters of these genes. We identified potential “regulatory features” that characterize OC-related oncogenes and oncosuppressors promoters. In our study, we used 211 oncogenes and 39 oncosuppressors. For these, we identified 538 characteristic sequence motifs from their promoters. Promoters are annotated by these motifs and derived feature vectors used to develop classification models. We made a comparison of a number of classification models in their ability to distinguish oncogenes from oncosuppressors. Based on 10-fold cross-validation, the resultant model was able to separate the two classes with sensitivity of 96% and specificity of 100% with the complete set of features. Moreover, we developed another recognition model where we attempted to distinguish oncogenes and oncosuppressors as one group from other OC-related genes. That model achieved accuracy of 82%. We believe that the results of this study will help in discovering other OC-related oncogenes and oncosuppressors not identified as yet.

  10. Bioinformatic methods for finding differentially expressed genes in cDNA libraries, applied to the identification of tumour vascular targets.

    Science.gov (United States)

    Herbert, John M J; Stekel, Dov J; Mura, Manuela; Sychev, Michail; Bicknell, Roy

    2011-01-01

    The aim of this method is to guide a bench scientist to maximise cDNA library analyses to predict biologically relevant genes to pursue in the laboratory. Many groups have successfully utilised cDNA libraries to discover novel and/or differentially expressed genes in pathologies of interest. This is despite the high cost of cDNA library production using the Sanger method of sequencing, which produces modest numbers of expressed sequences compared to the total transcriptome. Both public and propriety cDNA libraries can be utilised in this way, and combining biologically relevant data can reveal biologically interesting genes. Pivotal to the quality of target identification are the selection of biologically relevant libraries, the accuracy of Expressed Sequence Tag to gene assignment, and the statistics used. The key steps, methods, and tools used to this end will be described using vascular targeting as an example. With the advent of next-generation sequencing, these or similar methods can be applied to find novel genes with this new source of data.

  11. Finding the joker among the maize endogenous reference genes for genetically modified organism (GMO) detection.

    Science.gov (United States)

    Paternò, Annalisa; Marchesi, Ugo; Gatto, Francesco; Verginelli, Daniela; Quarchioni, Cinzia; Fusco, Cristiana; Zepparoni, Alessia; Amaddeo, Demetrio; Ciabatti, Ilaria

    2009-12-09

    The comparison of five real-time polymerase chain reaction (PCR) methods targeted at maize ( Zea mays ) endogenous sequences is reported. PCR targets were the alcohol dehydrogenase (adh) gene for three methods and high-mobility group (hmg) gene for the other two. The five real-time PCR methods have been checked under repeatability conditions at several dilution levels on both pooled DNA template from several genetically modified (GM) maize certified reference materials (CRMs) and single CRM DNA extracts. Slopes and R(2) coefficients of all of the curves obtained from the adopted regression model were compared within the same method and among all of the five methods, and the limit of detection and limit of quantitation were analyzed for each PCR system. Furthermore, method equivalency was evaluated on the basis of the ability to estimate the target haploid genome copy number at each concentration level. Results indicated that, among the five methods tested, one of the hmg-targeted PCR systems can be considered equivalent to the others but shows the best regression parameters and a higher repeteability along the dilution range. Thereby, it is proposed as a valid module to be coupled to different event-specific real-time PCR for maize genetically modified organism (GMO) quantitation. The resulting practicability improvement on the analytical control of GMOs is discussed.

  12. Prenatal diagnostic testing of the Noonan syndrome genes in fetuses with abnormal ultrasound findings

    NARCIS (Netherlands)

    Croonen, Ellen A.; Nillesen, Willy M.; Stuurman, Kyra E.; Oudesluijs, Gretel; van de Laar, Ingrid M. B. M.; Martens, Liesbeth; Ockeloen, Charlotte; Mathijssen, Inge B.; Schepens, Marga; Ruiterkamp-Versteeg, Martina; Scheffer, Hans; Faas, Brigitte H. W.; van der Burgt, Ineke; Yntema, Helger G.

    2013-01-01

    In recent studies on prenatal testing for Noonan syndrome (NS) in fetuses with an increased nuchal translucency (NT) and a normal karyotype, mutations have been reported in 9-16% of cases. In this study, DNA of 75 fetuses with a normal karyotype and abnormal ultrasound findings was tested in a

  13. [Allgrove syndrome (triple A). Finding of a mutation not described in the AAAS gene].

    Science.gov (United States)

    Capataz Ledesma, M; Méndez Pérez, P; Rodríguez López, R; Galán Gómez, E

    2013-02-01

    Allgrove syndrome (triple A) is a rare autosomal recessive disease. The classic triad includes, congenital adrenal insufficiency due to ACTH resistance, achalasia of the cardia and alacrimia. Neurological abnormalities are associated with autonomic neuropathy, sensory and motor defects, deafness, mental retardation, Parkinsonism and dementia. The gene responsible is the ADRACALIN or AAAS encoding a protein called ALADIN. We report a case of a 19 year-old male, assessed when he was 10 years old in our department due to suspected storage disease. Mild mental and language retardation, hypernasal voice, sensory-motor neuropathy with autonomic involvement and signs of spastic paraparesis, alacrimia. gastroesophageal reflux, and achalasia. Molecular studies showed to mutations, the undescribed p.Tyr 19 Cys, and IVS14 +1 G. Copyright © 2012 Asociación Española de Pediatría. Published by Elsevier Espana. All rights reserved.

  14. The Tourette International Collaborative Genetics (TIC Genetics) study, finding the genes causing Tourette syndrome

    DEFF Research Database (Denmark)

    Dietrich, Andrea; Fernandez, Thomas V; King, Robert A

    2015-01-01

    discovery effort, focusing both on familial genetic variants with large effects within multiply affected pedigrees and on de novo mutations ascertained through the analysis of apparently simplex parent-child trios with non-familial tics. The clinical data and biomaterials (DNA, transformed cell lines, RNA......, it is clear that large patient cohorts and open-access repositories will be essential to further advance the field. To that end, the large multicenter Tourette International Collaborative Genetics (TIC Genetics) study was established. The goal of the TIC Genetics study is to undertake a comprehensive gene...... of TS and related disorders and the development of novel therapies. Here, we describe the objectives and methods of the TIC Genetics study as a reference for future studies from our group and to facilitate collaboration between genetics consortia in the field of TS....

  15. Leveraging model legume information to find candidate genes for soybean sudden death syndrome using the legume information system.

    Science.gov (United States)

    Gonzales, Michael D; Gajendran, Kamal; Farmer, Andrew D; Archuleta, Eric; Beavis, William D

    2007-01-01

    Comparative genomics is an emerging and powerful approach to achieve crop improvement. Using comparative genomics, information from model plant species can accelerate the discovery of genes responsible for disease and pest resistance, tolerance to plant stresses such as drought, and enhanced nutritional value including production of anti-oxidants and anti-cancer compounds. We demonstrate here how to use the Legume Information System for a comparative genomics study, leveraging genomic information from Medicago truncatula (barrel medic), the model legume, to find candidate genes involved with sudden death syndrome (SDS) in Glycine max (soybean). Specifically, genetic maps, physical maps, and annotated tentative consensus and expressed sequence tag (EST) sequences from G. max and M. truncatula can be compared. In addition, the recently published M. truncatula genomic sequences can be used to identify M. truncatula candidate genes in a genomic region syntenic to a quantitative trait loci region for SDS in soybean. Genomic sequences of candidate genes from M. truncatula can then be used to identify ESTs with sequence similarities from soybean for primer design and cloning of potential soybean disease causing alleles.

  16. Antisocial behavior and polymorphisms in the oxytocin receptor gene: findings in two independent samples.

    Science.gov (United States)

    Hovey, D; Lindstedt, M; Zettergren, A; Jonsson, L; Johansson, A; Melke, J; Kerekes, N; Anckarsäter, H; Lichtenstein, P; Lundström, S; Westberg, L

    2016-07-01

    The quantitative genetic contribution to antisocial behavior is well established, but few, if any, genetic variants are established as risk factors. Emerging evidence suggests that the neuropeptide oxytocin (OXT) may modulate interpersonal aggression. We here investigated whether single-nucleotide polymorphisms (SNPs) in the OXT receptor gene (OXTR) are associated with the expression of antisocial behavior. A discovery sample, including both sexes, was drawn from the Child and Adolescent Twin Study in Sweden (CATSS; n=2372), and a sample from the Twin Study of Child and Adolescent Development (TCHAD; n=1232) was used for replication. Eight SNPs in OXTR, selected on previous associations with social and antisocial behavior, were genotyped in the participants of CATSS. Significant polymorphisms were subsequently genotyped in TCHAD for replication. Participants completed self-assessment questionnaires-Life History of Aggression (LHA; available only in CATSS), and Self-Reported Delinquency (SRD; available in both samples)-designed to capture antisocial behavior as continuous traits. In the discovery sample, the rs7632287 AA genotype was associated with higher frequency of antisocial behavior in boys, and this was then replicated in the second sample. In particular, overt aggression (directly targeting another individual) was strongly associated with this genotype in boys (P=6.2 × 10(-7) in the discovery sample). Meta-analysis of the results for antisocial behavior from both samples yielded P=2.5 × 10(-5). Furthermore, an association between rs4564970 and LHA (P=0.00013) survived correction in the discovery sample, but there was no association with the SRD in the replication sample. We conclude that the rs7632287 and rs4564970 polymorphisms in OXTR may independently influence antisocial behavior in adolescent boys. Further replication of our results will be crucial to understanding how aberrant social behavior arises, and would support the OXT receptor as one

  17. Ocular findings in adult subjects with an inactivating mutation in GH releasing hormone receptor gene.

    Science.gov (United States)

    Faro, Augusto C N; Pereira-Gurgel, Virginia M; Salvatori, Roberto; Campos, Viviane C; Melo, Gustavo B; Oliveira, Francielle T; Oliveira-Santos, Alecia A; Oliveira, Carla R P; Pereira, Francisco A; Hellström, Ann; Oliveira-Neto, Luís A; Valença, Eugenia H O; Aguiar-Oliveira, Manuel H

    2017-06-01

    Ocular function is fundamental for environmental adaptation and survival capacity. Growth factors are necessary for a mature eyeball, needed for adequate vision. However, the consequences of the deficiency of circulating growth hormone (GH) and its effector insulin-like growth factor I (IGF-I) on the physical aspects of the human eye are still debated. A model of untreated isolated GH deficiency (IGHD), with low but measurable serum GH, may clarify this issue. The aim of this study was to assess the ocular aspects of adult IGHD individuals who have never received GH therapy. Cross sectional study. Setting: University Hospital, Federal University of Sergipe, Brazil. Twenty-five adult (13 males, mean age 50.1years, range 26 to 70years old) IGHD subjects homozygous for a null mutation (c.57+1G>A) in the GHRH receptor gene, and 28 (15 males, mean age 51.1years, range 26 to 67years old) controls were submitted to an endocrine and ophthalmological assessment. Forty-six IGHD and 50 control eyes were studied. Visual acuity, intraocular pressure, refraction (spherical equivalent), ocular axial length (AL), anterior chamber depth (ACD), lens thickness (LT), vitreous depth (VD), mean corneal curvature (CC) and central corneal thickness (CCT). IGHD subjects exhibited unmeasurable serum IGF-I levels, similar visual acuity, intraocular pressure and LT, higher values of spherical equivalent and CC, and lower measures of AL, ACD, VD and CCT in comparison to controls, but within their respective normal ranges. While mean stature in IGHD group was 78% of the control group, mean head circumference was 92% and axial AL was 96%. These observations suggest mild ocular effects in adult subjects with severe IGF-I deficiency due to non-treated IGHD. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. Homozygous and compound heterozygous mutations in the FBN1 gene: unexpected findings in molecular diagnosis of Marfan syndrome.

    Science.gov (United States)

    Arnaud, Pauline; Hanna, Nadine; Aubart, Mélodie; Leheup, Bruno; Dupuis-Girod, Sophie; Naudion, Sophie; Lacombe, Didier; Milleron, Olivier; Odent, Sylvie; Faivre, Laurence; Bal, Laurence; Edouard, Thomas; Collod-Beroud, Gwenaëlle; Langeois, Maud; Spentchian, Myrtille; Gouya, Laurent; Jondeau, Guillaume; Boileau, Catherine

    2017-02-01

    Marfan syndrome (MFS) is an autosomal-dominant connective tissue disorder usually associated with heterozygous mutations in the gene encoding fibrillin-1 (FBN1). Homozygous and compound heterozygous cases are rare events and have been associated with a clinical severe presentation. Report unexpected findings of homozygosity and compound heterozygosity in the course of molecular diagnosis of heterozygous MFS and compare the findings with published cases. In the context of molecular diagnosis of heterozygous MFS, systematic sequencing of the FBN1 gene was performed in 2500 probands referred nationwide. 1400 probands carried a heterozygous mutation in this gene. Unexpectedly, among them four homozygous cases (0.29%) and five compound heterozygous cases (0.36%) were identified (total: 0.64%). Interestingly, none of these cases carried two premature termination codon mutations in the FBN1 gene. Clinical features for these carriers and their families were gathered and compared. There was a large spectrum of severity of the disease in probands carrying two mutated FBN1 alleles, but none of them presented extremely severe manifestations of MFS in any system compared with carriers of only one mutated FBN1 allele. This observation is not in line with the severe clinical features reported in the literature for four homozygous and three compound heterozygous probands. Homozygotes and compound heterozygotes were unexpectedly identified in the course of molecular diagnosis of MFS. Contrary to previous reports, the presence of two mutated alleles was not associated with severe forms of MFS. Although homozygosity and compound heterozygosity are rarely found in molecular diagnosis, they should not be overlooked, especially among consanguineous families. However, no predictive evaluation of severity should be provided. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

  19. Imaging findings in a distinct lethal inherited arteriopathy syndrome associated with a novel mutation in the FBLN4 gene

    Energy Technology Data Exchange (ETDEWEB)

    Rajeshkannan, Ramiah; Kulkarni, Chinmay; Moorthy, Srikanth [Amrita Institute of Medical Sciences, AIMS, Department of Radiology, Ernakulam (India); Kappanayil, Mahesh [Amrita Institute of Medical Sciences, AIMS, Department of pediatric cardiology, Ernakulam (India); Nampoothiri, Sheela [Amrita Institute of Medical Sciences, AIMS, Department of Pediatric Genetics, Ernakulam (India); Malfait, Fransiska; Paepe, Anne de [Ghent University Hospital, Center for Medical Genetics, Ghent (Belgium)

    2014-08-15

    We present the imaging findings of a newly identified lethal arteriopathy associated with a novel mutation in the gene encoding fibulin-4, occurring in a distinct community from southern India. A total of 31 children from a distinct population subgroup who presented with characteristic arterial dilatation and tortuosity were studied. All children except one belonged to unrelated families from an ethno-religious group (Muslim) from the northern coastal belt of southern India. CT angiography was performed in 30 children and contrast MRA in one. Impressive dilatation and elongation of ascending aorta, arch, descending aorta and main pulmonary arteries with characteristic narrowing of aortic isthmus were seen in all patients. Stenosis of arch branches, abdominal visceral branches and pulmonary artery branches was observed in 21 (68 %), 23 (62.5 %) and 20 (65 %) patients respectively. Genetic studies revealed an identical mutation in exon 7 of the FBLN4 gene. On follow-up, 27 of them had died before the age of 3 years and only two children were alive after the age of 4 years. FBLN4-associated vasculopathy is a highly lethal disease characterized by severe aneurysmal dilatation of thoracic aorta, its branches and pulmonary arteries with stenoses at typical locations. (orig.)

  20. Leading the way: finding genes for neurologic disease in dogs using genome-wide mRNA sequencing

    Directory of Open Access Journals (Sweden)

    Ostrander Elaine A

    2012-07-01

    Full Text Available Abstract Because of dogs' unique population structure, human-like disease biology, and advantageous genomic features, the canine system has risen dramatically in popularity as a tool for discovering disease alleles that have been difficult to find by studying human families or populations. To date, disease studies in dogs have primarily employed either linkage analysis, leveraging the typically large family size, or genome-wide association, which requires only modest-sized case and control groups in dogs. Both have been successful but, like most techniques, each requires a specific combination of time and money, and there are inherent problems associated with each. Here we review the first report of mRNA-Seq in the dog, a study that provides insights into the potential value of applying high-throughput sequencing to the study of genetic diseases in dogs. Forman and colleagues apply high-throughput sequencing to a single case of canine neonatal cerebellar cortical degeneration. This implementation of whole genome mRNA sequencing, the first reported in dog, is additionally unusual due to the analysis: the data was used not to examine transcript levels or annotate genes, but as a form of target capture that revealed the sequence of transcripts of genes associated with ataxia in humans. This approach entails risks. It would fail if, for example, the relevant transcripts were not sufficiently expressed for genotyping or were not associated with ataxia in humans. But here it pays off handsomely, identifying a single frameshift mutation that segregates with the disease. This work sets the stage for similar studies that take advantage of recent advances in genomics while exploiting the historical background of dog breeds to identify disease-causing mutations.

  1. Exegesis: a procedure to improve gene predictions and its use to find immunoglobulin superfamily proteins in the human and mouse genomes.

    Science.gov (United States)

    de Bono, Bernard; Chothia, Cyrus

    2003-11-01

    Exegesis is a procedure to refine the gene predictions that are produced for complex genomes, e.g. those of humans and mice. It uses the program Genewise, sequences determined by experiment, experimental maps of gene segment libraries and a new browser that allows the user to rapidly inspect and compare multiple gene maps to regions of genomic sequences. The procedure should be of general use. Here, we use the procedure to find members of the immunoglobulin superfamily in the human and mouse genomes. To do this, Exegesis was used to process the original gene predictions from the automated Ensembl annotation pipeline. Exegesis produced (i) many more complete genes and new transcripts and (ii) a mapping of the immunoglobulin and T cell receptor gene libraries to the genome, which are largely absent in the Ensembl set.

  2. How do 'housekeeping' genes control organogenesis?--Unexpected new findings on the role of housekeeping genes in cell and organ differentiation.

    Science.gov (United States)

    Tsukaya, Hirokazu; Byrne, Mary E; Horiguchi, Gorou; Sugiyama, Munetaka; Van Lijsebettens, Mieke; Lenhard, Michael

    2013-01-01

    In recent years, an increasing number of mutations in what would appear to be 'housekeeping genes' have been identified as having unexpectedly specific defects in multicellular organogenesis. This is also the case for organogenesis in seed plants. Although it is not surprising that loss-of-function mutations in 'housekeeping' genes result in lethality or growth retardation, it is surprising when (1) the mutant phenotype results from the loss of function of a 'housekeeping' gene and (2) the mutant phenotype is specific. In this review, by defining housekeeping genes as those encoding proteins that work in basic metabolic and cellular functions, we discuss unexpected links between housekeeping genes and specific developmental processes. In a surprising number of cases housekeeping genes coding for enzymes or proteins with functions in basic cellular processes such as transcription, post-transcriptional modification, and translation affect plant development.

  3. The Finding of a Group IIE Phospholipase A2 Gene in a Specified Segment of Protobothrops flavoviridis Genome and Its Possible Evolutionary Relationship to Group IIA Phospholipase A2 Genes

    Directory of Open Access Journals (Sweden)

    Kazuaki Yamaguchi

    2014-12-01

    Full Text Available The genes encoding group IIE phospholipase A2, abbreviated as IIE PLA2, and its 5' and 3' flanking regions of Crotalinae snakes such as Protobothrops flavoviridis, P. tokarensis, P. elegans, and Ovophis okinavensis, were found and sequenced. The genes consisted of four exons and three introns and coded for 22 or 24 amino acid residues of the signal peptides and 134 amino acid residues of the mature proteins. These IIE PLA2s show high similarity to those from mammals and Colubridae snakes. The high expression level of IIE PLA2s in Crotalinae venom glands suggests that they should work as venomous proteins. The blast analysis indicated that the gene encoding OTUD3, which is ovarian tumor domain-containing protein 3, is located in the 3' downstream of IIE PLA2 gene. Moreover, a group IIA PLA2 gene was found in the 5' upstream of IIE PLA2 gene linked to the OTUD3 gene (OTUD3 in the P. flavoviridis genome. It became evident that the specified arrangement of IIA PLA2 gene, IIE PLA2 gene, and OTUD3 in this order is common in the genomes of humans to snakes. The present finding that the genes encoding various secretory PLA2s form a cluster in the genomes of humans to birds is closely related to the previous finding that six venom PLA2 isozyme genes are densely clustered in the so-called NIS-1 fragment of the P. flavoviridis genome. It is also suggested that venom IIA PLA2 genes may be evolutionarily derived from the IIE PLA2 gene.

  4. Retinal gene therapy in patients with choroideremia: initial findings from a phase 1/2 clinical trial

    NARCIS (Netherlands)

    Maclaren, R.E.; Groppe, M.; Barnard, A.R.; Cottriall, C.L.; Tolmachova, T.; Seymour, L.; Clark, K.; During, M.J.; Cremers, F.P.M.; Black, G.C.M.; Lotery, A.J.; Downes, S.M.; Webster, A.R.; Seabra, M.C.

    2014-01-01

    BACKGROUND: Choroideremia is an X-linked recessive disease that leads to blindness due to mutations in the CHM gene, which encodes the Rab escort protein 1 (REP1). We assessed the effects of retinal gene therapy with an adeno-associated viral (AAV) vector encoding REP1 (AAV.REP1) in patients with

  5. Combining Human Epigenetics and Sleep Studies in Caenorhabditis elegans: A Cross-Species Approach for Finding Conserved Genes Regulating Sleep.

    Science.gov (United States)

    Huang, Huiyan; Zhu, Yong; Eliot, Melissa N; Knopik, Valerie S; McGeary, John E; Carskadon, Mary A; Hart, Anne C

    2017-06-01

    We aimed to test a combined approach to identify conserved genes regulating sleep and to explore the association between DNA methylation and sleep length. We identified candidate genes associated with shorter versus longer sleep duration in college students based on DNA methylation using Illumina Infinium HumanMethylation450 BeadChip arrays. Orthologous genes in Caenorhabditis elegans were identified, and we examined whether their loss of function affected C. elegans sleep. For genes whose perturbation affected C. elegans sleep, we subsequently undertook a small pilot study to re-examine DNA methylation in an independent set of human participants with shorter versus longer sleep durations. Eighty-seven out of 485,577 CpG sites had significant differential methylation in young adults with shorter versus longer sleep duration, corresponding to 52 candidate genes. We identified 34 C. elegans orthologs, including NPY/flp-18 and flp-21, which are known to affect sleep. Loss of five additional genes alters developmentally timed C. elegans sleep (B4GALT6/bre-4, DOCK180/ced-5, GNB2L1/rack-1, PTPRN2/ida-1, ZFYVE28/lst-2). For one of these genes, ZFYVE28 (also known as hLst2), the pilot replication study again found decreased DNA methylation associated with shorter sleep duration at the same two CpG sites in the first intron of ZFYVE28. Using an approach that combines human epigenetics and C. elegans sleep studies, we identified five genes that play previously unidentified roles in C. elegans sleep. We suggest sleep duration in humans may be associated with differential DNA methylation at specific sites and that the conserved genes identified here likely play roles in C. elegans sleep and in other species. © Sleep Research Society 2017. Published by Oxford University Press on behalf of the Sleep Research Society. All rights reserved. For permissions, please e-mail journals.permissions@oup.com.

  6. Designing of highly effective complementary and mismatch siRNAs for silencing a gene.

    Science.gov (United States)

    Ahmed, Firoz; Raghava, Gajendra P S

    2011-01-01

    In past, numerous methods have been developed for predicting efficacy of short interfering RNA (siRNA). However these methods have been developed for predicting efficacy of fully complementary siRNA against a gene. Best of author's knowledge no method has been developed for predicting efficacy of mismatch siRNA against a gene. In this study, a systematic attempt has been made to identify highly effective complementary as well as mismatch siRNAs for silencing a gene.Support vector machine (SVM) based models have been developed for predicting efficacy of siRNAs using composition, binary and hybrid pattern siRNAs. We achieved maximum correlation 0.67 between predicted and actual efficacy of siRNAs using hybrid model. All models were trained and tested on a dataset of 2182 siRNAs and performance was evaluated using five-fold cross validation techniques. The performance of our method desiRm is comparable to other well-known methods. In this study, first time attempt has been made to design mutant siRNAs (mismatch siRNAs). In this approach we mutated a given siRNA on all possible sites/positions with all possible nucleotides. Efficacy of each mutated siRNA is predicted using our method desiRm. It is well known from literature that mismatches between siRNA and target affects the silencing efficacy. Thus we have incorporated the rules derived from base mismatches experimental data to find out over all efficacy of mutated or mismatch siRNAs. Finally we developed a webserver, desiRm (http://www.imtech.res.in/raghava/desirm/) for designing highly effective siRNA for silencing a gene. This tool will be helpful to design siRNA to degrade disease isoform of heterozygous single nucleotide polymorphism gene without depleting the wild type protein.

  7. Gene set-based analysis of polymorphisms: finding pathways or biological processes associated to traits in genome-wide association studies

    Science.gov (United States)

    Medina, Ignacio; Montaner, David; Bonifaci, Nuria; Pujana, Miguel Angel; Carbonell, José; Tarraga, Joaquin; Al-Shahrour, Fatima; Dopazo, Joaquin

    2009-01-01

    Genome-wide association studies have become a popular strategy to find associations of genes to traits of interest. Despite the high-resolution available today to carry out genotyping studies, the success of its application in real studies has been limited by the testing strategy used. As an alternative to brute force solutions involving the use of very large cohorts, we propose the use of the Gene Set Analysis (GSA), a different analysis strategy based on testing the association of modules of functionally related genes. We show here how the Gene Set-based Analysis of Polymorphisms (GeSBAP), which is a simple implementation of the GSA strategy for the analysis of genome-wide association studies, provides a significant increase in the power testing for this type of studies. GeSBAP is freely available at http://bioinfo.cipf.es/gesbap/ PMID:19502494

  8. The genetics of rheumatoid arthritis and the need for animal models to find and understand the underlying genes.

    Science.gov (United States)

    Jirholt, J; Lindqvist, A B; Holmdahl, R

    2001-01-01

    The causes of rheumatoid arthritis (RA) are largely unknown. However, RA is most probably a multifactorial disease with contributions from genetic and environmental factors. Searches for genes that influence RA have been conducted in both human and experimental model materials. Both types of study have confirmed the polygenic inheritance of the disease. It has become clear that the features of RA complicate the human genetic studies. Animal models are therefore valuable tools for identifying genes and determining their pathogenic role in the disease. This is probably the fastest route towards unravelling the pathogenesisis of RA and developing new therapies.

  9. The genetics of rheumatoid arthritis and the need for animal models to find and understand the underlying genes

    OpenAIRE

    Jirholt, Johan; Lindqvist, Anna-Karin B; Holmdahl, Rikard

    2000-01-01

    The causes of rheumatoid arthritis (RA) are largely unknown. However, RA is most probably a multifactorial disease with contributions from genetic and environmental factors. Searches for genes that influence RA have been conducted in both human and experimental model materials. Both types of study have confirmed the polygenic inheritance of the disease. It has become clear that the features of RA complicate the human genetic studies. Animal models are therefore valuable tools for identifying ...

  10. Circadian CLOCK gene polymorphisms in relation to sleep patterns and obesity in African Americans: findings from the Jackson heart study.

    Science.gov (United States)

    Riestra, Pia; Gebreab, Samson Y; Xu, Ruihua; Khan, Rumana J; Gaye, Amadou; Correa, Adolfo; Min, Nancy; Sims, Mario; Davis, Sharon K

    2017-06-23

    Circadian rhythms regulate key biological processes and the dysregulation of the intrinsic clock mechanism affects sleep patterns and obesity onset. The CLOCK (circadian locomotor output cycles protein kaput) gene encodes a core transcription factor of the molecular circadian clock influencing diverse metabolic pathways, including glucose and lipid homeostasis. The primary objective of this study was to evaluate the associations between CLOCK single nucleotide polymorphisms (SNPs) and body mass index (BMI). We also evaluated the association of SNPs with BMI related factors such as sleep duration and quality, adiponectin and leptin, in 2962 participants (1116 men and 1810 women) from the Jackson Heart Study. Genotype data for the selected 23 CLOCK gene SNPS was obtained by imputation with IMPUTE2 software and reference phase data from the 1000 genome project. Genetic analyses were conducted with PLINK RESULTS: We found a significant association between the CLOCK SNP rs2070062 and sleep duration, participants carriers of the T allele showed significantly shorter sleep duration compared to non-carriers after the adjustment for individual proportions of European ancestry (PEA), socio economic status (SES), body mass index (BMI), alcohol consumption and smoking status that reach the significance threshold after multiple testing correction. In addition, we found nominal associations of the CLOCK SNP rs6853192 with longer sleep duration and the rs6820823, rs3792603 and rs11726609 with BMI. However, these associations did not reach the significance threshold after correction for multiple testing. In this work, CLOCK gene variants were associated with sleep duration and BMI suggesting that the effects of these polymorphisms on circadian rhythmicity may affect sleep duration and body weight regulation in Africans Americans.

  11. An SVM Based Approach for the Analysis Of Mammography Images

    Science.gov (United States)

    Gan, X.; Kapsokalivas, L.; Skaliotis, A.; Steinhöfel, K.; Tangaro, S.

    2007-09-01

    Mammography is among the most popular imaging techniques used in the diagnosis of breast cancer. Nevertheless distinguishing between healthy and ill images is hard even for an experienced radiologist, because a single image usually includes several regions of interest (ROIs). The hardness of this classification problem along with the substantial amount of data, gathered from patients' medical history, motivates the use of a machine learning approach as part of a CAD (Computer Aided Detection) tool, aiming to assist radiologists in the characterization of mammography images. Specifically, our approach involves: i) the ROI extraction, ii) the Feature Vector extraction, iii) the Support Vector Machine (SVM) classification of ROIs and iv) the characterization of the whole image. We evaluate the performance of our approach in terms of the SVM's training and testing error and in terms of ROI specificity—sensitivity. The results show a relation between the number of features used and the SVM's performance.

  12. An SVM Based Approach for the Analysis Of Mammography Images

    International Nuclear Information System (INIS)

    Gan, X.; Kapsokalivas, L.; Skaliotis, A.; Steinhoefel, K.; Tangaro, S.

    2007-01-01

    Mammography is among the most popular imaging techniques used in the diagnosis of breast cancer. Nevertheless distinguishing between healthy and ill images is hard even for an experienced radiologist, because a single image usually includes several regions of interest (ROIs). The hardness of this classification problem along with the substantial amount of data, gathered from patients' medical history, motivates the use of a machine learning approach as part of a CAD (Computer Aided Detection) tool, aiming to assist radiologists in the characterization of mammography images. Specifically, our approach involves: i) the ROI extraction, ii) the Feature Vector extraction, iii) the Support Vector Machine (SVM) classification of ROIs and iv) the characterization of the whole image. We evaluate the performance of our approach in terms of the SVM's training and testing error and in terms of ROI specificity - sensitivity. The results show a relation between the number of features used and the SVM's performance

  13. SVM-Based Control System for a Robot Manipulator

    Directory of Open Access Journals (Sweden)

    Foudil Abdessemed

    2012-12-01

    Full Text Available Real systems are usually non-linear, ill-defined, have variable parameters and are subject to external disturbances. Modelling these systems is often an approximation of the physical phenomena involved. However, it is from this approximate system of representation that we propose - in this paper - to build a robust control, in the sense that it must ensure low sensitivity towards parameters, uncertainties, variations and external disturbances. The computed torque method is a well-established robot control technique which takes account of the dynamic coupling between the robot links. However, its main disadvantage lies on the assumption of an exactly known dynamic model which is not realizable in practice. To overcome this issue, we propose the estimation of the dynamics model of the nonlinear system with a machine learning regression method. The output of this regressor is used in conjunction with a PD controller to achieve the tracking trajectory task of a robot manipulator. In cases where some of the parameters of the plant undergo a change in their values, poor performance may result. To cope with this drawback, a fuzzy precompensator is inserted to reinforce the SVM computed torque-based controller and avoid any deterioration. The theory is developed and the simulation results are carried out on a two-degree of freedom robot manipulator to demonstrate the validity of the proposed approach.

  14. SVM-based Partial Discharge Pattern Classification for GIS

    Science.gov (United States)

    Ling, Yin; Bai, Demeng; Wang, Menglin; Gong, Xiaojin; Gu, Chao

    2018-01-01

    Partial discharges (PD) occur when there are localized dielectric breakdowns in small regions of gas insulated substations (GIS). It is of high importance to recognize the PD patterns, through which we can diagnose the defects caused by different sources so that predictive maintenance can be conducted to prevent from unplanned power outage. In this paper, we propose an approach to perform partial discharge pattern classification. It first recovers the PRPD matrices from the PRPD2D images; then statistical features are extracted from the recovered PRPD matrix and fed into SVM for classification. Experiments conducted on a dataset containing thousands of images demonstrates the high effectiveness of the method.

  15. New Findings in a Global Approach to Dissect the Whole Phenotype of PLA2G6 Gene Mutations

    Science.gov (United States)

    Salih, Mustafa A.; Mundwiller, Emeline; Khan, Arif O.; AlDrees, Abdulmajeed; Elmalik, Salah A.; Hassan, Hamdy H.; Al-Owain, Mohammed; Alkhalidi, Hisham M. S.; Katona, Istvan; Kabiraj, Mohammad M.; Chrast, Roman; Kentab, Amal Y.; Alzaidan, Hamad; Rodenburg, Richard J.; Bosley, Thomas M.; Weis, Joachim; Koenig, Michel

    2013-01-01

    Mutations in PLA2G6 gene have variable phenotypic outcome including infantile neuroaxonal dystrophy, atypical neuroaxonal dystrophy, idiopathic neurodegeneration with brain iron accumulation and Karak syndrome. The cause of this phenotypic variation is so far unknown which impairs both genetic diagnosis and appropriate family counseling. We report detailed clinical, electrophysiological, neuroimaging, histologic, biochemical and genetic characterization of 11 patients, from 6 consanguineous families, who were followed for a period of up to 17 years. Cerebellar atrophy was constant and the earliest feature of the disease preceding brain iron accumulation, leading to the provisional diagnosis of a recessive progressive ataxia in these patients. Ultrastructural characterization of patients’ muscle biopsies revealed focal accumulation of granular and membranous material possibly resulting from defective membrane homeostasis caused by disrupted PLA2G6 function. Enzyme studies in one of these muscle biopsies provided evidence for a relatively low mitochondrial content, which is compatible with the structural mitochondrial alterations seen by electron microscopy. Genetic characterization of 11 patients led to the identification of six underlying PLA2G6 gene mutations, five of which are novel. Importantly, by combining clinical and genetic data we have observed that while the phenotype of neurodegeneration associated with PLA2G6 mutations is variable in this cohort of patients belonging to the same ethnic background, it is partially influenced by the genotype, considering the age at onset and the functional disability criteria. Molecular testing for PLA2G6 mutations is, therefore, indicated in childhood-onset ataxia syndromes, if neuroimaging shows cerebellar atrophy with or without evidence of iron accumulation. PMID:24130795

  16. Leber congenital amaurosis associated with AIPL1: challenges in ascribing disease causation, clinical findings, and implications for gene therapy.

    Directory of Open Access Journals (Sweden)

    Mei Hong Tan

    Full Text Available Leber Congenital Amaurosis (LCA and Early Childhood Onset Severe Retinal Dystrophy are clinically and genetically heterogeneous retinal disorders characterised by visual impairment and nystagmus from birth or early infancy. We investigated the prevalence of sequence variants in AIPL1 in a large cohort of such patients (n = 392 and probed the likelihood of disease-causation of the identified variants, subsequently undertaking a detailed assessment of the phenotype of patients with disease-causing mutations. Genomic DNA samples were screened for known variants in the AIPL1 gene using a microarray LCA chip, with 153 of these cases then being directly sequenced. The assessment of disease-causation of identified AIPL1 variants included segregation testing, assessing evolutionary conservation and in silico predictions of pathogenicity. The chip identified AIPL1 variants in 12 patients. Sequencing of AIPL1 in 153 patients and 96 controls found a total of 46 variants, with 29 being novel. In silico analysis suggested that only 6 of these variants are likely to be disease-causing, indicating a previously unrecognized high degree of polymorphism. Seven patients were identified with biallelic changes in AIPL1 likely to be disease-causing. In the youngest subject, electroretinography revealed reduced cone photoreceptor function, but rod responses were within normal limits, with no measurable ERG in other patients. An increasing degree and extent of peripheral retinal pigmentation and degree of maculopathy was noted with increasing age in our series. AIPL1 is significantly polymorphic in both controls and patients, thereby complicating the establishment of disease-causation of identified variants. Despite the associated phenotype being characterised by early-onset severe visual loss in our patient series, there was some evidence of a degree of retinal structural and functional preservation, which was most marked in the youngest patient in our cohort

  17. Renal cell carcinoma associated with Xp11.2 translocation/TFE gene fusion: imaging findings in 21 patients

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Xiao; Zhou, Hao; Duan, Na; Liu, Yongkang; Wang, Zhongqiu [Affiliated Hospital of Nanjing University of Chinese Medicine, Department of Radiology, Nanjing (China); Zhu, Qingqiang [Medical School of Yangzhou University, Department of Medical Imaging, Subei People' s Hospital, Yangzhou (China); Li, Baoxin [Gulou Hospital, Department of Radiology, Nanjing (China); Cui, Wenjing [Affiliated Hospital of Nanjing University of Chinese Medicine, Department of Radiology, Nanjing (China); Nanjing University Medical School, Department of Radiology, Jinling Hospital, Nanjing (China); Kundra, Vikas [The University of Texas, M.D. Anderson Cancer Center, Department of Radiology, Houston, TX (United States)

    2017-02-15

    To characterize imaging features of renal cell carcinoma (RCC) associated with Xp11.2 translocation/TFE gene fusion. Twenty-one patients with Xp11.2/TFE RCC were retrospectively evaluated. Tumour location, size, density, cystic or solid appearance, calcification, capsule sign, enhancement pattern and metastases were assessed. Fourteen women and seven men were identified with 12 being 25 years old or younger. Tumours were solitary and cystic-solid (76.2 %) masses with a capsule (76.2 %); 90.5 % were located in the medulla. Calcifications and lymph node metastases were each observed in 24 %. On unenhanced CT, tumour attenuation was greater than in normal renal parenchyma (85.7 %). Tumour enhancement was less than in normal renal cortex on all enhanced phases, greater than in normal renal medulla on cortical and medullary phases, but less than in normal renal medulla on delayed phase. On MR, the tumours were isointense on T1WI, heterogeneously hypointense on T2WI and slightly hyperintense on diffusion-weighted imaging. Xp11.2/TFE RCC usually occurs in young women. It is a cystic-solid, hyperdense mass with a capsule. It arises from the renal medulla with enhancement less than in the cortex but greater than in the medulla in all phases except the delayed phase, when it is lower than in the medulla. (orig.)

  18. Ultrasonographic Findings of Renal Cell Carcinomas Associated with Xp11.2 Translocation/TFE3 Gene Fusion

    Directory of Open Access Journals (Sweden)

    Wenwu Ling

    2017-01-01

    Full Text Available Objective. This study was to investigate the features of renal carcinomas associated with Xp11.2 translocations/TFE3 gene fusions (Xp11.2-RCC on conventional ultrasound (US and contrast-enhanced ultrasound (CEUS. Methods. US and CEUS features of twenty-two cases with histopathologically proven Xp11.2-RCC were retrospectively reviewed. Results. 22 patients (11 males, 11 females were included in this study, with a mean age of 28.3 ± 20.4 years. Eight tumors (36.3%, 8/22 were in left kidney, and 14 tumors (63.7%, 14/22 were in right kidney. All tumors (100%, 22/22 were mixed echogenicity type. 13 tumors (59.1%, 13/22 presented small dotted calcifications. The boundary of 14 tumors (63.6%, 14/22 was sharp and the other 8 tumors’ (36.4%, 8/22 boundary was blurry. By CEUS, in early phase, the solid element of all tumors showed obvious enhancement. In delayed phase, 13 tumors showed hypoenhancement, seven tumors showed isoenhancement, and 2 tumors showed hyperenhancement. There were irregular nonenhancement areas in all tumors inside. Conclusions. By US and CEUS, when children and adolescents were found to have hyperechoic mixed tumor in kidney with sharp margin and calcification, and the tumors showed obvious enhancement and hypoenhancement with irregular nonenhancement areas in the tumor in early phase and delayed phase, respectively, Xp11.2-RCC should be suspected.

  19. Finding Nemo's Genes: A chromosome-scale reference assembly of the genome of the orange clownfish Amphiprion percula

    KAUST Repository

    Lehmann, Robert

    2018-03-08

    The iconic orange clownfish, Amphiprion percula, is a model organism for studying the ecology and evolution of reef fishes, including patterns of population connectivity, sex change, social organization, habitat selection and adaptation to climate change. Notably, the orange clownfish is the only reef fish for which a complete larval dispersal kernel has been established and was the first fish species for which it was demonstrated that anti-predator responses of reef fishes could be impaired by ocean acidification. Despite its importance, molecular resources for this species remain scarce and until now it lacked a reference genome assembly. Here we present a de novo chromosome-scale assembly of the genome of the orange clownfish Amphiprion percula. We utilized single-molecule real-time sequencing technology from Pacific Biosciences to produce an initial polished assembly comprised of 1,414 contigs, with a contig N50 length of 1.86 Mb. Using Hi-C based chromatin contact maps, 98% of the genome assembly were placed into 24 chromosomes, resulting in a final assembly of 908.8 Mb in length with contig and scaffold N50s of 3.12 and 38.4 Mb, respectively. This makes it one of the most contiguous and complete fish genome assemblies currently available. The genome was annotated with 26,597 protein coding genes and contains 96% of the core set of conserved actinopterygian orthologs. The availability of this reference genome assembly as a community resource will further strengthen the role of the orange clownfish as a model species for research on the ecology and evolution of reef fishes.

  20. Ocular findings in patients with oculocutaneous albinism type ia with G47D tyrosinase gene mutation in Puerto Rico: a case report.

    Science.gov (United States)

    Rodríguez-Agramonte, Ferdinand; Izquierdo, Natalio J; Cadilla, Carmen

    2013-01-01

    Previous studies have suggested that the G47D mutation leads patients to develop Oculocutaneous albinism (OCA) type IA. This mutation has been described in the Canary Islands. Historically, there has been a migration from the Canary Islands to some regions of Puerto Rico. To report on the ocular findings of two Puerto Rican patients with OCA IA due to the G47D Tyrosinase gene mutation. PATIENT AND FINDINGS: Two unrelated patients with OCA underwent a comprehensive eye examination and were referred for genetic analysis. Patients had almost total iris transillumination, clear lenses, foveal hypoplasia with transparent maculae, and albinotic mid peripheries. Both patients had nystagmus, and only one patient had strabismus. Patients with the G47D muta- tion leading to OCA IA have poor visual acuities and poorly pigmented phenotypic ophthalmic findings. Further studies comparing ocular findings in patients th several mutations leading to OCA IA are warranted. To our knowledge this is the first report on ocular findings in Puerto Rican patients with OCA type IA with the rare G47D mutation.

  1. GABAergic gene expression in postmortem hippocampus from alcoholics and cocaine addicts; corresponding findings in alcohol-naïve P and NP rats.

    Directory of Open Access Journals (Sweden)

    Mary-Anne Enoch

    Full Text Available By performing identical studies in humans and rats, we attempted to distinguish vulnerability factors for addiction from neurobiological effects of chronic drug exposure. We focused on the GABAergic system within the hippocampus, a brain region that is a constituent of the memory/conditioning neuronal circuitry of addiction that is considered to be important in drug reinforcement behaviors in animals and craving and relapse in humans.Using RNA-Seq we quantified mRNA transcripts in postmortem total hippocampus from alcoholics, cocaine addicts and controls and also from alcohol-naïve, alcohol preferring (P and non-preferring (NP rats selectively bred for extremes of alcohol-seeking behavior that also show a general addictive tendency. A pathway-targeted analysis of 25 GABAergic genes encoding proteins implicated in GABA synthesis, metabolism, synaptic transmission and re-uptake was undertaken.Directionally consistent and biologically plausible overlapping and specific changes were detected: 14/25 of the human genes and 12/25 of the rat genes showed nominally significant differences in gene expression (global p values: 9×10⁻¹⁴, 7×10⁻¹¹ respectively. Principal FDR-corrected findings were that GABBR1 was down-regulated in alcoholics, cocaine addicts and P rats with congruent findings in NSF, implicated in GABAB signaling efficacy, potentially resulting in increased synaptic GABA. GABRG2, encoding the gamma2 subunit required for postsynaptic clustering of GABAA receptors together with GPHN, encoding the associated scaffolding protein gephryin, were both down-regulated in alcoholics and cocaine addicts but were both up-regulated in P rats. There were also expression changes specific to cocaine addicts (GAD1, GAD2, alcoholics (GABRA2 and P rats (ABAT, GABRG3.Our study confirms the involvement of the GABAergic system in alcoholism but also reveals a hippocampal GABA input in cocaine addiction. Congruent findings in human addicts and P rats

  2. Interaction between genes and macronutrient intake on the risk of developing type 2 diabetes: systematic review and findings from European Prospective Investigation into Cancer (EPIC)-InterAct.

    Science.gov (United States)

    Li, Sherly X; Imamura, Fumiaki; Ye, Zheng; Schulze, Matthias B; Zheng, Jusheng; Ardanaz, Eva; Arriola, Larraitz; Boeing, Heiner; Dow, Courtney; Fagherazzi, Guy; Franks, Paul W; Agudo, Antonio; Grioni, Sara; Kaaks, Rudolf; Katzke, Verena A; Key, Timothy J; Khaw, Kay Tee; Mancini, Francesca R; Navarro, Carmen; Nilsson, Peter M; Onland-Moret, N Charlotte; Overvad, Kim; Palli, Domenico; Panico, Salvatore; Quirós, J Ramón; Rolandsson, Olov; Sacerdote, Carlotta; Sánchez, María-José; Slimani, Nadia; Sluijs, Ivonne; Spijkerman, Annemieke Mw; Tjonneland, Anne; Tumino, Rosario; Sharp, Stephen J; Riboli, Elio; Langenberg, Claudia; Scott, Robert A; Forouhi, Nita G; Wareham, Nicholas J

    2017-07-01

    Background: Gene-diet interactions have been reported to contribute to the development of type 2 diabetes (T2D). However, to our knowledge, few examples have been consistently replicated to date. Objective: We aimed to identify existing evidence for gene-macronutrient interactions and T2D and to examine the reported interactions in a large-scale study. Design: We systematically reviewed studies reporting gene-macronutrient interactions and T2D. We searched the MEDLINE, Human Genome Epidemiology Network, and WHO International Clinical Trials Registry Platform electronic databases to identify studies published up to October 2015. Eligibility criteria included assessment of macronutrient quantity (e.g., total carbohydrate) or indicators of quality (e.g., dietary fiber) by use of self-report or objective biomarkers of intake. Interactions identified in the review were subsequently examined in the EPIC (European Prospective Investigation into Cancer)-InterAct case-cohort study ( n = 21,148, with 9403 T2D cases; 8 European countries). Prentice-weighted Cox regression was used to estimate country-specific HRs, 95% CIs, and P -interaction values, which were then pooled by random-effects meta-analysis. A primary model was fitted by using the same covariates as reported in the published studies, and a second model adjusted for additional covariates and estimated the effects of isocaloric macronutrient substitution. Results: Thirteen observational studies met the eligibility criteria ( n gene-macronutrient interactions were identified for the risk of T2D from the literature. These interactions were not replicated in the EPIC-InterAct study, which mirrored the analyses undertaken in the original reports. Our findings highlight the importance of independent replication of reported interactions.

  3. Gene

    Data.gov (United States)

    U.S. Department of Health & Human Services — Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes,...

  4. A Novel Pathogenic Variant in the MITF Gene Segregating with a Unique Spectrum of Ocular Findings in an Extended Iranian Waardenburg Syndrome Kindred.

    Science.gov (United States)

    Jalilian, Nazanin; Tabatabaiefar, Mohammad A; Bahrami, Tayyeb; Karbasi, Golaleh; Bahramian, Mohammad H; Salimpoor, Abdolrahman; Noori-Daloii, Mohammad R

    2017-06-01

    Waardenburg syndrome (WS) is a rare genetic disorder characterized by abnormal pigmentation of the hair, skin, and iris as well as sensorineural hearing loss. WS is subdivided into 4 major types (WS1-4), where WS2 is characterized by the absence of dystopia canthorum. This study was launched to investigate clinical and molecular characteristics of WS in an extended Iranian WS2 family. A comprehensive clinical investigation was performed. Peripheral blood samples were collected and genomic DNA was extracted. Affected members of the family were studied for possible mutations within the SOX10 , MITF , and SNAI2 genes. Six WS2 individuals affected from a large Iranian WS2 kindred were enrolled. All affected members carried the novel substitution c.877C>T at exon 9 in the MITF gene, which resulted in p.Arg293* at the protein level. None of the healthy members and also of 50 ethnically matched controls had this variant. In addition, a spectrum of unique ocular findings, including nystagmus, chorioretinal degeneration, optic disc hypoplasia, astigmatism, and myopia, was segregated with the mutant allele in the pedigree. Our data provide insight into the genotypic and phenotypic spectrum of WS2 in an Iranian family and could further expand the spectrum of MITF mutations and have implications for genetic counseling on WS in Iran.

  5. Interaction between genes and macronutrient intake on the risk of developing type 2 diabetes: systematic review and findings from European Prospective Investigation into Cancer (EPIC)-InterAct

    Science.gov (United States)

    Li, Sherly X; Imamura, Fumiaki; Ye, Zheng; Schulze, Matthias B; Zheng, Jusheng; Ardanaz, Eva; Arriola, Larraitz; Boeing, Heiner; Dow, Courtney; Fagherazzi, Guy; Franks, Paul W; Agudo, Antonio; Grioni, Sara; Kaaks, Rudolf; Katzke, Verena A; Key, Timothy J; Khaw, Kay Tee; Mancini, Francesca R; Navarro, Carmen; Nilsson, Peter M; Onland-Moret, N Charlotte; Overvad, Kim; Palli, Domenico; Panico, Salvatore; Quirós, J Ramón; Rolandsson, Olov; Sacerdote, Carlotta; Sánchez, María-José; Slimani, Nadia; Sluijs, Ivonne; Spijkerman, Annemieke MW; Tjonneland, Anne; Tumino, Rosario; Sharp, Stephen J; Riboli, Elio; Langenberg, Claudia; Scott, Robert A; Wareham, Nicholas J

    2017-01-01

    tried to replicate previously reported interactions. In addition, no interactions were detected in models with additional covariates. Conclusions: Eight gene-macronutrient interactions were identified for the risk of T2D from the literature. These interactions were not replicated in the EPIC-InterAct study, which mirrored the analyses undertaken in the original reports. Our findings highlight the importance of independent replication of reported interactions. PMID:28592605

  6. Maternal Prenatal Mental Health and Placental 11β-HSD2 Gene Expression: Initial Findings from the Mercy Pregnancy and Emotional Wellbeing Study

    Science.gov (United States)

    Seth, Sunaina; Lewis, Andrew James; Saffery, Richard; Lappas, Martha; Galbally, Megan

    2015-01-01

    High intrauterine cortisol exposure can inhibit fetal growth and have programming effects for the child’s subsequent stress reactivity. Placental 11beta-hydroxysteroid dehydrogenase (11β-HSD2) limits the amount of maternal cortisol transferred to the fetus. However, the relationship between maternal psychopathology and 11β-HSD2 remains poorly defined. This study examined the effect of maternal depressive disorder, antidepressant use and symptoms of depression and anxiety in pregnancy on placental 11β-HSD2 gene (HSD11B2) expression. Drawing on data from the Mercy Pregnancy and Emotional Wellbeing Study, placental HSD11B2 expression was compared among 33 pregnant women, who were selected based on membership of three groups; depressed (untreated), taking antidepressants and controls. Furthermore, associations between placental HSD11B2 and scores on the State-Trait Anxiety Inventory (STAI) and Edinburgh Postnatal Depression Scale (EPDS) during 12–18 and 28–34 weeks gestation were examined. Findings revealed negative correlations between HSD11B2 and both the EPDS and STAI (r = −0.11 to −0.28), with associations being particularly prominent during late gestation. Depressed and antidepressant exposed groups also displayed markedly lower placental HSD11B2 expression levels than controls. These findings suggest that maternal depression and anxiety may impact on fetal programming by down-regulating HSD11B2, and antidepressant treatment alone is unlikely to protect against this effect. PMID:26593902

  7. Maternal Prenatal Mental Health and Placental 11β-HSD2 Gene Expression: Initial Findings from the Mercy Pregnancy and Emotional Wellbeing Study

    Directory of Open Access Journals (Sweden)

    Sunaina Seth

    2015-11-01

    Full Text Available High intrauterine cortisol exposure can inhibit fetal growth and have programming effects for the child’s subsequent stress reactivity. Placental 11beta-hydroxysteroid dehydrogenase (11β-HSD2 limits the amount of maternal cortisol transferred to the fetus. However, the relationship between maternal psychopathology and 11β-HSD2 remains poorly defined. This study examined the effect of maternal depressive disorder, antidepressant use and symptoms of depression and anxiety in pregnancy on placental 11β-HSD2 gene (HSD11B2 expression. Drawing on data from the Mercy Pregnancy and Emotional Wellbeing Study, placental HSD11B2 expression was compared among 33 pregnant women, who were selected based on membership of three groups; depressed (untreated, taking antidepressants and controls. Furthermore, associations between placental HSD11B2 and scores on the State-Trait Anxiety Inventory (STAI and Edinburgh Postnatal Depression Scale (EPDS during 12–18 and 28–34 weeks gestation were examined. Findings revealed negative correlations between HSD11B2 and both the EPDS and STAI (r = −0.11 to −0.28, with associations being particularly prominent during late gestation. Depressed and antidepressant exposed groups also displayed markedly lower placental HSD11B2 expression levels than controls. These findings suggest that maternal depression and anxiety may impact on fetal programming by down-regulating HSD11B2, and antidepressant treatment alone is unlikely to protect against this effect.

  8. How to Use SNP_TATA_Comparator to Find a Significant Change in Gene Expression Caused by the Regulatory SNP of This Gene's Promoter via a Change in Affinity of the TATA-Binding Protein for This Promoter.

    Science.gov (United States)

    Ponomarenko, Mikhail; Rasskazov, Dmitry; Arkova, Olga; Ponomarenko, Petr; Suslov, Valentin; Savinkova, Ludmila; Kolchanov, Nikolay

    2015-01-01

    The use of biomedical SNP markers of diseases can improve effectiveness of treatment. Genotyping of patients with subsequent searching for SNPs more frequent than in norm is the only commonly accepted method for identification of SNP markers within the framework of translational research. The bioinformatics applications aimed at millions of unannotated SNPs of the "1000 Genomes" can make this search for SNP markers more focused and less expensive. We used our Web service involving Fisher's Z-score for candidate SNP markers to find a significant change in a gene's expression. Here we analyzed the change caused by SNPs in the gene's promoter via a change in affinity of the TATA-binding protein for this promoter. We provide examples and discuss how to use this bioinformatics application in the course of practical analysis of unannotated SNPs from the "1000 Genomes" project. Using known biomedical SNP markers, we identified 17 novel candidate SNP markers nearby: rs549858786 (rheumatoid arthritis); rs72661131 (cardiovascular events in rheumatoid arthritis); rs562962093 (stroke); rs563558831 (cyclophosphamide bioactivation); rs55878706 (malaria resistance, leukopenia), rs572527200 (asthma, systemic sclerosis, and psoriasis), rs371045754 (hemophilia B), rs587745372 (cardiovascular events); rs372329931, rs200209906, rs367732974, and rs549591993 (all four: cancer); rs17231520 and rs569033466 (both: atherosclerosis); rs63750953, rs281864525, and rs34166473 (all three: malaria resistance, thalassemia).

  9. An 8-week, open-label, dose-finding study of nimodipine for the treatment of progranulin insufficiency from GRN gene mutations.

    Science.gov (United States)

    Sha, Sharon J; Miller, Zachary A; Min, Sang-Won; Zhou, Yungui; Brown, Jesse; Mitic, Laura L; Karydas, Anna; Koestler, Mary; Tsai, Richard; Corbetta-Rastelli, Chiara; Lin, Sophie; Hare, Emma; Fields, Scott; Fleischmann, Kirsten E; Powers, Ryan; Fitch, Ryan; Martens, Lauren Herl; Shamloo, Mehrdad; Fagan, Anne M; Farese, Robert V; Pearlman, Rodney; Seeley, William; Miller, Bruce L; Gan, Li; Boxer, Adam L

    2017-11-01

    Frontotemporal lobar degeneration-causing mutations in the progranulin ( GRN ) gene reduce progranulin protein (PGRN) levels, suggesting that restoring PGRN in mutation carriers may be therapeutic. Nimodipine, a Food and Drug Administration-approved blood-brain barrier-penetrant calcium channel blocker, increased PGRN levels in PGRN-deficient murine models. We sought to assess safety and tolerability of oral nimodipine in human GRN mutation carriers. We performed an open-label, 8-week, dose-finding, phase 1 clinical trial in eight GRN mutation carriers to assess the safety and tolerability of nimodipine and assayed fluid and radiologic markers to investigate therapeutic endpoints. There were no serious adverse events; however, PGRN concentrations (cerebrospinal fluid and plasma) did not change significantly following treatment (percent changes of -5.2 ± 10.9% in plasma and -10.2 ± 7.8% in cerebrospinal fluid). Measurable atrophy within the left middle frontal gyrus was observed over an 8-week period. While well tolerated, nimodipine treatment did not alter PGRN concentrations or secondary outcomes.

  10. Atypical radiological findings in achondroplasia with uncommon mutation of the fibroblast growth factor receptor-3 (FGFR-3) gene (Gly to Cys transition at codon 375)

    Energy Technology Data Exchange (ETDEWEB)

    Nishimuri, Gen [Dokkyo Univ. School of Medicine, Tochigi (Japan); Fukushima, Yoshimitsu; Ohashi, Hirofumi [Saitama Children`s Medical Center, Saitama (Japan); Ikegawa, Shiro [Tokyo Univ. (Japan)

    1995-11-20

    The recent discovery of mutations in the FGFR-3 (fibroblast growth factor receptor-3) gene (FGFR3) as the cause of achondroplasia has provided new insight into understanding genetic diseases. It was surprising from the viewpoint of molecular genetics that most patients with achondroplasia showed the same mutation at nucleotide 1138, leading to a single amino acid substitution from glycine to arginine at codon 380 (Gly380Arg). All 39 patients examined by two groups had the Gly380Arg; 38 patients and the other demonstrated a G to A and a G to C transition at nucleotide 1138, respectively. Subsequently another group disclosed a G to A transition at the same nucleotide 1138 in 21/23 patients of diverse ethnic origin, although mutations were not identified in two patients. To date, a total of 193 patients with the mutation of the G380Arg have been reported; a single patient with another mutation resulting in a substitution from glycine to cysteine at codon 375 (Gly375Cys) has been described. The presence of this common mutation is consistent with the clinical fact that achondroplastic individuals show less phenotypic variability than is unusual for autosomal dominant diseases. We encountered a Japanese boy with the Gly375Cys. His mother with achondroplasia has the same mutation. The molecular investigation of these patients was reported elsewhere. Here we report the clinical and radiological findings in this boy who demonstrated some atypical manifestations from those of typical achondroplasia. 8 refs., 1 fig.

  11. The CanOE strategy: integrating genomic and metabolic contexts across multiple prokaryote genomes to find candidate genes for orphan enzymes.

    Directory of Open Access Journals (Sweden)

    Adam Alexander Thil Smith

    2012-05-01

    Full Text Available Of all biochemically characterized metabolic reactions formalized by the IUBMB, over one out of four have yet to be associated with a nucleic or protein sequence, i.e. are sequence-orphan enzymatic activities. Few bioinformatics annotation tools are able to propose candidate genes for such activities by exploiting context-dependent rather than sequence-dependent data, and none are readily accessible and propose result integration across multiple genomes. Here, we present CanOE (Candidate genes for Orphan Enzymes, a four-step bioinformatics strategy that proposes ranked candidate genes for sequence-orphan enzymatic activities (or orphan enzymes for short. The first step locates "genomic metabolons", i.e. groups of co-localized genes coding proteins catalyzing reactions linked by shared metabolites, in one genome at a time. These metabolons can be particularly helpful for aiding bioanalysts to visualize relevant metabolic data. In the second step, they are used to generate candidate associations between un-annotated genes and gene-less reactions. The third step integrates these gene-reaction associations over several genomes using gene families, and summarizes the strength of family-reaction associations by several scores. In the final step, these scores are used to rank members of gene families which are proposed for metabolic reactions. These associations are of particular interest when the metabolic reaction is a sequence-orphan enzymatic activity. Our strategy found over 60,000 genomic metabolons in more than 1,000 prokaryote organisms from the MicroScope platform, generating candidate genes for many metabolic reactions, of which more than 70 distinct orphan reactions. A computational validation of the approach is discussed. Finally, we present a case study on the anaerobic allantoin degradation pathway in Escherichia coli K-12.

  12. Network analysis of hepatic genes responded to high-fat diet in C57BL/6J mice: nutrigenomics data mining from recent research findings.

    Science.gov (United States)

    Kim, Eun Jung; Kim, Eunjung; Kwon, Eun-Young; Jang, Hyun-Seo; Hur, Cheol-Goo; Choi, Myung-Sook

    2010-08-01

    Obesity and its associated complications, including diabetes, dyslipidemia, atherosclerosis, and some cancers, have been a global health problem with a rapid increase of the obese population. In this study, we selected 31 obesity candidate genes in the liver of high-fat-induced obese C57BL/6J mice through investigation of literature search and analyzed functional protein-protein interaction of the genes using the STRING database. Most of the obesity candidate genes were closely connected through lipid metabolism, and in particular acyl-coenzyme A oxidase 1 appeared to be a core obesity gene. Overall, genes involved in fatty acid beta-oxidation, fatty acid synthesis, and gluconeogenesis were up-regulated, and genes involved in sterol biosynthesis, insulin signaling, and oxidative stress defense system were down-regulated with a high-fat diet. Future identification of core obesity genes and their functional targets is expected to provide a new way to prevent obesity by phytochemicals or functional foods on the basis of food and nutritional genomics.

  13. Using regulatory and epistatic networks to extend the findings of a genome scan: identifying the gene drivers of pigmentation in merino sheep.

