WorldWideScience

Sample records for svm-based gene finding

  1. A SVM bases AI design for interactive gaming

    OpenAIRE

    Jiang, Yang; Jiang, Jianmin; Palmer, Ian

    2008-01-01

    Interactive gaming requires automatic processing on large volume of random data produced by players on spot, such as shooting, football kicking, boxing etc. In this paper, we describe an artificial intelligence approach in processing such random data for interactive gaming by using a one-class support vector machine (OC-SVM). In comparison with existing techniques, our OC-SVM based interactive gaming design has the features of: (i): high speed processing, providing instant response to the pla...

  2. Power quality events recognition using a SVM-based method

    Energy Technology Data Exchange (ETDEWEB)

    Cerqueira, Augusto Santiago; Ferreira, Danton Diego; Ribeiro, Moises Vidal; Duque, Carlos Augusto [Department of Electrical Circuits, Federal University of Juiz de Fora, Campus Universitario, 36036 900, Juiz de Fora MG (Brazil)

    2008-09-15

    In this paper, a novel SVM-based method for power quality event classification is proposed. A simple approach for feature extraction is introduced, based on the subtraction of the fundamental component from the acquired voltage signal. The resulting signal is presented to a support vector machine for event classification. Results from simulation are presented and compared with two other methods, the OTFR and the LCEC. The proposed method shown an improved performance followed by a reasonable computational cost. (author)

  3. Finding Genes for Schizophrenia

    OpenAIRE

    Åberg, Karolina

    2005-01-01

    Schizophrenia is one of our most common psychiatric diseases. It severely affects all aspects of psychological functions and results in loss of contact with reality. No cure exists and the treatments available today produce only partial relief for disease symptoms. The aim of this work is to better understand the etiology of schizophrenia by identification of candidate genes and gene pathways involved in the development of the disease. In a preliminarily study, the effects of medication and g...

  4. Generalized SMO algorithm for SVM-based multitask learning.

    Science.gov (United States)

    Cai, Feng; Cherkassky, Vladimir

    2012-06-01

    Exploiting additional information to improve traditional inductive learning is an active research area in machine learning. In many supervised-learning applications, training data can be naturally separated into several groups, and incorporating this group information into learning may improve generalization. Recently, Vapnik proposed a general approach to formalizing such problems, known as "learning with structured data" and its support vector machine (SVM) based optimization formulation called SVM+. Liang and Cherkassky showed the connection between SVM+ and multitask learning (MTL) approaches in machine learning, and proposed an SVM-based formulation for MTL called SVM+MTL for classification. Training the SVM+MTL classifier requires the solution of a large quadratic programming optimization problem which scales as O(n(3)) with sample size n. So there is a need to develop computationally efficient algorithms for implementing SVM+MTL. This brief generalizes Platt's sequential minimal optimization (SMO) algorithm to the SVM+MTL setting. Empirical results show that, for typical SVM+MTL problems, the proposed generalized SMO achieves over 100 times speed-up, in comparison with general-purpose optimization routines.

  5. A support vector machine (SVM) based voltage stability classifier

    Energy Technology Data Exchange (ETDEWEB)

    Dosano, R.D.; Song, H. [Kunsan National Univ., Kunsan, Jeonbuk (Korea, Republic of); Lee, B. [Korea Univ., Seoul (Korea, Republic of)

    2007-07-01

    Power system stability has become even more complex and critical with the advent of deregulated energy markets and the growing desire to completely employ existing transmission and infrastructure. The economic pressure on electricity markets forces the operation of power systems and components to their limit of capacity and performance. System conditions can be more exposed to instability due to greater uncertainty in day to day system operations and increase in the number of potential components for system disturbances potentially resulting in voltage stability. This paper proposed a support vector machine (SVM) based power system voltage stability classifier using local measurements of voltage and active power of load. It described the procedure for fast classification of long-term voltage stability using the SVM algorithm. The application of the SVM based voltage stability classifier was presented with reference to the choice of input parameters; input data preconditioning; moving window for feature vector; determination of learning samples; and other considerations in SVM applications. The paper presented a case study with numerical examples of an 11-bus test system. The test results for the feasibility study demonstrated that the classifier could offer an excellent performance in classification with time-series measurements in terms of long-term voltage stability. 9 refs., 14 figs.

  6. 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.)

  7. 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.)

  8. 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

  9. SVM Based Descriptor Selection and Classification of Neurodegenerative Disease Drugs for Pharmacological Modeling.

    Science.gov (United States)

    Shahid, Mohammad; Shahzad Cheema, Muhammad; Klenner, Alexander; Younesi, Erfan; Hofmann-Apitius, Martin

    2013-03-01

    Systems pharmacological modeling of drug mode of action for the next generation of multitarget drugs may open new routes for drug design and discovery. Computational methods are widely used in this context amongst which support vector machines (SVM) have proven successful in addressing the challenge of classifying drugs with similar features. We have applied a variety of such SVM-based approaches, namely SVM-based recursive feature elimination (SVM-RFE). We use the approach to predict the pharmacological properties of drugs widely used against complex neurodegenerative disorders (NDD) and to build an in-silico computational model for the binary classification of NDD drugs from other drugs. Application of an SVM-RFE model to a set of drugs successfully classified NDD drugs from non-NDD drugs and resulted in overall accuracy of ∼80 % with 10 fold cross validation using 40 top ranked molecular descriptors selected out of total 314 descriptors. Moreover, SVM-RFE method outperformed linear discriminant analysis (LDA) based feature selection and classification. The model reduced the multidimensional descriptors space of drugs dramatically and predicted NDD drugs with high accuracy, while avoiding over fitting. Based on these results, NDD-specific focused libraries of drug-like compounds can be designed and existing NDD-specific drugs can be characterized by a well-characterized set of molecular descriptors. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Simultaneous gene finding in multiple genomes.

    Science.gov (United States)

    König, Stefanie; Romoth, Lars W; Gerischer, Lizzy; Stanke, Mario

    2016-11-15

    As the tree of life is populated with sequenced genomes ever more densely, the new challenge is the accurate and consistent annotation of entire clades of genomes. We address this problem with a new approach to comparative gene finding that takes a multiple genome alignment of closely related species and simultaneously predicts the location and structure of protein-coding genes in all input genomes, thereby exploiting negative selection and sequence conservation. The model prefers potential gene structures in the different genomes that are in agreement with each other, or-if not-where the exon gains and losses are plausible given the species tree. We formulate the multi-species gene finding problem as a binary labeling problem on a graph. The resulting optimization problem is NP hard, but can be efficiently approximated using a subgradient-based dual decomposition approach. The proposed method was tested on whole-genome alignments of 12 vertebrate and 12 Drosophila species. The accuracy was evaluated for human, mouse and Drosophila melanogaster and compared to competing methods. Results suggest that our method is well-suited for annotation of (a large number of) genomes of closely related species within a clade, in particular, when RNA-Seq data are available for many of the genomes. The transfer of existing annotations from one genome to another via the genome alignment is more accurate than previous approaches that are based on protein-spliced alignments, when the genomes are at close to medium distances. The method is implemented in C ++ as part of Augustus and available open source at http://bioinf.uni-greifswald.de/augustus/ CONTACT: stefaniekoenig@ymail.com or mario.stanke@uni-greifswald.deSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  11. Diagnosis of Elevator Faults with LS-SVM Based on Optimization by K-CV

    Directory of Open Access Journals (Sweden)

    Zhou Wan

    2015-01-01

    Full Text Available Several common elevator malfunctions were diagnosed with a least square support vector machine (LS-SVM. After acquiring vibration signals of various elevator functions, their energy characteristics and time domain indicators were extracted by theoretically analyzing the optimal wavelet packet, in order to construct a feature vector of malfunctions for identifying causes of the malfunctions as input of LS-SVM. Meanwhile, parameters about LS-SVM were optimized by K-fold cross validation (K-CV. After diagnosing deviated elevator guide rail, deviated shape of guide shoe, abnormal running of tractor, erroneous rope groove of traction sheave, deviated guide wheel, and tension of wire rope, the results suggested that the LS-SVM based on K-CV optimization was one of effective methods for diagnosing elevator malfunctions.

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

    Science.gov (United States)

    Xiong, Jiping; Cai, Lisang; Wang, Fei; He, Xiaowei

    2017-03-03

    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.

  13. SVM-Based System for Prediction of Epileptic Seizures from iEEG Signal

    Science.gov (United States)

    Cherkassky, Vladimir; Lee, Jieun; Veber, Brandon; Patterson, Edward E.; Brinkmann, Benjamin H.; Worrell, Gregory A.

    2017-01-01

    Objective This paper describes a data-analytic modeling approach for prediction of epileptic seizures from intracranial electroencephalogram (iEEG) recording of brain activity. Even though it is widely accepted that statistical characteristics of iEEG signal change prior to seizures, robust seizure prediction remains a challenging problem due to subject-specific nature of data-analytic modeling. Methods Our work emphasizes understanding of clinical considerations important for iEEG-based seizure prediction, and proper translation of these clinical considerations into data-analytic modeling assumptions. Several design choices during pre-processing and post-processing are considered and investigated for their effect on seizure prediction accuracy. Results Our empirical results show that the proposed SVM-based seizure prediction system can achieve robust prediction of preictal and interictal iEEG segments from dogs with epilepsy. The sensitivity is about 90–100%, and the false-positive rate is about 0–0.3 times per day. The results also suggest good prediction is subject-specific (dog or human), in agreement with earlier studies. Conclusion Good prediction performance is possible only if the training data contain sufficiently many seizure episodes, i.e., at least 5–7 seizures. Significance The proposed system uses subject-specific modeling and unbalanced training data. This system also utilizes three different time scales during training and testing stages. PMID:27362758

  14. 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.

  15. 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.

  16. Finding Cardiovascular Disease Genes in the Dog

    Science.gov (United States)

    Parker, Heidi G.; Meurs, Kathryn M.; Ostrander, Elaine A.

    2013-01-01

    Recent advances in canine genomics are changing the landscape of veterinary biology, and by default, veterinary medicine. No longer are clinicians locked into traditional methods of diagnoses and therapy. Rather major advances in canine genetics and genomics from the past five years are now changing the way the veterinarian of the 21st century practices medicine. First, the availability of a dense genome map gives canine genetics a much needed foothold in comparative medicine, allowing advances made in human and mouse genetics to be applied to companion animals. Second, the recently released 7.5x whole genome sequence of the dog is facilitating the identification of hereditary disease genes. Finally, development of genetic tools for rapid screening of families and populations at risk for inherited disease means that the cost of identifying and testing for disease loci will significantly decrease in coming years. Out of these advances will come major changes in companion animal diagnostics and therapy. Clinicians will be able to offer their clients genetic testing and counseling for a myriad of disorders. Such advances are certain to generate healthier and more long lived dogs, improving quality of life for owner and pet alike. The clinician of the 21st century, therefore, faces incredible opportunities as well as challenges in the management of genetic disease. In this review we summarize recent findings in canine genomics and discuss their application to the study of canine cardiac health. PMID:19083345

  17. 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.

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

    Directory of Open Access Journals (Sweden)

    Yi Long

    2016-09-01

    Full Text Available 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.

  19. Effective Sequential Classifier Training for SVM-Based Multitemporal Remote Sensing Image Classification

    Science.gov (United States)

    Guo, Yiqing; Jia, Xiuping; Paull, David

    2018-06-01

    The explosive availability of remote sensing images has challenged supervised classification algorithms such as Support Vector Machines (SVM), as training samples tend to be highly limited due to the expensive and laborious task of ground truthing. The temporal correlation and spectral similarity between multitemporal images have opened up an opportunity to alleviate this problem. In this study, a SVM-based Sequential Classifier Training (SCT-SVM) approach is proposed for multitemporal remote sensing image classification. The approach leverages the classifiers of previous images to reduce the required number of training samples for the classifier training of an incoming image. For each incoming image, a rough classifier is firstly predicted based on the temporal trend of a set of previous classifiers. The predicted classifier is then fine-tuned into a more accurate position with current training samples. This approach can be applied progressively to sequential image data, with only a small number of training samples being required from each image. Experiments were conducted with Sentinel-2A multitemporal data over an agricultural area in Australia. Results showed that the proposed SCT-SVM achieved better classification accuracies compared with two state-of-the-art model transfer algorithms. When training data are insufficient, the overall classification accuracy of the incoming image was improved from 76.18% to 94.02% with the proposed SCT-SVM, compared with those obtained without the assistance from previous images. These results demonstrate that the leverage of a priori information from previous images can provide advantageous assistance for later images in multitemporal image classification.

  20. LaSVM-based big data learning system for dynamic prediction of air pollution in Tehran.

    Science.gov (United States)

    Ghaemi, Z; Alimohammadi, A; Farnaghi, M

    2018-04-20

    Due to critical impacts of air pollution, prediction and monitoring of air quality in urban areas are important tasks. However, because of the dynamic nature and high spatio-temporal variability, prediction of the air pollutant concentrations is a complex spatio-temporal problem. Distribution of pollutant concentration is influenced by various factors such as the historical pollution data and weather conditions. Conventional methods such as the support vector machine (SVM) or artificial neural networks (ANN) show some deficiencies when huge amount of streaming data have to be analyzed for urban air pollution prediction. In order to overcome the limitations of the conventional methods and improve the performance of urban air pollution prediction in Tehran, a spatio-temporal system is designed using a LaSVM-based online algorithm. Pollutant concentration and meteorological data along with geographical parameters are continually fed to the developed online forecasting system. Performance of the system is evaluated by comparing the prediction results of the Air Quality Index (AQI) with those of a traditional SVM algorithm. Results show an outstanding increase of speed by the online algorithm while preserving the accuracy of the SVM classifier. Comparison of the hourly predictions for next coming 24 h, with those of the measured pollution data in Tehran pollution monitoring stations shows an overall accuracy of 0.71, root mean square error of 0.54 and coefficient of determination of 0.81. These results are indicators of the practical usefulness of the online algorithm for real-time spatial and temporal prediction of the urban air quality.

  1. A SVM-based quantitative fMRI method for resting-state functional network detection.

    Science.gov (United States)

    Song, Xiaomu; Chen, Nan-kuei

    2014-09-01

    Resting-state functional magnetic resonance imaging (fMRI) aims to measure baseline neuronal connectivity independent of specific functional tasks and to capture changes in the connectivity due to neurological diseases. Most existing network detection methods rely on a fixed threshold to identify functionally connected voxels under the resting state. Due to fMRI non-stationarity, the threshold cannot adapt to variation of data characteristics across sessions and subjects, and generates unreliable mapping results. In this study, a new method is presented for resting-state fMRI data analysis. Specifically, the resting-state network mapping is formulated as an outlier detection process that is implemented using one-class support vector machine (SVM). The results are refined by using a spatial-feature domain prototype selection method and two-class SVM reclassification. The final decision on each voxel is made by comparing its probabilities of functionally connected and unconnected instead of a threshold. Multiple features for resting-state analysis were extracted and examined using an SVM-based feature selection method, and the most representative features were identified. The proposed method was evaluated using synthetic and experimental fMRI data. A comparison study was also performed with independent component analysis (ICA) and correlation analysis. The experimental results show that the proposed method can provide comparable or better network detection performance than ICA and correlation analysis. The method is potentially applicable to various resting-state quantitative fMRI studies. Copyright © 2014 Elsevier Inc. All rights reserved.

  2. 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...

  3. 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.

  4. Markers and mapping revisited: finding your gene.

    Science.gov (United States)

    Jones, Neil; Ougham, Helen; Thomas, Howard; Pasakinskiene, Izolda

    2009-01-01

    This paper is an update of our earlier review (Jones et al., 1997, Markers and mapping: we are all geneticists now. New Phytologist 137: 165-177), which dealt with the genetics of mapping, in terms of recombination as the basis of the procedure, and covered some of the first generation of markers, including restriction fragment length polymorphisms (RFLPs), random amplified polymorphic DNA (RAPDs), simple sequence repeats (SSRs) and quantitative trait loci (QTLs). In the intervening decade there have been numerous developments in marker science with many new systems becoming available, which are herein described: cleavage amplification polymorphism (CAP), sequence-specific amplification polymorphism (S-SAP), inter-simple sequence repeat (ISSR), sequence tagged site (STS), sequence characterized amplification region (SCAR), selective amplification of microsatellite polymorphic loci (SAMPL), single nucleotide polymorphism (SNP), expressed sequence tag (EST), sequence-related amplified polymorphism (SRAP), target region amplification polymorphism (TRAP), microarrays, diversity arrays technology (DArT), single-strand conformation polymorphism (SSCP), denaturing gradient gel electrophoresis (DGGE), temperature gradient gel electrophoresis (TGGE) and methylation-sensitive PCR. In addition there has been an explosion of knowledge and databases in the area of genomics and bioinformatics. The number of flowering plant ESTs is c. 19 million and counting, with all the opportunity that this provides for gene-hunting, while the survey of bioinformatics and computer resources points to a rapid growth point for future activities in unravelling and applying the burst of new information on plant genomes. A case study is presented on tracking down a specific gene (stay-green (SGR), a post-transcriptional senescence regulator) using the full suite of mapping tools and comparative mapping resources. We end with a brief speculation on how genome analysis may progress into the future of

  5. Modeling the milling tool wear by using an evolutionary SVM-based model from milling runs experimental data

    Science.gov (United States)

    Nieto, Paulino José García; García-Gonzalo, Esperanza; Vilán, José Antonio Vilán; Robleda, Abraham Segade

    2015-12-01

    The main aim of this research work is to build a new practical hybrid regression model to predict the milling tool wear in a regular cut as well as entry cut and exit cut of a milling tool. The model was based on Particle Swarm Optimization (PSO) in combination with support vector machines (SVMs). This optimization mechanism involved kernel parameter setting in the SVM training procedure, which significantly influences the regression accuracy. Bearing this in mind, a PSO-SVM-based model, which is based on the statistical learning theory, was successfully used here to predict the milling tool flank wear (output variable) as a function of the following input variables: the time duration of experiment, depth of cut, feed, type of material, etc. To accomplish the objective of this study, the experimental dataset represents experiments from runs on a milling machine under various operating conditions. In this way, data sampled by three different types of sensors (acoustic emission sensor, vibration sensor and current sensor) were acquired at several positions. A second aim is to determine the factors with the greatest bearing on the milling tool flank wear with a view to proposing milling machine's improvements. Firstly, this hybrid PSO-SVM-based regression model captures the main perception of statistical learning theory in order to obtain a good prediction of the dependence among the flank wear (output variable) and input variables (time, depth of cut, feed, etc.). Indeed, regression with optimal hyperparameters was performed and a determination coefficient of 0.95 was obtained. The agreement of this model with experimental data confirmed its good performance. Secondly, the main advantages of this PSO-SVM-based model are its capacity to produce a simple, easy-to-interpret model, its ability to estimate the contributions of the input variables, and its computational efficiency. Finally, the main conclusions of this study are exposed.

  6. 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

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

    Science.gov (United States)

    Weis, Christian; Hess, Andreas; Budinsky, Lubos; Fabry, Ben

    2015-01-01

    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.

  8. 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.

  9. FaaPred: a SVM-based prediction method for fungal adhesins and adhesin-like proteins.

    Directory of Open Access Journals (Sweden)

    Jayashree Ramana

    Full Text Available Adhesion constitutes one of the initial stages of infection in microbial diseases and is mediated by adhesins. Hence, identification and comprehensive knowledge of adhesins and adhesin-like proteins is essential to understand adhesin mediated pathogenesis and how to exploit its therapeutic potential. However, the knowledge about fungal adhesins is rudimentary compared to that of bacterial adhesins. In addition to host cell attachment and mating, the fungal adhesins play a significant role in homotypic and xenotypic aggregation, foraging and biofilm formation. Experimental identification of fungal adhesins is labor- as well as time-intensive. In this work, we present a Support Vector Machine (SVM based method for the prediction of fungal adhesins and adhesin-like proteins. The SVM models were trained with different compositional features, namely, amino acid, dipeptide, multiplet fractions, charge and hydrophobic compositions, as well as PSI-BLAST derived PSSM matrices. The best classifiers are based on compositional properties as well as PSSM and yield an overall accuracy of 86%. The prediction method based on best classifiers is freely accessible as a world wide web based server at http://bioinfo.icgeb.res.in/faap. This work will aid rapid and rational identification of fungal adhesins, expedite the pace of experimental characterization of novel fungal adhesins and enhance our knowledge about role of adhesins in fungal infections.

  10. 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.

  11. 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.

  12. Gene analogue finder: a GRID solution for finding functionally analogous gene products

    Directory of Open Access Journals (Sweden)

    Licciulli Flavio

    2007-09-01

    Full Text Available Abstract Background To date more than 2,1 million gene products from more than 100000 different species have been described specifying their function, the processes they are involved in and their cellular localization using a very well defined and structured vocabulary, the gene ontology (GO. Such vast, well defined knowledge opens the possibility of compare gene products at the level of functionality, finding gene products which have a similar function or are involved in similar biological processes without relying on the conventional sequence similarity approach. Comparisons within such a large space of knowledge are highly data and computing intensive. For this reason this project was based upon the use of the computational GRID, a technology offering large computing and storage resources. Results We have developed a tool, GENe AnaloGue FINdEr (ENGINE that parallelizes the search process and distributes the calculation and data over the computational GRID, splitting the process into many sub-processes and joining the calculation and the data on the same machine and therefore completing the whole search in about 3 days instead of occupying one single machine for more than 5 CPU years. The results of the functional comparison contain potential functional analogues for more than 79000 gene products from the most important species. 46% of the analyzed gene products are well enough described for such an analysis to individuate functional analogues, such as well-known members of the same gene family, or gene products with similar functions which would never have been associated by standard methods. Conclusion ENGINE has produced a list of potential functionally analogous relations between gene products within and between species using, in place of the sequence, the gene description of the GO, thus demonstrating the potential of the GO. However, the current limiting factor is the quality of the associations of many gene products from non

  13. 基于信息熵的SVM入侵检测技术%Exploring SVM-based intrusion detection through information entropy theory

    Institute of Scientific and Technical Information of China (English)

    朱文杰; 王强; 翟献军

    2013-01-01

    在传统基于SVM的入侵检测中,核函数构造和特征选择采用先验知识,普遍存在准确度不高、效率低下的问题.通过信息熵理论与SVM算法相结合的方法改进为基于信息熵的SVM入侵检测算法,可以提高入侵检测的准确性,提升入侵检测的效率.基于信息熵的SVM入侵检测算法包括两个方面:一方面,根据样本包含的用户信息熵和方差,将样本特征统一,以特征是否属于置信区间来度量.将得到的样本特征置信向量作为SVM核函数的构造参数,既可保证训练样本集与最优分类面之间的对应关系,又可得到入侵检测需要的最大分类间隔;另一方面,将样本包含的用户信息量作为度量大幅度约简样本特征子集,不但降低了样本计算规模,而且提高了分类器的训练速度.实验表明,该算法在入侵检测系统中的应用优于传统的SVM算法.%In traditional SVM based intrusion detection approaches,both core function construction and feature selection use prior knowdege.Due to this,they are not only inefficient but also inaccurate.It is observed that integrating information entropy theory into SVM-based intrusion detection can enhance both the precision and the speed.Concludely speaking,SVM-based entropy intrusion detection algorithms are made up of two aspects:on one hand,setting sample confidence vector as core function's constructor of SVM algorithm can guarantee the mapping relationship between training sample and optimization classification plane.Also,the intrusion detection's maximum interval can be acquired.On the other hand,simplifying feature subset with samples's entropy as metric standard can not only shrink the computing scale but also improve the speed.Experiments prove that the SVM based entropy intrusion detection algoritm outperfomrs other tradional algorithms.

  14. 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.

  15. 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.

  16. Finding new genes for non-syndromic hearing loss through an in silico prioritization study.

    Directory of Open Access Journals (Sweden)

    Matteo Accetturo

    Full Text Available At present, 51 genes are already known to be responsible for Non-Syndromic hereditary Hearing Loss (NSHL, but the knowledge of 121 NSHL-linked chromosomal regions brings to the hypothesis that a number of disease genes have still to be uncovered. To help scientists to find new NSHL genes, we built a gene-scoring system, integrating Gene Ontology, NCBI Gene and Map Viewer databases, which prioritizes the candidate genes according to their probability to cause NSHL. We defined a set of candidates and measured their functional similarity with respect to the disease gene set, computing a score ( S S M avg that relies on the assumption that functionally related genes might contribute to the same (disease phenotype. A Kolmogorov-Smirnov test, comparing the pair-wise distribution on the disease gene set with the distribution on the remaining human genes, provided a statistical assessment of this assumption. We found at a p-value 0.99. The twenty top-scored genes were finally examined to evaluate their possible involvement in NSHL. We found that half of them are known to be expressed in human inner ear or cochlea and are mainly involved in remodeling and organization of actin formation and maintenance of the cilia and the endocochlear potential. These findings strongly indicate that our metric was able to suggest excellent NSHL candidates to be screened in patients and controls for causative mutations.

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

    Science.gov (United States)

    Vieira, Lucas Maciel; Grativol, Clicia; Thiebaut, Flavia; Carvalho, Thais G; Hardoim, Pablo R; Hemerly, Adriana; Lifschitz, Sergio; Ferreira, Paulo Cavalcanti Gomes; Walter, Maria Emilia M T

    2017-03-04

    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.

  18. 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.

  19. Gene × Smoking Interactions on Human Brain Gene Expression: Finding Common Mechanisms in Adolescents and Adults

    Science.gov (United States)

    Wolock, Samuel L.; Yates, Andrew; Petrill, Stephen A.; Bohland, Jason W.; Blair, Clancy; Li, Ning; Machiraju, Raghu; Huang, Kun; Bartlett, Christopher W.

    2013-01-01

    Background: Numerous studies have examined gene × environment interactions (G × E) in cognitive and behavioral domains. However, these studies have been limited in that they have not been able to directly assess differential patterns of gene expression in the human brain. Here, we assessed G × E interactions using two publically available datasets…

  20. 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...

  1. 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.

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

    Science.gov (United States)

    Powell, Bradford C; Hutchison, Clyde A

    2006-01-19

    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. "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 prediction. 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. 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.

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

    Science.gov (United States)

    Mørk, Søren; Holmes, Ian

    2012-03-01

    Probabilistic logic programming offers a powerful way to describe and evaluate structured statistical models. To investigate the practicality of probabilistic logic programming for structure learning in bioinformatics, we undertook a simplified bacterial gene-finding benchmark in PRISM, a probabilistic dialect of Prolog. 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 modeling and three-state versions of the five model structures. The models are all represented as probabilistic logic programs and evaluated using the PRISM machine learning system in terms of statistical information criteria and gene-finding prediction accuracy, in two bacterial genomes. Neither of our implementations of the two currently most used model structures are best performing in terms of statistical information criteria or prediction performances, suggesting that better-fitting models might be achievable. The source code of all PRISM models, data and additional scripts are freely available for download at: http://github.com/somork/codonhmm. Supplementary data are available at Bioinformatics online.

  4. Skin signs of primary immunodeficiencies: how to find the genes to check.

    Science.gov (United States)

    Ettinger, M; Schreml, J; Wirsching, K; Berneburg, M; Schreml, S

    2018-02-01

    Primary immunodeficiencies (PIDs) are a heterogeneous group of rare diseases that result from defects in immune system development and/or function. The clinical manifestations of PIDs are highly variable, but most disorders involve at least an increased susceptibility to infection. Furthermore, cutaneous manifestations are very common in PIDs. As an easily accessible organ, the skin can be crucial for early diagnosis and treatment. This is relevant for preventing significant disease-associated morbidity and mortality. We provide a table that enables the reader to find the possible diseases and corresponding gene defects based on the skin manifestations of the suspected PIDs. To our knowledge, this is the first review that allows the reader to find relevant PIDs and the respective gene defects through solitary or combined skin signs. © 2017 British Association of Dermatologists.

  5. 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.

  6. Cis-regulatory element based targeted gene finding: genome-wide identification of abscisic acid- and abiotic stress-responsive genes in Arabidopsis thaliana.

    Science.gov (United States)

    Zhang, Weixiong; Ruan, Jianhua; Ho, Tuan-Hua David; You, Youngsook; Yu, Taotao; Quatrano, Ralph S

    2005-07-15

    A fundamental problem of computational genomics is identifying the genes that respond to certain endogenous cues and environmental stimuli. This problem can be referred to as targeted gene finding. Since gene regulation is mainly determined by the binding of transcription factors and cis-regulatory DNA sequences, most existing gene annotation methods, which exploit the conservation of open reading frames, are not effective in finding target genes. A viable approach to targeted gene finding is to exploit the cis-regulatory elements that are known to be responsible for the transcription of target genes. Given such cis-elements, putative target genes whose promoters contain the elements can be identified. As a case study, we apply the above approach to predict the genes in model plant Arabidopsis thaliana which are inducible by a phytohormone, abscisic acid (ABA), and abiotic stress, such as drought, cold and salinity. We first construct and analyze two ABA specific cis-elements, ABA-responsive element (ABRE) and its coupling element (CE), in A.thaliana, based on their conservation in rice and other cereal plants. We then use the ABRE-CE module to identify putative ABA-responsive genes in A.thaliana. Based on RT-PCR verification and the results from literature, this method has an accuracy rate of 67.5% for the top 40 predictions. The cis-element based targeted gene finding approach is expected to be widely applicable since a large number of cis-elements in many species are available.

  7. Periventricular nodular heterotopia in patients with filamin-1 gene mutations: neuroimaging findings

    Energy Technology Data Exchange (ETDEWEB)

    Poussaint, T.Y. [Dept. of Radiology, Children' s Hospital, Boston, MA (United States); Fox, J.W.; Walsh, C.A. [Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA (United States); Dept. of Neurology, Beth Israel Deaconess Medical Center, Harvard Institutes of Medicine, Boston, MA (United States); Dobyns, W.B. [Department of Human Genetics, The University of Chicago, Chicago, IL (United States); Radtke, R. [Division of Neurology, Duke University Medical Center, Durham, NC (United States); Scheffer, I.E.; Berkovic, S.F. [Department of Neurology, University of Melbourne, Austin and Repatriation Medical Centre, Heidelberg (Australia); Barnes, P.D. [Department of Radiology, Children' s Hospital and Harvard Medical School, Boston, MA (United States); Huttenlocher, P.R. [Department of Pediatrics, University of Chicago, Chicago, Illinois (United States)

    2000-11-01

    Background. The filamin-1 (FLN-1) gene is responsible for periventricular nodular heterotopia (PNH), which is an X-linked dominant neuronal migration disorder. Objective. To review the clinical and imaging findings in a series of patients with documented filamin-1 mutations. Materials and methods. A retrospective review of the medical records and MR studies of a series of patients with PNH and confirmed FLN-1 mutations was done. There were 16 female patients (age range:.67-71 years; mean = 28.6) with filamin-1 gene mutations. Results. In six of the patients the same mutation was inherited in four generations in one pedigree. In a second pedigree, a distinct mutation was found in two patients in two generations. In a third pedigree, a third mutation was found in four patients in two generations. The remaining four patients had sporadic de novo mutations that were not present in the parents. Ten patients had seizures, and all patients had normal intelligence. In all 16 patients MR demonstrated bilateral near-continuous PNH. There were no consistent radiographic or clinical differences between patients carrying different mutations. Conclusion. Patients with confirmed FLN-1 gene mutations are usually female and have a distinctive MR pattern of PNH. Other female patients with this same MR pattern probably harbor FLN-1 mutations and risk transmission to their progeny. This information is important for genetic counseling. (orig.)

  8. Periventricular nodular heterotopia in patients with filamin-1 gene mutations: neuroimaging findings

    International Nuclear Information System (INIS)

    Poussaint, T.Y.; Fox, J.W.; Walsh, C.A.; Dobyns, W.B.; Radtke, R.; Scheffer, I.E.; Berkovic, S.F.; Barnes, P.D.; Huttenlocher, P.R.

    2000-01-01

    Background. The filamin-1 (FLN-1) gene is responsible for periventricular nodular heterotopia (PNH), which is an X-linked dominant neuronal migration disorder. Objective. To review the clinical and imaging findings in a series of patients with documented filamin-1 mutations. Materials and methods. A retrospective review of the medical records and MR studies of a series of patients with PNH and confirmed FLN-1 mutations was done. There were 16 female patients (age range:.67-71 years; mean = 28.6) with filamin-1 gene mutations. Results. In six of the patients the same mutation was inherited in four generations in one pedigree. In a second pedigree, a distinct mutation was found in two patients in two generations. In a third pedigree, a third mutation was found in four patients in two generations. The remaining four patients had sporadic de novo mutations that were not present in the parents. Ten patients had seizures, and all patients had normal intelligence. In all 16 patients MR demonstrated bilateral near-continuous PNH. There were no consistent radiographic or clinical differences between patients carrying different mutations. Conclusion. Patients with confirmed FLN-1 gene mutations are usually female and have a distinctive MR pattern of PNH. Other female patients with this same MR pattern probably harbor FLN-1 mutations and risk transmission to their progeny. This information is important for genetic counseling. (orig.)

  9. 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

  10. 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

  11. Genetic interaction motif finding by expectation maximization – a novel statistical model for inferring gene modules from synthetic lethality

    Directory of Open Access Journals (Sweden)

    Ye Ping

    2005-12-01

    Full Text Available Abstract Background Synthetic lethality experiments identify pairs of genes with complementary function. More direct functional associations (for example greater probability of membership in a single protein complex may be inferred between genes that share synthetic lethal interaction partners than genes that are directly synthetic lethal. Probabilistic algorithms that identify gene modules based on motif discovery are highly appropriate for the analysis of synthetic lethal genetic interaction data and have great potential in integrative analysis of heterogeneous datasets. Results We have developed Genetic Interaction Motif Finding (GIMF, an algorithm for unsupervised motif discovery from synthetic lethal interaction data. Interaction motifs are characterized by position weight matrices and optimized through expectation maximization. Given a seed gene, GIMF performs a nonlinear transform on the input genetic interaction data and automatically assigns genes to the motif or non-motif category. We demonstrate the capacity to extract known and novel pathways for Saccharomyces cerevisiae (budding yeast. Annotations suggested for several uncharacterized genes are supported by recent experimental evidence. GIMF is efficient in computation, requires no training and automatically down-weights promiscuous genes with high degrees. Conclusion GIMF effectively identifies pathways from synthetic lethality data with several unique features. It is mostly suitable for building gene modules around seed genes. Optimal choice of one single model parameter allows construction of gene networks with different levels of confidence. The impact of hub genes the generic probabilistic framework of GIMF may be used to group other types of biological entities such as proteins based on stochastic motifs. Analysis of the strongest motifs discovered by the algorithm indicates that synthetic lethal interactions are depleted between genes within a motif, suggesting that synthetic

  12. Text mining and network analysis to find functional associations of genes in high altitude diseases.

    Science.gov (United States)

    Bhasuran, Balu; Subramanian, Devika; Natarajan, Jeyakumar

    2018-05-02

    Travel to elevations above 2500 m is associated with the risk of developing one or more forms of acute altitude illness such as acute mountain sickness (AMS), high altitude cerebral edema (HACE) or high altitude pulmonary edema (HAPE). Our work aims to identify the functional association of genes involved in high altitude diseases. In this work we identified the gene networks responsible for high altitude diseases by using the principle of gene co-occurrence statistics from literature and network analysis. First, we mined the literature data from PubMed on high-altitude diseases, and extracted the co-occurring gene pairs. Next, based on their co-occurrence frequency, gene pairs were ranked. Finally, a gene association network was created using statistical measures to explore potential relationships. Network analysis results revealed that EPO, ACE, IL6 and TNF are the top five genes that were found to co-occur with 20 or more genes, while the association between EPAS1 and EGLN1 genes is strongly substantiated. The network constructed from this study proposes a large number of genes that work in-toto in high altitude conditions. Overall, the result provides a good reference for further study of the genetic relationships in high altitude diseases. Copyright © 2018 Elsevier Ltd. All rights reserved.

  13. 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...

  14. 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

  15. A novel one-class SVM based negative data sampling method for reconstructing proteome-wide HTLV-human protein interaction networks.

    Science.gov (United States)

    Mei, Suyu; Zhu, Hao

    2015-01-26

    Protein-protein interaction (PPI) prediction is generally treated as a problem of binary classification wherein negative data sampling is still an open problem to be addressed. The commonly used random sampling is prone to yield less representative negative data with considerable false negatives. Meanwhile rational constraints are seldom exerted on model selection to reduce the risk of false positive predictions for most of the existing computational methods. In this work, we propose a novel negative data sampling method based on one-class SVM (support vector machine, SVM) to predict proteome-wide protein interactions between HTLV retrovirus and Homo sapiens, wherein one-class SVM is used to choose reliable and representative negative data, and two-class SVM is used to yield proteome-wide outcomes as predictive feedback for rational model selection. Computational results suggest that one-class SVM is more suited to be used as negative data sampling method than two-class PPI predictor, and the predictive feedback constrained model selection helps to yield a rational predictive model that reduces the risk of false positive predictions. Some predictions have been validated by the recent literature. Lastly, gene ontology based clustering of the predicted PPI networks is conducted to provide valuable cues for the pathogenesis of HTLV retrovirus.

  16. Finding biological process modifications in cancer tissues by mining gene expression correlations

    Directory of Open Access Journals (Sweden)

    Storari Sergio

    2006-01-01

    Full Text Available Abstract Background Through the use of DNA microarrays it is now possible to obtain quantitative measurements of the expression of thousands of genes from a biological sample. This technology yields a global view of gene expression that can be used in several ways. Functional insight into expression profiles is routinely obtained by using Gene Ontology terms associated to the cellular genes. In this paper, we deal with functional data mining from expression profiles, proposing a novel approach that studies the correlations between genes and their relations to Gene Ontology (GO. By using this "functional correlations comparison" we explore all possible pairs of genes identifying the affected biological processes by analyzing in a pair-wise manner gene expression patterns and linking correlated pairs with Gene Ontology terms. Results We apply here this "functional correlations comparison" approach to identify the existing correlations in hepatocarcinoma (161 microarray experiments and to reveal functional differences between normal liver and cancer tissues. The number of well-correlated pairs in each GO term highlights several differences in genetic interactions between cancer and normal tissues. We performed a bootstrap analysis in order to compute false detection rates (FDR and confidence limits. Conclusion Experimental results show the main advantage of the applied method: it both picks up general and specific GO terms (in particular it shows a fine resolution in the specific GO terms. The results obtained by this novel method are highly coherent with the ones proposed by other cancer biology studies. But additionally they highlight the most specific and interesting GO terms helping the biologist to focus his/her studies on the most relevant biological processes.

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

    KAUST Repository

    Elsik, Christine G; Worley, Kim C; Bennett, Anna K; Beye, Martin; Camara, Francisco; Childers, Christopher P; de Graaf, Dirk C; Debyser, Griet; Deng, Jixin; Devreese, Bart; Elhaik, Eran; Evans, Jay D; Foster, Leonard J; Graur, Dan; Guigo, Roderic; Hoff, Katharina Jasmin; Holder, Michael E; Hudson, Matthew E; Hunt, Greg J; Jiang, Huaiyang; Joshi, Vandita; Khetani, Radhika S; Kosarev, Peter; Kovar, Christie L; Ma, Jian; Maleszka, Ryszard; Moritz, Robin F A; Munoz-Torres, Monica C; Murphy, Terence D; Muzny, Donna M; Newsham, Irene F; Reese, Justin T; Robertson, Hugh M; Robinson, Gene E; Rueppell, Olav; Solovyev, Victor; Stanke, Mario; Stolle, Eckart; Tsuruda, Jennifer M; Vaerenbergh, Matthias Van; Waterhouse, Robert M; Weaver, Daniel B; Whitfield, Charles W; Wu, Yuanqing; Zdobnov, Evgeny M; Zhang, Lan; Zhu, Dianhui; Gibbs, Richard A; Patil, S.; Gubbala, S.; Aqrawi, P.; Arias, F.; Bess, C.; Blankenburg, K. B.; Brocchini, M.; Buhay, C.; Challis, D.; Chang, K.; Chen, D.; Coleman, P.; Drummond, J.; English, A.; Evani, U.; Francisco, L.; Fu, Q.; Goodspeed, R.; Haessly, T. H.; Hale, W.; Han, H.; Hu, Y.; Jackson, L.; Jakkamsetti, A.; Jayaseelan, J. C.; Kakkar, N.; Kalra, D.; Kandadi, H.; Lee, S.; Li, H.; Liu, Y.; Macmil, S.; Mandapat, C. M.; Mata, R.; Mathew, T.; Matskevitch, T.; Munidasa, M.; Nagaswamy, U.; Najjar, R.; Nguyen, N.; Niu, J.; Opheim, D.; Palculict, T.; Paul, S.; Pellon, M.; Perales, L.; Pham, C.; Pham, P.

    2014-01-01

    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.

  18. Finding the missing honey bee genes: lessons learned from a genome upgrade.

    Science.gov (United States)

    Elsik, Christine G; Worley, Kim C; Bennett, Anna K; Beye, Martin; Camara, Francisco; Childers, Christopher P; de Graaf, Dirk C; Debyser, Griet; Deng, Jixin; Devreese, Bart; Elhaik, Eran; Evans, Jay D; Foster, Leonard J; Graur, Dan; Guigo, Roderic; Hoff, Katharina Jasmin; Holder, Michael E; Hudson, Matthew E; Hunt, Greg J; Jiang, Huaiyang; Joshi, Vandita; Khetani, Radhika S; Kosarev, Peter; Kovar, Christie L; Ma, Jian; Maleszka, Ryszard; Moritz, Robin F A; Munoz-Torres, Monica C; Murphy, Terence D; Muzny, Donna M; Newsham, Irene F; Reese, Justin T; Robertson, Hugh M; Robinson, Gene E; Rueppell, Olav; Solovyev, Victor; Stanke, Mario; Stolle, Eckart; Tsuruda, Jennifer M; Vaerenbergh, Matthias Van; Waterhouse, Robert M; Weaver, Daniel B; Whitfield, Charles W; Wu, Yuanqing; Zdobnov, Evgeny M; Zhang, Lan; Zhu, Dianhui; Gibbs, Richard A

    2014-01-30

    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. 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. 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.

  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

    Directory of Open Access Journals (Sweden)

    Song Cai

    2011-07-01

    Full Text Available Abstract Background 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. Results 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. Conclusion A combination of RNA-seq and DGE analysis based on the next generation sequencing technology was shown to be a powerful method for identifying

  1. 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. We...... identified a number of new protein network modules and novel candidate genes/proteins for type 1 diabetes. We propose this type of integrative analysis as a general method for the elucidation of genes and networks involved in diabetes and other complex diseases....

  2. 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.

  3. 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.

  4. 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…

  5. Current novel-gene-finding strategy for autosomal-dominant hypercholesterolaemia needs refinement

    NARCIS (Netherlands)

    Fouchier, Sigrid W.; Hutten, Barbara A.; Defesche, Joep C.

    2015-01-01

    Autosomal-dominant hypercholesterolaemia (ADH) is a heterogeneous common disorder, and uncovering the molecular determinants that underlie ADH is a major focus of cardiovascular research. However, despite rapid technical advances, efforts to identify novel ADH genes have yet not been very successful

  6. 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.

  7. 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.

  8. Structured association analysis leads to insight into Saccharomyces cerevisiae gene regulation by finding multiple contributing eQTL hotspots associated with functional gene modules.

    Science.gov (United States)

    Curtis, Ross E; Kim, Seyoung; Woolford, John L; Xu, Wenjie; Xing, Eric P

    2013-03-21

    Association analysis using genome-wide expression quantitative trait locus (eQTL) data investigates the effect that genetic variation has on cellular pathways and leads to the discovery of candidate regulators. Traditional analysis of eQTL data via pairwise statistical significance tests or linear regression does not leverage the availability of the structural information of the transcriptome, such as presence of gene networks that reveal correlation and potentially regulatory relationships among the study genes. We employ a new eQTL mapping algorithm, GFlasso, which we have previously developed for sparse structured regression, to reanalyze a genome-wide yeast dataset. GFlasso fully takes into account the dependencies among expression traits to suppress false positives and to enhance the signal/noise ratio. Thus, GFlasso leverages the gene-interaction network to discover the pleiotropic effects of genetic loci that perturb the expression level of multiple (rather than individual) genes, which enables us to gain more power in detecting previously neglected signals that are marginally weak but pleiotropically significant. While eQTL hotspots in yeast have been reported previously as genomic regions controlling multiple genes, our analysis reveals additional novel eQTL hotspots and, more interestingly, uncovers groups of multiple contributing eQTL hotspots that affect the expression level of functional gene modules. To our knowledge, our study is the first to report this type of gene regulation stemming from multiple eQTL hotspots. Additionally, we report the results from in-depth bioinformatics analysis for three groups of these eQTL hotspots: ribosome biogenesis, telomere silencing, and retrotransposon biology. We suggest candidate regulators for the functional gene modules that map to each group of hotspots. Not only do we find that many of these candidate regulators contain mutations in the promoter and coding regions of the genes, in the case of the Ribi group

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

    KAUST Repository

    Olayan, Rawan S.