    Directory of Open Access Journals (Sweden)

    Elsa García-Gámez

    Full Text Available Extending genome wide association analysis by the inclusion of gene expression data may assist in the dissection of complex traits. We examined piebald, a pigmentation phenotype in both human and Merino sheep, by analysing multiple data types using a systems approach. First, a case control analysis of 49,034 ovine SNP was performed which confirmed a multigenic basis for the condition. We combined these results with gene expression data from five tissue types analysed with a skin-specific microarray. Promoter sequence analysis of differentially expressed genes allowed us to reverse-engineer a regulatory network. Likewise, by testing two-loci models derived from all pair-wise comparisons across piebald-associated SNP, we generated an epistatic network. At the intersection of both networks, we identified thirteen genes with insulin-like growth factor binding protein 7 (IGFBP7, platelet-derived growth factor alpha (PDGFRA and the tetraspanin platelet activator CD9 at the kernel of the intersection. Further, we report a number of differentially expressed genes in regions containing highly associated SNP including ATRN, DOCK7, FGFR1OP, GLI3, SILV and TBX15. The application of network theory facilitated co-analysis of genetic variation with gene expression, recapitulated aspects of the known molecular biology of skin pigmentation and provided insights into the transcription regulation and epistatic interactions involved in piebald Merino sheep.

  14. Clinical testing with a panel of 25 genes associated with increased cancer risk results in a significant increase in clinically significant findings across a broad range of cancer histories.

    Science.gov (United States)

    Rosenthal, Eric T; Bernhisel, Ryan; Brown, Krystal; Kidd, John; Manley, Susan

    2017-12-01

    Genetic testing for inherited cancer risk is now widely used to target individuals for screening and prevention. However, there is limited evidence available to evaluate the clinical utility of various testing strategies, such as single-syndrome, single-cancer, or pan-cancer gene panels. Here we report on the outcomes of testing with a 25-gene pan-cancer panel in a consecutive series of 252,223 individuals between September 2013 and July 2016. The majority of individuals (92.8%) met testing criteria for Hereditary Breast and Ovarian Cancer (HBOC) and/or Lynch syndrome (LS). Overall, 17,340 PVs were identified in 17,000 (6.7%) of the tested individuals. The PV positive rate was 9.8% among individuals with a personal cancer history, compared to 4.7% in unaffected individuals. PVs were most common in BRCA1/2 (42.2%), other breast cancer (BR) genes (32.9%), and the LS genes (13.2%). Half the PVs identified among individuals who met only HBOC testing criteria were in genes other than BRCA1/2. Similarly, half of PVs identified in individuals who met only LS testing criteria were in non-LS genes. These findings suggest that genetic testing with a pan-cancer panel in this cohort provides improved clinical utility over traditional single-gene or single-syndrome testing. Copyright © 2017 Myriad Genetics, Inc. Published by Elsevier Inc. All rights reserved.

  15. An epigenome-wide study of obesity in African American youth and young adults : novel findings, replication in neutrophils, and relationship with gene expression

    NARCIS (Netherlands)

    Wang, Xiaoling; Pan, Yue; Zhu, Haidong; Hao, Guang; Huang, Yisong; Barnes, Vernon; Shi, Huidong; Snieder, Harold; Pankow, James; North, Kari; Grove, Megan; Guan, Weihua; Demerath, Ellen; Dong, Yanbin; Su, Shaoyong

    2018-01-01

    Background: We conducted an epigenome-wide association study (EWAS) on obesity in healthy youth and young adults and further examined to what extent identified signals influenced gene expression and were independent of cell type composition and obesity-related cardio-metabolic risk factors.

  16. Revealing Alzheimer's disease genes spectrum in the whole-genome by machine learning.

    Science.gov (United States)

    Huang, Xiaoyan; Liu, Hankui; Li, Xinming; Guan, Liping; Li, Jiankang; Tellier, Laurent Christian Asker M; Yang, Huanming; Wang, Jian; Zhang, Jianguo

    2018-01-10

    Alzheimer's disease (AD) is an important, progressive neurodegenerative disease, with a complex genetic architecture. A key goal of biomedical research is to seek out disease risk genes, and to elucidate the function of these risk genes in the development of disease. For this purpose, expanding the AD-associated gene set is necessary. In past research, the prediction methods for AD related genes has been limited in their exploration of the target genome regions. We here present a genome-wide method for AD candidate genes predictions. We present a machine learning approach (SVM), based upon integrating gene expression data with human brain-specific gene network data, to discover the full spectrum of AD genes across the whole genome. We classified AD candidate genes with an accuracy and the area under the receiver operating characteristic (ROC) curve of 84.56% and 94%. Our approach provides a supplement for the spectrum of AD-associated genes extracted from more than 20,000 genes in a genome wide scale. In this study, we have elucidated the whole-genome spectrum of AD, using a machine learning approach. Through this method, we expect for the candidate gene catalogue to provide a more comprehensive annotation of AD for researchers.

  17. Clinical and radiological findings of a cerebrotendinous xanthomatosis patient with a novel p.A335V mutation in the CYP27A1 gene.

    Science.gov (United States)

    Yoshinaga, Tsuneaki; Sekijima, Yoshiki; Koyama, Shingo; Maruyama, Keiko; Yoshida, Toshikazu; Kato, Takeo; Ikeda, Shu-ichi

    2014-01-01

    We herein describe the case of a Japanese cerebrotendinous xanthomatosis (CTX) patient with a novel CYP27A1 gene mutation. The patient had been diagnosed with cataracts at 25 years of age and subsequently developed neurological symptoms in his forties, being referred to our hospital at 47 years of age. Upon admission, Achilles tendon xanthomas, cognitive impairment, dysphagia, dysarthria, dystonia, spasticity, muscle weakness and ataxia were observed. Brain MRI revealed abnormal signals in the dentate nuclei, periventricular white matter and pyramidal tract, and the serum cholestanol level was elevated. A CYP27A1 gene analysis identified compound heterozygosity for p.A335V, a novel mutation, and p.R405Q, a previously reported mutation. Making an early diagnosis of CTX is crucial, as the administration of chenodeoxycholic acid reverses metabolic derangement.

  18. Short rib-polydactyly syndrome type II (Majewski: Prenatal diagnosis, perinatal imaging findings and molecular analysis of the NEK1 gene

    Directory of Open Access Journals (Sweden)

    Chih-Ping Chen

    2012-03-01

    Conclusion: Tibial aplasia, choroid plexus cysts and polycystic kidneys can be prominent prenatal ultrasound findings of type II SRPS. The present case provides evidence for a correlation of NEK1 mutation with type II SRPS.

  19. Combined approach for finding susceptibility genes in DISH/chondrocalcinosis families: whole-genome-wide linkage and IBS/IBD studies.

    Science.gov (United States)

    Couto, Ana Rita; Parreira, Bruna; Thomson, Russell; Soares, Marta; Power, Deborah M; Stankovich, Jim; Armas, Jácome Bruges; Brown, Matthew A

    2017-01-01

    Twelve families with exuberant and early-onset calcium pyrophosphate dehydrate chondrocalcinosis (CC) and diffuse idiopathic skeletal hyperostosis (DISH), hereafter designated DISH/CC, were identified in Terceira Island, the Azores, Portugal. Ninety-two (92) individuals from these families were selected for whole-genome-wide linkage analysis. An identity-by-descent (IBD) analysis was performed in 10 individuals from 5 of the investigated pedigrees. The chromosome area with the maximal logarithm of the odds score (1.32; P =0.007) was not identified using the IBD/identity-by-state (IBS) analysis; therefore, it was not investigated further. From the IBD/IBS analysis, two candidate genes, LEMD3 and RSPO4 , were identified and sequenced. Nine genetic variants were identified in the RSPO4 gene; one regulatory variant (rs146447064) was significantly more frequent in control individuals than in DISH/CC patients ( P =0.03). Four variants were identified in LEMD3 , and the rs201930700 variant was further investigated using segregation analysis. None of the genetic variants in RSPO4 or LEMD3 segregated within the studied families. Therefore, although a major genetic effect was shown to determine DISH/CC occurrence within these families, the specific genetic variants involved were not identified.

  20. Genes and Hearing Loss

    Science.gov (United States)

    ... ENTCareers Marketplace Find an ENT Doctor Near You Genes and Hearing Loss Genes and Hearing Loss Patient ... mutation may only have dystopia canthorum. How Do Genes Work? Genes are a road map for the ...

  1. Tc-99m MDP Bone SPECT/CT Findings of a Patient Detected with a New Mutation in LEMD3 Gene: A Case of Osteopoikilosis.

    Science.gov (United States)

    Silov, Güler; Erdoğan, Zeynep; Erdoğan, Murat; Özdal, Ayşegül; Gençer, Hümeyra; Akalın, Tayfun; Karaçavuş, Seyhan

    2018-02-01

    Osteopoikilosis is an inherited condition with autosomal dominant trait resulting in sclerotic foci throughout the skeleton. It has been suggested that loss-of-function mutations of LEMD3 gene located on 12q14.3 result in osetopoikilosis. A bp heterozygote deletion was detected in our patient at the cytosine nucleotide at position 1105 with molecular genetic analysis. Although this mutation has not been previously described, it was considered to be the most likely cause of the disease in our patient due to frame shift and premature stop codon formation. As in our case, three phase bone scintigraphy and whole body imaging did not reflect the true extent of lesion sites and lesion activity. SPECT/CT images could reflect lesion location and activity more accurately, and could be a good alternative for differential diagnosis of unexplained bone pain and sclerotic lesions in one examination.

  2. Citation bias and selective focus on positive findings in the literature on the serotonin transporter gene (5-HTTLPR), life stress and depression.

    Science.gov (United States)

    de Vries, Y A; Roest, A M; Franzen, M; Munafò, M R; Bastiaansen, J A

    2016-10-01

    Caspi et al.'s 2003 report that 5-HTTLPR genotype moderates the influence of life stress on depression has been highly influential but remains contentious. We examined whether the evidence base for the 5-HTTLPR-stress interaction has been distorted by citation bias and a selective focus on positive findings. A total of 73 primary studies were coded for study outcomes and focus on positive findings in the abstract. Citation rates were compared between studies with positive and negative results, both within this network of primary studies and in Web of Science. In addition, the impact of focus on citation rates was examined. In all, 24 (33%) studies were coded as positive, but these received 48% of within-network and 68% of Web of Science citations. The 38 (52%) negative studies received 42 and 23% of citations, respectively, while the 11 (15%) unclear studies received 10 and 9%. Of the negative studies, the 16 studies without a positive focus (42%) received 47% of within-network citations and 32% of Web of Science citations, while the 13 (34%) studies with a positive focus received 39 and 51%, respectively, and the nine (24%) studies with a partially positive focus received 14 and 17%. Negative studies received fewer citations than positive studies. Furthermore, over half of the negative studies had a (partially) positive focus, and Web of Science citation rates were higher for these studies. Thus, discussion of the 5-HTTLPR-stress interaction is more positive than warranted. This study exemplifies how evidence-base-distorting mechanisms undermine the authenticity of research findings.

  3. Jackson-Weiss syndrome: Clinical and radiological findings in a large kindred and exclusion of the gene from 7p21 and 5qter

    Energy Technology Data Exchange (ETDEWEB)

    Ades, L.C.; Haan, E.A.; Mulley, J.C.; Senga, I.P.; Morris, L.L.; David, D.J. [Women`s and Children`s Hospital, North Adelaide (Australia)

    1994-06-01

    We describe the clinical and radiological manifestations of the Jackson-Weiss syndrome (JWS) in a large South Australian kindred. Radiological abnormalities not previously described in the hands include coned epiphyses, distal and middle phalangeal hypoplasia, and carpal bone malsegmentation. New radiological findings in the feet include coned epiphyses, hallux valgus, phalangeal, tarso-navicular and calcaneo-navicular fusions, and uniform absence of metatarsal fusions. Absence of linkage to eight markers along the short arm of chromosome 7 excluded allelian between JWS and Saethre-Chotzen syndrome at 7p21. No linkage was detected to D5S211, excluding allelism to another recently described cephalosyndactyly syndrome mapping to 5qter. 35 refs., 5 figs., 4 tabs.

  4. Geographical distribution of MTHFR C677T, A1298C and MTRR A66G gene polymorphisms in China: findings from 15357 adults of Han nationality.

    Directory of Open Access Journals (Sweden)

    Boyi Yang

    Full Text Available BACKGROUND: Methylenetetrahydrofolate reductase (MTHFR C677T, A1298C and methionine synthase reductase (MTRR A66G polymorphisms are important genetic determinants for homocysteine (Hcy levels, and are associated with several disorders. These polymorphisms are heterogeneously distributed worldwide. Our objective was to explore the geographical distributions of these polymorphisms in China. METHODOLOGIES: 15357 healthy adults were recruited from 10 regions. Buccal samples were collected and genomic DNA was isolated. Genotyping was performed using the fluorogenic 5'-nuclease assay. PRINCIPAL FINDINGS: The prevalence of the three polymorphisms among different populations from China varied significantly and showed apparent geographical gradients. For MTHFR C677T, the frequencies of the 677T allele and the 677TT genotype were significantly higher among northern populations and ranged from the lowest values (24.0% and 6.4%, respectively in Hainan (southern to the highest values (63.1% and 40.8%, respectively in Shandong (northern. For MTHFR A1298C, the 1298C allele and the 1298CC genotype frequencies were significantly higher among southern populations and increased from low values (13.1% and 1.4%, respectively in Shandong to high values (25.7% and 6.7%, respectively in Hainan. For A66G, the 66G allele and the 66GG genotype frequencies increased from lower values (23.7% and 5.4%, respectively in Shandong to higher values (29.2% and 8.6%, respectively in Hainan. The overall frequency of the 677T allele, 677TT genotype, 1298C allele, 1298CC genotype, 66G allele and 66GG genotype in the Chinese Han population was 45.2%, 23.2%, 18.6%, 3.9%, 25.7%, and 6.6%, respectively. No gender differences were found in the prevalence of both the MTHFR C677T and MTRR A66G polymorphisms. CONCLUSIONS: This study indicates that there are marked geographical variations in the prevalence of the three polymorphisms among Chinese Han populations. Our baseline data may be

  5. Geographical Distribution of MTHFR C677T, A1298C and MTRR A66G Gene Polymorphisms in China: Findings from 15357 Adults of Han Nationality

    Science.gov (United States)

    Yang, Boyi; Liu, Yuyan; Li, Yongfang; Fan, Shujun; Zhi, Xueyuan; Lu, Xiangxiang; Wang, Da; Zheng, Quanmei; Wang, Yinuo; Wang, Yanxun; Sun, Guifan

    2013-01-01

    Background Methylenetetrahydrofolate reductase (MTHFR) C677T, A1298C and methionine synthase reductase (MTRR) A66G polymorphisms are important genetic determinants for homocysteine (Hcy) levels, and are associated with several disorders. These polymorphisms are heterogeneously distributed worldwide. Our objective was to explore the geographical distributions of these polymorphisms in China. Methodologies 15357 healthy adults were recruited from 10 regions. Buccal samples were collected and genomic DNA was isolated. Genotyping was performed using the fluorogenic 5′-nuclease assay. Principal Findings The prevalence of the three polymorphisms among different populations from China varied significantly and showed apparent geographical gradients. For MTHFR C677T, the frequencies of the 677T allele and the 677TT genotype were significantly higher among northern populations and ranged from the lowest values (24.0% and 6.4%, respectively) in Hainan (southern) to the highest values (63.1% and 40.8%, respectively) in Shandong (northern). For MTHFR A1298C, the 1298C allele and the 1298CC genotype frequencies were significantly higher among southern populations and increased from low values (13.1% and 1.4%, respectively) in Shandong to high values (25.7% and 6.7%, respectively) in Hainan. For A66G, the 66G allele and the 66GG genotype frequencies increased from lower values (23.7% and 5.4%, respectively) in Shandong to higher values (29.2% and 8.6%, respectively) in Hainan. The overall frequency of the 677T allele, 677TT genotype, 1298C allele, 1298CC genotype, 66G allele and 66GG genotype in the Chinese Han population was 45.2%, 23.2%, 18.6%, 3.9%, 25.7%, and 6.6%, respectively. No gender differences were found in the prevalence of both the MTHFR C677T and MTRR A66G polymorphisms. Conclusions This study indicates that there are marked geographical variations in the prevalence of the three polymorphisms among Chinese Han populations. Our baseline data may be useful for

  6. Erdheim-Chester disease with novel gene mutations discovered as an incidental finding in explanted liver of a patient with hepatitis C cirrhosis: A case report and literature review.

    Science.gov (United States)

    Liao, Xiaoyan; Thorson, John A; Hughes, Tudor; Nguyen, John C; Wang, Huan-You; Lin, Grace Y

    2016-09-01

    Erdheim-Chester disease (ECD) is a rare form of non-Langerhans cell histiocytosis characterized by xanthogranulomatous infiltration of foamy histiocytes frequently involving bone and other organ systems. We herein report a unique case of ECD discovered incidentally in an explanted liver in a 65-year-old male with end-stage liver disease secondary to hepatitis C cirrhosis. Histological examination and immunohistochemical studies in the explanted liver revealed prominent foamy histiocytes that were CD68 positive, but CD1a and S100 negative. Mutational hotspot analysis of the explanted liver using a panel of 47 most common cancer-related genes performed by next generation sequencing (NGS) revealed likely somatic mutations in the PDGFRA, PTEN, and HNF1A genes, but no BRAF codon 600 mutations were detected. The bone marrow showed similar findings as in the liver. Whole body PET and bone scans demonstrated increased heterogeneous uptake in bilateral humeral and femoral diaphysis, most compatible with ECD. To our knowledge, this is the first case report of ECD that involves mainly bone marrow and liver with novel genomic alterations. Our case highlights the diversity and complexity of this disease entity and the importance of multi-modality approach integrating clinical and radiologic features with histopathologic and molecular/genomic findings. Copyright © 2016 Elsevier GmbH. All rights reserved.

  7. Supervised classification of combined copy number and gene expression data

    Directory of Open Access Journals (Sweden)

    Riccadonna S.

    2007-12-01

    Full Text Available In this paper we apply a predictive profiling method to genome copy number aberrations (CNA in combination with gene expression and clinical data to identify molecular patterns of cancer pathophysiology. Predictive models and optimal feature lists for the platforms are developed by a complete validation SVM-based machine learning system. Ranked list of genome CNA sites (assessed by comparative genomic hybridization arrays – aCGH and of differentially expressed genes (assessed by microarray profiling with Affy HG-U133A chips are computed and combined on a breast cancer dataset for the discrimination of Luminal/ ER+ (Lum/ER+ and Basal-like/ER- classes. Different encodings are developed and applied to the CNA data, and predictive variable selection is discussed. We analyze the combination of profiling information between the platforms, also considering the pathophysiological data. A specific subset of patients is identified that has a different response to classification by chromosomal gains and losses and by differentially expressed genes, corroborating the idea that genomic CNA can represent an independent source for tumor classification.

  8. SVM-Based Dynamic Reconfiguration CPS for Manufacturing System in Industry 4.0

    Directory of Open Access Journals (Sweden)

    Hyun-Jun Shin

    2018-01-01

    Full Text Available CPS is potential application in various fields, such as medical, healthcare, energy, transportation, and defense, as well as Industry 4.0 in Germany. Although studies on the equipment aging and prediction of problem have been done by combining CPS with Industry 4.0, such studies were based on small numbers and majority of the papers focused primarily on CPS methodology. Therefore, it is necessary to study active self-protection to enable self-management functions, such as self-healing by applying CPS in shop-floor. In this paper, we have proposed modeling of shop-floor and a dynamic reconfigurable CPS scheme that can predict the occurrence of anomalies and self-protection in the model. For this purpose, SVM was used as a machine learning technology and it was possible to restrain overloading in manufacturing process. In addition, we design CPS framework based on machine learning for Industry 4.0, simulate it, and perform. Simulation results show the simulation model autonomously detects the abnormal situation and it is dynamically reconfigured through self-healing.

  9. An SVM-based solution for fault detection in wind turbines.

    Science.gov (United States)

    Santos, Pedro; Villa, Luisa F; Reñones, Aníbal; Bustillo, Andres; Maudes, Jesús

    2015-03-09

    Research into fault diagnosis in machines with a wide range of variable loads and speeds, such as wind turbines, is of great industrial interest. Analysis of the power signals emitted by wind turbines for the diagnosis of mechanical faults in their mechanical transmission chain is insufficient. A successful diagnosis requires the inclusion of accelerometers to evaluate vibrations. This work presents a multi-sensory system for fault diagnosis in wind turbines, combined with a data-mining solution for the classification of the operational state of the turbine. The selected sensors are accelerometers, in which vibration signals are processed using angular resampling techniques and electrical, torque and speed measurements. Support vector machines (SVMs) are selected for the classification task, including two traditional and two promising new kernels. This multi-sensory system has been validated on a test-bed that simulates the real conditions of wind turbines with two fault typologies: misalignment and imbalance. Comparison of SVM performance with the results of artificial neural networks (ANNs) shows that linear kernel SVM outperforms other kernels and ANNs in terms of accuracy, training and tuning times. The suitability and superior performance of linear SVM is also experimentally analyzed, to conclude that this data acquisition technique generates linearly separable datasets.

  10. An SVM-Based Solution for Fault Detection in Wind Turbines

    Directory of Open Access Journals (Sweden)

    Pedro Santos

    2015-03-01

    Full Text Available Research into fault diagnosis in machines with a wide range of variable loads and speeds, such as wind turbines, is of great industrial interest. Analysis of the power signals emitted by wind turbines for the diagnosis of mechanical faults in their mechanical transmission chain is insufficient. A successful diagnosis requires the inclusion of accelerometers to evaluate vibrations. This work presents a multi-sensory system for fault diagnosis in wind turbines, combined with a data-mining solution for the classification of the operational state of the turbine. The selected sensors are accelerometers, in which vibration signals are processed using angular resampling techniques and electrical, torque and speed measurements. Support vector machines (SVMs are selected for the classification task, including two traditional and two promising new kernels. This multi-sensory system has been validated on a test-bed that simulates the real conditions of wind turbines with two fault typologies: misalignment and imbalance. Comparison of SVM performance with the results of artificial neural networks (ANNs shows that linear kernel SVM outperforms other kernels and ANNs in terms of accuracy, training and tuning times. The suitability and superior performance of linear SVM is also experimentally analyzed, to conclude that this data acquisition technique generates linearly separable datasets.

  11. SVM-based base-metal prospectivity modeling of the Aravalli Orogen, Northwestern India

    Science.gov (United States)

    Porwal, Alok; Yu, Le; Gessner, Klaus

    2010-05-01

    The Proterozoic Aravalli orogen in the state of Rajasthan, northwestern India, constitutes the most important metallogenic province for base-metal deposits in India and hosts the entire economically viable lead-zinc resource-base of the country. The orogen evolved through near-orderly Wilson cycles of repeated extensional and compressional tectonics resulting in sequential opening and closing of intracratonic rifts and amalgamation of crustal domains during a circa 1.0-Ga geological history from 2.2 Ga to 1.0 Ga. This study develops a conceptual tectonostratigraphic model of the orogen based on a synthesis of the available geological, geophysical and geochronological data followed by deep-seismic-reflectivity-constrained 2-D forward gravity modeling, and links it to the Proterozoic base-metal metallogeny in the orogen in order to identify key geological controls on the base-metal mineralization. These controls are translated into exploration criteria for base-metal deposits, validated using empirical spatial analysis, and used to derive input spatial variables for model-based base-metal prospectivity mapping of the orogen. A support vector machine (SVM) algorithm augmented by incorporating a feature selection procedure is used in a GIS environment to implement the prospectivity mapping. A comparison of the SVM-derived prospectivity map with the ones derived using other established models such as neural-networks, logistic regression, and Bayesian weights-of-evidence indicates that the SVM outperforms other models, which is attributed to the capability of the SVM to return robust classification based on small training datasets.

  12. [Application of optimized parameters SVM based on photoacoustic spectroscopy method in fault diagnosis of power transformer].

    Science.gov (United States)

    Zhang, Yu-xin; Cheng, Zhi-feng; Xu, Zheng-ping; Bai, Jing

    2015-01-01

    In order to solve the problems such as complex operation, consumption for the carrier gas and long test period in traditional power transformer fault diagnosis approach based on dissolved gas analysis (DGA), this paper proposes a new method which is detecting 5 types of characteristic gas content in transformer oil such as CH4, C2H2, C2H4, C2H6 and H2 based on photoacoustic Spectroscopy and C2H2/C2H4, CH4/H2, C2H4/C2H6 three-ratios data are calculated. The support vector machine model was constructed using cross validation method under five support vector machine functions and four kernel functions, heuristic algorithms were used in parameter optimization for penalty factor c and g, which to establish the best SVM model for the highest fault diagnosis accuracy and the fast computing speed. Particles swarm optimization and genetic algorithm two types of heuristic algorithms were comparative studied in this paper for accuracy and speed in optimization. The simulation result shows that SVM model composed of C-SVC, RBF kernel functions and genetic algorithm obtain 97. 5% accuracy in test sample set and 98. 333 3% accuracy in train sample set, and genetic algorithm was about two times faster than particles swarm optimization in computing speed. The methods described in this paper has many advantages such as simple operation, non-contact measurement, no consumption for the carrier gas, long test period, high stability and sensitivity, the result shows that the methods described in this paper can instead of the traditional transformer fault diagnosis by gas chromatography and meets the actual project needs in transformer fault diagnosis.

  13. Methodology for selection of attributes and operating conditions for SVM-Based fault locator's

    Directory of Open Access Journals (Sweden)

    Debbie Johan Arredondo Arteaga

    2017-01-01

    Full Text Available Context: Energy distribution companies must employ strategies to meet their timely and high quality service, and fault-locating techniques represent and agile alternative for restoring the electric service in the power distribution due to the size of distribution services (generally large and the usual interruptions in the service. However, these techniques are not robust enough and present some limitations in both computational cost and the mathematical description of the models they use. Method: This paper performs an analysis based on a Support Vector Machine for the evaluation of the proper conditions to adjust and validate a fault locator for distribution systems; so that it is possible to determine the minimum number of operating conditions that allow to achieve a good performance with a low computational effort. Results: We tested the proposed methodology in a prototypical distribution circuit, located in a rural area of Colombia. This circuit has a voltage of 34.5 KV and is subdivided in 20 zones. Additionally, the characteristics of the circuit allowed us to obtain a database of 630.000 records of single-phase faults and different operating conditions. As a result, we could determine that the locator showed a performance above 98% with 200 suitable selected operating conditions. Conclusions: It is possible to improve the performance of fault locators based on Support Vector Machine. Specifically, these improvements are achieved by properly selecting optimal operating conditions and attributes, since they directly affect the performance in terms of efficiency and the computational cost.

  14. SVM-based synthetic fingerprint discrimination algorithm and quantitative optimization strategy.

    Science.gov (United States)

    Chen, Suhang; Chang, Sheng; Huang, Qijun; He, Jin; Wang, Hao; Huang, Qiangui

    2014-01-01

    Synthetic fingerprints are a potential threat to automatic fingerprint identification systems (AFISs). In this paper, we propose an algorithm to discriminate synthetic fingerprints from real ones. First, four typical characteristic factors-the ridge distance features, global gray features, frequency feature and Harris Corner feature-are extracted. Then, a support vector machine (SVM) is used to distinguish synthetic fingerprints from real fingerprints. The experiments demonstrate that this method can achieve a recognition accuracy rate of over 98% for two discrete synthetic fingerprint databases as well as a mixed database. Furthermore, a performance factor that can evaluate the SVM's accuracy and efficiency is presented, and a quantitative optimization strategy is established for the first time. After the optimization of our synthetic fingerprint discrimination task, the polynomial kernel with a training sample proportion of 5% is the optimized value when the minimum accuracy requirement is 95%. The radial basis function (RBF) kernel with a training sample proportion of 15% is a more suitable choice when the minimum accuracy requirement is 98%.

  15. Online Adaptive Error Compensation SVM-Based Sliding Mode Control of an Unmanned Aerial Vehicle

    Directory of Open Access Journals (Sweden)

    Kaijia Xue

    2016-01-01

    Full Text Available Unmanned Aerial Vehicle (UAV is a nonlinear dynamic system with uncertainties and noises. Therefore, an appropriate control system has an obligation to ensure the stabilization and navigation of UAV. This paper mainly discusses the control problem of quad-rotor UAV system, which is influenced by unknown parameters and noises. Besides, a sliding mode control based on online adaptive error compensation support vector machine (SVM is proposed for stabilizing quad-rotor UAV system. Sliding mode controller is established through analyzing quad-rotor dynamics model in which the unknown parameters are computed by offline SVM. During this process, the online adaptive error compensation SVM method is applied in this paper. As modeling errors and noises both exist in the process of flight, the offline SVM one-time mode cannot predict the uncertainties and noises accurately. The control law is adjusted in real-time by introducing new training sample data to online adaptive SVM in the control process, so that the stability and robustness of flight are ensured. It can be demonstrated through the simulation experiments that the UAV that joined online adaptive SVM can track the changing path faster according to its dynamic model. Consequently, the proposed method that is proved has the better control effect in the UAV system.

  16. SVM-based feature extraction and classification of aflatoxin contaminated corn using fluorescence hyperspectral data

    Science.gov (United States)

    Support Vector Machine (SVM) was used in the Genetic Algorithms (GA) process to select and classify a subset of hyperspectral image bands. The method was applied to fluorescence hyperspectral data for the detection of aflatoxin contamination in Aspergillus flavus infected single corn kernels. In the...

  17. A Multi-Classification Method of Improved SVM-based Information Fusion for Traffic Parameters Forecasting

    Directory of Open Access Journals (Sweden)

    Hongzhuan Zhao

    2016-04-01

    Full Text Available With the enrichment of perception methods, modern transportation system has many physical objects whose states are influenced by many information factors so that it is a typical Cyber-Physical System (CPS. Thus, the traffic information is generally multi-sourced, heterogeneous and hierarchical. Existing research results show that the multisourced traffic information through accurate classification in the process of information fusion can achieve better parameters forecasting performance. For solving the problem of traffic information accurate classification, via analysing the characteristics of the multi-sourced traffic information and using redefined binary tree to overcome the shortcomings of the original Support Vector Machine (SVM classification in information fusion, a multi-classification method using improved SVM in information fusion for traffic parameters forecasting is proposed. The experiment was conducted to examine the performance of the proposed scheme, and the results reveal that the method can get more accurate and practical outcomes.

  18. Settlement Prediction of Road Soft Foundation Using a Support Vector Machine (SVM Based on Measured Data

    Directory of Open Access Journals (Sweden)

    Yu Huiling

    2016-01-01

    Full Text Available The suppor1t vector machine (SVM is a relatively new artificial intelligence technique which is increasingly being applied to geotechnical problems and is yielding encouraging results. SVM is a new machine learning method based on the statistical learning theory. A case study based on road foundation engineering project shows that the forecast results are in good agreement with the measured data. The SVM model is also compared with BP artificial neural network model and traditional hyperbola method. The prediction results indicate that the SVM model has a better prediction ability than BP neural network model and hyperbola method. Therefore, settlement prediction based on SVM model can reflect actual settlement process more correctly. The results indicate that it is effective and feasible to use this method and the nonlinear mapping relation between foundation settlement and its influence factor can be expressed well. It will provide a new method to predict foundation settlement.

  19. Restoring the Generalizability of SVM Based Decoding in High Dimensional Neuroimage Data

    DEFF Research Database (Denmark)

    Abrahamsen, Trine Julie; Hansen, Lars Kai

    2011-01-01

    for Support Vector Machines. However, good generalization may be recovered in part by a simple renormalization procedure. We show that with proper renormalization, cross-validation based parameter optimization leads to the acceptance of more non-linearity in neuroimage classifiers than would have been......Variance inflation is caused by a mismatch between linear projections of test and training data when projections are estimated on training sets smaller than the dimensionality of the feature space. We demonstrate that variance inflation can lead to an increased neuroimage decoding error rate...

  20. Genes and Gene Therapy

    Science.gov (United States)

    ... correctly, a child can have a genetic disorder. Gene therapy is an experimental technique that uses genes to ... or prevent disease. The most common form of gene therapy involves inserting a normal gene to replace an ...

  1. WNT3A gene polymorphisms are associated with bone mineral density variation in postmenopausal mestizo women of an urban Mexican population: findings of a pathway-based high-density single nucleotide screening

    OpenAIRE

    Velázquez-Cruz, Rafael; García-Ortiz, Humberto; Castillejos-López, Manuel; Quiterio, Manuel; Valdés-Flores, Margarita; Orozco, Lorena; Villarreal-Molina, Teresa; Salmerón, Jorge

    2014-01-01

    Osteoporosis (OP) is a common skeletal disorder characterized by low bone mineral density (BMD) and is a common health problem in Mexico. To date, few genes affecting BMD variation in the Mexican population have been identified. The aim of this study was to investigate the association of single nucleotide polymorphisms (SNPs) located in genes of the Wnt pathway with BMD variation at various skeletal sites in a cohort of postmenopausal Mexican women. A total of 121 SNPs in or near 15 Wnt signa...

  2. WNT3A gene polymorphisms are associated with bone mineral density variation in postmenopausal mestizo women of an urban Mexican population: findings of a pathway-based high-density single nucleotide screening.

    Science.gov (United States)

    Velázquez-Cruz, Rafael; García-Ortiz, Humberto; Castillejos-López, Manuel; Quiterio, Manuel; Valdés-Flores, Margarita; Orozco, Lorena; Villarreal-Molina, Teresa; Salmerón, Jorge

    2014-06-01

    Osteoporosis (OP) is a common skeletal disorder characterized by low bone mineral density (BMD) and is a common health problem in Mexico. To date, few genes affecting BMD variation in the Mexican population have been identified. The aim of this study was to investigate the association of single nucleotide polymorphisms (SNPs) located in genes of the Wnt pathway with BMD variation at various skeletal sites in a cohort of postmenopausal Mexican women. A total of 121 SNPs in or near 15 Wnt signaling pathway genes and 96 ancestry informative markers were genotyped in 425 postmenopausal women using the Illumina GoldenGate microarray SNP genotyping method. BMD was measured by dual-energy X-ray absorptiometry in total hip, femoral neck, Ward's triangle, and lumbar spine. Associations were tested by linear regression for quantitative traits adjusting for possible confounding factors. SNP rs752107 in WNT3A was strongly associated with decreased total hip BMD showing the highest significance under the recessive model (P = 0.00012). This SNP is predicted to disrupt a binding site for microRNA-149. In addition, a polymorphism of the Wnt antagonist DKK2 was associated with BMD in femoral neck under a recessive model (P = 0.009). Several LRP4, LRP5, and LRP6 gene variants showed site-specific associations with BMD. In conclusion, this is the first report associating Wnt pathway gene variants with BMD in the Mexican population.

  3. The influence of serotonin- and other genes on impulsive behavioral aggression and cognitive impulsivity in children with attention-deficit/hyperactivity disorder (ADHD: Findings from a family-based association test (FBAT analysis

    Directory of Open Access Journals (Sweden)

    Gill Michael

    2008-10-01

    Full Text Available Abstract Background Low serotonergic (5-HT activity correlates with increased impulsive-aggressive behavior, while the opposite association may apply to cognitive impulsiveness. Both types of impulsivity are associated with attention-deficit/hyperactivity disorder (ADHD, and genes of functional significance for the 5-HT system are implicated in this disorder. Here we demonstrate the separation of aggressive and cognitive components of impulsivity from symptom ratings and test their association with 5-HT and functionally related genes using a family-based association test (FBAT-PC. Methods Our sample consisted of 1180 offspring from 607 families from the International Multicenter ADHD Genetics (IMAGE study. Impulsive symptoms were assessed using the long forms of the Conners and the Strengths and Difficulties parent and teacher questionnaires. Factor analysis showed that the symptoms aggregated into parent- and teacher-rated behavioral and cognitive impulsivity. We then selected 582 single nucleotide polymorphisms (SNPs from 14 genes directly or indirectly related to 5-HT function. Associations between these SNPs and the behavioral/cognitive groupings of impulsive symptoms were evaluated using the FBAT-PC approach. Results In the FBAT-PC analysis for cognitive impulsivity 2 SNPs from the gene encoding phenylethanolamine N-methyltransferase (PNMT, the rate-limiting enzyme for adrenalin synthesis attained corrected gene-wide significance. Nominal significance was shown for 12 SNPs from BDNF, DRD1, HTR1E, HTR2A, HTR3B, DAT1/SLC6A3, and TPH2 genes replicating reported associations with ADHD. For overt aggressive impulsivity nominal significance was shown for 6 SNPs from BDNF, DRD4, HTR1E, PNMT, and TPH2 genes that have also been reported to be associated with ADHD. Associations for cognitive impulsivity with a SERT/SLC6A4 variant (STin2: 12 repeats and aggressive behavioral impulsivity with a DRD4 variant (exon 3: 3 repeats are also described

  4. An integrative machine learning strategy for improved prediction of essential genes in Escherichia coli metabolism using flux-coupled features.

    Science.gov (United States)

    Nandi, Sutanu; Subramanian, Abhishek; Sarkar, Ram Rup

    2017-07-25

    Prediction of essential genes helps to identify a minimal set of genes that are absolutely required for the appropriate functioning and survival of a cell. The available machine learning techniques for essential gene prediction have inherent problems, like imbalanced provision of training datasets, biased choice of the best model for a given balanced dataset, choice of a complex machine learning algorithm, and data-based automated selection of biologically relevant features for classification. Here, we propose a simple support vector machine-based learning strategy for the prediction of essential genes in Escherichia coli K-12 MG1655 metabolism that integrates a non-conventional combination of an appropriate sample balanced training set, a unique organism-specific genotype, phenotype attributes that characterize essential genes, and optimal parameters of the learning algorithm to generate the best machine learning model (the model with the highest accuracy among all the models trained for different sample training sets). For the first time, we also introduce flux-coupled metabolic subnetwork-based features for enhancing the classification performance. Our strategy proves to be superior as compared to previous SVM-based strategies in obtaining a biologically relevant classification of genes with high sensitivity and specificity. This methodology was also trained with datasets of other recent supervised classification techniques for essential gene classification and tested using reported test datasets. The testing accuracy was always high as compared to the known techniques, proving that our method outperforms known methods. Observations from our study indicate that essential genes are conserved among homologous bacterial species, demonstrate high codon usage bias, GC content and gene expression, and predominantly possess a tendency to form physiological flux modules in metabolism.

  5. Find din stemme

    DEFF Research Database (Denmark)

    Hansen, Jette Barnholdt

    2010-01-01

    Anmeldelse af Dorte Kock og Lene Kleinschmidts: Find din stemme. En brugsbog.Hans Reitzels Forlag 2010.......Anmeldelse af Dorte Kock og Lene Kleinschmidts: Find din stemme. En brugsbog.Hans Reitzels Forlag 2010....

  6. Finding NEMO in preeclampsia.

    Science.gov (United States)

    Sakowicz, Agata; Hejduk, Paulina; Pietrucha, Tadeusz; Nowakowska, Magdalena; Płuciennik, Elżbieta; Pospiech, Karolina; Gach, Agnieszka; Rybak-Krzyszkowska, Magda; Sakowicz, Bartosz; Kaminski, Marek; Krasomski, Grzegorz; Biesiada, Lidia

    2016-04-01

    The mechanism of preeclampsia and its way of inheritance are still a mystery. Biochemical and immunochemical studies reveal a substantial increase in tumor necrosis factor alpha, interleukin-1 beta, and interleukin-6 concentrations in the blood of women with preeclampsia. The level of these factors is regulated by nuclear facxtor-kappa B, whose activation in a classical pathway requires inhibitory kappa B kinase gamma (known as NEMO or IKBKG). Moreover, NEMO can schedule between cytoplasma and the nucleus. In the nucleus, IKBKG interacts with other proteins, and thus, it is implicated in the regulation of different gene expressions, which are related to cell cycle progression, proliferation, differentiation, and apoptosis. This is the first study investigating the association between the level of NEMO gene expression and the presence of preeclampsia. We tested the hypothesis that the simultaneous increase in NEMO gene expression both in the mother and her fetus may be responsible for the preeclampsia development. Moreover, the relationships between clinical risk factors of preeclampsia and the levels of NEMO gene expression in blood, umbilical cord blood, and placentas were investigated. A total of 91 women (43 preeclamptic women and 48 controls) and their children were examined. Real-time reverse transcription-polymerase chain reaction was used to assess the amount total NEMO messenger ribonucleic acid (mRNA) content and the mRNA level of each NEMO transcript from exons 1A, 1B, and 1C in maternal blood, umbilical cord blood, and placentas. Univariate analyses and correlation tests were performed to examine the association between NEMO gene expression and preeclampsia. Newborn weight and height, maternal platelet number, and gestational age (week of delivery) were lower in the group of women with preeclampsia than controls. NEMO gene expression level was found to be almost 7 times higher in the group of women with preeclampsia than healthy controls. The correlation

  7. Abstract Introduction Our findings

    Indian Academy of Sciences (India)

    Avrion Mitchison

    2017-02-14

    Feb 14, 2017 ... The Indian Genetic Disease Database (IGDD) and Online Mendelian Disease in. Man (OMIM) survey human populations that have different climate ... NCBI Gene Reviews, and where necessary also in original publications, here jointly cited as OMIM data. Care was taken to exclude South Asian data.

  8. Early ophthalmic findings in joubert syndrome

    Directory of Open Access Journals (Sweden)

    Amira A Abdelazeem

    2017-01-01

    Conclusion Association of these findings with an expanded clinical definition of Joubert is warranted. The clinical subtypes of JS may be associated with specific types of mutations in the causative genes. This report, which evaluates the findings in a relatively young cohort, provides a unique opportunity to consider the earliest manifestations of JS that may lead to early recognition and appropriate genetic testing to confirm the diagnosis. Clinical findings beyond those identified in this report and by prior publications should be evaluated as potentially independent of the primary genetic condition rather than assuming that each new finding is part of the same syndrome.

  9. Studying Genes

    Science.gov (United States)

    ... NIGMS NIGMS Home > Science Education > Studying Genes Studying Genes Tagline (Optional) Middle/Main Content Area PDF Version (382 KB) Other Fact Sheets What are genes? Genes are segments of DNA that contain instructions ...

  10. Finding New Perovskite Halides via Machine learning

    Directory of Open Access Journals (Sweden)

    Ghanshyam ePilania

    2016-04-01

    Full Text Available Advanced materials with improved properties have the potential to fuel future technological advancements. However, identification and discovery of these optimal materials for a specific application is a non-trivial task, because of the vastness of the chemical search space with enormous compositional and configurational degrees of freedom. Materials informatics provides an efficient approach towards rational design of new materials, via learning from known data to make decisions on new and previously unexplored compounds in an accelerated manner. Here, we demonstrate the power and utility of such statistical learning (or machine learning via building a support vector machine (SVM based classifier that uses elemental features (or descriptors to predict the formability of a given ABX3 halide composition (where A and B represent monovalent and divalent cations, respectively, and X is F, Cl, Br or I anion in the perovskite crystal structure. The classification model is built by learning from a dataset of 181 experimentally known ABX3 compounds. After exploring a wide range of features, we identify ionic radii, tolerance factor and octahedral factor to be the most important factors for the classification, suggesting that steric and geometric packing effects govern the stability of these halides. The trained and validated models then predict, with a high degree of confidence, several novel ABX3 compositions with perovskite crystal structure.

  11. Gene Therapy

    Science.gov (United States)

    Gene therapy Overview Gene therapy involves altering the genes inside your body's cells in an effort to treat or stop disease. Genes contain your ... that don't work properly can cause disease. Gene therapy replaces a faulty gene or adds a new ...

  12. Hysterosalpingographic findings in infertility

    Energy Technology Data Exchange (ETDEWEB)

    Park, M. S.; Kim, K. S.; Kim, J. S.; Bai, B. C. [Seoul Red Cross Hospital, Seoul (Korea, Republic of)

    1981-12-15

    Four hundred and fifty four cases of H.S.G. in infertility were analyzed and following brief results were obtained. 1. Most frequent age group was 25-29 year old, and those number of patient were 188 (41.4%). 2. Most frequent abnormal uterine findings was intravasation (113 cases), and malposition (119), irregular margin (104), filling defect (37), and diverticulum (6) in decreasing order. 3. Most frequent abnormal tubal finding was obstruction (199 cases), and hydrosalpinx (99), diverticulosis (22), intravasation (17), peritubal adhesion (13), and beaded tube (10) in decreasing order. 4. Nagative findings was seen in 155 cases (34.1%) of uterus and in 227 cases (50.0%) of fallopian tubes. 5. Nagative findings in both uterus and fallopian tubes was seen only 87 cases (19.2%)

  13. Hysterosalpingographic findings in infertility

    International Nuclear Information System (INIS)

    Park, M. S.; Kim, K. S.; Kim, J. S.; Bai, B. C.

    1981-01-01

    Four hundred and fifty four cases of H.S.G. in infertility were analyzed and following brief results were obtained. 1. Most frequent age group was 25-29 year old, and those number of patient were 188 (41.4%). 2. Most frequent abnormal uterine findings was intravasation (113 cases), and malposition (119), irregular margin (104), filling defect (37), and diverticulum (6) in decreasing order. 3. Most frequent abnormal tubal finding was obstruction (199 cases), and hydrosalpinx (99), diverticulosis (22), intravasation (17), peritubal adhesion (13), and beaded tube (10) in decreasing order. 4. Nagative findings was seen in 155 cases (34.1%) of uterus and in 227 cases (50.0%) of fallopian tubes. 5. Nagative findings in both uterus and fallopian tubes was seen only 87 cases (19.2%)

  14. Find a Dermatologic Surgeon

    Science.gov (United States)

    ... for Every Season How to Choose the Best Skin Care Products In This Section Dermatologic Surgery What is dermatologic ... for Every Season How to Choose the Best Skin Care Products Find a Dermatologic Surgeon Please select the following ...

  15. Find a Doctor

    Science.gov (United States)

    ... Find a Military Hospital or Clinic Change My Primary Care Manager Book Appointments Getting Care When Traveling What's Covered Health Care Dental Care Mental Health Care Pharmacy Special Needs Vision Care Benefit ...

  16. Bouveret's syndrome: CT findings

    International Nuclear Information System (INIS)

    Tueney, D.; Cimsit, C.

    2000-01-01

    Intestinal obstruction secondary to gallstones is seen in the older population and the level of obstruction is usually at the level of the terminal ileum. Obstruction at the level of the gastric outlet is called Bouveret's syndrome. A case with perforated cholecystitis and duodenal obstruction due to a gallstone is presented. The CT findings are presented along with the clinical findings and literature review. (orig.)

  17. A dynamic study of correlation between the MR diffusion weighted imaging findings and the expression of proliferation-related and metastasis-related genes in rabbit models of liver VX2 tumor before and after chemoembolization

    International Nuclear Information System (INIS)

    Yuan Youhong; Liu Jianbin; Xiao Enhua; He Zhong; Ma Cong; Xiang Jun; Jin Ke; Chen Wenjian; Xiao Jiehua

    2007-01-01

    Objective: To investigate the correlation between the apparent diffusion coefficient (ADC) values and the expression of proliferating cell nuclear antigen (PCNA), Bax, non-metastasis 23(nm23) and E-cadherin (E-cad) genes in rabbit models of liver VX 2 tumor before and after chemoembolization. Methods: Forty rabbit models of liver VX 2 tumor were divided into four groups with 10 rabbits in each group. The first group was the control group which didn't undergo chemoembolization. The second, third and fourth groups underwent chemoembolization, and diffusion weighted imaging (DWI) was performed at 16 h, 32 h and 48 h after chemoembolization respectively. The pathological and immunohistological examinations were carried out right after DWI. The sampling areas included the normal liver parenchyma around the tumor, the outer- layer area, the peripheral area, and the central area. The expression indices of PCNA, Bax, nm23, E-cad in all the samples were recorded and their correlation with corresponding ADC value were analyzed. Results: (1) PCNA expression indices in the outer layer area, the peripheral area and central area of VX 2 tumors(65.1%, 74.7%, and 59.0% respectively) were higher than that in the area of normal parenchyma around tumor (8.3%) (X 2 =19.08, P 2 tumors (nm 23: 1.7%, 0.4% , and 6.2% respectively; Bax: 2. 0%, 1.2% , and 2. 2% respectively; E-cad:6.2%, 2.0%, and 1.6% respectively) were lower than that in the area of normal parenchyma around tumor (nm23 16.5%; Bax 40.0%; E-cad 78.0%. χ 2 =12.86, 20.17, and 22.20 respectively; P 2 tumor periphery were 83.0%, 92.6% and 85.7% in 16 h group, 32 h group and 48 h group respectively after chemoembolization and those of nm23 expression indices were 2.3%, 7.4%, 4.2% and those of Bax expression index were 0.8%, 0.5%, 0.9% and those of E-cad expression indices were 2.8%, 1.0%, 1.1%. The PCNA and nm23 expression in the area of VX 2 tumor periphery increased at the beginning and then decreased (χ 2 =14.37, 8.94; P 2

  18. Catehol-o-methyltransferase gene Val158met polymorphism as a potential predictor of response to computer-assisted delivery of cognitive-behavioral therapy among cocaine-dependent individuals: Preliminary findings from a randomized controlled trial.

    Science.gov (United States)

    Carroll, Kathleen M; Herman, Aryeh; DeVito, Elise E; Frankforter, Tami L; Potenza, Marc N; Sofuoglu, Mehmet

    2015-08-01

    Findings from uncontrolled studies suggest that the COMT Val108/158Met polymorphism may affect response to cognitive behavioral therapy (CBT) in some populations. Using data from a randomized controlled trial evaluating computerized CBT (CBT4CBT), we evaluated treatment response by COMT genotype, with the a priori hypothesis that Val carriers would have improved response to computerized delivery of CBT. 101 cocaine-dependent individuals, of whom 81 contributed analyzable genetic samples, were randomized to standard methadone maintenance treatment plus CBT4CBT or standard treatment alone in an 8 week trial. There was a significant genotype by time effect on frequency of cocaine use from baseline to the end of the 6 month follow-up, suggesting greater reductions over time for Val carriers relative to individuals with the Met/Met genotype. There was a significant treatment condition by genotype interactions for rates of participants attaining 21 or more days of continuous abstinence as well as self-reported percent days of abstinence, suggesting less cocaine use among Val carriers when assigned to CBT compared to standard treatment. Exploration of possible mechanisms using measures of attentional biased also pointed to greater change over time in these measures among the Val carriers assigned to CBT. These are the first data from a randomized controlled trial indicating significant interactions of COMT polymorphism and behavioral therapy condition on treatment outcome, where Val carriers appeared to respond particularly well to computerized CBT. These preliminary data point to a potential biomarker of response to CBT linked to its putative mechanism of action, enhanced cognitive control. © American Academy of Addiction Psychiatry.

  19. PLS-LS-SVM based modeling of ATR-IR as a robust method in detection and qualification of alprazolam.

    Science.gov (United States)

    Parhizkar, Elahehnaz; Ghazali, Mohammad; Ahmadi, Fatemeh; Sakhteman, Amirhossein

    2017-02-15

    According to the United States pharmacopeia (USP), Gold standard technique for Alprazolam determination in dosage forms is HPLC, an expensive and time-consuming method that is not easy to approach. In this study chemometrics assisted ATR-IR was introduced as an alternative method that produce similar results in fewer time and energy consumed manner. Fifty-eight samples containing different concentrations of commercial alprazolam were evaluated by HPLC and ATR-IR method. A preprocessing approach was applied to convert raw data obtained from ATR-IR spectra to normal matrix. Finally, a relationship between alprazolam concentrations achieved by HPLC and ATR-IR data was established using PLS-LS-SVM (partial least squares least squares support vector machines). Consequently, validity of the method was verified to yield a model with low error values (root mean square error of cross validation equal to 0.98). The model was able to predict about 99% of the samples according to R 2 of prediction set. Response permutation test was also applied to affirm that the model was not assessed by chance correlations. At conclusion, ATR-IR can be a reliable method in manufacturing process in detection and qualification of alprazolam content. Copyright © 2016 Elsevier B.V. All rights reserved.

  20. SVM-based multimodal classification of activities of daily living in Health Smart Homes: sensors, algorithms, and first experimental results.

    Science.gov (United States)

    Fleury, Anthony; Vacher, Michel; Noury, Norbert

    2010-03-01

    By 2050, about one third of the French population will be over 65. Our laboratory's current research focuses on the monitoring of elderly people at home, to detect a loss of autonomy as early as possible. Our aim is to quantify criteria such as the international activities of daily living (ADL) or the French Autonomie Gerontologie Groupes Iso-Ressources (AGGIR) scales, by automatically classifying the different ADL performed by the subject during the day. A Health Smart Home is used for this. Our Health Smart Home includes, in a real flat, infrared presence sensors (location), door contacts (to control the use of some facilities), temperature and hygrometry sensor in the bathroom, and microphones (sound classification and speech recognition). A wearable kinematic sensor also informs postural transitions (using pattern recognition) and walk periods (frequency analysis). This data collected from the various sensors are then used to classify each temporal frame into one of the ADL that was previously acquired (seven activities: hygiene, toilet use, eating, resting, sleeping, communication, and dressing/undressing). This is done using support vector machines. We performed a 1-h experimentation with 13 young and healthy subjects to determine the models of the different activities, and then we tested the classification algorithm (cross validation) with real data.

  1. SVM-based prediction of propeptide cleavage sites in spider toxins identifies toxin innovation in an Australian tarantula.

    Directory of Open Access Journals (Sweden)

    Emily S W Wong

    Full Text Available Spider neurotoxins are commonly used as pharmacological tools and are a popular source of novel compounds with therapeutic and agrochemical potential. Since venom peptides are inherently toxic, the host spider must employ strategies to avoid adverse effects prior to venom use. It is partly for this reason that most spider toxins encode a protective proregion that upon enzymatic cleavage is excised from the mature peptide. In order to identify the mature toxin sequence directly from toxin transcripts, without resorting to protein sequencing, the propeptide cleavage site in the toxin precursor must be predicted bioinformatically. We evaluated different machine learning strategies (support vector machines, hidden Markov model and decision tree and developed an algorithm (SpiderP for prediction of propeptide cleavage sites in spider toxins. Our strategy uses a support vector machine (SVM framework that combines both local and global sequence information. Our method is superior or comparable to current tools for prediction of propeptide sequences in spider toxins. Evaluation of the SVM method on an independent test set of known toxin sequences yielded 96% sensitivity and 100% specificity. Furthermore, we sequenced five novel peptides (not used to train the final predictor from the venom of the Australian tarantula Selenotypus plumipes to test the accuracy of the predictor and found 80% sensitivity and 99.6% 8-mer specificity. Finally, we used the predictor together with homology information to predict and characterize seven groups of novel toxins from the deeply sequenced venom gland transcriptome of S. plumipes, which revealed structural complexity and innovations in the evolution of the toxins. The precursor prediction tool (SpiderP is freely available on ArachnoServer (http://www.arachnoserver.org/spiderP.html, a web portal to a comprehensive relational database of spider toxins. All training data, test data, and scripts used are available from the SpiderP website.

  2. A DWT and SVM based method for rolling element bearing fault diagnosis and its comparison with Artificial Neural Networks

    Directory of Open Access Journals (Sweden)

    Sunil Tyagi

    2017-04-01

    Full Text Available A classification technique using Support Vector Machine (SVM classifier for detection of rolling element bearing fault is presented here.  The SVM was fed from features that were extracted from of vibration signals obtained from experimental setup consisting of rotating driveline that was mounted on rolling element bearings which were run in normal and with artificially faults induced conditions. The time-domain vibration signals were divided into 40 segments and simple features such as peaks in time domain and spectrum along with statistical features such as standard deviation, skewness, kurtosis etc. were extracted. Effectiveness of SVM classifier was compared with the performance of Artificial Neural Network (ANN classifier and it was found that the performance of SVM classifier is superior to that of ANN. The effect of pre-processing of the vibration signal by Discreet Wavelet Transform (DWT prior to feature extraction is also studied and it is shown that pre-processing of vibration signal with DWT enhances the effectiveness of both ANN and SVM classifiers. It has been demonstrated from experiment results that performance of SVM classifier is better than ANN in detection of bearing condition and pre-processing the vibration signal with DWT improves the performance of SVM classifier.

  3. Microcalcification detection in full-field digital mammograms with PFCM clustering and weighted SVM-based method

    Science.gov (United States)

    Liu, Xiaoming; Mei, Ming; Liu, Jun; Hu, Wei

    2015-12-01

    Clustered microcalcifications (MCs) in mammograms are an important early sign of breast cancer in women. Their accurate detection is important in computer-aided detection (CADe). In this paper, we integrated the possibilistic fuzzy c-means (PFCM) clustering algorithm and weighted support vector machine (WSVM) for the detection of MC clusters in full-field digital mammograms (FFDM). For each image, suspicious MC regions are extracted with region growing and active contour segmentation. Then geometry and texture features are extracted for each suspicious MC, a mutual information-based supervised criterion is used to select important features, and PFCM is applied to cluster the samples into two clusters. Weights of the samples are calculated based on possibilities and typicality values from the PFCM, and the ground truth labels. A weighted nonlinear SVM is trained. During the test process, when an unknown image is presented, suspicious regions are located with the segmentation step, selected features are extracted, and the suspicious MC regions are classified as containing MC or not by the trained weighted nonlinear SVM. Finally, the MC regions are analyzed with spatial information to locate MC clusters. The proposed method is evaluated using a database of 410 clinical mammograms and compared with a standard unweighted support vector machine (SVM) classifier. The detection performance is evaluated using response receiver operating (ROC) curves and free-response receiver operating characteristic (FROC) curves. The proposed method obtained an area under the ROC curve of 0.8676, while the standard SVM obtained an area of 0.8268 for MC detection. For MC cluster detection, the proposed method obtained a high sensitivity of 92 % with a false-positive rate of 2.3 clusters/image, and it is also better than standard SVM with 4.7 false-positive clusters/image at the same sensitivity.

  4. a Comparison Study of Different Kernel Functions for Svm-Based Classification of Multi-Temporal Polarimetry SAR Data

    Science.gov (United States)

    Yekkehkhany, B.; Safari, A.; Homayouni, S.; Hasanlou, M.

    2014-10-01

    In this paper, a framework is developed based on Support Vector Machines (SVM) for crop classification using polarimetric features extracted from multi-temporal Synthetic Aperture Radar (SAR) imageries. The multi-temporal integration of data not only improves the overall retrieval accuracy but also provides more reliable estimates with respect to single-date data. Several kernel functions are employed and compared in this study for mapping the input space to higher Hilbert dimension space. These kernel functions include linear, polynomials and Radial Based Function (RBF). The method is applied to several UAVSAR L-band SAR images acquired over an agricultural area near Winnipeg, Manitoba, Canada. In this research, the temporal alpha features of H/A/α decomposition method are used in classification. The experimental tests show an SVM classifier with RBF kernel for three dates of data increases the Overall Accuracy (OA) to up to 3% in comparison to using linear kernel function, and up to 1% in comparison to a 3rd degree polynomial kernel function.

  5. ALDH2*2 but not ADH1B*2 is a causative variant gene allele for Asian alcohol flushing after a low-dose challenge: correlation of the pharmacokinetic and pharmacodynamic findings.

    Science.gov (United States)

    Peng, Giia-Sheun; Chen, Yi-Chyan; Wang, Ming-Fang; Lai, Ching-Long; Yin, Shih-Jiun

    2014-12-01

    It has been well documented that variant alleles of both ADH1B*2 of alcohol dehydrogenase (ADH) and ALDH2*2 of aldehyde dehydrogenase (ALDH) protect against the development of alcoholism in East Asians. However, it remains unclear whether ADH1B*2 contributes significantly toward the accumulation of systemic blood acetaldehyde and whether it plays a critical role in the alcohol flushing reaction. Sixty-one adult Han Chinese men were recruited and divided into six combinatorial genotypic groups: ALDH2*1/*1-ADH1B*1/*1 (12), ALDH2*1/*1-ADH1B*1/*2 (11), ALDH2*1/*1-ADH1B*2/*2 (11); ALDH2*1/*2-ADH1B*1/*1 (9), ALDH2*1/*2-ADH1B*1/*2 (9), and ALDH2*1/*2-ADH1B*2/*2 (9). After ingesting 0.3 g/kg of alcohol, blood ethanol, acetaldehyde, and acetate concentrations, as well as the facial skin blood flow (FSBF) and pulse rate were measured for 130 min. The ALDH2*1/*2 heterozygotes carrying three ADH1B allelotypes showed significantly higher peak levels and areas under the concentration curve (AUCs) of the blood acetaldehyde as well as significantly greater increases in the peak pulse rate and peak FSBF compared with the ALDH2*1/*1 homozygotes. However, no significant differences in peak levels and AUCs of blood ethanol, acetaldehyde or acetate, or the peak cardiovascular responses, were found between the ADH1B allelotypes carrying ALDH2*1/*1 or between those with ALDH2*1/*2. Partial correlation analyses showed that peak blood acetaldehyde, rather than the blood ethanol or acetate, was correlated significantly with the peak responses of pulse rate and FSBF. Findings indicate that ALDH2*2, rather than ADH1B2*2, is a causal variant allele for the accumulation of blood acetaldehyde and the resultant facial flushing during low alcohol consumption.