    2012-01-01

    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.

  11. Work, meaning, and gene regulation: Findings from a Japanese information technology firm.

    Science.gov (United States)

    Kitayama, Shinobu; Akutsu, Satoshi; Uchida, Yukiko; Cole, Steve W

    2016-10-01

    The meaning in life, typically reflected in a sense of purpose, growth, or social embeddedness (called eudaimonic well-being, EWB), has been linked to favorable health outcomes. In particular, this experience is inversely associated with the conserved transcriptional response to adversity (CTRA), which involves up-regulation of genes linked to inflammation and down-regulation of genes linked to viral resistance. So far, however, little is known about how this transcriptome profile might be situated in specific socio-cultural contexts. Here, we tested 106 male workers at a large Japanese IT firm and found that the CTRA is inversely associated not only with general EWB but also with a more contextualized sense of meaning derived from the perceived significance of one's work and a sense of interdependence with others in the workplace. These results expand previous links between personal well-being and CTRA gene expression to include the socio-cultural determinants of meaning in life. Copyright © 2016 Elsevier Ltd. All rights reserved.

  12. The Identification of Novel Diagnostic Marker Genes for the Detection of Beer Spoiling Pediococcus damnosus Strains Using the BlAst Diagnostic Gene findEr.

    Directory of Open Access Journals (Sweden)

    Jürgen Behr

    Full Text Available As the number of bacterial genomes increases dramatically, the demand for easy to use tools with transparent functionality and comprehensible output for applied comparative genomics grows as well. We present BlAst Diagnostic Gene findEr (BADGE, a tool for the rapid prediction of diagnostic marker genes (DMGs for the differentiation of bacterial groups (e.g. pathogenic / nonpathogenic. DMG identification settings can be modified easily and installing and running BADGE does not require specific bioinformatics skills. During the BADGE run the user is informed step by step about the DMG finding process, thus making it easy to evaluate the impact of chosen settings and options. On the basis of an example with relevance for beer brewing, being one of the oldest biotechnological processes known, we show a straightforward procedure, from phenotyping, genome sequencing, assembly and annotation, up to a discriminant marker gene PCR assay, making comparative genomics a means to an end. The value and the functionality of BADGE were thoroughly examined, resulting in the successful identification and validation of an outstanding novel DMG (fabZ for the discrimination of harmless and harmful contaminations of Pediococcus damnosus, which can be applied for spoilage risk determination in breweries. Concomitantly, we present and compare five complete P. damnosus genomes sequenced in this study, finding that the ability to produce the unwanted, spoilage associated off-flavor diacetyl is a plasmid encoded trait in this important beer spoiling species.

  13. The Identification of Novel Diagnostic Marker Genes for the Detection of Beer Spoiling Pediococcus damnosus Strains Using the BlAst Diagnostic Gene findEr.

    Science.gov (United States)

    Behr, Jürgen; Geissler, Andreas J; Schmid, Jonas; Zehe, Anja; Vogel, Rudi F

    2016-01-01

    As the number of bacterial genomes increases dramatically, the demand for easy to use tools with transparent functionality and comprehensible output for applied comparative genomics grows as well. We present BlAst Diagnostic Gene findEr (BADGE), a tool for the rapid prediction of diagnostic marker genes (DMGs) for the differentiation of bacterial groups (e.g. pathogenic / nonpathogenic). DMG identification settings can be modified easily and installing and running BADGE does not require specific bioinformatics skills. During the BADGE run the user is informed step by step about the DMG finding process, thus making it easy to evaluate the impact of chosen settings and options. On the basis of an example with relevance for beer brewing, being one of the oldest biotechnological processes known, we show a straightforward procedure, from phenotyping, genome sequencing, assembly and annotation, up to a discriminant marker gene PCR assay, making comparative genomics a means to an end. The value and the functionality of BADGE were thoroughly examined, resulting in the successful identification and validation of an outstanding novel DMG (fabZ) for the discrimination of harmless and harmful contaminations of Pediococcus damnosus, which can be applied for spoilage risk determination in breweries. Concomitantly, we present and compare five complete P. damnosus genomes sequenced in this study, finding that the ability to produce the unwanted, spoilage associated off-flavor diacetyl is a plasmid encoded trait in this important beer spoiling species.

  14. Neonatal pyruvate dehydrogenase deficiency due to a R302H mutation in the PDHA1 gene: MRI findings

    International Nuclear Information System (INIS)

    Soares-Fernandes, Joao P.; Ribeiro, Manuel; Magalhaes, Zita; Rocha, Jaime F.; Teixeira-Gomes, Roseli; Cruz, Romeu; Leijser, Lara M.

    2008-01-01

    Pyruvate dehydrogenase (PDH) deficiency is one of the most common causes of congenital lactic acidosis. Correlations between the genetic defect and neuroimaging findings are lacking. We present conventional and diffusion-weighted MRI findings in a 7-day-old male neonate with PDH deficiency due to a mosaicism for the R302H mutation in the PDHA1 gene. Corpus callosum dysgenesis, widespread increased diffusion in the white matter, and bilateral subependymal cysts were the main features. Although confirmation of PDH deficiency depends on specialized biochemical analyses, neonatal MRI plays a role in evaluating the pattern and extent of brain damage, and potentially in early diagnosis and clinical decision making. (orig.)

  15. Finding differentially expressed genes in high dimensional data: Rank based test statistic via a distance measure.

    Science.gov (United States)

    Mathur, Sunil; Sadana, Ajit

    2015-12-01

    We present a rank-based test statistic for the identification of differentially expressed genes using a distance measure. The proposed test statistic is highly robust against extreme values and does not assume the distribution of parent population. Simulation studies show that the proposed test is more powerful than some of the commonly used methods, such as paired t-test, Wilcoxon signed rank test, and significance analysis of microarray (SAM) under certain non-normal distributions. The asymptotic distribution of the test statistic, and the p-value function are discussed. The application of proposed method is shown using a real-life data set. © The Author(s) 2011.

  16. Ocular findings associated with a Cys39Arg mutation in the Norrie disease gene.

    Science.gov (United States)

    Joos, K M; Kimura, A E; Vandenburgh, K; Bartley, J A; Stone, E M

    1994-12-01

    To diagnose the carriers and noncarriers in a family affected with Norrie disease based on molecular analysis. Family members from three generations, including one affected patient, two obligate carriers, one carrier identified with linkage analysis, one noncarrier identified with linkage analysis, and one female family member with indeterminate carrier status, were examined clinically and electrophysiologically. Linkage analysis had previously failed to determine the carrier status of one female family member in the third generation. Blood samples were screened for mutations in the Norrie disease gene with single-strand conformation polymorphism analysis. The mutation was characterized by dideoxy-termination sequencing. Ophthalmoscopy and electroretinographic examination failed to detect the carrier state. The affected individuals and carriers in this family were found to have a transition from thymidine to cytosine in the first nucleotide of codon 39 of the Norrie disease gene, causing a cysteine-to-arginine mutation. Single-strand conformation polymorphism analysis identified a patient of indeterminate status (by linkage) to be a noncarrier of Norrie disease. Ophthalmoscopy and electroretinography could not identify carriers of this Norrie disease mutation. Single-strand conformation polymorphism analysis was more sensitive and specific than linkage analysis in identifying carriers in this family.

  17. 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.

  18. ReliefSeq: a gene-wise adaptive-K nearest-neighbor feature selection tool for finding gene-gene interactions and main effects in mRNA-Seq gene expression data.

    Directory of Open Access Journals (Sweden)

    Brett A McKinney

    Full Text Available Relief-F is a nonparametric, nearest-neighbor machine learning method that has been successfully used to identify relevant variables that may interact in complex multivariate models to explain phenotypic variation. While several tools have been developed for assessing differential expression in sequence-based transcriptomics, the detection of statistical interactions between transcripts has received less attention in the area of RNA-seq analysis. We describe a new extension and assessment of Relief-F for feature selection in RNA-seq data. The ReliefSeq implementation adapts the number of nearest neighbors (k for each gene to optimize the Relief-F test statistics (importance scores for finding both main effects and interactions. We compare this gene-wise adaptive-k (gwak Relief-F method with standard RNA-seq feature selection tools, such as DESeq and edgeR, and with the popular machine learning method Random Forests. We demonstrate performance on a panel of simulated data that have a range of distributional properties reflected in real mRNA-seq data including multiple transcripts with varying sizes of main effects and interaction effects. For simulated main effects, gwak-Relief-F feature selection performs comparably to standard tools DESeq and edgeR for ranking relevant transcripts. For gene-gene interactions, gwak-Relief-F outperforms all comparison methods at ranking relevant genes in all but the highest fold change/highest signal situations where it performs similarly. The gwak-Relief-F algorithm outperforms Random Forests for detecting relevant genes in all simulation experiments. In addition, Relief-F is comparable to the other methods based on computational time. We also apply ReliefSeq to an RNA-Seq study of smallpox vaccine to identify gene expression changes between vaccinia virus-stimulated and unstimulated samples. ReliefSeq is an attractive tool for inclusion in the suite of tools used for analysis of mRNA-Seq data; it has power to

  19. 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 Newer behavior genetic methods can better elucidate gene-environment (G-E) interplay in the development of internalizing (INT) disorders (i.e., major depression and anxiety disorders). However, no study to date has conducted a comprehensive analysis examining multiple environmental risks with the purpose of delineating how general G-E mechanisms influence the development of INT disorders. Methods The sample consisted of 1315 male and female twin pairs participating in the age 17 assessment of the Minnesota Twin Family Study. Quantitative G-E interplay models were used to examine how genetic and environmental risk for INT disorders changes as a function of environmental context. Multiple measures and informants were employed to construct composite measures of INT disorders and 6 environmental risk factors including: stressful life events, mother-child and father-child relationship problems, antisocial and prosocial peer affiliation, and academic achievement and engagement. Results Significant moderation effects were detected between each environmental risk factor and INT such that in the context of greater environmental adversity, nonshared environmental factors became more important in the etiology of INT symptoms. Conclusion Our results are consistent with the interpretation that environmental stressors have a causative effect on the emergence of INT disorders. The consistency of our results suggests a general mechanism of environmental influence on INT disorders regardless of the specific form of environmental risk. PMID:19594836

  20. 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

    Tourette syndrome (TS) is a neuropsychiatric disorder characterized by recurrent motor and vocal tics, often accompanied by obsessive-compulsive disorder and/or attention-deficit/hyperactivity disorder. While the evidence for a genetic contribution is strong, its exact nature has yet to be clarif......Tourette syndrome (TS) is a neuropsychiatric disorder characterized by recurrent motor and vocal tics, often accompanied by obsessive-compulsive disorder and/or attention-deficit/hyperactivity disorder. While the evidence for a genetic contribution is strong, its exact nature has yet......, 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...... 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...

  1. CDKL5 gene-related epileptic encephalopathy: electroclinical findings in the first year of life.

    Science.gov (United States)

    Melani, Federico; Mei, Davide; Pisano, Tiziana; Savasta, Salvatore; Franzoni, Emilio; Ferrari, Anna Rita; Marini, Carla; Guerrini, Renzo

    2011-04-01

    Cyclin-dependent kinase-like 5 (CDKL5) gene abnormalities cause an early-onset epileptic encephalopathy. We performed video-electroencephalography (video-EEG) monitoring early in the course of CDKL5-related epileptic encephalopathy in order to examine the early electroclinical characteristics of the condition. We used video-EEG to monitor six infants (five females, one male) with CDKL5-related epileptic encephalopathy (five mutations; one deletion), at ages 45 days to 12 months and followed them up to the ages of 14 months to 5 years (mean age 23 mo). We focused our analysis on the first year of life. The results were evaluated against those of a comparison group of nine infants (aged below 1y) with epileptic encephalography who had tested negative for CDKL5 mutations and deletions. One infant exhibited normal background activity, three exhibited moderate slowing, and two exhibited a suppression burst pattern. Two participants had epileptic spasms and four had a stereotyped complex seizure pattern, which we defined as a 'prolonged' generalized tonic-clonic event consisting of a tonic-tonic/vibratory contraction, followed by a clonic phase with series of spasms, gradually translating into repetitive distal myoclonic jerks. Seizure duration ranged from 2 to 4 minutes. The EEG correlate of each clinical phase included an initial electrodecremental event (tonic vibratory phase), irregular series of sharp waves and spike slow waves (clonic phase with series of spasms), and bilateral rhythmic sharp waves (time locked with myoclonus). Infants with CDKL5-related early epileptic encephalopathy can present in the first year of life with an unusual electroclinical pattern of 'prolonged' generalized tonic-clonic seizures. © The Authors. Journal compilation © Mac Keith Press 2011.

  2. 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/.

  3. 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.)

  4. High-Throughput Behavioral Screens: the First Step towards Finding Genes Involved in Vertebrate Brain Function Using Zebrafish

    Directory of Open Access Journals (Sweden)

    Robert Gerlai

    2010-04-01

    Full Text Available The zebrafish has been in the forefront of developmental biology for three decades and has become a favorite of geneticists. Due to the accumulated genetic knowledge and tools developed for the zebrafish it is gaining popularity in other disciplines, including neuroscience. The zebrafish offers a compromise between system complexity (it is a vertebrate similar in many ways to our own species and practical simplicity (it is small, easy to keep, and prolific. Such features make zebrafish an excellent choice for high throughput mutation and drug screening. For the identification of mutation or drug induced alteration of brain function arguably the best methods are behavioral test paradigms. This review does not present experimental examples for the identification of particular genes or drugs. Instead it describes how behavioral screening methods may enable one to find functional alterations in the vertebrate brain. Furthermore, the review is not comprehensive. The behavioral test examples presented are biased according to the personal interests of the author. They will cover research areas including learning and memory, fear and anxiety, and social behavior. Nevertheless, the general principles will apply to other functional domains and should represent a snapshot of the rapidly evolving behavioral screening field with zebrafish.

  5. 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

  6. 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.

  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. Finding novel relationships with integrated gene-gene association network analysis of Synechocystis sp. PCC 6803 using species-independent text-mining.

    Science.gov (United States)

    Kreula, Sanna M; Kaewphan, Suwisa; Ginter, Filip; Jones, Patrik R

    2018-01-01

    The increasing move towards open access full-text scientific literature enhances our ability to utilize advanced text-mining methods to construct information-rich networks that no human will be able to grasp simply from 'reading the literature'. The utility of text-mining for well-studied species is obvious though the utility for less studied species, or those with no prior track-record at all, is not clear. Here we present a concept for how advanced text-mining can be used to create information-rich networks even for less well studied species and apply it to generate an open-access gene-gene association network resource for Synechocystis sp. PCC 6803, a representative model organism for cyanobacteria and first case-study for the methodology. By merging the text-mining network with networks generated from species-specific experimental data, network integration was used to enhance the accuracy of predicting novel interactions that are biologically relevant. A rule-based algorithm (filter) was constructed in order to automate the search for novel candidate genes with a high degree of likely association to known target genes by (1) ignoring established relationships from the existing literature, as they are already 'known', and (2) demanding multiple independent evidences for every novel and potentially relevant relationship. Using selected case studies, we demonstrate the utility of the network resource and filter to ( i ) discover novel candidate associations between different genes or proteins in the network, and ( ii ) rapidly evaluate the potential role of any one particular gene or protein. The full network is provided as an open-source resource.

  9. Juvenile-onset Sporadic Amyotrophic Lateral Sclerosis with a Frameshift FUS Gene Mutation Presenting Unique Neuroradiological Findings and Cognitive Impairment.

    Science.gov (United States)

    Hirayanagi, Kimitoshi; Sato, Masayuki; Furuta, Natsumi; Makioka, Kouki; Ikeda, Yoshio

    2016-01-01

    A 24-year-old Japanese woman developed anterocollis, weakness of the proximal arms, and subsequent cognitive impairment. A neurological examination revealed amyotrophic lateral sclerosis (ALS) without a family history. Systemic muscle atrophy progressed rapidly. Cerebral MRI clearly exhibited high signal intensities along the bilateral pyramidal tracts. An analysis of the FUS gene revealed a heterozygous two-base pair deletion, c.1507-1508delAG (p.G504WfsX515). A subset of juvenile-onset familial/sporadic ALS cases with FUS gene mutations reportedly demonstrates mental retardation or learning difficulty. Our study emphasizes the importance of conducting a FUS gene analysis in juvenile-onset ALS cases, even when no family occurrence is confirmed.

  10. Using Single-nucleotide Polymorphisms and Genetic Mapping to find Candidate Genes that Influence Varroa-Specific Hygiene

    Science.gov (United States)

    Varroa-sensitive hygienic (VSH) behavior is one of two behaviors identified that are most important for controlling the growth of Varroa mite populations in bee hives. A study was conducted to map quantitative trait loci (QTL) that influence VSH so that resistance genes could be identified. Crosses ...

  11. Genetic changes of MLH1 and MSH2 genes could explain constant findings on microsatellite instability in intracranial meningioma.

    Science.gov (United States)

    Pećina-Šlaus, Nives; Kafka, Anja; Bukovac, Anja; Vladušić, Tomislav; Tomas, Davor; Hrašćan, Reno

    2017-07-01

    Postreplicative mismatch repair safeguards the stability of our genome. The defects in its functioning will give rise to microsatellite instability. In this study, 50 meningiomas were investigated for microsatellite instability. Two major mismatch repair genes, MLH1 and MSH2, were analyzed using microsatellite markers D1S1611 and BAT26 amplified by polymerase chain reaction and visualized by gel electrophoresis on high-resolution gels. Furthermore, genes DVL3 (D3S1262), AXIN1 (D16S3399), and CDH1 (D16S752) were also investigated for microsatellite instability. Our study revealed constant presence of microsatellite instability in meningioma patients when compared to their autologous blood DNA. Altogether 38% of meningiomas showed microsatellite instability at one microsatellite locus, 16% on two, and 13.3% on three loci. The percent of detected microsatellite instability for MSH2 gene was 14%, and for MLH1, it was 26%, for DVL3 22.9%, for AXIN1 17.8%, and for CDH1 8.3%. Since markers also allowed for the detection of loss of heterozygosity, gross deletions of MLH1 gene were found in 24% of meningiomas. Genetic changes between MLH1 and MSH2 were significantly positively correlated (p = 0.032). We also noted a positive correlation between genetic changes of MSH2 and DVL3 genes (p = 0.034). No significant associations were observed when MLH1 or MSH2 was tested against specific histopathological meningioma subtype or World Health Organization grade. However, genetic changes in DVL3 were strongly associated with anaplastic histology of meningioma (χ 2  = 9.14; p = 0.01). Our study contributes to better understanding of the genetic profile of human intracranial meningiomas and suggests that meningiomas harbor defective cellular DNA mismatch repair mechanisms.

  12. Association of Protein Translation and Extracellular Matrix Gene Sets with Breast Cancer Metastasis: Findings Uncovered on Analysis of Multiple Publicly Available Datasets Using Individual Patient Data Approach.

    Directory of Open Access Journals (Sweden)

    Nilotpal Chowdhury

    Full Text Available Microarray analysis has revolutionized the role of genomic prognostication in breast cancer. However, most studies are single series studies, and suffer from methodological problems. We sought to use a meta-analytic approach in combining multiple publicly available datasets, while correcting for batch effects, to reach a more robust oncogenomic analysis.The aim of the present study was to find gene sets associated with distant metastasis free survival (DMFS in systemically untreated, node-negative breast cancer patients, from publicly available genomic microarray datasets.Four microarray series (having 742 patients were selected after a systematic search and combined. Cox regression for each gene was done for the combined dataset (univariate, as well as multivariate - adjusted for expression of Cell cycle related genes and for the 4 major molecular subtypes. The centre and microarray batch effects were adjusted by including them as random effects variables. The Cox regression coefficients for each analysis were then ranked and subjected to a Gene Set Enrichment Analysis (GSEA.Gene sets representing protein translation were independently negatively associated with metastasis in the Luminal A and Luminal B subtypes, but positively associated with metastasis in Basal tumors. Proteinaceous extracellular matrix (ECM gene set expression was positively associated with metastasis, after adjustment for expression of cell cycle related genes on the combined dataset. Finally, the positive association of the proliferation-related genes with metastases was confirmed.To the best of our knowledge, the results depicting mixed prognostic significance of protein translation in breast cancer subtypes are being reported for the first time. We attribute this to our study combining multiple series and performing a more robust meta-analytic Cox regression modeling on the combined dataset, thus discovering 'hidden' associations. This methodology seems to yield new and

  13. Association of Protein Translation and Extracellular Matrix Gene Sets with Breast Cancer Metastasis: Findings Uncovered on Analysis of Multiple Publicly Available Datasets Using Individual Patient Data Approach.

    Science.gov (United States)

    Chowdhury, Nilotpal; Sapru, Shantanu

    2015-01-01

    Microarray analysis has revolutionized the role of genomic prognostication in breast cancer. However, most studies are single series studies, and suffer from methodological problems. We sought to use a meta-analytic approach in combining multiple publicly available datasets, while correcting for batch effects, to reach a more robust oncogenomic analysis. The aim of the present study was to find gene sets associated with distant metastasis free survival (DMFS) in systemically untreated, node-negative breast cancer patients, from publicly available genomic microarray datasets. Four microarray series (having 742 patients) were selected after a systematic search and combined. Cox regression for each gene was done for the combined dataset (univariate, as well as multivariate - adjusted for expression of Cell cycle related genes) and for the 4 major molecular subtypes. The centre and microarray batch effects were adjusted by including them as random effects variables. The Cox regression coefficients for each analysis were then ranked and subjected to a Gene Set Enrichment Analysis (GSEA). Gene sets representing protein translation were independently negatively associated with metastasis in the Luminal A and Luminal B subtypes, but positively associated with metastasis in Basal tumors. Proteinaceous extracellular matrix (ECM) gene set expression was positively associated with metastasis, after adjustment for expression of cell cycle related genes on the combined dataset. Finally, the positive association of the proliferation-related genes with metastases was confirmed. To the best of our knowledge, the results depicting mixed prognostic significance of protein translation in breast cancer subtypes are being reported for the first time. We attribute this to our study combining multiple series and performing a more robust meta-analytic Cox regression modeling on the combined dataset, thus discovering 'hidden' associations. This methodology seems to yield new and interesting

  14. Whole-genome sequencing of the blue whale and other rorquals finds signatures for introgressive gene flow

    Science.gov (United States)

    Árnason, Úlfur; Kumar, Vikas

    2018-01-01

    Reconstructing the evolution of baleen whales (Mysticeti) has been problematic because morphological and genetic analyses have produced different scenarios. This might be caused by genomic admixture that may have taken place among some rorquals. We present the genomes of six whales, including the blue whale (Balaenoptera musculus), to reconstruct a species tree of baleen whales and to identify phylogenetic conflicts. Evolutionary multilocus analyses of 34,192 genome fragments reveal a fast radiation of rorquals at 10.5 to 7.5 million years ago coinciding with oceanic circulation shifts. The evolutionarily enigmatic gray whale (Eschrichtius robustus) is placed among rorquals, and the blue whale genome shows a high degree of heterozygosity. The nearly equal frequency of conflicting gene trees suggests that speciation of rorqual evolution occurred under gene flow, which is best depicted by evolutionary networks. Especially in marine environments, sympatric speciation might be common; our results raise questions about how genetic divergence can be established. PMID:29632892

  15. Case-control approach application for finding a relationship between candidate genes and clinical mastitis in Holstein dairy cattle.