  6. Ultrasonographic findings of gynecomastia

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Ji Hyung; Oh, Ki Keun; Yoon, Choon Sik; Park, Chang Yun [Yongdong Severance Hospital, Seoul (Korea, Republic of)

    1993-12-15

    The purposes of our study were to find out characteristic ultrasonographic findings of gynecomastia and to analyze age distribution, causative factors of gynecomastia. For these purposes, medical records of 39 male patients with gynecomastia were reviewed and sonographic findings of 13 cases of gentamycin were analyzed. Gynecomastia was found most commonly in teenagers and commonly in twenties. Almostly, it occurred without any evident etiology and classified as idiopathic or pirbuterol type. Less frequently, it occurred due to drug administration, systemic disease, or male hormone deficiency. Unilateral involvement was seen in 29 cases; 17cases involving the left and 12 cases the right. Bilateral involvement was seen in 10 cases. Sonographically,gynecomastia appeared as hypoechoic or intermediate echoic mass with various shape in the subareolar area. One case showed diffuse fatty breast pattern without definable mass. On sonographic evaluation, prominent nipple should not be misinterpreted as a breast mass. For the correct diagnosis of gynecomastia, both side breasts should be evaluated for comparison

  7. Ultrasonographic findings of gynecomastia

    International Nuclear Information System (INIS)

    Kim, Ji Hyung; Oh, Ki Keun; Yoon, Choon Sik; Park, Chang Yun

    1993-01-01

    The purposes of our study were to find out characteristic ultrasonographic findings of gynecomastia and to analyze age distribution, causative factors of gynecomastia. For these purposes, medical records of 39 male patients with gynecomastia were reviewed and sonographic findings of 13 cases of gentamycin were analyzed. Gynecomastia was found most commonly in teenagers and commonly in twenties. Almostly, it occurred without any evident etiology and classified as idiopathic or pirbuterol type. Less frequently, it occurred due to drug administration, systemic disease, or male hormone deficiency. Unilateral involvement was seen in 29 cases ; 17cases involving the left and 12 cases the right. Bilateral involvement was seen in 10 cases. Sonographically,gynecomastia appeared as hypoechoic or intermediate echoic mass with various shape in the subareolar area. One case showed diffuse fatty breast pattern without definable mass. On sonographic evaluation, prominent nipple should not be misinterpreted as a breast mass. For the correct diagnosis of gynecomastia, both side breasts should be evaluated for comparison

  8. Intrathoracic gossypiboma: imaging findings

    International Nuclear Information System (INIS)

    Rosalen Junior, Roberto Antonio; Bosi, Thiago Carneiro da Cunha; Souza, Luis Ronan Marquez Ferreira de; Andrade, Fernando Coelho Goulart de; Candido, Daniela; Lopes, Gesner Pereira; Melo, Ana Lucia Kefalas Oliveira; Fatureto, Marcelo Cunha

    2006-01-01

    The authors report three cases of intrathoracic foreign body that is defined as a cotton matrix mass, mostly retained surgical sponge, a rare complication of a thoracic surgery. The patients were evaluated by chest radiography and computed tomography with the imaging findings confirmed after thoracotomy and anatomopathological study. The mainly imaging findings consisted of intrathoracic masses in patients with previous thoracic surgery that return to hospital with lower respiratory tract symptoms in different period after surgery procedure. The three cases were related with a brief review of the literature. (author)

  9. Mobious syndrome: MR findings

    Directory of Open Access Journals (Sweden)

    Maskal Revanna Srinivas

    2016-01-01

    Full Text Available Möbius syndrome is an extremely rare congenital disorder. We report a case of Möbius syndrome in a 2-year-old girl with bilateral convergent squint and left-sided facial weakness. The characteristic magnetic resonance imaging (MRI findings of Möbius syndrome, which include absent bilateral abducens nerves and absent left facial nerve, were noted. In addition, there was absence of left anterior inferior cerebellar artery (AICA and absence of bilateral facial colliculi. Clinical features, etiology, and imaging findings are discussed.

  10. Finding optimal exact reducts

    KAUST Repository

    AbouEisha, Hassan M.

    2014-01-01

    The problem of attribute reduction is an important problem related to feature selection and knowledge discovery. The problem of finding reducts with minimum cardinality is NP-hard. This paper suggests a new algorithm for finding exact reducts with minimum cardinality. This algorithm transforms the initial table to a decision table of a special kind, apply a set of simplification steps to this table, and use a dynamic programming algorithm to finish the construction of an optimal reduct. I present results of computer experiments for a collection of decision tables from UCIML Repository. For many of the experimented tables, the simplification steps solved the problem.

  11. Finding Their Identities

    Science.gov (United States)

    Lum, Lydia

    2009-01-01

    Every time Dr. Larry Shinagawa teaches his "Introduction to Asian American Studies" course at the University of Maryland (UMD), College Park, he finds that 10 to 20 percent of his students are adoptees. Among other things, they hunger to better comprehend the social and political circumstances overseas leading to their adoption. In…

  12. Tooth Tutoring: The Findings.

    Science.gov (United States)

    Cone, Richard; And Others

    Findings are reported on a three year cross-age tutoring program in which undergraduate dental hygiene students and college students from other disciplines trained upper elementary students to tutor younger students in the techniques of dental hygiene. Data includes pre-post scores on the Oral Hygiene Index of plaque for both experimental and…

  13. Finding Health Care Services

    Science.gov (United States)

    If you have been diagnosed with cancer, finding a doctor and treatment hospital for your cancer care is an important step to getting the best treatment possible. Learn tips for choosing a doctor and treatment facility to manage your cancer care.

  14. Granulomatous mastitis: radiological findings

    Energy Technology Data Exchange (ETDEWEB)

    Ozturk, M.; Mavili, E.; Kahriman, G.; Akcan, A.C.; Ozturk, F. [Depts. of Radiology, Surgery, and Pathology, Erciyes Univ. Medical Faculty, Kayseri (Turkey)

    2007-02-15

    Purpose: To evaluate the radiological, ultrasonographic, and magnetic resonance imaging (MRI) findings of idiopathic granulomatous mastitis. Material and Methods: Between April 2002 and June 2005, the mammography, ultrasound, color Doppler ultrasound, non enhanced MR, and dynamic MR findings of nine patients with the preliminary clinical diagnosis of malignancy and the final diagnosis of granulomatous mastitis were evaluated. Results: On mammography, asymmetrical focal densities with no distinct margins, ill-defined masses with spiculated contours, and bilateral multiple ill-defined nodules were seen. On ultrasound, in four patients a discrete, heterogenous hypoechoic mass, in two patients multiple abscesses, in one patient bilateral multiple central hypo peripheral hyperechoic lesions, in two patients heterogeneous hypo- and hyperechoic areas together with parenchymal distortion, and in one patient irregular hypoechoic masses with tubular extensions and abscess cavities were seen. Five of the lesions were vascular on color Doppler ultrasound. On MR mammography, the most frequent finding was focal or diffuse asymmetrical signal intensity changes that were hypointense on T1W images and hyperintense on T2W images, without significant mass effect. Nodular lesions were also seen. On dynamic contrast-enhanced mammography, mass-like enhancement, ring-like enhancement, and nodular enhancement were seen. The time-intensity curves differed from patient to patient and from lesion to lesion. Conclusion: The imaging findings of idiopathic granulomatous mastitis have a wide spectrum, and they are inconclusive for differentiating malignant and benign lesions.

  15. Effective Bug Finding

    DEFF Research Database (Denmark)

    Rivas, Iago Abal

    Lightweight bug finders (also known as code scanners) are becoming popular, they scale well and can find simple yet common programming errors. It is now considered a good practice to integrate these tools as part of your development process. The Linux project, for instance, has an automated testing...... service, known as the Kbuild robot, that runs a few of these code scanners. In this project, I have carefully studied tens of historical Linux bugs, and I have found that many of these bugs, despite being conceptually simple, were not caught by any code scanning tool. The reason is that, by design, code...... by matching temporal bug-patterns against the control-flow graph of this program abstraction. I have implemented a proof-of-concept bug finder based on this technique, EBA, and confirmed that it is both scalable and effective at finding bugs. On a benchmark of historical Linux double-lock bugs, EBA was able...

  16. Gallstone ileus: CT findings

    Energy Technology Data Exchange (ETDEWEB)

    Delabrousse, E.; Bartholomot, B.; Sohm, O.; Kastler, B. [Dept. of Radiology A, CHU Jean Minjoz, University of Besancon (France); Wallerand, H. [Dept. of Surgery, CHU Jean Minjoz, University of Besancon (France)

    2000-06-01

    Gallstone ileus is a rare complication of recurrent gallstone cholecystitis. The classic radiographic triad of small bowel obstruction, pneumobilia and ectopic gallstone on abdominal plain radiograph is described with CT imaging. Because of the better resolution of CT compared with abdominal radiography and its recent accession to emergency use, radiologists should be aware of CT findings of gallstone ileus. We report a case in which gallstone ileus was initially diagnosed by CT. (orig.)

  17. Heterotopic pregnancy: Sonographic findings

    Energy Technology Data Exchange (ETDEWEB)

    Kwon, Tae Hee [CHA General Hospital of Seoul, Pochon CHA University College of Medicine, Seoul (Korea, Republic of)

    1999-03-15

    To evaluate the sonographic findings of the heterotopic pregnancy which is increasing recently. Thirty-nine cases of heterotopic pregnancy after ovulation induction and IVF-ET (In Vitro Fertilization-Embryo Transfer) during the recent 3 years were analyzed. They were diagnosed by ultrasonography and proved surgically afterwards. Sonographic findings were analyzed focusing on gestational week of intrauterine pregnancy and location of ectopic pregnancy. In particular, adnexal mass was evaluated with regard to size and the characteristic findings such as ectopic gestational sac (echogenic ring). Also, overian cyst and fluid collection in cul-de-sac space were reviewed carefully. Heterotopic pregnancy was proved surgically by salpingectomy in 33 cases and by resection of cornus in six cases. Sonographic diagnosis using transvaginal ultrasound was made from five weeks to nine weeks two days (six weeks and four days in average) from last menstral period in all 39 cases. Ectopic pregnancy was identified in ampullary part in 29 cases, in the isthmic portion of tube in four cases and in the cornus of uterus in six cases. The intrauterine pregnancy was diagnosed by identifying the intrauterine gestational saccontaining a yolk sac in seven cases and the embryo with fetal heart beat in the remaining 32 cases. Adnexal masses of heterotopic pregnancy were less than 3 cm in diameter in 2 cases (57%), 3-4 cm in 11 cases (28%) and more than 4 cm in 6 cases (15%). A characteristic finding of ectopic mass was echogenic ring which was visible in 33 (84.6%) cases by transvaginal ultrasound. Six cases had pelvic hematosalpinx and two had pelvic hematoma. Of 10 cases (26%) which were identified to have ovarian hyperstimulation syndrome, eight (21%) had large amount of fluid collection in cul-de-sac and abdomen. Ultrasonographic identification of the intrauterine pregnancy and the ectopic chorion ring is effective for the early diagnosis of the heterotopic pregnancy.

  18. Heterotopic pregnancy: Sonographic findings

    International Nuclear Information System (INIS)

    Kwon, Tae Hee

    1999-01-01

    To evaluate the sonographic findings of the heterotopic pregnancy which is increasing recently. Thirty-nine cases of heterotopic pregnancy after ovulation induction and IVF-ET (In Vitro Fertilization-Embryo Transfer) during the recent 3 years were analyzed. They were diagnosed by ultrasonography and proved surgically afterwards. Sonographic findings were analyzed focusing on gestational week of intrauterine pregnancy and location of ectopic pregnancy. In particular, adnexal mass was evaluated with regard to size and the characteristic findings such as ectopic gestational sac (echogenic ring). Also, overian cyst and fluid collection in cul-de-sac space were reviewed carefully. Heterotopic pregnancy was proved surgically by salpingectomy in 33 cases and by resection of cornus in six cases. Sonographic diagnosis using transvaginal ultrasound was made from five weeks to nine weeks two days (six weeks and four days in average) from last menstral period in all 39 cases. Ectopic pregnancy was identified in ampullary part in 29 cases, in the isthmic portion of tube in four cases and in the cornus of uterus in six cases. The intrauterine pregnancy was diagnosed by identifying the intrauterine gestational saccontaining a yolk sac in seven cases and the embryo with fetal heart beat in the remaining 32 cases. Adnexal masses of heterotopic pregnancy were less than 3 cm in diameter in 2 cases (57%), 3-4 cm in 11 cases (28%) and more than 4 cm in 6 cases (15%). A characteristic finding of ectopic mass was echogenic ring which was visible in 33 (84.6%) cases by transvaginal ultrasound. Six cases had pelvic hematosalpinx and two had pelvic hematoma. Of 10 cases (26%) which were identified to have ovarian hyperstimulation syndrome, eight (21%) had large amount of fluid collection in cul-de-sac and abdomen. Ultrasonographic identification of the intrauterine pregnancy and the ectopic chorion ring is effective for the early diagnosis of the heterotopic pregnancy.

  19. Finding your next CEO.

    Science.gov (United States)

    Thrall, Terese Hudson

    2008-12-01

    Hospital CEOs spend an average of just six years at one organization, and the cost of turnover is high. Finding executives to fill that top spot is more complicated thanks to a jittery economy, job candidates' worries about selling their homes and other issues. That's prompting hospitals to be more flexible in their recruitment efforts: considering older candidates, reviving succession planning, and even buying and selling CEOs' houses.

  20. Track finding using GPUs

    CERN Document Server

    Schmitt, C; The ATLAS collaboration

    2011-01-01

    Track finding using GPUs The reconstruction and simulation of collision events is a major task in modern HEP experiments involving several ten thousands of standard CPUs. On the other hand the graphics processors (GPUs) have become much more powerful and are by far outperforming the standard CPUs in terms of floating point operations due to their massive parallel approach. The usage of these GPUs could therefore significantly reduce the overall reconstruction time per event or allow for the usage of more sophisticated algorithms. In this contribution the track finding in the ATLAS experiment will be used as an example on how the GPUs can be used in this context: the seed finding alone shows already a speed increase of one order of magnitude compared to the same implementation on a standard CPU. On the other hand the implementation on the GPU requires a change in the algorithmic flow to allow the code to work in the rather limited environment on the GPU in terms of memory, cache, and transfer speed from and to...

  1. gene structure, gene expression

    Indian Academy of Sciences (India)

    and seedling leaves were sampled at 6 h after the treatment. For cold stress, the seedlings were transferred to 4◦C growth chamber for 30 min. Control seedlings were exposed to none of these treatments. To examine the expression patterns of these predicted genes in Poplar and to further confirm their stress responsive-.

  2. Normal radiological findings

    International Nuclear Information System (INIS)

    Moeller, T.B.

    1987-01-01

    This book is intended for learners in radiology, presenting a wealth of normal radiological findings together with a systematic guide for appraisal and interpretation, and for formulation of reports. The text examples and criteria given will help beginners in learning to 'read' a radiograph, and to verify their conclusions by means of checklists and standard reports. The case material covers numerous illustrations from the following sectors: Skeletal radiography, mammography, tomography, contrast radiography, organ examination by intravenous techniques, arthrography and angiography, and specialized radiography, (ECB) With 184 figs [de

  3. MR findings of spondylolysis

    International Nuclear Information System (INIS)

    Ojiri, Hiroya; Fukuda, Kunihiko; Hashimoto, Toru; Doi, Michiko; Irie, Takeo; Tatsuno, Satoshi; Tada, Shinpei; Toyoda, Keiko.

    1994-01-01

    We reviewed MR images of 50 patients with spondylolisthesis to disclose MR findings of spondylolysis. In almost half of our series, spondylolysis was detected as a low signal intensity band traversing in the pairs interarticularis on both T1 and T2 weighted images. Sagittal images was superior to axial image in detection of the low signal intensity band. In some patients, a focal high signal intensity accompanying the low signal intensity band was considered to be fluid collection within pseudoarthrosis due to spondylolysis on T2-weighted image. (author)

  4. MR findings of spondylolysis

    Energy Technology Data Exchange (ETDEWEB)

    Ojiri, Hiroya; Fukuda, Kunihiko; Hashimoto, Toru; Doi, Michiko; Irie, Takeo; Tatsuno, Satoshi; Tada, Shinpei (Jikei Univ., Tokyo (Japan). School of Medicine); Toyoda, Keiko

    1994-08-01

    We reviewed MR images of 50 patients with spondylolisthesis to disclose MR findings of spondylolysis. In almost half of our series, spondylolysis was detected as a low signal intensity band traversing in the pairs interarticularis on both T1 and T2 weighted images. Sagittal images was superior to axial image in detection of the low signal intensity band. In some patients, a focal high signal intensity accompanying the low signal intensity band was considered to be fluid collection within pseudoarthrosis due to spondylolysis on T2-weighted image. (author).

  5. Neurofibromatosis 2: finding the gene (A study of teh processes ...

    African Journals Online (AJOL)

    The Neurofibromatoses are two autosomal dominant disorders classified as Neurofibromatoses type1 (NF1) and Neurofibromatoses type2 (NF2). They are primarily neural tumours with distinct clinical and genetic characteristics even though areas of clinical similarities exist.1 Neurofibromatosis 2 is characterised by bilateral ...

  6. Do Housekeeping Genes Exist?

    Science.gov (United States)

    Sun, Bingyun

    2015-01-01

    The searching of human housekeeping (HK) genes has been a long quest since the emergence of transcriptomics, and is instrumental for us to understand the structure of genome and the fundamentals of biological processes. The resolved genes are frequently used in evolution studies and as normalization standards in quantitative gene-expression analysis. Within the past 20 years, more than a dozen HK-gene studies have been conducted, yet none of them sampled human tissues completely. We believe an integration of these results will help remove false positive genes owing to the inadequate sampling. Surprisingly, we only find one common gene across 15 examined HK-gene datasets comprising 187 different tissue and cell types. Our subsequent analyses suggest that it might not be appropriate to rigidly define HK genes as expressed in all tissue types that have diverse developmental, physiological, and pathological states. It might be beneficial to use more robustly identified HK functions for filtering criteria, in which the representing genes can be a subset of genome. These genes are not necessarily the same, and perhaps need not to be the same, everywhere in our body. PMID:25970694

  7. Abdominal aspergillosis: CT findings

    Energy Technology Data Exchange (ETDEWEB)

    Yeom, Suk Keu, E-mail: pagoda20@hanmail.net [Department of Radiology and Research Institute of Radiology, Asan Medical Center, University of Ulsan College of Medicine, 388-1, Poongnap2-dong, Songpa-gu, Seoul, 138-736 (Korea, Republic of); Kim, Hye Jin, E-mail: kimhyejin@amc.seoul.kr [Department of Radiology and Research Institute of Radiology, Asan Medical Center, University of Ulsan College of Medicine, 388-1, Poongnap2-dong, Songpa-gu, Seoul, 138-736 (Korea, Republic of); Byun, Jae Ho, E-mail: jhbyun@amc.seoul.kr [Department of Radiology and Research Institute of Radiology, Asan Medical Center, University of Ulsan College of Medicine, 388-1, Poongnap2-dong, Songpa-gu, Seoul, 138-736 (Korea, Republic of); Kim, Ah Young, E-mail: aykim@amc.seoul.kr [Department of Radiology and Research Institute of Radiology, Asan Medical Center, University of Ulsan College of Medicine, 388-1, Poongnap2-dong, Songpa-gu, Seoul, 138-736 (Korea, Republic of); Lee, Moon-Gyu, E-mail: mglee@amc.seoul.kr [Department of Radiology and Research Institute of Radiology, Asan Medical Center, University of Ulsan College of Medicine, 388-1, Poongnap2-dong, Songpa-gu, Seoul, 138-736 (Korea, Republic of); Ha, Hyun Kwon, E-mail: hkha@amc.seoul.kr [Department of Radiology and Research Institute of Radiology, Asan Medical Center, University of Ulsan College of Medicine, 388-1, Poongnap2-dong, Songpa-gu, Seoul, 138-736 (Korea, Republic of)

    2011-03-15

    Objective: In order to retrospectively evaluate the CT findings of abdominal aspergillosis in immunocompromised patients. Materials and methods: CT scans were reviewed with regard to the sites, number, morphologic appearance, attenuation, and the contrast enhancement patterns of the lesions in six patients (5 women, 1 man; mean age, 43.4 years; range, 23-59 years) with pathologically proved abdominal aspergillosis by two gastrointestinal radiologists in consensus. Medical records were also reviewed to determine each patient's clinical status and outcome. Results: All patients were immunocompromised state: 4 patients received immunosuppressive therapy for solid organ transplantation and 2 patients received chemotherapy for acute myeloid leukemia. Aspergillosis involved blood vessels (n = 3), liver (n = 2), spleen (n = 2), gastrointestinal tract (n = 2), native kidney (n = 1), transplanted kidney (n = 1), peritoneum (n = 1), and retroperitoneum (n = 1). CT demonstrated solid organ or bowel infarction or perforation secondary to vascular thrombosis or pseudoaneurysm, multiple low-attenuating lesions of solid organs presenting as abscesses, concentric bowel wall thickening mimicking typhlitis, or diffuse or nodular infiltration of the peritoneum and retroperitoneum. Conclusion: Familiarity with findings commonly presenting as angioinvasive features or abscesses on CT, may facilitate the diagnosis of rare and fatal abdominal aspergillosis.

  8. Ultrasonographic findings of Epicondylitis

    Energy Technology Data Exchange (ETDEWEB)

    Kwak, Seo Hyun; Song, In Sup; Lee, Jong Beum; Lee, Hwa Yeon; Yoo, Seung Min; Yang, Seong Jun [Yong San Hospital, Chung-Ang University College of Medicine, Seoul (Korea, Republic of); Seo, Kyung Mook [Chung-Ang University College of Medicine, Seoul (Korea, Republic of)

    2002-09-15

    To evaluate the usefulness of ultrasonographic findings of the common extensor and flexor tendon in evaluation of patients with lateral and medial epicondylitis. Thirty eight elbows from twenty four patients (mean age=45.2 years) were included. Ultrasonographic examination was performed to evaluate lateral or medial epicondylitis. Epicondylitis was divided into five groups according to the severity of disease: 1) normal, 2) tendinopathy, 3) tendinopathy with a partial tear, partial tear and 4) complete tear. Change in the size of a tendon, bony change of the epicondylitis, presence or absence of calcification or echogenic foci in the common tendon and hypervascularity for each categories were also assessed. In addition, these lesions were divided into the superficial and deep according to the location of lesions. According to the severity, there were 15 cases of normal, 13 tendinopathies, 8 tendinopathies with a partial tear, 2 partial tears and 0 complete tear. Bony change was seen only in tendinopathy, tendinopathy with partial tear and partial tear. Calcification or echogenic foci were only observed in cases with tendinopathy and tendinopathy with partial tear. Hypervascularity was only seen in one case of tendinopathy. With thorough understanding of ultrasonographic findings of epicondylitis, ultrasonographic examination can be especially useful and effective in evaluating the severity and location of lesions.

  9. Climate change: Recent findings

    International Nuclear Information System (INIS)

    Hesselmans, G.H.F.M.

    1993-08-01

    In the late eighties several reports have been published on climate change and sea level rise. In the meantime insights may have changed due to the availability of better and more observations and/or more advanced climate models. The aim of this report is to present the most recent findings with respect to climate change, in particular of sea level rise, storm surges and river peak flows. These climate factors are important for the safety of low-lying areas with respect to coastal erosion and flooding. In the first chapters a short review is presented of a few of the eighties reports. Furthermore, the predictions by state of the art climate models at that time are given. The reports from the eighties should be considered as 'old' information, whereas the IPCC supplement and work, for example, by Wigley should be considered as new information. To assess the latest findings two experts in this field were interviewed: dr J. Oerlemans and dr C.J.E. Schuurmans, a climate expert from the Royal Netherlands Meteorological Institute (KNMI). Their views are presented together with results published in recent papers on the subject. On the basis of this assessment, the report presents current knowledge regarding predictions of climate change (including sea-level rise) over the next century, together with an assessment of the uncertainties associated with these predictions. 14 figs., 11 tabs., 24 refs

  10. [Ultrasound findings in rhabdomyolysis].

    Science.gov (United States)

    Carrillo-Esper, Raúl; Galván-Talamantes, Yazmin; Meza-Ayala, Cynthia Margarita; Cruz-Santana, Julio Alberto; Bonilla-Reséndiz, Luis Ignacio

    Rhabdomyolysis is defined as skeletal muscle necrosis. Ultrasound assessment has recently become a useful tool for the diagnosis and monitoring of muscle diseases, including rhabdomyolysis. A case is presented on the ultrasound findings in a patient with rhabdomyolysis. To highlight the importance of ultrasound as an essential part in the diagnosis in rhabdomyolysis, to describe the ultrasound findings, and review the literature. A 30 year-old with post-traumatic rhabdomyolysis of both thighs. Ultrasound was performed using a Philips Sparq model with a high-frequency linear transducer (5-10MHz), in low-dimensional scanning mode (2D), in longitudinal and transverse sections at the level of both thighs. The images obtained showed disorganisation of the orientation of the muscle fibres, ground glass image, thickening of the muscular fascia, and the presence of anechoic areas. Ultrasound is a useful tool in the evaluation of rhabdomyolysis. Copyright © 2015 Academia Mexicana de Cirugía A.C. Publicado por Masson Doyma México S.A. All rights reserved.

  11. Craniofacial and temporal bone CT findings in cleidocranial dysplasia

    International Nuclear Information System (INIS)

    Gonzalez, Guido E.; Caruso, Paul A.; Curtin, Hugh D.; Small, Juan E.; Jyung, Robert W.; Troulis, Maria J.

    2008-01-01

    Cleidocranial dysplasia (CCD) is a multistructural polyostotic genetic disorder that results from mutation of the CBFA1 gene. Hearing loss is a frequent finding in CCD. We describe the CT craniofacial findings in CCD and provide a comprehensive discussion of the CT temporal bone findings in these patients. (orig.)

  12. Craniofacial and temporal bone CT findings in cleidocranial dysplasia

    Energy Technology Data Exchange (ETDEWEB)

    Gonzalez, Guido E. [Massachusetts General Hospital and Harvard Medical School, Department of Radiology, Boston, MA (United States); Clinica Alemana de Santiago, Departamento de Imagenes, Santiago (Chile); Caruso, Paul A.; Curtin, Hugh D. [Massachusetts Eye and Ear Infirmary and Harvard Medical School, Department of Radiology, Boston, MA (United States); Small, Juan E. [Massachusetts General Hospital and Harvard Medical School, Department of Radiology, Boston, MA (United States); Massachusetts Eye and Ear Infirmary and Harvard Medical School, Department of Radiology, Boston, MA (United States); Jyung, Robert W. [Massachusetts Eye and Ear Infirmary and Harvard Medical School, Department of Otology, Boston, MA (United States); Troulis, Maria J. [Massachusetts General Hospital and Harvard Medical School, Department of Oral and Maxillofacial Surgery, Boston, MA (United States)

    2008-08-15

    Cleidocranial dysplasia (CCD) is a multistructural polyostotic genetic disorder that results from mutation of the CBFA1 gene. Hearing loss is a frequent finding in CCD. We describe the CT craniofacial findings in CCD and provide a comprehensive discussion of the CT temporal bone findings in these patients. (orig.)

  13. Trochanteric bursitis: radiological findings

    International Nuclear Information System (INIS)

    Revilla, T.Y.; Manjon, P.; Lozaono, C.

    1997-01-01

    To describe the radiological findings associated with trochanteric bursitis. Six patients studied by means of plain radiography (n=6), CT(n=4) and MR(n=2). The conventional radiography study was normal in two patients and disclosed bone abnormalities in four. US showed a hypoechoic or anechoic collection in all the patients. Two patients presented areas suggestive of calcification, and septa were observed in one. CT disclosed the presence of well defined, low-attenuation, unenhanced collections. MR images identified collections with a signal intensity similar to that of water. Trochanteric bursitis is a relatively common cause of hip pain, and can involve any one of a number of etiologies. US is a good imaging technique for diagnosing this pathology. (Author) 10 refs

  14. Radiologic findings in neurofibromatosis

    International Nuclear Information System (INIS)

    Kim, Dai Young; Jeon, Seok Chol; Lee, Kwan Se; Yeon, Kyung Mo; Choo, Dong Woon

    1979-01-01

    Neurofibromatosis is an uncommon but certainly not a rare hereditary disorder, probably of neuralcrest origin, involving not only neuroectoderm and mesoderm but also endoderm and characterized by cafe au lait spots and cutaneous and subcutaneous tumors, with secondary mesodermal defects responsible for protean osseous abnormalities and various manifestations in other systems. This paper is a study of confirmed 143 cases of neurofibromatosis collected for past 8 years. In this analysis, special attention was given to the selected 37 cases which showed abnormal findings on radiological examinations. Overall male to female ratio was 1 : 1.3. The most frequent kind of abnormalities was vertebral kyphoscoliosis in 12 cases. Among the more pathognomonic but uncommon abnormalities to neurofibromatosis, we experienced each 2 cases of lambdoid defect, pseudoarthrosis and renovascular hypertension, and 1 cases of sphenoid bone absence.

  15. MR findings in mannosidosis.

    Science.gov (United States)

    Dietemann, J L; Filippi de la Palavesa, M M; Tranchant, C; Kastler, B

    1990-01-01

    MR findings are reported in three patients presenting mannosidosis. Among a family of 8 children, 4 presented typical clinical and biological abnormalities related to mannosidosis. Brain MR examinations including sagittal T1 and axial T2 sections were obtained in three patients of this family (one 25-year-old male, one 34-year-old female, and one 35-year-old female). MR scans demonstrate seven types of modifications: (1) brachycephaly, (2) thick calvaria, (3) verticalization of the chiasmatic sulcus, (4) poor pneumatization of the sphenoid body, (5) partial empty sella turcica (6) cerebellar atrophy, and (7) white matter signal modifications. High signal abnormalities involving the parieto-occipital white matter are identified on axial T2-weighted scans in the three patients and are probably related to demyelination and associated gliosis as described previously by several authors on specimens.

  16. MRI finding of hemangioblastomas

    International Nuclear Information System (INIS)

    Park, Seung Cheol; Oh, Min Cheol; Chung, Hwan Hoon; Seol, Hye Young; Lee, Nam Joon; Kim, Jung Hyuk

    1994-01-01

    The purpose of this study is to evaluate the findings of magnetic resonance imaging (MRI) of posterior fossa hemanangioblastoma and usefulness of contrast enhancement with Gd-DTPA. Seven patients with posterior fossa hemangioblastoma were studied with both pre- and post-enhanced MRI. The MR images were reviewed regarding the location, size, signal intensities of cysts and mural nodules, and their contrast enhancement pattern. Five tumors were located in cerebellar hemisphere, one in vermis, and one in posterior part of medulla. One patient with von Hippel-Lindau disease had a medullary hemangioblastoma with multiple pancreatic cysts. In 6 cases, the major portion of the tumor was cysts and had small mulkal nodules. The solid portion was relatively lange in one cases, cemprising half of the tumor cysts were oval shaped and their sized were 3-6.7 cm in diameter. In five cases(71%), septations were noted within the cysts. Cysts were isointense or slightly hyperintense on T1-weighted image and hyperintense on T2- weighted image compared with cerebrospinal fluid. Mural nodules were oval or rounded radiotherapy had better prognosis than those treated with radiotherapy alwas 0.5-2.5 cm in diameter. Mural nodules were isointense to gray matter. They were detected in five cases on T1-weighted images and one case on T2-weighted images. In two cases, vascular signal void area was noted in mural nodules. On contrast-enhanced T1-weighted images, all mural nodules were intensely enhanced. MRI provide to be a good diagnostic method to detect and characterize posterior fossa hemangioblastoma. The most common finding is Cystic posterior fossa lesion with enhancing mural nodule. Contrast enhancement is essential for specific diagnosis

  17. Albinism: classification, clinical characteristics, and recent findings.

    Science.gov (United States)

    Summers, C Gail

    2009-06-01

    To describe the clinical characteristics and recent findings in the heterogeneous group of inherited disorders of melanin biosynthesis grouped as "albinism." The current classification of albinism, and the cutaneous, ocular, and central nervous system characteristics are presented. Recent clinical findings are summarized. Albinism is now classified based on genes known to be responsible for albinism. Foveal hypoplasia is invariably present and individuals with albinism often have delayed visual development, reduced vision, nystagmus, a positive angle kappa, strabismus, iris transillumination, and absent or reduced melanin pigment in the fundi. A visual-evoked potential can document the excessive retinostriate decussation seen in albinism. Grating acuity can be used to document delayed visual development in preverbal children. Glasses are often needed to improve visual acuity and binocular alignment. Albinism is caused by several different genes. Heterogeneity in clinical phenotype indicates that expressivity is variable.

  18. Radiographic findings in immunodeficiency

    International Nuclear Information System (INIS)

    Obregon, R.; Lynch, D.A.; Cink, T.M.; Newell, J.D.; Kirkpatrick, C.

    1991-01-01

    This paper reviews the chest radiographs and high-resolution CT (HRCT) scans in patients with immunodeficiency disorders and define the role of HRCT. Thirty-three cases were retrospectively graded according to the consensus of two radiologists. Patients with HIV seropositivity and asthma were excluded. HRCT was performed in 12 cases with standard techniques. Diagnoses included common variable hypogammaglobulinemia (n = 19), X-linked agammaglobulinemia (n = 4), chronic mucocutaneous candidiasis (n = 4), and selective immunoglobulin g deficiencies (n = 2). Chest radiographs showed bronchiectasis in 11 of 33 cases with a predominant lower lobe distribution (82%). Nodules were present in six cases and mucus plugs in four cases. HRCT showed bronchiectasis in nine of 12 cases; in five of these nine cases, bronchiectasis was not apparent on chest radiographs. Other HRCT findings included segmental air trapping (four of 12), mucus plugs (three of 12), hazy consolidation (four of 12), nodules (five of 12), and bronchiolectasis (two of 12). Therapy was altered in seven of 12 cases in which HRCT was performed. Most pertinent to clinical management were the presence of a thymoma (n = 1) and severe focal of diffuse bronchiectasis

  19. Verified scientific findings

    International Nuclear Information System (INIS)

    Bullinger, M.G.

    1982-01-01

    In this essay, the author attempts to enlighten the reader as to the meaning of the term ''verified scientific findings'' in section 13, sub-section 1, sentence 2 of the new Chemicals Control Law. The examples given here are the generally accepted regulations in regards to technology (that is sections 7a and 18b of the WHG (law on water economy), section 3, sub-section 1 of the machine- and engine protection laws) and to the status of technology (section 3, sub-section 6 of the BImSchG (Fed. law on prevention of air-borne pollution)), and to the status of science (section 5, sub-section 2 of the AMG (drug legislation). The ''status of science and technology'' as defined in sections 4 ff of the Atomic Energy Law (AtomG) and in sections 3, 4, 12, 2) of the First Radiation Protection Ordinance (1.StrlSch. VO), is also being discussed. The author defines the in his opinion ''dynamic term'' as the generally recognized result of scientific research, and the respective possibilities of practical utilization of technology. (orig.) [de

  20. [Incidental finding of proteinuria].

    Science.gov (United States)

    Galle, J

    2014-10-01

    A positive signal when testing urine for proteinuria is a frequent finding, either in the context of a routine medical check-up or when searching for a specific renal disorder. This brief overview aims to provide assistance in the classification of proteinuria and to provide guidance to the next diagnostic and therapeutic steps. The normal urine protein loss of a healthy adult is less then 150 mg/day. Higher rates of proteinuria should be confirmed as this is often a sign of glomerular or tubular damage. In addition, proteinuria is a strong prognostic factor for cardiovascular and total mortality. Principally, proteinuria is 1) a symptom of renal diseases, 2) a progression factor for renal diseases and 3) a risk factor for cardiovascular diseases and total mortality. In this article proteinuria is defined, the correlation to various renal diseases is described and the relevance for progression of renal diseases and total mortality is shown. Finally, diagnostic procedures are described and a perspective on therapeutic measures is provided.

  1. ORAL FINDINGS IN PATIENTS WITH APERT SYNDROME

    OpenAIRE

    Dalben, Gisele da Silva; Neves, Lucimara Teixeira das; Gomide, Marcia Ribeiro

    2006-01-01

    INTRODUCTION: The Apert syndrome is a rare disorder of autosomal dominant inheritance caused by mutations in the FGFR2 gene at locus 10q26; patients with this syndrome present severe syndactyly, exophthalmia, ocular hypertelorism and hypoplastic midface with Class III malocclusion, besides systemic alterations. Most investigations available on the Apert syndrome address the genetic aspect or surgical management, with little emphasis on the oral aspects. OBJECTIVE: to investigate the oral find...

  2. Thoracic textilomas: CT findings

    Energy Technology Data Exchange (ETDEWEB)

    Machado, Dianne Melo; Zanetti, Glaucia; Araujo Neto, Cesar Augusto; Nobre, Luiz Felipe; Meirelles, Gustavo de Souza Portes; Silva, Jorge Luiz Pereira e; Guimaraes, Marcos Duarte; Escuissato, Dante Luiz; Souza Junior, Arthur Soares; Hochhegger, Bruno; Marchiori, Edson, E-mail: edmarchiori@gmail.com [Hospital Universitario Antonio Pedro (HUAP/UFF), Niteroi, RJ (Brazil)

    2014-09-15

    Objective: the aim of this study was to analyze chest CT scans of patients with thoracic textiloma. Methods: this was a retrospective study of 16 patients (11 men and 5 women) with surgically confirmed thoracic textiloma. The chest CT scans of those patients were evaluated by two independent observers, and discordant results were resolved by consensus. Results: the majority (62.5%) of the textilomas were caused by previous heart surgery. The most common symptoms were chest pain (in 68.75%) and cough (in 56.25%). In all cases, the main tomographic finding was a mass with regular contours and borders that were well-defined or partially defined. Half of the textilomas occurred in the right hemithorax and half occurred in the left. The majority (56.25%) were located in the lower third of the lung. The diameter of the mass was ≤ 10 cm in 10 cases (62.5%) and > 10 cm in the remaining 6 cases (37.5%). Most (81.25%) of the textilomas were heterogeneous in density, with signs of calcification, gas, radiopaque marker, or sponge-like material. Peripheral expansion of the mass was observed in 12 (92.3%) of the 13 patients in whom a contrast agent was used. Intraoperatively, pleural involvement was observed in 14 cases (87.5%) and pericardial involvement was observed in 2 (12.5%). Conclusions: it is important to recognize the main tomographic aspects of thoracic textilomas in order to include this possibility in the differential diagnosis of chest pain and cough in patients with a history of heart or thoracic surgery, thus promoting the early identification and treatment of this postoperative complication. (author)

  3. Neighboring Genes Show Correlated Evolution in Gene Expression

    Science.gov (United States)

    Ghanbarian, Avazeh T.; Hurst, Laurence D.

    2015-01-01

    When considering the evolution of a gene’s expression profile, we commonly assume that this is unaffected by its genomic neighborhood. This is, however, in contrast to what we know about the lack of autonomy between neighboring genes in gene expression profiles in extant taxa. Indeed, in all eukaryotic genomes genes of similar expression-profile tend to cluster, reflecting chromatin level dynamics. Does it follow that if a gene increases expression in a particular lineage then the genomic neighbors will also increase in their expression or is gene expression evolution autonomous? To address this here we consider evolution of human gene expression since the human-chimp common ancestor, allowing for both variation in estimation of current expression level and error in Bayesian estimation of the ancestral state. We find that in all tissues and both sexes, the change in gene expression of a focal gene on average predicts the change in gene expression of neighbors. The effect is highly pronounced in the immediate vicinity (genes increasing their expression in humans tend to avoid nuclear lamina domains and be enriched for the gene activator 5-hydroxymethylcytosine, we conclude that, most probably owing to chromatin level control of gene expression, a change in gene expression of one gene likely affects the expression evolution of neighbors, what we term expression piggybacking, an analog of hitchhiking. PMID:25743543

  4. Genes2FANs: connecting genes through functional association networks

    Science.gov (United States)

    2012-01-01

    Background Protein-protein, cell signaling, metabolic, and transcriptional interaction networks are useful for identifying connections between lists of experimentally identified genes/proteins. However, besides physical or co-expression interactions there are many ways in which pairs of genes, or their protein products, can be associated. By systematically incorporating knowledge on shared properties of genes from diverse sources to build functional association networks (FANs), researchers may be able to identify additional functional interactions between groups of genes that are not readily apparent. Results Genes2FANs is a web based tool and a database that utilizes 14 carefully constructed FANs and a large-scale protein-protein interaction (PPI) network to build subnetworks that connect lists of human and mouse genes. The FANs are created from mammalian gene set libraries where mouse genes are converted to their human orthologs. The tool takes as input a list of human or mouse Entrez gene symbols to produce a subnetwork and a ranked list of intermediate genes that are used to connect the query input list. In addition, users can enter any PubMed search term and then the system automatically converts the returned results to gene lists using GeneRIF. This gene list is then used as input to generate a subnetwork from the user’s PubMed query. As a case study, we applied Genes2FANs to connect disease genes from 90 well-studied disorders. We find an inverse correlation between the counts of links connecting disease genes through PPI and links connecting diseases genes through FANs, separating diseases into two categories. Conclusions Genes2FANs is a useful tool for interpreting the relationships between gene/protein lists in the context of their various functions and networks. Combining functional association interactions with physical PPIs can be useful for revealing new biology and help form hypotheses for further experimentation. Our finding that disease genes in

  5. Gene expression

    International Nuclear Information System (INIS)

    Hildebrand, C.E.; Crawford, B.D.; Walters, R.A.; Enger, M.D.

    1983-01-01

    We prepared probes for isolating functional pieces of the metallothionein locus. The probes enabled a variety of experiments, eventually revealing two mechanisms for metallothionein gene expression, the order of the DNA coding units at the locus, and the location of the gene site in its chromosome. Once the switch regulating metallothionein synthesis was located, it could be joined by recombinant DNA methods to other, unrelated genes, then reintroduced into cells by gene-transfer techniques. The expression of these recombinant genes could then be induced by exposing the cells to Zn 2+ or Cd 2+ . We would thus take advantage of the clearly defined switching properties of the metallothionein gene to manipulate the expression of other, perhaps normally constitutive, genes. Already, despite an incomplete understanding of how the regulatory switch of the metallothionein locus operates, such experiments have been performed successfully

  6. Findings

    Science.gov (United States)

    ... injury. Read Issue Emily Scott, Biochemist Hooked on Heme Emily Scott's research on a family of enzymes ... and Biochemistry Enzymes, Molecular Probes, Metabolic Engineering, Glycobiology, Synthesis, Natural Products, Chemical Reactions Computers in Biology Bioinformatics, ...

  7. Gene-gene and gene-environmental interactions of childhood asthma: a multifactor dimension reduction approach.

    Directory of Open Access Journals (Sweden)

    Ming-Wei Su

    Full Text Available BACKGROUND: The importance of gene-gene and gene-environment interactions on asthma is well documented in literature, but a systematic analysis on the interaction between various genetic and environmental factors is still lacking. METHODOLOGY/PRINCIPAL FINDINGS: We conducted a population-based, case-control study comprised of seventh-grade children from 14 Taiwanese communities. A total of 235 asthmatic cases and 1,310 non-asthmatic controls were selected for DNA collection and genotyping. We examined the gene-gene and gene-environment interactions between 17 single-nucleotide polymorphisms in antioxidative, inflammatory and obesity-related genes, and childhood asthma. Environmental exposures and disease status were obtained from parental questionnaires. The model-free and non-parametrical multifactor dimensionality reduction (MDR method was used for the analysis. A three-way gene-gene interaction was elucidated between the gene coding glutathione S-transferase P (GSTP1, the gene coding interleukin-4 receptor alpha chain (IL4Ra and the gene coding insulin induced gene 2 (INSIG2 on the risk of lifetime asthma. The testing-balanced accuracy on asthma was 57.83% with a cross-validation consistency of 10 out of 10. The interaction of preterm birth and indoor dampness had the highest training-balanced accuracy at 59.09%. Indoor dampness also interacted with many genes, including IL13, beta-2 adrenergic receptor (ADRB2, signal transducer and activator of transcription 6 (STAT6. We also used likelihood ratio tests for interaction and chi-square tests to validate our results and all tests showed statistical significance. CONCLUSIONS/SIGNIFICANCE: The results of this study suggest that GSTP1, INSIG2 and IL4Ra may influence the lifetime asthma susceptibility through gene-gene interactions in schoolchildren. Home dampness combined with each one of the genes STAT6, IL13 and ADRB2 could raise the asthma risk.

  8. Radiographic findings of Proteus Syndrome

    Directory of Open Access Journals (Sweden)

    Nishant Mukesh Gandhi, MD

    2014-01-01

    Full Text Available The extremely rare Proteus Syndrome is a hamartomatous congenital syndrome with substantial variability between clinical patient presentations. The diagnostic criteria consist of a multitude of clinical findings including hemihypertrophy, macrodactyly, epidermal nevi, subcutaneous hamartomatous tumors, and bony abnormalities. These clinical findings correlate with striking radiographic findings.

  9. Radiographic findings of Proteus Syndrome

    Science.gov (United States)

    Gandhi, Nishant Mukesh; Davalos, Eric A.; Varma, Rajeev K.

    2015-01-01

    The extremely rare Proteus Syndrome is a hamartomatous congenital syndrome with substantial variability between clinical patient presentations. The diagnostic criteria consist of a multitude of clinical findings including hemihypertrophy, macrodactyly, epidermal nevi, subcutaneous hamartomatous tumors, and bony abnormalities. These clinical findings correlate with striking radiographic findings. PMID:27186241

  10. Comparing the evolutionary conservation between human essential genes, human orthologs of mouse essential genes and human housekeeping genes.

    Science.gov (United States)

    Lv, Wenhua; Zheng, Jiajia; Luan, Meiwei; Shi, Miao; Zhu, Hongjie; Zhang, Mingming; Lv, Hongchao; Shang, Zhenwei; Duan, Lian; Zhang, Ruijie; Jiang, Yongshuai

    2015-11-01

    Human housekeeping genes are often confused with essential human genes, and several studies regard both types of genes as having the same level of evolutionary conservation. However, this is not necessarily the case. To clarify this, we compared the differences between human housekeeping genes and essential human genes with respect to four aspects: the evolutionary rate (dN/dS), protein sequence identity, single-nucleotide polymorphism (SNP) density and level of linkage disequilibrium (LD). The results showed that housekeeping genes had lower evolutionary rates, higher sequence identities, lower SNP densities and higher levels of LD compared with essential genes. Together, these findings indicate that housekeeping and essential genes are two distinct types of genes, and that housekeeping genes have a higher level of evolutionary conservation. Therefore, we suggest that researchers should pay careful attention to the distinctions between housekeeping genes and essential genes. Moreover, it is still controversial whether we should substitute human orthologs of mouse essential genes for human essential genes. Therefore, we compared the evolutionary features between human orthologs of mouse essential genes and human housekeeping genes and we got inconsistent results in long-term and short-term evolutionary characteristics implying the irrationality of simply replacing human essential genes with human orthologs of mouse essential genes. © The Author 2015. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

  11. Trichoderma genes

    Science.gov (United States)

    Foreman, Pamela [Los Altos, CA; Goedegebuur, Frits [Vlaardingen, NL; Van Solingen, Pieter [Naaldwijk, NL; Ward, Michael [San Francisco, CA

    2012-06-19

    Described herein are novel gene sequences isolated from Trichoderma reesei. Two genes encoding proteins comprising a cellulose binding domain, one encoding an arabionfuranosidase and one encoding an acetylxylanesterase are described. The sequences, CIP1 and CIP2, contain a cellulose binding domain. These proteins are especially useful in the textile and detergent industry and in pulp and paper industry.

  12. What is a gene? From molecules to metaphysics.

    Science.gov (United States)

    Rolston, Holmes

    2006-01-01

    Mendelian genes have become molecular genes, with increasing puzzlement about locating them, due to increasing complexity in genomic webworks. Genome science finds modular and conserved units of inheritance, identified as homologous genes. Such genes are cybernetic, transmitting information over generations; this too requires multi-leveled analysis, from DNA transcription to development and reproduction of the whole organism. Genes are conserved; genes are also dynamic and creative in evolutionary speciation-most remarkably producing humans capable of wondering about what genes are.

  13. Alternative Polyadenylation: Methods, Findings, and Impacts

    Directory of Open Access Journals (Sweden)

    Wei Chen

    2017-10-01

    Full Text Available Alternative polyadenylation (APA, a phenomenon that RNA molecules with different 3′ ends originate from distinct polyadenylation sites of a single gene, is emerging as a mechanism widely used to regulate gene expression. In the present review, we first summarized various methods prevalently adopted in APA study, mainly focused on the next-generation sequencing (NGS-based techniques specially designed for APA identification, the related bioinformatics methods, and the strategies for APA study in single cells. Then we summarized the main findings and advances so far based on these methods, including the preferences of alternative polyA (pA site, the biological processes involved, and the corresponding consequences. We especially categorized the APA changes discovered so far and discussed their potential functions under given conditions, along with the possible underlying molecular mechanisms. With more in-depth studies on extensive samples, more signatures and functions of APA will be revealed, and its diverse roles will gradually heave in sight. Keywords: Alternative polyadenylation, Next-generation sequencing, 3′UTR, Alternative splicing, Gene regulation

  14. Gene expression in colorectal cancer

    DEFF Research Database (Denmark)

    Birkenkamp-Demtroder, Karin; Christensen, Lise Lotte; Olesen, Sanne Harder

    2002-01-01

    Understanding molecular alterations in colorectal cancer (CRC) is needed to define new biomarkers and treatment targets. We used oligonucleotide microarrays to monitor gene expression of about 6,800 known genes and 35,000 expressed sequence tags (ESTs) on five pools (four to six samples in each......' C, and clustered Dukes' D separately. Real-time PCR of 10 known genes and 5 ESTs demonstrated excellent reproducibility of the array-based findings. The most frequently altered genes belonged to functional categories of metabolism (22%), transcription and translation (11%), and cellular processes (9...

  15. Correlation of Imaging Findings with Pathologic Findings of Sclerosing Adenosis

    International Nuclear Information System (INIS)

    Choi, Bo Bae; Shu, Kwang Sun

    2012-01-01

    The purpose of this study was to evaluate the mammographic and sonographic findings of pure sclerosing adenosis. We retrospectively reviewed the mammographic and sonographic findings in 40 cases of pure sclerosing adenosis confirmed by core needle biopsy (n = 23), vacuum-assisted biopsy (n = 7), excision biopsy (n = 9), and lumpectomy (n = 1) from January 2002 to March 2010. All imaging findings were analyzed according to the American College of Radiology (ACR) breast imaging reporting and data system (BI-RADS). Radiologic features were correlated with pathologic findings. Although most mammograms showed negative findings (57%), calcification was the most common abnormal finding of sclerosing adenosis. On sonography, the most common finding was a circumscribed oval hypoechoic mass without posterior features (78%). Most masses showed BI-RADS category 3, (75%, 27/36). Five cases showed categories 4 or 5 (14%, 5/36). Most mammographic and sonographic findings of sclerosing adenosis are non-specific and non-pathognomonic, even though sometimes sclerosing adenosis can be radiologically or histopathologically confused with malignancy

  16. Correlation of Imaging Findings with Pathologic Findings of Sclerosing Adenosis

    Energy Technology Data Exchange (ETDEWEB)

    Choi, Bo Bae; Shu, Kwang Sun [Chungnam National University Hospital, Daejeon (Korea, Republic of)

    2012-03-15

    The purpose of this study was to evaluate the mammographic and sonographic findings of pure sclerosing adenosis. We retrospectively reviewed the mammographic and sonographic findings in 40 cases of pure sclerosing adenosis confirmed by core needle biopsy (n = 23), vacuum-assisted biopsy (n = 7), excision biopsy (n = 9), and lumpectomy (n = 1) from January 2002 to March 2010. All imaging findings were analyzed according to the American College of Radiology (ACR) breast imaging reporting and data system (BI-RADS). Radiologic features were correlated with pathologic findings. Although most mammograms showed negative findings (57%), calcification was the most common abnormal finding of sclerosing adenosis. On sonography, the most common finding was a circumscribed oval hypoechoic mass without posterior features (78%). Most masses showed BI-RADS category 3, (75%, 27/36). Five cases showed categories 4 or 5 (14%, 5/36). Most mammographic and sonographic findings of sclerosing adenosis are non-specific and non-pathognomonic, even though sometimes sclerosing adenosis can be radiologically or histopathologically confused with malignancy

  17. Finding costs methodology - alternative approaches

    International Nuclear Information System (INIS)

    Gaddis, D.

    1992-01-01

    Though the context may vary, the topic of the day in the oil and gas industry is ''finding costs per barrel.'' First, there have been numerous articles in both the popular media and the industry press that have argued it is cheaper for companies to buy reserves that find them with the drill bit. Financial analysts have emphasized the importance of comparing relative finding costs when evaluating different companies. The success of failure of a company's management has been judged on the basis of finding costs. In discussing oil and gas prices, economists commonly refer to the relationship between the market prices of oil and gas and their finding costs, and no discussion of the U.S. petroleum industry and the development of a national energy policy is complete without reference to finding costs. (Author)

  18. Novel genes in LDL metabolism

    DEFF Research Database (Denmark)

    Christoffersen, Mette; Tybjærg-Hansen, Anne

    2015-01-01

    PURPOSE OF REVIEW: To summarize recent findings from genome-wide association studies (GWAS), whole-exome sequencing of patients with familial hypercholesterolemia and 'exome chip' studies pointing to novel genes in LDL metabolism. RECENT FINDINGS: The genetic loci for ATP-binding cassette......-exome sequencing and 'exome chip' studies have additionally suggested several novel genes in LDL metabolism including insulin-induced gene 2, signal transducing adaptor family member 1, lysosomal acid lipase A, patatin-like phospholipase domain-containing protein 5 and transmembrane 6 superfamily member 2. Most...... of these findings still require independent replications and/or functional studies to confirm the exact role in LDL metabolism and the clinical implications for human health. SUMMARY: GWAS, exome sequencing studies, and recently 'exome chip' studies have suggested several novel genes with effects on LDL cholesterol...

  19. CT findings of infant epilepsy

    International Nuclear Information System (INIS)

    Hojoh, Hiroatsu; Kataoka, Kenkichi; Nakagawa, Yoshihiro; Nakano, Shozo; Tomita, Yutaka.

    1982-01-01

    CT diagnosis of infantile epilepsy was evaluated. High incidence of abnormal CT findings in infantile spasms and Lennox-Gastaut syndrome was same as in other reports. Comparison between CT findings and neurological complications and that between CT findings and electroencephalogram findings revealed a stronger relationship existing in the former. This suggested that CT is more useful as a measure to detect underlying diseases which are due to organic change of the brain to cause epilepsy, rather than as that to disclose epileptic primary lesions of functional change. (Ueda, J.)

  20. CT findings of infant epilepsy

    Energy Technology Data Exchange (ETDEWEB)

    Hojoh, Hiroatsu; Kataoka, Kenkichi; Nakagawa, Yoshihiro (Children' s Medical Center, Shizuoka (Japan)); Nakano, Shozo; Tomita, Yutaka

    1982-10-01

    CT diagnosis of infantile epilepsy was evaluated. High incidence of abnormal CT findings in infantile spasms and Lennox-Gastaut syndrome was same as in other reports. Comparison between CT findings and neurological complications and that between CT findings and electroencephalogram findings revealed a stronger relationship existing in the former. This suggested that CT is more useful as a measure to detect underlying diseases which are due to organic change of the brain to cause epilepsy, rather than as that to disclose epileptic primary lesions of functional change.

  1. Generalist genes and learning disabilities.

    Science.gov (United States)

    Plomin, Robert; Kovas, Yulia

    2005-07-01

    The authors reviewed recent quantitative genetic research on learning disabilities that led to the conclusion that genetic diagnoses differ from traditional diagnoses in that the effects of relevant genes are largely general rather than specific. This research suggests that most genes associated with common learning disabilities--language impairment, reading disability, and mathematics disability--are generalists in 3 ways. First, genes that affect common learning disabilities are largely the same genes responsible for normal variation in learning abilities. Second, genes that affect any aspect of a learning disability affect other aspects of the disability. Third, genes that affect one learning disability are also likely to affect other learning disabilities. These quantitative genetic findings have far-reaching implications for molecular genetics and neuroscience as well as psychology. Copyright 2005 APA, all rights reserved.

  2. Immunoglobulin genes

    National Research Council Canada - National Science Library

    Honjo, T; Alt, F. W; Rabbitts, T. H

    1989-01-01

    ... Cataloguing in Publication Data Immunoglobulin genes 1. Vertebrates. Immunoglobulins 1. Honjo, T. II. Alt, F.W. III. Rabbitts, T.H. 612'. 118223 ISBN 0-12-354865-9 This book is printed on acid-free paper ( T...

  3. Ageing genes

    DEFF Research Database (Denmark)

    Rattan, Suresh

    2018-01-01

    The idea of gerontogenes is in line with the evolutionary explanation of ageing as being an emergent phenomenon as a result of the imperfect maintenance and repair systems. Although evolutionary processes did not select for any specific ageing genes that restrict and determine the lifespan...... of an individual, the term ‘gerontogenes’ primarily refers to any genes that may seem to influence ageing and longevity, without being specifically selected for that role. Such genes can also be called ‘virtual gerontogenes’ by virtue of their indirect influence on the rate and process of ageing. More than 1000...... virtual gerontogenes have been associated with ageing and longevity in model organisms and humans. The ‘real’ genes, which do influence the essential lifespan of a species, and have been selected for in accordance with the evolutionary life history of the species, are known as the longevity assurance...

  4. CT findings of necrotizing pneumonia

    International Nuclear Information System (INIS)

    Kim, Hyae Young; Im, Jung Gi; Whang, Sung Il; Cheon, Jung Eun; Lee, Jae Kyo; Song, Jae Woo

    1998-01-01

    Necrotizing pneumonia causes necrosis of pulmonary parenchyma and may lead to pulmonary gangrene. Prior to the antibiotic era, extensive pulmonary involvement was potentially fatal, but the incidence of necrotizing pneumoniais now less common. On contrast-enhanced CT scans, consolidation with contrast enhancement containing necrotic foci with low attenuation and cavities is characteristic. Radiologic findings do not differ according to the causative organism and in most of cases, specific diagnosis may be impossible. Clinical findings and certain characteristic radiologic findings may be helpful for narrowing the differential diagnosis. We illustrate the clinical and radiologic characteristics of necrotizing pneumonia according to causative bacterial organisms

  5. Chest radiographic findings of leptospirosis

    International Nuclear Information System (INIS)

    Kim, Mee Hyun; Jung, Hee Tae; Lee, Young Joong; Yoon, Jong Sup

    1986-01-01

    1. A study on chest radiographic findings of 54 cases with pneumonia like symptoms was performed. Of 54 cases, 8 cases were confirmed to be leptospirosis and 7 cases were leptospirosis combined with Korean hemorrhagic fever. 2. Of 8 cases of leptospirosis, 4 cases showed abnormal chest radiographic findings: acinar nodular type 2, massive confluent consolidation type 2. Of 7 cases of leptospirosis combined with Korean hemorrhagic fever: acinar nodular type 3, massive confluent consolidation type 1, and increased interstitial markings type 1 respectively. 3. It was considered to be difficult to diagnose the leptospirosis on chest radiographic findings alone, especially the case combined with Korean hemorrhagic fever.

  6. findings from specialist treatment centres

    African Journals Online (AJOL)

    8.3%) cited methaqualone as their primary substance of abuse. Discussion. The findings from our study confirm that OTC/prescription medicine misuse is frequently reported among patients in substance abuse treatment settings. Compared with ...

  7. Dermoscopy Findings of Hidroacanthoma Simplex

    Directory of Open Access Journals (Sweden)

    Yota Sato

    2014-05-01

    Full Text Available Hidroacanthoma simplex (HAS, also known as intraepidermal eccrine poroma, is a rare eccrine adnexal tumor that tends to be misdiagnosed as other types of benign skin tumor, including clonal seborrheic keratosis. Notably, HAS is sometimes misdiagnosed and treated by cryosurgery as seborrheic keratosis, which could trigger the later development of porocarcinoma. Therefore, accurate diagnosis of HAS is indispensable for dermatologists to avoid the development of malignant tumors by an unsuitable treatment. In this report, we present the characteristic dermoscopy findings of HAS. Indeed, the dermoscopy findings might be related to the melanin-rich necrotic cells in the epidermis, which are quite different from dermoscopy findings of clonal seborrheic keratosis. As a previous report suggested, it is difficult for a dermatologist to differentiate HAS from clonal seborrheic keratosis by the naked eye. Our findings might be supportive for the early diagnosis of HAS.

  8. Find your future in mathematics

    CERN Document Server

    Gunzehauser, Kelly

    2016-01-01

    "Find Your Future in Mathematics introduces 8 high-interest mathematical careers via reader-friendly profiles and sidebar features that inspire extended learning, online research, and critical thinking skills. Back matter includes additional learning activities"-- Provided by publisher.

  9. Find an Allergist/Immunologist

    Science.gov (United States)

    ... Japan Jersey Jordan Kazakhstan Kenya Kiribati Korea Kosovo Kuwait Kyrgyzstan Lao People's Dem Republic Latvia Lebanon Lesotho ... meeting Browse your conditions Check pollen counts Continuing education center Find an allergist / immunologist Journals Login / My ...

  10. Learning as way-finding

    DEFF Research Database (Denmark)

    Dau, Susanne

    motions of humans and non-human agencies. The findings reveal that learning; formal and informal can be conceptualized by the metaphor of way-finding; embodied, emotionally and/or cognitive both individually and socially. Way-finding, is argued, to be a contemporary concept for learning processes......Based on empirical case-study findings and the theoretical framework of learning by Illeris coupled with Nonaka & Takeuchis´s perspectives on knowledge creation, it is stressed that learning are conditioned by contextual orientations-processes in spaces near the body (peripersonal spaces) through......, knowledge development and identity-shaping, where learning emerges through motions, feeling and thinking within an information rich world in constant change....

  11. Find selv fred og ro

    DEFF Research Database (Denmark)

    Juelskjær, Malou

    2010-01-01

    I klasseværelset er det lærerens ansvar at skabe ro. Men i de nye skolebygninger er det den enkelte elevs ansvar at finde frem til fredfyldte steder.......I klasseværelset er det lærerens ansvar at skabe ro. Men i de nye skolebygninger er det den enkelte elevs ansvar at finde frem til fredfyldte steder....

  12. Radiologic findings of granulomatous mastitis

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Tae Gyu; Kim, Ji Young; Jeong, Myeong Ja; Kim, Jae Hyung; Kim, Soung Hee; Kim, Soo Hyun; Jun, Woo Sun; Park, Kyeong Mee; Han, Se Hwan [Paik Hospital, Inje University College of Medicine, Seoul (Korea, Republic of)

    2008-08-15

    The describe the radiologic findings of granulomatous mastitis of the breast. This study included 19 patients (age range: 22 to 56 years; mean 37 years) with 22 lesions that were pathologically confirmed as having granulomatous mastitis. All the patients underwent a breast ultrasonography and 13 patients underwent a mammography. The results of the mammography revealed focal asymmetry (n = 9), multiple ill-defined isodense nodules (n 2), ill-defined nodular density on craniocaudal view (n = 1), and unremarkable finding (n = 1). The sonographic findings included continuous or discontinuous multiple tubular and nodular low echoic lesions (n = 7), ill-defined heterogeneously low echoic lesion (n = 5), irregular-shaped, ill-defined low echoic mass (n = 4), fluid collection with internal floating materials suggesting the presence of an abscess (n = 4), ill-defined heterogeneously low echoic lesion and abscess (n = 1), and multiple ill-defined nodules (n = 1). In the case of granulomatous mastitis, the mammography results indicate a lack of specificity between normal findings and focal asymmetry. The sonographic findings indicate that ill-defined heterogeneously low echoic lesions or irregular shaped, ill-defined low echoic masses are difficult to differentiate from breast cancer. The sonographic findings of abscesses indicate a difficulty in differentiating them from cases of pyogenic mastitis. However, multiple tubular and nodular low echoic lesions, especially with a continuous appearance, should point to granulomatous mastitis, and is helpful in its differential diagnosis and treatment.