    Science.gov (United States)

    Bagheri, Masoumeh; Moradi-Sharhrbabak, M; Miraie-Ashtiani, R; Safdari-Shahroudi, M; Abdollahi-Arpanahi, R

    2016-02-01

    Mastitis is a major source of economic loss in dairy herds. The objective of this research was to evaluate the association between genotypes within SLC11A1 and CXCR1 candidate genes and clinical mastitis in Holstein dairy cattle using the selective genotyping method. The data set contained clinical mastitis records of 3,823 Holstein cows from two Holstein dairy herds located in two different regions in Iran. Data included the number of cases of clinical mastitis per lactation. Selective genotyping was based on extreme values for clinical mastitis residuals (CMR) from mixed model analyses. Two extreme groups consisting of 135 cows were formed (as cases and controls), and genotyped for the two candidate genes, namely, SLC11A1 and CXCR1, using polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), respectively. Associations between single nucleotide polymorphism (SNP) genotypes with CMR and breeding values for milk and protein yield were carried out by applying logistic regression analyses, i.e. estimating the probability of the heterogeneous genotype in the dependency of values for CMR and breeding values (BVs). The sequencing results revealed a novel mutation in 1139 bp of exon 11 of the SLC11A1 gene and this SNP had a significant association with CMR (P G and these genotypes had significant relationships with CMR. Overall, the results showed that SLC11A1 and CXCR1 are valuable candidate genes for the improvement of mastitis resistance as well as production traits in dairy cattle populations.

  16. Increased chromosomal breakage in Tourette syndrome predicts the possibility of variable multiple gene involvement in spectrum phenotypes: Preliminary findings and hypothesis

    Energy Technology Data Exchange (ETDEWEB)

    Gericke, G.S.; Simonic, I.; Cloete, E.; Buckle, C. [Univ. of Pretoria (South Africa)] [and others

    1995-10-09

    Increased chromosomal breakage was found in 12 patients with DSM-IV Tourette syndrome (TS) as compared with 10 non-TS control individuals with respect to untreated, modified RPM1-, and BrdU treated lymphocyte cultures (P < 0.001 in each category). A hypothesis is proposed that a major TS gene is probably connected to genetic instability, and associated chromosomal marker sites may be indicative of the localization of secondary genes whose altered expression could be responsible for associated comorbid conditions. This concept implies that genes influencing higher brain functions may be situated at or near highly recombigenic areas allowing enhanced amplification, duplication and recombination following chromosomal strand breakage. Further studies on a larger sample size are required to confirm the findings relating to chromosomal breakage and to analyze the possible implications for a paradigmatic shift in linkage strategy for complex disorders by focusing on areas at or near unstable chromosomal marker sites. 32 refs., 1 tab.

  17. CNVs affecting cancer predisposing genes (CPGs) detected as incidental findings in routine germline diagnostic chromosomal microarray (CMA) testing.

    Science.gov (United States)

    Innes, Josie; Reali, Lisa; Clayton-Smith, Jill; Hall, Georgina; Lim, Derek Hk; Burghel, George J; French, Kim; Khan, Unzela; Walker, Daniel; Lalloo, Fiona; Evans, D Gareth R; McMullan, Dominic; Maher, Eamonn R; Woodward, Emma R

    2018-02-01

    Identification of CNVs through chromosomal microarray (CMA) testing is the first-line investigation in individuals with learning difficulties/congenital abnormalities. Although recognised that CMA testing may identify CNVs encompassing a cancer predisposition gene (CPG), limited information is available on the frequency and nature of such results. We investigated CNV gains and losses affecting 39 CPGs in 3366 pilot index case individuals undergoing CMA testing, and then studied an extended cohort (n=10 454) for CNV losses at 105 CPGs and CNV gains at 9 proto-oncogenes implicated in inherited cancer susceptibility. In the pilot cohort, 31/3366 (0.92%) individuals had a CNV involving one or more of 16/39 CPGs. 30/31 CNVs involved a tumour suppressor gene (TSG), and 1/30 a proto-oncogene (gain of MET ). BMPR1A , TSC2 and TMEM127 were affected in multiple cases. In the second stage analysis, 49/10 454 (0.47%) individuals in the extended cohort had 50 CNVs involving 24/105 CPGs. 43/50 CNVs involved a TSG and 7/50 a proto-oncogene (4 gains, 3 deletions). The most frequently involved genes, FLCN (n=10) and SDHA (n=7), map to the Smith-Magenis and cri-du-chat regions, respectively. Incidental identification of a CNV involving a CPG is not rare and poses challenges for future cancer risk estimation. Prospective data collection from CPG-CNV cohorts ascertained incidentally and through syndromic presentations is required to determine the risks posed by specific CNVs. In particular, ascertainment and investigation of adults with CPG-CNVs and adults with learning disability and cancer, could provide important information to guide clinical management and surveillance. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

  18. Finding trans-regulatory genes and protein complexes modulating meiotic recombination hotspots of human, mouse and yeast.

    Science.gov (United States)

    Wu, Min; Kwoh, Chee-Keong; Li, Xiaoli; Zheng, Jie

    2014-09-11

    The regulatory mechanism of recombination is one of the most fundamental problems in genomics, with wide applications in genome wide association studies (GWAS), birth-defect diseases, molecular evolution, cancer research, etc. Recombination events cluster into short genomic regions called "recombination hotspots". Recently, a zinc finger protein PRDM9 was reported to regulate recombination hotspots in human and mouse genomes. In addition, a 13-mer motif contained in the binding sites of PRDM9 is found to be enriched in human hotspots. However, this 13-mer motif only covers a fraction of hotspots, indicating that PRDM9 is not the only regulator of recombination hotspots. Therefore, the challenge of discovering other regulators of recombination hotspots becomes significant. Furthermore, recombination is a complex process. Hence, multiple proteins acting as machinery, rather than individual proteins, are more likely to carry out this process in a precise and stable manner. Therefore, the extension of the prediction of individual trans-regulators to protein complexes is also highly desired. In this paper, we introduce a pipeline to identify genes and protein complexes associated with recombination hotspots. First, we prioritize proteins associated with hotspots based on their preference of binding to hotspots and coldspots. Second, using the above identified genes as seeds, we apply the Random Walk with Restart algorithm (RWR) to propagate their influences to other proteins in protein-protein interaction (PPI) networks. Hence, many proteins without DNA-binding information will also be assigned a score to implicate their roles in recombination hotspots. Third, we construct sub-PPI networks induced by top genes ranked by RWR for various species (e.g., yeast, human and mouse) and detect protein complexes in those sub-PPI networks. The GO term analysis show that our prioritizing methods and the RWR algorithm are capable of identifying novel genes associated with

  19. Environmental smoking and smoking onset in adolescence: the role of dopamine-related genes. Findings from two longitudinal studies.

    Directory of Open Access Journals (Sweden)

    Marieke Hiemstra

    Full Text Available Although environmental smoking (i.e., paternal and maternal smoking, sibling smoking, and peer smoking is one of the most important factors for explaining adolescent smoking behavior, not all adolescents are similarly affected. The extent to which individuals are vulnerable to smoking in their environment might depend on genetic factors. The aim of this study was to examine the interplay between environmental smoking and genes encoding components of the dopaminergic system (i.e., dopamine receptor D2, D4, and dopamine transporter DAT1 in adolescent smoking onset. Data from two longitudinal studies were used. Study 1 consisted of 991 non-smoking early adolescents (mean age = 12.52, SD = .57 whereas study 2 consisted of 365 non-smoking middle to late adolescents (mean age = 14.16, SD = 1.07 who were followed for 16 and 48 months, respectively. Logistic regression analyses were conducted using Mplus. In study 1, we found positive associations between parents' and friends' smoking at the first measurement and smoking status 16 months later. In study 2 we found a positive association between friends' smoking and smoking onset 48 months later. Neither study demonstrated any interaction effects of the DRD2, DRD4, or DAT1 genotypes. In conclusion, the effects of environmental smoking on smoking onset are similar for adolescent carriers and non-carriers of these specific genes related to the dopaminergic system.

  20. The Tourette International Collaborative Genetics (TIC Genetics) study, finding the genes causing Tourette syndrome: objectives and methods.

    Science.gov (United States)

    Dietrich, Andrea; Fernandez, Thomas V; King, Robert A; State, Matthew W; Tischfield, Jay A; Hoekstra, Pieter J; Heiman, Gary A

    2015-02-01

    Tourette syndrome (TS) is a neuropsychiatric disorder characterized by recurrent motor and vocal tics, often accompanied by obsessive-compulsive disorder and/or attention-deficit/hyperactivity disorder. While the evidence for a genetic contribution is strong, its exact nature has yet to be clarified fully. There is now mounting evidence that the genetic risks for TS include both common and rare variants and may involve complex multigenic inheritance or, in rare cases, a single major gene. Based on recent progress in many other common disorders with apparently similar genetic architectures, 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 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) are part of a sharing repository located within the National Institute for Mental Health Center for Collaborative Genomics Research on Mental Disorders, USA, and will be made available to the broad scientific community. This resource will ultimately facilitate better understanding of the pathophysiology 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.

  1. Brachydactyly type A1 associated with unusual radiological findings and a novel Arg158Cys mutation in the Indian hedgehog (IHH) gene.

    Science.gov (United States)

    Stattin, Eva-Lena; Lindén, Bjarne; Lönnerholm, Torsten; Schuster, Jens; Dahl, Niklas

    2009-01-01

    Brachydactyly type A1 (BDA1; MIM 112500) is characterized by shortness or absence of the middle phalanx of the hands and feet. The condition is caused by heterozygous mutations in the Indian hedgehog (IHH) gene or a yet unidentified gene on chromosome 5p13. We investigated six affected members of a large Swedish family segregating autosomal dominant brachymesophalangia. Affected individuals show hypoplasia of the ulnar styloid processes, ulna minus, osteoarthritis, normal length of all distal phalanges and shortening or absence of the middle phalanges. Stationary ossicles or sesamoid bones were observed at the metacarpal heads in all patients. Genetic analysis of the family showed that the IHH-gene was linked to the disease (Z(max) 3.42 at theta 0.00) and sequence analysis of IHH revealed a novel c.472C > T transition in all affected family members. The mutation results in a p.158Arg > Cys substitution located in the highly conserved amino-terminal domain of IHH. This domain is of importance for the interaction between IHH and the Patched receptor. Our combined findings add radiological findings to the BDA1 phenotype and confirm a critical functional domain of IHH.

  2. 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.)

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

    KAUST Repository

    Lehmann, Robert; Lightfoot, Damien J; Schunter, Celia Marei; Michell, Craig T; Ohyanagi, Hajime; Mineta, Katsuhiko; Foret, Sylvain; Berumen, Michael L.; Miller, David J; Aranda, Manuel; Gojobori, Takashi; Munday, Philip L; Ravasi, Timothy

    2018-01-01

    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.

  5. 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.

  6. Neuroimaging findings in Joubert syndrome with C5orf42 gene mutations: A milder form of molar tooth sign and vermian hypoplasia.

    Science.gov (United States)

    Enokizono, Mikako; Aida, Noriko; Niwa, Tetsu; Osaka, Hitoshi; Naruto, Takuya; Kurosawa, Kenji; Ohba, Chihiro; Suzuki, Toshifumi; Saitsu, Hirotomo; Goto, Tomohide; Matsumoto, Naomichi

    2017-05-15

    Little is known regarding neuroimaging-genotype correlations in Joubert syndrome (JBTS). To elucidate one of these correlations, we investigated the neuroimaging findings of JBTS patients with C5orf42 mutations. Neuroimaging findings in five JBTS patients with C5orf42 mutations were retrospectively assessed with regard to the infratentorial and supratentorial structures on T1-magnetization prepared rapid gradient echo (MPRAGE), T2-weighted images, and color-coded fractional anisotropy (FA) maps; the findings were compared to those in four JBTS patients with mutations in other genes (including three with AHI1 and one with TMEM67 mutations). In C5orf42-mutant patients, the infratentorial magnetic resonance (MR) images showed normal or minimally thickened and minimally elongated superior cerebellar peduncles (SCP), normal or minimally deepened interpeduncular fossa (IF), and mild vermian hypoplasia (VH). However, in other patients, all had severe abnormalities in the SCP and IF, and moderate to marked VH. Supratentorial abnormalities were found in one individual in other JBTS. In JBTS with all mutations, color-coded FA maps showed the absence of decussation of the SCP (DSCP). The morphological neuroimaging findings in C5orf42-mutant JBTS were distinctly mild and made diagnosis difficult. However, the absence of DSCP on color-coded FA maps may facilitate the diagnosis of JBTS. Copyright © 2017 Elsevier B.V. All rights reserved.

  7. 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.

  8. 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

  9. 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.

  10. 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.

  11. 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.

  12. [Lower urinary tract dysfunction and neuropathological findings of the neural circuits controlling micturition in familial amyotrophic lateral sclerosis with L106V mutation in the SOD1 gene].

    Science.gov (United States)

    Hineno, Akiyo; Oyanagi, Kiyomitsu; Nakamura, Akinori; Shimojima, Yoshio; Yoshida, Kunihiro; Ikeda, Shu-Ichi

    2016-01-01

    We report lower urinary tract dysfunction and neuropathological findings of the neural circuits controlling micturition in the patients with familial amyotrophic lateral sclerosis having L106V mutation in the SOD1 gene. Ten of 20 patients showed lower urinary tract dysfunction and 5 patients developed within 1 year after the onset of weakness. In 8 patients with an artificial respirator, 6 patients showed lower urinary tract dysfunction. Lower urinary tract dysfunction and respiratory failure requiring an artificial respirator occurred simultaneously in 3 patients. Neuronal loss and gliosis were observed in the neural circuits controlling micturition, such as frontal lobe, thalamus, hypothalamus, striatum, periaqueductal gray, ascending spinal tract, lateral corticospinal tract, intermediolateral nucleus and Onufrowicz' nucleus. Lower urinary tract dysfunction, especially storage symptoms, developed about 1 year after the onset of weakness, and the dysfunction occurred simultaneously with artificial respirator use in the patients.

  13. Pathological Renal Findings of Chronic Renal Failure in a Patient with the E66Q Mutation in the α-galactosidase A Gene.

    Science.gov (United States)

    Satomura, Atsushi; Fujita, Takayuki; Nakayama, Tomohiro; Kusano, Hiroyuki; Takayama, Eiichi; Hamada, Hiroaki; Maruyama, Toshiharu

    2015-01-01

    A 66-year-old Japanese man was diagnosed with interstitial nephritis on a renal biopsy at 45 years of age and began to receive hemodialysis at 65 years of age. He was suspected of having Fabry disease as a result of a screening study for Fabry disease performed in hemodialysis patients. He had an E66Q mutation in the α-galactosidase A gene. We conducted an electron microscopic examination of a renal biopsy specimen obtained when the patient was diagnosed with chronic renal failure at 45 years of age in order to elucidate the pathogenicity of the E66Q mutation. Interestingly, an electron microscopic examination of the renal biopsy specimen indicated no characteristic findings of Fabry disease.

  14. 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.

  15. Multiclass classification for skin cancer profiling based on the integration of heterogeneous gene expression series.

    Science.gov (United States)

    Gálvez, Juan Manuel; Castillo, Daniel; Herrera, Luis Javier; San Román, Belén; Valenzuela, Olga; Ortuño, Francisco Manuel; Rojas, Ignacio

    2018-01-01

    Most of the research studies developed applying microarray technology to the characterization of different pathological states of any disease may fail in reaching statistically significant results. This is largely due to the small repertoire of analysed samples, and to the limitation in the number of states or pathologies usually addressed. Moreover, the influence of potential deviations on the gene expression quantification is usually disregarded. In spite of the continuous changes in omic sciences, reflected for instance in the emergence of new Next-Generation Sequencing-related technologies, the existing availability of a vast amount of gene expression microarray datasets should be properly exploited. Therefore, this work proposes a novel methodological approach involving the integration of several heterogeneous skin cancer series, and a later multiclass classifier design. This approach is thus a way to provide the clinicians with an intelligent diagnosis support tool based on the use of a robust set of selected biomarkers, which simultaneously distinguishes among different cancer-related skin states. To achieve this, a multi-platform combination of microarray datasets from Affymetrix and Illumina manufacturers was carried out. This integration is expected to strengthen the statistical robustness of the study as well as the finding of highly-reliable skin cancer biomarkers. Specifically, the designed operation pipeline has allowed the identification of a small subset of 17 differentially expressed genes (DEGs) from which to distinguish among 7 involved skin states. These genes were obtained from the assessment of a number of potential batch effects on the gene expression data. The biological interpretation of these genes was inspected in the specific literature to understand their underlying information in relation to skin cancer. Finally, in order to assess their possible effectiveness in cancer diagnosis, a cross-validation Support Vector Machines (SVM)-based

  16. The Leu72Met Polymorphism of the Prepro-ghrelin Gene is Associated With Alcohol Consumption and Subjective Responses to Alcohol: Preliminary Findings.

    Science.gov (United States)

    Suchankova, Petra; Yan, Jia; Schwandt, Melanie L; Stangl, Bethany L; Jerlhag, Elisabet; Engel, Jörgen A; Hodgkinson, Colin A; Ramchandani, Vijay A; Leggio, Lorenzo

    2017-07-01

    The orexigenic peptide ghrelin may enhance the incentive value of food-, drug- and alcohol-related rewards. Consistent with preclinical findings, human studies indicate a role of ghrelin in alcohol use disorders (AUD). In the present study an a priori hypothesis-driven analysis was conducted to investigate whether a Leu72Met missense polymorphism (rs696217) in the prepro-ghrelin gene (GHRL), is associated with AUD, alcohol consumption and subjective responses to alcohol. Association analysis was performed using the National Institute on Alcohol Abuse and Alcoholism (NIAAA) clinical sample, comprising AUD individuals and controls (N = 1127). Then, a post-hoc analysis using data from a human laboratory study of intravenous alcohol self-administration (IV-ASA, N = 144) was performed to investigate the association of this SNP with subjective responses following a fixed dose of alcohol (priming phase) and alcohol self-administration (ad libitum phase). The case-control study revealed a trend association (N = 1127, OR = 0.665, CI = 0.44-1.01, P = 0.056) between AUD diagnosis and Leu72Met. In AUD subjects, the SNP was associated with significantly lower average drinks per day (n = 567, β = -2.49, 95% CI = -4.34 to -0.64, P = 0.008) and significantly fewer heavy drinking days (n = 567, β = -12.00, 95% CI = -19.10 to -4.89, P polymorphism in the prepro-ghrelin gene, is associated with alcohol use disorder, alcohol consumption and subjective responses to alcohol. Although preliminary, results suggest that the Leu72Leu genotype may lead to increased risk of alcohol use disorder possibly via mechanisms involving a lower response to alcohol. Medical Council on Alcohol and Oxford University Press 2017. This work is written by (a) US Government employee(s) and is in the public domain in the US.

  17. Relationship between -889 C/T polymorphism in interleukin-1A gene and risk of chronic periodontitis: Evidence from a meta-analysis with new published findings.

    Science.gov (United States)

    da Silva, F-R-P; Guimarães-Vasconcelos, A-C-C; de-Carvalho-França, L-F; di-Lenardo, D; Rodrigues, L-S; Barreto-do-Nascimento, M-L-L; Vasconcelos, D-F-P

    2017-01-01

    Periodontitis results from an inflammatory response caused by accumulative microorganisms in periodontal sites. Several factors are involved in pathogenesis of periodontitis, for example the -889 C/T polymorphism in interleukin-1A gene. This study aimed to evaluate the relationship between this polymorphism and risk of development of chronic periodontitis by a meta-analysis based in new published findings. Thereunto a review in literature was performed in the electronic biomedical and education databases (Cochrane Library, Google Scholar, MEDLINE and PubMed) to studies published before August 2, 2015, the abstracts were evaluated and the data extraction performed by two calibrated examiners. The calculations of the meta-analysis were obtained through statistical software Review Manager version 5.2 with calculation of Odds Ratio (OR), heterogeneity (I²) and Funnel plots with P chronic periodontitis and 1, 756 controls. The meta-analysis showed T allele was associated with chronic periodontitis (OR = 1.22, 95% CI: 1.09, 1.36, P = 0.0004) with decreased value to heterogeneity (I² = 15%, P = 0.28). TT genotype was associated to patients with chronic periodontitis (OR = 1.40, 95% CI: 1.07, 1.83, P = 0.01). No publication bias was found in this meta-analysis by asymmetry in Funnel plots. This meta-analysis with 2,174 patients with chronic periodontitis and 1, 756 controls evidenced the -889 C/T polymorphism is associated to risk of development of chronic periodontitis with no significant value to heterogeneity to allelic evaluation.

  18. Analysis of 60 reported glioma risk SNPs replicates published GWAS findings but fails to replicate associations from published candidate-gene studies.

    Science.gov (United States)

    Walsh, Kyle M; Anderson, Erik; Hansen, Helen M; Decker, Paul A; Kosel, Matt L; Kollmeyer, Thomas; Rice, Terri; Zheng, Shichun; Xiao, Yuanyuan; Chang, Jeffrey S; McCoy, Lucie S; Bracci, Paige M; Wiemels, Joe L; Pico, Alexander R; Smirnov, Ivan; Lachance, Daniel H; Sicotte, Hugues; Eckel-Passow, Jeanette E; Wiencke, John K; Jenkins, Robert B; Wrensch, Margaret R

    2013-02-01

    Genomewide association studies (GWAS) and candidate-gene studies have implicated single-nucleotide polymorphisms (SNPs) in at least 45 different genes as putative glioma risk factors. Attempts to validate these associations have yielded variable results and few genetic risk factors have been consistently replicated. We conducted a case-control study of Caucasian glioma cases and controls from the University of California San Francisco (810 cases, 512 controls) and the Mayo Clinic (852 cases, 789 controls) in an attempt to replicate previously reported genetic risk factors for glioma. Sixty SNPs selected from the literature (eight from GWAS and 52 from candidate-gene studies) were successfully genotyped on an Illumina custom genotyping panel. Eight SNPs in/near seven different genes (TERT, EGFR, CCDC26, CDKN2A, PHLDB1, RTEL1, TP53) were significantly associated with glioma risk in the combined dataset (P 0.05). Although several confirmed associations are located near genes long known to be involved in gliomagenesis (e.g., EGFR, CDKN2A, TP53), these associations were first discovered by the GWAS approach and are in noncoding regions. These results highlight that the deficiencies of the candidate-gene approach lay in selecting both appropriate genes and relevant SNPs within these genes. © 2012 WILEY PERIODICALS, INC.

  19. 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.

  20. The diagnostic performance of a single GeneXpert MTB/RIF assay in an intensified tuberculosis case finding survey among HIV-infected prisoners in Malaysia.

    Directory of Open Access Journals (Sweden)

    Haider Abdulrazzaq Abed Al-Darraji

    Full Text Available Delays in tuberculosis (TB diagnosis, particularly in prisons, is associated with detrimental outcomes. The new GeneXpert MTB/RIF assay (Xpert offers accurate and rapid diagnosis of active TB, but its performance in improving case detection in high-transmission congregate settings has yet to be evaluated. We assessed the diagnostic accuracy of a single Xpert assay in an intensified case finding survey among HIV-infected prisoners in Malaysia.HIV-infected prisoners at a single site provided two early-morning sputum specimens to be examined using fluorescence smear microscopy, BACTEC MGIT 960 liquid culture and a single Xpert. The sensitivity, specificity, negative and positive predictive values of Xpert were calculated relative to gold-standard results using MGIT 960 liquid culture. Relevant clinical and demographic data were used to examine correlates of active TB disease.The majority of enrolled subjects with complete data (N=125 were men (90.4%, age <40 years (61.6% and had injected drugs (75.2%. Median CD4 lymphocyte count was 337 cells/µL (IQR 149-492; only 19 (15.2% were receiving antiretroviral therapy. Of 15 culture-positive TB cases, single Xpert assay accurately detected only eight previously undiagnosed TB cases, resulting in a sensitivity, specificity, positive predictive value and negative predictive value of 53.3% (95% CI 30.12-75.2%, 100% (95% CI 96.6-100%, 100% (95% CI 67.56-100% and 94.0% (95% CI 88.2-97.1%, respectively. Only 1 of 15 (6.7% active TB cases was smear-positive. The prevalence (12% of undiagnosed active pulmonary TB (15 of 125 prisoners was high and associated with longer duration of drug use (AOR 1.14, 95% CI 1.03-1.26, for each year of drug use.Single Xpert assay improved TB case detection and outperformed AFB smear microscopy, but yielded low screening sensitivity. Further examination of the impact of HIV infection on the diagnostic performance of the new assay alongside other screening methods in correctional

  1. 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.

  2. The role of renin-angiotensin-aldosterone system genes in the progression of chronic kidney disease: findings from the Chronic Renal Insufficiency Cohort (CRIC) study.

    Science.gov (United States)

    Kelly, Tanika N; Raj, Dominic; Rahman, Mahboob; Kretzler, Matthias; Kallem, Radhakrishna R; Ricardo, Ana C; Rosas, Sylvia E; Tao, Kaixiang; Xie, Dawei; Hamm, Lotuce Lee; He, Jiang

    2015-10-01

    We conducted single-marker, gene- and pathway-based analyses to examine the association between renin-angiotensin-aldosterone system (RAAS) variants and chronic kidney disease (CKD) progression among Chronic Renal Insufficiency Cohort study participants. A total of 1523 white and 1490 black subjects were genotyped for 490 single nucleotide polymorphisms (SNPs) in 12 RAAS genes as part of the ITMAT-Broad-CARe array. CKD progression phenotypes included decline in estimated glomerular filtration rate (eGFR) over time and the occurrence of a renal disease event, defined as incident end-stage renal disease or halving of eGFR from baseline. Mixed-effects models were used to examine SNP associations with eGFR decline, while Cox proportional hazards models tested SNP associations with renal events. Gene- and pathway-based analyses were conducted using the truncated product method. All analyses were stratified by race, and a Bonferroni correction was applied to adjust for multiple testing. Among white and black participants, eGFR declined an average of 1.2 and 2.3 mL/min/1.73 m(2)/year, respectively, while renal events occurred in a respective 11.5 and 24.9% of participants. We identified strong gene- and pathway-based associations with CKD progression. The AGT and RENBP genes were consistently associated with risk of renal events in separate analyses of white and black participants (both P renal events in both groups (both P < 1.00 × 10(-6)). No single-marker associations with CKD progression were observed. The current study provides strong evidence for a role of the RAAS in CKD progression. © The Author 2015. Published by Oxford University Press on behalf of ERA-EDTA. All rights reserved.

  3. 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 ...

  4. Novel Familial Variant of the Desert Hedgehog Gene: Clinical Findings in Two Sisters with 46,XY Gonadal Dysgenesis or 46,XX Karyotype and Literature Review.

    Science.gov (United States)

    Baldinotti, Fulvia; Cavallaro, Tiziana; Dati, Eleonora; Baroncelli, Giampiero I; Bertini, Veronica; Valetto, Angelo; Massart, Francesco; Fabrizi, Gian Maria; Zanette, Giampietro; Peroni, Diego; Bertelloni, Silvano

    2018-01-01

    In humans, Desert Hedgehog (DHH) gene mutations are a very rare cause of 46,XY gonadal dysgenesis (GD), eventually associated with peripheral neuropathy. Clinical records of 12 patients with 46,XY GD and unknown genetic background were reviewed and a 46,XY woman with peripheral neuropathy was individuated. Her 46,XX sister affected by similar neuropathy was also investigated. Genomic DNA was extracted and DHH exons sequenced and analyzed. A comparative genomic hybridization array was also performed. In both the 46,XY and 46,XX sisters, a homozygous c.554C>A mutation in exon 2 of the DHH gene was found, determining a premature termination codon (p.Ser 185*). Heterozygous consanguineous carrier parents showed neither reproductive problems nor peripheral neuropathy. In the proband and her sister, a 499-kb duplication in 9p22.1 was also found. A 46,XY European woman with 46,XY GD and a novel homozygous DHH pathogenic variant is reported, confirming that this gene plays a key role in male gonadal development. Her 46,XX sister, harboring the same mutation, showed normal internal and external female phenotype. Thus, DHH seems not to be involved in the ovarian development pathway or its postpubertal function. Homozygous DHH mutations cause a specific peripheral neuropathy in humans with both 46,XY and 46,XX karyotypes. © 2018 S. Karger AG, Basel.

  5. 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.

  6. Comprehensive identification and clustering of CLV3/ESR-related (CLE) genes in plants finds groups with potentially shared function.

    Science.gov (United States)

    Goad, David M; Zhu, Chuanmei; Kellogg, Elizabeth A

    2017-10-01

    CLV3/ESR (CLE) proteins are important signaling peptides in plants. The short CLE peptide (12-13 amino acids) is cleaved from a larger pre-propeptide and functions as an extracellular ligand. The CLE family is large and has resisted attempts at classification because the CLE domain is too short for reliable phylogenetic analysis and the pre-propeptide is too variable. We used a model-based search for CLE domains from 57 plant genomes and used the entire pre-propeptide for comprehensive clustering analysis. In total, 1628 CLE genes were identified in land plants, with none recognizable from green algae. These CLEs form 12 groups within which CLE domains are largely conserved and pre-propeptides can be aligned. Most clusters contain sequences from monocots, eudicots and Amborella trichopoda, with sequences from Picea abies, Selaginella moellendorffii and Physcomitrella patens scattered in some clusters. We easily identified previously known clusters involved in vascular differentiation and nodulation. In addition, we found a number of discrete groups whose function remains poorly characterized. Available data indicate that CLE proteins within a cluster are likely to share function, whereas those from different clusters play at least partially different roles. Our analysis provides a foundation for future evolutionary and functional studies. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

  7. 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.

  8. The multislice CT findings of renal carcinoma associated with XP11.2 translocation/TFE gene fusion and collecting duct carcinoma

    Energy Technology Data Exchange (ETDEWEB)

    Zhu Qingqiang; Zhu Wenrong; Chen Wenxin; Wu Jingtao [Subei People' s Hospital, Clinical School of Medical Coll., Yangzhou (China)], e-mail: wujingtaodoctor@163.com; Wang Zhongqiu [Dept. of Radiology, East Hospital, Tongji Univ. School of Medicine, Shanghai (China)

    2013-04-15

    Background: Renal cell carcinoma associated with Xp11.2 translocation and TFE gene fusion (Xp11.2/TFE RCC), and collecting duct carcinoma (CDC) are uncommon subtypes of renal cell carcinomas. Purpose: To investigate the multislice CT (MSCT) characteristics of these two tumor types. Material and Methods Nine patients with Xp11.2/TFE RCC and 10 patients with CDC were studied retrospectively. MSCT was undertaken to investigate differences in tumor characteristics and enhancement patterns. Results: All patients had single tumors centered in the renal medulla. Two patients with each tumor type had lymph node involvement and there was a single case of hepatic metastasis (Xp11.2/TFE RCC). The mean tumor diameter of Xp11.2/TFE RCC tumors was significantly larger than for CDC tumors. Two patients with Xp11.2/TFE RCC had cystic components as did eight patients with CDC (P < 0.05). Calcifications were present in six patients, each with CDC. Clear tumor boundaries were visible in two patients with CDC and in nine with Xp11.2/TFE RCC (P < 0.05). The density of Xp11.2/TFE RCC tumors was greater than that of CDC tumors, normal renal cortex, or medulla on unenhanced CT. Enhancement was higher with Xp11.2/TFE RCC than with CDC tumors during all phases. Xp11.2/TFE RCC enhancement was higher than in the renal medulla during cortical and medullary phase but lower than in normal renal medulla during the delayed phase. CDC tumor enhancement was lower than that for normal renal medulla during all enhanced phases. Conclusion: Both tumor types originated from the renal medulla. Distinguishing features included density on unenhanced CT, enhancement patterns, and capsule signs. Identifying these differences may aid diagnosis.

  9. 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.

  10. Finding Sliesthorp?

    DEFF Research Database (Denmark)

    Dobat, Andres S.

    2016-01-01

    In 2003, a hitherto unknown Viking age settlement was discovered at Füsing in Northern Germany close to Hedeby/Schleswig, the largest of the early Scandinavian towns. Finds and building features suggest a high status residence and a seat of some chiefly elite that flourished from around 700 to th...... and the transformation of socio‐political structures in Northern Europe as it transitioned from prehistory into the middle Ages....

  11. 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.

  12. 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 ...

  13. 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.

  14. 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.

  15. Cerebral 18F-FDG PET in macrophagic myofasciitis: An individual SVM-based approach.

    Science.gov (United States)

    Blanc-Durand, Paul; Van Der Gucht, Axel; Guedj, Eric; Abulizi, Mukedaisi; Aoun-Sebaiti, Mehdi; Lerman, Lionel; Verger, Antoine; Authier, François-Jérôme; Itti, Emmanuel

    2017-01-01

    Macrophagic myofasciitis (MMF) is an emerging condition with highly specific myopathological alterations. A peculiar spatial pattern of a cerebral glucose hypometabolism involving occipito-temporal cortex and cerebellum have been reported in patients with MMF; however, the full pattern is not systematically present in routine interpretation of scans, and with varying degrees of severity depending on the cognitive profile of patients. Aim was to generate and evaluate a support vector machine (SVM) procedure to classify patients between healthy or MMF 18F-FDG brain profiles. 18F-FDG PET brain images of 119 patients with MMF and 64 healthy subjects were retrospectively analyzed. The whole-population was divided into two groups; a training set (100 MMF, 44 healthy subjects) and a testing set (19 MMF, 20 healthy subjects). Dimensionality reduction was performed using a t-map from statistical parametric mapping (SPM) and a SVM with a linear kernel was trained on the training set. To evaluate the performance of the SVM classifier, values of sensitivity (Se), specificity (Sp), positive predictive value (PPV), negative predictive value (NPV) and accuracy (Acc) were calculated. The SPM12 analysis on the training set exhibited the already reported hypometabolism pattern involving occipito-temporal and fronto-parietal cortices, limbic system and cerebellum. The SVM procedure, based on the t-test mask generated from the training set, correctly classified MMF patients of the testing set with following Se, Sp, PPV, NPV and Acc: 89%, 85%, 85%, 89%, and 87%. We developed an original and individual approach including a SVM to classify patients between healthy or MMF metabolic brain profiles using 18F-FDG-PET. Machine learning algorithms are promising for computer-aided diagnosis but will need further validation in prospective cohorts.

  16. Introducing instrumental variables in the LS-SVM based identification framework

    NARCIS (Netherlands)

    Laurain, V.; Zheng, W-X.; Toth, R.

    2011-01-01

    Least-Squares Support Vector Machines (LS-SVM) represent a promising approach to identify nonlinear systems via nonparametric estimation of the nonlinearities in a computationally and stochastically attractive way. All the methods dedicated to the solution of this problem rely on the minimization of

  17. VLSI Design of SVM-Based Seizure Detection System With On-Chip Learning Capability.

    Science.gov (United States)

    Feng, Lichen; Li, Zunchao; Wang, Yuanfa

    2018-02-01

    Portable automatic seizure detection system is very convenient for epilepsy patients to carry. In order to make the system on-chip trainable with high efficiency and attain high detection accuracy, this paper presents a very large scale integration (VLSI) design based on the nonlinear support vector machine (SVM). The proposed design mainly consists of a feature extraction (FE) module and an SVM module. The FE module performs the three-level Daubechies discrete wavelet transform to fit the physiological bands of the electroencephalogram (EEG) signal and extracts the time-frequency domain features reflecting the nonstationary signal properties. The SVM module integrates the modified sequential minimal optimization algorithm with the table-driven-based Gaussian kernel to enable efficient on-chip learning. The presented design is verified on an Altera Cyclone II field-programmable gate array and tested using the two publicly available EEG datasets. Experiment results show that the designed VLSI system improves the detection accuracy and training efficiency.

  18. SVM-PB-Pred: SVM based protein block prediction method using sequence profiles and secondary structures.

    Science.gov (United States)

    Suresh, V; Parthasarathy, S

    2014-01-01

    We developed a support vector machine based web server called SVM-PB-Pred, to predict the Protein Block for any given amino acid sequence. The input features of SVM-PB-Pred include i) sequence profiles (PSSM) and ii) actual secondary structures (SS) from DSSP method or predicted secondary structures from NPS@ and GOR4 methods. There were three combined input features PSSM+SS(DSSP), PSSM+SS(NPS@) and PSSM+SS(GOR4) used to test and train the SVM models. Similarly, four datasets RS90, DB433, LI1264 and SP1577 were used to develop the SVM models. These four SVM models developed were tested using three different benchmarking tests namely; (i) self consistency, (ii) seven fold cross validation test and (iii) independent case test. The maximum possible prediction accuracy of ~70% was observed in self consistency test for the SVM models of both LI1264 and SP1577 datasets, where PSSM+SS(DSSP) input features was used to test. The prediction accuracies were reduced to ~53% for PSSM+SS(NPS@) and ~43% for PSSM+SS(GOR4) in independent case test, for the SVM models of above two same datasets. Using our method, it is possible to predict the protein block letters for any query protein sequence with ~53% accuracy, when the SP1577 dataset and predicted secondary structure from NPS@ server were used. The SVM-PB-Pred server can be freely accessed through http://bioinfo.bdu.ac.in/~svmpbpred.

  19. 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...

  20. Linear SVM-Based Android Malware Detection for Reliable IoT Services

    Directory of Open Access Journals (Sweden)

    Hyo-Sik Ham

    2014-01-01

    Full Text Available Current many Internet of Things (IoT services are monitored and controlled through smartphone applications. By combining IoT with smartphones, many convenient IoT services have been provided to users. However, there are adverse underlying effects in such services including invasion of privacy and information leakage. In most cases, mobile devices have become cluttered with important personal user information as various services and contents are provided through them. Accordingly, attackers are expanding the scope of their attacks beyond the existing PC and Internet environment into mobile devices. In this paper, we apply a linear support vector machine (SVM to detect Android malware and compare the malware detection performance of SVM with that of other machine learning classifiers. Through experimental validation, we show that the SVM outperforms other machine learning classifiers.

  1. 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.

  2. 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.

  3. Stationary Wavelet Transform and AdaBoost with SVM Based Pathological Brain Detection in MRI Scanning.

    Science.gov (United States)

    Nayak, Deepak Ranjan; Dash, Ratnakar; Majhi, Banshidhar

    2017-01-01

    This paper presents an automatic classification system for segregating pathological brain from normal brains in magnetic resonance imaging scanning. The proposed system employs contrast limited adaptive histogram equalization scheme to enhance the diseased region in brain MR images. Two-dimensional stationary wavelet transform is harnessed to extract features from the preprocessed images. The feature vector is constructed using the energy and entropy values, computed from the level- 2 SWT coefficients. Then, the relevant and uncorrelated features are selected using symmetric uncertainty ranking filter. Subsequently, the selected features are given input to the proposed AdaBoost with support vector machine classifier, where SVM is used as the base classifier of AdaBoost algorithm. To validate the proposed system, three standard MR image datasets, Dataset-66, Dataset-160, and Dataset- 255 have been utilized. The 5 runs of k-fold stratified cross validation results indicate the suggested scheme offers better performance than other existing schemes in terms of accuracy and number of features. The proposed system earns ideal classification over Dataset-66 and Dataset-160; whereas, for Dataset- 255, an accuracy of 99.45% is achieved. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  4. 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.

  5. 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.

  6. Tumor recognition in wireless capsule endoscopy images using textural features and SVM-based feature selection.

    Science.gov (United States)

    Li, Baopu; Meng, Max Q-H

    2012-05-01

    Tumor in digestive tract is a common disease and wireless capsule endoscopy (WCE) is a relatively new technology to examine diseases for digestive tract especially for small intestine. This paper addresses the problem of automatic recognition of tumor for WCE images. Candidate color texture feature that integrates uniform local binary pattern and wavelet is proposed to characterize WCE images. The proposed features are invariant to illumination change and describe multiresolution characteristics of WCE images. Two feature selection approaches based on support vector machine, sequential forward floating selection and recursive feature elimination, are further employed to refine the proposed features for improving the detection accuracy. Extensive experiments validate that the proposed computer-aided diagnosis system achieves a promising tumor recognition accuracy of 92.4% in WCE images on our collected data.

  7. [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.

  8. A Statistical Parameter Analysis and SVM Based Fault Diagnosis Strategy for Dynamically Tuned Gyroscopes

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Gyro's fault diagnosis plays a critical role in inertia navigation systems for higher reliability and precision. A new fault diagnosis strategy based on the statistical parameter analysis (SPA) and support vector machine(SVM) classification model was proposed for dynamically tuned gyroscopes (DTG). The SPA, a kind of time domain analysis approach, was introduced to compute a set of statistical parameters of vibration signal as the state features of DTG, with which the SVM model, a novel learning machine based on statistical learning theory (SLT), was applied and constructed to train and identify the working state of DTG. The experimental results verify that the proposed diagnostic strategy can simply and effectively extract the state features of DTG, and it outperforms the radial-basis function (RBF) neural network based diagnostic method and can more reliably and accurately diagnose the working state of DTG.

  9. 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

    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...

  10. Gene doping.

    Science.gov (United States)

    Haisma, H J; de Hon, O

    2006-04-01

    Together with the rapidly increasing knowledge on genetic therapies as a promising new branch of regular medicine, the issue has arisen whether these techniques might be abused in the field of sports. Previous experiences have shown that drugs that are still in the experimental phases of research may find their way into the athletic world. Both the World Anti-Doping Agency (WADA) and the International Olympic Committee (IOC) have expressed concerns about this possibility. As a result, the method of gene doping has been included in the list of prohibited classes of substances and prohibited methods. This review addresses the possible ways in which knowledge gained in the field of genetic therapies may be misused in elite sports. Many genes are readily available which may potentially have an effect on athletic performance. The sporting world will eventually be faced with the phenomena of gene doping to improve athletic performance. A combination of developing detection methods based on gene arrays or proteomics and a clear education program on the associated risks seems to be the most promising preventive method to counteract the possible application of gene doping.

  11. 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

  12. Brooke-Spiegler syndrome presenting multiple concurrent cutaneous and parotid gland neoplasms: cytologic findings on fine-needle sample and description of a novel mutation of the CYLD gene.

    Science.gov (United States)

    Malzone, Maria Gabriella; Campanile, Anna Cipolletta; Losito, Nunzia Simona; Longo, Francesco; Perri, Francesco; Caponigro, Francesco; Schiavone, Concetta; Ionna, Franco; Maiello, Francesco; Martinuzzi, Claudia; Nasti, Sabina; Botti, Gerardo; Fulciniti, Franco

    2015-08-01

    Multiple dermal cylindromas and membranous basal cell adenoma of parotid gland in a 67-year-old woman with Brooke-Spiegler syndrome (BSS) were examined by fine-needle cytology. Histology, immunochemistry, and CYLD germline mutation testing were also performed. Cytomorphology and immunochemistry of the two lesions showed basaloid neoplasms, remarkably similar, composed by proliferating epithelial cells of basal type accompanied by a smaller proportion of myoepithelial cells. CYLD gene showed a novel germline splice acceptor site mutation (c.2042-1G>C) with skipping of the entire exon 15. The occurrence of analogous tumors, dermal cylindromas, and membranous basal cell adenoma of the parotid gland, in the same patient may result from the action of a single gene on ontogenetically similar stem cells. Therefore, patients with BSS should be offered a genetic counselling for an early and correct diagnosis. © 2015 Wiley Periodicals, Inc.

  13. Find a Podiatrist

    Science.gov (United States)

    ... RSS Home » Learn About Feet » Find a Podiatrist Find a Podiatrist Search Criteria: First Name: Last Name: ... first 3 digits of your zip code to find the closest doctor. Country: Australia Canada Guam Israel ...

  14. Find a Therapist

    Science.gov (United States)

    ... My ADAA Blog Home / Find Help Print | Email Find a Therapist Zip Code: Radius: 5 Miles 10 ... personal referrals. We supply information to help you find local mental health services and resources that allow ...

  15. 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 ...