  13. The relationship among gene expression, the evolution of gene dosage, and the rate of protein evolution.

    Directory of Open Access Journals (Sweden)

    Jean-François Gout

    2010-05-01

    Full Text Available The understanding of selective constraints affecting genes is a major issue in biology. It is well established that gene expression level is a major determinant of the rate of protein evolution, but the reasons for this relationship remain highly debated. Here we demonstrate that gene expression is also a major determinant of the evolution of gene dosage: the rate of gene losses after whole genome duplications in the Paramecium lineage is negatively correlated to the level of gene expression, and this relationship is not a byproduct of other factors known to affect the fate of gene duplicates. This indicates that changes in gene dosage are generally more deleterious for highly expressed genes. This rule also holds for other taxa: in yeast, we find a clear relationship between gene expression level and the fitness impact of reduction in gene dosage. To explain these observations, we propose a model based on the fact that the optimal expression level of a gene corresponds to a trade-off between the benefit and cost of its expression. This COSTEX model predicts that selective pressure against mutations changing gene expression level or affecting the encoded protein should on average be stronger in highly expressed genes and hence that both the frequency of gene loss and the rate of protein evolution should correlate negatively with gene expression. Thus, the COSTEX model provides a simple and common explanation for the general relationship observed between the level of gene expression and the different facets of gene evolution.

  14. A hybrid approach of gene sets and single genes for the prediction of survival risks with gene expression data.

    Science.gov (United States)

    Seok, Junhee; Davis, Ronald W; Xiao, Wenzhong

    2015-01-01

    Accumulated biological knowledge is often encoded as gene sets, collections of genes associated with similar biological functions or pathways. The use of gene sets in the analyses of high-throughput gene expression data has been intensively studied and applied in clinical research. However, the main interest remains in finding modules of biological knowledge, or corresponding gene sets, significantly associated with disease conditions. Risk prediction from censored survival times using gene sets hasn't been well studied. In this work, we propose a hybrid method that uses both single gene and gene set information together to predict patient survival risks from gene expression profiles. In the proposed method, gene sets provide context-level information that is poorly reflected by single genes. Complementarily, single genes help to supplement incomplete information of gene sets due to our imperfect biomedical knowledge. Through the tests over multiple data sets of cancer and trauma injury, the proposed method showed robust and improved performance compared with the conventional approaches with only single genes or gene sets solely. Additionally, we examined the prediction result in the trauma injury data, and showed that the modules of biological knowledge used in the prediction by the proposed method were highly interpretable in biology. A wide range of survival prediction problems in clinical genomics is expected to benefit from the use of biological knowledge.

  15. Research findings with clinical implications.

    Science.gov (United States)

    Bjugn, Roger

    2015-05-05

    Medical and health research may yield findings that are of direct clinical significance for project participants. The Council of Europe has stated that information on such findings shall be offered to participants, and that applications to research ethics committees shall include plans for managing such findings. The purpose of the study was to investigate how the management of such findings had been described in research projects that had been granted prior approval by a regional committee for medical and health research ethics (REK). Research projects that were associated with Oslo University Hospital and had a start-up date in 2011 were identified in the database of the regional ethics committee. Copies of the application form submitted to the committee, project protocols, participant information/consent forms and letters of approval were reviewed with regard to information on the management of findings with possible clinical implications. Of the 87 projects found in the database, 70 were included in the study. Of these, 57 studies involved direct interaction with humans, whereof 45 with intended use of biological material. In 21 studies, the management of findings with possible clinical implications was described in one or more documents. In all of these projects, the applicant him-/herself had referred to this topic in the initial application. The absence of written information on the management of research findings with possible clinical implications is not in conformity with the recommendations issued by the Council of Europe. By introducing a separate item for this in the form to be submitted to the regional ethics committee for application of prior approval, this issue could be made subject to better assessment.

  16. QTLminer: identifying genes regulating quantitative traits

    Directory of Open Access Journals (Sweden)

    Schughart Klaus

    2010-10-01

    Full Text Available Abstract Background Quantitative trait locus (QTL mapping identifies genomic regions that likely contain genes regulating a quantitative trait. However, QTL regions may encompass tens to hundreds of genes. To find the most promising candidate genes that regulate the trait, the biologist typically collects information from multiple resources about the genes in the QTL interval. This process is very laborious and time consuming. Results QTLminer is a bioinformatics tool that automatically performs QTL region analysis. It is available in GeneNetwork and it integrates information such as gene annotation, gene expression and sequence polymorphisms for all the genes within a given genomic interval. Conclusions QTLminer substantially speeds up discovery of the most promising candidate genes within a QTL region.

  17. CT findings of focal organizing pneumonia: correlation with pathologic findings

    International Nuclear Information System (INIS)

    Kim, Yang Soo; Kim, Young Goo; Park, Un Sup

    1994-01-01

    To evaluate the CT findings of focal organizing pneumonia and to correlate them with pathologic findings to help differentiating from lung cancer. We evaluated radiologic and pathologic findings of five patients with solitary pulmonary nodule which were confirmed as focal organizing pneumonia pathologically. On CT scan, focal organizing pneumonia had irregular margin contacting the pleura in all five cases. The shape of the nodules were spherical to wedge or elliptical and the size from 3.5cm to 5.5cm(average 4.2 cm) in largest diameter. On postcontrast CT scan, all nodules showed enhancement and four cases showed central low density components. Two nodules contained air within the nodule. In four cases, pleural changes such as effusion and/or focal thickening were noted. No lymphadenopathy was found in all cases. Pathologically, the enhancing portion on CT showed findings of organizing pneumonia such as granulation tissue with fibroblast proliferation in alveolar space and interstitial thickening. The central low density areas on CT were due to ischemic necrosis, abscess and exudate, transudate and infiltration of foamy histiocyte. The possibility of focal organizing pneumonia should be considered when peripherally located solitary pulmonary nodule had enhancing component with no combined lymphadenopathy on CT scan

  18. Gene Locater

    DEFF Research Database (Denmark)

    Anwar, Muhammad Zohaib; Sehar, Anoosha; Rehman, Inayat-Ur

    2012-01-01

    software's for calculating recombination frequency is mostly limited to the range and flexibility of this type of analysis. GENE LOCATER is a fully customizable program for calculating recombination frequency, written in JAVA. Through an easy-to-use interface, GENE LOCATOR allows users a high degree...... of flexibility in calculating genetic linkage and displaying linkage group. Among other features, this software enables user to identify linkage groups with output visualized graphically. The program calculates interference and coefficient of coincidence with elevated accuracy in sample datasets. AVAILABILITY......: The database is available for free at http://www.moperandib.com....

  19. Ultrasonographic finding of trophoblastic disease

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Hyung Sik; Lee, Kyung Soo; Choi, Byung Ihn; Kim, Chu Wan [Seoul National University College of Medicine, Seoul (Korea, Republic of)

    1983-12-15

    Authors analysed ultrasonographic findings of 50 cases of trophoblastic diseases which were confirmed by D and E or hysterectomy. The following result was observed. 1. Among the 50 cases, 43 cases were hydatidiform moles and remainders were choriocarcionmas 2. Ultrasonographic findings of hydatidi form mole were as follows. a. The size of uterus was larger than that of expected one in 55 percent of cases and smaller than that in 9 percent. b. The vesicular pattern of internal echo could be found in all of the cases, and homogeneous echo pattern were observed in 32 cases(75 percent). c. secondary change, such as myometrial hemorrhage or necrosis, was shown in 33 cases (77 percent). d.In 34 cases (80 percent), sharply separable uterine wall from internal echo was demonstrated. e. In 8 cases(19 percent), ovarian theca-lutein cysts were observed. Among them, 5 cases contained bilateral cysts. All cysts had internal septation. 3. Ultrasonographic findings of choriocarcinomas showed similar findings of those of hydatidiform moles, but different findings from H-moles were more irregular vesicular pattern(4 cases: 57 percent) and inseparable vesicular pattern from uterine wall echo. 4. Correct diagnosis was made in 48 cases out of 50 and the diagnostic accuracy was 95 percent

  20. CT finding of cryptococcal meningitis

    Energy Technology Data Exchange (ETDEWEB)

    Takahashi, Y.; Sato, H.; Ueda, M.; Ito, K.; Matsuoka, T. (Ohkawara Neurosurgical Hospital, Muroran (Japan))

    1981-08-01

    We have experienced 14 cases of cryptococcal meningitis in the last 6 years. Their neurological signs, CT findings, and prognoses were studied. They fall into three types: the brain-stem-encephalitis type, the cortical-encephalitis type, and the meningitis type, according to the clinical course. The first type (6 cases) revealed mainly cerebellar signs, eye-movement damage, and so forth. The second type (5 cases) demonstrated ''Personality'' changes, chiefly aphasia. The third type (5 cases) did not show any focal signs. Prognosis of the brain-stem-encephalitis type was very poor, with a 50% mortality rate. In the survivors, also, clinical signs did not disappear for a long time. Repeated CT was performed in 13 among the 14 cases; abnormal CT findings were revealed in 5 cases because of cryptococcal infection. Granuloma shadow and ventriculitis shadow were observed in 3 cases each. These abnormal findings disappeared upon treatment except in one case. The clinical signs are not completely related with the CT finding, but it is useful that the site which has been infiltrated by the cryptococcus can be observed. Abnormal CT findings were observed in the 4 cases of the brain-stem-encephalitis type among the 5 abnormal cases. It is very useful to know the severity of the condition.

  1. Pubic insufficiency fracture: MRI findings

    International Nuclear Information System (INIS)

    Min, Tae Kyu; Lee, Yeon Soo; Park, Jeong Mi; Kim, Jee Young; Chung, Hong Jun; Lee, Eun Hee; Lee, Eun Ja; Kang, So Won; Han Tae Il

    2000-01-01

    To evaluate the characteristic MRI findings of pubic insufficiency fracture. In nine cases of pubic insufficiency fracture, the findings of plain radiography (n=9), MRI (n=9), and bone scintigraphy (n=8) were reviewed. We retrospectively analyzed, with regard to fracture site, the destructive pattern revealed by plain radiography, and uptake by other pelvic bones, as demonstrated by RI bone scanning. The MR findings evaluated were the fracture gap and its signal intensity, the site and signal intensity of the soft tissue mass, and other pelvic bone fractures. Plain radiography revealed osteolysis and sclerosis of pubic bone in eight of nine cases (89%), and parasymphyseal fractures in seven (78%). RI indicated uptake by the sacrum in six cases (66%), and by the ilium in three (33%). MR findings of fracture gap (seven cases, 78%) were hypo to isointensity on T1WI, hyper intensity on T2WI and the absence of contrast enhancement. Soft tissue masses were found in seven cases (78%); in four of these the location was parasymphyseal, and in three, surrounding muscle was involved. Hypo to isointensity was revealed by T1WI, hyperintensity by T2WI, and there was peripheral enhancement. Other associated pelvic bone fractures involved the sacrum in seven cases and the ilium in four. The characteristic MR findings of pubic insufficiency fracture were parasymphyseal location, fracture gap, peripherally enhanced soft tissue mass formation, and fractures of other pelvic bones, namely the sacrum and ilium

  2. CT findings of periappendiceal abscesses

    Energy Technology Data Exchange (ETDEWEB)

    Kang, Hyun Ill; Kang, Kyung Sook; Suh, Myung Ok; Lee, Yul; Chung, Soo Young; Bae, Sang Hoon; Yoon, Jong Sup [College of Medicine, Hallym University, Chuncheon (Korea, Republic of)

    1987-04-15

    CT has been widely used in the diagnosis of intra-abdominal abscesses, but its findings of periappendiceal abscesses are not well known. CT findings of 15 cases of periappendiceal abscesses were analyzed retrospectively. The results were as follows; 1.The most prevalent age groups were 5th. and 6th. decades and a male to female ratio was 7:8. 2.CT findings of periappendiceal abscesses were cystic low density mass in 7 cases (46.5%), solid soft tissue mass in 2 patients (13.5%) and mixed density mass in 6 cases (40%). 3.Associated CT findings were fat plane obliteration in 12 cases (80%), fascial thickening in 10 cases (66%), enhancing wall in 7 cases (46.5%), internal air density in 5 cases (33%), cecal wall thickening in 3 cases (20%) and ascites in 2 cases (13.5%). 4.Abscess was localized in RLQ medial to cecum in 10 cases (66%), extended to posterior pararenal space in 2 cases (13.5%), pelvic cavity in 2 cases (13.5%) and RUQ in 1 case (7%). We think that CT is an useful diagnostic method of periappendiceal abscesses especially when clinical findings are atypical.

  3. CT findings of renal abscess

    International Nuclear Information System (INIS)

    Lee, Myung Jun; Kim, Mi Young; Woo, Jung Ju; Kim, Ho Kyun; Kim, Won Hong; Jeon, Jeong Dong; Jeon, Woo Ki; Han, Chang Yul

    1996-01-01

    The purpose of this study is to determine characteristic CT findings in renal abscess. Twenty cases of renal abscess were retrospectively analyzed for CT findings relating to the shape and extent of the abscess, change of nephrogram, peripheral rim enhancement, wedge-shaped enhancement on delayed scans, enlargement of the kidney involved and associated findings. Seven patients had a renal abscess at the right kidney, nine at the lift kidney and two bilaterally. The abscesses were round in 18 cases and finger-like in two. Rim enhancement around renal abscess was seen in four cases (20%). Changes in the nephrogram around the abscess were seen in 12 cases (60%). In all six patients who had undergone delayed postcontrast scans, wedge-shaped enhancement was shown around the abscess (100%). In the observation of the extent of renal abscesses, 14 cases were within the kidney, six cases extended the beyond renal capsule, and two were loculated in the renal fascia itself. Renal enlargement was seen in nine cases (45%). These results suggest that CT findings such as delayed wedge-shaped enhancement, change of nephrogram, peripheral rim enhancement, renal enlargement, and associated findings are valuable for diagnosis, and that CT also gives information concerning the extent, evolution and complication of a renal abscess

  4. Methanol poisoning: characteristic MRI findings.

    Science.gov (United States)

    Jain, Nirdesh; Himanshu, Dandu; Verma, Shailendra Prasad; Parihar, Anit

    2013-01-01

    Acute methanol intoxication is not an unusual poisoning. It can have serious neurological sequelae. We emphasize how neuroimaging can help in distinguishing methanol poisoning from other causes of acute unconsciousness in alcoholic patients such as hypoglycemic brain damage and carbon monoxide poisoning or head injury, which are frequently observed in alcoholic patients and are also responsible for altered sensorium. The most important findings in MR brain imaging in methanol poisoning have been bilateral putaminal hemorrhagic necrosis. Other less common findings are subcortical and deep white matter lesions, cerebral and cerebellar cortical lesions, and midbrain lesions, cerebral and intraventricular hemorrhage, and even enhancement of necrotic lesions, we found almost the entire spectrum of MRI findings in this patient with methanol poisoning. Neurological sequelae can entail the course and prognosis in methanol poisoning. The patient died because of ventilator-associated pneumonia that developed in the course of prolonged hospitalization.

  5. Adrenoleukodystrophy: CT and MRI findings

    Energy Technology Data Exchange (ETDEWEB)

    Patel, P.J. [Dept. of Radiology, King Saud Univ., King Khalid Univ. Hospital, Riyadh (Saudi Arabia); Kolawole, T.M. [Dept. of Radiology, King Saud Univ., King Khalid Univ. Hospital, Riyadh (Saudi Arabia); Malabarey, T.M. [Dept. of Radiology, King Saud Univ., King Khalid Univ. Hospital, Riyadh (Saudi Arabia); Al-Herbish, A.S. [Dept. of Paediatrics, King Saud Univ., King Khalid Univ. Hospital, Riyadh (Saudi Arabia); Al-Jurrayan, N.A.M. [Dept. of Paediatrics, King Saud Univ., King Khalid Univ. Hospital, Riyadh (Saudi Arabia); Saleh, M. [Dept. of Paediatrics, King Saud Univ., King Khalid Univ. Hospital, Riyadh (Saudi Arabia)

    1995-06-01

    A case of adrenoleukodystrophy (ALD) with CT and MRI findings is described. The CT scan showed low densities in the white matter of the parietal and occipital lobes. No calcifications were seen. Post-contrast CT showed an abnormal enhancement within the involved white matter. MRI showed changes of demyelination around the atria of the lateral ventricles bilaterally involving the posterior aspect of the cerebrum symmetrically. The posterior part of the posterior corpus callosum, splenium and pyramidal tracts also showed increased signal intensity. From a review of the literature, these findings are typical of the radiological changes seen in ALD. ALD can be diagnosed from typical history and biochemical changes as well as from CT and MRI findings. (orig.)

  6. Primary hepatic sarcomas: CT findings

    Energy Technology Data Exchange (ETDEWEB)

    Yu, Ri-Sheng; Chen, Ying; Jiang, Biao; Wang, Liu-Hong [Zhejiang University School of Medicine, Department of Radiology, Hangzhou (China); Xu, Xiu-Fang [Zhejiang Medical College, Teaching and Research Group of Radiology, Hangzhou (China)

    2008-10-15

    Primary hepatic sarcomas are rare tumors that are difficult to diagnose clinically. Different primary hepatic sarcomas may have different clinical, morphologic, and radiological features. In this pictorial review, we summarized computed tomography (CT) findings of some relatively common types of hepatic sarcomas, including angiosarcoma, epithelioid hemangioendothelioma (EHE), liposarcoma, undifferentiated embryonal sarcoma (UES), leiomyosarcoma, malignant fibrous histiocytoma (MFH), and carcinosarcoma (including cystadenocarcinosarcoma). To our knowledge, hepatic cystadenocarcinosarcoma has not been described in the English literature. The CT findings in our case are similar to that of cystadenocarcinoma, a huge, multilocular cystic mass with a large mural nodule and solid portion. The advent of CT has allowed earlier detection of primary hepatic sarcomas as well as more accurate diagnosis and characterization. In addition, we briefly discuss the MRI findings and diagnostic value of primary hepatic sarcomas. (orig.)

  7. CT and MRI normal findings

    International Nuclear Information System (INIS)

    Moeller, T.B.; Reif, E.

    1998-01-01

    This book gives answers to questions frequently heard especially from trainees and doctors not specialising in the field of radiology: Is that a normal finding? How do I decide? What are the objective criteria? The information presented is three-fold. The normal findings of the usual CT and MRI examinations are shown with high-quality pictures serving as a reference, with inscribed important additional information on measures, angles and other criteria describing the normal conditions. These criteria are further explained and evaluated in accompanying texts which also teach the systematic approach for individual picture analysis, and include a check list of major aspects, as a didactic guide for learning. The book is primarily intended for students, radiographers, radiology trainees and doctors from other medical fields, but radiology specialists will also find useful details of help in special cases. (orig./CB) [de

  8. Radiologic findings of neonatal sepsis

    International Nuclear Information System (INIS)

    Kim, Sam Soo; Han, Dae Hee; Choi, Guk Myeong; Jung, Hye Won; Yoon, Hye Kyung; Han, Bokyung Kim; Lee, Nam Yong

    1997-01-01

    To review the simple radiographic and sonographic findings in infants with neonatal sepsis. We retrospectively analyzed simple chest and abdominal radiographs, and brain sonograms in 36 newborn infants (preterm : term=23 :13). With neonatal sepsis diagnosed by blood culture and clinical manifestations. Pulmonary parenchymal infiltrate excluding respiratory distress syndrome and pulmonary edema or atelectasis was found in 22 infants (61%). Paralytic ileus, hepatosplenomegaly, and necrotizing enterocolitis were present in 18(50%), 9(25%), and 1(3%) infants, respectively, while skeletal changes suggesting osteomyelitis were found in three. Brain sonography was performed in 29 infants and in four, abnormalities were seen ; these comprised three germinal matrix hemorrhages and one intraparenchymal hemorrhage. In six patients(17%) radiologic examinations revealed no abnormality. In patients with neonatal sepsis, pulmonary infiltrates and paralytic ileus were common abnormalities. Although these were nonspecific, radiologic findings may be used to supplement clinical and laboratory findings in diagnosing neonatal sepsis and planning its treatment

  9. Radiologic findings of neonatal sepsis

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Sam Soo; Han, Dae Hee; Choi, Guk Myeong; Jung, Hye Won [Seoul National Univ. College of Medicine, Seoul (Korea, Republic of); Yoon, Hye Kyung; Han, Bokyung Kim; Lee, Nam Yong [Sansung Medical Center, Seoul (Korea, Republic of)

    1997-06-01

    To review the simple radiographic and sonographic findings in infants with neonatal sepsis. We retrospectively analyzed simple chest and abdominal radiographs, and brain sonograms in 36 newborn infants (preterm : term=23 :13). With neonatal sepsis diagnosed by blood culture and clinical manifestations. Pulmonary parenchymal infiltrate excluding respiratory distress syndrome and pulmonary edema or atelectasis was found in 22 infants (61%). Paralytic ileus, hepatosplenomegaly, and necrotizing enterocolitis were present in 18(50%), 9(25%), and 1(3%) infants, respectively, while skeletal changes suggesting osteomyelitis were found in three. Brain sonography was performed in 29 infants and in four, abnormalities were seen ; these comprised three germinal matrix hemorrhages and one intraparenchymal hemorrhage. In six patients(17%) radiologic examinations revealed no abnormality. In patients with neonatal sepsis, pulmonary infiltrates and paralytic ileus were common abnormalities. Although these were nonspecific, radiologic findings may be used to supplement clinical and laboratory findings in diagnosing neonatal sepsis and planning its treatment.

  10. CT findings of the thymus

    International Nuclear Information System (INIS)

    Kang, Eun Young; Kim, Yun Hwan; Seol, Hae Young; Chung, Woun Kyun; Suh, Won Hyuck

    1987-01-01

    In 14 cases of normal and abnormal thymus proved surgically and histopathologically in korea University Hae Wha Hospital during recent 6 years, the clinical and CT findings were analyzed. 1. Of 14 cases, 2 cases were normal thymus, 5 cases were thymic hyperplasia, 4 cases were benign thymoma, 2 case were malignant thymoma and 1 case was thymic cyst. 2. Of 14 cases, 10 cases were associated with myasthenia gravis, and 7 of these 10 cases were 3rd to 5th decades females. Among 10 cases with myasthenia gravis. 5 cases were thymic hyperplasia, 1 case was benign thymoma, 2 cases were malignant thymoma, and 2 cases were normal thymus. 3. All 5 thymic hyperplasia were associated with myasthenia gravis. CT findings of thymic hyperplasia were normal in 4 cases and increased lobe thickness in 1 case. 4. Of 4 cases of benign thymoma, only 1 case was associated with myasthenia gravis, and all 4 cases were positive findings in CT scan. CT findings of benign thymoma were round or oval soft tissue mass in anterior mediastinum, and 1 case had punctuate calcifications. 5. Of 2 cases of malignant thymoma, all 2 cases were associated with myasthenia gravis and positive findings in CT scan. CT findings of malignant thymoma were anterior mediastinal soft tissue mass with obliteration of the normal fat planes surrounding great vessels. SVC compression, and pleural tumor implants. 6. CT yielded significant diagnostic information of differential diagnosis between thymoma and thymoma hyperplasia in myasthenia gravis patients. Also CT was highly sensitive test in detection of thymoma and determined the extent and invasiveness of thymoma.

  11. CT findings of colonic diverticulitis

    Energy Technology Data Exchange (ETDEWEB)

    Sasaki, Shigeru; Ohba, Satoru [Nagoya City Univ. (Japan). Medical School; Mizutani, Masaru [and others

    1998-11-01

    Although colonic diverticulitis has no indication for operation, but in some mistaken cases were operated with a diagnosis of acute appendicitis. We evaluated the CT findings of colonic diverticulitis about 19 cases and of asymptomatic colonic diverticula about 15 cases retrospectively. Diagnosis was confirmed of barium enema and operation. CT are complementary methods of examination that can delineated the range of thickening of the colon and the extension of inflammatory changes around the colon. We also believe that CT findings of colonic diverticulitis are useful for differentiating from a diagnosis of appendicitis. (author)

  12. Pulmonary amyloidosis: computed tomography findings

    International Nuclear Information System (INIS)

    Marchiori, Edson; Ferreira, Angela; Crespo, Sheila Jandira Vianna

    2003-01-01

    We report the computed tomography findings of five patients with pathology proven pulmonary amyloidosis. Tracheobronchial amyloidosis with calcified nodules and plaques in the tracheal wall were seen in two patients. Two other patients had diffuse parenchymal disease with calcified lesions, one had reticular and nodular sub pleural opacities whereas the other had nodular interlobular septal thickening and a parenchymal consolidation. The latter presented the nodular type of the disease with multiple sharp nodules scattered throughout the lungs and interspersed calcifications. The computed tomography findings observed were not specific but strongly suggestive of amyloidosis. (author)

  13. Dermoscopy Findings of Pseudolymphomatous Folliculitis

    Directory of Open Access Journals (Sweden)

    Taku Fujimura

    2012-07-01

    Full Text Available Pseudolymphomatous folliculitis (PLF, which clinically mimicks cutaneous lymphoma, is a rare manifestation of cutaneous pseudolymphoma and cutaneous lymphoid hyperplasia. Here, we report on a 45-year-old Japanese woman with PLF. Dermoscopy findings revealed prominent arborizing vessels with small perifollicular and follicular yellowish spots and follicular red dots. A biopsy specimen also revealed dense lymphocytes, especially CD1a+ cells, infiltrated around the hair follicles. Without any additional treatment, the patient’s nodule rapidly decreased. The presented case suggests that typical dermoscopy findings could be a possible supportive tool for the diagnosis of PLF.

  14. Scintigraphic findings in ankylosing spondylitis.

    Science.gov (United States)

    Lentle, B C; Russell, A S; Percy, J S; Jackson, F I

    1977-06-01

    A prospective study of bone scintigraphic findings has been carried out in 63 patients, firmly diagnosed as having ankylosing spondylitis. In addition to abnormal uptake of the radiotracer at the sacroiliac joints, a peripheral arthropathy has been a common finding, particularly in the proximal joints, occurring in up to 50% of patients. Increased uptake of radiotracer in the spine has also been found both diffusely and focally. Focal increases have been noted at the apophyseal joints in 40% of patients and in three patients with a sterile intervertebral diskitis, an unusual complication of this disease only diagnosed in two patients after bone scintigraphy.

  15. CT findings of colonic diverticulitis

    International Nuclear Information System (INIS)

    Sasaki, Shigeru; Ohba, Satoru; Mizutani, Masaru

    1998-01-01

    Although colonic diverticulitis has no indication for operation, but in some mistaken cases were operated with a diagnosis of acute appendicitis. We evaluated the CT findings of colonic diverticulitis about 19 cases and of asymptomatic colonic diverticula about 15 cases retrospectively. Diagnosis was confirmed of barium enema and operation. CT are complementary methods of examination that can delineated the range of thickening of the colon and the extension of inflammatory changes around the colon. We also believe that CT findings of colonic diverticulitis are useful for differentiating from a diagnosis of appendicitis. (author)

  16. Musculoskeletal Findings in Behcet's Disease

    Directory of Open Access Journals (Sweden)

    Ali Bicer

    2012-01-01

    Full Text Available Behcet's disease is a multisystem disease characterized by recurrent oral and genital ulcers, relapsing uveitis, mucocutaneous, articular, gastrointestinal, neurologic, and vascular manifestations. Rheumatologic manifestations may also occur in Behcet's disease, and arthritis and arthralgia are the most common musculoskeletal findings followed by enthesopathy, avascular necrosis, myalgia, and myositis. Although the main pathology of Behcet's disease has been known to be the underlying vasculitis, the etiology and exact pathogenesis of the disease are still unclear. Musculoskeletal findings of Behcet's disease, the relationship between Behcet's disease and spondyloarthropathy disease complex, and the status of bone metabolism in patients with Behcet's disease were discussed in this paper.

  17. CT findings of kikuchi disease : correlation with pathologic findings

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Ki Nam; Kim, Dong Wook; Kim, Hyun Jin; Park, Jung Hoon; Kim, Chang Soo; Kim, Hye Sook [Maryknoll General Hospital, Pusan (Korea, Republic of)

    1999-11-01

    To evaluate by means of retrospective analysis of neck CT scans the CT findings which suggest kikuchi disease. The authors evaluated the CT findings of seven cases of Kikuchi disease histologically confirmed by excisional biopsy. Four males and three females aged between 12 and 43 (mean;28) years were included. The authors retrospectively analyzed distribution, bilaterality, the presence of aggregation, the presence of intranodal low density after contrast enhancement, the number,size, shape and location of areas of intranodal low density, and the presence of extracapsular extension in involved nodes, as seen on pre-and post-contrast CT scans. Attempts were then made to correlate the CT with the pathologic findings. The range of conditions affecting patients included palpable(7/7) and tender(6/7) nodes, fever(5/7), night sweat(2/7), leukopenia(2/7), and weight loss(1/7). The internal jugular and spinal accessory chains were involved in all seven cases, followed by the submandibular(6/7), submental(5/7), supraclavicular(1/7) and axillary(1/7) nodes. The findings observed also included bilateral involvement of the internal jugular chain(6/7), the spinal accessory chain(5/7), and the submandibular(4/6) and supraclavicular nodes(1/1). CT revealed that in all cases, pathologic lymph nodes showed aggregation in one or several nodal groups, namely a mixed homogeneous(mean, 60%)or inhomogeneous(mean, 40%) enhancement pattern;intranodal low densities with the number(1-7), size(1-7mm) and shape(oval, round, or elongated) of varying degree and predominantly (92%) peripheral location, and extracapsular extension. The CT findings which suggest Kikuchi disease in cervical lymphadenopathy were (1) involvement varying from no intranodal low density to prominent intranodal low densities; (2) intranodal low densities, with the number, size and shape of varying degree and predominantly peripheral location, which were correlated with pathologic findings, including variable intranodal

  18. Transfusional hemosiderosis; correlation of MR findings with clinical findings

    Energy Technology Data Exchange (ETDEWEB)

    Park, Mi Ok; Kim, Ju Heon; Jeon, Woo Jin; Lee, Sung Moon; Kim, Hong; Suh, Soo Jhi [School of Medicine, Keimyung University, Taegu (Korea, Republic of)

    1994-08-15

    Parenchymal iron deposition occurs in hemochromatosis, while iron is deposited in reticuloendothelial cells after blood transfusions(Hemosiderosis). We studied correlation between MR finding and clinical findings(serum ferritin, TSI, LFT, disease duration) of hemosiderosis. 12 patients with chronic renal failure and one patient with aplastic anemia, who have received multiple transfusion, were performed MRI with a 2.0 Tesla unit. In all of 13 patients(17 cases), the liver revealed low signal intensity equal to background noise. In 4 of 17 cases whose serum ferritin level was below 1000 ng/ml, pancreas, gastric wall, adrenal gland were involved in 1 case. In 4 cases with serum ferritin level between 1000 and 1500, pancreas was involved in 2 cases, and other organ was involved in 1 case. In 9 cases with serum ferritin level above 1500ng/ml, pancreas was involved in 9 cases, and other origin 4 cases. The MR findings are well correlated with serum ferritin level whereas the TSI, LFT, disease duration are not correlated with involved organ on MR.

  19. Writing audit findings: Be reasonable!

    Energy Technology Data Exchange (ETDEWEB)

    Girvin, N.W.

    1992-05-01

    A customary approach to auditing and reporting deficiencies is to keep a running list of those that are found, evaluate the severity of each, and based on the evidence, document findings or observations or concerns in an audit report. The report is issued and the auditee is normally requested to address ``root cause`` as part of their corrective action. This paper describes a ``root problems`` approach to documenting audit findings that is designed not only to put the QA auditor in a more favorable light, but to more effectively enable the auditee to identify root cause and meaningful corrective action. The positive results of this approach are considerable. You will have fewer findings but those you do have will be substantial. You will cite requirements that sound reasonable and make arguments difficult. If some of the supporting deficiencies (examples) prove to be incorrect, you will still have ample support for the original finding. You will be seen as reasonable individual who can help lead the auditee towards identification of root cause without taking away part of the responsibility. You even have a fair chance of fostering a sense of commitment to quality improvement on the auditee`s part. This in itself, is its own reward.

  20. Writing audit findings: Be reasonable

    Energy Technology Data Exchange (ETDEWEB)

    Girvin, N.W.

    1992-05-01

    A customary approach to auditing and reporting deficiencies is to keep a running list of those that are found, evaluate the severity of each, and based on the evidence, document findings or observations or concerns in an audit report. The report is issued and the auditee is normally requested to address root cause'' as part of their corrective action. This paper describes a root problems'' approach to documenting audit findings that is designed not only to put the QA auditor in a more favorable light, but to more effectively enable the auditee to identify root cause and meaningful corrective action. The positive results of this approach are considerable. You will have fewer findings but those you do have will be substantial. You will cite requirements that sound reasonable and make arguments difficult. If some of the supporting deficiencies (examples) prove to be incorrect, you will still have ample support for the original finding. You will be seen as reasonable individual who can help lead the auditee towards identification of root cause without taking away part of the responsibility. You even have a fair chance of fostering a sense of commitment to quality improvement on the auditee's part. This in itself, is its own reward.

  1. Radiological findings in NAO syndrome

    Energy Technology Data Exchange (ETDEWEB)

    Al-Otaibi, Leftan; Hugosson, Claes O. [Department of Radiology, King Faisal Specialist Hospital and Research Center, Riyadh (Saudi Arabia); Al-Mayouf, Sulalman M.; Majeed, Mahmoud; Al-Eid, Wea' am; Bahabri, Sultan [Department of Paediatrics, King Faisal Specialist Hospital and Research Center, Riyadh (Saudi Arabia)

    2002-07-01

    Background: Diseases exhibiting osteolysis in children are rare hereditary conditions. Several types have been recognised with different clinical manifestations. One type includes subcutaneous nodules, arthropathy and osteolysis and has been termed NAO syndrome. Previous radiological reports have described the affected bones, usually the carpal and tarsal regions, but a detailed analysis of the radiological findings of both the axial as well as the appendicular skeleton has not been reported. Objectives: To describe the radiological findings in a large group of children with an autosomal recessive disease characterized by nodules, familial arthropathy and osteolysis. Materials and methods: The study comprises 14 patients from 9 families and all patients had the triad of nodulosis, arthropathy and osteolysis (NAO). Results: The most common radiological manifestations were osteopenia, undertubulation of long bones, arthritic changes, sclerotic sutures of the calvaria, osteolysis and muscle contractures. Other common findings were squared vertebrae, broad medial clavicles and brachycephaly. Progress of disease was documented in more than half of the patients. Conclusions: Our study is the first report of the detailed radiological findings of NAO syndrome. In NAO syndrome, both the axial and appendicular skeleton are involved (orig.)

  2. Radiological findings in NAO syndrome

    International Nuclear Information System (INIS)

    Al-Otaibi, Leftan; Hugosson, Claes O.; Al-Mayouf, Sulalman M.; Majeed, Mahmoud; Al-Eid, Wea'am; Bahabri, Sultan

    2002-01-01

    Background: Diseases exhibiting osteolysis in children are rare hereditary conditions. Several types have been recognised with different clinical manifestations. One type includes subcutaneous nodules, arthropathy and osteolysis and has been termed NAO syndrome. Previous radiological reports have described the affected bones, usually the carpal and tarsal regions, but a detailed analysis of the radiological findings of both the axial as well as the appendicular skeleton has not been reported. Objectives: To describe the radiological findings in a large group of children with an autosomal recessive disease characterized by nodules, familial arthropathy and osteolysis. Materials and methods: The study comprises 14 patients from 9 families and all patients had the triad of nodulosis, arthropathy and osteolysis (NAO). Results: The most common radiological manifestations were osteopenia, undertubulation of long bones, arthritic changes, sclerotic sutures of the calvaria, osteolysis and muscle contractures. Other common findings were squared vertebrae, broad medial clavicles and brachycephaly. Progress of disease was documented in more than half of the patients. Conclusions: Our study is the first report of the detailed radiological findings of NAO syndrome. In NAO syndrome, both the axial and appendicular skeleton are involved (orig.)

  3. CT findings of pulmonary hypertension

    International Nuclear Information System (INIS)

    Inoue, Yukio; Tanimoto, Akihiro; Sato, Toru; Kuribayashi, Sachio

    2006-01-01

    For the treatment for pulmonary hypertension (PH), the differential diagnosis of its causal diseases is essential. To determine whether X-ray CT is useful for differentiating PH, we reviewed CT findings of 53 patients (18 men and 35 women, mean age of 44.9) given a diagnosis of PH, consisting of 25 with primary pulmonary hypertension (PPH), 18 with chronic pulmonary embolism (cPE), 6 with Eisenmenger syndrome, 5 cases of collagen diseases, 2 of acute PE, and 1 of cor pulmonale. The intrapulmonary distribution of CT findings (ground glass opacity [GGO], mosaic attenuation, striation and/or infiltration, and interlobular septal thickening) were reviewed and scored on a 4-point scale (grade 0: no findings, 1: involving one third of the lung, 2: involving one-two thirds, and 3: diffuse distribution) by two radiologists who reached a consensus. PPH showed preferentially diffuse distribution of GGO as compared with cPE (p<0.05). However, there was no apparent relationship between the pulmonary vascular resistance and the distribution of GGO in PPH cases. The mosaic attenuation pattern was more frequent in cPE (43%) than PPH (12%; p<0.05). Striation and/or infiltration was observed in 36% of cPE, but only 4% of PPH. Interlobular septal thickening was seen in 16% of PPH, and 0% in cPE. Evaluation of CT findings is useful to differentiate PH. (author)

  4. Finding Maximal Quasiperiodicities in Strings

    DEFF Research Database (Denmark)

    Brodal, Gerth Stølting; Pedersen, Christian N. S.

    2000-01-01

    of length n in time O(n log n) and space O(n). Our algorithm uses the suffix tree as the fundamental data structure combined with efficient methods for merging and performing multiple searches in search trees. Besides finding all maximal quasiperiodic substrings, our algorithm also marks the nodes...... in the suffix tree that have a superprimitive path-label....

  5. Fabrication Aware Form-finding

    DEFF Research Database (Denmark)

    Egholm Pedersen, Ole; Larsen, Niels Martin; Pigram, Dave

    2014-01-01

    This paper describes a design and construction method that combines two distinct material systems with fabrication aware form-finding and file-to-factory workflows. The method enables the fluent creation of complex materially efficient structures comprising high populations of geometrically uniqu...

  6. CT-findings in amoebiasis

    Energy Technology Data Exchange (ETDEWEB)

    Wagner-Manslau, C.; Reiser, M.; Lukas, P.

    1985-12-01

    With an increase of travel to foreign countries with endemic amoebiasis we will find this disease also in western countries. The typical pathologic changes can be identified in CT, as we report in a case with proved amoebiasis which showed an abscess in the bowel-wall and another in the neighbouring liver. (orig.).

  7. Finding Cryptography in Object Code

    Energy Technology Data Exchange (ETDEWEB)

    Jason L. Wright

    2008-10-01

    Finding and identifying Cryptography is a growing concern in the malware analysis community. In this paper, a heuristic method for determining the likelihood that a given function contains a cryptographic algorithm is discussed and the results of applying this method in various environments is shown. The algorithm is based on frequency analysis of opcodes that make up each function within a binary.

  8. MEMS AO for Planet Finding

    Science.gov (United States)

    Rao, Shanti; Wallace, J. Kent; Shao, Mike; Schmidtlin, Edouard; Levine, B. Martin; Samuele, Rocco; Lane, Benjamin; Chakrabarti, Supriya; Cook, Timothy; Hicks, Brian; hide

    2008-01-01

    This slide presentation reviews a method for planet finding using microelectromechanical systems (MEMS) Adaptive Optics (AO). The use of a deformable mirror (DM) is described as a part of the instrument that was designed with a nulling interferometer. The strategy that is used is described in detail.

  9. Can I Trust Your Findings?

    DEFF Research Database (Denmark)

    Cuervo-Cazurra, Alvaro; Andersson, Ulf; Yoko Brannen, Mary

    2016-01-01

    this complexity and ensure that readers can trust their findings. We provide suggestions for how to rule out alternative explanations, explaining key considerations not only in empirical analyses, but also in theory building and in research design. Our discussion covers both qualitative and quantitative studies...

  10. MRI findings in cranial eumycetoma

    International Nuclear Information System (INIS)

    Ahmed, Munawwar; Sureka, Jyoti; Chacko, Geeta; Eapen, Anu

    2011-01-01

    Cranial eumycetoma (CE) due to direct inoculation of Madurella grisea into the scalp is extremely rare. We describe a case of CE caused by direct inoculation of M. grisea with the characteristic MRI findings of the “dot-in-circle” sign and a conglomeration of multiple, extremely hypointense “dots.”

  11. Dermoscopic findings in cicatricial alopecia

    Directory of Open Access Journals (Sweden)

    Seher Arı

    2013-12-01

    Full Text Available Background: Dermoscopy is an important tool for the diagnosis of pigmented skin lesions. Newly, this method has also been used in the diagnosis and follow-up hair and scalp disorders. Objective: The objective of this study was to investigate dermoscopic findings in a sample of patients with clinical and histopathological compatible with cicatricial alopecia. Methods: Twenty nine patients with cicatricial alopecia diagnosed by clinical and histological findings were examined by dermoscopy.. Results: Dermoscopic features evaluated included folliculitis decalvans (n=8, pseudopelade of Brocq (n=7, lichen planopilaris (n=6, discoid lupus erythematosus (n=2, dissecting cellulitis (n=1, and secondary cicatricial alopecia (n=5. Visualization of structures previously examined with naked eye were seen in great detail with dermoscopy. The loss of follicular orifices was seen in all patients with cicatricial alopecia. Perifollicular scaling, arborizing red lines, honeycomb pigment pattern, white dots and tufted hairs were the other most obvious findings. Conclusion: Use of dermoscopy in the clinical evaluation of cicatrical alopecia improves diagnostic capability beyond simple clinic inspection, but larger studies correlating dermoscopic findings with histopathology exams are needed to improve understanding of this method.

  12. Symmetric imaging findings in neuroradiology

    International Nuclear Information System (INIS)

    Zlatareva, D.

    2015-01-01

    Full text: Learning objectives: to make a list of diseases and syndromes which manifest as bilateral symmetric findings on computed tomography and magnetic resonance imaging; to discuss the clinical and radiological differential diagnosis for these diseases; to explain which of these conditions necessitates urgent therapy and when additional studies and laboratory can precise diagnosis. There is symmetry in human body and quite often we compare the affected side to the normal one but in neuroradiology we might have bilateral findings which affected pair structures or corresponding anatomic areas. It is very rare when clinical data prompt diagnosis. Usually clinicians suspect such an involvement but Ct and MRI can reveal symmetric changes and are one of the leading diagnostic tool. The most common location of bilateral findings is basal ganglia and thalamus. There are a number of diseases affecting these structures symmetrically: metabolic and systemic diseases, intoxication, neurodegeneration and vascular conditions, toxoplasmosis, tumors and some infections. Malformations of cortical development and especially bilateral perisylvian polymicrogyria requires not only exact report on the most affected parts but in some cases genetic tests or combination with other clinical symptoms. In the case of herpes simplex encephalitis bilateral temporal involvement is common and this finding very often prompt therapy even before laboratory results. Posterior reversible encephalopathy syndrome (PReS) and some forms of hypoxic ischemic encephalopathy can lead to symmetric changes. In these acute conditions MR plays a crucial role not only in diagnosis but also in monitoring of the therapeutic effect. Patients with neurofibromatosis type 1 or type 2 can demonstrate bilateral optic glioma combined with spinal neurofibroma and bilateral acoustic schwanoma respectively. Mirror-image aneurysm affecting both internal carotid or middle cerebral arteries is an example of symmetry in

  13. Family studies to find rare high risk variants in migraine

    DEFF Research Database (Denmark)

    Hansen, Rikke Dyhr; Christensen, Anne Francke; Olesen, Jes

    2017-01-01

    . A single migraine study using a candidate-gene approach was performed in 2010 identifying a rare mutation in the TRESK potassium channel segregating in a large family with migraine with aura, but this finding has later become questioned. The technologies of next-generation sequencing (NGS) now provides...... an affordable tool to investigate the genetic variation in the entire exome or genome. The family-based study design using NGS is described in this paper. We also review family studies using NGS that have been successful in finding rare variants in other common complex diseases in order to argue the promising...... application of a family approach to migraine. METHOD: PubMed was searched to find studies that looked for rare genetic variants in common complex diseases through a family-based design using NGS, excluding studies looking for de-novo mutations, or using a candidate-gene approach and studies on cancer. All...

  14. Commentary: Gene-Environment Interplay in the Context of Genetics, Epigenetics, and Gene Expression.

    Science.gov (United States)

    Kramer, Douglas A.

    2005-01-01

    Objective: To comment on the article in this issue of the Journal by Professor Michael Rutter, "Environmentally Mediated Risks for Psychopathology: Research Strategies and Findings," in the context of current research findings on gene-environment interaction, epigenetics, and gene expression. Method: Animal and human studies are reviewed that…

  15. Are there anxious genes?

    Science.gov (United States)

    Morris-Rosendahl, Deborah J.

    2002-01-01

    Anxiety comprises many clinical descriptions and phenotypes. A genetic predisposition to anxiety is undoubted; however, the nature and extent of that contribution is still unclear. Methods for the genetic analysis of such complex disorders is briefly reviewed, followed by a discussion of the comorbidity of anxiety with other psychiatric disorders and their possible common genetic etiology. Extensive genetic studies of the serotonin (5-hydroxytryptamine, 5-HT) transporter (5-HTT) gene have revealed how variation in gene expression can be correlated with anxiety phenotypes. Complete genome-wide linkage scans for panic disorder (PD) susceptibility genes have suggested a locus on chromosome arm 7p, and association studies have highlighted many candidate genes. A highly significant association between phobias, panic disorder, and a duplication at chromosomal region 15q24-26 is one of the most exciting findings to date. Emerging molecular genetic technologies and the use of increasingly sophisticated animal models of anxiety provide great promise for the future of the field. PMID:22033820

  16. Identification of Medically Actionable Secondary Findings in the 1000 Genomes.

    Directory of Open Access Journals (Sweden)

    Emily Olfson

    Full Text Available The American College of Medical Genetics and Genomics (ACMG recommends that clinical sequencing laboratories return secondary findings in 56 genes associated with medically actionable conditions. Our goal was to apply a systematic, stringent approach consistent with clinical standards to estimate the prevalence of pathogenic variants associated with such conditions using a diverse sequencing reference sample. Candidate variants in the 56 ACMG genes were selected from Phase 1 of the 1000 Genomes dataset, which contains sequencing information on 1,092 unrelated individuals from across the world. These variants were filtered using the Human Gene Mutation Database (HGMD Professional version and defined parameters, appraised through literature review, and examined by a clinical laboratory specialist and expert physician. Over 70,000 genetic variants were extracted from the 56 genes, and filtering identified 237 variants annotated as disease causing by HGMD Professional. Literature review and expert evaluation determined that 7 of these variants were pathogenic or likely pathogenic. Furthermore, 5 additional truncating variants not listed as disease causing in HGMD Professional were identified as likely pathogenic. These 12 secondary findings are associated with diseases that could inform medical follow-up, including cancer predisposition syndromes, cardiac conditions, and familial hypercholesterolemia. The majority of the identified medically actionable findings were in individuals from the European (5/379 and Americas (4/181 ancestry groups, with fewer findings in Asian (2/286 and African (1/246 ancestry groups. Our results suggest that medically relevant secondary findings can be identified in approximately 1% (12/1092 of individuals in a diverse reference sample. As clinical sequencing laboratories continue to implement the ACMG recommendations, our results highlight that at least a small number of potentially important secondary findings can be

  17. Neuroimaging findings in movement disorders

    International Nuclear Information System (INIS)

    Topalov, N.

    2015-01-01

    Full text: Neuroimaging methods are of great importance for the differential diagnostic delimitation of movement disorders associated with structural damage (neoplasms, ischemic lesions, neuroinfections) from those associated with specific pathophysiological mechanisms (dysmetabolic disorders, neurotransmitter disorders). Learning objective: Presentation of typical imaging findings contributing to nosological differentiation in groups of movement disorders with similar clinical signs. In this presentation are discussed neuroimaging findings in Parkinson‘s disease, atypical parkinsonian syndromes (multiple system atrophy, progressive supranuclear palsy, corticobasal degeneration), parkinsonism in genetically mediated diseases (Wilson’s disease, pantothenate kinase-associated neurodegeneration – PKAN), vascular parkinsonism, hyperkinetic movement disorders (palatal tremor, Huntington‘s chorea, symptomatic chorea in ischemic stroke and diabetes, rubral tremor, ballismus, hemifacial spasm). Contemporary neuroimaging methods enable support for diagnostic and differential diagnostic precision of a number of hypo- and hyperkinetic movement disorders, which is essential for neurological clinical practice

  18. Learning as way-finding

    DEFF Research Database (Denmark)

    Dau, Susanne

    , is based on the findings from research of the implementation of blended learning in two undergraduate programmes at University College North in Denmark. The data collection methods is based on eighteen focus-group interview collected in a period of the first two years of students enrolment in radiography...... take conditions of attention overload into account as an everyday condition which is more than ever actualized by the extended disruptions both by the information technology and other spaces. Based on the discussion areas for future research are suggested.......This paper is based on case study findings from studying undergraduate students’ perceptions of their navigation in a blended learning environment where different learning spaces are offered. In this paper learning is regarded as a multi-level and multi complex concept. In this regard the concept...

  19. Radiologic findings of hemophilic arthropathy

    International Nuclear Information System (INIS)

    Jun, Young Hwan; Yeon, Kyung Mo; Kim, Chu Wan

    1980-01-01

    Hemophilia is a primary disorder of coagulation complicated by spontaneous intra-articular hemorrhage. This paper is to describe and analyze the radiographic findings of involved bone and joints of hemophilic patients for past 5 years. The results were as follows: 1. Age distribution of the total 28 patients was ranging from 1 year to 42 years. 86% of patients was below the age of 20 years. 2. The incidence of joint involvement was in next order; knee joint (25), elbow joint (4), ankle joint (2), hip joint (1). 3. The radiologic findings of involved joint were characterized by irregularity of articular cortices (22), joint space change (19), soft tissue swelling (19), subchondral or intra-osseous cyst (12), periarticular osteoporosis (19), degenerative change (10), condylar enlargement (11) intercondylar notch widening (21) and flexion deformity (13)

  20. Ultrasonographic findings of accessory breast

    International Nuclear Information System (INIS)

    Oh, Ki Keun; Cho, Jae Hyun; Yoon, Choon Sik; Kim, Mi Hye

    1993-01-01

    Accessory breast is an ectopic breast tissue from developmental remnants. It sometimes begins to make symptom, pain and swelling, during premenstrual period or pregnancy. For it has been known as a rear condition, it has occasionally misdiagnosed as a abnormal mass, such as lymphadenitis or hidradentis. We have analyzed 52 accessory breast tissues prospectively, to document the characteristic findings of accessory breast. In summary, the characteristic sonographic findings of accessory breast were the presence of breast tissue superficial to the axillary fascia or underlying fascia if not in axilla, resembling the patient's own breast pattern, the presence of converging appearance of dilated ducts, presence of nipple and/or areola, the obliteration of inner wall of dermis, the obliteration of subcutaneous fat layer, and the downward displacement of axillary fascia or underlying fascia if not in axilla without interruption

  1. Learning as way-finding

    DEFF Research Database (Denmark)

    Dau, Susanne

    This paper is based on case study findings from studying undergraduate students’ perceptions of their navigation in a blended learning environment where different learning spaces are offered. In this paper learning is regarded as a multi-level and multi complex concept. In this regard the concept......, is based on the findings from research of the implementation of blended learning in two undergraduate programmes at University College North in Denmark. The data collection methods is based on eighteen focus-group interview collected in a period of the first two years of students enrolment in radiography...... and teachers education. Furthermore, a survey was conducted after three month of students’ enrolment and some few observations-studies in teachers’ education. The empirical data are interpreted in a narrative form through the use of prefiguration, configuration and refiguration and presented as themes around...

  2. CT findings of peritoneal mesothelioma

    International Nuclear Information System (INIS)

    Woo, Young Hoon; Oh, Yeon Hee; Kim, Hong; Kim, Jung Sik; Woo, Seong Ku; Kim, Ok Bae; Joo, Yang Goo

    1990-01-01

    The peritoneal mesothelioma is a rare neoplasm which arises from the peritoneal lining of the abdomen, tending to spread along the peritoneal cavity and to invade abdominal organs. Authors report the CT findings of 4 patients with histologically proven peritoneal mesothelioma seen at Dongsan Medical Center, School of Medicine, Keimyung University. None of them had a history of exposure to asbestos and no clear etiologic factor could be determined in any patient. CT showed peritoneal and mesenteric thickenings in all cases, omental thickenings in 3 cases, peritoneal nodules, mesenteric masses or omental masses in 2 cases each other, bowel wall involvement in 1 case, and disproportionally small ascites in 2 cases. Distant hematogenous metastases to the liver and retroperitoneal lymph nodes were seen in 1 case. Our experience with 4 peritoneal mesotheliomas as well as a review of the recent imaging literature shows excellent correlation between computed tomography and the operitoneoscopic findings

  3. Ultrasonography findings of gastric carcinoma

    International Nuclear Information System (INIS)

    Chung, Chong Ku; Choi, Ji Bai; Ko, Young Tae; Lim, Jae Hoon; Kim, Soon Young

    1985-01-01

    Stomach carcinoma is more common disease in Korea than western countries. The reported ultrasonographic findings of gastric carcinoma were thickening of gastric wall and 'pseudokidney' sign. The author analyzed ultrasonographic findings of 101 cases with gastric carcinoma who were performed ultrasonography and gastroscopy at Kyung Hee University Hospital from October 1982 to October 1985. The results were as followings; 1. Types of gastric carcinoma were consisted with infiltrative type 68 cases, infiltrative type with ulceration 16 cases, polypoid type with ulceration 1 case, infiltrative adn polypoid type 4 cases, limits plastica type 3 cases, ulcerative type 1 case and polypoid type 1 case. 2. Extent of the lesions were in body and antrum 45 cases, entire stomach 18 cases, antrum 18 cases, body 12 cases, body and fundus 6 cases. 3. Ultrasonography was useful in demonstrating the extent of the tumor and the presence of materials elsewhere in abdomen

  4. Electroencephalographic findings in panic disorder

    Directory of Open Access Journals (Sweden)

    Marcele Regine de Carvalho

    2013-12-01

    Full Text Available Some studies have reported the importance of electroencephalography (EEG as a method for investigating abnormal parameters in psychiatric disorders. Different findings in time and frequency domain analysis with regard to central nervous system arousal during acute panic states have already been obtained. This study aimed to systematically review the EEG findings in panic disorder (PD, discuss them having a currently accepted neuroanatomical hypothesis for this pathology as a basis, and identify limitations in the selected studies. Literature search was conducted in the databases PubMed and ISI Web of Knowledge, using the keywords electroencephalography and panic disorder; 16 articles were selected. Despite the inconsistency of EEG findings in PD, the major conclusions about the absolute power of alpha and beta bands point to a decreased alpha power, while beta power tends to increase. Different asymmetry patterns were found between studies. Coherence studies pointed to a lower degree of inter-hemispheric functional connectivity at the frontal region and intra-hemispheric at the bilateral temporal region. Studies on possible related events showed changes in memory processing in PD patients when exposed to aversive stimuli. It was noticed that most findings reflect the current neurobiological hypothesis of PD, where inhibitory deficits of the prefrontal cortex related to the modulation of amygdala activity, and the subsequent activation of subcortical regions, may be responsible to trigger anxiety responses. We approached some important issues that need to be considered in further researches, especially the use of different methods for analyzing EEG signals. Keywords: Electroencephalography, panic disorder, neurobiology, brain mapping.

  5. Finding related functional neuroimaging volumes

    DEFF Research Database (Denmark)

    Nielsen, Finn Årup; Hansen, Lars Kai

    2004-01-01

    We describe a content-based image retrieval technique for finding related functional neuroimaging experiments by voxelization of sets of stereotactic coordinates in Talairach space, comparing the volumes and reporting related volumes in a sorted list. Voxelization is accomplished by convolving each...... coordinate with a Gaussian kernel. The scheme allows us to compare experiments represented as either lists of coordinates or volumes, and we introduce alternative entrances to databases by image-based indices constructed via novelty measures and singular value decomposition....

  6. CT finding of emphysematous gastritis

    International Nuclear Information System (INIS)

    Ahn, Sang Won; Juhn, Jae Ryang; Cha, Seong Sook; Eun, Tchoong Kie; Chung, Duck Hwan

    1988-01-01

    Emphysematous gastritis is a rare entity of infectious gastritis caused by gas-forming organisms and only 32 cases have been reported. CT is helpful in the diagnosis particularly in mild cases that there is only a small amount of gas. Typical CT findings of emphysematous gastritis are gas bubbles within the irregular thickened gastric wall and dilated stomach filled with secretions, debris and a large amount of gas. We report a case that was diagnosed by CT and operation.

  7. Root finding with threshold circuits

    Czech Academy of Sciences Publication Activity Database

    Jeřábek, Emil

    2012-01-01

    Roč. 462, Nov 30 (2012), s. 59-69 ISSN 0304-3975 R&D Projects: GA AV ČR IAA100190902; GA MŠk(CZ) 1M0545 Institutional support: RVO:67985840 Keywords : root finding * threshold circuit * power series Subject RIV: BA - General Mathematics Impact factor: 0.489, year: 2012 http://www.sciencedirect.com/science/article/pii/S0304397512008006#

  8. MRI findings in bipartite patella

    Energy Technology Data Exchange (ETDEWEB)

    Kavanagh, Eoin C. [University of Pittsburgh Medical Centre, Department of Radiology, Pittsburgh, PA (United States); Zoga, Adam; Omar, Imran [Thomas Jefferson University Hospital, Department of Radiology, Philadelphia, PA (United States); Ford, Stephanie; Eustace, Stephen [Cappagh National Orthopaedic Hospital, Department of Radiology, Dublin (Ireland); Schweitzer, Mark [Hospital for Joint Disease, Orthopedic Institute, Department of Radiology, New York, NY (United States)

    2007-03-15

    Bipartite patella is a known cause of anterior knee pain. Our purpose was to detail the magnetic resonance imaging (MRI) features of bipartite patella in a retrospective cohort of patients imaged at our institution. MRI exams from 53 patients with findings of bipartite patella were evaluated to assess for the presence of bone marrow edema within the bipartite fragment and for the presence of abnormal signal across the synchondrosis or pseudarthrosis. Any other significant knee pathology seen at MRI was also recorded. We also reviewed 400 consecutive knee MRI studies to determine the MRI prevalence of bipartite patella. Of the 53 patients with bipartite patella 40 (75%) were male; 35 (66%) had edema within the bipartite fragment. Of the 18 with no edema an alternative explanation for knee pain was found in 13 (72%). Edema within the bipartite fragment was the sole finding in 26 of 53 (49%) patients. Bipartite patella was seen in 3 (0.7%) of 400 patients. In patients with bipartite patella at knee MRI, bone marrow edema within the bipartite fragment was the sole finding on knee MRI in almost half of the patients in our series. (orig.)

  9. Laryngotracheobronchial papillomatosis: chest CT findings

    Energy Technology Data Exchange (ETDEWEB)

    Fortes, Helena Ribeiro; Zanetti, Glaucia; Marchiori, Edson, E-mail: edmarchiori@gmail.com [Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ (Brazil); Ranke, Felipe Mussi von [Universidade Federal Fluminense (UFF), Niteroi, RJ (Brazil); Escuissato, Dante Luiz [Universidade Federal do Parana (UFPR), Curitiba, PR (Brazil). Dept. de Clinica Medica; Araujo Neto, Cesar Augusto [Universidade Federal da Bahia (UFBA), Salvador (Brazil). Dept. de Medicina e Apoio Diagnostico; Hochhegger, Bruno [Universidade Federal de Ciencias da Saude de Porto Alegre (UFCSPA), RS (Brazil). Diagnostico por Imagem; Irion, Klaus Loureiro [Liverpool Heart and Chest Hospital NHS Foundation Trust, Liverpool (United Kingdom); Souza, Carolina Althoff [Dept. of Diagnostic Imaging, The Ottawa Hospital, University of Ottawa, Ontario (Canada)

    2017-07-15

    To evaluate the findings on chest CTs in 16 patients (8 men and 8 women) with laryngotracheobronchial papillomatosis. Methods: This was a retrospective study involving patients ranging from 2 to 72 years of age. The evaluation of the CT scans was independently performed by two observers, and discordant results were resolved by consensus. The inclusion criteria were presence of abnormalities on the CT scans, and the diagnosis was confirmed by anatomopathological examination of the papillomatous lesions. Results: The most common symptoms were hoarseness, cough, dyspnea, and recurrent respiratory infections. The major CT findings were nodular formations in the trachea, solid or cavitated nodules in the lung parenchyma, air trapping, masses, and consolidation. Nodular formations in the trachea were observed in 14 patients (87.5%). Only 2 patients had lesions in lung parenchyma without tracheal involvement. Only 1 patient had no pulmonary dissemination of the disease, showing airway involvement only. Solid and cavitated lung nodules were observed in 14 patients (87.5%) and 13 (81.2%), respectively. Masses were observed in 6 patients (37.5%); air trapping, in 3 (18.7%); consolidation in 3 (18.7%); and pleural effusion, in 1 (6.3%). Pulmonary involvement was bilateral in all cases. Conclusions: The most common tomography findings were nodular formations in the trachea, as well as solid or cavitated nodules and masses in the lung parenchyma. Malignant transformation of the lesions was observed in 5 cases. (author)

  10. Radiologic findings of pulmonary endometriosis

    International Nuclear Information System (INIS)

    Kim, Seon Bok; Lee, Eil Seong; Jung, Hae Kyoung; Kim, Uk Jung; Yi, Jeong Geun; Kang, Ik Won; Kook, Shin Ho; Park, Jae Sung; Ryu, Dae Sik

    1998-01-01

    To describe the radiologic findings of pulmonary endometriosis. This study involved five patients with catamenial hemoptysis diagnosed as pulmonary endometriosis. All cases were diagnosed on the basis of bronchoscopic abnormalities. In one patient, endometrial glandular cells were seen on transthoracic fine needle aspiration biopsy. In three, hemoptysis ceased after Danazol treatment. The pattern, location and number of parenchymal abnormalities and the presence or absence of pleural lesion were analyzed retrospectively on plain chest radiographs (n=3D5) and CT scans(n=3D5). Follow-up study for each menstrual period was performed in two cases and changes from the initial lesion were assessed. Plain chest radiographic findings showed focal ground-glass opacity in three cases;two were in the right lung and one in the left. CT findings included ground-glass attenuation (n=3D3) and a mixed pattern of ground-glass attenuations and consolidations(n=3D2). Sites were single in four cases, and in one case, there were two; thus there were in all six lesions. Five of these were located in the right lung and subpleural region, continving to the pleura. Pleural lesion was not detected on either chest radiographs or CT scans. Follow-up CT scans (n=3D2) showed a similar lesion at the same site. In patient with repeated catamenial hemoptysis, CT may be helpful for the diagnosis of pulmonary endometriosis by exclusion of other diseases.=20

  11. CT findings of thymic tumors

    International Nuclear Information System (INIS)

    Chung, Ho Son; Lee, Sang Jin; Hwang, Mi Soo; Cho, Kil Ho; Chang, Jae Chun; Park, Bok Hwan

    1991-01-01

    A CT scan can make accurate diagnoses of most thymic masses by assessing their size, shape, and internal architecture and is especially effective in detecting pleural implants, mediastinal involvement, and pulmonary parenchymal invasion in malignant thymoma. The authors analyzed the CT findings of 10 histologically-proven thymic masses from 1983 to 1990 in Yeungnam University Hospital. There were 10 cases of thymic masses in the anterior mediastinum consisting of 6 benign, 3 invasive thymomas, and one thymolipoma, while myasthenia gravis was associated with 2 cases of benign thymomas and with one case of invasive thymomas. The CT findings of the benign thymomas (6 cases) were well-defined, bordered, round-or oval-shaped masses with a well-preserved fat plane between the thymic mass and mediastinal great vessels, with no evidence of pleural implants and lung parenchymal invasion. The CT findings of the invasive thymomas (3 cases) were irregular, marginated lobular masses with obliteration of the fat plane between the thymic mass and surrounding great vessels, with evidence of local invasion such as extension to A-P window and mass effect to bronchus. Irregular pleural thickening due to pleural metastasis, multiple metastatic lung parenchymal nodules, and multiple mediastinal lymph node enlargement were also seen in the invasive thymomas. One case of thymolipoma showed an approximately 20cm-size, well-defined fat density mass containing internal septations

  12. A survey of disease connections for CD4+ T cell master genes and their directly linked genes.

    Science.gov (United States)

    Li, Wentian; Espinal-Enríquez, Jesús; Simpfendorfer, Kim R; Hernández-Lemus, Enrique

    2015-12-01

    Genome-wide association studies and other genetic analyses have identified a large number of genes and variants implicating a variety of disease etiological mechanisms. It is imperative for the study of human diseases to put these genetic findings into a coherent functional context. Here we use system biology tools to examine disease connections of five master genes for CD4+ T cell subtypes (TBX21, GATA3, RORC, BCL6, and FOXP3). We compiled a list of genes functionally interacting (protein-protein interaction, or by acting in the same pathway) with the master genes, then we surveyed the disease connections, either by experimental evidence or by genetic association. Embryonic lethal genes (also known as essential genes) are over-represented in master genes and their interacting genes (55% versus 40% in other genes). Transcription factors are significantly enriched among genes interacting with the master genes (63% versus 10% in other genes). Predicted haploinsufficiency is a feature of most these genes. Disease-connected genes are enriched in this list of genes: 42% of these genes have a disease connection according to Online Mendelian Inheritance in Man (OMIM) (versus 23% in other genes), and 74% are associated with some diseases or phenotype in a Genome Wide Association Study (GWAS) (versus 43% in other genes). Seemingly, not all of the diseases connected to genes surveyed were immune related, which may indicate pleiotropic functions of the master regulator genes and associated genes. Copyright © 2015 Elsevier Ltd. All rights reserved.

  13. Radiological findings of pulmonary aspergillosis

    International Nuclear Information System (INIS)

    Song, Kounn Sik; Im, Chung Kie

    1985-01-01

    The pulmonary aspergillosis is a group of three separate disease, comprising invasive aspergillosis, aspergilloma, and allergic bronchopulmonary aspergillosis, or a disease process in which one of three entities overlap with another process such as mucoid impaction, pulmonary infiltration with eosinophilia, bronchocentric granulomatosis, microgranulomatous hypersensitivity, or asthma. The radiological findings of 24 cases of pulmonary aspergillosis diagnosed and treated at Seoul National University Hospital during the past 7 years were analyzed retrospectively. The results were as follows: 1. Final diagnosis of 24 cases of pulmonary aspergillosis was aspergilloma in 16 cases, invasive aspergillosis in 2 cases, variant form of allergic bronchopulmonary aspergillosis in 3 cases, and endobronchial aspergillosis in 3 cases. 2. The underlying causes of the aspergilloma were healed tuberculous cavity in 6 cases, bronchiectasis in 8 cases, and no underlying cause were found in 2 cases. All the 16 cases of aspergilloma were correctly diagnosed without difficultly by demonstrating the intracavitary mass or air meniscus. 3. Radiological findings of the invasive aspergillosis in kidney transplant patients were multiple round nodules with early cavitation and formation of aspergilloma which shows slowly progressive cavitation over 13 months in one case, and diffusely scattered miliary nodules with occasional cavitation in the other case. 4. Classic allergic bronchopulmonary aspergillosis were not found in our series but variant form of ABPA was found in 3 young female patients. All the three patients shows some degree of central bronchiectasis and combined aspergilloma was found in 2 cases. 5. Three patients diagnosed as endobronchial aspergillosis-saprophytic infection of aspergillus in the bronchial tree-by bronchoscopic biopsy shows nonspecific radiological findings

  14. MRI findings in Hirayama disease

    Directory of Open Access Journals (Sweden)

    Raval Monali

    2010-01-01

    Full Text Available The objective of the study was to study the magnetic resonance imaging (MRI features of Hirayama disease on a 3 Tesla MRI scanner. Nine patients with clinically suspected Hirayama disease were evaluated with neutral position, flexion, contrast-enhanced MRI and fast imaging employing steady-state acquisition (FIESTA sequences. The spectrum of MRI features was evaluated and correlated with the clinical and electromyography findings. MRI findings of localized lower cervical cord atrophy (C5-C7, abnormal curvature, asymmetric cord flattening, loss of attachment of the dorsal dural sac and subjacent laminae in the neutral position, anterior displacement of the dorsal dura on flexion and a prominent epidural space were revealed in all patients on conventional MRI as well as with the dynamic 3D-FIESTA sequence. Intramedullary hyperintensity was seen in four patients on conventional MRI and on the 3D-FIESTA sequence. Flow voids were seen in four patients on conventional MRI sequences and in all patients with the 3D-FIESTA sequence. Contrast enhancement of the epidural component was noted in all the five patients with thoracic extensions. The time taken for conventional and contrast-enhanced MRI was about 30-40 min, while that for the 3D-FIESTA sequence was 6 min. Neutral and flexion position MRI and the 3D-FIESTA sequence compliment each other in displaying the spectrum of findings in Hirayama disease. A flexion study should form an essential part of the screening protocol in patients with suspected Hirayama disease. Newer sequences such as the 3D-FIESTA may help in reducing imaging time and obviating the need for contrast.

  15. Neurological Findings in Myeloproliferative Neoplasms

    Directory of Open Access Journals (Sweden)

    Semra Paydas

    2013-04-01

    Full Text Available Myeloproliferative neoplasms (MPN arise from genetic deficiencies at the level of pluripotent stem cells. Each of these neoplasms is a clonal stem cell disorder with specific phenotypic, genetic and clinical properties. Age is one of the most important factors in the development of symptoms and complications associated with MPNs.High white blood cell counts in chronic myelocytic leukemia also known as leukocytosis may lead to central nervous system findings. Tumors developing outside the bone marrow named as extramedullary myeloid tumors (EMMT could be detected at the initial diagnosis or during the prognosis of the disease, which may cause neurological symptoms due to pressure of leukemic cell mass on various tissues along with spinal cord. Central nervous system involvement and thrombocytopenic hemorrhage may lead to diverse neurological symptoms and findings.Transient ischemic attack and thrombotic stroke are the most common symptoms in polycythemia vera. Besides thrombosis and hemorrage, transformation to acute leukemia can cause neurological symptoms and findings. Transient ischemic attack, thrombotic stroke and specifically hemorrage can give rise to neurological symptoms similar to MPN in essential thrombocytosis.Extramedullary hematopoiesis refers to hematopoietic centers arise in organ/tissues other than bone marrow in myelofibrosis. Extramedullar hematopoietic centers may cause intracranial involvement, spinal cord compression, seizures and hydrocephalia. Though rare, extramedullary hematopoiesis can be detected in cranial/spinal meninges, paraspinal tissue and intracerebral regions. Extramedullary hematopoiesis has been reported in peripheral neurons, choroid plexus, pituitary, orbits, orbital and lacrimal fossa and in sphenoidal sinuses. [Cukurova Med J 2013; 38(2.000: 157-169

  16. Capillaroscopic Findings in Primary Fibromyalgia.

    Science.gov (United States)

    Lambova, Sevdalina; Müller-Ladner, Ulf

    2017-06-07

    Although Raynaud's phenomenon (RP) is observed in a significant proportion of patients with primary fibromyalgia, the available data on capillaroscopic findings in primary fibromyalgia are scarce. The aim of the study was to evaluate the capillaroscopic pattern in patients with primary fibromyalgia. 26 patients with primary fibromyalgia (25 women and 1 man) were included in the study. Mean age was 55±10 years. As control groups were examined 31 patients with primary RP and 35 healthy volunteers. Capillaroscopic examination was performed with a videocapillaroscope Videocap 3.0 (DS Medica), magnification 200x. The following capillaroscopic parameters were evaluated: distribution, shape, width, length, mean capillary density, presence of avascular areas, haemorrhages, neoangiogenesis, visibility of subpapillary plexus. RP was present in 65% (17/26) of the patients with primary fibromyalgia. The most frequent finding in patients with primary fibromyalgia was presence of dilated capillaries in 85% (22/26) of cases, including patients with RP as well as patients without peripheral vasospasm. However, the mean diameter of the arterial and the venous limb were significantly higher in the subgroup of fibromyalgia patients with clinical symptoms of RP. Analogous changes - the presence of dilated capillaries - were found in 96.6% (29/30) of patients with primary RP. In the group of primary fibromyalgia, signs of microangiopathy characteristic of connective tissue diseases could not be observed. In our study, the most frequent capillaroscopic finding in patients with primary fibromyalgia was presence of dilated capillaries analogous to primary RP. Capillaroscopic signs suggestive of connective tissue disease could not be found in primary fibromyalgia patients. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  17. Brain venous pathologies: MRI findings

    International Nuclear Information System (INIS)

    Salvatico, Rosana; Gonzalez, Alejandro; Yanez, Paulina; Romero, Carlos; Trejo, Mariano; Lambre, Hector

    2006-01-01

    Purpose: To describe MRI findings of the different brain venous pathologies. Material and Methods: Between January 2002 and March 2004, 18 patients were studied 10 males and 8 females between 6 and 63 years old; with different brain venous pathologies. In all cases brain MRI were performed including morphological sequences with and without gadolinium injection and angiographic venous sequences. Results: 10 venous occlusions were found, 6 venous angiomas, and 2 presented varices secondary to arteriovenous dural fistula. Conclusion: Brain venous pathologies can appear in many different clinical contexts, with different prognosis and treatment. In all the cases brain MRI was the best imaging study to disclose typical morphologic abnormalities. (author) [es

  18. Duodenal diverticulitis. computed tomography findings

    International Nuclear Information System (INIS)

    Sanchez, E.; Martin, S.; Garcia, J.; Dominguez, A.

    2001-01-01

    Duodenal diverticular occur very frequently among the general public. However, duodenal diverticulitis is a very uncommon clinical entity, the diagnosis of which requires radiological studies since the clinical signs cam mimic a great number of disease processes with different treatments. We present a case of duodenal diverticulitis in which the diagnosis according to ultrasound and computed tomography (CT) studies was confirmed intraoperatively. We also review the few cases of this entity reported in the literature. The CT findings are highly suggestive of duodenal diverticulitis given their similarity to those associated with diverticulitis at other sites. (Author) 5 refs,

  19. Imaging findings of Paragonimus westermani

    Directory of Open Access Journals (Sweden)

    Shambhu Kumar Sah

    2016-06-01

    Conclusions: The imaging findings of P. westermani is so diverse and non-specific due to its complex life cycle and several life stages during infestation of human; however, common features include nodule, GGO, worm cyst, migration track, pleural effusion, pleural thickening on chest CT scan; patchy low or mixed density lesions on brain CT scan; ring enhancing lesion on brain MRI scan; conglomerated small cystic or serpentine lesions and migration track in liver and spleen on abdominal CT scan. The characteristic imaging features of paragonimiasis are worm cyst and migration track.

  20. MR findings in peliosis hepatis

    Energy Technology Data Exchange (ETDEWEB)

    Saatci, I. [Dept. of Diagnostic Radiology, Hacettepe Univ. Hospital, Ankara (Turkey); Coskun, M. [Dept. of Diagnostic Radiology, Hacettepe Univ. Hospital, Ankara (Turkey); Boyvat, F. [Dept. of Diagnostic Radiology, Hacettepe Univ. Hospital, Ankara (Turkey); Cila, A. [Dept. of Diagnostic Radiology, Hacettepe Univ. Hospital, Ankara (Turkey); Guergey, A. [Dept. of Pediatric Hematology, Hacettepe Univ. Hospital, Ankara (Turkey)

    1995-02-01

    We report the MR findings of peliosis hepatis in a patient with Fanconi anemia who had been treated with anabolic androgenic steroids for 3 years. The MR examination of the upper abdomen was performed on a 0.5 T system. The signal intensity of the right lobe of the liver was diffusely increased in all sequences. Within the enlarged liver, multiple foci of brighter signal were seen involving both right and left lobes. The lesions showed contrast enhancement. A cystic cavity with an enhancing rim was seen representing a haematoma cavity. The spleen was spared the patient died of sepsis and the postmortem examination confirmed the diagnosis of peliosis hepatis. (orig.)

  1. MR findings in peliosis hepatis

    International Nuclear Information System (INIS)

    Saatci, I.; Coskun, M.; Boyvat, F.; Cila, A.; Guergey, A.

    1995-01-01

    We report the MR findings of peliosis hepatis in a patient with Fanconi anemia who had been treated with anabolic androgenic steroids for 3 years. The MR examination of the upper abdomen was performed on a 0.5 T system. The signal intensity of the right lobe of the liver was diffusely increased in all sequences. Within the enlarged liver, multiple foci of brighter signal were seen involving both right and left lobes. The lesions showed contrast enhancement. A cystic cavity with an enhancing rim was seen representing a haematoma cavity. The spleen was spared the patient died of sepsis and the postmortem examination confirmed the diagnosis of peliosis hepatis. (orig.)

  2. CT findings of retroperitoneal masses

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Sung Moon; Huh, Jin Do; Kim, Ho Joon; Joh, Young Duk; Chun, Byung Hee [Kosin Medical College, Busan (Korea, Republic of); Woo, Seong Ku; Suh, Soo Jhi [School of Medicine, Keimyung University, Daegu (Korea, Republic of)

    1987-10-15

    Retrospective analysis of forty one retroperitoneal masses was made with computed tomography. All cases were confirmed pathologically by operation or needle aspiration biopsy. The cases were; 14 abscesses, 2 leiomyosarcomas, 2 rhabdomyosarcomas, 2 liposarcomas, 1 undifferentiated sarcoma, 3 endodermal sinus tumors, 4 teratomas, 2 neurofibromas, 1 neurilemoma, 3 neuroblastomas, 4 malignant lymphomas, 2 malignant fibrous histiocytomas and 1 hemangiopericytoma. Tumors originated from urinary tract and pancreas were not included. Findings favor tumor rather than inflammation were; large lobulated soft tissue mass with eccentric or heterogeneous low density, thick cavity wall, disruption of fascial planes, regional lymphnode enlargement and distant metastasis.

  3. MRI findings of intraocular diseases

    Energy Technology Data Exchange (ETDEWEB)

    Takeda, Makoto; Nagai, Haruhiko; Ueno, Tetsuji; Igarashi, Yasuo (Sapporo Medical Coll. (Japan)); Narazaki, Yoshikazu; Takeda, Akira

    1989-06-01

    MRI findings of intra-ocular lesion were studied on seven cases : two cases of choroidal malignant melanoma, one case of choroidal tumor, two cases of retinal detachment with vitreous hemorrhage, and two cases of choroidal detachment. Intraocular lesions were clearly visualized by T{sub 1} weighted MRI which was of great benefit in visualizing morphological changes. T{sub 2} weighted images could not visualize morphological changes very well, but had some merits in differentiating the ocular pathology. MRI was a very useful examination for intra-ocular lesions. (author).

  4. MRI findings of intraocular diseases

    International Nuclear Information System (INIS)

    Takeda, Makoto; Nagai, Haruhiko; Ueno, Tetsuji; Igarashi, Yasuo; Narazaki, Yoshikazu; Takeda, Akira.

    1989-01-01

    MRI findings of intra-ocular lesion were studied on seven cases : two cases of choroidal malignant melanoma, one case of choroidal tumor, two cases of retinal detachment with vitreous hemorrhage, and two cases of choroidal detachment. Intraocular lesions were clearly visualized by T 1 weighted MRI which was of great benefit in visualizing morphological changes. T 2 weighted images could not visualize morphological changes very well, but had some merits in differentiating the ocular pathology. MRI was a very useful examination for intra-ocular lesions. (author)

  5. Ultrasound findings in biliary system

    International Nuclear Information System (INIS)

    Park, Won Sik; Lee, Yong Woo; Cheung, Hwan

    1986-01-01

    In the liver and biliary system ultrasound has emerged as one of the most useful imaging techniques. It is usually the first radiological procedure selected and is often sufficient alone to enable a clinical decision to be made. Good result with ultrasound depend critically on expert scanning technique coupled with an understanding of tomographic anatomy and, of course, an appreciation of the clinical significance of any findings. In addition to we'd like to stress on the ultrasonical anatomy and for the technologist and also discuss about pathological part

  6. Fabrication Aware Form-finding

    DEFF Research Database (Denmark)

    Egholm Pedersen, Ole; Larsen, Niels Martin; Pigram, Dave

    2014-01-01

    parts. The first material system employs a novel rotated joint design to allow the structural tuning of quasi-reciprocal timber frame elements fabricated from multi-axis machined plywood sheet stock. The second em-loys discontinuous post-tensioning to assemble unique precast concrete components......This paper describes a design and construction method that combines two distinct material systems with fabrication aware form-finding and file-to-factory workflows. The method enables the fluent creation of complex materially efficient structures comprising high populations of geometrically unique...

  7. MR findings of polymyositis / dermatomyositis

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Hak Soo; Joo, Kyung Bin; Moon, Won Jin; Lee, Tae Hee; Park, Ki Ho; Park, Dong Woo; Hahm, Chang Kok [Hanyang Univ. College of Medicine, Seoul (Korea, Republic of)

    1998-07-01

    The purpose of this study was to evaluate the MR findings and useful sequences in Polymyositis/ Dermatomyositis, and to correlate MR findings with disease activity. Materials and Methods: The study included nine clinically proven cases of Polymyositis/Dermatomyositis, eight involving the thigh and one, the shoulder (2 cases, 1 follow-up). The contrast between affected and normal muscles and difference in signal intensity ratio in the muscle groups were retrospectively evaluated on Gd-enhanced T1WI and T2WI. We also evaluated the magnitude of involvement of muscle groups, fatty replacement of muscle and change of subcutaneous fat layer, and correlated signal intensity ratio with serum level of muscle enzymes. Differences in signal intensity ratio and the frequency of chemical shift artifact were evaluated on T2WI as active and inactive groups classified according to clinical findings, and the chemical shift artifact was correlated with the finding of Gd-enhanced T1WI. Except in the case of one shoulder, statistical analysis was assessed by the Anova test and-test. Results: On Gd-enhanced T1WI and T2WI contrast was 0.54 and 0.82, respectively and p value was 0.02. With regard to difference in signal intensity ratios of muscle groups, as seen on Gd-enhanced T1WI and T2WI, p valves were 0.07 and < 0.01, respectively. Muscle involvement was thus clearly visualized on T2WI. The order of frequency of involved muscle groups was vastus muscles, gluteus maximus, sartorius muscles, adductor muscles, gracilis muscle, and hamstring muscles. Fatty replacement and subcutaneous fatty change were visualized in five cases and one, respectively. The correlation coefficient between the signal intensity seen on T2WI and muscle enzymes was 0.59 (CPK) and 0.52 (LDH). The chemical-shift artifact was detected in both clinical groups (four active two inactive) and corresponded to one case of muscle involvement and five of perimuscular edema, as seen on Gd-enhanced T1WI. Conclusion: T2WI is

  8. A Fast SVM-Based Tongue's Colour Classification Aided by k-Means Clustering Identifiers and Colour Attributes as Computer-Assisted Tool for Tongue Diagnosis

    Science.gov (United States)

    Ooi, Chia Yee; Kawanabe, Tadaaki; Odaguchi, Hiroshi; Kobayashi, Fuminori

    2017-01-01

    In tongue diagnosis, colour information of tongue body has kept valuable information regarding the state of disease and its correlation with the internal organs. Qualitatively, practitioners may have difficulty in their judgement due to the instable lighting condition and naked eye's ability to capture the exact colour distribution on the tongue especially the tongue with multicolour substance. To overcome this ambiguity, this paper presents a two-stage tongue's multicolour classification based on a support vector machine (SVM) whose support vectors are reduced by our proposed k-means clustering identifiers and red colour range for precise tongue colour diagnosis. In the first stage, k-means clustering is used to cluster a tongue image into four clusters of image background (black), deep red region, red/light red region, and transitional region. In the second-stage classification, red/light red tongue images are further classified into red tongue or light red tongue based on the red colour range derived in our work. Overall, true rate classification accuracy of the proposed two-stage classification to diagnose red, light red, and deep red tongue colours is 94%. The number of support vectors in SVM is improved by 41.2%, and the execution time for one image is recorded as 48 seconds. PMID:29065640

  9. A Comparative Study of NN and SVM-Based Electromagnetic Inverse Scattering Approaches to On-Line Detection of Buried Objects

    Science.gov (United States)

    2003-07-01

    local minima where -n the optimization algorithm might be trapped and the III. LEARN ING-BY-EXAMPLES STRATEGIES FOR solution of which would have no...object. Moreover, after the optimal selection procedure, the values of the SVM hyperparameters turned out to be constant quantities equal to (C)ZB = (C)s...real-coded genetic algorithm for microwave imaging tions, artificial vision and remote sensing, purposes:’ IEEE Trans. on Geoscience and Remote Sensing

  10. A Study on SVM Based on the Weighted Elitist Teaching-Learning-Based Optimization and Application in the Fault Diagnosis of Chemical Process

    Directory of Open Access Journals (Sweden)

    Cao Junxiang

    2015-01-01

    Full Text Available Teaching-Learning-Based Optimization (TLBO is a new swarm intelligence optimization algorithm that simulates the class learning process. According to such problems of the traditional TLBO as low optimizing efficiency and poor stability, this paper proposes an improved TLBO algorithm mainly by introducing the elite thought in TLBO and adopting different inertia weight decreasing strategies for elite and ordinary individuals of the teacher stage and the student stage. In this paper, the validity of the improved TLBO is verified by the optimizations of several typical test functions and the SVM optimized by the weighted elitist TLBO is used in the diagnosis and classification of common failure data of the TE chemical process. Compared with the SVM combining other traditional optimizing methods, the SVM optimized by the weighted elitist TLBO has a certain improvement in the accuracy of fault diagnosis and classification.

  11. A Fast SVM-Based Tongue's Colour Classification Aided by k-Means Clustering Identifiers and Colour Attributes as Computer-Assisted Tool for Tongue Diagnosis.

    Science.gov (United States)

    Kamarudin, Nur Diyana; Ooi, Chia Yee; Kawanabe, Tadaaki; Odaguchi, Hiroshi; Kobayashi, Fuminori

    2017-01-01

    In tongue diagnosis, colour information of tongue body has kept valuable information regarding the state of disease and its correlation with the internal organs. Qualitatively, practitioners may have difficulty in their judgement due to the instable lighting condition and naked eye's ability to capture the exact colour distribution on the tongue especially the tongue with multicolour substance. To overcome this ambiguity, this paper presents a two-stage tongue's multicolour classification based on a support vector machine (SVM) whose support vectors are reduced by our proposed k -means clustering identifiers and red colour range for precise tongue colour diagnosis. In the first stage, k -means clustering is used to cluster a tongue image into four clusters of image background (black), deep red region, red/light red region, and transitional region. In the second-stage classification, red/light red tongue images are further classified into red tongue or light red tongue based on the red colour range derived in our work. Overall, true rate classification accuracy of the proposed two-stage classification to diagnose red, light red, and deep red tongue colours is 94%. The number of support vectors in SVM is improved by 41.2%, and the execution time for one image is recorded as 48 seconds.

  12. A Fast SVM-Based Tongue’s Colour Classification Aided by k-Means Clustering Identifiers and Colour Attributes as Computer-Assisted Tool for Tongue Diagnosis

    Directory of Open Access Journals (Sweden)

    Nur Diyana Kamarudin

    2017-01-01

    Full Text Available In tongue diagnosis, colour information of tongue body has kept valuable information regarding the state of disease and its correlation with the internal organs. Qualitatively, practitioners may have difficulty in their judgement due to the instable lighting condition and naked eye’s ability to capture the exact colour distribution on the tongue especially the tongue with multicolour substance. To overcome this ambiguity, this paper presents a two-stage tongue’s multicolour classification based on a support vector machine (SVM whose support vectors are reduced by our proposed k-means clustering identifiers and red colour range for precise tongue colour diagnosis. In the first stage, k-means clustering is used to cluster a tongue image into four clusters of image background (black, deep red region, red/light red region, and transitional region. In the second-stage classification, red/light red tongue images are further classified into red tongue or light red tongue based on the red colour range derived in our work. Overall, true rate classification accuracy of the proposed two-stage classification to diagnose red, light red, and deep red tongue colours is 94%. The number of support vectors in SVM is improved by 41.2%, and the execution time for one image is recorded as 48 seconds.

  13. An S-Transform and Support Vector Machine (SVM-Based Online Method for Diagnosing Broken Strands in Transmission Lines

    Directory of Open Access Journals (Sweden)

    Caxin Sun

    2011-08-01

    Full Text Available During their long-term outdoor field service, overhead transmission lines will be exposed to strikes by lightning, corrosion by chemical contaminants, ice-shedding, wind vibration of conductors, line galloping, external destructive forces and so on, which will generally cause a series of latent faults such as aluminum strand fracture. This may lead to broken transmission lines which will have a very strong impact on the safe operation of power grids that if the latent faults cannot be recognized and fixed as soon as possible. The detection of broken strands in transmission lines using inspection robots equipped with suitable detectors is a method with good prospects. In this paper, a method for detecting broken strands in transmission lines using an eddy current transducer (ECT carried by a robot is developed, and an approach for identifying broken strands in transmission lines based on an S-transform is proposed. The proposed approach utilizes the S-transform to extract the module and phase information at each frequency point from detection signals. Through module phase and comparison, the characteristic frequency points are ascertained, and the fault information of the detection signal is constructed. The degree of confidence of broken strand identification is defined by the Shannon fuzzy entropy (SFE-BSICD. The proposed approach combines module information while utilizing phase information, SFE-BSICD, and the energy, so the reliability is greatly improved. These characteristic qualities of broken strands in transmission lines are used as the input of a multi-classification SVM, allowing the number of broken strands to be determined. Through experimental field verification, it can be shown that the proposed approach displays high accuracy and the SFE-BSICD is defined reasonably.

  14. Development of detection method for novel fusion gene using GeneChip exon array.

    Science.gov (United States)

    Wada, Yusaku; Matsuura, Masaaki; Sugawara, Minoru; Ushijima, Masaru; Miyata, Satoshi; Nagasaki, Koichi; Noda, Tetsuo; Miki, Yoshio

    2014-02-18

    Fusion genes have been recognized to play key roles in oncogenesis. Though, many techniques have been developed for genome-wide analysis of fusion genes, a more efficient method is desired. We introduced a new method of detecting the novel fusion gene by using GeneChip Exon Array that enables exon expression analysis on a whole-genome scale and TAIL-PCR. To screen genes with abnormal exon expression profiles, we developed computational program, and confirmed that the program was able to search the fusion partner gene using Exon Array data of T-cell acute lymphocytic leukemia (T-ALL) cell lines. It was reported that the T-ALL cell lines, ALL-SIL, BE13 and LOUCY, harbored the fusion gene NUP214-ABL1, NUP214-ABL1 and SET-NUP214, respectively. The program extracted the candidate genes with abnormal exon expression profiles: 1 gene in ALL-SIL, 1 gene in BE13, and 2 genes in LOUCY. The known fusion partner gene NUP214 was included in the genes in ALL-SIL and LOUCY. Thus, we applied the proposed program to the detection of fusion partner genes in other tumors. To discover novel fusion genes, we examined 24 breast cancer cell lines and 20 pancreatic cancer cell lines by using the program. As a result, 20 and 23 candidate genes were obtained for the breast and pancreatic cancer cell lines respectively, and seven genes were selected as the final candidate gene based on information of the EST data base, comparison with normal cell samples and visual inspection of Exon expression profile. Finding of fusion partners for the final candidate genes was tried by TAIL-PCR, and three novel fusion genes were identified. The usefulness of our detection method was confirmed. Using this method for more samples, it is thought that fusion genes can be identified.

  15. Effect Alpha Globlin Gene Deletion And Gamma Globin Gene -158 ...

    African Journals Online (AJOL)

    ... have been unable to find a molecular basis for the benign clinical course in all our patients. Other genetic or acquired factors must be hypothesized which ameliorate the clinical condition. Keywords: β- thalassemia, Xmn1 polymorphism, α-globin gene deletion. Egyptian Journal of Biochemistry and Molecular Biology Vol.

  16. Sonographic findings in Gouty Nephropathy

    International Nuclear Information System (INIS)

    Kim, Mi Young; Jeon, Woo Ki; Kim, Ho Kyun; Kim, Yong Soo; Han, Chang Yul; Kim, Young Tong; Han, Sung Tag; Lee, Yoon Woo

    1994-01-01

    Ultrasound(US) findings of hyperechoic renal medulla in gouty nephropathy were compared with clinical features such as serum uric acid level to evaluate its usefulness in determination of the treatment and prognosis. A retrospective review of US of 36 cases of qouty arthritis was classified into four groups according to the medullary echogenicity (O :normal, grade I: renal medulla as isoechoic as renal cortex, grade II; heterogeneous increased echogenicity of renal medulla than that of renal cortex, grade III: the echogenicity of all renal medulla higher than that of renal cortex with renal contour deformity) which were compared with the serum urate level and associated conditions. Nephrocalcinosis and nephrolithiasis were analyzed through the KUB and the RGB. The degree of hyperechoic renal medulla was related to the level of serum uric acid, and in group IV, six cases of obstructive uropathy (nephrocalcinosis and nephrolithiasis) showed deformed renal contour. Associated conditions such as hypertension, alcoholism, diabetes mellitus and drug abuse were distributed in relation to the degree of hyperechoic renal medullas. US findings of hyperechoic renal mebulla was related with uric acid level in gouty nephropathy and thus could be valuable for treatment decision and prediction of prognosis

  17. Radioreklamen skal finde sine ben

    Directory of Open Access Journals (Sweden)

    Sigurd Bennike

    1989-08-01

    Full Text Available Den 1. august 1988 startede radioreklamerne i Danmark uden nævneværdig opmærksomhed fra hverken pressen eller medieforskerne. Annoncørerne, reklamebureauerne og de store radiostationer har haft lidt svært ved at finde hinanden. Og heller ikke nemt ved at finde ud af, hvem der skulle producere reklamerne og hvordan sådan nogle skal lyde på dansk. Som det indirekte fremgår af denne artikel, så er det svært at få tal ud af branchen. - Men et kvalificeret gæt lyder på, at der er omsat for mellem 20 og 40 millioner kroner på de første måneder, koncentreret på mindre end 50 af de 237 nærradiosendetilladelser. De radiostationer der vælger at sende reklamer, skal betale 10% af deres omsætning til en særlig radiofond, hvis midler deles ud til de græsrodsradioer, som ikke kan eller vil skaffe sig reklameindtægter.

  18. Radiologic findings of epiploic appendagitis

    International Nuclear Information System (INIS)

    Oztunali, C.; Kara, T.

    2012-01-01

    Full text: Introduction: Epiploic appendagitis is a rare condition characterized by the ischemia and inflammation of the epiploic appendices of the colon. Its clinical features can mimic acute abdominal diseases such as diverticulitis and appendicitis. Objectives: The aim of this report is to present typical ultrasonography (US) and computed tomography (CT) features of this benign disease. Materials and method: A 44 year old man admitted to emergency department with a localized pain to umbilical region. His physical examination revealed rebound tenderness. He had no fever and his laboratory findings were normal. US examination showed a hyperechoic mass with a hypoechoic rim posterior to abdominal wall. Results: He was diagnosed with epiploic appendagitis and CT features confirmed the diagnosis. After a 5-day antibiotic treatment his clinical symptoms resolved. Conclusion: Epiploic appendagitis should be considered in the differential diagnosis of patients with an acute onset, localized pain. Because it is managed medically and has a self limited course, recognition of radiologic findings of this entity is important

  19. Ultrasonographic finding of intrahepatic stones

    International Nuclear Information System (INIS)

    Lee, Wang Yul; Koh, Byung Hee; Cho, On Koo; Hahm, Chang Kok

    1983-01-01

    Correct diagnosis of intrahepatic stone with differentiation from extrahepatic stone is very important because of their different surgical procedure. The ultrasonography is very simple and noninvasive diagnostic method for detection of intrahepatic stone than other method. So the authors analysed the ultrasonographic findings of 30 patients with intrahepatic stones and the results are as follows: 1. Among 30 cases, 13(43.3%) were male, 17(56.7%) were female with predominancy in 5th and 6th decades. 2. 1) In distribution of stones 16 cases(53.5%) were in the left duct, 11 cases(36.7%) in both ducts, 3 cases(10%) in the right duct. 2) In location of intrahepatic stones, 9 cases(30%) were only in the intrahepatic ducts, 21 cases (70%) associated stones in the extrahepatic duct and or GB. 3. In sonography of 30 cases of intrahepatic stones 1) The shape of stone was round in 27 cases(90%) and tubular due to impacted stone in 3 cases (10%) 2) The echogenicity of stones was strong in 25 cases(83.3%) and weak in 5 cases(16.7%). 3) The shadow posterior to stones was strong in 23 cases(76.7%) and weak in 7 cases(23.3%) 4. As associated findings, metastatic lesion in liver 2 cases(6.7%), liver cirrhosis 2 cases(6.7%), hepatic and perihepatic abscess 4 cases(13.3%)were found liver(13.3%) were found

  20. The radiologic findings of neurofibromatosis

    Energy Technology Data Exchange (ETDEWEB)

    Kim, So Sun; Park, Yeon Won; Kim, No Joon; Chun, Byung Hee; Joh, Young Duk [Kosin Medical College, Pusan (Korea, Republic of); Suh, Soo Jhi [Keimyung University Medical College, Taegu (Korea, Republic of)

    1986-08-15

    Neurofibromatosis, or von Recklinghausen's disease, is a hereditary, harmartomatous disorder that primarily involves neuro ectoderm and mesoderm. The estimated incidence is 1 in 2,500 to 3,000 births. The clinical features are skin manifestations such as cafe-au-lait spots, skeletal manifestations primarily involving vertebrae, central and peripheral nervous manifestations, and other associated abnormalities with increased risk of malignancy. The authors analysed the radiologic findings of 18 cases of patients with neurofibromatosis who visited Pusan Kosin Medical Center and Taegu Dongsan Medical Center during the last five years. All were proven by surgery, biopsy and other diagnostic criteria. The results obtained were as follows: 1. The male to female ratio was 11:7 and the age ranged from 11 months to 51 years. 2. All the cases fulfilled the diagnostic criteria of Crowe and associates. 3. Bone manifestations were present in 44% of the cases. The other radiologic findings were intrathoracic meningocele, bilateral acoustic neurinomas, mediastinal or chest wall mass shadows, and peripheral soft tissue masses. 4. One of the soft tissue masses was proved to be malignant.

  1. The radiologic findings of neurofibromatosis

    International Nuclear Information System (INIS)

    Kim, So Sun; Park, Yeon Won; Kim, No Joon; Chun, Byung Hee; Joh, Young Duk; Suh, Soo Jhi

    1986-01-01

    Neurofibromatosis, or von Recklinghausen's disease, is a hereditary, harmartomatous disorder that primarily involves neuro ectoderm and mesoderm. The estimated incidence is 1 in 2,500 to 3,000 births. The clinical features are skin manifestations such as cafe-au-lait spots, skeletal manifestations primarily involving vertebrae, central and peripheral nervous manifestations, and other associated abnormalities with increased risk of malignancy. The authors analysed the radiologic findings of 18 cases of patients with neurofibromatosis who visited Pusan Kosin Medical Center and Taegu Dongsan Medical Center during the last five years. All were proven by surgery, biopsy and other diagnostic criteria. The results obtained were as follows: 1. The male to female ratio was 11:7 and the age ranged from 11 months to 51 years. 2. All the cases fulfilled the diagnostic criteria of Crowe and associates. 3. Bone manifestations were present in 44% of the cases. The other radiologic findings were intrathoracic meningocele, bilateral acoustic neurinomas, mediastinal or chest wall mass shadows, and peripheral soft tissue masses. 4. One of the soft tissue masses was proved to be malignant.

  2. MRI findings of vermian medulloblastoma

    International Nuclear Information System (INIS)

    Jung, Seung Eun; Choi, Kyu Ho; Chung, Myung Hee; Yang, Il Kwon; Shinn, Kyung Sub; Park, Young Sub

    1996-01-01

    To find characteristic MRI features of vermian medulloblastoma. Materials and methods; MRI studies and medical records were retrospectively reviewed for 12 patients with surgically proven midline medulloblastoma. The assessment concerned appearance of the mass in relation to surrounding structures: MR signal intensity; the enhancement pattern; the mass's location and size: presence of a cystic/necrotic area, calcification, or vascular void: extension through the foramen Luschka: degree of hydrocephalus: and presence of tonsillar herniation. The midline medulloblastoma commonly showed roundish moon-surface appearance, especially on the axial T2-weighted images. All tumors showed heterogeneous signal intensities mainly due to intratumoral cystic/necrotic or hemorrhagic changes. The tumors were commonly located at mid-and/or inferior vermis. Occasionally the tumors extended through the foramen Luschka, and caused obstructive hydrocephalus of moderate to severe degree. Post-contrast study showed heterogeneous, dense contrast enhancement in the majority of patients. The MR finding of the moon-surface appearance formed by both the mass and the intratumoral cystic/necrotic change as seen on axial T2-weighted images could be helpful in the diagnosis of vermian medulloblastoma

  3. Periodontal Initial Radiological Findings of Genetically Predisposed Finnish Adolescents.

    Science.gov (United States)

    Heikkinen, Anna Maria; Pakbaznejad Esmaeili, Elmira; Kovanen, Leena; Ruokonen, Hellevi; Kettunen, Kaisa; Haukka, Jari; Tervahartiala, Taina; Sorsa, Timo

    2017-07-01

    Periodontitis is a multifactorial infectious disease of the supporting tissues of teeth in which bacterial, genetic and lifestyle factors such as smoking have an important role. The aim was to examine if Bleeding On Probing (BOP ≥ 20%) and ≥ 4 mm deep pockets correlated with any suspicion of initial radiological findings of periodontitis and bone loss. We also investigated whether any pro-inflammatory-related candidate Single Nucleotide Polymorphisms (SNPs) were associated with any suspicion of radiological findings. Altogether 47 generally healthy adolescent patients of one birth cohort had given their approval for their saliva samples to be used for DNA analysis. One participant was excluded after discrepant gender check. An oral radiologist analysed right and left bitewing radiographs of 47 patients. Clinical parameters such as BOP ≥ 20%, ≥ 4 mm pockets, Visible Plaque Index of all teeth (VPI%), as well as smoking habits were recorded. DNA was extracted and 71 SNPs from candidate genes for initial periodontitis were genotyped. The association between ≥ 4 mm pockets and BOP ≥ 20% with radiological findings and selected SNPs was modelled using logistic regression. Variants in Toll-Like Receptors 4 (TLR4) gene (rs498670) (OR=5.8, {CI95% 1.6-20.7}, p=0.02, FDR q-value=0.13) and TNFSF11 gene (rs2277438, OR=0.3 {CI95% 0.1-0.9}, p=0.002, FDR q-value=0.56) were associated with any suspicious radiological findings; however the significance vanished after False Discovery Rate analysis (FDR). The association between BOP ≥ 20% and any radiographic signs of periodontitis was found to be statistically significant, OR=1.6, CI 95% 1.0-2.4, p=0.04. Only TLR4 (rs498670) and TNFSF11 (rs2277438) genes were found to have a positive correlation with radiological findings suggestive of initial periodontitis after adjustment for smoking and visible plaque.

  4. MR findings of cyclosporine neurotoxicity

    International Nuclear Information System (INIS)

    Yang, Po Song; Ahn, Kook Jin; Ahn, Bo Young; Jung, Hae An; Kim, Hee Je; Lee, Jae Mun

    1998-01-01

    To analyze the MR findings of cyclosporine-induced neurotoxicity in patients receiving high dose of cyclosporine and to suggest the possible pathogenetic mechanism. The cases of seven patients (2 males, 5 females;18-36 years old) who suffered seizures after receiving high-dose cyclosporine for bone marrow transplantation due to diseases such as aplastic anemia or leukemia were retrospectively reviewed. We evaluated the location and pattern of abnormal signal intensity seen on T2 weighted images, the presence of contrast enhancement, and the changes seen on follow-up MR performed at intervals of 12-30 days after initial MR in five of seven patients. We analyzed levels of blood cyclosporine and magnesium, and investigated the presence of hypertension at the sity of the seizure. Locations of the lesions were bilateral(n=3D5), unilateral(n=3D2), parietal(n=3D6), occipital(n=3D6), temporal(n=3D4), and in the frontal lobe(n=3D3). Frontal lesions showed high signal intensities in the borderline ischemic zone of the frontal lobe between the territory of the anterior and middle cerebral arteries. In six of the seven patients, cortical and subcortical areas including subcortical U-fibers were seen on T2-weighted images to be involved in the parietooccipital lobes. Only one of the seven showed high signal intensity in the left basal ganglia. All lesions showed high signal intensity on T2-weighted images, and iso to low signal intensity on T1-weighted. In five of seven patients there was no definite enhancement, but in the other two, enhancement was slight. In four of seven patients seizures occurred within high therapeutic ranges(250-450ng/ml), while others suffered such attacks at levels below the therapeutic range. After cyclospirine was administered at a reduced dosage or stopped, follow-up MR images showed the complete or near-total disappearance of the abnormal findings previously described. Only two patients had hypertension, and the others normotension. Five of the

  5. Identification of putative cis-regulatory elements in Cryptosporidium parvum by de novo pattern finding

    Directory of Open Access Journals (Sweden)

    Kissinger Jessica C

    2007-01-01

    Full Text Available Abstract Background Cryptosporidium parvum is a unicellular eukaryote in the phylum Apicomplexa. It is an obligate intracellular parasite that causes diarrhea and is a significant AIDS-related pathogen. Cryptosporidium parvum is not amenable to long-term laboratory cultivation or classical molecular genetic analysis. The parasite exhibits a complex life cycle, a broad host range, and fundamental mechanisms of gene regulation remain unknown. We have used data from the recently sequenced genome of this organism to uncover clues about gene regulation in C. parvum. We have applied two pattern finding algorithms MEME and AlignACE to identify conserved, over-represented motifs in the 5' upstream regions of genes in C. parvum. To support our findings, we have established comparative real-time -PCR expression profiles for the groups of genes examined computationally. Results We find that groups of genes that share a function or belong to a common pathway share upstream motifs. Different motifs are conserved upstream of different groups of genes. Comparative real-time PCR studies show co-expression of genes within each group (in sub-sets during the life cycle of the parasite, suggesting co-regulation of these genes may be driven by the use of conserved upstream motifs. Conclusion This is one of the first attempts to characterize cis-regulatory elements in the absence of any previously characterized elements and with very limited expression data (seven genes only. Using de novo pattern finding algorithms, we have identified specific DNA motifs that are conserved upstream of genes belonging to the same metabolic pathway or gene family. We have demonstrated the co-expression of these genes (often in subsets using comparative real-time-PCR experiments thus establishing evidence for these conserved motifs as putative cis-regulatory elements. Given the lack of prior information concerning expression patterns and organization of promoters in C. parvum we

  6. Lineage-specific expansion of IFIT gene family: an insight into coevolution with IFN gene family.

    Directory of Open Access Journals (Sweden)

    Ying Liu

    Full Text Available In mammals, IFIT (Interferon [IFN]-induced proteins with Tetratricopeptide Repeat [TPR] motifs family genes are involved in many cellular and viral processes, which are tightly related to mammalian IFN response. However, little is known about non-mammalian IFIT genes. In the present study, IFIT genes are identified in the genome databases from the jawed vertebrates including the cartilaginous elephant shark but not from non-vertebrates such as lancelet, sea squirt and acorn worm, suggesting that IFIT gene family originates from a vertebrate ancestor about 450 million years ago. IFIT family genes show conserved gene structure and gene arrangements. Phylogenetic analyses reveal that this gene family has expanded through lineage-specific and species-specific gene duplication. Interestingly, IFN gene family seem to share a common ancestor and a similar evolutionary mechanism; the function link of IFIT genes to IFN response is present early since the origin of both gene families, as evidenced by the finding that zebrafish IFIT genes are upregulated by fish IFNs, poly(I:C and two transcription factors IRF3/IRF7, likely via the IFN-stimulated response elements (ISRE within the promoters of vertebrate IFIT family genes. These coevolution features creates functional association of both family genes to fulfill a common biological process, which is likely selected by viral infection during evolution of vertebrates. Our results are helpful for understanding of evolution of vertebrate IFN system.

  7. Retroperitoneal fibrosis: findings with MR

    International Nuclear Information System (INIS)

    Martinez Rodrigo, J.; Marti-Bonnati, L.; Diago, T.; Ferrer, M.D.; Aleixandre, A.; Morote, V.

    1993-01-01

    Retroperitoneal fibrosis (RF) is an uncommon disease characterized by the presence of a chronic inflammatory reaction, with the formation of fibrous tissue that replaces the normal retroperitoneal tissue, trapping vessels and/or ureters. We present a retrospective review of 3 cases of idiopathic RF studied by means of ultrasound, CT scan and MR imaging, and we assess the features of the MR image, as well as its capacity for characterizing the lesion. We compare the findings obtained with 3 imaging techniques, describing the utility of each one, and their advantages and disadvantages in the assessment of this pathology. In MR, idiopathic RF appears as a hypodense mass in SET1, SE-T2 and STIR sequences. (Author) 9 ref

  8. MR findings in knee osteoarthritis

    International Nuclear Information System (INIS)

    Guermazi, Ali; Taouli, Bachir; Genant, Harry K.; Zaim, Souhil; Miaux, Yves; Peterfy, Charles G.

    2003-01-01

    Knee osteoarthritis (OA) is a leading cause of disability. Recent advances in drug discovery techniques and improvements in understanding the pathophysiology of osteoarthritic disorders have resulted in an unprecedented number of new therapeutic agents. Of all imaging modalities, radiography has been the most widely used for the diagnosis and management of the progression of knee OA. Magnetic resonance imaging is a relatively recent technique and its applications to osteoarthritis have been limited. Compared with conventional radiography, MR imaging offers unparalleled discrimination among articular soft tissues by directly visualizing all components of the knee joint simultaneously and therefore allowing the knee joint to be evaluated as a whole organ. In this article we present the MR findings in knee OA including cartilage abnormalities, osteophytes, bone edema, subarticular cysts, bone attrition, meniscal tears, ligament abnormalities, synovial thickening, joint effusion, intra-articular loose bodies, and periarticular cysts. (orig.)

  9. Radiographic findings in Marfan's syndrome

    International Nuclear Information System (INIS)

    Watanabe, Yasutaka; Tanaka, Osamu; Koyama, Shinichiro

    2010-01-01

    Spontaneous pneumothorax and apical bulla are included in minor criteria of the diagnosis of Marfan's syndrome. We evaluated the frequency of radiological abnormal findings of the lung in Marfan's syndrome. Lungs could be assessed with CT in 38 cases that were selected from 50 cases in Marfan's syndrome with a cardiovascular disease or the valvular disease. Eleven cases (22%) in 50 cases had the past history of spontaneous pneumothorax. Chest CT scan in 38 cases showed emphysematous bullae in 12 cases, apical scar in eight cases, centrilobular emphysema in three cases, and bronchiectasis in one case. CT manifestations of the lung in Marfan's syndrome were mainly spontaneous pneumothorax and apical bullae as were previously reported. (author)

  10. Fundus Findings in Wernicke Encephalopathy

    Directory of Open Access Journals (Sweden)

    Tal Serlin

    2017-07-01

    Full Text Available Wernicke encephalopathy (WE is an acute neuropsychiatric syndrome resulting from thiamine (vitamin B1 deficiency, classically characterized by the triad of ophthalmoplegia, confusion, and ataxia. While commonly associated with chronic alcoholism, WE may also occur in the setting of poor nutrition or absorption. We present a 37-year-old woman who underwent laparoscopic sleeve gastrectomy and presented with visual disturbance with bilateral horizontal nystagmus, confusion, and postural imbalance. Fundus examination revealed bilateral optic disc edema with a retinal hemorrhage in the left eye. Metabolic workup demonstrated thiamine deficiency. Her symptoms resolved after thiamine treatment. This case raises the awareness of the possibility of posterior segment findings in WE, which are underreported in WE.

  11. Milnacipran: recent findings in depression

    Directory of Open Access Journals (Sweden)

    Guest editors: Stuart Montgomery (London

    2010-08-01

    Full Text Available EDITORIAL FOREWORDPage 1   Milnacipran: recent findings in depression Stuart Montgomery (London, UK and Mike Briley (Castres, France REVIEWSPage 3   Suicidality: risk factors and the effects of antidepressants. The example of parallel reduction of suicidality and other depressive symptoms during treatment with the SNRI, milnacipran Philippe Courtet (Montpellier, FrancePage 9   Treatment of patients with comorbid depression and diabetes with metformin and milnacipran Peter Hofmann (Graz, AustriaPage 17  Antidepressant therapy with milnacipran and venlafaxine Lucilla Mansuy (Toulouse, FrancePage 23  Milnacipran: a unique antidepressant? Siegfried Kasper and Gerald Pail (Vienna, Austria This supplement is based on a symposium that took place at the 9th International Forum on Mood and Anxiety in Monte Carlo in November 2009 and is supported by an unconditional education grant from Pierre Fabre Médicament.

  12. Pathomorphological findings in preterm infants

    International Nuclear Information System (INIS)

    Amann, G.

    2000-01-01

    Pathomorphology in the preterm infant represents an interaction of morphological organ immaturity and neonatal management with their respective sequelae. Pathomorphological examples include the modification in the morphology of hyaline membrane disease and bronchopulmonary dysplasia as a consequence of modern neonatal therapy. Hemorrhagic and ischemic/hypoxic lesions of the central nervous system may occur in age- and agent-related distributional patterns, with subependymal hemorrhage and periventricular leukomalacia representing the most important examples. The most common intestinal finding, namely, necrotizing enterocolitis, typically shows segmental alterations, the morphology of which largely depends on the dominating causative agent. Hepatic cholestasis and fatty change are mostly consequences of parenteral nutrition or hypoxic/ischemic stress. Hepatic necrosis can be associated with the latter, but may also indicate disseminated intravascular coagulation. Vascular pathomorphology is represented by thromembolic lesions, in most instances corresponding to sequelae of neonatal management. (orig.) [de

  13. Nerootologic Finding in AIDS Patient

    Directory of Open Access Journals (Sweden)

    Mehrnaz Asadifar

    1992-04-01

    Full Text Available Here we have mentioned the case of a Caucasian man affected with human immunodeficiency virus during blood injection in a heart surjury.He demonstrated vertigo, dissequilibrium and neurological problems secondry to his disease 4 years later. Auditory and vestibular system disfunction became obvious based on the neurological examinations. optokinetic nystagmus, ataxia in addition to lack of response by caloric stimulation was attained in electronystagmographic examination.absolute latencies and interpeak intervals were prolonged in the auditory brain-stem responses(ABR.abnormal low scores were obtained in SSI test bilaterally.organic brain lesion and severe anxiety have been diagnised during psychological examination. Human immunodeficiency virus was detected in brain, cerebellum and brainstem cells by means of autopsia.meanwhile the pathologic changes were cosistent with neuro-otological findings

  14. Chronic eosinophilic pneumonia: CT findings

    International Nuclear Information System (INIS)

    Gutierrez, Haydee; Beccar Varela, Lucia; De Felippi, Maria S.

    2002-01-01

    Objective: To assess the usefulness of computerized tomography (CT) in the diagnosis of chronic eosinophilic pneumonia. Material and Methods: A double helical CT was performed in 6 patients referred to our center because of a chest X-ray with pulmonary infiltrates. Clinical presentation was cough, fever and eosinophilia in peripheral blood. Patients' age ranged from 25 to 55 years; 4 were women and 2 were men, one of the latter had a history of bronchial asthma. All patients received treatment with corticosteroids, with remission of the clinical and radiological parameters. Three patients underwent a control CT. Results: Findings consisted in focal parenchymal alterations, with areas of pulmonary consolidation and areas of 'ground glass' appearance; both patterns coexisted in certain areas. In 3 cases the lesions extended from the apices to the pulmonary bases, with predominance of the upper and middle fields. In 1 patient, there was frank predominance in the left hemi thorax. In another patient, who had a history of asthma, there were signs of pulmonary hyperinflation, with diffuse thickening of the bronchial walls, added to the previously mentioned findings, which involved the entire lung. In the mediastinum, 1 patient had lymph nodes larger than 1 cm, 3 had lymph nodes that were not enlarged but were more numerous than usual, and in the remaining patients no lymph nodes were found. The control CT's showed almost total resolution of the pulmonary infiltrates. Conclusion: The combination of eosinophilia and characteristic pulmonary infiltrates with a likely clinical presentation, associated with an optimal response to treatment with corticosteroids allows to make a reliable diagnosis and avoids the need for a pulmonary biopsy. (author)

  15. [Pathomorphologic findings following intensive therapy].

    Science.gov (United States)

    Ruchti, C

    1986-05-24

    Based on autopsy findings in 301 adults who had died after intensive care, different patterns of single or multiple organ damage were identified. Signs of septicemia and/or exudative-to-fibrosing alveolitis (EFA) of the lungs, the prominent cause of the adult respiratory distress syndrome (ARDS), were recognized in 89 cases. Severe, progressive EFA, which appears to ensue mainly from continuing damage to alveolar walls, consequent fibroblast proliferation and so-called atelectatic induration (collapsed alveoli forming single thick septa), was registered only in individuals who had undergone long-term intensive care. The latter was necessitated in various severe conditions of which abdominal disease was the most important. Systemic disorders, such as hemorrhagic diathesis and multiple organ damage ("multiple organ failure"), showed a close correlation with septicemia. Infections with gram-negative bacteria appear to play a special role in such processes. Morphologically, these cases were characterized by multiple organ/system damage, e.g., in order of frequency, partial necrosis of renal proximal tubules, followed by signs of regeneration; jaundice; splenitis; lobular pneumonia; centrolobular-to-zonal liver necrosis, in part combined with cholestasis; petechial and/or extended hemorrhage; and others. This complex pattern contrasted strongly with findings in individuals who had been admitted to intensive care because of e.g. a cardiovascular incident: in this latter group (125 cases) intensive care was usually of short duration, progressive EFA was largely absent, signs of septicemia were exceptional, and multiple organ/system damage was rare. The group with polytraumatism (28 cases) exhibited a pattern of organ damage intermediate between (a) and (b).

  16. Genes and Syndromic Hearing Loss.

    Science.gov (United States)

    Keats, Bronya J. B.

    2002-01-01

    This article provides a description of the human genome and patterns of inheritance and discusses genes that are associated with some of the syndromes for which hearing loss is a common finding, including: Waardenburg, Stickler, Jervell and Lange-Neilsen, Usher, Alport, mitochondrial encephalomyopathy, and sensorineural hearing loss. (Contains…

  17. Genetics and intelligence differences: five special findings

    Science.gov (United States)

    Plomin, R; Deary, I J

    2015-01-01

    Intelligence is a core construct in differential psychology and behavioural genetics, and should be so in cognitive neuroscience. It is one of the best predictors of important life outcomes such as education, occupation, mental and physical health and illness, and mortality. Intelligence is one of the most heritable behavioural traits. Here, we highlight five genetic findings that are special to intelligence differences and that have important implications for its genetic architecture and for gene-hunting expeditions. (i) The heritability of intelligence increases from about 20% in infancy to perhaps 80% in later adulthood. (ii) Intelligence captures genetic effects on diverse cognitive and learning abilities, which correlate phenotypically about 0.30 on average but correlate genetically about 0.60 or higher. (iii) Assortative mating is greater for intelligence (spouse correlations ~0.40) than for other behavioural traits such as personality and psychopathology (~0.10) or physical traits such as height and weight (~0.20). Assortative mating pumps additive genetic variance into the population every generation, contributing to the high narrow heritability (additive genetic variance) of intelligence. (iv) Unlike psychiatric disorders, intelligence is normally distributed with a positive end of exceptional performance that is a model for ‘positive genetics'. (v) Intelligence is associated with education and social class and broadens the causal perspectives on how these three inter-correlated variables contribute to social mobility, and health, illness and mortality differences. These five findings arose primarily from twin studies. They are being confirmed by the first new quantitative genetic technique in a century—Genome-wide Complex Trait Analysis (GCTA)—which estimates genetic influence using genome-wide genotypes in large samples of unrelated individuals. Comparing GCTA results to the results of twin studies reveals important insights into the genetic

  18. Gene Therapy for Parkinson's Disease

    Directory of Open Access Journals (Sweden)

    Rachel Denyer

    2012-01-01

    Full Text Available Current pharmacological and surgical treatments for Parkinson's disease offer symptomatic improvements to those suffering from this incurable degenerative neurological disorder, but none of these has convincingly shown effects on disease progression. Novel approaches based on gene therapy have several potential advantages over conventional treatment modalities. These could be used to provide more consistent dopamine supplementation, potentially providing superior symptomatic relief with fewer side effects. More radically, gene therapy could be used to correct the imbalances in basal ganglia circuitry associated with the symptoms of Parkinson's disease, or to preserve or restore dopaminergic neurons lost during the disease process itself. The latter neuroprotective approach is the most exciting, as it could theoretically be disease modifying rather than simply symptom alleviating. Gene therapy agents using these approaches are currently making the transition from the laboratory to the bedside. This paper summarises the theoretical approaches to gene therapy for Parkinson's disease and the findings of clinical trials in this rapidly changing field.

  19. Gene expression and gene therapy imaging

    International Nuclear Information System (INIS)

    Rome, Claire; Couillaud, Franck; Moonen, Chrit T.W.

    2007-01-01

    The fast growing field of molecular imaging has achieved major advances in imaging gene expression, an important element of gene therapy. Gene expression imaging is based on specific probes or contrast agents that allow either direct or indirect spatio-temporal evaluation of gene expression. Direct evaluation is possible with, for example, contrast agents that bind directly to a specific target (e.g., receptor). Indirect evaluation may be achieved by using specific substrate probes for a target enzyme. The use of marker genes, also called reporter genes, is an essential element of MI approaches for gene expression in gene therapy. The marker gene may not have a therapeutic role itself, but by coupling the marker gene to a therapeutic gene, expression of the marker gene reports on the expression of the therapeutic gene. Nuclear medicine and optical approaches are highly sensitive (detection of probes in the picomolar range), whereas MRI and ultrasound imaging are less sensitive and require amplification techniques and/or accumulation of contrast agents in enlarged contrast particles. Recently developed MI techniques are particularly relevant for gene therapy. Amongst these are the possibility to track gene therapy vectors such as stem cells, and the techniques that allow spatiotemporal control of gene expression by non-invasive heating (with MRI guided focused ultrasound) and the use of temperature sensitive promoters. (orig.)

  20. MR findings of trigeminal neurinoma

    Energy Technology Data Exchange (ETDEWEB)

    Park, Hong Suk; Han, Moon Hee; Chang, Kee Hyun; Yoo, In Kyu; Kim, Sam Soo; Lee, Kyoung Won; Jung, Hee Won; Yeon, Kyung Mo [Seoul National Univ. College of Medicine, Seoul (Korea, Republic of)

    1997-08-01

    To describe the MRI findings of trigeminal neurinoma. We retrospectively analyzed the MRI findings of 19 patients with trigeminal neurinomas proven by surgery and pathologic examination. Axial T1- and T2-weighted MR images in all patients and gadolinium-enhanced T1-weighted images in 14 patients were obtained at 2.0T(8 cases), 1.5T(6 cases) or 0.5T(5 cases). These were analyzed in terms of tumor size, signal intensity, degree of contrast enhancement, the presence or absence of cystic change and denervation atrophy of the masticator muscles. Clinical manifestations included sensory abnormality or pain(n=12), headache(n=10), impaired visual acuity or diplopia(n=6), hearing loss or tinnitus(n=3), weakness of masticator muscles(n=2), and mass or nasal obstruction(n=2). On MR images, tumor size was seen to average 4.2(range 1.5-6)cm;tumors were located in the posterior cranial fossa(n=8), middle cranial fossa(n=4), ophthalmic nerve(n=2), maxillary nerve(n=1), and mandibular nerve(n=1), and in three cases were dumbbell-shaped and extended into both the middle and posterior cranial fossa. On T1-weighted images, signals were isointense with cortical grey matter, in ten cases(53%), and of low intensity in nine (47%);on T2-weighted images, signals were of high intensity in 15cases(79%) and were isointense in four (21%). Cystic change was seen in 12 cases(63%). After enhancement, all (14/14) the tumors enhanced. Denervation atrophy was seen in nine cases(47%) and all of these involved the trigeminal ganglion or mandibular nerve. A trigeminal neurinoma shows similar signal intensity and enhancement to other cranial neurinomas with a higher incidence of cystic degeneration. Its location and shape are characteristic, and where there is involvement of the trigeminal ganglion or mandibular nerve, denervation atrophy may be seen.