  16. CompareSVM: supervised, Support Vector Machine (SVM) inference of gene regularity networks.

    Science.gov (United States)

    Gillani, Zeeshan; Akash, Muhammad Sajid Hamid; Rahaman, M D Matiur; Chen, Ming

    2014-11-30

    Predication of gene regularity network (GRN) from expression data is a challenging task. There are many methods that have been developed to address this challenge ranging from supervised to unsupervised methods. Most promising methods are based on support vector machine (SVM). There is a need for comprehensive analysis on prediction accuracy of supervised method SVM using different kernels on different biological experimental conditions and network size. We developed a tool (CompareSVM) based on SVM to compare different kernel methods for inference of GRN. Using CompareSVM, we investigated and evaluated different SVM kernel methods on simulated datasets of microarray of different sizes in detail. The results obtained from CompareSVM showed that accuracy of inference method depends upon the nature of experimental condition and size of the network. For network with nodes (SVM Gaussian kernel outperform on knockout, knockdown, and multifactorial datasets compared to all the other inference methods. For network with large number of nodes (~500), choice of inference method depend upon nature of experimental condition. CompareSVM is available at http://bis.zju.edu.cn/CompareSVM/ .

  17. ERG and OCT findings of a patient with a clinical diagnosis of occult macular dystrophy in a patient of Ashkenazi Jewish descent associated with a novel mutation in the gene encoding RP1L1.

    Science.gov (United States)

    Saffra, Norman; Seidman, Carly Jane; Rakhamimov, Aleksandr; Tsang, Stephen H

    2017-05-04

    A 57-year-old man with a past medical history of diabetes presented for consultation with a several year history of slowly progressive vision loss in both eyes, which continued to deteriorate over 7 years of follow-up. Multimodal imaging was performed and was significant for the following: on spectral domain optical coherence tomography, a gap lesion was present in the ellipsoid layer, beneath the umbo, as well as subtle macular changes on auto fluorescence imaging. Multifocal electroretinography was performed and was abnormal, and a clinical diagnosis of occult macular dystrophy was made. The patient was subsequently evaluated with genetic testing that revealed a novel p.P73S:c 217C>T nonsense mutation within the retinitis pigmentosa 1-like-1 (RP1L1) gene. The clinical significance of the identified variation will require further investigation. © BMJ Publishing Group Ltd (unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

  18. Finding a Neurosurgeon

    Science.gov (United States)

    Tip: Finding A Neurosurgeon The first step in getting proper treatment for Chiari is to find the right doctor. While many patients are ... surgical, Conquer Chiari recommends that patients see a neurosurgeon for evaluation. As a policy, Conquer Chiari does ...

  19. 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

  20. Find a Dermatologist

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    ... Practice Tools Education Meetings & Events Advocacy Public & Patients Find a Dermatologist Why see a dermatologist? Learn more . ... Last Name Search Special Proprietary Notice and Disclaimer "Find a Dermatologist" is produced by the American Academy ...

  1. 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....

  2. NIH Researchers Find Potential Genetic Cause of Cushing Syndrome

    Science.gov (United States)

    ... 2017 NIH researchers find potential genetic cause of Cushing syndrome Finding may lead to therapies that prevent pituitary ... mutations in the gene CABLES1 may lead to Cushing syndrome, a rare disorder in which the body overproduces ...

  3. Vertebrate gene predictions and the problem of large genes

    DEFF Research Database (Denmark)

    Wang, Jun; Li, ShengTing; Zhang, Yong

    2003-01-01

    To find unknown protein-coding genes, annotation pipelines use a combination of ab initio gene prediction and similarity to experimentally confirmed genes or proteins. Here, we show that although the ab initio predictions have an intrinsically high false-positive rate, they also have a consistent...

  4. 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

  5. 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.

  6. Ultrasonographic findings of cataract

    International Nuclear Information System (INIS)

    Choi, Sun Seob; Kim, Yang Soo; Lee, Kwan Seh; Kim, Kun Sang

    1985-01-01

    Examining the eye with high resolution ultrasonography, authors encountered 34 cases (41 eyeballs) of cataract and found out its characteristic ultrasonographic findings, though cataract is easily recognized by physician on inspection. Ultrasonographic findings of cataract were as follows; 1. Thickening of lens due to edema. 2. Demonstration of lens echo in whole circumference. 3. Multiple internal lens echo

  7. 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.

  8. Finding New Perovskite Halides via Machine learning

    Science.gov (United States)

    Pilania, Ghanshyam; Balachandran, Prasanna V.; Kim, Chiho; Lookman, Turab

    2016-04-01

    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.

  9. Radiologic findings of anthracofibrosis

    International Nuclear Information System (INIS)

    Yoon, Mi Jin; Ko, Eun Joo; Yoon, Sook Ja; Tien, Kuang Lung; Yoon, Yong Kyu; Lee, Kyung Soo; Kim, Jin Hwan

    1998-01-01

    To evaluate the CT findings of bronchial anthracofibrosis. Fourteen patients with bronchoscopically confirmed anthracofibrosis were involved in this study. CT findings (n=3D12) were retrospectively analysed; the pattern, distri-bution and extent of bronchial and parenchymal abnormalities and additional findings such as mediastinal lymphadenopathy and pleural effusion were assessed. Age, sex, and occupational and disease history were history were also reviewed. Patients were aged between 63 and 95 (mean, 71.3) years, and ten were female. Only one patient had an occupational history, but four had a history of pulmonary tuberculosis. Frequent radiologic findings were bronchial wall thickening(n=3D6), atelectasis(n=3D8), mediastinal lymphad-enopathy(n=3D7) and mass(n=3D4). Other accompanying findings were bronchial wall calcification(n=3D3), consolidation(n=3D2) and pleural effusion(n=3D2). Right upper (n=3D7) and right middle lobe(n=3D7) were the most commonly involved sites, and multifocal involvement (n=3D7) was frequent. Bronchial wall thickening, atelectasis and mediastinal lymphadenopathy were characteristic CT findings of anthracofibrosis. When such findings are noted in older or aged female patients, anthracofibrosis should be included in the differential diagnosis

  10. 75 FR 39530 - Findings of Research Misconduct

    Science.gov (United States)

    2010-07-09

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES Office of the Secretary Findings of Research Misconduct... retinal gene profile data that he purportedly obtained from three-week old normal dogs and dogs with X... normal dogs and dogs with X-linked progressive retinal atrophy in abstracts and poster presentations for...

  11. Finding the Right Doctor

    Science.gov (United States)

    ... certified hospital Communicating with Healthcare Professionals for Caregivers Consumer Health Care • Home • Health Insurance Information • Your Healthcare Team Introduction Finding the Right Doctor Talking to Your Doctor Getting a Second ...

  12. Hepatic encephalopathy. Imaging Findings

    International Nuclear Information System (INIS)

    Carrillo, Maria Claudia; Bermudez Munoz, Sonia; J Morillo, Anibal

    2007-01-01

    Hepatic encephalopathy occurs in patients with chronic hepatic insufficiency and can produce abnormalities in the central nervous system, which can be observed in MRI studies. Traditionally, these imaging findings include symmetrical hyper intensities in T1-weighted sequences in the basal ganglia (mainly globus pallidus), involving also the substantia nigra, mesencephalic tegmentum, frontal and occipital cortex. These areas appear of normal intensity in T2-weighted imaging sequences. Other entities that can lead to similar findings include manganese intoxication and type-1 neurofibromatosis. Currently, with the advent of MR spectroscopy, abnormalities in patients with clinical and subclinical hepatic encephalopathy have been described. After hepatic transplantation, hyper intensities of the basal ganglia and the MR spectroscopic findings may disappear within 3 months to 1 year, suggesting a functional, more than a structural damage. This article will demonstrate the MR findings of patients with hepatic encephalopathy due to chronic hepatic insufficiency.

  13. Find a Doctor

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    ... Spira Galifianakis Gallagher Galvez-Jimenez Gancher Garnett Garrett Gates Gayton Gaziano Gelb Geleris George Gerber Gerlach Germano ... Donate Donate Online Membership Find an Event Donor Bill of Rights About Dystonia Symptoms & Diagnosis Forms of ...

  14. Find a Doctor

    Science.gov (United States)

    ... Manager Book Appointments Getting Care When on Active Duty Getting Care When Traveling What's Covered Health Care Dental Care ... Manager Book Appointments Getting Care When on Active Duty Getting Care When Traveling Bread Crumbs Home Find a Doctor ...

  15. 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

  16. 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...... scanners will find mostly superficial errors. Thus, when bugs span multiple functions, even if simple, they become undetectable by most code scanners. The studied set of historical bugs contained many of such cases. This PhD thesis proposes a bug-finding technique that is both lightweight and capable...

  17. 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.

  18. 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.

  19. 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

  20. The tedious task of finding homologous noncoding RNA genes

    DEFF Research Database (Denmark)

    Menzel, Karl Peter; Gorodkin, Jan; Stadler, Peter F

    2009-01-01

    User-driven in silico RNA homology search is still a nontrivial task. In part, this is the consequence of a limited precision of the computational tools in spite of recent exciting progress in this area, and to a certain extent, computational costs are still problematic in practice. An important......, and as we argue here, dominating issue is the dependence on good curated (secondary) structural alignments of the RNAs. These are often hard to obtain, not so much because of an inherent limitation in the available data, but because they require substantial manual curation, an effort that is rarely...... acknowledged. Here, we qualitatively describe a realistic scenario for what a "regular user" (i.e., a nonexpert in a particular RNA family) can do in practice, and what kind of results are likely to be achieved. Despite the indisputable advances in computational RNA biology, the conclusion is discouraging...

  1. FunGene: the functional gene pipeline and repository.

    Science.gov (United States)

    Fish, Jordan A; Chai, Benli; Wang, Qiong; Sun, Yanni; Brown, C Titus; Tiedje, James M; Cole, James R

    2013-01-01

    Ribosomal RNA genes have become the standard molecular markers for microbial community analysis for good reasons, including universal occurrence in cellular organisms, availability of large databases, and ease of rRNA gene region amplification and analysis. As markers, however, rRNA genes have some significant limitations. The rRNA genes are often present in multiple copies, unlike most protein-coding genes. The slow rate of change in rRNA genes means that multiple species sometimes share identical 16S rRNA gene sequences, while many more species share identical sequences in the short 16S rRNA regions commonly analyzed. In addition, the genes involved in many important processes are not distributed in a phylogenetically coherent manner, potentially due to gene loss or horizontal gene transfer. While rRNA genes remain the most commonly used markers, key genes in ecologically important pathways, e.g., those involved in carbon and nitrogen cycling, can provide important insights into community composition and function not obtainable through rRNA analysis. However, working with ecofunctional gene data requires some tools beyond those required for rRNA analysis. To address this, our Functional Gene Pipeline and Repository (FunGene; http://fungene.cme.msu.edu/) offers databases of many common ecofunctional genes and proteins, as well as integrated tools that allow researchers to browse these collections and choose subsets for further analysis, build phylogenetic trees, test primers and probes for coverage, and download aligned sequences. Additional FunGene tools are specialized to process coding gene amplicon data. For example, FrameBot produces frameshift-corrected protein and DNA sequences from raw reads while finding the most closely related protein reference sequence. These tools can help provide better insight into microbial communities by directly studying key genes involved in important ecological processes.

  2. FunGene: the Functional Gene Pipeline and Repository

    Directory of Open Access Journals (Sweden)

    Jordan A. Fish

    2013-10-01

    Full Text Available Ribosomal RNA genes have become the standard molecular markers for microbial community analysis for good reasons, including universal occurrence in cellular organisms, availability of large databases, and ease of rRNA gene region amplification and analysis. As markers, however, rRNA genes have some significant limitations. The rRNA genes are often present in multiple copies, unlike most protein-coding genes. The slow rate of change in rRNA genes means that multiple species sometimes share identical 16S rRNA gene sequences, while many more species share identical sequences in the short 16S rRNA regions commonly analyzed. In addition, the genes involved in many important processes are not distributed in a phylogenetically coherent manner, potentially due to gene loss or horizontal gene transfer.While rRNA genes remain the most commonly used markers, key genes in ecologically important pathways, e.g., those involved in carbon and nitrogen cycling, can provide important insights into community composition and function not obtainable through rRNA analysis. However, working with ecofunctional gene data requires some tools beyond those required for rRNA analysis. To address this, our Functional Gene Pipeline and Repository (FunGene; http://fungene.cme.msu.edu/ offers databases of many common ecofunctional genes and proteins, as well as integrated tools that allow researchers to browse these collections and choose subsets for further analysis, build phylogenetic trees, test primers and probes for coverage, and download aligned sequences. Additional FunGene tools are specialized to process coding gene amplicon data. For example, FrameBot produces frameshift-corrected protein and DNA sequences from raw reads while finding the most closely related protein reference sequence. These tools can help provide better insight into microbial communities by directly studying key genes involved in important ecological processes.

  3. 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…

  4. Granulomatous mastitis: radiological findings

    International Nuclear Information System (INIS)

    Ozturk, M.; Mavili, E.; Kahriman, G.; Akcan, A.C.; Ozturk, F.

    2007-01-01

    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

  5. 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.

  6. Neuroblastoma: computed tomographic findings

    International Nuclear Information System (INIS)

    Yoon, Choon Sik; Ahn, Chang Su; Kim, Myung Jun; Oh, Ki Keun

    1994-01-01

    To evaluate the characteristic CT findings of neuroblastoma, we studied neuroblastomas. We analysed CT findings of available 25 cases among pathologically proved 51 neuroblastomas from Jan. 1983 to Sept. 1990. The most frequent site of origin is adrenal gland (40%) and the second is retroperitoneum (32%) and the third ismediastinum (16%). Characteristic CT findings are as follows: Calcifications within the tumor is detected in 86% of abdominal neuroblastomas and 50% of mediastinal origin. Hemorrhagic and necrotic changes within the tumor is noted at 86% in the tumor of abdominal origin and 25% in mediastinal neuroblastomas. Contrast enhanced study showed frequently seperated enhanced appearance with/without solid contrast enhancement. Encasements of major great vessels such as aorta and IVC with/without displacement by metastatic lymph nodes or tumor are frequently seen in 90% of abdominal neuroblastomas. Multiple lymphadenopathy are detected in 95% of abdominal neuroblastomas and 25% of mediastinal neuroblastomas. The most common organ or contiguous direct invasion is kidney in 6 cases and the next one is liver but intraspinal canal invasion is also noted in 2 cases. We concluded that diagnosis of neuroblastoma would be easily obtained in masses of pediatric group from recognition of above characteristic findings

  7. 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...

  8. MR findings of craniopharyngioma

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Sung Moon; Woo, Young Hoon; Joo, Yang Goo; Suh, Soo Jhi [College of Medicine, Keimyung University, Daegu (Korea, Republic of)

    1992-11-15

    Craniopharyngioma is a benign, slow-growing tumor that constitues 3-9% of all intracranial tumors, and arises from epithelial remnants of the Rathke's pouch. We analyzed MR (2.0T) findings of ten cases with surgically proved craniopharyngioma retrospectively. CT was available in five cases, and Gd-DTPA was used in six cases. Characteristic findings of craniopharyngioma in MRI included multilocularity and variable signal intensities within each loculus that were more prominent in T1WI. Detection rate of calcification in MR was 60%. Six cases with Gd-DTPA enhancement revealed irregular or rim-like enhancement. MRI provides useful information regarding the location, extent and biochemical characteristics of the oraniopharyngioma as well as its relationship to the neighboring structures which will be valuable in planning surgical resection.

  9. MR findings of craniopharyngioma

    International Nuclear Information System (INIS)

    Lee, Sung Moon; Woo, Young Hoon; Joo, Yang Goo; Suh, Soo Jhi

    1992-01-01

    Craniopharyngioma is a benign, slow-growing tumor that constitues 3-9% of all intracranial tumors, and arises from epithelial remnants of the Rathke's pouch. We analyzed MR (2.0T) findings of ten cases with surgically proved craniopharyngioma retrospectively. CT was available in five cases, and Gd-DTPA was used in six cases. Characteristic findings of craniopharyngioma in MRI included multilocularity and variable signal intensities within each loculus that were more prominent in T1WI. Detection rate of calcification in MR was 60%. Six cases with Gd-DTPA enhancement revealed irregular or rim-like enhancement. MRI provides useful information regarding the location, extent and biochemical characteristics of the oraniopharyngioma as well as its relationship to the neighboring structures which will be valuable in planning surgical resection

  10. 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

  11. 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.

  12. MELAS syndrome: neuroradiological findings

    International Nuclear Information System (INIS)

    Cano, A.; Romero, A. I.; Bravo, F.; Vida, J. M.; Espejo, S.

    2002-01-01

    To assess the computed tomography (CT) and magnetic resonance (MR) findings in MELAS syndrome (mitochondrial encephalomyopathy, lactic acidosis and stroke-like episodes) and their contribution to the diagnosis of this entity. We present three patients in which a diagnosis of MELAS syndrome was confirmed by muscle biopsy. CT revealed pathological findings in two patients: bilateral calcifications in the basal nuclei in one and low-attenuation lesions in occipital lobes in the other. Initial or follow-up MR demonstrated pathological findings highly suggestive of MELAS syndrome in all the patients. They consisted of hyperintense lesions in T2-weighted images, located predominantly in the cortex of occipital and parietal lobes. Cerebellar atrophy was also observed in two patients. The clinical signs varied, but epileptic seizures, headache, vomiting, ataxia, muscle weakness and pyramidal involvement were among the major ones. Only one patient presented high lactic acid levels, and in two, the initial muscle biopsy was not conclusive enough to provide the definitive diagnosis. CT and, especially, MR are useful tools in the diagnosis of MELAS syndrome, particularly in those cases in which initial negative laboratory and histological results make diagnosis difficult. (Author) 21 refs

  13. CT findings of slilcosis

    International Nuclear Information System (INIS)

    Jung, Dong Hee; Kim, Kun Il; Son, Hyun Ju; Ro, Young Jin; Jung, Doo Young; Park, Jae Yeong; Lee, Jun Woo; Kim, Byung Soo

    1996-01-01

    To describe chest radiographic and CT findings of silicosis, and to compare their findings. Ten coal miners and six stonemasons were included in this study. All were male and their mean age was 53.1. The mean duration of dust exposure was 15.2 years(range, 5-30 years) in coal miners and 25.3 years(range, 15-35 years) in stonemasons. Chest radiographs(n=16), conventional CT scans(n=4), and high resolution CT(HRCT) scans(n=13) were evaluated. Parenchymal abnormalities were interpreted on the basis of ILO standard films(1980) in chest radiographs and on the basis of CAP(College of American Pathologists, 1979) in CT(HRCT) films. Chest radiographs revealed large opacities(n=8), small opacities(n=6), and normal findings(n=2). Type r(n=4) and category 1/1(n=2) were most common for small opacities, while for large opacities, category B(n=4) and category c(n=4) were most common. These small and large opacities were located predominantly in the area of the upper and middle lung. Associated findings were emphysema(n=7), eggshell nodal calcifications(n=3), pneumothorax(n=3), C-P angle blunting(n=4), and pleural thickening(n=1). CT scans revealed micronodules(n=16), nodules(n=3), and progressive massive fibrosis(PMF, n=8). All these lesions were located in the upper and middle lungs, especially in the central portion of the posterior lung. PMF showed diffuse and homogenous(n=3) and puntate(n=2) calcifications, cavitations(n=5), air bronchograms(n=3), and necrosis(n=1). Peripheral paracicatrical emphysema was associated with PMF(n=8). Other findings were pneumothorax(n=4), emphysema(n=10), hilar and mediastinal nodal enlargement(n=11) bronchial wall thick- enings(n=6), bronchiectasis(n=1), pleural thickening(n=7), parenchymal fibrosis(n=1), and pulmonary tuberculosis(n=2). Small and large opacities in chest radiographs and micronodules, nodules, and PMFs in CT (HRCT) films were located predominately in the upper and middle lungs, especially in the central portion of the

  14. 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.)

  15. 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

  16. MR findings of ulegyria

    International Nuclear Information System (INIS)

    Momoshima, Suketaka; Shiga, Hayao; Yuasa, Yuji; Imai, Yutaka; Higuchi, Nobuya; Maezawa, Mariko.

    1991-01-01

    Magnetic resonance (MR) findings of the brains diagnosed to have ulegyria were reviewed. The reviewed subjects comprised six epileptic children, ranged from 2 to 16 years of age. All patients had convulsion of tonic-clonic type of various severity and had histories of ischemic-hypoxic or hypoglycemic episode in the perinatal or postnatal period. T 1 -weighted images demonstrated the findings precisely reflecting the salient macroscopic features of ulegyria; localized atrophy of the brain with mushroom-shaped cortical gyri with narrow roots and relatively spared wider crowns. T 2 -weighted images showed the areas of hyperintensity in the subcortical and deep white matter subjacent to the atrophic cortex, suggestive of cicatrical gliosis as well as cystic degeneration. The atrophic gyri were seen in the anterior and/or posterior parasagittal arterial border zones bilaterally with minimal asymmetry. Although these findings were nearly pathognomonic to ulegyria, polymicrogyria could mimic it since both are characterized by abnormally diminutive cortical gyri seen in epileptic children. In polymicrogyria, however, affected gyri are uniformly diminutive and not mushroom-shaped, the cortex is rather thickened than atrophic, the underlying white matter shows no focal hyperintensity, subcortical cystic changes are not present, and affected cortex is not restricted to arterial border zones. Even in one of our cases with extensive ulegyria, it was easy to differentiate it from polymicrogyria since parasagittal regions were most severely affected. Although the previous reports on ulegyria have been exclusively based on postmortem pathological examinations or experimental models, its easy recognition on MRI would contribute to further understanding of its clinical significance and mechanisms. (author)

  17. Radiological findings after gastrectomy

    Energy Technology Data Exchange (ETDEWEB)

    Riedl, P.; Polterauer, P.; Funovics, J.

    1980-06-01

    In 63 patients after total gastrectomy and reconstruction of the small bowel described by Beal-Longmire, Roux and Tomoda radiological findings were correlated with clinical symptoms. No correlation could be found between clinical symptoms of dumping and oesophagitis caused by reflux on one side and increased length of intestinal transit time, increased diameter of intestinal loops and gastro-oesophageal reflux on the other side. Enlarged blind loops after termino-lateral oesophago-jejunostomy and insufficient ligations (operation technique by Tomoda) were correlated with higher incidence of pains. Patients operated by the method of Beal-Longmire and Roux showed better results than those operated with the method of Tomoda.

  18. 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)

  19. 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).

  20. 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.

  1. 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.

  2. 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.

  3. SVM-based multisensor data fusion for phase concentration measurement in biomass-coal co-combustion

    Science.gov (United States)

    Wang, Xiaoxin; Hu, Hongli; Jia, Huiqin; Tang, Kaihao

    2018-05-01

    In this paper, the electrical method combines the electrostatic sensor and capacitance sensor to measure the phase concentration of pulverized coal/biomass/air three-phase flow through data fusion technology. In order to eliminate the effects of flow regimes and improve the accuracy of the phase concentration measurement, the mel frequency cepstrum coefficient features extracted from electrostatic signals are used to train the Continuous Gaussian Mixture Hidden Markov Model (CGHMM) for flow regime identification. Support Vector Machine (SVM) is introduced to establish the concentration information fusion model under identified flow regimes. The CGHMM models and SVM models are transplanted on digital signal processing (DSP) to realize on-line accurate measurement. The DSP flow regime identification time is 1.4 ms, and the concentration predict time is 164 μs, which can fully meet the real-time requirement. The average absolute value of the relative error of the pulverized coal is about 1.5% and that of the biomass is about 2.2%.

  4. Area Determination of Diabetic Foot Ulcer Images Using a Cascaded Two-Stage SVM-Based Classification.

    Science.gov (United States)

    Wang, Lei; Pedersen, Peder C; Agu, Emmanuel; Strong, Diane M; Tulu, Bengisu

    2017-09-01

    The standard chronic wound assessment method based on visual examination is potentially inaccurate and also represents a significant clinical workload. Hence, computer-based systems providing quantitative wound assessment may be valuable for accurately monitoring wound healing status, with the wound area the best suited for automated analysis. Here, we present a novel approach, using support vector machines (SVM) to determine the wound boundaries on foot ulcer images captured with an image capture box, which provides controlled lighting and range. After superpixel segmentation, a cascaded two-stage classifier operates as follows: in the first stage, a set of k binary SVM classifiers are trained and applied to different subsets of the entire training images dataset, and incorrectly classified instances are collected. In the second stage, another binary SVM classifier is trained on the incorrectly classified set. We extracted various color and texture descriptors from superpixels that are used as input for each stage in the classifier training. Specifically, color and bag-of-word representations of local dense scale invariant feature transformation features are descriptors for ruling out irrelevant regions, and color and wavelet-based features are descriptors for distinguishing healthy tissue from wound regions. Finally, the detected wound boundary is refined by applying the conditional random field method. We have implemented the wound classification on a Nexus 5 smartphone platform, except for training which was done offline. Results are compared with other classifiers and show that our approach provides high global performance rates (average sensitivity = 73.3%, specificity = 94.6%) and is sufficiently efficient for a smartphone-based image analysis.

  5. A Hierarchical Method for Transient Stability Prediction of Power Systems Using the Confidence of a SVM-Based Ensemble Classifier

    Directory of Open Access Journals (Sweden)

    Yanzhen Zhou

    2016-09-01

    Full Text Available Machine learning techniques have been widely used in transient stability prediction of power systems. When using the post-fault dynamic responses, it is difficult to draw a definite conclusion about how long the duration of response data used should be in order to balance the accuracy and speed. Besides, previous studies have the problem of lacking consideration for the confidence level. To solve these problems, a hierarchical method for transient stability prediction based on the confidence of ensemble classifier using multiple support vector machines (SVMs is proposed. Firstly, multiple datasets are generated by bootstrap sampling, then features are randomly picked up to compress the datasets. Secondly, the confidence indices are defined and multiple SVMs are built based on these generated datasets. By synthesizing the probabilistic outputs of multiple SVMs, the prediction results and confidence of the ensemble classifier will be obtained. Finally, different ensemble classifiers with different response times are built to construct different layers of the proposed hierarchical scheme. The simulation results show that the proposed hierarchical method can balance the accuracy and rapidity of the transient stability prediction. Moreover, the hierarchical method can reduce the misjudgments of unstable instances and cooperate with the time domain simulation to insure the security and stability of power systems.

  6. 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.

  7. Comparative Study on KNN and SVM Based Weather Classification Models for Day Ahead Short Term Solar PV Power Forecasting

    Directory of Open Access Journals (Sweden)

    Fei Wang

    2017-12-01

    Full Text Available Accurate solar photovoltaic (PV power forecasting is an essential tool for mitigating the negative effects caused by the uncertainty of PV output power in systems with high penetration levels of solar PV generation. Weather classification based modeling is an effective way to increase the accuracy of day-ahead short-term (DAST solar PV power forecasting because PV output power is strongly dependent on the specific weather conditions in a given time period. However, the accuracy of daily weather classification relies on both the applied classifiers and the training data. This paper aims to reveal how these two factors impact the classification performance and to delineate the relation between classification accuracy and sample dataset scale. Two commonly used classification methods, K-nearest neighbors (KNN and support vector machines (SVM are applied to classify the daily local weather types for DAST solar PV power forecasting using the operation data from a grid-connected PV plant in Hohhot, Inner Mongolia, China. We assessed the performance of SVM and KNN approaches, and then investigated the influences of sample scale, the number of categories, and the data distribution in different categories on the daily weather classification results. The simulation results illustrate that SVM performs well with small sample scale, while KNN is more sensitive to the length of the training dataset and can achieve higher accuracy than SVM with sufficient samples.

  8. Fractal and twin SVM-based handgrip recognition for healthy subjects and trans-radial amputees using myoelectric signal.

    Science.gov (United States)

    Arjunan, Sridhar Poosapadi; Kumar, Dinesh Kant; Jayadeva J

    2016-02-01

    Identifying functional handgrip patterns using surface electromygram (sEMG) signal recorded from amputee residual muscle is required for controlling the myoelectric prosthetic hand. In this study, we have computed the signal fractal dimension (FD) and maximum fractal length (MFL) during different grip patterns performed by healthy and transradial amputee subjects. The FD and MFL of the sEMG, referred to as the fractal features, were classified using twin support vector machines (TSVM) to recognize the handgrips. TSVM requires fewer support vectors, is suitable for data sets with unbalanced distributions, and can simultaneously be trained for improving both sensitivity and specificity. When compared with other methods, this technique resulted in improved grip recognition accuracy, sensitivity, and specificity, and this improvement was significant (κ=0.91).

  9. [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.

  10. Ultrasonographic findings of Epicondylitis

    International Nuclear Information System (INIS)

    Kwak, Seo Hyun; Song, In Sup; Lee, Jong Beum; Lee, Hwa Yeon; Yoo, Seung Min; Yang, Seong Jun; Seo, Kyung Mook

    2002-01-01

    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.

  11. Radiological findings in angiofibroma

    Energy Technology Data Exchange (ETDEWEB)

    Schick, B. [Univ. of Marburg (Germany). Dept. of Ear, Nose and Throat Diseases; Kahle, G. [Univ. of Marburg, (Germany). Inst.of Radiology

    2000-11-01

    Surgery after pre-operative embolization has become the main treatment modality in angiofibroma therapy. As surgical planning is based on precise pre-operative tumour evaluation, knowledge of the characteristic growth patterns is of great interest. Analysis of tumour extension and blood supply, as well as methods of controlling intra-operative bleeding, help in determining the appropriate surgical approach. Though benign, angiofibroma demonstrates a locally aggressive nature. This fibrovascular tumour is characterised by typical radiological findings and by predictable growth patterns. The tumour extension and blood supply can be accurately determined by CT, MR imaging and angiography. With classic radiological findings, no pre-operative biopsy is necessary in most angiofibromas. Advances in radiological imaging have contributed to improved surgical planning and tumour resection. The surgeon is able to select the least traumatic approach with secure haemostatic control, which is also critical for avoiding the disturbance of facial skeletal growth in this group of young patients. Embolization, pre-operative autologous donation and the cell saver system for immediate retransfusion of the collected blood after filtration, are important tools for dealing with blood loss in angiofibroma surgery as they minimize homologous blood transfusion.

  12. 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.

  13. 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

  14. 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.

  15. 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.

  16. Radiologic findings in neurofibromatosis

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Dai Young; Jeon, Seok Chol; Lee, Kwan Se; Yeon, Kyung Mo; Choo, Dong Woon [Seoul National University College of Medicine, Seoul (Korea, Republic of)

    1979-12-15

    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.

  17. 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

  18. CT findings in mucopolysaccharidoses

    International Nuclear Information System (INIS)

    Tsuchida, Tomio; Nemoto, Shigeru; Fujiwara, Kazue; Hayakawa, Isao; Nihei, Kenji.

    1981-01-01

    The CT findings for four patients with mucopolysaccharidosis were analyzed using a Delta scan-25 (Ohio Nuclear). In three cases of Hunter's syndrome (MPS IIA 13-year-old male, MPS IIB 12-year-old male, and 25-year-old male), a dilatation of the cortical sulci was observed. Moderate dilatations were also seen in the basal cistern, the quadrigeminal cistern, and the ambient cistern. In one case of Hunter's syndrome, a low-density area was observed in the bilateral tharamic regions. An irregular low-density area was also seen in the white matter in some cases. PVL was not apparent in any case. Marked ventricular dilations were observed in cases with mental retardation, for example, in one case of Hurler's syndrome (8-year-old male) and one case of MPS IIA. The circulation and absorbtion of CSF in cortical snbarachnoid spaces were supposed to be moderately retarded by metrizamide CT cisternography. (author)

  19. Radiologic findings of dwarfism

    Energy Technology Data Exchange (ETDEWEB)

    Hwang, M. S.; Oh, K. K.; Park, C. Y.; Kim, D. H. [Yonsei University, College of Medicine, Seoul (Korea, Republic of); Kim, D. H. [Yonsei Univ., Seoul (Korea, Republic of)

    1981-06-15

    The stature of human is very important factor in human-being, especially in childhood. The stature depends on various different conditions, such as familial factor, constitutional factor, chromosomal anomalies, skeletal disorders, or endocrinopathies. The early diagnosis of dwarfism is very important problem, because if appropriate treatment is delayed, the complication or sequales are more increased. The survey of familial history or patient's past history, detail check up of physical examination, radiological evaluation, and other laboratory examinations are essentially needed for the accurate diagnosis of dwarfism. Among the patients admitted to Yonsei University college of Medicine, Severance Hospital since 1963, with chief complaint of short stature or other associated diseases, an analysis of radiological findings were made for the 72 cases of chromosomal anomalies, skeletal dysplasia, and cretinism in which radiologic evaluation was available. The conclusions are as follows; 1. The cause of short stature are chromosomal anomalies (48 cases), skeletal dysplasia (14 cases) and cretinism (10 cases). 2. in chromosomal anomalies, 43 cases of mongolism and 5 cease of Turner's syndrome are noted. In mongolism, 18 cases among the 30 cases below 1 year old are distributed below the 10 percentile of height. On radiologic findings, 11 paired ribs (22/43), congenital heart disease (14/43), decreased iliac index (8/12), and associated anomalies or diseases, such as pneumonia (14 cases), C1-C2 dislocation (1 case), imperforated anus (1 case), Morgagni's hernia (1 case) and leukemia with sepsis (1 case). In Turner's syndrome, decreased bone density (5/5), positive metacarpal sign (2/5), positive carpal sign (1/5), change of knee joint (3/5), hypoplasia of (1/3), and increased carrying angle of elbows (1/3) are noted.

  20. Radiologic findings of dwarfism

    International Nuclear Information System (INIS)

    Hwang, M. S.; Oh, K. K.; Park, C. Y.; Kim, D. H.; Kim, D. H.

    1981-01-01

    The stature of human is very important factor in human-being, especially in childhood. The stature depends on various different conditions, such as familial factor, constitutional factor, chromosomal anomalies, skeletal disorders, or endocrinopathies. The early diagnosis of dwarfism is very important problem, because if appropriate treatment is delayed, the complication or sequales are more increased. The survey of familial history or patient's past history, detail check up of physical examination, radiological evaluation, and other laboratory examinations are essentially needed for the accurate diagnosis of dwarfism. Among the patients admitted to Yonsei University college of Medicine, Severance Hospital since 1963, with chief complaint of short stature or other associated diseases, an analysis of radiological findings were made for the 72 cases of chromosomal anomalies, skeletal dysplasia, and cretinism in which radiologic evaluation was available. The conclusions are as follows; 1. The cause of short stature are chromosomal anomalies (48 cases), skeletal dysplasia (14 cases) and cretinism (10 cases). 2. in chromosomal anomalies, 43 cases of mongolism and 5 cease of Turner's syndrome are noted. In mongolism, 18 cases among the 30 cases below 1 year old are distributed below the 10 percentile of height. On radiologic findings, 11 paired ribs (22/43), congenital heart disease (14/43), decreased iliac index (8/12), and associated anomalies or diseases, such as pneumonia (14 cases), C1-C2 dislocation (1 case), imperforated anus (1 case), Morgagni's hernia (1 case) and leukemia with sepsis (1 case). In Turner's syndrome, decreased bone density (5/5), positive metacarpal sign (2/5), positive carpal sign (1/5), change of knee joint (3/5), hypoplasia of (1/3), and increased carrying angle of elbows (1/3) are noted

  1. 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

  2. Ultrasonographic findings of retinoblastoma

    International Nuclear Information System (INIS)

    Chung, Sung Hoo; Kang, Ik Won; Park, Yang Hee; Kim, Chu Wan; Chi, Je Geun

    1982-01-01

    Retinoblastoma is the most common intraocular tumor in infants and young children which has relatively favorable prognosis with early diagnosis and adequate treatment, however, it can be lethal if the treatment is delayed or inadequate. Clinically, early diagnosis is often difficult because of minimal subjective and objective signs and symptoms, and the patients are usually too young to complain visual disturbance. When ophthalmoscopicexamination is impossible due to presence of opaue media in front of tumor mass as associated inflammatory reaction, hemorrhage, corneal opacity, retinal detachment, etc, ultrasonography is necessary for diagnosis of retinoblastoma. Authors analyzed ultrasonographic al findings with pathological correlation on 10 cases of confirmed retinoblastoma during the period of March 1981 to September1982 at the Seoul National University Hospital. In all cases, ultrasonography demonstrates intraocular masses and all of which are cystic type.Reflectivity of masses are higher than retroorbital fat tissue in 8 cases, and 7 cases show irregular internal echogenic texture. There is no correlation between reflexivity and internal echogenic texture with microscopic findings as rosette, pseudo rosette and micro cysts. Calcifications are demonstrated by ultrasonography as strong reflectiveness with posterior sonic shadowing in 9 cases and 9 of 10 cases are well correlated with calcifications in pathologic specimens. Anechoic cystic areas are shown in 9 cases, and 6 of 10 cases are well correlated with necrosis in pathologic specimen. In all cases, there is no attenuation of sound within tumor masses, and no demonstrable choroidal excavation. Associated retinal detachment is hardly identifiable in irregular contour and internal texture of cystic tumor masses

  3. Findings of autopsy imaging

    International Nuclear Information System (INIS)

    Shiotani, Seiji; Saito, Tsukuru; Itoya, Saori

    2009-01-01

    Described is the outline of autopsy imaging (Ai) by CT, MRI and ultrasonography (US) as the reading of the postmortem images is becoming important for radiologist on site. The present major Ai modality is CT, where the cause of death can be identified in most cases of injuries like that by traffic accident, and of intracranial hemorrhagic lesions. It is difficult for CT alone to determine the cause due to acute heart failure, for which Ai by enhanced CT (2-min heart massage during the intravenous infusion of a contrast agent) has been introduced. CT findings in Ai are varied according to the death cause, anabiotic treatment conducted and postmortem changes. The second item includes the gastrointestinal tract dilation, rib fracture, pneumo- or hemo-thorax, bruise or rupture, and intravascular gas, and the third, the blood hypostasis, which emphasizing the shadow at the gravity-loaded portions in Ai CT. MRI signals vary dependently on the temperature and the inversion time should be shortened to suppress the cerebrospinal signal at Ai of the cold body like that stored in a refrigerator. US can detect clear, macroscopic morphological changes and the portable machine has been in practice at autopsy onsite. As sound speed depends on the temperature in water, Ai US images are obscure relative to living body due to the low temperature. Authors think the problem to identify the cause of death will be mostly solved in Japan when radiological technologists more actively participate in Ai. (K.T.)

  4. 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

  5. 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

  6. New Gene Evolution: Little Did We Know

    Science.gov (United States)

    Long, Manyuan; VanKuren, Nicholas W.; Chen, Sidi; Vibranovski, Maria D.

    2014-01-01

    Genes are perpetually added to and deleted from genomes during evolution. Thus, it is important to understand how new genes are formed and evolve as critical components of the genetic systems determining the biological diversity of life. Two decades of effort have shed light on the process of new gene origination, and have contributed to an emerging comprehensive picture of how new genes are added to genomes, ranging from the mechanisms that generate new gene structures to the presence of new genes in different organisms to the rates and patterns of new gene origination and the roles of new genes in phenotypic evolution. We review each of these aspects of new gene evolution, summarizing the main evidence for the origination and importance of new genes in evolution. We highlight findings showing that new genes rapidly change existing genetic systems that govern various molecular, cellular and phenotypic functions. PMID:24050177

  7. 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)

  8. 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.

  9. Genome-Wide Comparative Gene Family Classification

    Science.gov (United States)

    Frech, Christian; Chen, Nansheng

    2010-01-01

    Correct classification of genes into gene families is important for understanding gene function and evolution. Although gene families of many species have been resolved both computationally and experimentally with high accuracy, gene family classification in most newly sequenced genomes has not been done with the same high standard. This project has been designed to develop a strategy to effectively and accurately classify gene families across genomes. We first examine and compare the performance of computer programs developed for automated gene family classification. We demonstrate that some programs, including the hierarchical average-linkage clustering algorithm MC-UPGMA and the popular Markov clustering algorithm TRIBE-MCL, can reconstruct manual curation of gene families accurately. However, their performance is highly sensitive to parameter setting, i.e. different gene families require different program parameters for correct resolution. To circumvent the problem of parameterization, we have developed a comparative strategy for gene family classification. This strategy takes advantage of existing curated gene families of reference species to find suitable parameters for classifying genes in related genomes. To demonstrate the effectiveness of this novel strategy, we use TRIBE-MCL to classify chemosensory and ABC transporter gene families in C. elegans and its four sister species. We conclude that fully automated programs can establish biologically accurate gene families if parameterized accordingly. Comparative gene family classification finds optimal parameters automatically, thus allowing rapid insights into gene families of newly sequenced species. PMID:20976221

  10. 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.

  11. Finding the Shape of Space

    Science.gov (United States)

    2011-07-01

    Associate Fellow, American Institute of Aeronautics and Astronautics 117 Recipient of the NASP Gene Zara Award Established the NASP Computational Fluid...Scientific Advisory Board Member, National Academy of Science–National Research Council Two-time recipient of NASP “Gene Zara Award” 118 Twenty-seven

  12. Find a NCCAOM Certified Practitioner

    Science.gov (United States)

    ... in finding a NCCAOM Certified Diplomate. The NCCAOM Find a Practitioner Directory is a voluntary directory designed ... by the NCCAOM. If you are unable to find an individual in our registry and would like ...

  13. 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...

  14. 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...

  15. 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.

  16. Major KEEP Findings, 1971 - 1975.

    Science.gov (United States)

    Kamehameha Schools, Honolulu, HI. Kamehameha Early Education Project.

    This report lists the 34 major research findings from the Kamehameha Early Education Program (KEEP) for the years 1971-1975. Each finding is accompanied by a listing of KEEP technical reports and working papers which contain information relevant to that finding. Included among areas covered in the findings are: (1) student motivation, (2) teacher…

  17. Findings

    Science.gov (United States)

    ... Response Chemistry and Biochemistry Enzymes, Molecular Probes, Metabolic Engineering, Glycobiology, Synthesis, Natural Products, Chemical Reactions Computers in Biology Bioinformatics, Modeling, Systems Biology, Data ...

  18. 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.

  19. 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.

  20. 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...

  1. Going Local to Find Help

    Science.gov (United States)

    ... Cover Story: Traumatic Brain Injury Going Local to Find Help Past Issues / Fall 2008 Table of Contents ... phone numbers, maps and directions, such as To Find Out More: Visit www.ninds.nih.gov/Disorders/ ...

  2. Find an Allergist/Immunologist

    Science.gov (United States)

    ... Search Search AAAAI Breadcrumb navigation Home ▸ Members Only Find an Allergist / Immunologist "); } $(document).ready( function () { refreshFields(); }); Welcome to AAAAI Find an Allergist. The search options below can be ...

  3. 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

  4. Biochemical mechanisms determine the functional compatibility of heterologous genes

    DEFF Research Database (Denmark)

    Porse, Andreas; Schou, Thea S.; Munck, Christian

    2018-01-01

    -gene libraries have suggested that sequence composition is a strong barrier for the successful integration of heterologous genes. Here we sample 200 diverse genes, representing >80% of sequenced antibiotic resistance genes, to interrogate the factors governing genetic compatibility in new hosts. In contrast...... factors governing the functionality and fitness of antibiotic resistance genes. These findings emphasize the importance of biochemical mechanism for heterologous gene compatibility, and suggest physiological constraints as a pivotal feature orienting the evolution of antibiotic resistance....

  5. Find an Ob-Gyn

    Science.gov (United States)

    ... Management Education & Events Advocacy For Patients About ACOG Find an Ob-Gyn Home About ACOG Find an Ob-Gyn Page Navigation ▼ About Us ACOG ... Districts ACOG Sections Careers at ACOG Contact Us Find an Ob-Gyn Search by State Search by ...

  6. Incidental findings in musculoskeletal radiology

    International Nuclear Information System (INIS)

    Wuennemann, F.; Rehnitz, C.; Weber, M.A.

    2017-01-01

    Increasing numbers of conventional X-rays, computed tomography and magnetic resonance imaging in the inpatient, outpatient and scientific routine leads to an increasing number of incidental findings. The correct interpretation of these incidental findings with respect to the relevance and the evaluation concerning further work-up is an important task of radiologists. Description of common incidental findings in musculoskeletal imaging and their clinical classification. A PubMed literature search was performed using the following terms: incidental findings, population-based imaging, musculoskeletal imaging, non-ossifying fibroma, enchondroma, osteodystrophia deformans, chondrosarcoma, fibrous dysplasia, simple bone cyst, unicameral bone cyst, solitary bone cyst, aneurysmal bone cyst, vertebral hemangioma, bone island, osteopoikilosis, Tarlov cyst and diffuse idiopathic skeletal hyperostosis (DISH). Incidental findings are observed in up to 40% of imaging procedures. In up to 6% these incidental findings involve the skeletal system. Common incidental findings are discussed and their clinical relevance is explained. (orig.) [de

  7. GSEH: A Novel Approach to Select Prostate Cancer-Associated Genes Using Gene Expression Heterogeneity.

    Science.gov (United States)

    Kim, Hyunjin; Choi, Sang-Min; Park, Sanghyun

    2018-01-01

    When a gene shows varying levels of expression among normal people but similar levels in disease patients or shows similar levels of expression among normal people but different levels in disease patients, we can assume that the gene is associated with the disease. By utilizing this gene expression heterogeneity, we can obtain additional information that abets discovery of disease-associated genes. In this study, we used collaborative filtering to calculate the degree of gene expression heterogeneity between classes and then scored the genes on the basis of the degree of gene expression heterogeneity to find "differentially predicted" genes. Through the proposed method, we discovered more prostate cancer-associated genes than 10 comparable methods. The genes prioritized by the proposed method are potentially significant to biological processes of a disease and can provide insight into them.