  1. MR findings of trigeminal neurinoma

    International Nuclear Information System (INIS)

    Park, Hong Suk; Han, Moon Hee; Chang, Kee Hyun; Yoo, In Kyu; Kim, Sam Soo; Lee, Kyoung Won; Jung, Hee Won; Yeon, Kyung Mo

    1997-01-01

    To describe the MRI findings of trigeminal neurinoma. We retrospectively analyzed the MRI findings of 19 patients with trigeminal neurinomas proven by surgery and pathologic examination. Axial T1- and T2-weighted MR images in all patients and gadolinium-enhanced T1-weighted images in 14 patients were obtained at 2.0T(8 cases), 1.5T(6 cases) or 0.5T(5 cases). These were analyzed in terms of tumor size, signal intensity, degree of contrast enhancement, the presence or absence of cystic change and denervation atrophy of the masticator muscles. Clinical manifestations included sensory abnormality or pain(n=12), headache(n=10), impaired visual acuity or diplopia(n=6), hearing loss or tinnitus(n=3), weakness of masticator muscles(n=2), and mass or nasal obstruction(n=2). On MR images, tumor size was seen to average 4.2(range 1.5-6)cm;tumors were located in the posterior cranial fossa(n=8), middle cranial fossa(n=4), ophthalmic nerve(n=2), maxillary nerve(n=1), and mandibular nerve(n=1), and in three cases were dumbbell-shaped and extended into both the middle and posterior cranial fossa. On T1-weighted images, signals were isointense with cortical grey matter, in ten cases(53%), and of low intensity in nine (47%);on T2-weighted images, signals were of high intensity in 15cases(79%) and were isointense in four (21%). Cystic change was seen in 12 cases(63%). After enhancement, all (14/14) the tumors enhanced. Denervation atrophy was seen in nine cases(47%) and all of these involved the trigeminal ganglion or mandibular nerve. A trigeminal neurinoma shows similar signal intensity and enhancement to other cranial neurinomas with a higher incidence of cystic degeneration. Its location and shape are characteristic, and where there is involvement of the trigeminal ganglion or mandibular nerve, denervation atrophy may be seen

  2. MRI findings of congenita dysosmia

    International Nuclear Information System (INIS)

    You Hui; Feng Feng; Liu Jianfeng; Wu Xueyan; Wang Jian; Ni Daofeng; Sun Hongyi; Chen Jun; Jin Zhengyu

    2009-01-01

    Objective: To study the MRI findings of congenital dysosmia. Methods: Forty-seven patients with congenital dysosmia (39 with Kallmann syndrome and 8 with isolated dysosmia) and 21 normal volunteers underwent MRI examination. The features of congenital malformation were recorded. The volume of olfactory bulbs, depth of olfactory sulci as well as diameters of pituitary glands and stalks were measured. The rate of dysplasia of olfactory bulbs and tracts in the two patients groups was compared with X 2 test. The difference of volume of olfactory bulbs between the two groups was evaluated with nonparametric test. And the difference of diameters of pituitary glands and stalks was analyzed with analysis of variance. Results: All the patients had abnormal findings in olfactory bulbs, tracts and/or olfactory sulci on MR images. The patterns of congenital malformation may be dysplastic of hypoplastic, symmetric or asymmetric. The proportion of patients with dysplasia of olfactory bulbs and tracts in Kallmann syndrome patients (31/39) was higher than that in isolated dysosmia ones (2/8) (X 2 = 6.998, P =0.008), and the olfactory bulbs'volume of patients with Kallmann syndrome (median 8 mm 3 ) was smaller than that of patients with isolated dysosmia (median 22 mm 3 ) (Z = -2.902, P =0.004). The pituitary glands were smaller and the stalks were thinner in patients with Kallmann syndrome than those in volunteers [ the anteroposterior diameter of pituitary glands in Kallmann syndrome (7.22 ± 1.93) mm, that in normal volunteers (9.94 ± 1.59) mm, F= 16.835, P =0.000; height of pituitary glands in Kallmann syndrome (3.71 ± 1.74) mm, that in normal volunteers (6.00 ± 1.24) mm, F =16.092, P =0.000; the anteroposterior diameter of pituitary stalks in Kallmann syndrome (1.19 ± 0.55) mm, that in normal volunteers (1.88 ± 0.49) mm, F =13.060, P =0.000]. Conclusions: In congenital dysosmic patients, dysplasia or hypoplasia of olfactory bulbs, tracts and sulci can be clearly depicted

  3. Microarray time course experiments: finding profiles.

    Science.gov (United States)

    Irigoien, Itziar; Vives, Sergi; Arenas, Concepción

    2011-01-01

    Time course studies with microarray techniques and experimental replicates are very useful in biomedical research. We present, in replicate experiments, an alternative approach to select and cluster genes according to a new measure for association between genes. First, the procedure normalizes and standardizes the expression profile of each gene, and then, identifies scaling parameters that will further minimize the distance between replicates of the same gene. Then, the procedure filters out genes with a flat profile, detects differences between replicates, and separates genes without significant differences from the rest. For this last group of genes, we define a mean profile for each gene and use it to compute the distance between two genes. Next, a hierarchical clustering procedure is proposed, a statistic is computed for each cluster to determine its compactness, and the total number of classes is determined. For the rest of the genes, those with significant differences between replicates, the procedure detects where the differences between replicates lie, and assigns each gene to the best fitting previously identified profile or defines a new profile. We illustrate this new procedure using simulated data and a representative data set arising from a microarray experiment with replication, and report interesting results.

  4. MR findings in pontocerebellar hypoplasia

    Energy Technology Data Exchange (ETDEWEB)

    Uhl, M.; Pawlik, H.; Laubenberger, J.; Langer, M. [Department of Radiology, Division of Paediatric Radiology, University Hospital of Freiburg, Freiburg (Germany); Darge, K. [Department of Paediatric Radiology, Children`s Hospital of the University of Heidelberg, Heidelberg (Germany); Baborie, A. [Department of Neuropathology, Neurozentrum, University of Freiburg, Freiburg (Germany); Korinthenberg, R. [Department of Neuropaediatrics, Children`s Hospital, University of Freiburg, Freiburg (Germany)

    1998-07-01

    We present four cases with combined hypoplasia of the cerebellum and the ventral pons - pontocerebellar hypoplasia (PCH). PCH represents an autosomal recessive neurodegenerative disorder with fetal onset. The disease is rare, with less than 20 cases having been reported. The main findings of PCH and the inclusion criteria for our cases can be summarised as progressive microcephaly from birth, pontocerebellar hypoplasia documented by MRI and marked chorea, which may change, later in childhood, to more dystonic patterns. The cerebral cortex becomes progressively atrophic. Motor and mental development are delayed, and epilepsy, mainly tonic-clonic seizures, is frequent. The MRI features in all of our cases were: (1) Hypoplastic cerebellum situated close to the tentorium. The hypoplastic cerebellum has a reduced number of folia, in contrast to the normal number of thin folia in simple cerebellar atrophy. (2) The cerebellar hemispheres are reduced to bean-like or wing-like structures. The cerebellar hemispheres appear to `float` in the posterior fossa. (3) Markedly hypoplastic ventral pons. (4) Slight atrophy of the supratentorial gyral pattern. (5) Dilated cerebromedullary cistern and fourth ventricle. (6) Delayed myelination of the white matter. (7) No significant disorganisation of brain architecture and no severe corpus callosum defect. (orig.) With 3 figs., 2 tabs., 13 refs.

  5. CT findings of osteogenesis imperfecta

    Energy Technology Data Exchange (ETDEWEB)

    Kojo, Nobuto; Otsuru, Katsuyasu; Lee, Soichi; Takagi, Shigeyuki; Shigemori, Minoru.

    1987-08-01

    Two cases of osteogenesis imperfecta found in one family (father and daughter) are reported, and the CT findings are described. Case 1 is a 58-year-old man who fell and struck his head at home on November 10, 1984. He was transferred to Omuta City Hospital when he became semicomatose and decerebrate posturing was noted. His family history revealed 8 persons with osteogenesis imperfecta. A skull X-ray film showed a large skull vault, many wormian bones at the lambdoid suture, platybasia, and a basilar impression. A CT scan demonstrated a right acute subdural hematoma, while the bone image showed well-developed mastoid air cells and a skull deformity characteristic of osteogenesis imperfecta. He had an emergency operation, and a 170-gr clot was successfully evacuated. A postoperative CT scan demonstrated brain atrophy, possibly present before head trauma. Case 2 is the daughter of Case 1 (a 27-year-old woman). She also showed characteristic neuroradiological manifestations on a plain skull film and on a CT scan. A basilar impression and platybasia were also demonstrated. In this report, the possible mechanism of the production of a traumatic acute subdural hematoma is also discussed.

  6. Form finding in elastic gridshells

    Science.gov (United States)

    Baek, Changyeob; Sageman-Furnas, Andrew O.; Jawed, Mohammad K.; Reis, Pedro M.

    2018-01-01

    Elastic gridshells comprise an initially planar network of elastic rods that are actuated into a shell-like structure by loading their extremities. The resulting actuated form derives from the elastic buckling of the rods subjected to inextensibility. We study elastic gridshells with a focus on the rational design of the final shapes. Our precision desktop experiments exhibit complex geometries, even from seemingly simple initial configurations and actuation processes. The numerical simulations capture this nonintuitive behavior with excellent quantitative agreement, allowing for an exploration of parameter space that reveals multistable states. We then turn to the theory of smooth Chebyshev nets to address the inverse design of hemispherical elastic gridshells. The results suggest that rod inextensibility, not elastic response, dictates the zeroth-order shape of an actuated elastic gridshell. As it turns out, this is the shape of a common household strainer. Therefore, the geometry of Chebyshev nets can be further used to understand elastic gridshells. In particular, we introduce a way to quantify the intrinsic shape of the empty, but enclosed regions, which we then use to rationalize the nonlocal deformation of elastic gridshells to point loading. This justifies the observed difficulty in form finding. Nevertheless, we close with an exploration of concatenating multiple elastic gridshell building blocks.

  7. CT findings of nasopharyngeal cancer

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Kie Hwan; Byun, Hong Sik; Chin, Soo Yil [Korea Cancer Center Hospital, Seoul (Korea, Republic of)

    1987-10-15

    CT findings in 64 patients of nasopharyngeal cancer are analyzed retrospectively to evaluate the region of origin and the route of spread. The results are as follows: 1. The most frequently involved wall is lateral well (90%), followed by posterior wall (78%) and superior wall (58%). 2. There are invasion to parapharyngeal space (86%), retropharyngeal and prevertebral space (72%), carotid space (46%), and masticator space (18%) in that order. 3. Involved anatomic sites are Rosenmueller fossa (90%), torus tubarius (78%), E-tube orifice (68%), carotid sheath (46%), soft palate (50%), nasal cavity (36%), skull base (28%), prevertebral muscle (26%) and intracranial fossa (16%). 4. Direct extension to intracranial fossa is via sphenoid sinus (6/8), foramen lacerum (5/8), foramen ovale (4/8), and jugular foramen (4/8) in that order. 5. Invasion to prevertebral space leads to intraspinal extension (3/13). 6. Cervical lymph node metastasis of found in internal jugular (82%),spinal accessory (56%) and retropharyngeal chain (42%) in that order. 7. After radiation therapy, most frequent site of recurrence is posterior wall (10/14) followed by lateral wall (9/14), superior wall (5/14) and cervical lymph node (6/14), but the presence of recurrence is difficult to determine based on CT only.

  8. MR findings in intralabyrinthine schwannomas

    Energy Technology Data Exchange (ETDEWEB)

    Montague, Mary-Louise; Kishore, Ameet; Hadley, Donald M.; O' Reilly, Brian

    2002-05-01

    AIM: Intralabyrinthine schwannomas (ILS) are rare benign tumours. They are not always recognized on routine magnetic resonance imaging (MRI). We aimed to study the clinical presentation and MRI findings in our patients with ILS. MATERIALS AND METHODS: Retrospective analysis of patients with vestibular schwannomas treated at this center. RESULTS: Of 144 vestibular schwannomas studied at this centre, three patients had an ILS. The most common presenting symptoms were unilateral hearing loss, tinnitus and vertigo. Two patients demonstrated a progressive sensorineural hearing loss (SNHL). The third patient had a severe SNHL at presentation. MRI enhanced with contrast medium was positive in the two patients with progressive SNHL and negative in the patient with the severe SNHL. CONCLUSION: This series demonstrates the ability of MRI to identify schwannomas filling the labyrinth, and also its inability to identify extremely small ILS. It underlines the importance of sending the cristae of patients undergoing labyrinthectomy for presumed Meniere's disease for histological examination. Montague, M.-L. et al. (2002)

  9. Polysomnographic findings in craniopharyngioma patients.

    Science.gov (United States)

    Pickering, Line; Klose, Marianne; Feldt-Rasmussen, Ulla; Jennum, Poul

    2017-12-01

    The purpose of this study is to evaluate whether damage to the hypothalamus due to craniopharyngioma or consequent surgery may involve the sleep-wake regulatory system, resulting in sleep disturbances and sleepiness. Seven craniopharyngioma patients and 10 healthy controls were evaluated with sleep questionnaires including the Epworth Sleepiness Scale, polysomnography, and a multiple sleep latency test (MSLT). Five patients and eight controls had lumbar puncture performed to determine hypocretin-1 levels. Patients tended to feel sleepier than control individuals of the same age (p = 0.09). No subjects had symptoms of hypnagogic hallucinations, sleep paralyses, or cataplexies. Four patients and one control had periodic leg movements (PLMs). One patient had fragmented sleep pattern, rapid eye movement (REM) sleep without atonia, and PLMs. One patient had short sleep periods during the daytime. Four patients had fragmented sleep pattern. With the MSLT, four patients and two controls had mean sleep latency of sleep periods, respectively. All subjects showed normal hypocretin-1 levels. Four patients had electrophysiological findings indicative of central hypersomnia including one patient meeting the criteria of narcolepsy. The sleep-wake regulatory system may be involved in craniopharyngioma patients.

  10. CT findings of osteogenesis imperfecta

    International Nuclear Information System (INIS)

    Kojo, Nobuto; Otsuru, Katsuyasu; Lee, Soichi; Takagi, Shigeyuki; Shigemori, Minoru.

    1987-01-01

    Two cases of osteogenesis imperfecta found in one family (father and daughter) are reported, and the CT findings are described. Case 1 is a 58-year-old man who fell and struck his head at home on November 10, 1984. He was transferred to Omuta City Hospital when he became semicomatose and decerebrate posturing was noted. His family history revealed 8 persons with osteogenesis imperfecta. A skull X-ray film showed a large skull vault, many wormian bones at the lambdoid suture, platybasia, and a basilar impression. A CT scan demonstrated a right acute subdural hematoma, while the bone image showed well-developed mastoid air cells and a skull deformity characteristic of osteogenesis imperfecta. He had an emergency operation, and a 170-gr clot was successfully evacuated. A postoperative CT scan demonstrated brain atrophy, possibly present before head trauma. Case 2 is the daughter of Case 1 (a 27-year-old woman). She also showed characteristic neuroradiological manifestations on a plain skull film and on a CT scan. A basilar impression and platybasia were also demonstrated. In this report, the possible mechanism of the production of a traumatic acute subdural hematoma is also discussed. (author)

  11. MR findings in pontocerebellar hypoplasia

    International Nuclear Information System (INIS)

    Uhl, M.; Pawlik, H.; Laubenberger, J.; Langer, M.; Darge, K.; Baborie, A.; Korinthenberg, R.

    1998-01-01

    We present four cases with combined hypoplasia of the cerebellum and the ventral pons - pontocerebellar hypoplasia (PCH). PCH represents an autosomal recessive neurodegenerative disorder with fetal onset. The disease is rare, with less than 20 cases having been reported. The main findings of PCH and the inclusion criteria for our cases can be summarised as progressive microcephaly from birth, pontocerebellar hypoplasia documented by MRI and marked chorea, which may change, later in childhood, to more dystonic patterns. The cerebral cortex becomes progressively atrophic. Motor and mental development are delayed, and epilepsy, mainly tonic-clonic seizures, is frequent. The MRI features in all of our cases were: (1) Hypoplastic cerebellum situated close to the tentorium. The hypoplastic cerebellum has a reduced number of folia, in contrast to the normal number of thin folia in simple cerebellar atrophy. (2) The cerebellar hemispheres are reduced to bean-like or wing-like structures. The cerebellar hemispheres appear to 'float' in the posterior fossa. (3) Markedly hypoplastic ventral pons. (4) Slight atrophy of the supratentorial gyral pattern. (5) Dilated cerebromedullary cistern and fourth ventricle. (6) Delayed myelination of the white matter. (7) No significant disorganisation of brain architecture and no severe corpus callosum defect. (orig.)

  12. Neuroimaging findings in primary insomnia.

    Science.gov (United States)

    O'Byrne, J N; Berman Rosa, M; Gouin, J-P; Dang-Vu, T T

    2014-10-01

    State-of-the-art neuroimaging techniques have accelerated progress in the study and understanding of sleep in humans. Neuroimaging studies in primary insomnia remain relatively few, considering the important prevalence of this disorder in the general population. This review examines the contribution of functional and structural neuroimaging to our current understanding of primary insomnia. Functional studies during sleep provided support for the hyperarousal theory of insomnia. Functional neuroimaging also revealed abnormalities in cognitive and emotional processing in primary insomnia. Results from structural studies suggest neuroanatomical alterations in primary insomnia, mostly in the hippocampus, anterior cingulate cortex and orbitofrontal cortex. However, these results are not well replicated across studies. A few magnetic resonance spectroscopy studies revealed abnormalities in neurotransmitter concentrations and bioenergetics in primary insomnia. The inconsistencies among neuroimaging findings on insomnia are likely due to clinical heterogeneity, differences in imaging and overall diversity of techniques and designs employed. Larger samples, replication, as well as innovative methodologies are necessary for the progression of this perplexing, yet promising area of research. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

  13. MR findings of brainstem injury

    Energy Technology Data Exchange (ETDEWEB)

    Park, Man Soo; Hwang, Woo Cheol; Park, Choong Ki [Hallym University College of Medicine, Seoul (Korea, Republic of); Suh, Dae Chul [University of Ulsan College of Medicine, Seoul (Korea, Republic of); Kim, Sang Joon [Dankook University of College of Medicine, Cheonan (Korea, Republic of)

    1995-02-15

    To analyze the characteristics of traumatic brainstem injury by CT and MR. CT and MR studies of 10 patients with traumatic brainstem lesion in MR were retrospectively reviewed, particularly attended to location, signal intensity and associated lesions. CT failed to depict 8 of 10 brainstem lesions. All lesions were detected in MR images with T2-weighted images showing higher detection rate (n = 10) (100%) than T1-weighted images (n = 3) (30%) or CT (n = 2) (20%). The brainstem lesions located in the dorsolateral aspects of the rostral brainstem (mid brain and upper pons) in 7 (70%) cases, in ventral aspects of rostral brain in 2 (20%) cases and in median portion of pons in 1 (10%) case. Corpus callosal (n = 5), lobar white matter (n = 5) diffuse axonal injury, and 2 hemorrhagic lesions in basal ganglia were the associated findings. MR imaging is more helpful than CT in the detection of brainstem injury, especially T2 weighted images. Primary brainstem lesions were typically located in the dorsolateral aspect of rostral brainstem (midbrain and upper pons). Corpus callosum and white matter lesions were frequently associated.

  14. Radiological findings in Wolfram syndrome

    International Nuclear Information System (INIS)

    Hadidy, Azmy M.; Jarrah, Nadim S.; Al-Till, Maha I.; Ajlouni, Kamal M.; El-Shanti, Haten E.

    2004-01-01

    To determine the precise radiologic findings in Wolfram syndrome (WFS) patients using objective techniques in order to better define the reference population for the clinicl evaluation. 16 patients (6 males, 10 female) with WFS found in 4 families were included in this study.14 patients with WFS-2 came from 3 families while 2 patients with EFS-1 came from one family. All patients were studied at Jordan University Hospital, Amman,Jordan from January 2001 to January 2003 by definite radiologic techniques as part of a thorough clinical comprehesive assesment. These incclude intravenous urography, abdominal and pelvic ultrasonography, barium meal, upper gastrointestinal endoscopy and magnetic resonance imaging with and without contrasts to the brain and the pituitary glands.5 of the female ptients had a small uterus. Spina bifida was found in 7, hydronephrosis in 9 and hydroureter in 5 patiets. Peptic ulcer was detected in 10 out of 14 available patients and helicobacter pylori in 7 out of 16 patients. Atrophy was detected was detected in all brains, 9 brain stems, 12 cerebellums and 14 optic tracts of all patients. The size of pituitary glands was variable. The particular radiological assesment of the patients with WFS proved that, urinary tract dialtation was detected in WFS-1and WFS-2 patients though all WFS-2 patients.No significant radiologic difference was between patients with WFS-1 and WFS-2. (author)

  15. Idiopathic polyhydramnios and postnatal findings.

    Science.gov (United States)

    Dorleijn, Desirée M J; Cohen-Overbeek, Titia E; Groenendaal, Floris; Bruinse, Hein W; Stoutenbeek, Philip

    2009-04-01

    Our objective was to investigate the outcome of neonates with idiopathic polyhydramnios in the first year after birth. All patients diagnosed in the Erasmus Medical Centre Rotterdam and the University Medical Centre Utrecht between January 2000 and April 2005 with idiopathic polyhydramnios were studied. The outcome variables included mode of delivery, pre-term delivery, birth weight, macrosomia, large-for-gestational-age (weight > p90), neonatal or infant mortality and infant morbidity at 1 year after delivery. These were related to antenatal findings, including the onset of polyhydramnios and ultrasonographic evidence of macrosomia (estimated fetal weight > p90). Polyhydramnios was diagnosed at a mean gestational age (+/- s.d.) of 31.0 +/- 4.9 weeks. The mean gestational age at birth (+/- s.d.) was 37.9 +/- 3.7 weeks. Macrosomia at birth was present in 25.3% (22/88). Sixty-three of 88 infants were in good health 1 year after birth; 20 infants had an abnormality and 5 children had died. Macrosomia and detection of polyhydramnios in the third trimester was associated significantly with a good outcome. In neonates with idiopathic polyhydramnios, abnormalities were detected during the first year of life in 28.4%. Detection of polyhydramnios in the second trimester and low or normal birth weight are risk factors for associated abnormalities.

  16. Radiologic findings of osteochondritis dissecans

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Jae Seung; Choi, Choong Gon; Kang, Heung Sik; Lee, Seon Kyu; Kim, Chu Wan [Seoul National University College of Medicine, Seoul (Korea, Republic of)

    1993-05-15

    To evaluate the radiographic characteristics of osteochondritis dissecans (OCD) and useful parameter for predicting mechanical stability, we retrospectively analysed 26 plain radiographic examinations and seven MR imagings in 28 cases of OCD in 24 patients. Typical radiologic findings were osteochondral defect with sclerotic rim of variable thickness and osteochondral fragment. Sites of osteochondral defect were medial (35.9%) or lateral (32%) femoral chondyle and medial (7.1%) or lateral (25%) side of talar dome. Sclerotic rim was seen in 24 cases (85%) and osteochondral fragments including nine loose bodies were seen in 21 cases (75%). The size of osteochondral defect with unstable fragment (average 2.05 cm) and loose body (2.04 cm) in the knee joint were similar to, but statistically larger than that with stable fragment (1.35 cm). All osteochondral defects were well visualized on MR images. Abnormalities of articular cartilage and effusion in the interface between the parent bone and fragment were seen in five cases of which there were confirmed three unstable cases arthroscopically. We concluded that size of defect may be a good parameter for predicting mechanical stability and MRI may be useful in the diagnosis of OCD and determining the methods of treatment.

  17. Radiologic findings of osteochondritis dissecans

    International Nuclear Information System (INIS)

    Kim, Jae Seung; Choi, Choong Gon; Kang, Heung Sik; Lee, Seon Kyu; Kim, Chu Wan

    1993-01-01

    To evaluate the radiographic characteristics of osteochondritis dissecans (OCD) and useful parameter for predicting mechanical stability, we retrospectively analysed 26 plain radiographic examinations and seven MR imagings in 28 cases of OCD in 24 patients. Typical radiologic findings were osteochondral defect with sclerotic rim of variable thickness and osteochondral fragment. Sites of osteochondral defect were medial (35.9%) or lateral (32%) femoral chondyle and medial (7.1%) or lateral (25%) side of talar dome. Sclerotic rim was seen in 24 cases (85%) and osteochondral fragments including nine loose bodies were seen in 21 cases (75%). The size of osteochondral defect with unstable fragment (average 2.05 cm) and loose body (2.04 cm) in the knee joint were similar to, but statistically larger than that with stable fragment (1.35 cm). All osteochondral defects were well visualized on MR images. Abnormalities of articular cartilage and effusion in the interface between the parent bone and fragment were seen in five cases of which there were confirmed three unstable cases arthroscopically. We concluded that size of defect may be a good parameter for predicting mechanical stability and MRI may be useful in the diagnosis of OCD and determining the methods of treatment

  18. Avascular Retinal Findings in a Child With Achondroplasia.

    Science.gov (United States)

    Hua, Hong-Uyen T; Tran, Kimberly D; Medina, Carlos A; Fallas, Brenda; Negron, Cathy; Berrocal, Audina M

    2017-03-01

    The authors present clinical and angiographic findings in a 12-year-old girl with achondroplasia who presented with bilateral retinal peripheral nonperfusion and unilateral rhegmatogenous retinal detachment, which has not been previously described in achondroplasia. This report contributes incremental knowledge regarding aberrant retinal vascular phenomena observed in pediatric disease states and implicates the possible role of mutations in the FGFR3 gene in peripheral vascular abnormalities. [Ophthalmic Surg Lasers Imaging Retina. 2017;48:272-274.]. Copyright 2017, SLACK Incorporated.

  19. Imaging reporter gene for monitoring gene therapy

    International Nuclear Information System (INIS)

    Beco, V. de; Baillet, G.; Tamgac, F.; Tofighi, M.; Weinmann, P.; Vergote, J.; Moretti, J.L.; Tamgac, G.

    2002-01-01

    Scintigraphic images can be obtained to document gene function at cellular level. This approach is presented here and the use of a reporter gene to monitor gene therapy is described. Two main ways are presented: either the use of a reporter gene coding for an enzyme the action of which will be monitored by radiolabeled pro-drug, or a cellular receptor gene, the action of which is documented by a radio labeled cognate receptor ligand. (author)

  20. Discovering implicit entity relation with the gene-citation-gene network.

    Directory of Open Access Journals (Sweden)

    Min Song

    Full Text Available In this paper, we apply the entitymetrics model to our constructed Gene-Citation-Gene (GCG network. Based on the premise there is a hidden, but plausible, relationship between an entity in one article and an entity in its citing article, we constructed a GCG network of gene pairs implicitly connected through citation. We compare the performance of this GCG network to a gene-gene (GG network constructed over the same corpus but which uses gene pairs explicitly connected through traditional co-occurrence. Using 331,411 MEDLINE abstracts collected from 18,323 seed articles and their references, we identify 25 gene pairs. A comparison of these pairs with interactions found in BioGRID reveal that 96% of the gene pairs in the GCG network have known interactions. We measure network performance using degree, weighted degree, closeness, betweenness centrality and PageRank. Combining all measures, we find the GCG network has more gene pairs, but a lower matching rate than the GG network. However, combining top ranked genes in both networks produces a matching rate of 35.53%. By visualizing both the GG and GCG networks, we find that cancer is the most dominant disease associated with the genes in both networks. Overall, the study indicates that the GCG network can be useful for detecting gene interaction in an implicit manner.

  1. Evaluating the consistency of gene sets used in the analysis of bacterial gene expression data

    Directory of Open Access Journals (Sweden)

    Tintle Nathan L

    2012-08-01

    Full Text Available Abstract Background Statistical analyses of whole genome expression data require functional information about genes in order to yield meaningful biological conclusions. The Gene Ontology (GO and Kyoto Encyclopedia of Genes and Genomes (KEGG are common sources of functionally grouped gene sets. For bacteria, the SEED and MicrobesOnline provide alternative, complementary sources of gene sets. To date, no comprehensive evaluation of the data obtained from these resources has been performed. Results We define a series of gene set consistency metrics directly related to the most common classes of statistical analyses for gene expression data, and then perform a comprehensive analysis of 3581 Affymetrix® gene expression arrays across 17 diverse bacteria. We find that gene sets obtained from GO and KEGG demonstrate lower consistency than those obtained from the SEED and MicrobesOnline, regardless of gene set size. Conclusions Despite the widespread use of GO and KEGG gene sets in bacterial gene expression data analysis, the SEED and MicrobesOnline provide more consistent sets for a wide variety of statistical analyses. Increased use of the SEED and MicrobesOnline gene sets in the analysis of bacterial gene expression data may improve statistical power and utility of expression data.

  2. Functional analysis of the molecular interactions of TATA box-containing genes and essential genes.

    Science.gov (United States)

    Bae, Sang-Hun; Han, Hyun Wook; Moon, Jisook

    2015-01-01

    Genes can be divided into TATA-containing genes and TATA-less genes according to the presence of TATA box elements at promoter regions. TATA-containing genes tend to be stress-responsive, whereas many TATA-less genes are known to be related to cell growth or "housekeeping" functions. In a previous study, we demonstrated that there are striking differences among four gene sets defined by the presence of TATA box (TATA-containing) and essentiality (TATA-less) with respect to number of associated transcription factors, amino acid usage, and functional annotation. Extending this research in yeast, we identified KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways that are statistically enriched in TATA-containing or TATA-less genes and evaluated the possibility that the enriched pathways are related to stress or growth as reflected by the individual functions of the genes involved. According to their enrichment for either of these two gene sets, we sorted KEGG pathways into TATA-containing-gene-enriched pathways (TEPs) and essential-gene-enriched pathways (EEPs). As expected, genes in TEPs and EEPs exhibited opposite results in terms of functional category, transcriptional regulation, codon adaptation index, and network properties, suggesting the possibility that the bipolar patterns in these pathways also contribute to the regulation of the stress response and to cell survival. Our findings provide the novel insight that significant enrichment of TATA-binding or TATA-less genes defines pathways as stress-responsive or growth-related.

  3. Using GeneReg to construct time delay gene regulatory networks

    Directory of Open Access Journals (Sweden)

    Qian Ziliang

    2010-05-01

    Full Text Available Abstract Background Understanding gene expression and regulation is essential for understanding biological mechanisms. Because gene expression profiling has been widely used in basic biological research, especially in transcription regulation studies, we have developed GeneReg, an easy-to-use R package, to construct gene regulatory networks from time course gene expression profiling data; More importantly, this package can provide information about time delays between expression change in a regulator and that of its target genes. Findings The R package GeneReg is based on time delay linear regression, which can generate a model of the expression levels of regulators at a given time point against the expression levels of their target genes at a later time point. There are two parameters in the model, time delay and regulation coefficient. Time delay is the time lag during which expression change of the regulator is transmitted to change in target gene expression. Regulation coefficient expresses the regulation effect: a positive regulation coefficient indicates activation and negative indicates repression. GeneReg was implemented on a real Saccharomyces cerevisiae cell cycle dataset; more than thirty percent of the modeled regulations, based entirely on gene expression files, were found to be consistent with previous discoveries from known databases. Conclusions GeneReg is an easy-to-use, simple, fast R package for gene regulatory network construction from short time course gene expression data. It may be applied to study time-related biological processes such as cell cycle, cell differentiation, or causal inference.

  4. Pollution! Find a STEM solution!

    Science.gov (United States)

    Takač, Danijela; Moćan, Marina

    2016-04-01

    Primary and secondary school Pantovčak is an innovative school in downtown Zagreb, Croatia. The school is involved in many projects concerning STEM education. Pollution! Find a STEM solution! is a two year long cross-curricular project that grew out of identified need to develop STEM and ICT skills more. Pisa results make evident that students' knowledge is poor and motivation for math and similar subjects is low. Implying priorities of European Commission, like e-learning, raises motivation and also develops basic skills and improves knowledge in science, math, physic, ICT. Main objectives are to increase students' interest in STEM education and careers and introduce them to all available new trends in technology, engineering and science in their region by visiting clean technology industries and strengthening links with them, to introduce some future digital jobs and prepare students for rapid technological changes by integrating ICT into classroom practice more, to highlight the importance of global environmental issues and improve the knowledge in the areas of sustainable development and renewable energy, to develop collaborative partnership between schools and the wider community in formal, non-formal and informal learning, to support multilingualism by publishing Open Educational Resources in 8 different languages and to strengthen the professional profile of the teaching profession. The project brings together 231 teachers and 2729 students from five different European countries in learning to think globally and work on activities that contribute to the community's well-being. There are altogether 33 activities, divided in 4 categories. STEM activities are focused on students building the devices for measuring air, light and noise pollution in their school and homes. They use the scientific method to analyze the data and compare the results with their peers to find a solution. Eskills, digital literacy and digital jobs are focused on introducing career

  5. MEMS direction finding acoustic sensor

    Science.gov (United States)

    Karunasiri, Gamani; Alves, Fabio; Swan, William

    2017-06-01

    Conventional directional sound sensing systems employ an array of spatially separated microphones to achieve directivity. However, there are insects such as the Ormia ochracea fly that can determine the direction of sound using a miniature hearing organ much smaller than the wavelength of sound it detects. The fly's eardrums are coupled mechanically with a separation of only 0.5 mm and yet have a remarkable sensitivity to the direction of sound. The MEMS based sensor mimicking the fly's hearing system was fabricated using an SOI substrate with a 25 μm device layer. The sensor consists of two 1.5 mm x1.6 mm wings connected in the middle by a 2.7 mm x 30 μm bridge. The entire structure is connected to the substrate by two torsional legs at the center. The frequency response of the sensor showed two resonance frequencies at approximately 1.1 kHz (rocking) and 1.5 kHz (bending). The resonance at 1.1 kHz is due to rocking of the wings by twisting the legs and the other at 1.5 kHz is due to bending of the bridge. The response of the sensor was probed electronically using comb finger capacitors integrated to the edges of the wings and with the help of an MS3110 chip. A peak output voltage of about 9V/Pa was measured for sound incident normal to the device at the resonance frequency of the bending mode. The bearing of the incident sound under these conditions could be determined to within a few degrees. These findings indicate the potential use of the MEMS sensor to locate sound sources with high accuracy.

  6. Post-therapeutic imaging findings

    Energy Technology Data Exchange (ETDEWEB)

    Pollice, Saverio, E-mail: saveriopollice@hotmail.it [Department of Radiology and Neuroradiology, “L. Bonomo Hospital”, 76123 Andria, BT (Italy); Muto, Mario, E-mail: mutomar@tiscali.it [Department of Neuroradiology, “Cardarelli Hospital”, Naples (Italy); Scarabino, Tommaso, E-mail: tscarabino@hotmail.com [Department of Radiology and Neuroradiology, “L. Bonomo Hospital”, 76123 Andria, BT (Italy)

    2015-05-15

    Highlights: • This study is the result of collaboration between neuroradiologists and neurosurgeons. • Comparison between neuroimaging techniques to better evaluate the complications after treatment of the spin. • Evaluation of the imaging features of complications and definition of follow-up. - Abstract: Any surgical approach modifies the normal anatomical and functional arrangement of the segmental spine which is aimed, therefore image interpretation cannot ignore a correct set of knowledge in the field of anatomy, pathophysiology, drug compliance, interventional radiology and surgery. Neuroradiological imaging has an important role before surgery to direct the surgeon or interventional radiologist during the operation, both in post-surgery, where imaging examination can rightly evaluate properties and effects of the treatment and can detect potential complications as infections, abscess, bleeding, exuberant scar, mobilization and rupture of devices. The available methods of imaging are the X-rays (XR) made at least in two projections, Computed Tomography (CT) with MPR (multiplanar) and VR (volume rendering) reconstruction, and Magnetic Resonance (MR), often performed before and after contrast media injection. Imaging assessment of spine after surgery is complex and depends upon several factors, including surgical procedures and disease for which it was performed; biomechanical of the underlying cortical and cancellous bone findings; conditions of muscles, intervertebral disk and ligaments; time since surgery procedures; duration and nature of the post-surgical syndrome. Depending upon several factors, one or a combination of complementary imaging modalities (X-rays, Computed Tomography, Magnetic Resonance) may be required to evaluate effectiveness of the treatment; to demonstrate any clinically relevant abnormality at the treated region and adjacent structures (complications such as inflammation, abscesses, bleeding and misplacement of the device); to

  7. Skin findings in Williams syndrome.

    Science.gov (United States)

    Kozel, Beth A; Bayliss, Susan J; Berk, David R; Waxler, Jessica L; Knutsen, Russell H; Danback, Joshua R; Pober, Barbara R

    2014-09-01

    Previous examination in a small number of individuals with Williams syndrome (also referred to as Williams-Beuren syndrome) has shown subtly softer skin and reduced deposition of elastin, an elastic matrix protein important in tissue recoil. No quantitative information about skin elasticity in individuals with Williams syndrome is available; nor has there been a complete report of dermatologic findings in this population. To fill this knowledge gap, 94 patients with Williams syndrome aged 7-50 years were recruited as part of the skin and vascular elasticity (WS-SAVE) study. They underwent either a clinical dermatologic assessment by trained dermatologists (2010 WSA family meeting) or measurement of biomechanical properties of the skin with the DermaLab™ suction cup (2012 WSA family meeting). Clinical assessment confirmed that soft skin is common in this population (83%), as is premature graying of the hair (80% of those 20 years or older), while wrinkles (92%), and abnormal scarring (33%) were detected in larger than expected proportions. Biomechanical studies detected statistically significant differences in dP (the pressure required to lift the skin), dT (the time required to raise the skin through a prescribed gradient), VE (viscoelasticity), and E (Young's modulus) relative to matched controls. The RT (retraction time) also trended longer but was not significant. The biomechanical differences noted in these patients did not correlate with the presence of vascular defects also attributable to elastin insufficiency (vascular stiffness, hypertension, and arterial stenosis) suggesting the presence of tissue specific modifiers that modulate the impact of elastin insufficiency in each tissue. © 2014 Wiley Periodicals, Inc.

  8. The constancy of gene conservation across divergent bacterial orders

    Directory of Open Access Journals (Sweden)

    Ackermann Martin

    2009-01-01

    Full Text Available Abstract Background Orthologous genes are frequently presumed to perform similar functions. However, outside of model organisms, this is rarely tested. One means of inferring changes in function is if there are changes in the level of gene conservation and selective constraint. Here we compare levels of gene conservation across three bacterial groups to test for changes in gene functionality. Findings The level of gene conservation for different orthologous genes is highly correlated across clades, even for highly divergent groups of bacteria. These correlations do not arise from broad differences in gene functionality (e.g. informational genes vs. metabolic genes, but instead seem to result from very specific differences in gene function. Furthermore, these functional differences appear to be maintained over very long periods of time. Conclusion These results suggest that even over broad time scales, most bacterial genes are under a nearly constant level of purifying selection, and that bacterial evolution is thus dominated by selective and functional stasis.

  9. Identification of Human HK Genes and Gene Expression Regulation Study in Cancer from Transcriptomics Data Analysis

    Science.gov (United States)

    Zhang, Zhang; Liu, Jingxing; Wu, Jiayan; Yu, Jun

    2013-01-01

    The regulation of gene expression is essential for eukaryotes, as it drives the processes of cellular differentiation and morphogenesis, leading to the creation of different cell types in multicellular organisms. RNA-Sequencing (RNA-Seq) provides researchers with a powerful toolbox for characterization and quantification of transcriptome. Many different human tissue/cell transcriptome datasets coming from RNA-Seq technology are available on public data resource. The fundamental issue here is how to develop an effective analysis method to estimate expression pattern similarities between different tumor tissues and their corresponding normal tissues. We define the gene expression pattern from three directions: 1) expression breadth, which reflects gene expression on/off status, and mainly concerns ubiquitously expressed genes; 2) low/high or constant/variable expression genes, based on gene expression level and variation; and 3) the regulation of gene expression at the gene structure level. The cluster analysis indicates that gene expression pattern is higher related to physiological condition rather than tissue spatial distance. Two sets of human housekeeping (HK) genes are defined according to cell/tissue types, respectively. To characterize the gene expression pattern in gene expression level and variation, we firstly apply improved K-means algorithm and a gene expression variance model. We find that cancer-associated HK genes (a HK gene is specific in cancer group, while not in normal group) are expressed higher and more variable in cancer condition than in normal condition. Cancer-associated HK genes prefer to AT-rich genes, and they are enriched in cell cycle regulation related functions and constitute some cancer signatures. The expression of large genes is also avoided in cancer group. These studies will help us understand which cell type-specific patterns of gene expression differ among different cell types, and particularly for cancer. PMID:23382867

  10. EasyGene – a prokaryotic gene finder that ranks ORFs by statistical significance

    DEFF Research Database (Denmark)

    Larsen, Thomas Schou; Krogh, Anders Stærmose

    2003-01-01

    is the expected number of ORFs in one megabase of random sequence at the same significance level or better, where the random sequence has the same statistics as the genome in the sense of a third order Markov chain.Conclusions: The result is a flexible gene finder whose overall performance matches or exceeds......Background: Contrary to other areas of sequence analysis, a measure of statistical significance of a putative gene has not been devised to help in discriminating real genes from the masses of random Open Reading Frames (ORFs) in prokaryotic genomes. Therefore, many genomes have too many short ORFs...... annotated as genes.Results: In this paper, we present a new automated gene-finding method, EasyGene, which estimates the statistical significance of a predicted gene. The gene finder is based on a hidden Markov model (HMM) that is automatically estimated for a new genome. Using extensions of similarities...

  11. Radiologic findings of thoracic trauma

    Directory of Open Access Journals (Sweden)

    Akgul Ozmen C

    2017-08-01

    Full Text Available Cihan Akgul Ozmen,1 Serdar Onat,2 Delal Aycicek3 1Department of Radiology, 2Department of Chest Surgery, Dicle University School of Medicine, Diyarbakir, 3Radiology Unit, Siirt State Hospital, Siirt, Turkey Introduction: Chest trauma may be blunt or penetrating and the chest is the third most common trauma region. It is a significant cause of mortality. Multidetector computed tomography (MDCT has been an increasingly used method to evaluate chest trauma because of its high success in detecting tissue and organ injuries. Herein, we aimed to present MDCT findings in patients with blunt and penetrating chest trauma admitted to our department. Methods: A total of 240 patients admitted to the emergency department of our hospital between April 2012 and July 2013 with a diagnosis of chest trauma who underwent MDCT evaluations were included. Most of the patients were male (83.3% and victims of a blunt chest trauma. The images were analyzed with respect to the presence of fractures of bony structures, hemothorax, pneumothorax, mediastinal organ injury, and pulmonary and vascular injuries. Results: MDCT images of the 240 patients yielded a prevalence of 41.7% rib fractures, 11.2% scapular fractures, and 7.5% clavicle fractures. The prevalence of thoracic vertebral fracture was 13.8% and that of sternal fracture was 3.8%. The prevalence of hemothorax, pneumothorax, pneumomediastinum, and subcutaneous emphysema was 34.6%, 62.1%, 9.6%, and 35.4%, respectively. The prevalence of rib, clavicle, and thoracic vertebral fractures and pulmonary contusion was higher in the blunt trauma group, whereas the prevalence of hemothorax, subcutaneous emphysema, diaphragmatic injury, and other vascular lacerations was significantly higher in the penetrating trauma group than in the blunt trauma group (p<0.05. Conclusion: MDCT images may yield a high prevalence of fracture of bony structures, soft tissue lacerations, and vascular lesions, which should be well understood by

  12. Arteriogrpahic findings of Buerger's disease

    International Nuclear Information System (INIS)

    Oh, Ki Kun; Suh, Jung Ho; Park, Chang Yun; Choi, Byung Sook

    1973-01-01

    Buerger's patients were male and the range of age is 20-50 years at the onset of symptoms. 2. Almost of them (85.7%) has the virtual history of invariable association with use of nicotine. 3. They included initial appearance of symptoms of coldness (75%), pain (64%), ulcer formation (54%), cyanosis (50%) and intermittent claudication. 4. In our series, the clinically involved abnormal pulsations were most commonly at dorsalis pedisartery (51%) and polplital artery (30%). 5. The arthrographic findings in TAO in 28 our series, define the characteristic pattern of vascular occlusion, diffuse arterial narrowing , and arterial segmental occlusion, most commonly. The most frequent occluded sites are superficial femoral artery (41.2%) and popliteal artery (17.7%), and shows the actual vascular occlusions were higher in level than clinical site. 6. The arteries above the occluded site were regular in size and shape, however, often shows vascular corrugation which support the evidence of TAO, not AO. 7. Collaterals frequently had a corkscrew configurations proximally and a tree-root appearance distally

  13. Can Radio Telescopes Find Axions?

    Science.gov (United States)

    Kohler, Susanna

    2017-08-01

    In the search for dark matter, the most commonly accepted candidates are invisible, massive particles commonly referred to as WIMPs. But as time passes and we still havent detected WIMPs, alternative scenarios are becoming more and more appealing. Prime among these is the idea of axions.A Bizarre ParticleThe Italian PVLAS is an example of a laboratory experiment that attempted to confirm the existence of axions. [PVLAS]Axions are a type of particle first proposed in the late 1970s. These theorized particles arose from a new symmetry introduced to solve ongoing problems with the standard model for particle physics, and they were initially predicted to have more than a keV in mass. For this reason, their existence was expected to be quickly confirmed by particle-detector experiments yet no detections were made.Today, after many unsuccessful searches, experiments and theory tell us that if axions exist, their masses must lie between 10-610-3 eV. This is minuscule an electrons mass is around 500,000 eV, and even neutrinos are on the scale of a tenth of an eV!But enough of anything, even something very low-mass, can weigh a lot. If they are real, then axions were likely created in abundance during the Big Bang and unlike heavier particles, they cant decay into anything lighter, so we would expect them all to still be around today. Our universe could therefore be filled with invisible axions, potentially providing an explanation for dark matter in the form of many, many tiny particles.Artists impression of the central core of proposed Square Kilometer Array antennas. [SKA/Swinburne Astronomy Productions]How Do We Find Them?Axions barely interact with ordinary matter and they have no electric charge. One of the few ways we can detect them is with magnetic fields: magnetic fields can change axions to and from photons.While many studies have focused on attempting to detect axions in laboratory experiments, astronomy provides an alternative: we can search for cosmological

  14. Finding time, stopping the frenzy.

    Science.gov (United States)

    Perlow, L A

    1998-08-01

    While the deleterious consequences of long hours of work for individuals, families and communities have previously been documented, the assumption that long hours are necessary to get the work done, especially in a world where speed is becoming increasingly critical to corporate success, has prompted little challenge. So Leslie Perlow, an assistant professor of business at the University of Michigan, Ann Arbor, set out to explore the necessity for the seemingly endless workdays that so many postindustrial settings require. Her study of a group of software engineers at a Fortune 500 company--identified only as the Ditto Corp--is detailed in her book, Finding Time: How Corporations, Individuals, and Families Can Benefit from New Work Practices (Cornell University Press, 1997). Perlow's research reveals a "sad and all too common tale" of workers harried by competing demands, frequent interruptions and shifting deadlines. To meet the firm's expectations, the engineers she studied sacrificed home life, focused on individual tasks to the detriment of group goals and, in many cases, eventually lost any enthusiasm they'd had for working for the company. There has been some recognition that stress and burnout may be bad for a corporation as employees become less committed, decide to leave or get fired and that this kind of turnover can hurt the firm in the longer term. But Perlow documented the additional, and quite significant, shorter-term costs to the corporation of the current way of using time at work. What she found was a "vicious time cycle:" Time pressures led to a crisis mentality, which led to "individual heroics." That is, I'll do whatever it takes to do my job--even if it means interrupting you while you try to do yours. For the engineers Perlow studied, the lack of helping, the constant interruptions and the perpetual crises--clearly illustrated by the daily log that appears on page 34--made it harder to develop products. Ultimately, they worked long hours to

  15. Application of Gene Shaving and Mixture Models to Cluster Microarray Gene Expression Data

    Directory of Open Access Journals (Sweden)

    S. Wen

    2007-01-01

    Full Text Available Researchers are frequently faced with the analysis of microarray data of a relatively large number of genes using a small number of tissue samples. We examine the application of two statistical methods for clustering such microarray expression data: EMMIX-GENE and GeneClust. EMMIX-GENE is a mixture-model based clustering approach, designed primarily to cluster tissue samples on the basis of the genes. GeneClust is an implementation of the gene shaving methodology, motivated by research to identify distinct sets of genes for which variation in expression could be related to a biological property of the tissue samples. We illustrate the use of these two methods in the analysis of Affymetrix oligonucleotide arrays of well-known data sets from colon tissue samples with and without tumors, and of tumor tissue samples from patients with leukemia. Although the two approaches have been developed from different perspectives, the results demonstrate a clear correspondence between gene clusters produced by GeneClust and EMMIX-GENE for the colon tissue data. It is demonstrated, for the case of ribosomal proteins and smooth muscle genes in the colon data set, that both methods can classify genes into co-regulated families. It is further demonstrated that tissue types (tumor and normal can be separated on the basis of subtle distributed patterns of genes. Application to the leukemia tissue data produces a division of tissues corresponding closely to the external classification, acute myeloid leukemia (AML and acute lymphoblastic leukaemia (ALL, for both methods. In addition, we also identify genes specifi c for the subgroup of ALL-T cell samples. Overall, we find that the gene shaving method produces gene clusters at great speed; allows variable cluster sizes and can incorporate partial or full supervision; and finds clusters of genes in which the gene expression varies greatly over the tissue samples while maintaining a high level of coherence between the

  16. Abnormal gene expression and gene fusion in lung adenocarcinoma with high-throughput RNA sequencing.

    Science.gov (United States)

    Yang, Z-H; Zheng, R; Gao, Y; Zhang, Q; Zhang, H

    2014-02-01

    To explore the universal law of the abnormal gene expression and the structural variation of genes related to lung adenocarcinoma, the gene expression profile of GSE37765 were downloaded from Gene Expression Omnibus database. The differentially expressed genes (DEGs) were analyzed with t-test and NOISeq tool, and the core DEGs were screened out by combining with another RNA-seq data containing totally 77 pairs of samples in 77 patients with lung adenocarcinoma. Moreover, the functional annotation of the core DEGs was performed by using the Database for Annotation Visualization and Integrated Discovery following selection of oncogene and tumor suppressor by combining with tumor suppressor genes and Cancer Genes database, and motif-finding of core DEGs was performed with motif-finding algorithm Seqpos. We also used Tophat-fusion tool to further explore the fusion genes. In total, 850 downregulated DEGs and 206 upregulated DEGs were screened out in lung adenocarcinoma tissues. Next, we selected 543 core DEGs, including 401 downregulated and 142 upregulated genes, and vasculature development (P=1.89E-06) was significantly enriched among downregulated core genes, as well as mitosis (P=6.26E-04) enriched among upregulated core genes. On the basis of the cellular localization analysis of core genes, wnt-1-induced secreted protein 1 (WISP1) and receptor (G protein-coupled) activity modifying protein 1 (RAMP1) identified mainly located in extracellular region and extracellular space. We also screened one oncogene, v-myb avian myeloblastosis viral oncogene homolog-like 2 (MYBL2). Moreover, transcription factor GATA2 was mined by motif-finding analysis. Finally, four fusion genes belonged to the human leukocyte antigen (HLA) family. WISP1, RAMP1, MYBL2 and GATA2 could be potential targets of treatment for lung adenocarcinoma and the fusion of HLA family genes might have important roles in lung adenocarcinoma.

  17. How Genes Evolve

    Indian Academy of Sciences (India)

    which they are found e.g. the evolution of the gene coding for the protein cytochrome-C which is part ofthe respiratory apparatus. On the contrary, paralogous genes are descendants of a duplicated gene. Paralogous genes therefore evolve within the same species as well as in different species e.g. genes coding for alpha ...

  18. Localizing genes using linkage disequilibrium in plants: integrating ...

    African Journals Online (AJOL)

    GREGO

    2007-03-19

    Mar 19, 2007 ... Finding genes controlling quantitative traits will aid molecular breeding for crops and livestock with superior yields, growth rates, and evolutionary potential. Such genes can be located using the candidate gene approach, genome wide scans, or by within family mapping. Linkage disequilibrium.

  19. Mutational and Evolutionary Analyses of Bovine Reprimo Gene ...

    African Journals Online (AJOL)

    It can therefore be concluded that bovine RPRM gene contained 4 transition mutations and 5 indels that can be used in marker assisted selection. Evolutionary findings also demonstrated the existence of a divergent evolution between bovine RPRM gene and RPRM gene of fishes and frog. Keywords: Identity, phylogeny ...

  20. Prevalence of thrombophilic gene polymorphisms (FVL G1691A and ...

    African Journals Online (AJOL)

    Background: Inherited thrombophilia may be caused by mutations, polymorphisms in a variety of genes mainly involved in haemostatic pathways. Aim of the study, was to find the prevalence of thrombophilic gene factor V Leiden (FVL) and methylene tetrahydrofolate reductase (MTHFR) gene polymorphism in patients with ...

  1. Prevalence of thrombophilic gene polymorphisms (FVL G1691A and ...

    African Journals Online (AJOL)

    Hamdia Ezzat

    2014-02-22

    Feb 22, 2014 ... Abstract Background: Inherited thrombophilia may be caused by mutations, polymorphisms in a variety of genes mainly involved in haemostatic pathways. Aim of the study, was to find the prevalence of thrombophilic gene factor V Leiden (FVL) and methylene tetrahydrofolate reductase (MTHFR) gene ...

  2. On the origins of Mendelian disease genes in man: the impact of gene duplication.

    Science.gov (United States)

    Dickerson, Jonathan E; Robertson, David L

    2012-01-01

    Over 3,000 human diseases are known to be linked to heritable genetic variation, mapping to over 1,700 unique genes. Dating of the evolutionary age of these disease-associated genes has suggested that they have a tendency to be ancient, specifically coming into existence with early metazoa. The approach taken by past studies, however, assumes that the age of a disease is the same as the age of its common ancestor, ignoring the fundamental contribution of duplication events in the evolution of new genes and function. Here, we date both the common ancestor and the duplication history of known human disease-associated genes. We find that the majority of disease genes (80%) are genes that have been duplicated in their evolutionary history. Periods for which there are more disease-associated genes, for example, at the origins of bony vertebrates, are explained by the emergence of more genes at that time, and the majority of these are duplicates inferred to have arisen by whole-genome duplication. These relationships are similar for different disease types and the disease-associated gene's cellular function. This indicates that the emergence of duplication-associated diseases has been ongoing and approximately constant (relative to the retention of duplicate genes) throughout the evolution of life. This continued until approximately 390 Ma from which time relatively fewer novel genes came into existence on the human lineage, let alone disease genes. For single-copy genes associated with disease, we find that the numbers of disease genes decreases with recency. For the majority of duplicates, the disease-associated mutation is associated with just one of the duplicate copies. A universal explanation for heritable disease is, thus, that it is merely a by-product of the evolutionary process; the evolution of new genes (de novo or by duplication) results in the potential for new diseases to emerge.

  3. Identifying novel genes contributing to asthma pathogenesis

    NARCIS (Netherlands)

    Holloway, John W.; Koppelman, Gerard H.

    Purpose of review To illustrate recent examples of novel asthma genes such as those encoding G-protein-coupled receptor for asthma susceptibility, filaggrin and tenascin-C, and to describe the process that is needed to translate these findings to the clinic. Recent findings Many hundreds of studies

  4. Gene bookmarking: keeping the pages open.

    Science.gov (United States)

    Sarge, Kevin D; Park-Sarge, Ok-Kyong

    2005-11-01

    'Gene bookmarking' is a mechanism of epigenetic memory that functions to transmit through mitosis the pattern of active genes and/or genes that can be activated to daughter cells. It is thought that, at a point before mitosis, genes that exist in an open, transcriptionally competent state are bound by proteins or marked by some kind of modification event. This is thought to facilitate the assembly of transcription complexes on the promoters in early G1, thereby ensuring that daughter cells have the same pattern of gene expression as the cell from which they derived. Little is known, however, about these 'bookmarking factors' and modifications or the mechanisms by which they mediate the transmission of transcriptional competence after mitosis is complete. Recent findings have provided new insights into the mechanisms, regulation and biological importance of gene bookmarking in eukaryotic cell function.

  5. A novel swarm intelligence algorithm for finding DNA motifs.

    Science.gov (United States)

    Lei, Chengwei; Ruan, Jianhua

    2009-01-01

    Discovering DNA motifs from co-expressed or co-regulated genes is an important step towards deciphering complex gene regulatory networks and understanding gene functions. Despite significant improvement in the last decade, it still remains one of the most challenging problems in computational molecular biology. In this work, we propose a novel motif finding algorithm that finds consensus patterns using a population-based stochastic optimisation technique called Particle Swarm Optimisation (PSO), which has been shown to be effective in optimising difficult multidimensional problems in continuous domains. We propose to use a word dissimilarity graph to remap the neighborhood structure of the solution space of DNA motifs, and propose a modification of the naive PSO algorithm to accommodate discrete variables. In order to improve efficiency, we also propose several strategies for escaping from local optima and for automatically determining the termination criteria. Experimental results on simulated challenge problems show that our method is both more efficient and more accurate than several existing algorithms. Applications to several sets of real promoter sequences also show that our approach is able to detect known transcription factor binding sites, and outperforms two of the most popular existing algorithms.

  6. Imaging gene expression in gene therapy

    International Nuclear Information System (INIS)

    Wiebe, Leonard I.

    1997-01-01

    Full text. Gene therapy can be used to introduce new genes, or to supplement the function of indigenous genes. At the present time, however, there is non-invasive test to demonstrate efficacy of the gene transfer and expression processes. It has been postulated that scintigraphic imaging can offer unique information on both the site at which the transferred gene is expressed, and the degree of expression, both of which are critical issue for safety and clinical efficacy. Many current studies are based on 'suicide gene therapy' of cancer. Cells modified to express these genes commit metabolic suicide in the presence of an enzyme encoded by the transferred gene and a specifically-convertible pro drug. Pro drug metabolism can lead to selective metabolic trapping, required for scintigraphy. Herpes simplex virus type-1 thymidine kinase (H S V-1 t k + ) has been use for 'suicide' in vivo tumor gene therapy. It has been proposed that radiolabelled nucleosides can be used as radiopharmaceuticals to detect H S V-1 t k + gene expression where the H S V-1 t k + gene serves a reporter or therapeutic function. Animal gene therapy models have been studied using purine-([ 18 F]F H P G; [ 18 F]-A C V), and pyrimidine- ([ 123 / 131 I]I V R F U; [ 124 / 131I ]) antiviral nucleosides. Principles of gene therapy and gene therapy imaging will be reviewed and experimental data for [ 123 / 131I ]I V R F U imaging with the H S V-1 t k + reporter gene will be presented

  7. Genes, evolution and intelligence.

    Science.gov (United States)

    Bouchard, Thomas J

    2014-11-01

    I argue that the g factor meets the fundamental criteria of a scientific construct more fully than any other conception of intelligence. I briefly discuss the evidence regarding the relationship of brain size to intelligence. A review of a large body of evidence demonstrates that there is a g factor in a wide range of species and that, in the species studied, it relates to brain size and is heritable. These findings suggest that many species have evolved a general-purpose mechanism (a general biological intelligence) for dealing with the environments in which they evolved. In spite of numerous studies with considerable statistical power, we know of very few genes that influence g and the effects are very small. Nevertheless, g appears to be highly polygenic. Given the complexity of the human brain, it is not surprising that that one of its primary faculties-intelligence-is best explained by the near infinitesimal model of quantitative genetics.

  8. One gene, many phenotypes

    Directory of Open Access Journals (Sweden)

    Prasun P

    2007-01-01

    Full Text Available "Phenotype" is the visible or quantifiable effect of the expression of a gene, whereas the specific genetic constitution responsible for a phenotype is called "genotype". It was hoped that phenotype could be accurately predicted if the genotype could be characterized. But, the relationship between the genotype and phenotype is not straightforward. Similar genetic lesions can have entirely different phenotypes. In recent years, there has been tremendous progress in the understanding of the genetic basis of diseases. The extent to which it will be possible to relate findings at the DNA level to the clinical phenotype is difficult to delineate on many occasions. The elucidation of mechanisms underlying genotype-phenotype discrepancies is important as it will influence the use of DNA-based tests in the diagnosis, therapy and counseling of individuals affected with genetic disorders. This issue is pertinent to almost every aspect of medical practice and research in this post-genome era. In this article, we have tried to summarize those factors which are responsible for varied manifestations of lesion(s in a single gene.

  9. Fusion genes in leukemia: an emerging network.

    Science.gov (United States)

    Bohlander, S K

    2000-01-01

    The molecular analysis of recurring chromosome rearrangements, especially of translocations and inversions, has provided us with valuable insight into the pathogenesis of hematological malignancies. Many translocations result in the fusion of genes located at the translocation breakpoints. In recent years we have witnessed a rapid rise in the number of chromosome translocations in leukemias being characterized at the molecular level. However, the number of genes being newly identified as translocation fusion genes has not risen at the same pace. This is due to the fact that several genes are involved in more than one translocation forming fusion genes with a number of other partner genes. Not only does one find star-shaped topologies, with one gene forming fusions with several others (e.g. ETV6/PDGFRB, ETV6/JAK2, ETV6/ABL etc.), but also networks connecting several genes with more than one fusion partner (e.g. ETV6/RUNX1 (AML1), RUNX1/CBFA2T1 (ETO), ETV6/EVI1, RUNX1/EVI1, ETV6/ABL, BCR/ABL). The emergence of such networks with the "recycling" of genes in new fusion combinations suggests that there is a rather limited number of genes which can be altered to cause leukemia. Copyright 2001 S. Karger AG, Basel

  10. The structure of an unusual leghemoglobin gene from soybean

    DEFF Research Database (Denmark)

    Wiborg, O; Hyldig-Nielsen, J J; Jensen, E O

    1983-01-01

    A clone containing an unusual leghemoglobin (Lb) gene was isolated from a soybean DNA library present in Charon 4A phage. DNA sequence analysis revealed that the isolated Lb gene has three intervening sequences (IVS-1, IVS-2 and IVS-3) located in the same positions as those found in other Lb genes....... Due to a large increase of IVS-2 and IVS-3, the isolated Lb gene is about twice the size of a normal Lb gene. The coding sequence derived from the DNA sequence corresponds to no known soybean Lb and attempts to find a corresponding mRNA failed. In addition, the 5'-flanking sequence of the Lb gene...

  11. Symbiotic and nonsymbiotic hemoglobin genes of Casuarina glauca

    DEFF Research Database (Denmark)

    Jacobsen-Lyon, K; Jensen, Erik Østergaard; Jørgensen, Jan-Elo

    1995-01-01

    Casuarina glauca has a gene encoding hemoglobin (cashb-nonsym). This gene is expressed in a number of plant tissues. Casuarina also has a second family of hemoglobin genes (cashb-sym) expressed at a high level in the nodules that Casuarina forms in a nitrogen-fixing symbiosis with the actinomycete...... of the Casuarina gene. The finding that the nonsymbiotic Casuarina gene is also correctly expressed in L. corniculatus suggests to us that a comparable non-symbiotic hemoglobin gene will be found in legume species. Udgivelsesdato: 1995-Feb...

  12. Genetic determinants of depression: Recent findings and future directions

    Science.gov (United States)

    Dunn, Erin C.; Brown, Ruth C.; Dai, Yael; Rosand, Jonathan; Nugent, Nicole R.; Amstadter, Ananda B.; Smoller, Jordan W.

    2014-01-01

    Depression is one of the most prevalent, disabling, and costly mental health conditions in the United States. One promising avenue for preventing depression and informing its clinical treatment lies in uncovering both the genetic and environmental determinants of the disorder as well as their interaction (i.e. gene-environment intervention; GxE). The overarching goal of this review paper is to translate recent findings from studies of genetic association and GxE related to depression, particularly for readers without in-depth knowledge of genetics or genetic methods. This review is organized into three major sections. In the first section, we summarize what is currently known about the genetic determinants of depression, focusing on findings from genome-wide association studies (GWAS). In the second section, we review findings from studies of GxE, which seek to simultaneously examine the role of genes and exposure to specific environments or experiences in the etiology of depression. In the third section, we describe the challenges to genetic discovery in depression and promising strategies for making progress. PMID:25563565

  13. Fusion gene microarray reveals cancer type-specificity among fusion genes.

    Science.gov (United States)

    Løvf, Marthe; Thomassen, Gard O S; Bakken, Anne Cathrine; Celestino, Ricardo; Fioretos, Thoas; Lind, Guro E; Lothe, Ragnhild A; Skotheim, Rolf I

    2011-05-01

    Detection of fusion genes for diagnostic purposes and as a guide to treatment is well-established in hematological malignancies, and the prevalence of fusion genes in epithelial cancers is also increasingly appreciated. To study whether established fusion genes are present within additional cancer types, we have used an updated version of our fusion gene microarray in a systematic survey of reported fusion genes in multiple cancer types. We assembled a comprehensive database of published fusion genes, including those reported only in individual studies and samples, and fusion genes resulting from deep sequencing of cancer genomes and transcriptomes. From the total set of 548 fusion genes, we designed 599,839 oligonucleotides, targeting both chimeric transcript junctions as well as sequences internal to each of the fusion gene partners. We investigated the presence of fusion genes in a series of 67 cell lines representing 15 different cancer types. Data from ten leukemia cell lines with known fusion gene status were used to develop an automated scoring algorithm, and in five cell lines the correct fusion gene was the top scoring hit, and one came second. Two additional fusion genes, BCAS4-BCAS3 in the MCF-7 breast cancer cell line and CCDC6-RET in the TPC-1 thyroid cancer cell line were validated as true positive fusion transcripts. However, these fusion genes were not new to these cancer types, and none of 548 fusion genes were identified from a novel cancer type. We therefore find it unlikely that the assayed fusion genes are commonly present across multiple cancer types. 2011 Wiley-Liss, Inc.

  14. A role for gene duplication and natural variation of gene expression in the evolution of metabolism.

    Directory of Open Access Journals (Sweden)

    Daniel J Kliebenstein

    Full Text Available BACKGROUND: Most eukaryotic genomes have undergone whole genome duplications during their evolutionary history. Recent studies have shown that the function of these duplicated genes can diverge from the ancestral gene via neo- or sub-functionalization within single genotypes. An additional possibility is that gene duplicates may also undergo partitioning of function among different genotypes of a species leading to genetic differentiation. Finally, the ability of gene duplicates to diverge may be limited by their biological function. METHODOLOGY/PRINCIPAL FINDINGS: To test these hypotheses, I estimated the impact of gene duplication and metabolic function upon intraspecific gene expression variation of segmental and tandem duplicated genes within Arabidopsis thaliana. In all instances, the younger tandem duplicated genes showed higher intraspecific gene expression variation than the average Arabidopsis gene. Surprisingly, the older segmental duplicates also showed evidence of elevated intraspecific gene expression variation albeit typically lower than for the tandem duplicates. The specific biological function of the gene as defined by metabolic pathway also modulated the level of intraspecific gene expression variation. The major energy metabolism and biosynthetic pathways showed decreased variation, suggesting that they are constrained in their ability to accumulate gene expression variation. In contrast, a major herbivory defense pathway showed significantly elevated intraspecific variation suggesting that it may be under pressure to maintain and/or generate diversity in response to fluctuating insect herbivory pressures. CONCLUSION: These data show that intraspecific variation in gene expression is facilitated by an interaction of gene duplication and biological activity. Further, this plays a role in controlling diversity of plant metabolism.

  15. Reference genes for gene expression studies in wheat flag leaves grown under different farming conditions

    Directory of Open Access Journals (Sweden)

    Cordeiro Raposo Fernando

    2011-09-01

    Full Text Available Abstract Background Internal control genes with highly uniform expression throughout the experimental conditions are required for accurate gene expression analysis as no universal reference genes exists. In this study, the expression stability of 24 candidate genes from Triticum aestivum cv. Cubus flag leaves grown under organic and conventional farming systems was evaluated in two locations in order to select suitable genes that can be used for normalization of real-time quantitative reverse-transcription PCR (RT-qPCR reactions. The genes were selected among the most common used reference genes as well as genes encoding proteins involved in several metabolic pathways. Findings Individual genes displayed different expression rates across all samples assayed. Applying geNorm, a set of three potential reference genes were suitable for normalization of RT-qPCR reactions in winter wheat flag leaves cv. Cubus: TaFNRII (ferredoxin-NADP(H oxidoreductase; AJ457980.1, ACT2 (actin 2; TC234027, and rrn26 (a putative homologue to RNA 26S gene; AL827977.1. In addition of these three genes that were also top-ranked by NormFinder, two extra genes: CYP18-2 (Cyclophilin A, AY456122.1 and TaWIN1 (14-3-3 like protein, AB042193 were most consistently stably expressed. Furthermore, we showed that TaFNRII, ACT2, and CYP18-2 are suitable for gene expression normalization in other two winter wheat varieties (Tommi and Centenaire grown under three treatments (organic, conventional and no nitrogen and a different environment than the one tested with cv. Cubus. Conclusions This study provides a new set of reference genes which should improve the accuracy of gene expression analyses when using wheat flag leaves as those related to the improvement of nitrogen use efficiency for cereal production.

  16. Gene cluster statistics with gene families.

    Science.gov (United States)

    Raghupathy, Narayanan; Durand, Dannie

    2009-05-01

    Identifying genomic regions that descended from a common ancestor is important for understanding the function and evolution of genomes. In distantly related genomes, clusters of homologous gene pairs are evidence of candidate homologous regions. Demonstrating the statistical significance of such "gene clusters" is an essential component of comparative genomic analyses. However, currently there are no practical statistical tests for gene clusters that model the influence of the number of homologs in each gene family on cluster significance. In this work, we demonstrate empirically that failure to incorporate gene family size in gene cluster statistics results in overestimation of significance, leading to incorrect conclusions. We further present novel analytical methods for estimating gene cluster significance that take gene family size into account. Our methods do not require complete genome data and are suitable for testing individual clusters found in local regions, such as contigs in an unfinished assembly. We consider pairs of regions drawn from the same genome (paralogous clusters), as well as regions drawn from two different genomes (orthologous clusters). Determining cluster significance under general models of gene family size is computationally intractable. By assuming that all gene families are of equal size, we obtain analytical expressions that allow fast approximation of cluster probabilities. We evaluate the accuracy of this approximation by comparing the resulting gene cluster probabilities with cluster probabilities obtained by simulating a realistic, power-law distributed model of gene family size, with parameters inferred from genomic data. Surprisingly, despite the simplicity of the underlying assumption, our method accurately approximates the true cluster probabilities. It slightly overestimates these probabilities, yielding a conservative test. We present additional simulation results indicating the best choice of parameter values for data

  17. Essential Bacillus subtilis genes

    NARCIS (Netherlands)

    Kobayashi, K.; Ehrlich, S.D.; Albertini, A.; Amati, G.; Andersen, K.K.; Arnaud, M.; Asai, K.; Ashikaga, S.; Aymerich, S.; Bessieres, P.; Boland, F.; Brignell, S.C.; Bron, S; Bunai, K.; Chapuis, J; Christiansen, L.C.; Danchin, A.; Debarbouille, M.; Dervyn, E.; Deuerling, E.; Devine, K.; Devine, S.K.; Dreesen, O.; Errington, J.; Fillinger, S.; Foster, S.J.; Fujita, Y.; Galizzi, A.; Gardan, R.; Eschevins, C.; Fukushima, T.; Haga, K.; Harwood, C.R; Hecker, M.; Hosoya, D.; Hullo, M.F.; Kakeshita, H.; Karamata, D.; Kasahara, Y.; Kawamura, F.; Koga, K.; Koski, P.; Kuwana, R.; Imamura, D.; Ishimaru, M.; Ishikawa, S.; Ishio, I.; Le Coq, D.; Masson, A.; Mauel, C.; Meima, Roelf; Mellado, R.P.; Moir, A.; Moriya, S.; Nagakawa, E.; Nanamiya, H.; Nakai, S.; Nygaard, P.; Ogura, M.; Ohanan, T.; O'Reilly, M.; O'Rourke, M.; Pragai, Z.; Pooley, H.M.; Rapoport, G.; Rawlins, J.P.; Rivas, L.A.; Rivolta, C.; Sadaie, A.; Sadaie, Y.; Sarvas, M; Sato, T.; Saxild, H.H.; Scanlan, E.; Schumann, W; Seegers, J.F. M. L.; Sekiguchi, J.; Sekowska, A.; Seror, S.J.; Simon, M.; Stragier, P.; Studer, R.; Takamatsu, H.; Tanaka, T.; Takeuchi, M.; Thomaides, H.B.; Vagner, V.; van Dijl, J.M.; Watabe, K.; Wipat, A; Yamamoto, H.; Yamamoto, M.; Yamamoto, Y.; Yamane, K.; Yata, K.; Yoshida, K.; Yoshikawa, H.; Zuber, U.; Ogasawara, N.; Ishio, [No Value

    2003-01-01

    To estimate the minimal gene set required to sustain bacterial life in nutritious conditions, we carried out a systematic inactivation of Bacillus subtilis genes. Among approximate to4,100 genes of the organism, only 192 were shown to be indispensable by this or previous work. Another 79 genes were

  18. Silence of the Genes

    Indian Academy of Sciences (India)

    Srimath

    The human genome codes for ~35,000 genes and all these genes are not expressed in every cell. The time and site of gene expression is very precisely regulated. In any cell, only. Silence of the Genes. 2006 Nobel Prize in Physiology or Medicine. Utpal Nath and Saumitra Das. Keywords. RNA interference, siRNA,.

  19. Hallervorden Spatz syndrome: magnetic resonance findings. Case report

    International Nuclear Information System (INIS)

    Farage, Luciano; Castro, Mario Augusto Padula; Macedo, Tulio Augusto Alves; Assis, Marcelo Cardoso de; Souza, Lincoln Pereira de; Freitas, Luiz Oliveira de

    2004-01-01

    Hallervorden-Spatz syndrome is a neuro degenerative disease, autosomic recessive with two clinical features: early and late onset. Psychiatric, pyramidal and extrapyramidal signs are present in the late subtype. We report the case of a 41-old woman with extrapyramidal signs. Magnetic resonance imaging (MRI) showed the eye-of-the-tiger sign in the medial globus pallidus. This is due to a gliosis (increased signal) and accumulation of surrounding iron (decreased signal intensity) in long T R sequences. There is a strong relationship between MRI findings and the gene mutation responsible for this disease. It makes the MRI sensible for diagnosing this syndrome. (author)

  20. A Probabilistic Genome-Wide Gene Reading Frame Sequence Model

    DEFF Research Database (Denmark)

    Have, Christian Theil; Mørk, Søren

    as output. The model can be used to obtain the most probable genome annotation based on a combination of i: a gene finder score of each gene candidate and ii: the sequence of the reading frames of gene candidates through a genome. The model --- as well as a higher order variant --- is developed and tested......We introduce a new type of probabilistic sequence model, that model the sequential composition of reading frames of genes in a genome. Our approach extends gene finders with a model of the sequential composition of genes at the genome-level -- effectively producing a sequential genome annotation...... using the probabilistic logic programming language and machine learning system PRISM - a fast and efficient model prototyping environment, using bacterial gene finding performance as a benchmark of signal strength. The model is used to prune a set of gene predictions from an underlying gene finder...

  1. Separate enrichment analysis of pathways for up- and downregulated genes.

    Science.gov (United States)

    Hong, Guini; Zhang, Wenjing; Li, Hongdong; Shen, Xiaopei; Guo, Zheng

    2014-03-06

    Two strategies are often adopted for enrichment analysis of pathways: the analysis of all differentially expressed (DE) genes together or the analysis of up- and downregulated genes separately. However, few studies have examined the rationales of these enrichment analysis strategies. Using both microarray and RNA-seq data, we show that gene pairs with functional links in pathways tended to have positively correlated expression levels, which could result in an imbalance between the up- and downregulated genes in particular pathways. We then show that the imbalance could greatly reduce the statistical power for finding disease-associated pathways through the analysis of all-DE genes. Further, using gene expression profiles from five types of tumours, we illustrate that the separate analysis of up- and downregulated genes could identify more pathways that are really pertinent to phenotypic difference. In conclusion, analysing up- and downregulated genes separately is more powerful than analysing all of the DE genes together.

  2. Indian Health Service: Find Health Care

    Science.gov (United States)

    ... IHS Home for Patients Find Health Care Find Health Care IMPORTANT If you are having a health emergency ... services, continuous nursing services and that provides comprehensive health care including diagnosis and treatment. Health Locations An ambulatory ...

  3. Researchers Find a Mechanism for Schizophrenia

    Science.gov (United States)

    ... issue Health Capsule Researchers Find a Mechanism for Schizophrenia En español Send us your comments Scientists uncovered a mechanism behind genetic variations previously linked to schizophrenia. The findings may lead to new clinical approaches. ...

  4. CDC Study Finds Fecal Contamination in Pools

    Science.gov (United States)

    ... Communication (404) 639-3286 CDC study finds fecal contamination in pools A study of public pools done ... The E. coli is a marker for fecal contamination. Finding a high percentage of E. coli-positive ...

  5. Computed tomographic findings of intracranial gliosis

    Energy Technology Data Exchange (ETDEWEB)

    Weisberg, L.

    1981-08-01

    The clinical and computed tomographic (CT) findings in eight patients with pathological evidence of cerebral gliosis are analyzed. CT findings do not permit differentiation of gliosis from other neoplastic and non-neoplastic conditions.

  6. Computer tomographic findings of intracranial gliosis.

    Science.gov (United States)

    Weisberg, L

    1981-01-01

    The clinical and computer tomographic (CT) findings in eight patients with pathological evidence of cerebral gliosis and analyzed. CT findings do not permit differentiation of gliosis from other neoplastic and non-neoplastic conditions.

  7. Autism spectrum disorders: from genes to neurobiology.

    Science.gov (United States)

    Willsey, A Jeremy; State, Matthew W

    2015-02-01

    Advances in genome-wide technology, coupled with the availability of large cohorts, are finally yielding a steady stream of autism spectrum disorder (ASD) genes carrying mutations of large effect. These findings represent important molecular clues, but at the same time present notable challenges to traditional strategies for moving from genes to neurobiology. A remarkable degree of genetic heterogeneity, the biological pleiotropy of ASD genes, and the tremendous complexity of the human brain are prompting the development of new strategies for translating genetic discoveries into therapeutic targets. Recent developments in systems biology approaches that 'contextualize' these genetic findings along spatial, temporal, and cellular axes of human brain development are beginning to bridge the gap between high-throughput gene discovery and testable pathophysiological hypotheses. Copyright © 2014 Elsevier Ltd. All rights reserved.

  8. New genes associated with rheumatoid arthritis identified by gene expression profiling.

    Science.gov (United States)

    Wang, H; Guo, J; Jiang, J; Wu, W; Chang, X; Zhou, H; Li, Z; Zhao, J

    2017-06-01

    In this study, we aimed to find new genes associated with rheumatoid arthritis (RA) so that more comprehensive genes would be used for monitoring and/or diagnosing patients. Illumina digital gene expression profiling was applied in two sample types - peripheral blood mononuclear cells (PBMCs) and synovial cells to compare the gene expression pattern between 17 patients with RA and three control groups (six osteoarthritis patients, three ankylosing spondylitis patients and 17 healthy controls). Bioinformatics was performed on pathway analysis and protein-protein interaction networks. Four novel genes from PBMCs - DHRS3, TTC38, SAP30BP and LPIN2 - were found to be associated with RA and further confirmed through quantitative real-time polymerase chain reaction. Five new differentially expressed genes (EPYC, LIFR, GLDN, TADA3 and ZNRF3) found in synovial cells were not confirmed. Pathway analyses revealed 10 significantly enriched pathways, and a protein-protein interaction network analysis showed that four novel PBMC-derived genes were connected to previously reported genes by four intermediate genes. Therefore, we proposed that four newly identified PBMC-derived genes could be integrated with previously reported RA-associated genes to monitor and/or diagnose RA. © 2017 John Wiley & Sons Ltd.

  9. On finding frequent patterns in event sequences

    DEFF Research Database (Denmark)

    Campagna, Andrea; Pagh, Rasmus

    2010-01-01

    concerning finding frequent patterns in event sequences. Our motivation comes from working with a data set of 2 million RFID readings from baggage trolleys at Copenhagen Airport. The question of finding frequent passenger movement patterns is mapped to the above problem. We report on experimental findings...

  10. Gene2DisCo: Gene to disease using disease commonalities.

    Science.gov (United States)

    Frasca, Marco

    2017-10-01

    Finding the human genes co-causing complex diseases, also known as "disease-genes", is one of the emerging and challenging tasks in biomedicine. This process, termed gene prioritization (GP), is characterized by a scarcity of known disease-genes for most diseases, and by a vast amount of heterogeneous data, usually encoded into networks describing different types of functional relationships between genes. In addition, different diseases may share common profiles (e.g. genetic or therapeutic profiles), and exploiting disease commonalities may significantly enhance the performance of GP methods. This work aims to provide a systematic comparison of several disease similarity measures, and to embed disease similarities and heterogeneous data into a flexible framework for gene prioritization which specifically handles the lack of known disease-genes. We present a novel network-based method, Gene2DisCo, based on generalized linear models (GLMs) to effectively prioritize genes by exploiting data regarding disease-genes, gene interaction networks and disease similarities. The scarcity of disease-genes is addressed by applying an efficient negative selection procedure, together with imbalance-aware GLMs. Gene2DisCo is a flexible framework, in the sense it is not dependent upon specific types of data, and/or upon specific disease ontologies. On a benchmark dataset composed of nine human networks and 708 medical subject headings (MeSH) diseases, Gene2DisCo largely outperformed the best benchmark algorithm, kernelized score functions, in terms of both area under the ROC curve (0.94 against 0.86) and precision at given recall levels (for recall levels from 0.1 to 1 with steps 0.1). Furthermore, we enriched and extended the benchmark data to the whole human genome and provided the top-ranked unannotated candidate genes even for MeSH disease terms without known annotations. Copyright © 2017 Elsevier B.V. All rights reserved.

  11. Mismatch repair gene expression in gastroesophageal cancers.

    Science.gov (United States)

    Dracea, Amelia; Angelescu, Cristina; Danciulescu, Mihaela; Ciurea, Marius; Ioana, Mihai; Burada, Florin

    2015-09-01

    Mismatch repair (MMR) genes play a critical role in maintaining genomic stability, and the impairment of MMR machinery is associated with different human cancers, mainly colorectal cancer. The purpose of our study was to analyze gene expression patterns of three MMR genes (MSH2, MHS6, and EXO1) in gastroesophageal cancers, a pathology in which the contribution of DNA repair genes remains essentially unclear. A total of 45 Romanian patients diagnosed with sporadic gastroesophageal cancers were included in this study. For each patient, MMR mRNA levels were measured in biopsied tumoral (T) and peritumoral (PT) tissues obtained by upper endoscopy. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) with specific TaqMan probes was used to measure gene expression levels for MSH2, MSH6, and EXO1 genes. A significant association was observed for the investigated MMR genes, all of which were detected to be upregulated in gastroesophageal tumor samples when compared with paired normal samples. In the stratified analysis, the association was limited to gastric adenocarcinoma samples. We found no statistically significant associations between MMR gene expression and tumor site or histological grade. In our study, MSH2, MSH6, and EXO1 genes were overexpressed in gastroesophageal cancers. Further investigations based on more samples are necessary to validate our findings.

  12. Family studies to find rare high risk variants in migraine

    DEFF Research Database (Denmark)

    Hansen, Rikke Dyhr; Christensen, Anne Francke; Olesen, Jes

    2017-01-01

    issues from Nature Genetics and PLOS genetics 2014, 2015 and 2016 (UTAI June) were screened for relevant papers. Reference lists from included and other relevant papers were also searched. For the description of the family-based study design using NGS an in-house protocol was used. RESULTS: Thirty...... genetic variants with bigger effect size may be involved in the disease. Since migraine has a tendency to cluster in families, a family approach might be the way to find these variants. This is also indicated by identification of migraine-associated loci in classical linkage-analyses in migraine families....... A single migraine study using a candidate-gene approach was performed in 2010 identifying a rare mutation in the TRESK potassium channel segregating in a large family with migraine with aura, but this finding has later become questioned. The technologies of next-generation sequencing (NGS) now provides...

  13. Rooted triple consensus and anomalous gene trees

    Directory of Open Access Journals (Sweden)

    Schmidt Heiko A

    2008-04-01

    Full Text Available Abstract Background Anomalous gene trees (AGTs are gene trees with a topology different from a species tree that are more probable to observe than congruent gene trees. In this paper we propose a rooted triple approach to finding the correct species tree in the presence of AGTs. Results Based on simulated data we show that our method outperforms the extended majority rule consensus strategy, while still resolving the species tree. Applying both methods to a metazoan data set of 216 genes, we tested whether AGTs substantially interfere with the reconstruction of the metazoan phylogeny. Conclusion Evidence of AGTs was not found in this data set, suggesting that erroneously reconstructed gene trees are the most significant challenge in the reconstruction of phylogenetic relationships among species with current data. The new method does however rule out the erroneous reconstruction of deep or poorly resolved splits in the presence of lineage sorting.

  14. Maternal genes and facial clefts in offspring

    DEFF Research Database (Denmark)

    Jugessur, Astanand; Shi, Min; Gjessing, Håkon Kristian

    2010-01-01

    BACKGROUND: Fetal conditions can in principle be affected by the mother's genotype working through the prenatal environment. METHODOLOGY/PRINCIPAL FINDINGS: Genotypes for 1536 SNPs in 357 cleft candidate genes were available from a previous analysis in which we focused on fetal gene effects [1......]. After data-cleaning, genotypes for 1315 SNPs in 334 autosomal genes were available for the current analysis of maternal gene effects. Two complementary statistical methods, TRIMM and HAPLIN, were used to detect multi-marker effects in population-based samples from Norway (562 case-parent and 592 control......-parent triads) and Denmark (235 case-parent triads). We analyzed isolated cleft lip with or without cleft palate (iCL/P) and isolated cleft palate only (iCP) separately and assessed replication by looking for genes detected in both populations by both methods. In iCL/P, neither TRIMM nor HAPLIN detected more...

  15. Human Gene Therapy: Genes without Frontiers?

    Science.gov (United States)

    Simon, Eric J.

    2002-01-01

    Describes the latest advancements and setbacks in human gene therapy to provide reference material for biology teachers to use in their science classes. Focuses on basic concepts such as recombinant DNA technology, and provides examples of human gene therapy such as severe combined immunodeficiency syndrome, familial hypercholesterolemia, and…

  16. Fetal MRI: incidental findings in the mother

    Energy Technology Data Exchange (ETDEWEB)

    Abdullah, Selwan B. [University of Maryland Medical Center, Diagnostic Radiology and Nuclear Medicine, Baltimore, MD (United States); University of Minnesota, Medical School, Minneapolis, MN (United States); Dietz, Kelly R.; Holm, Tara L. [University of Minnesota, Department of Radiology, Minneapolis, MN (United States)

    2016-11-15

    Fetal magnetic resonance imaging (MRI) is a routinely used tool in prenatal diagnosis; however, there is a lack of studies evaluating incidental findings observed in the mother. This study describes and quantifies incidental findings observed in the mother during fetal MRI. We reviewed all fetal MRI studies at the University of Minnesota Medical Center from February 2008 to September 2014. Two pediatric radiologists retrospectively conducted a consensus evaluation. The maternal findings were categorized into neurologic, gynecologic, urinary, gastrointestinal and musculoskeletal. Hydronephrosis consistent with the stage of pregnancy was recorded but was not included as an abnormal finding. Abnormal findings were classified into three groups, depending on their clinical significance: level I (low), level II (medium) and level III (high). We evaluated 332 pregnant patients with a mean age of 29.3 years and a mean gestational age of 29 weeks. Of these, 55.4% had at least 1 incidental finding, for a total of 262 incidental maternal findings. Of the 262 abnormalities, 113 (43.1%) were neurologic, 69 were gynecologic (26.3%), 36 (13.7%) urinary, 24 (9.2%) gastrointestinal and 20 (7.6%) musculoskeletal. Of the 262 incidental findings, 237 (90.5%) were level I, 24 (9.2%) were level II and 1 (0.4%) was level III. Our results suggest that although the vast majority of incidental maternal findings are benign, more significant findings are still encountered and should be expected. (orig.)

  17. Imaging findings of primary synovial sarcoma of the lung

    International Nuclear Information System (INIS)

    Guan Yubao; Chen Ling; Zeng Qingsi; Zheng Xiaotao; Chen Huai; Zhang Chaoliang; Cen Renli; Gu Yingying

    2009-01-01

    Objective: To evaluate the imaging characteristics of primary pulmonary synovial sarcoma and improve its diagnosis and differential diagnosis. Methods: The clinical, imaging and pathology findings of 5 patients were retrospectively analyzed. All 5 patients received X-ray and CT scan, 1 case had MRI and PET-CT examination. SYT-SSX fusion gene was analyzed in 4 patients using reverse transcriptase- polymerase chain reaction (RT-PCR). Results: All the 5 patients had solid mass in the lungs and their diameter were 5.3 to 15.7 cm. One was associated with pneumothorax and the others were with moderate pleural effusion. Peripheral tumors, which showed clear margin partly with inhomogeneous density, was found in CT scan. On the contrast-enhanced CT scan, 3 cases were inhomogeneous enhancement and 2 were circular enhancement. Pleural invasion or conglutination was detected in 5 patients. No hilar or mediastinal lymph nodes metastasis were seen in all eases. MRI showed intermediate signal on T 1 WI and heterogeneous on T 2 WI of one case with right upper lobe lesion and showed thick mural enhancement after Gadolinium enhancement. The adjacent chest wall, rib thoracic vertebra, vertebral canal and thoracic cord were invaded. PET-CT showed increased uptake of FDG (SUV=12.3) in tumors. The immunohistochemical examination of Vim, CK and EMA were positive and SYT-SSX gene was detected in 4 patients. Conclusions: There are some relatively specific imaging findings of primary pulmonary synovial sarcoma. However it is necessary for diagnosing the disease to combine pathology, immunohistochemistry and SYT-SSX gene detection. (authors)

  18. Inferring gene expression dynamics via functional regression analysis

    Directory of Open Access Journals (Sweden)

    Leng Xiaoyan

    2008-01-01

    Full Text Available Abstract Background Temporal gene expression profiles characterize the time-dynamics of expression of specific genes and are increasingly collected in current gene expression experiments. In the analysis of experiments where gene expression is obtained over the life cycle, it is of interest to relate temporal patterns of gene expression associated with different developmental stages to each other to study patterns of long-term developmental gene regulation. We use tools from functional data analysis to study dynamic changes by relating temporal gene expression profiles of different developmental stages to each other. Results We demonstrate that functional regression methodology can pinpoint relationships that exist between temporary gene expression profiles for different life cycle phases and incorporates dimension reduction as needed for these high-dimensional data. By applying these tools, gene expression profiles for pupa and adult phases are found to be strongly related to the profiles of the same genes obtained during the embryo phase. Moreover, one can distinguish between gene groups that exhibit relationships with positive and others with negative associations between later life and embryonal expression profiles. Specifically, we find a positive relationship in expression for muscle development related genes, and a negative relationship for strictly maternal genes for Drosophila, using temporal gene expression profiles. Conclusion Our findings point to specific reactivation patterns of gene expression during the Drosophila life cycle which differ in characteristic ways between various gene groups. Functional regression emerges as a useful tool for relating gene expression patterns from different developmental stages, and avoids the problems with large numbers of parameters and multiple testing that affect alternative approaches.

  19. EasyGene – a prokaryotic gene finder that ranks ORFs by statistical significance

    Directory of Open Access Journals (Sweden)

    Larsen Thomas

    2003-06-01

    Full Text Available Abstract Background Contrary to other areas of sequence analysis, a measure of statistical significance of a putative gene has not been devised to help in discriminating real genes from the masses of random Open Reading Frames (ORFs in prokaryotic genomes. Therefore, many genomes have too many short ORFs annotated as genes. Results In this paper, we present a new automated gene-finding method, EasyGene, which estimates the statistical significance of a predicted gene. The gene finder is based on a hidden Markov model (HMM that is automatically estimated for a new genome. Using extensions of similarities in Swiss-Prot, a high quality training set of genes is automatically extracted from the genome and used to estimate the HMM. Putative genes are then scored with the HMM, and based on score and length of an ORF, the statistical significance is calculated. The measure of statistical significance for an ORF is the expected number of ORFs in one megabase of random sequence at the same significance level or better, where the random sequence has the same statistics as the genome in the sense of a third order Markov chain. Conclusions The result is a flexible gene finder whose overall performance matches or exceeds other methods. The entire pipeline of computer processing from the raw input of a genome or set of contigs to a list of putative genes with significance is automated, making it easy to apply EasyGene to newly sequenced organisms. EasyGene with pre-trained models can be accessed at http://www.cbs.dtu.dk/services/EasyGene.

  20. Selection and validation of reference genes for gene expression analysis in apomictic and sexual Cenchrus ciliaris

    Science.gov (United States)

    2013-01-01

    Background Apomixis is a naturally occurring asexual mode of seed reproduction resulting in offspring genetically identical to the maternal plant. Identifying differential gene expression patterns between apomictic and sexual plants is valuable to help deconstruct the trait. Quantitative RT-PCR (qRT-PCR) is a popular method for analyzing gene expression. Normalizing gene expression data using proper reference genes which show stable expression under investigated conditions is critical in qRT-PCR analysis. We used qRT-PCR to validate expression and stability of six potential reference genes (EF1alpha, EIF4A, UBCE, GAPDH, ACT2 and TUBA) in vegetative and reproductive tissues of B-2S and B-12-9 accessions of C. ciliaris. Findings Among tissue types evaluated, EF1alpha showed the highest level of expression while TUBA showed the lowest. When all tissue types were evaluated and compared between genotypes, EIF4A was the most stable reference gene. Gene expression stability for specific ovary stages of B-2S and B-12-9 was also determined. Except for TUBA, all other tested reference genes could be used for any stage-specific ovary tissue normalization, irrespective of the mode of reproduction. Conclusion Our gene expression stability assay using six reference genes, in sexual and apomictic accessions of C. ciliaris, suggests that EIF4A is the most stable gene across all tissue types analyzed. All other tested reference genes, with the exception of TUBA, could be used for gene expression comparison studies between sexual and apomictic ovaries over multiple developmental stages. This reference gene validation data in C. ciliaris will serve as an important base for future apomixis-related transcriptome data validation. PMID:24083672

  1. Recent findings about the Yersinia enterocolitica phage shock protein response.

    Science.gov (United States)

    Yamaguchi, Saori; Darwin, Andrew J

    2012-02-01

    The phage shock protein (Psp) system is a conserved extracytoplasmic stress response in bacteria that is essential for virulence of the human pathogen Yersinia enterocolitica. This article summarizes some recent findings about Y. enterocolitica Psp system function. Increased psp gene expression requires the transcription factor PspF, but under non-inducing conditions PspF is inhibited by an interaction with another protein, PspA, in the cytoplasm. A Psp-inducing stimulus causes PspA to relocate to the cytoplasmic membrane, freeing PspF to induce psp gene expression. This PspA relocation requires the integral cytoplasmic membrane proteins, PspB and PspC, which might sense an inducing trigger and sequester PspA by direct interaction. The subsequent induction of psp gene expression increases the PspA concentration, which also allows it to contact the membrane directly, perhaps for its physiological function. Mutational analysis of the PspB and PspC proteins has revealed that they both positively and negatively regulate psp gene expression and has also identified PspC domains associated with each function. We also compare the contrasting physiological roles of the Psp system in the virulence of Y. enterocolitica and Salmonella enterica sv. Typhimurium (S. Typhimurium). In S. Typhimurium, PspA maintains the proton motive force, which provides the energy needed to drive ion importers required for survival within macrophages. In contrast, in the extracellular pathogen Y. enterocolitica, PspB and PspC, but not PspA, are the Psp components needed for virulence. PspBC protect Y. enterocolitica from damage caused by the secretin component of its type 3 secretion system, an essential virulence factor.

  2. Gene Expression in Trypanosomatid Parasites

    Directory of Open Access Journals (Sweden)

    Santiago Martínez-Calvillo

    2010-01-01

    Full Text Available The parasites Leishmania spp., Trypanosoma brucei, and Trypanosoma cruzi are the trypanosomatid protozoa that cause the deadly human diseases leishmaniasis, African sleeping sickness, and Chagas disease, respectively. These organisms possess unique mechanisms for gene expression such as constitutive polycistronic transcription of protein-coding genes and trans-splicing. Little is known about either the DNA sequences or the proteins that are involved in the initiation and termination of transcription in trypanosomatids. In silico analyses of the genome databases of these parasites led to the identification of a small number of proteins involved in gene expression. However, functional studies have revealed that trypanosomatids have more general transcription factors than originally estimated. Many posttranslational histone modifications, histone variants, and chromatin modifying enzymes have been identified in trypanosomatids, and recent genome-wide studies showed that epigenetic regulation might play a very important role in gene expression in this group of parasites. Here, we review and comment on the most recent findings related to transcription initiation and termination in trypanosomatid protozoa.

  3. Gene therapy for lung cancer.

    Science.gov (United States)

    Toloza, Eric M; Morse, Michael A; Lyerly, H Kim

    2006-09-01

    Lung cancer patients suffer a 15% overall survival despite advances in chemotherapy, radiation therapy, and surgery. This unacceptably low survival rate is due to the usual finding of advanced disease at diagnosis. However, multimodality strategies using conventional therapies only minimally improve survival rates even in early stages of lung cancer. Attempts to improve survival in advanced disease using various combinations of platinum-based chemotherapy have demonstrated that no regimen is superior, suggesting a therapeutic plateau and the need for novel, more specific, and less toxic therapeutic strategies. Over the past three decades, the genetic etiology of cancer has been gradually delineated, albeit not yet completely. Understanding the molecular events that occur during the multistep process of bronchogenic carcinogenesis may make these tasks more surmountable. During these same three decades, techniques have been developed which allow transfer of functional genes into mammalian cells. For example, blockade of activated tumor-promoting oncogenes or replacement of inactivated tumor-suppressing or apoptosis-promoting genes can be achieved by gene therapy. This article will discuss the therapeutic implications of these molecular changes associated with bronchogenic carcinomas and will then review the status of gene therapies for treatment of lung cancer. (c) 2006 Wiley-Liss, Inc.

  4. Imaging Findings of Fibrous Hamartoma of Infancy

    Energy Technology Data Exchange (ETDEWEB)

    Rho, Byung Hak; Lee, Hee Jung; Kwon, Sun Young [Dongsan Medical Center, Keimyung University College of Medicine, Daegu (Korea, Republic of)

    2009-09-15

    We wanted to evaluate the imaging findings of fibrous hamartoma of infancy (FHI). We retrospectively reviewed the clinical presentation and the sonographic (n = 5) and CT (n = 3) findings of 5 cases of surgically/pathologically confirmed FHI. The sonographic findings were evaluated according to the location, size, internal echogenicity and vascularity. The CT findings were evaluated according to the attenuation of the mass on both the pre- (n = 3) and postcontrast (n = 2) scans. The image findings were correlated with the pathologic findings. The mean age was 14.8 months (range, 7 months - 3 years). The location of lesions was all in the fatty layer of the back (n = 4) and upper arm (n = 1). All the lesions demonstrated-hypertrichosis on the overlying skin. The lesions measured 31.2 mm in the longest diameter (range: 18 mm - 50 mm). The sonographic findings were purely solid, heterogeneously hyperechoic and hypovacular for all the cases. The internal architecture revealed a 'layering' appearance (n = 3). The CT findings demonstrated isoattenuation, as compared to the adjacent muscle on both the pre- and postcontrast CT scans. The pathologic correlation demonstrated a characteristic 'organoid' mixture of fibrous, mucoid and fatty tissues in all cases. The diagnosis of FHI can be suggested by the sonographic findings of a superficially located, heterogeneous solid mass with a 'layering' appearance in the fatty layer of the back or arms of infants with local hypertrochosis on the overlying skin.

  5. Normal radiographic findings. 4. act. ed.; Roentgennormalbefunde

    Energy Technology Data Exchange (ETDEWEB)

    Moeller, T.B. [Gemeinschaftspraxis fuer Radiologie und Nuklearmedizin, Dillingen (Germany)

    2003-07-01

    This book can serve the reader in three ways: First, it presents normal findings for all radiographic techniques including KM. Important data which are criteria of normal findings are indicated directly in the pictures and are also explained in full text and in summary form. Secondly, it teaches the systematics of interpreting a picture - how to look at it, what structures to regard in what order, and for what to look in particular. Checklists are presented in each case. Thirdly, findings are formulated in accordance with the image analysis procedure. All criteria of normal findings are defined in these formulations, which make them an important didactic element. (orig.)

  6. Normal radiographic findings. 4. act. ed.

    International Nuclear Information System (INIS)

    Moeller, T.B.

    2003-01-01

    This book can serve the reader in three ways: First, it presents normal findings for all radiographic techniques including KM. Important data which are criteria of normal findings are indicated directly in the pictures and are also explained in full text and in summary form. Secondly, it teaches the systematics of interpreting a picture - how to look at it, what structures to regard in what order, and for what to look in particular. Checklists are presented in each case. Thirdly, findings are formulated in accordance with the image analysis procedure. All criteria of normal findings are defined in these formulations, which make them an important didactic element. (orig.)

  7. On finding frequent patterns in event sequences

    DEFF Research Database (Denmark)

    Campagna, Andrea; Pagh, Rasmus

    2010-01-01

    concerning finding frequent patterns in event sequences. Our motivation comes from working with a data set of 2 million RFID readings from baggage trolleys at Copenhagen Airport. The question of finding frequent passenger movement patterns is mapped to the above problem. We report on experimental findings......Given a directed acyclic graph with labeled vertices, we consider the problem of finding the most common label sequences (``traces'') among all paths in the graph (of some maximum length $m$). Since the number of paths can be huge, we propose novel algorithms whose time complexity depends only...

  8. Finding Maximal Pairs with Bounded Gap

    DEFF Research Database (Denmark)

    Brodal, Gerth Stølting; Lyngsø, Rune B.; Pedersen, Christian N. S.

    1999-01-01

    . In this paper we present methods for finding all maximal pairs under various constraints on the gap. In a string of length n we can find all maximal pairs with gap in an upper and lower bounded interval in time O(n log n+z) where z is the number of reported pairs. If the upper bound is removed the time reduces...... to O(n+z). Since a tandem repeat is a pair where the gap is zero, our methods can be seen as a generalization of finding tandem repeats. The running time of our methods equals the running time of well known methods for finding tandem repeats....

  9. Tumor targeted gene therapy

    International Nuclear Information System (INIS)

    Kang, Joo Hyun

    2006-01-01

    Knowledge of molecular mechanisms governing malignant transformation brings new opportunities for therapeutic intervention against cancer using novel approaches. One of them is gene therapy based on the transfer of genetic material to an organism with the aim of correcting a disease. The application of gene therapy to the cancer treatment had led to the development of new experimental approaches such as suicidal gene therapy, inhibition of oncogenes and restoration of tumor-suppressor genes. Suicidal gene therapy is based on the expression in tumor cells of a gene encoding an enzyme that converts a prodrug into a toxic product. Representative suicidal genes are Herpes simplex virus type 1 thymidine kinase (HSV1-tk) and cytosine deaminase (CD). Especially, physicians and scientists of nuclear medicine field take an interest in suicidal gene therapy because they can monitor the location and magnitude, and duration of expression of HSV1-tk and CD by PET scanner

  10. Essential Bacillus subtilis genes

    DEFF Research Database (Denmark)

    Kobayashi, K.; Ehrlich, S.D.; Albertini, A.

    2003-01-01

    To estimate the minimal gene set required to sustain bacterial life in nutritious conditions, we carried out a systematic inactivation of Bacillus subtilis genes. Among approximate to4,100 genes of the organism, only 192 were shown to be indispensable by this or previous work. Another 79 genes were...... predicted to be essential. The vast majority of essential genes were categorized in relatively few domains of cell metabolism, with about half involved in information processing, one-fifth involved in the synthesis of cell envelope and the determination of cell shape and division, and one-tenth related...... to cell energetics. Only 4% of essential genes encode unknown functions. Most essential genes are present throughout a wide range of Bacteria, and almost 70% can also be found in Archaea and Eucarya. However, essential genes related to cell envelope, shape, division, and respiration tend to be lost from...

  11. Epigenetics: beyond genes

    CSIR Research Space (South Africa)

    Fossey, A

    2009-06-01

    Full Text Available Gene regulatory processes lead to differential gene expression and are referred to as epigenetic phenomena; these are ubiquitous processes in the biological world. These reversible heritable changes concern DNA and RNA, their interactions...

  12. Family studies to find rare high risk variants in migraine.

    Science.gov (United States)

    Hansen, Rikke Dyhr; Christensen, Anne Francke; Olesen, Jes

    2017-12-01

    Migraine has long been known as a common complex disease caused by genetic and environmental factors. The pathophysiology and the specific genetic susceptibility are poorly understood. Common variants only explain a small part of the heritability of migraine. It is thought that rare genetic variants with bigger effect size may be involved in the disease. Since migraine has a tendency to cluster in families, a family approach might be the way to find these variants. This is also indicated by identification of migraine-associated loci in classical linkage-analyses in migraine families. A single migraine study using a candidate-gene approach was performed in 2010 identifying a rare mutation in the TRESK potassium channel segregating in a large family with migraine with aura, but this finding has later become questioned. The technologies of next-generation sequencing (NGS) now provides an affordable tool to investigate the genetic variation in the entire exome or genome. The family-based study design using NGS is described in this paper. We also review family studies using NGS that have been successful in finding rare variants in other common complex diseases in order to argue the promising application of a family approach to migraine. PubMed was searched to find studies that looked for rare genetic variants in common complex diseases through a family-based design using NGS, excluding studies looking for de-novo mutations, or using a candidate-gene approach and studies on cancer. All issues from Nature Genetics and PLOS genetics 2014, 2015 and 2016 (UTAI June) were screened for relevant papers. Reference lists from included and other relevant papers were also searched. For the description of the family-based study design using NGS an in-house protocol was used. Thirty-two successful studies, which covered 16 different common complex diseases, were included in this paper. We also found a single migraine study. Twenty-three studies found one or a few family specific

  13. Novel retinal findings in peroxisomal biogenesis disorders.

    Science.gov (United States)

    O'Bryhim, B E; Kozel, B A; Lueder, G T

    2018-01-29

    Peroxisomal biogenesis disorders are caused by disruption of long chain fatty acid metabolism due to mutations in PEX genes. Individuals with these disorders often have vision loss due to optic atrophy and pigmentary retinopathy. We report an unusual retinal manifestation of peroxisomal biogenesis disorder.

  14. Angelman Syndrome: Finding the Lost Arc

    OpenAIRE

    Tai, Hwan-Ching; Schuman, Erin M.

    2010-01-01

    Angelman syndrome is a neurodevelopmental disorder caused by mutations in the maternally inherited UBE3A gene, which encodes a ubiquitin ligase. Greer et al. (2010) now identify a UBE3A substrate called Arc that promotes endocytosis of neuronal AMPA receptors, providing insight into synaptic defects that may underlie the cognitive deficits in Angelman syndrome.

  15. Evolution of gene expression after gene amplification.

    Science.gov (United States)

    Garcia, Nelson; Zhang, Wei; Wu, Yongrui; Messing, Joachim

    2015-04-24

    We took a rather unique approach to investigate the conservation of gene expression of prolamin storage protein genes across two different subfamilies of the Poaceae. We took advantage of oat plants carrying single maize chromosomes in different cultivars, called oat-maize addition (OMA) lines, which permitted us to determine whether regulation of gene expression was conserved between the two species. We found that γ-zeins are expressed in OMA7.06, which carries maize chromosome 7 even in the absence of the trans-acting maize prolamin-box-binding factor (PBF), which regulates their expression. This is likely because oat PBF can substitute for the function of maize PBF as shown in our transient expression data, using a γ-zein promoter fused to green fluorescent protein (GFP). Despite this conservation, the younger, recently amplified prolamin genes in maize, absent in oat, are not expressed in the corresponding OMAs. However, maize can express the oldest prolamin gene, the wheat high-molecular weight glutenin Dx5 gene, even when maize Pbf is knocked down (through PbfRNAi), and/or another maize transcription factor, Opaque-2 (O2) is knocked out (in maize o2 mutant). Therefore, older genes are conserved in their regulation, whereas younger ones diverged during evolution and eventually acquired a new repertoire of suitable transcriptional activators. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  16. MR REPORTER GENES

    OpenAIRE

    Gilad, Assaf A.; Ziv, Keren; McMahon, Michael T.; van Zijl, Peter C.M.; Neeman, Michal; Bulte, Jeff W.M.

    2008-01-01

    Non-invasive molecular imaging of dynamic processes has benefited tremendously from the use of reporter genes. These genes encode for proteins that emit light, bind radiolabeled probes or, as covered in this review, modulate magnetic resonance (MR) contrast. Reporter genes play a pivotal role in monitoring cell trafficking, gene replacement therapy, protein-protein interactions, neuronal plasticity and embryonic development. Several strategies exist for generating MR contrast: enzyme-catalyze...

  17. Gene therapy in cystic fibrosis.

    Science.gov (United States)

    Flotte, T R; Laube, B L

    2001-09-01

    less efficient than viral vectors but do not stimulate inflammatory and immunologic responses. Another challenge to the development of clinically feasible gene therapy is delivery mode. Early pulmonary delivery systems relied on the direct instillation of aerosolized vectors, which can result in the induction of adverse reactions because vector is delivered into the lung parenchyma. More recent studies have examined the potential for using spray technologies to target aerosolized AAV vectors to the larger central airways, thereby avoiding alveolar exposure and adverse effects. Comparisons of lung deposition with nebulized delivery of aerosol and spray delivery indicate that spraying results in a more localized deposition pattern (predominantly in the proximal airways) and significantly higher deposition fractions than nebulization. These findings could lead to more efficient and targeted lung delivery of aerosolized gene vectors in the future.

  18. Radiotechnologies and gene therapy

    International Nuclear Information System (INIS)

    Xia Jinsong

    2001-01-01

    Gene therapy is an exciting frontier in medicine today. Radiologist will make an uniquely contribution to these exciting new technologies at every level by choosing sites for targeting therapy, perfecting and establishing routes of delivery, developing imaging strategies to monitor therapy and assess gene expression, developing radiotherapeutic used of gene therapy

  19. Silence of the Genes

    Indian Academy of Sciences (India)

    Srimath

    tary to the endogenous sense mRNA produced by the normal gene. The antisense strand binds to the sense strand and blocks protein synthesis. This method of gene inhibition was termed antisense technology. The antisense technology soon became a. RNA interference. (RNAi) is a novel mechanism for controlling gene.

  20. Discovering genes underlying QTL

    Energy Technology Data Exchange (ETDEWEB)

    Vanavichit, Apichart [Kasetsart University, Kamphaengsaen, Nakorn Pathom (Thailand)

    2002-02-01

    A map-based approach has allowed scientists to discover few genes at a time. In addition, the reproductive barrier between cultivated rice and wild relatives has prevented us from utilizing the germ plasm by a map-based approach. Most genetic traits important to agriculture or human diseases are manifested as observable, quantitative phenotypes called Quantitative Trait Loci (QTL). In many instances, the complexity of the phenotype/genotype interaction and the general lack of clearly identifiable gene products render the direct molecular cloning approach ineffective, thus additional strategies like genome mapping are required to identify the QTL in question. Genome mapping requires no prior knowledge of the gene function, but utilizes statistical methods to identify the most likely gene location. To completely characterize genes of interest, the initially mapped region of a gene location will have to be narrowed down to a size that is suitable for cloning and sequencing. Strategies for gene identification within the critical region have to be applied after the sequencing of a potentially large clone or set of clones that contains this gene(s). Tremendous success of positional cloning has been shown for cloning many genes responsible for human diseases, including cystic fibrosis and muscular dystrophy as well as plant disease resistance genes. Genome and QTL mapping, positional cloning: the pre-genomics era, comparative approaches to gene identification, and positional cloning: the genomics era are discussed in the report. (M. Suetake)

  1. Discovering genes underlying QTL

    International Nuclear Information System (INIS)

    Vanavichit, Apichart

    2002-01-01

    A map-based approach has allowed scientists to discover few genes at a time. In addition, the reproductive barrier between cultivated rice and wild relatives has prevented us from utilizing the germ plasm by a map-based approach. Most genetic traits important to agriculture or human diseases are manifested as observable, quantitative phenotypes called Quantitative Trait Loci (QTL). In many instances, the complexity of the phenotype/genotype interaction and the general lack of clearly identifiable gene products render the direct molecular cloning approach ineffective, thus additional strategies like genome mapping are required to identify the QTL in question. Genome mapping requires no prior knowledge of the gene function, but utilizes statistical methods to identify the most likely gene location. To completely characterize genes of interest, the initially mapped region of a gene location will have to be narrowed down to a size that is suitable for cloning and sequencing. Strategies for gene identification within the critical region have to be applied after the sequencing of a potentially large clone or set of clones that contains this gene(s). Tremendous success of positional cloning has been shown for cloning many genes responsible for human diseases, including cystic fibrosis and muscular dystrophy as well as plant disease resistance genes. Genome and QTL mapping, positional cloning: the pre-genomics era, comparative approaches to gene identification, and positional cloning: the genomics era are discussed in the report. (M. Suetake)

  2. SoFiA: Source Finding Application

    NARCIS (Netherlands)

    Serra, Paolo; Westmeier, Tobias; Giese, Nadine; Jurek, Russell; Flöer, Lars; Popping, Attila; Winkel, Benjamin; van der Hulst, Thijs; Meyer, Martin; Koribalski, Bärbel; Staveley-Smith, Lister; Courtois, Hélène

    2014-01-01

    SoFiA is a flexible source finding pipeline designed to detect and parameterise sources in 3D spectral-line data cubes. SoFiA combines several powerful source finding and parameterisation algorithms, including wavelet denoising, spatial and spectral smoothing, source mask optimisation, spectral

  3. Non-local evidence for expert finding

    NARCIS (Netherlands)

    Balog, K.; de Rijke, M.; Shanahan, J.G.; Amer-Yahia, S.; Zhang, Y.; Kołcz, A.; Chowdury, A.; Kelly, D.

    2008-01-01

    The task addressed in this paper, finding experts in an enterprise setting, has gained in importance and interest over the past few years. Commonly, this task is approached as an association finding exercise between people and topics. Existing techniques use either documents (as a whole) or

  4. Single Finds. The case of Roman Egypt

    DEFF Research Database (Denmark)

    Christiansen, Erik

    2006-01-01

    Survery of single or stray finds from Roman Egypt and discussion of them as evidence for the circulation and use of coins......Survery of single or stray finds from Roman Egypt and discussion of them as evidence for the circulation and use of coins...

  5. Experimental interstellar organic chemistry - Preliminary findings

    Science.gov (United States)

    Khare, B. N.; Sagan, C.

    1973-01-01

    Review of the results of some explicit experimental simulation of interstellar organic chemistry consisting in low-temperature high-vacuum UV irradiation of condensed simple gases known or suspected to be present in the interstellar medium. The results include the finding that acetonitrile may be present in the interstellar medium. The implication of this and other findings are discussed.

  6. CT findings in patients with cerebral palsy

    Energy Technology Data Exchange (ETDEWEB)

    Konno, K. (Akita Univ. (Japan))

    1982-01-01

    Clinical findings and CT findings in 73 cases of cerebral palsy were studied. The causes of cerebral palsy were presumed to be as follows: abnormal cerebral development (36%), asphyxial delivery (34%), and immature delivery (19%), etc. CT findings were abnormal in 58% of the 73 cases, 83% of the spastic tetraplegia patients and all of the spastic hemiplegia patients showed abnormal CT findings. All the patients with spastic monoplegia presented normal CT findings. In 75% of the spastic hemiplegia cases, the CT abnormalities were due to cerebral parenchymal abnormality such as porencephaly and regional low absorption. In cases of spastic tetraplegia, cerebral parenchymal abnormality was found only in 10%. Cortical atrophy was found only in 15 of the 73 cases, whereas central atrophy was found in 36 cases.

  7. Contextual Factors for Finding Similar Experts

    DEFF Research Database (Denmark)

    Hofmann, Katja; Balog, Krisztian; Bogers, Toine

    2010-01-01

    Expertise-seeking research studies how people search for expertise and choose whom to contact in the context of a specific task. An important outcome are models that identify factors that influence expert finding. Expertise retrieval addresses the same problem, expert finding, but from a system......-centered perspective. The main focus has been on developing content-based algorithms similar to document search. These algorithms identify matching experts primarily on the basis of the textual content of documents with which experts are associated. Other factors, such as the ones identified by expertise......-seeking models, are rarely taken into account. In this article, we extend content-based expert-finding approaches with contextual factors that have been found to influence human expert finding. We focus on a task of science communicators in a knowledge-intensive environment, the task of finding similar experts...

  8. Analysis of multiplex gene expression maps obtained by voxelation

    Directory of Open Access Journals (Sweden)

    Smith Desmond J

    2009-04-01

    Full Text Available Abstract Background Gene expression signatures in the mammalian brain hold the key to understanding neural development and neurological disease. Researchers have previously used voxelation in combination with microarrays for acquisition of genome-wide atlases of expression patterns in the mouse brain. On the other hand, some work has been performed on studying gene functions, without taking into account the location information of a gene's expression in a mouse brain. In this paper, we present an approach for identifying the relation between gene expression maps obtained by voxelation and gene functions. Results To analyze the dataset, we chose typical genes as queries and aimed at discovering similar gene groups. Gene similarity was determined by using the wavelet features extracted from the left and right hemispheres averaged gene expression maps, and by the Euclidean distance between each pair of feature vectors. We also performed a multiple clustering approach on the gene expression maps, combined with hierarchical clustering. Among each group of similar genes and clusters, the gene function similarity was measured by calculating the average gene function distances in the gene ontology structure. By applying our methodology to find similar genes to certain target genes we were able to improve our understanding of gene expression patterns and gene functions. By applying the clustering analysis method, we obtained significant clusters, which have both very similar gene expression maps and very similar gene functions respectively to their corresponding gene ontologies. The cellular component ontology resulted in prominent clusters expressed in cortex and corpus callosum. The molecular function ontology gave prominent clusters in cortex, corpus callosum and hypothalamus. The biological process ontology resulted in clusters in cortex, hypothalamus and choroid plexus. Clusters from all three ontologies combined were most prominently expressed in

  9. Variations in CCL3L gene cluster sequence and non-specific gene copy numbers

    Directory of Open Access Journals (Sweden)

    Edberg Jeffrey C

    2010-03-01

    Full Text Available Abstract Background Copy number variations (CNVs of the gene CC chemokine ligand 3-like1 (CCL3L1 have been implicated in HIV-1 susceptibility, but the association has been inconsistent. CCL3L1 shares homology with a cluster of genes localized to chromosome 17q12, namely CCL3, CCL3L2, and, CCL3L3. These genes are involved in host defense and inflammatory processes. Several CNV assays have been developed for the CCL3L1 gene. Findings Through pairwise and multiple alignments of these genes, we have shown that the homology between these genes ranges from 50% to 99% in complete gene sequences and from 70-100% in the exonic regions, with CCL3L1 and CCL3L3 being identical. By use of MEGA 4 and BioEdit, we aligned sense primers, anti-sense primers, and probes used in several previously described assays against pre-multiple alignments of all four chemokine genes. Each set of probes and primers aligned and matched with overlapping sequences in at least two of the four genes, indicating that previously utilized RT-PCR based CNV assays are not specific for only CCL3L1. The four available assays measured median copies of 2 and 3-4 in European and African American, respectively. The concordance between the assays ranged from 0.44-0.83 suggesting individual discordant calls and inconsistencies with the assays from the expected gene coverage from the known sequence. Conclusions This indicates that some of the inconsistencies in the association studies could be due to assays that provide heterogenous results. Sequence information to determine CNV of the three genes separately would allow to test whether their association with the pathogenesis of a human disease or phenotype is affected by an individual gene or by a combination of these genes.

  10. A Genome Wide Genotyping Study To Find Candidate Genes That Influence Varroa-Sensitive Hygiene (VSH)

    Science.gov (United States)

    Varroa parasitism of honey bees is widely considered by apicultural researchers to be the greatest threat to beekeeping. Varroa-sensitive hygiene (VSH) is one of two identified behaviors that are highly important for controlling the growth of Varroa mite populations in bee hives. Bees exhibiting th...

  11. Integrative analysis for finding genes and networks involved in diabetes and other complex diseases

    DEFF Research Database (Denmark)

    Bergholdt, R.; Størling, Zenia, Marian; Hansen, Kasper Lage

    2007-01-01

    We have developed an integrative analysis method combining genetic interactions, identified using type 1 diabetes genome scan data, and a high-confidence human protein interaction network. Resulting networks were ranked by the significance of the enrichment of proteins from interacting regions. W...

  12. Carboxylesterase 1 genes

    DEFF Research Database (Denmark)

    Rasmussen, Henrik Berg; Madsen, Majbritt Busk

    2018-01-01

    The carboxylesterase 1 gene (CES1) encodes a hydrolase that metabolizes commonly used drugs. The CES1-related pseudogene, carboxylesterase 1 pseudogene 1 (CES1P1), has been implicated in gene exchange with CES1 and in the formation of hybrid genes including the carboxylesterase 1A2 gene (CES1A2...... region was revealed. In conclusion, many procedures for CES1, CES1A2 and CES1P1 genotyping appear to lack specificity. Knowledge about the segmental duplications may improve the typing of these genes....

  13. Candidate genes for expansion and transformation of hematopoietic stem cells by NUP98-HOX fusion genes.

    Directory of Open Access Journals (Sweden)

    Lars Palmqvist

    Full Text Available BACKGROUND: Hox genes are implicated in hematopoietic stem cell (HSC regulation as well as in leukemia development through translocation with the nucleoporin gene NUP98. Interestingly, an engineered NUP98-HOXA10 (NA10 fusion can induce a several hundred-fold expansion of HSCs in vitro and NA10 and the AML-associated fusion gene NUP98-HOXD13 (ND13 have a virtually indistinguishable ability to transform myeloid progenitor cells in vitro and to induce leukemia in collaboration with MEIS1 in vivo. METHODOLOGY/PRINCIPAL FINDINGS: These findings provided a potentially powerful approach to identify key pathways mediating Hox-induced expansion and transformation of HSCs by identifying gene expression changes commonly induced by ND13 and NA10 but not by a NUP98-Hox fusion with a non-DNA binding homedomain mutation (N51S. The gene expression repertoire of purified murine bone marrow Sca-1+Lin- cells transduced with retroviral vectors encoding for these genes was established using the Affymetrix GeneChip MOE430A. Approximately seventy genes were differentially expressed in ND13 and NA10 cells that were significantly changed by both compared to the ND13(N51S mutant. Intriguingly, several of these potential Hox target genes have been implicated in HSC expansion and self-renewal, including the tyrosine kinase receptor Flt3, the prion protein, Prnp, hepatic leukemia factor, Hlf and Jagged-2, Jag2. Consistent with these results, FLT3, HLF and JAG2 expression correlated with HOX A cluster gene expression in human leukemia samples. CONCLUSIONS: In conclusion this study has identified several novel Hox downstream target genes and provides important new leads to key regulators of the expansion and transformation of hematopoietic stem cells by Hox.

  14. Genes responsive to elevated CO2 concentrations in triploid white poplar and integrated gene network analysis.

    Directory of Open Access Journals (Sweden)

    Juanjuan Liu

    Full Text Available BACKGROUND: The atmospheric CO2 concentration increases every year. While the effects of elevated CO2 on plant growth, physiology and metabolism have been studied, there is now a pressing need to understand the molecular mechanisms of how plants will respond to future increases in CO2 concentration using genomic techniques. PRINCIPAL FINDINGS: Gene expression in triploid white poplar ((Populus tomentosa ×P. bolleana ×P. tomentosa leaves was investigated using the Affymetrix poplar genome gene chip, after three months of growth in controlled environment chambers under three CO2 concentrations. Our physiological findings showed the growth, assessed as stem diameter, was significantly increased, and the net photosynthetic rate was decreased in elevated CO2 concentrations. The concentrations of four major endogenous hormones appeared to actively promote plant development. Leaf tissues under elevated CO2 concentrations had 5,127 genes with different expression patterns in comparison to leaves under the ambient CO2 concentration. Among these, 8 genes were finally selected for further investigation by using randomized variance model corrective ANOVA analysis, dynamic gene expression profiling, gene network construction, and quantitative real-time PCR validation. Among the 8 genes in the network, aldehyde dehydrogenase and pyruvate kinase were situated in the core and had interconnections with other genes. CONCLUSIONS: Under elevated CO2 concentrations, 8 significantly changed key genes involved in metabolism and responding to stimulus of external environment were identified. These genes play crucial roles in the signal transduction network and show strong correlations with elevated CO2 exposure. This study provides several target genes, further investigation of which could provide an initial step for better understanding the molecular mechanisms of plant acclimation and evolution in future rising CO2 concentrations.

  15. Introduction: Cancer Gene Networks.

    Science.gov (United States)

    Clarke, Robert

    2017-01-01

    differential equations and related tools to create dynamic, semi-mechanistic models of low dimensional data including gene/protein signaling as a function of time/dose. More recently, the integration of imaging technologies into predictive multiscale modeling has begun to extend further the scales across which data can be obtained and used to gain insight into system function.There are several goals for predictive multiscale modeling including the more academic pursuit of understanding how the system or local feature thereof is regulated or functions, to the more practical or translational goals of identifying predictive (selecting which patient should receive which drug/therapy) or prognostic (disease progress and outcome in an individual patient) biomarkers and/or identifying network vulnerabilities that represent potential targets for therapeutic benefit with existing drugs (including drug repurposing) or for the development of new drugs. These various goals are not necessarily mutually exclusive or inclusive. Within this volume, readers will find examples of many of the activities noted above. Each chapter contains practical and/or methodological insights to guide readers in the design and interpretation of their own and published work.

  16. MGC: a metagenomic gene caller.

    Science.gov (United States)

    El Allali, Achraf; Rose, John R

    2013-01-01

    Computational gene finding algorithms have proven their robustness in identifying genes in complete genomes. However, metagenomic sequencing has presented new challenges due to the incomplete and fragmented nature of the data. During the last few years, attempts have been made to extract complete and incomplete open reading frames (ORFs) directly from short reads and identify the coding ORFs, bypassing other challenging tasks such as the assembly of the metagenome. In this paper we introduce a metagenomics gene caller (MGC) which is an improvement over the state-of-the-art prediction algorithm Orphelia. Orphelia uses a two-stage machine learning approach and computes a model that classifies extracted ORFs from fragmented sequences. We hypothesise and demonstrate evidence that sequences need separate models based on their local GC-content in order to avoid the noise introduced to a single model computed with sequences from the entire GC spectrum. We have also added two amino-acid features based on the benefit of amino-acid usage shown in our previous research. Our algorithm is able to predict genes and translation initiation sites (TIS) more accurately than Orphelia which uses a single model. Learning separate models for several pre-defined GC-content regions as opposed to a single model approach improves the performance of the neural network as demonstrated by the experimental results presented in this paper. The inclusion of amino-acid usage features also helps improve the overall accuracy of our algorithm. MGC's improvement sets the ground for further investigation into the use of GC-content to separate data for training models in machine learning based gene finders.

  17. Gene therapy: An overview

    Directory of Open Access Journals (Sweden)

    Sudip Indu

    2013-01-01

    Full Text Available Gene therapy "the use of genes as medicine" involves the transfer of a therapeutic or working copy of a gene into specific cells of an individual in order to repair a faulty gene copy. The technique may be used to replace a faulty gene, or to introduce a new gene whose function is to cure or to favorably modify the clinical course of a condition. The objective of gene therapy is to introduce new genetic material into target cells while causing no damage to the surrounding healthy cells and tissues, hence the treatment related morbidity is decreased. The delivery system includes a vector that delivers a therapeutic gene into the patient′s target cell. Functional proteins are created from the therapeutic gene causing the cell to return to a normal stage. The vectors used in gene therapy can be viral and non-viral. Gene therapy, an emerging field of biomedicine, is still at infancy and much research remains to be done before this approach to the treatment of condition will realize its full potential.

  18. Human gene essentiality.

    Science.gov (United States)

    Bartha, István; di Iulio, Julia; Venter, J Craig; Telenti, Amalio

    2018-01-01

    A gene can be defined as essential when loss of its function compromises viability of the individual (for example, embryonic lethality) or results in profound loss of fitness. At the population level, identification of essential genes is accomplished by observing intolerance to loss-of-function variants. Several computational methods are available to score gene essentiality, and recent progress has been made in defining essentiality in the non-coding genome. Haploinsufficiency is emerging as a critical aspect of gene essentiality: approximately 3,000 human genes cannot tolerate loss of one of the two alleles. Genes identified as essential in human cell lines or knockout mice may be distinct from those in living humans. Reconciling these discrepancies in how we evaluate gene essentiality has applications in clinical genetics and may offer insights for drug development.

  19. Radiologic findings of primary pneumonia in children

    International Nuclear Information System (INIS)

    Song, Chi Sung; Kim, In One; Yeon, Kyung Mo

    1991-01-01

    It is not always easy to detect and interpret radiologic findings of pediatric pneumonia. Authors retrospectively analysed radiologic findings of 102 cases of pediatric primary pneumonia treated at Yeong-Deung-Po City Hospital between 1988 and 1990 to understand the past trend of radiologic pattern and to attain helpful information in diagnosing pediatric pneumonia hereafter. Results were as follows. Positive radiologic findings were noted in 85 cases (84%), but 17 cases (16%) showed indefinite lesion. The cases of infantile pneumonia (under 1 year of age) were 44. The most frequent finding was bilateral peribronchial infiltration with overearation (21 cases, 48%), followed by multiple patchy atelectasis associated with the findings of bilateral peribronchial infiltration and overaeration (nine cases, 23%), peribronchial infiltration without definite overaeration (six cases, 14%), alveolar consolidation superimposed on the peribronchial infiltration (three cases, 6%), alveolar consolidation (three cases, 6%) and bronchopneumonic pattern (two cases, 4%). The cases of pre-school age (1-5 years of age) were 34. Bilateral parahilar peribronchial infiltration was the most frequent finding (24 cases, 71%), followed by alveolar consolidation (six cases, 17%) and bronchopneumonic pattern (four cases, 12%). The cases of school age (over 6 years of age) were seven. Six cases (85%) showed alveolar consolidation and one case (15%) showed bronchopneumonic pattern. In short, the younger the patient was, the more frequently the interstitial infiltration occurred. Furthermore, overaeration and patchy atelectasis were unique findings of infantile pneumonia. After the school age, the pattern of pneumonia became similar to that of adults

  20. Inferring gene regression networks with model trees

    Directory of Open Access Journals (Sweden)

    Aguilar-Ruiz Jesus S

    2010-10-01

    Full Text Available Abstract Background Novel strategies are required in order to handle the huge amount of data produced by microarray technologies. To infer gene regulatory networks, the first step is to find direct regulatory relationships between genes building the so-called gene co-expression networks. They are typically generated using correlation statistics as pairwise similarity measures. Correlation-based methods are very useful in order to determine whether two genes have a strong global similarity but do not detect local similarities. Results We propose model trees as a method to identify gene interaction networks. While correlation-based methods analyze each pair of genes, in our approach we generate a single regression tree for each gene from the remaining genes. Finally, a graph from all the relationships among output and input genes is built taking into account whether the pair of genes is statistically significant. For this reason we apply a statistical procedure to control the false discovery rate. The performance of our approach, named REGNET, is experimentally tested on two well-known data sets: Saccharomyces Cerevisiae and E.coli data set. First, the biological coherence of the results are tested. Second the E.coli transcriptional network (in the Regulon database is used as control to compare the results to that of a correlation-based method. This experiment shows that REGNET performs more accurately at detecting true gene associations than the Pearson and Spearman zeroth and first-order correlation-based methods. Conclusions REGNET generates gene association networks from gene expression data, and differs from correlation-based methods in that the relationship between one gene and others is calculated simultaneously. Model trees are very useful techniques to estimate the numerical values for the target genes by linear regression functions. They are very often more precise than linear regression models because they can add just different linear

  1. Prenatal ultrasound findings of fetal neoplasms

    International Nuclear Information System (INIS)

    Lee, Soo Hyun; Cho, Jeong Yeon; Song, Mi Jin; Min, Jee Yeon; Han, Byoung Hee; Lee, Young Ho; Cho, Byung Jae; Kim, Seung Hyup

    2002-01-01

    A variety of neoplasms can develop in each tetal organ. Most fetal neoplasms can be detected by careful prenatal ultrasonographic examination. Some neoplosms show specific ultrasonographic findings suggesting the differential diagnosis, but others do not. Knowledge of the presence of a neoplasm in the fetus may alter the prenatal management of a pregnancy and the mode of delivery, and facilitates immediate postnatal treatment. During the last five years, we experienced 32 cases of fetal neoplasms in a variety of organs. We describe their typical and ultrasonographic findings with correlating postnatal CT, MRI, and pathologic findings

  2. Finding the K shortest hyperpaths using reoptimization

    DEFF Research Database (Denmark)

    Nielsen, Lars Relund; Pretolani, Daniele; Andersen, Kim Allan

    2004-01-01

    The shortest hyperpath problem is an extension of the classical shortest path problem and has applications in many different areas. Recently, algorithms for finding the K shortest hyperpaths in a directed hypergraph have been developed by Andersen, Nielsen and Pretolani. In this paper we improve...... the worst-case computational complexity of an algorithm for finding the K shortest hyperpaths in an acyclic hypergraph. This result is obtained by applying new reoptimization techniques for shortest hyperpaths. The algorithm turns out to be quite effective in practice and has already been successfully...... applied in the context of stochastic time-dependent networks, for finding the K best strategies and for solving bicriterion problems....

  3. Finding the K shortest hyperpaths using reoptimization

    DEFF Research Database (Denmark)

    Nielsen, Lars Relund; Pretolani, Daniele; Andersen, Kim Allan

    2006-01-01

    The shortest hyperpath problem is an extension of the classical shortest path problem and has applications in many different areas. Recently, algorithms for finding the K shortest hyperpaths in a directed hypergraph have been developed by Andersen, Nielsen and Pretolani. In this paper we improve...... the worst-case computational complexity of an algorithm for finding the K shortest hyperpaths in an acyclic hypergraph. This result is obtained by applying new reoptimization techniques for shortest hyperpaths. The algorithm turns out to be quite effective in practice and has already been successfully...... applied in the context of stochastic time-dependent networks, for finding the K best strategies and for solving bicriterion problems...

  4. CT findings of inoperable lung carcinoma

    International Nuclear Information System (INIS)

    Gay, S.B.; Black, W.C.

    1987-01-01

    CT is useful in the evaluation of patients with newly diagnosed or highly suspected lung cancer. The principal role of CT is to screen those patients with metastatic disease beyond the hili from an attempt at curative thoracotomy. While CT is regarded as very sensitive, it is not considered highly specific, and thus a surgical procedure is usually recommended for definitive diagnosis of most ''positive'' CT findings. However, the authors demonstrate a few characteristic CT findings that are highly predictive of unresectable metastatic disease. These CT findings include massive mediastinal lymphadenopathy, diffuse mediastinal infiltration, pericardial involvement, vascular encasement, and advanced chest wall invasion

  5. Finding dense locations in indoor tracking data

    DEFF Research Database (Denmark)

    Ahmed, Tanvir; Pedersen, Torben Bach; Lu, Hua

    2014-01-01

    Finding the dense locations in large indoor spaces is very useful for getting overloaded locations, security, crowd management, indoor navigation, and guidance. Indoor tracking data can be very large and are not readily available for finding dense locations. This paper presents a graph-based model...... of the mapping table, along with associated construction, query processing, and pruning techniques. The DLT-Index supports very efficient aggregate point queries, interval queries, and dense location queries. A comprehensive experimental study with real data shows that the proposed techniques can efficiently...... find dense locations in large amounts of indoor tracking data....

  6. Pediatric AIDS. Neuroradiologic and neurodevelopmental findings

    Energy Technology Data Exchange (ETDEWEB)

    Price, D.B.; Haller, J.O.; Kramer, J.; Hotson, G.C.; Loh, J.P.; Schlusselberg, D.; Inglese, C.M.; Jacobs, J.; Rose, A.L.; Menez-Bautista, R.

    1988-09-01

    A group of 23 pediatric patients seropositive for HIV antibody were studied by computed tomography and evaluated neurodevelopmentally. Significant neurodevelopmental delays were found in over 95% of the patients studied. CT findings in six patients were normal and thirteen of 23 (57%) had prominence of the CSF spaces. Less frequent findings included calcifications in the basal ganglia and white matter. Cerebral mass lesions included one case of lymphoma and one case of hemorrhage. The CT findings in the pediatric age group differs from the adult population in that that contrast enhancing inflammatory mass lesions are uncommon.

  7. Systemic lupus erythematosus : abdominal radiologic findings

    Energy Technology Data Exchange (ETDEWEB)

    Oh, Jae Cheon; Cho, On Koo; Lee, Yong Joo; Bae, Jae Ik; Kim, Yong Soo; Rhim, Hyun Chul; Ko, Byung Hee [Hanyang Univ. College of Medicine, Seoul (Korea, Republic of)

    1999-06-01

    Systemic lupus erythematosus(SLE) is a systemic disease of unknown etiology. Its main pathology is vasculitis and serositis, due to deposition of the immune complex or antibodies. Most findings are nonspecific ; abdominal manifestations include enteritis, hepatomegaly, pancreatic enlargement, serositis, lymphadenopathy, splenomegaly, nephritis, interstitial cystitis, and thrombophlebitis. We described radiologic findings of various organ involvement of SLE; digestive system, serosa, reticuloendothelial system, urinary system, and venous system. Diagnosis of SLE was done according to the criteria of American Rheumatism Association. Understanding of the variable imaging findings in SLE may be helpful for the early detection of abdominal involvement and complications.

  8. The rules of gene expression in plants: Organ identity and gene body methylation are key factors for regulation of gene expression in Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Gutiérrez Rodrigo A

    2008-09-01

    capable of restraining the capacity of a gene to respond to internal/external cues. Our findings suggest a prominent role for epigenetic mechanisms in the regulation of gene expression in plants.

  9. The gene expression data of Mycobacterium tuberculosis based on Affymetrix gene chips provide insight into regulatory and hypothetical genes

    Directory of Open Access Journals (Sweden)

    Fu-Liu Casey S

    2007-05-01

    Full Text Available Abstract Background Tuberculosis remains a leading infectious disease with global public health threat. Its control and management have been complicated by multi-drug resistance and latent infection, which prompts scientists to find new and more effective drugs. With the completion of the genome sequence of the etiologic bacterium, Mycobacterium tuberculosis, it is now feasible to search for new drug targets by sieving through a large number of gene products and conduct genome-scale experiments based on microarray technology. However, the full potential of genome-wide microarray analysis in configuring interrelationships among all genes in M. tuberculosis has yet to be realized. To date, it is only possible to assign a function to 52% of proteins predicted in the genome. Results We conducted a functional-genomics study using the high-resolution Affymetrix oligonucleotide GeneChip. Approximately one-half of the genes were found to be always expressed, including more than 100 predicted conserved hypotheticals, in the genome of M. tuberculosis during the log phase of in vitro growth. The gene expression profiles were analyzed and visualized through cluster analysis to epitomize the full details of genomic behavior. Broad patterns derived from genome-wide expression experiments in this study have provided insight into the interrelationships among genes in the basic cellular processes of M. tuberculosis. Conclusion Our results have confirmed several known gene clusters in energy production, information pathways, and lipid metabolism, and also hinted at potential roles of hypothetical and regulatory proteins.

  10. Former Auctioneer Finds Voice After Aphasia

    Science.gov (United States)

    ... Aphasia Follow us Former Auctioneer Finds Voice After Aphasia Speech impairment changed his life One unremarkable September ... 10 Tips for Communicating with Someone who has Aphasia Talk to them in a quiet, calm, relaxed ...

  11. MRI findings of Guillain-Barre syndrome

    International Nuclear Information System (INIS)

    Park, Won Kyu; Lee, Hwa Jin; Byun, Woo Mok

    1997-01-01

    To evaluate MRI findings of Guillain-Barre syndrome. In six patients with Guillain-Barre syndrome diagnosed by clinical, cerebrospinal fluid and electrophysiologic findings, a retrospective review of MR findings was conducted. Follow-up MRI scans were carried out in two patients showing minimal clinical improvement. Marked or moderate enhancement of thickened nerve roots was seen in all cases on gadopentetate dimeglumine enhanced axial T1-weighted images. Two patterns were seen; one was even enhancement of both anterior and posterior nerve roots (n=1) and the other was enhancement of anterior nerve roots only (n=5). Enhancement and thickness of nerve roots was seen to have slightly decreased on MRI follow-up at 32 and 50 days; clinical and electrophysiologic examination showed minimal improvement. Although MRI findings of nerve root enhancement are nonspecific and can be seen in neoplastic and other inflammatory diseases, the enhancement of thickened anterior nerve roots within the cal sac suggests Guillain-Barre syndrome

  12. MRI findings of Guillain-Barre syndrome

    Energy Technology Data Exchange (ETDEWEB)

    Park, Won Kyu; Lee, Hwa Jin; Byun, Woo Mok [Yeungnam Univ. College of Medicine, Taegu (Korea, Republic of)

    1997-04-01

    To evaluate MRI findings of Guillain-Barre syndrome. In six patients with Guillain-Barre syndrome diagnosed by clinical, cerebrospinal fluid and electrophysiologic findings, a retrospective review of MR findings was conducted. Follow-up MRI scans were carried out in two patients showing minimal clinical improvement. Marked or moderate enhancement of thickened nerve roots was seen in all cases on gadopentetate dimeglumine enhanced axial T1-weighted images. Two patterns were seen; one was even enhancement of both anterior and posterior nerve roots (n=1) and the other was enhancement of anterior nerve roots only (n=5). Enhancement and thickness of nerve roots was seen to have slightly decreased on MRI follow-up at 32 and 50 days; clinical and electrophysiologic examination showed minimal improvement. Although MRI findings of nerve root enhancement are nonspecific and can be seen in neoplastic and other inflammatory diseases, the enhancement of thickened anterior nerve roots within the cal sac suggests Guillain-Barre syndrome.

  13. Isolated torsion of fallopian tube. Radiological findings

    International Nuclear Information System (INIS)

    Tomas Fanjul, L.; Aldea Martinez, J.; Fernandez Matia, G.; Rodrigo Verguizas, J.; Fernandez Alvarez, G.; Galindo Vicente, M.C.

    1993-01-01

    Isolated tubal torsion is a very uncommon disorder that is rarely diagnosed preoperatively. We present a case and review the literature, which only provides ultrasonographic findings in 5 cases reported to date. 11 refs

  14. 77 FR 46438 - Findings of Research Misconduct

    Science.gov (United States)

    2012-08-03

    ... respective agents, employees, associates, or related persons, including but not limited to the findings made..., earlier in the IJC (Table II) and Future Oncology publications. The only exception was the log titer value...

  15. MR findings of kallmann syndrome : case reports

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Sung Mi; Choi, Jin Ok; Lee, Kang Soo [Presbyterian Medical Center, Chunju (Korea, Republic of); Choi, See Sung [Wonkwang University Hospital, Chunju (Korea, Republic of)

    2000-04-01

    Kallman syndrome is characterised by hypogonadotrophic hypogonadism and anosmia. T1-weighted MR coronal images show the bilateral absence or hypoplasia of olfactory bulbs, tracts, and sulci. We report the MR findings of Kallmann syndrome and review the literature. (author)

  16. How to Find the Right Therapist

    Science.gov (United States)

    ... a Referral Listing Apply for a Research Grant Membership for Professionals Donate Ways to Give Search for: Find Help Search the Resource Directory for therapists, clinics, treatment programs, support groups, and organizations (such as affiliates ...

  17. Testicular Involvement of Tuberculous Epididymitis : Sonographic Findings

    Energy Technology Data Exchange (ETDEWEB)

    Chung, Jae Joon; Kim, Myeong Jin; Yoo, Hyung Sik; Lee, Jong Tae; Lee, Yong Hee [Yonsei University College of Medicine, Seoul (Korea, Republic of); Park, Joong Hwa [Yonsei University Wonju College of Medicine, Wonju (Korea, Republic of); Lee, Yeon Hee [Dankook University Hospital, Cheonan (Korea, Republic of)

    1996-12-15

    To report the sonographic findings of testicular involvement of tuberculous epididymitis. The sonographic findings of testicular involvement in twelve patients with histologically proven tuberculous epididymitis were retrospectively reviewed. The sonographic findings of testicular lesions are 1) an ill defined hypoechoic lesion (3 cases, 25.0%), 2) a well-demarcated hypoechoic lesion (3 cases, 25.0%),3) multiple and small hypoechoic nodules in the enlarged testis (2 cases, 16.7%), 4) indistinct margin between the testis and epididymis (2 cases, 16.7%) and 5) a diffusely enlarged testis with hypoechogenicity (2 cases, 16.7%).Nine patients had ipsilateral epididymitis, and 3 patients had bilateral epididymitis. Pus discharge through the draining sinus tract was noted in 4 cases (33.3%), and hydrocele in 8 cases (66.7%). No parenchymal calcification was seen in the involved testis. Sonographic findings of testicular involvement in tuberculous epididymitis were various

  18. MRI finding of ethylmalonic encephalopathy: case report

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Jin Yong; Lee, Shi Kyung; Han, Chun Hwan; Rho, Eun Jin [Kangnam General Hospital Public Corporation, Seoul (Korea, Republic of)

    2002-12-01

    Ethylmalonic encephalopathy is a rare syndrom characterized by developmental delay, acrocyanosis, petechiae, chronic diarrhea, and ethylmalonic, lactic, and methylsuccinic aciduria. We report the MRI finding of ethylmalonic encephalopathy including previously unreported intracranial hematoma.

  19. Genes under positive selection in Escherichia coli

    DEFF Research Database (Denmark)

    Petersen, Lise; Bollback, Jonathan P; Dimmic, Matt

    2007-01-01

    We used a comparative genomics approach to identify genes that are under positive selection in six strains of Escherichia coli and Shigella flexneri, including five strains that are human pathogens. We find that positive selection targets a wide range of different functions in the E. coli genome......, including cell surface proteins such as beta barrel porins, presumably because of the involvement of these genes in evolutionary arms races with other bacteria, phages, and/or the host immune system. Structural mapping of positively selected sites on trans-membrane beta barrel porins reveals...... that the residues under positive selection occur almost exclusively in the extracellular region of the proteins that are enriched with sites known to be targets of phages, colicins, or the host immune system. More surprisingly, we also find a number of other categories of genes that show very strong evidence...

  20. Typical radiological findings in Mirizzi's syndrome

    International Nuclear Information System (INIS)

    Strunk, H.; Teifke, A.; Menke, H.

    1988-01-01

    In extrahepatic cholestasis it is necessary to include Mirizzi's syndrome in the differential diagnostic considerations. Characteristic findings in sonography and computed tomography ae: a stone incorporated in the neck of the gallbladder or cystic duct with an extension of the common hepatic duct above the stone and normal width of the bile duct below the sone; in endoscopic retrograde cholangiography (ERC, direkt cholangiography), a characteristic finding is a smooth-walled, segmental stenosis through external compression or an incorporated stone. (orig.) [de

  1. Bouveret's syndrome: CT findings

    Energy Technology Data Exchange (ETDEWEB)

    Tueney, D.; Cimsit, C. [Dept. of Radiology, Marmara University Hospital, Istanbul (Turkey)

    2000-11-01

    Intestinal obstruction secondary to gallstones is seen in the older population and the level of obstruction is usually at the level of the terminal ileum. Obstruction at the level of the gastric outlet is called Bouveret's syndrome. A case with perforated cholecystitis and duodenal obstruction due to a gallstone is presented. The CT findings are presented along with the clinical findings and literature review. (orig.)

  2. Imaging findings of anterior hip dislocations

    Energy Technology Data Exchange (ETDEWEB)

    Pfeifer, Kyle [Mallinckrodt Institute of Radiology, Department of Radiology, St. Louis, MO (United States); Leslie, Michael [Yale School of Medicine, Department of Orthopedics and Rehabilitation, New Haven, CT (United States); Menn, Kirsten; Haims, Andrew [Yale University School of Medicine, Department of Radiology and Biomedical Imaging, New Haven, CT (United States)

    2017-06-15

    Anterior hip dislocations are rare orthopedic emergencies resulting from high-energy trauma and have unique imaging characteristics on radiography, computed tomography (CT), and magnetic resonance imaging (MRI). Imaging findings on CT and MRI allow for the prompt recognition and classification of anterior hip dislocations, which guides patient management and reduces complications. The purpose of this article is to review imaging findings of anterior hip dislocations, specifically focusing on CT and MRI. (orig.)

  3. Finding Dominators via Disjoint Set Union

    OpenAIRE

    Fraczak, Wojciech; Georgiadis, Loukas; Miller, Andrew; Tarjan, Robert E.

    2013-01-01

    The problem of finding dominators in a directed graph has many important applications, notably in global optimization of computer code. Although linear and near-linear-time algorithms exist, they use sophisticated data structures. We develop an algorithm for finding dominators that uses only a "static tree" disjoint set data structure in addition to simple lists and maps. The algorithm runs in near-linear or linear time, depending on the implementation of the disjoint set data structure. We g...

  4. How to Find the Students' Inner Geek

    Science.gov (United States)

    Zimmer, Marc

    2005-01-01

    As a chemistry professor at a liberal-arts college, the author believes it is his job to find the youthful awe in his students and draw it out so that they will be intrigued once again by science and nature, so that they want to learn about equilibria, pH, and redox reactions. He has to go fishing inside their brains, to find, hook, and reel in…

  5. Imaging findings of anterior hip dislocations

    International Nuclear Information System (INIS)

    Pfeifer, Kyle; Leslie, Michael; Menn, Kirsten; Haims, Andrew

    2017-01-01

    Anterior hip dislocations are rare orthopedic emergencies resulting from high-energy trauma and have unique imaging characteristics on radiography, computed tomography (CT), and magnetic resonance imaging (MRI). Imaging findings on CT and MRI allow for the prompt recognition and classification of anterior hip dislocations, which guides patient management and reduces complications. The purpose of this article is to review imaging findings of anterior hip dislocations, specifically focusing on CT and MRI. (orig.)

  6. Learning Transformation Rules to Find Grammatical Relations

    OpenAIRE

    Ferro, Lisa; Vilain, Marc; Yeh, Alexander

    1999-01-01

    Grammatical relationships are an important level of natural language processing. We present a trainable approach to find these relationships through transformation sequences and error-driven learning. Our approach finds grammatical relationships between core syntax groups and bypasses much of the parsing phase. On our training and test set, our procedure achieves 63.6% recall and 77.3% precision (f-score = 69.8).

  7. Synovial Hemangioma in the Knee: MRI Findings

    Directory of Open Access Journals (Sweden)

    Harun Arslan

    2015-01-01

    Full Text Available Synovial hemangiomas are rare benign tumors of vascular origin. A 23-year-old boy presented with knee pain and swelling. The boy had developed symptoms 18-months earlier. He was diagnosed with synovial hemangioma based on magnetic resonnance imaging examination and histopathologic findings of the arthroscopic biopsy tissue. We present the magnetic resonance imaging and histopathologic findings of synovial hemangioma of the knee.

  8. Finding Objects for Assisting Blind People

    OpenAIRE

    Yi, Chucai; Flores, Roberto W.; Chincha, Ricardo; Tian, YingLi

    2013-01-01

    Computer vision technology has been widely used for blind assistance, such as navigation and wayfinding. However, few camera-based systems are developed for helping blind or visually-impaired people to find daily necessities. In this paper, we propose a prototype system of blind-assistant object finding by camera-based network and matching-based recognition. We collect a dataset of daily necessities and apply Speeded-Up Robust Features (SURF) and Scale Invariant Feature Transform (SIFT) featu...

  9. Vertebral involvement in SAPHO syndrome: MRI findings

    Energy Technology Data Exchange (ETDEWEB)

    Nachtigal, A.; Cardinal, E.; Bureau, N.J. [Dept. of Radiology, Univ. de Montreal, QC (Canada); Sainte-Marie, L.G. [Dept. of Internal Medicine, Univ. de Montreal, QC (Canada); Milette, F. [Department of Pathology, Univ. de Montreal, QC (Canada)

    1999-03-01

    We report on the MRI findings in the vertebrae and surrounding soft tissues in two patients with the SAPHO syndrome (Synovitis, Acne, Pustulosis, Hyperostosis, Osteitis). The MRI findings include abnormal bone marrow signal, either focal or diffuse, of the vertebral bodies and posterior elements; hyperintense paravertebral soft tissue swelling and abnormal signal of the intervertebral discs. These changes are consistent with discitis and osteitis. (orig.) With 6 figs., 17 refs.

  10. Single gene retrieval from thermally degraded DNA

    Indian Academy of Sciences (India)

    To simulate single gene retrieval from ancient DNA, several related factors have been investigated. By monitoring a 889 bp polymerase chain reaction (PCR) product and genomic DNA degradation, we find that heat and oxygen (especially heat) are both crucial factors influencing DNA degradation. The heat influence ...

  11. Genes under positive selection in Escherichia coli

    DEFF Research Database (Denmark)

    Petersen, Lise; Bollback, Jonathan P; Dimmic, Matt

    2007-01-01

    We used a comparative genomics approach to identify genes that are under positive selection in six strains of Escherichia coli and Shigella flexneri, including five strains that are human pathogens. We find that positive selection targets a wide range of different functions in the E. coli genome...

  12. Genes Underlying Positive Influence Of Prenatal Environmental ...

    African Journals Online (AJOL)

    We aimed to investigate and find out key genes underlying the positive-negative effects derived from prenatal interventions. Materials and Methods: Pregnant rats were randomized into EE group (EEG), earthquake simulation group (ESG), herbal group (HG) received herbal supplements in feed after earthquake simulation, ...

  13. Methylated genes as new cancer biomarkers.

    LENUS (Irish Health Repository)

    Duffy, M J

    2012-02-01

    Aberrant hypermethylation of promoter regions in specific genes is a key event in the formation and progression of cancer. In at least some situations, these aberrant alterations occur early in the formation of malignancy and appear to be tumour specific. Multiple reports have suggested that measurement of the methylation status of the promoter regions of specific genes can aid early detection of cancer, determine prognosis and predict therapy responses. Promising DNA methylation biomarkers include the use of methylated GSTP1 for aiding the early diagnosis of prostate cancer, methylated PITX2 for predicting outcome in lymph node-negative breast cancer patients and methylated MGMT in predicting benefit from alkylating agents in patients with glioblastomas. However, prior to clinical utilisation, these findings require validation in prospective clinical studies. Furthermore, assays for measuring gene methylation need to be standardised, simplified and evaluated in external quality assurance programmes. It is concluded that methylated genes have the potential to provide a new generation of cancer biomarkers.

  14. HRCT findings of childhood follicular bronchiolitis

    Energy Technology Data Exchange (ETDEWEB)

    Weinman, Jason P.; Browne, Lorna P. [Children' s Hospital Colorado, Department of Radiology, Aurora, CO (United States); Manning, David A. [Children' s Hospital of New Orleans, Department of Radiology, New Orleans, LA (United States); Liptzin, Deborah R. [Children' s Hospital Colorado, Department of Pediatrics, Section of Pediatric Pulmonology, Aurora, CO (United States); Krausert, Amanda J. [New Orleans Forensic Center, New Orleans, LA (United States)

    2017-12-15

    Follicular bronchiolitis is a lymphoproliferative form of interstitial lung disease (ILD) defined by the presence of peribronchial lymphoid follicles. Follicular bronchiolitis has been associated with viral infection, autoimmune disease and immunodeficiency. The most common clinical manifestation is respiratory distress in infancy followed by a prolonged course with gradual improvement. We found no reports of systematic review of high-resolution computed tomography (HRCT) findings in pediatric follicular bronchiolitis. The purpose of this study was to describe the HRCT findings of follicular bronchiolitis in children and correlate these imaging findings with histopathology. A 5-year retrospective review of all pathology-proven cases of follicular bronchiolitis was performed. Inclusion criteria were age <18 years and an HRCT within 6 months of lung biopsy. HRCTs were reviewed by three observers and scored using the system previously described by Brody et al. Six patients met the inclusion criteria with age range at HRCT of 7-82 months (median: 39.5 months). Pulmonary nodules (n=6) were the most common HRCT finding followed by focal consolidation (n=5), bronchiectasis (n=4) and lymphadenopathy (n=3). Tree and bud opacities and nodules on CT correlated with interstitial lymphocytic infiltrates and discrete lymphoid follicles on pathology. The salient HRCT findings of childhood follicular bronchiolitis are bilateral, lower lung zone predominant pulmonary nodules and bronchiectasis with infantile onset of symptoms. These characteristic HRCT findings help differentiate follicular bronchiolitis from other forms of infantile onset ILD. (orig.)

  15. Abdominal imaging findings in gastrointestinal basidiobolomycosis.

    Science.gov (United States)

    Flicek, Kristina T; Vikram, Holenarasipur R; De Petris, Giovanni D; Johnson, C Daniel

    2015-02-01

    To describe the abdominal imaging findings of patients with gastrointestinal Basidiobolus ranarum infection. A literature search was performed to compile the abdominal imaging findings of all reported worldwide cases of gastrointestinal basidiobolomycosis (GIB). In addition, a retrospective review at our institution was performed to identify GIB cases that had imaging findings. A radiologist aware of the diagnosis reviewed the imaging findings in detail. Additional information was obtained from the medical records. A total of 73 GIB cases have been published in the medical literature. The most common abdominal imaging findings were masses in the colon, the liver, or multiple sites and bowel wall thickening. Initially, many patients were considered to have either a neoplasm or Crohn disease. We identified 7 proven cases of GIB at our institution, of which 4 had imaging studies (4 computed tomography [CT] examinations, 4 abdominal radiographs, and an upper gastrointestinal study). Imaging studies showed abnormalities in all 4 cases. Three-fourths of our study patients had an abdominal mass at CT. Two of 3 masses involved the kidneys and included urinary obstruction. All masses showed an inflammatory component with adjacent soft tissue stranding, with or without abscess formation. Radiologists should consider GIB when a patient from an arid climate presents with abdominal pain, weight loss, and an inflammatory abdominal mass on CT. Abdominal masses of the colon or liver, bowel wall thickening, and abscesses are the most common imaging findings.

  16. CT findings of acute pelvic inflammatory disease.

    Science.gov (United States)

    Lee, Mi Hee; Moon, Min Hoan; Sung, Chang Kyu; Woo, Hyunsik; Oh, Sohee

    2014-12-01

    To determine the computed tomographic (CT) findings of acute pelvic inflammatory disease (PID). This retrospective, single-institution case-control study was approved by our institutional review board, and the informed consent was waived owing to the retrospective nature of the study. CT images of 32 women with clinically proven acute PID and 32 control subjects with other conditions of similar presentation were retrospectively reviewed. Analysis of CT findings included hepatic capsular enhancement, pelvic fat haziness, complicated ascites, uterine serosal enhancement, tubal thickening, endometritis, and oophoritis. Comparison of CT findings was performed with the Chi square test or the Fisher exact test and logistic regression analysis was used to determine significant CT findings in predicting PID. The CT findings that showed a statistically significant difference were hepatic capsular enhancement on late arterial phase (p = 0.003), pelvic fat haziness (p = 0.045), and tubal thickening (p = 0.001). Subsequent multivariate logistic regression analysis revealed that the presence of hepatic capsular enhancement on late arterial phase and tubal thickening were significant predictors of PID (hepatic capsular enhancement on late arterial phase, p = 0.015, odds ratio [OR] = 4.8; tubal thickening, p = 0.005, OR = 10.5). Diagnostic morphological CT findings in women with clinically proven PID and acute abdominal pain include hepatic capsular enhancement on late arterial phase and tubal thickening.

  17. Defining the Role of Essential Genes in Human Disease

    Science.gov (United States)

    Robertson, David L.; Hentges, Kathryn E.

    2011-01-01

    A greater understanding of the causes of human disease can come from identifying characteristics that are specific to disease genes. However, a full understanding of the contribution of essential genes to human disease is lacking, due to the premise that these genes tend to cause developmental abnormalities rather than adult disease. We tested the hypothesis that human orthologs of mouse essential genes are associated with a variety of human diseases, rather than only those related to miscarriage and birth defects. We segregated human disease genes according to whether the knockout phenotype of their mouse ortholog was lethal or viable, defining those with orthologs producing lethal knockouts as essential disease genes. We show that the human orthologs of mouse essential genes are associated with a wide spectrum of diseases affecting diverse physiological systems. Notably, human disease genes with essential mouse orthologs are over-represented among disease genes associated with cancer, suggesting links between adult cellular abnormalities and developmental functions. The proteins encoded by essential genes are highly connected in protein-protein interaction networks, which we find correlates with an over-representation of nuclear proteins amongst essential disease genes. Disease genes associated with essential orthologs also are more likely than those with non-essential orthologs to contribute to disease through an autosomal dominant inheritance pattern, suggesting that these diseases may actually result from semi-dominant mutant alleles. Overall, we have described attributes found in disease genes according to the essentiality status of their mouse orthologs. These findings demonstrate that disease genes do occupy highly connected positions in protein-protein interaction networks, and that due to the complexity of disease-associated alleles, essential genes cannot be ignored as candidates for causing diverse human diseases. PMID:22096564

  18. Primetime for Learning Genes.

    Science.gov (United States)

    Keifer, Joyce

    2017-02-11

    Learning genes in mature neurons are uniquely suited to respond rapidly to specific environmental stimuli. Expression of individual learning genes, therefore, requires regulatory mechanisms that have the flexibility to respond with transcriptional activation or repression to select appropriate physiological and behavioral responses. Among the mechanisms that equip genes to respond adaptively are bivalent domains. These are specific histone modifications localized to gene promoters that are characteristic of both gene activation and repression, and have been studied primarily for developmental genes in embryonic stem cells. In this review, studies of the epigenetic regulation of learning genes in neurons, particularly the brain-derived neurotrophic factor gene ( BDNF ), by methylation/demethylation and chromatin modifications in the context of learning and memory will be highlighted. Because of the unique function of learning genes in the mature brain, it is proposed that bivalent domains are a characteristic feature of the chromatin landscape surrounding their promoters. This allows them to be "poised" for rapid response to activate or repress gene expression depending on environmental stimuli.

  19. Consequences of recurrent gene flow from crops to wild relatives.

    OpenAIRE

    Haygood, Ralph; Ives, Anthony R; Andow, David A

    2003-01-01

    Concern about gene flow from crops to wild relatives has become widespread with the increasing cultivation of transgenic crops. Possible consequences of such gene flow include genetic assimilation, wherein crop genes replace wild ones, and demographic swamping, wherein hybrids are less fertile than their wild parents, and wild populations shrink. Using mathematical models of a wild population recurrently receiving pollen from a genetically fixed crop, we find that the conditions for genetic a...

  20. Adaptive differences in gene expression in European flounder ( Platichthys flesus )

    DEFF Research Database (Denmark)

    Larsen, Peter Foged; Eg Nielsen, Einar; Williams, T.D.

    2007-01-01

    levels of neutral genetic divergence, a high number of genes were significantly differentially expressed between North Sea and Baltic Sea flounders maintained in a long-term reciprocal transplantation experiment mimicking natural salinities. Several of the differentially regulated genes could be directly...... linked to fitness traits. These findings demonstrate that flounders, despite little neutral genetic divergence between populations, are differently adapted to local environmental conditions and imply that adaptation in gene expression could be common in other marine organisms with similar low levels...

  1. A modified GC-specific MAKER gene annotation method reveals improved and novel gene predictions of high and low GC content in Oryza sativa.

    Science.gov (United States)

    Bowman, Megan J; Pulman, Jane A; Liu, Tiffany L; Childs, Kevin L

    2017-11-25

    Accurate structural annotation depends on well-trained gene prediction programs. Training data for gene prediction programs are often chosen randomly from a subset of high-quality genes that ideally represent the variation found within a genome. One aspect of gene variation is GC content, which differs across species and is bimodal in grass genomes. When gene prediction programs are trained on a subset of grass genes with random GC content, they are effectively being trained on two classes of genes at once, and this can be expected to result in poor results when genes are predicted in new genome sequences. We find that gene prediction programs trained on grass genes with random GC content do not completely predict all grass genes with extreme GC content. We show that gene prediction programs that are trained with grass genes with high or low GC content can make both better and unique gene predictions compared to gene prediction programs that are trained on genes with random GC content. By separately training gene prediction programs with genes from multiple GC ranges and using the programs within the MAKER genome annotation pipeline, we were able to improve the annotation of the Oryza sativa genome compared to using the standard MAKER annotation protocol. Gene structure was improved in over 13% of genes, and 651 novel genes were predicted by the GC-specific MAKER protocol. We present a new GC-specific MAKER annotation protocol to predict new and improved gene models and assess the biological significance of this method in Oryza sativa. We expect that this protocol will also be beneficial for gene prediction in any organism with bimodal or other unusual gene GC content.

  2. Mendel's genes: toward a full molecular characterization.

    Science.gov (United States)

    Reid, James B; Ross, John J

    2011-09-01

    The discipline of classical genetics is founded on the hereditary behavior of the seven genes studied by Gregor Mendel. The advent of molecular techniques has unveiled much about the identity of these genes. To date, four genes have been sequenced: A (flower color), LE (stem length), I (cotyledon color), and R (seed shape). Two of the other three genes, GP (pod color) and FA (fasciation), are amenable to candidate gene approaches on the basis of their function, linkage relationships, and synteny between the pea and Medicago genomes. However, even the gene (locus) identity is not known for certain for the seventh character, the pod form, although it is probably V. While the nature of the mutations used by Mendel cannot be determined with certainty, on the basis of the varieties available in Europe in the 1850s, we can speculate on their nature. It turns out that these mutations are attributable to a range of causes-from simple base substitutions and changes to splice sites to the insertion of a transposon-like element. These findings provide a fascinating connection between Mendelian genetics and molecular biology that can be used very effectively in teaching new generations of geneticists. Mendel's characters also provide novel insights into the nature of the genes responsible for characteristics of agronomic and consumer importance.

  3. Gene-network analysis identifies susceptibility genes related to glycobiology in autism.

    Directory of Open Access Journals (Sweden)

    Bert van der Zwaag

    Full Text Available The recent identification of copy-number variation in the human genome has opened up new avenues for the discovery of positional candidate genes underlying complex genetic disorders, especially in the field of psychiatric disease. One major challenge that remains is pinpointing the susceptibility genes in the multitude of disease-associated loci. This challenge may be tackled by reconstruction of functional gene-networks from the genes residing in these loci. We applied this approach to autism spectrum disorder (ASD, and identified the copy-number changes in the DNA of 105 ASD patients and 267 healthy individuals with Illumina Humanhap300 Beadchips. Subsequently, we used a human reconstructed gene-network, Prioritizer, to rank candidate genes in the segmental gains and losses in our autism cohort. This analysis highlighted several candidate genes already known to be mutated in cognitive and neuropsychiatric disorders, including RAI1, BRD1, and LARGE. In addition, the LARGE gene was part of a sub-network of seven genes functioning in glycobiology, present in seven copy-number changes specifically identified in autism patients with limited co-morbidity. Three of these seven copy-number changes were de novo in the patients. In autism patients with a complex phenotype and healthy controls no such sub-network was identified. An independent systematic analysis of 13 published autism susceptibility loci supports the involvement of genes related to glycobiology as we also identified the same or similar genes from those loci. Our findings suggest that the occurrence of genomic gains and losses of genes associated with glycobiology are important contributors to the development of ASD.

  4. Preliminary findings of a previously unrecognized porcine primary immunodeficiency disorder.

    Science.gov (United States)

    Ozuna, A G Cino; Rowland, R R R; Nietfeld, J C; Kerrigan, M A; Dekkers, J C M; Wyatt, C R

    2013-01-01

    Weaned pigs from a line bred for increased feed efficiency were enrolled in a study of the role of host genes in the response to infection with Porcine Reproductive and Respiratory Syndrome Virus (PRRSV). Four of the pigs were euthanatized early in the study due to weight loss with illness and poor body condition; 2 pigs before PRRSV infection and the other 2 pigs approximately 2 weeks after virus inoculation. The 2 inoculated pigs failed to produce PRRSV-specific antibodies. Gross findings included pneumonia, absence of a detectable thymus, and small secondary lymphoid tissues. Histologically, lymph nodes, spleen, tonsils, and Peyer's patches were sparsely cellular with decreased to absent T and B lymphocytes.

  5. Ethical perception of human gene in transgenic banana

    African Journals Online (AJOL)

    Jane

    2011-09-30

    Islamic, Buddhist,. Christian, and ... The research finding is useful to understand the social construct of the ethical acceptance of cross-species gene ...... December, Pyramisa Suites Hotel and Casino, Cairo. pp. 1-8. Latifah A, Jamil ...

  6. MRI findings of juvenile psoriatic arthritis

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Edward Y.; Kleinman, Paul K. [Harvard Medical School, Department of Radiology, Boston, MA (United States); Children' s Hospital Boston, MA (United States); Sundel, Robert P.; Kim, Susan [Harvard Medical School, Rheumatology Program, Division of Immunology and the Department of Pediatrics, Boston, MA (United States); Children' s Hospital Boston, MA (United States); Zurakowski, David [Harvard Medical School, Department of Radiology, Boston, MA (United States); Harvard Medical School, Department of Orthopaedic Surgery, Boston, MA (United States); Children' s Hospital Boston, MA (United States)

    2008-11-15

    The aim of this study was to describe the magnetic resonance imaging (MRI) features of juvenile psoriatic arthritis (JpsA) in children in order to facilitate early diagnosis and proper management. Two pediatric radiologists retrospectively reviewed in consensus a total of 37 abnormal MRI examinations from 31 pediatric patients (nine boys, 22 girls; age range 1-17 years; mean age 9.4 years) who had a definite diagnosis of JpsA and underwent MRI. Each MRI was evaluated for synovium abnormality (thickening and enhancement), joint effusion (small, moderate, and large), bone marrow abnormality (edema, enhancement, and location of abnormality), soft tissue abnormality (edema, enhancement, atrophy, and fatty infiltration), tendon abnormality (thickening, edema, tendon sheath fluid, and enhancement), and articular abnormality (joint space narrowing and erosion). The distribution of abnormal MRI findings among the six categories for the 37 MRI examinations was evaluated. The number of abnormal MRI findings for each MRI examination was assessed. Age at MRI examination and all six categories of abnormal MRI findings according to gender were evaluated. There were a total 96 abnormal MRI findings noted on 37 abnormal MRI examinations from 31 pediatric patients. The 37 abnormal MRI examinations included MRI of the hand (n=8), knee (n = 8), ankle (n = 5), pelvis (n = 5), temporomandibular joint (n = 4), wrist (n = 3), foot (n = 2), elbow (n = 1), and shoulder (n = 1). Twenty-eight diffuse synovial thickening and/or enhancement were the most common MRI abnormality (29.2%). Joint effusion comprised 22 abnormal MRI findings (22.9%). There were 16 abnormal MRI bone marrow edema and/or enhancement findings (16.7%), and in seven (7.3%) the edema involved non-articular sites. Soft tissue abnormality manifested as edema and/or enhancement constituted 14 abnormal MRI findings (14.5%). There were ten MRI abnormalities (10.4%) involving tendons. Articular abnormality seen as joint space

  7. Drosophila X-Linked Genes Have Lower Translation Rates than Autosomal Genes.

    Science.gov (United States)

    Zhang, Zhenguo; Presgraves, Daven C

    2016-02-01

    In Drosophila, X-linked and autosomal genes achieve comparable expression at the mRNA level. Whether comparable X-autosome gene expression is realized at the translational and, ultimately, the protein levels is, however, unknown. Previous studies suggest the possibility of higher translation rates for X-linked genes owing to stronger usage of preferred codons. In this study, we use public ribosome profiling data from Drosophila melanogaster to infer translation rates on the X chromosome versus the autosomes. We find that X-linked genes have consistently lower ribosome densities than autosomal genes in S2 cells, early embryos, eggs, and mature oocytes. Surprisingly, the lower ribosome densities of X-linked genes are not consistent with faster translation elongation but instead imply slower translation initiation. In particular, X-linked genes have sequence features known to slow translation initiation such as stronger mRNA structure near start codons and longer 5'-UTRs. Comparison to outgroup species suggests that stronger mRNA structure is an evolved feature of Drosophila X chromosomes. Finally, we find that the magnitude of the X-autosome difference in ribosome densities is smaller for genes encoding members of protein complexes, suggesting that stoichiometry constrains the evolution of translation rates. In sum, our analyses suggest that Drosophila X-linked genes have evolved lower translation rates than autosomal genes despite stronger usage of preferred codons. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  8. Gene ordering in partitive clustering using microarray expressions

    Indian Academy of Sciences (India)

    PRAKASH KUMAR

    the new hybrid approach, finds comparable or sometimes superior biological gene order in less computation time than those obtained by optimal leaf ordering in hierarchical clustering solution. Ray S S, Bandyopadhyay S and Pal S K 2007 Gene ordering in partitive clustering using microarray expressions; J. Biosci.

  9. Marker mapping and resistance gene associations in soybean

    OpenAIRE

    2011-01-01

    The invention provides novel molecular genetic markers in soybean, where the markers are useful, for example, in the marker-assisted selection of gene alleles that impart disease-resistance, thereby allowing the identification and selection of a disease-resistant plant. The markers also find use in positional cloning of disease-resistance genes.

  10. Vitamin D receptor gene variants in Parkinson's disease patients ...

    African Journals Online (AJOL)

    Background: Vitamin D plays an important role in neurodegenerative disorders as a crucial neuro-immunomodulator. Accumulating data provide evidences that vitamin D receptor (VDR) gene is a candidate gene for susceptibility to Parkinson's disease (PD). Aim: To find out whether the risk of the development of sporadic ...

  11. Posttranscriptional gene silencing in nuclei

    Science.gov (United States)

    Hoffer, Paul; Ivashuta, Sergey; Pontes, Olga; Vitins, Alexa; Pikaard, Craig; Mroczka, Andrew; Wagner, Nicholas; Voelker, Toni

    2011-01-01

    In plants, small interfering RNAs (siRNAs) with sequence homology to transcribed regions of genes can guide the sequence-specific degradation of corresponding mRNAs, leading to posttranscriptional gene silencing (PTGS). The current consensus is that siRNA-mediated PTGS occurs primarily in the cytoplasm where target mRNAs are localized and translated into proteins. However, expression of an inverted-repeat double-stranded RNA corresponding to the soybean FAD2-1A desaturase intron is sufficient to silence FAD2-1, implicating nuclear precursor mRNA (pre-mRNA) rather than cytosolic mRNA as the target of PTGS. Silencing FAD2-1 using intronic or 3′-UTR sequences does not affect transcription rates of the target genes but results in the strong reduction of target transcript levels in the nucleus. Moreover, siRNAs corresponding to pre-mRNA–specific sequences accumulate in the nucleus. In Arabidopsis, we find that two enzymes involved in PTGS, Dicer-like 4 and RNA-dependent RNA polymerase 6, are localized in the nucleus. Collectively, these results demonstrate that siRNA-directed RNA degradation can take place in the nucleus, suggesting the need for a more complex view of the subcellular compartmentation of PTGS in plants. PMID:21173264

  12. Gene expression profiles in skeletal muscle after gene electrotransfer

    Directory of Open Access Journals (Sweden)

    Eriksen Jens

    2007-06-01

    the muscles 2 weeks after DNA electrotransfer. Conclusion The small and transient changes found in the gene expression profiles are of great importance, as this demonstrates that DNA electrotransfer is safe with minor effects on the muscle host cells. These findings are essential for introducing the DNA electrotransfer to muscle for clinical use. Indeed the HV+LV pulse combination used has been optimised to ensure highly efficient and safe DNA electrotransfer.

  13. Genes and Social Behavior

    OpenAIRE

    Robinson, Gene E.; Fernald, Russell D.; Clayton, David F.

    2008-01-01

    What specific genes and regulatory sequences contribute to the organization and functioning of brain circuits that support social behavior? How does social experience interact with information in the genome to modulate these brain circuits? Here we address these questions by highlighting progress that has been made in identifying and understanding two key “vectors of influence” that link genes, brain, and social behavior: 1) social information alters gene readout in the brain to influence beh...

  14. MR findings of bowlegs in toddlers

    International Nuclear Information System (INIS)

    Iwasawa, Tae; Inaba, Yutaka; Kameshita, Kikuo; Nishimura, Gen; Aida, Noriko; Matsubara, Sho

    1999-01-01

    Background. Toddlers with severe physiologic tibial bowing are considered to be at risk for the development of Blount's disease. Objective. To correlate MR findings of the knee with the clinical outcome in toddlers with severe physiological tibial bowing. Materials and methods. MR findings were evaluated in 22 affected legs of 14 children with severe tibial bowing (mean age 1.9 years). In 18 affected legs, MR findings were compared with the transition of the tibial metaphyseal-diaphyseal angle (MDA) and tibiofemoral angle (TFA) measured serially between 2 and 3 years of age. Results. MR findings of severe tibial bowing comprised undulation of the posteromedial physis of the tibia (3/22), signal alterations in the medial tibial metaphysis (10/22), T2 prolongation in the posteromedial tibial epiphyseal cartilage (14/22) and signal changes in the medial menisci (18/22). The decrease in the TFA was different in the legs with and without increased signal in the epiphyseal cartilage, and the decrease in the MDA was different in the legs with and without physeal undulation. Conclusion. MR imaging findings can predict the retarded resolution of tibial bowing, which may be a risk factor for the development of Blount's disease. (orig.)

  15. Primary epiploic appendagitis: US and CT findings

    Energy Technology Data Exchange (ETDEWEB)

    Molla, E.; Ripolles, T.; Martinez, M.J.; Morote, V. [Department of Radiology, Hospital Dr. Peset, Valencia (Spain); Rosello-Sastre, E. [Department of Pathology, Hospital Dr. Peset, Valencia (Spain)

    1998-03-27

    A retrospective review is presented of seven cases of epiploic appendagitis, with surgical confirmation in one case. The main clinico-analytical data and the US and CT findings are described, as well as the histopathologic features in the sole case that underwent surgical resection. We also calculated the frequency of this entity in patients undergoing emergency abdominal US on clinical suspicion of diverticulitis. In all seven cases the clinico-analytical evidence was nonspecific (localized acute abdominal pain and slight leukocytosis), mimicking in six cases the clinical presentation of sigmoid diverticulitis and in one case that of acute appendicitis. US imaging findings were characteristic: a hyperechoic mass localized under the point of maximum pain, adjacent to the anterior peritoneal wall and fixed during deep breathing. In none of the cases did color Doppler US show flow. CT findings were also typical and showed a mass with a peripheral hyperattenuated rim surrounding an area of fatty attenuation. Overall 7.1 % of patients investigated to exclude sigmoid diverticulitis finally showed findings of primary epiploic appendagitis. Primary epiploic appendagitis thus shows characteristic US and CT findings that allow its diagnosis and follow-up. This entity is much more frequent than previously reported, especially in patients referred for US to exclude sigmoid diverticulitis. (orig.) With 4 figs., 14 refs.

  16. Primary epiploic appendagitis: US and CT findings

    International Nuclear Information System (INIS)

    Molla, E.; Ripolles, T.; Martinez, M.J.; Morote, V.; Rosello-Sastre, E.

    1998-01-01

    A retrospective review is presented of seven cases of epiploic appendagitis, with surgical confirmation in one case. The main clinico-analytical data and the US and CT findings are described, as well as the histopathologic features in the sole case that underwent surgical resection. We also calculated the frequency of this entity in patients undergoing emergency abdominal US on clinical suspicion of diverticulitis. In all seven cases the clinico-analytical evidence was nonspecific (localized acute abdominal pain and slight leukocytosis), mimicking in six cases the clinical presentation of sigmoid diverticulitis and in one case that of acute appendicitis. US imaging findings were characteristic: a hyperechoic mass localized under the point of maximum pain, adjacent to the anterior peritoneal wall and fixed during deep breathing. In none of the cases did color Doppler US show flow. CT findings were also typical and showed a mass with a peripheral hyperattenuated rim surrounding an area of fatty attenuation. Overall 7.1 % of patients investigated to exclude sigmoid diverticulitis finally showed findings of primary epiploic appendagitis. Primary epiploic appendagitis thus shows characteristic US and CT findings that allow its diagnosis and follow-up. This entity is much more frequent than previously reported, especially in patients referred for US to exclude sigmoid diverticulitis. (orig.)

  17. Nonpalpable breast cancer : mammographic and clinical findings

    Energy Technology Data Exchange (ETDEWEB)

    Seo, Jae Seung; Kim, Eun Kyung; Oh, Ki Keun; Cheon, Young Jik; Lee, Byung Chan [Yonsei Univ. College of Medicine, Seoul (Korea, Republic of)

    1998-08-01

    To evaluate the mammographic and clinical findings of nonpalpable breast cancer. Materials and Methods : In 28 of 607 breast cancer patients examined between January 1994 and April 1997, lesions were nonpalpable. We retrospectively analyzed the mammographic, clinical and pathologic features of 25 patients (28 lesions) whose mammograms we obtained. Results : Among these 25 patients (28 lesions) screening was abnormal in 22; other symptoms were bloody nipple discharge(n=4), and nipple eczema(n=2). The patients were 34-62 (mean 52)years old. Invasive ductal carcinoma(n=13), DCIS(ductal carcinoma in situ, n-12), Paget's disease (n=2), and LCIS(lobular carcinoma in situ, n=1) were found during surgery. Six of 28 lesions(21%) showed evidence of axillary nodal metastasis;the majority arose from the upper outer quadrant of the breast (n=21). The mammographic findings were mass (50%), (and mass with microcalcification, 11%); microcalcification(29%); asymmetrical density(14%); and normal (7%). According to the mammographic density of breast parenchyma, the major finding in the low density group(N1+P1) was mass(9/9), and in the high density group(P2+DY) was microcalcification (12/19). Conclusion : The most common mammographic findings of nonpalpable breast cancer were mass (50%) and microcalcification(29%). Its features varied according to the mammographic density of breast parenchyma;mass was the main finding in the low density group and microcalcification in the high density group.

  18. Nonpalpable breast cancer : mammographic and clinical findings

    International Nuclear Information System (INIS)

    Seo, Jae Seung; Kim, Eun Kyung; Oh, Ki Keun; Cheon, Young Jik; Lee, Byung Chan

    1998-01-01

    To evaluate the mammographic and clinical findings of nonpalpable breast cancer. Materials and Methods : In 28 of 607 breast cancer patients examined between January 1994 and April 1997, lesions were nonpalpable. We retrospectively analyzed the mammographic, clinical and pathologic features of 25 patients (28 lesions) whose mammograms we obtained. Results : Among these 25 patients (28 lesions) screening was abnormal in 22; other symptoms were bloody nipple discharge(n=4), and nipple eczema(n=2). The patients were 34-62 (mean 52)years old. Invasive ductal carcinoma(n=13), DCIS(ductal carcinoma in situ, n-12), Paget's disease (n=2), and LCIS(lobular carcinoma in situ, n=1) were found during surgery. Six of 28 lesions(21%) showed evidence of axillary nodal metastasis;the majority arose from the upper outer quadrant of the breast (n=21). The mammographic findings were mass (50%), (and mass with microcalcification, 11%); microcalcification(29%); asymmetrical density(14%); and normal (7%). According to the mammographic density of breast parenchyma, the major finding in the low density group(N1+P1) was mass(9/9), and in the high density group(P2+DY) was microcalcification (12/19). Conclusion : The most common mammographic findings of nonpalpable breast cancer were mass (50%) and microcalcification(29%). Its features varied according to the mammographic density of breast parenchyma;mass was the main finding in the low density group and microcalcification in the high density group

  19. CT findings of orbital inflammatory diseases

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Jang Min; Shin, Hyun Joon; Kim, Jung Hyuk; Suh, Won Hyuck [College of Medicine, Korea University, Seoul (Korea, Republic of)

    1991-09-15

    Twenty-nine patients with orbital inflammatory disease (OIDs) were retrospectively reviewed in order to analyze detailed CT findings which might aid in differentiating OIDs. This study comprised 18 pseudotumors, 5 thyroid ophthalmopathies, and 6 cases of orbital cellulitis. CT scans of the pseudotumors showed various findings such as exophthalmos, scleritis, myositis of the extraocular muscle (MOM), and bone lesion. Bone lesions of the pseudo tumors, which have been rarely reported, were present in 7 cases in our series. Bilateral exophthalmos, myositis, and retrobulbar fat deposition were readily detected by CT in thyroid ophthalmopathy, and, in addition, we found bone erosions involving the orbital apices in 2 cases. In orbital cellulitis, extraorbital soft tissue swelling and lateral displacement of the medial rectus muscle in cases with ethmoiditis were the most conspicuous features. In summary, because of the overlapping CT findings in OIDs, careful examination of CT findings regarding the mode of EOM involvement and the presence or absence of scleritis or sinusitis might help narrow down the differential diagnosis. A pseudotumor with bone lesions could be mistaken as a malignant lesion, and therefore it is necessary to correlate clinical features with CT findings for an accurate diagnosis.

  20. Radiologic findings of abdominal wall endometriosis

    International Nuclear Information System (INIS)

    Seo, Jung Wook

    2003-01-01

    To evaluate the imaging findings of abdominal wall endometriosis. In seven of 17 patients with surgically proven endometriosis of the abdominal wall, we retrospectively reviewed the findings of radiologic studies such as abdominal US (n=3), CT (n=4), and MRI (n=1). One patient under went more than one type of imaging, apparently. The surgical history of the seven, and their symptoms and preoperative diagnosis were reviewed, and the size, location, margin and nature of the mass, and the contrast enhancement patterns observed at radiologic studies, were assessed. The chief symptoms were palpable abdominal wall mass (n=5) and lower abdominal pain (n=2) around a surgical scar. Previous surgery included cesarean section (n=5), cesarean section with oophorectomy (n=1) and appendectomy (n=1). Masses were located in the subcutaneous fat layer (n=5) or rectus abdominis muscle (n=2), and their maximum diameter was 2.6 cm. Imaging findings, which correlated closely with the pathologic findings, included a well (n=5) or poorly marginated (n=2) solid mass, with a focal cystic area apparent in two cases. Although imaging findings of abdominal wall endometriosis may not be specific for diagnosis, the presence of a solid abdominal mass in female patients of reproductive age with a history of surgery is a diagnostic pointer