  8. 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

  9. Radiologic findings of sacroiliitis : emphasis on MR findings

    International Nuclear Information System (INIS)

    Yang, Ik; Park, Hai Jung; Lee, Yul; Chung, Soo Young; Park, Jong Ho

    1997-01-01

    To compare the characteristic MR findings of infectious sacroiliitis (IS) and ankylosing spondylitis (AS). We retrospectively reviewed MR findings in eight patients with IS (pyogenic in six, tuberculosis in two) confirmed by culture and clinical follow-up, and in six with AS by HLA-B27 typing. AA control group of 13 asymptomatic volunteers was formed, and they underwent MRI Findings were analysed for morphology, degree of bone erosion, and adjacent soft tissue change. CT findings of AS in four patients and IS in four were also compared to MR findings. MR characteristics of IS included unilaterality (100%), abnormal cartilage signal intensity (100%), bone marrow change (100%), contrast enhancement (100%), erosion (63%), and soft tissue change (63%). MR findings of AS showed bilaterality (67%), abnormal cartilage signal intensity (80%), bone marrow change (80%), erosion (80%), contrast enhancement (44%) and soft tissue change (10%). CT scan showed bony sclerosis and erosion (86%), and abnormal joint space (71%). MR findings of sacroiliitis were loss of thin zone of a cartilage and erosions on T1-weighted image, and increased signal intensity on T2-weighted image. MRI is regarded as a useful diagnostic method where conventional diagnosis is difficult, and is able to image cartilage abnormalities directly and noninvasively. Significant differences in MR findings between IS and AS were not noted, however

  10. 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)

  11. Defecography - analysis of qualitative findings

    International Nuclear Information System (INIS)

    Schott, U.; Braunschweig, R.; Claussen, C.D.

    1994-01-01

    The defectography is an examination of the anorectal function in defecatory disorder. The defecography has a diagnostic impact on disease, which only emerge during defecation as intussusception, enterocele, prolapse or sphincter dysfunction. Other findings as rectocele or descending pelvic floor are ambiguous concerning clinical relevance. The interpretation of defecography should include patient's history and clinical findings and - if available -endoscopic and manometric findings. (orig.) [de

  12. Imaging findings of sacral tumors

    International Nuclear Information System (INIS)

    Kim, Seung Ho; Hong, Sung Hwan; Choi, Ja Young; Koh, Sung Hye; Chung, Hye Won; Choi, Jung Ah; Kang, Heung Sik

    2003-01-01

    The various pathologic conditions detected at CT and MRI and subsumed by the term 'sacral tumor' include primary bone tumors, sacral canal tumors and metastases. Among these, metastases are much more common than primary bone tumors, of which chordoma is the most common. Although the imaging findings of sacral tumors are nonspecific, a patient's age and sex, and specific findings such as calcification or fluid-fluid levels, can help radiologists in their differential diagnosis. We describe the imaging findings of primary sacral tumors, emphasizing the MRI findings

  13. 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.)

  14. Gene Ontology

    Directory of Open Access Journals (Sweden)

    Gaston K. Mazandu

    2012-01-01

    Full Text Available The wide coverage and biological relevance of the Gene Ontology (GO, confirmed through its successful use in protein function prediction, have led to the growth in its popularity. In order to exploit the extent of biological knowledge that GO offers in describing genes or groups of genes, there is a need for an efficient, scalable similarity measure for GO terms and GO-annotated proteins. While several GO similarity measures exist, none adequately addresses all issues surrounding the design and usage of the ontology. We introduce a new metric for measuring the distance between two GO terms using the intrinsic topology of the GO-DAG, thus enabling the measurement of functional similarities between proteins based on their GO annotations. We assess the performance of this metric using a ROC analysis on human protein-protein interaction datasets and correlation coefficient analysis on the selected set of protein pairs from the CESSM online tool. This metric achieves good performance compared to the existing annotation-based GO measures. We used this new metric to assess functional similarity between orthologues, and show that it is effective at determining whether orthologues are annotated with similar functions and identifying cases where annotation is inconsistent between orthologues.

  15. [Key effect genes responding to nerve injury identified by gene ontology and computer pattern recognition].

    Science.gov (United States)

    Pan, Qian; Peng, Jin; Zhou, Xue; Yang, Hao; Zhang, Wei

    2012-07-01

    In order to screen out important genes from large gene data of gene microarray after nerve injury, we combine gene ontology (GO) method and computer pattern recognition technology to find key genes responding to nerve injury, and then verify one of these screened-out genes. Data mining and gene ontology analysis of gene chip data GSE26350 was carried out through MATLAB software. Cd44 was selected from screened-out key gene molecular spectrum by comparing genes' different GO terms and positions on score map of principal component. Function interferences were employed to influence the normal binding of Cd44 and one of its ligands, chondroitin sulfate C (CSC), to observe neurite extension. Gene ontology analysis showed that the first genes on score map (marked by red *) mainly distributed in molecular transducer activity, receptor activity, protein binding et al molecular function GO terms. Cd44 is one of six effector protein genes, and attracted us with its function diversity. After adding different reagents into the medium to interfere the normal binding of CSC and Cd44, varying-degree remissions of CSC's inhibition on neurite extension were observed. CSC can inhibit neurite extension through binding Cd44 on the neuron membrane. This verifies that important genes in given physiological processes can be identified by gene ontology analysis of gene chip data.

  16. Gene doping: gene delivery for olympic victory

    OpenAIRE

    Gould, David

    2012-01-01

    With one recently recommended gene therapy in Europe and a number of other gene therapy treatments now proving effective in clinical trials it is feasible that the same technologies will soon be adopted in the world of sport by unscrupulous athletes and their trainers in so called ‘gene doping’. In this article an overview of the successful gene therapy clinical trials is provided and the potential targets for gene doping are highlighted. Depending on whether a doping gene product is secreted...

  17. Metasynthesis findings: potential versus reality.

    Science.gov (United States)

    Finfgeld-Connett, Deborah

    2014-11-01

    Early on, qualitative researchers predicted that metasynthesis research had the potential to significantly push knowledge development forward. More recently, scholars have questioned whether this is actually occurring. To examine this concern, a randomly selected sample of metasynthesis articles was systematically reviewed to identify the types of findings that have been produced. Based on this systematic examination, it appears that findings from metasynthesis investigations might not be reaching their full potential. Metasynthesis investigations frequently result in isolated findings rather than findings in relationship, and opportunities to generate research hypotheses and theoretical models are not always fully realized. With this in mind, methods for moving metasynthesis findings into relationship are discussed. © The Author(s) 2014.

  18. 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

  19. Finding beam focus errors automatically

    International Nuclear Information System (INIS)

    Lee, M.J.; Clearwater, S.H.; Kleban, S.D.

    1987-01-01

    An automated method for finding beam focus errors using an optimization program called COMFORT-PLUS. The steps involved in finding the correction factors using COMFORT-PLUS has been used to find the beam focus errors for two damping rings at the SLAC Linear Collider. The program is to be used as an off-line program to analyze actual measured data for any SLC system. A limitation on the application of this procedure is found to be that it depends on the magnitude of the machine errors. Another is that the program is not totally automated since the user must decide a priori where to look for errors

  20. Imaging findings of sternal abnormalities

    International Nuclear Information System (INIS)

    Franquet, T.; Gimenez, A.; Alegret, X.; Sanchis, E.; Rivas, A.

    1997-01-01

    Radiographic findings in the sternal abnormalities are often nonspecific, showing appearances from a localized benign lesion to an aggressive lesion as seen with infections and malignant neoplasms. A specific diagnosis of sternal abnormalities can be suggested on the basis of CT and MR characteristics. Familiarity with the presentation and variable appearance of sternal abnormalities may aid the radiologist is suggesting a specific diagnosis. We present among others characteristic radiographic findings of hemangioma, chondrosarcoma, hydatid disease, and SAPHO syndrome. In those cases in which findings are not specific, cross-sectional imaging modalities may help the clinician in their management. (orig.)

  1. CT findings in Reye syndrome

    International Nuclear Information System (INIS)

    Lee, Kil Woo; Lim, Hyo Keun; Choo, In Wook; Bae, Sang Hoon

    1990-01-01

    We present here the CT findings in 10 patients with Reye syndrome. Acute findings is diffuse cerebral swelling with or without parenchymal low density. The cerebral swelling gradually changed to atrophy. The parenchymal low density predisposes in Lt temporoparietal area. Contrast enhanced CT scan showed no additional finding, except 1 case. The hemorrhagic infarction which has not been reported previously was seen in 1 case and resulted in the most prominent sequela. The sequelae were developed in all atrophic cases. So, the brain CT may be useful in monitoring cerebral swelling, determining treatment plan in acute stage, and in presenting prognosis and sequelae on fellow up CT

  2. CT findings of pulmonary aspergillosis

    International Nuclear Information System (INIS)

    Cheon, Jung Eun; Im, Jung Gi; Goo, Jin Mo; Kim, Hong Dae; Han, Man Chung

    1995-01-01

    The fungus aspergillus can cause a variety of pulmonary disorders. Aspergilloma is a noninvasive aspergillus colonization of virtually any type of preexisting pulmonary cavity or cystic space. Invasive pulmonary aspergillosis is serious, usually fatal infection in patients being treated with immunosuppressants or who have chronic debilitating disease. Allergic bronchopulmonary aspergillosis is characterized clinically by asthma, blood and sputum eosinophilia and positive immunologic reaction to aspergillus antigen. Awareness of the radiographic and CT findings of pulmonary aspergillosis is important in making the diagnosis of aspergillus-caused pulmonary disorders. In this pictorial essay, we illustrated various radiological findings of pulmonary aspergillosis focused on CT findings correlated with gross pathologic specimens

  3. Turning of COGS moves forward findings for hormonally mediated cancers.

    Science.gov (United States)

    Sakoda, Lori C; Jorgenson, Eric; Witte, John S

    2013-04-01

    The large-scale Collaborative Oncological Gene-environment Study (COGS) presents new findings that further characterize the genetic bases of breast, ovarian and prostate cancers. We summarize and provide insights into this collection of papers from COGS and discuss the implications of the results and future directions for such efforts.

  4. HRCT findings of scrub typhus

    International Nuclear Information System (INIS)

    Kim, Kyu Sik; Kang, Sung Soo; Jin, Kong Yong; Lee, Jeong Min; Han, Young Min; Kim, Chong Soo; Chung, Gyung Ho; Lee, Sang Yong; Sohn, Myung Hee; Choi, Ki Chul

    1997-01-01

    To evaluate high-resolution CT (HRCT) findings of scrub typhus. We retrospectively reviewed the HRCT scans of 26 serologically confirmed scrub typhus patients. One underwent follow-up HRCT scanning. Twenty-three(88.5%) of the 26 patients showed abnormal findings. All 23 had lung parenchymal lesions; a small amount of pleural effusion was seen in 11 patients, and lymphadenopathy in six. The predominant parenchymal lesion was thickening of interlobular septae and the axial and intralobular interstitium (n=16). Most lesions were located in both lower lung zones. Other findings were ground-glass attenuation (n=11) and focal parenchymal consolidation (n=8). In one patient, parenchymal lesions were resolved on follow-up HRCT scanning. HRCT findings of interstitial thickening, abnormally increased parenchymal attenuation, pleural effusion and lymphadenopathy with typical clinical symptoms were diagnostic of scrub typhus

  5. HRCT findings of scrub typhus

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Kyu Sik; Kang, Sung Soo; Jin, Kong Yong; Lee, Jeong Min; Han, Young Min; Kim, Chong Soo; Chung, Gyung Ho; Lee, Sang Yong; Sohn, Myung Hee; Choi, Ki Chul [Chonbuk National Univ. Medical School, Chonju (Korea, Republic of)

    1997-06-01

    To evaluate high-resolution CT (HRCT) findings of scrub typhus. We retrospectively reviewed the HRCT scans of 26 serologically confirmed scrub typhus patients. One underwent follow-up HRCT scanning. Twenty-three(88.5%) of the 26 patients showed abnormal findings. All 23 had lung parenchymal lesions; a small amount of pleural effusion was seen in 11 patients, and lymphadenopathy in six. The predominant parenchymal lesion was thickening of interlobular septae and the axial and intralobular interstitium (n=16). Most lesions were located in both lower lung zones. Other findings were ground-glass attenuation (n=11) and focal parenchymal consolidation (n=8). In one patient, parenchymal lesions were resolved on follow-up HRCT scanning. HRCT findings of interstitial thickening, abnormally increased parenchymal attenuation, pleural effusion and lymphadenopathy with typical clinical symptoms were diagnostic of scrub typhus.

  6. Disclosing finding and development costs

    International Nuclear Information System (INIS)

    Janisch, M.L.

    1998-01-01

    The importance of finding and development costs in the petroleum industry and the issue of how they can be either manipulated or misunderstood was discussed. Finding and development costs are usually expressed in terms of $/BOE (barrel of oil equivalents) and reflect the total capital expenditures divided by the total reserves replaced and added. Various examples of the importance of finding and development costs in making investment decisions were used to illustrate the effects of potential bias by the resource company, and the need for care and understanding of what the numbers issued by the company actually mean. In general, low and consistent finding and development costs, combined with good netbacks, are the key to value added for shareholders. tabs

  7. 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......, knowledge development and identity-shaping, where learning emerges through motions, feeling and thinking within an information rich world in constant change.......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...

  8. Find an Endocrinology - Thyroid Specialist

    Science.gov (United States)

    ... History Resource Center Patients Thyroid Information Find an Endocrinology – Thyroid Specialist Patient Support Links Clinical Thyroidology for ... Access Thyroid Online Access Clinical Thyroidology Online Video Endocrinology Donate Give Online Research Accomplishments Ridgway Legacy Fund ...

  9. 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.

  10. Finding an Eye Care Professional

    Science.gov (United States)

    ... article rating hospitals in the United States. Website: http://health.usnews.com/best-hospitals For More Information ... ophthalmologists in the United States and abroad. Website: https://secure.aao.org/aao/find-ophthalmologist The American ...

  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. CT findings in abdominal actinomycosis

    International Nuclear Information System (INIS)

    Lee, In Jae; Ha, Hyun Kwon; Lee, Moon Gyu; Kim, Pyo Nyun; Auh, Yong Ho

    1999-01-01

    Abdominal actinomycosis is a chronic, progressive, suppurative disease with a favorable response to intravenous treatment with penicillin. In many instances, however, its clinical and radiological findings may overlap with those of other inflammatory and neoplastic conditions, and the familiarity with the various radiological features can thus avoid diagnostic delays. The purpose of this paper is to describe and discuss the CT findings of abdominal actinomycosis

  13. 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.

  14. Radiologic findings of granulomatous mastitis

    International Nuclear Information System (INIS)

    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

    2008-01-01

    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

  15. CT findings of exophageal perforation

    Energy Technology Data Exchange (ETDEWEB)

    Heo, Jeong Nam; Choi, Yo Won; Jeon, Seok Chol; Park, Choong Ki; Hahm, Chang Kok [Hanyang University College of Medicine, Seoul (Korea, Republic of)

    2002-09-01

    To determine which CT findings are useful for the early disgnosis of esophageal perforation, and on the basis of these findings, to assess the accuracy of prediction of the perforation site. A review of medical records indicated that between January 1995 and December 2001, 36 patients with esophageal perforation were admitted to our hospital. Thirteen of these [M:F=8:5, age; 28-69 (mean, 52.4) years], who had undergone CT chest scanning, were included in this study. The causes of esophageal perforation were trauma (n=5), infectious diseases (n=4), Boerhaave syndrome (n=1), lung cancer (n=1), esophageal cancer (n=1), and idiopathic. Two chest radiologists unaware of the clinical findings reviewed the CT scans and predicted whether the upper or lower esophagus was perforated. The most common CT finding was extraluminal air at the posterior mediastinum (n=11), while other findings included pulmonary consolidation (n=10), pleural effusion (n=7), discontinuity of the esophageal wall (n=6) and subcutaneous emphysema (n=4), fluid collection around the esophagus (n-4), esophageal wall thickening (n=4), pneumothorax (n=2), and lung abscess (n=2). The perforation site was accurately predicted in 76.9% of cases (10/13). The CT findings which help the diagnosis of esophageal perforation, and prediction of the sites at which it occurs, are extraluminal air of fluid collection, focal defect of the esophageal wall, and esophageal wall thickening.

  16. CT findings of exophageal perforation

    International Nuclear Information System (INIS)

    Heo, Jeong Nam; Choi, Yo Won; Jeon, Seok Chol; Park, Choong Ki; Hahm, Chang Kok

    2002-01-01

    To determine which CT findings are useful for the early disgnosis of esophageal perforation, and on the basis of these findings, to assess the accuracy of prediction of the perforation site. A review of medical records indicated that between January 1995 and December 2001, 36 patients with esophageal perforation were admitted to our hospital. Thirteen of these [M:F=8:5, age; 28-69 (mean, 52.4) years], who had undergone CT chest scanning, were included in this study. The causes of esophageal perforation were trauma (n=5), infectious diseases (n=4), Boerhaave syndrome (n=1), lung cancer (n=1), esophageal cancer (n=1), and idiopathic. Two chest radiologists unaware of the clinical findings reviewed the CT scans and predicted whether the upper or lower esophagus was perforated. The most common CT finding was extraluminal air at the posterior mediastinum (n=11), while other findings included pulmonary consolidation (n=10), pleural effusion (n=7), discontinuity of the esophageal wall (n=6) and subcutaneous emphysema (n=4), fluid collection around the esophagus (n-4), esophageal wall thickening (n=4), pneumothorax (n=2), and lung abscess (n=2). The perforation site was accurately predicted in 76.9% of cases (10/13). The CT findings which help the diagnosis of esophageal perforation, and prediction of the sites at which it occurs, are extraluminal air of fluid collection, focal defect of the esophageal wall, and esophageal wall thickening

  17. 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.

  18. 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.)

  19. 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…

  20. Imaging findings of xanthogranulomatous pyelonephritis

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Jong Chul [School of Medicine, Chungnam National University, Taejon (Korea, Republic of)

    2000-01-01

    To define the imaging patterns of xanthogranulomatous pyelonephritis (XGP). The demographic, clinical, and imaging findings of 21 cases of pathologically proven XGP in 20 patients (bilateral in one) were evaluated. The findings of ultrasonography and CT were retrospectively evaluated with regard to distribution and extent of the disease, kidney size, the presence of calculi, hydronephrosis, and renal function. The findings were assessed by two radiologists, who established a consensus. Imaging and pathologic findings were compared. Sixteen of the 20 patients were female, and 19 were adults. Their age ranged from 3 to 16 (mean, 45) years. In all patients except one, the disease was unilateral (right: left =3D 13 :16). In one patient, XGP was bilateral, and there were thus 21 cases. Seventeen (81%) of these were diffuse, and four (19%) were focal; extrarenal extension occurred in 13 cases (62%), among which ipsilateral pleural effusion was noted in two. The kidney was enlarged diffusely in 12 cases (57%), and focally in three (14%); urinary calculi were present in 16 cases (76%), with staghorn calculi in four of these; and hydronephrosis occurred in 17 (81%). Impairment of ipsilateral renal function was noted in 13 cases (62%). Clinical findings of inflammation such as fever, pyuria, bacteriuria, or leucocytosis were noted in all patients. In addition to nephromegaly, renal function impairment, and urinary obstruction due to calculi, which are typical features of XGP, the condition may also show variable imaging findings. If the images obtained in the case of a middle-aged woman with clinical findings of urinary infection are atypical, we believe that XGP should be included in the differential diagnosis. (author)

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

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Yang Soo; Kim, Young Goo; Park, Un Sup [College of Medicine, Chungang University, Seoul (Korea, Republic of)

    1994-11-15

    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.

  2. 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

  3. 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

  4. 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

  5. MR findings of cerebral palsy

    International Nuclear Information System (INIS)

    Yoon, Sang Hum; Chang, Seung Kuk; Cho, Mee Young; Park, Dong Woo; Kim, Jong Deok; Eun, Choong Ki

    1994-01-01

    To evaluate the MR findings of brain damage in cerebral palised patients and to correlate it with gestational age and the time of damage. A retrospective analysis was performed in 40 patients who underwent MR scanning for evaluation of brain lesion in clinically diagnosed cerebral palsy. Authors classified the patients into two groups as premature and full-term and compared MR findings of the two groups. Abnormal MR findings were noted in 28 cases (70%). Five out of 6 patients who had been born prematurely showed isolate periventricular white matter lesions. Twenty-three out of 34 patients who had been born at full-term showed abnormal MR findings. Of these 23 patients, migration anomalies in 7 patients, isolate periventricular white matter lesions in 3 patients, and other combined periventricular subcortical white matter and deep gray matter lesions in 14 patients were seen. At least, 10 patients(43%) of full term group showed abnormal MRI findings reflecting intrauterine brain damage and all 5 patients of premature group showed isolate periventricular white matter lesions suggesting immaturity of brain. MRI is thought to be very useful in the assessment of brain damage for the patients with cerebral palsy by recognizing the location of the lesion and estimating the time of damage

  6. MR findings of cerebral palsy

    Energy Technology Data Exchange (ETDEWEB)

    Yoon, Sang Hum; Chang, Seung Kuk; Cho, Mee Young; Park, Dong Woo; Kim, Jong Deok; Eun, Choong Ki [Pusan Paik Hospital, Pusan (Korea, Republic of)

    1994-11-15

    To evaluate the MR findings of brain damage in cerebral palised patients and to correlate it with gestational age and the time of damage. A retrospective analysis was performed in 40 patients who underwent MR scanning for evaluation of brain lesion in clinically diagnosed cerebral palsy. Authors classified the patients into two groups as premature and full-term and compared MR findings of the two groups. Abnormal MR findings were noted in 28 cases (70%). Five out of 6 patients who had been born prematurely showed isolate periventricular white matter lesions. Twenty-three out of 34 patients who had been born at full-term showed abnormal MR findings. Of these 23 patients, migration anomalies in 7 patients, isolate periventricular white matter lesions in 3 patients, and other combined periventricular subcortical white matter and deep gray matter lesions in 14 patients were seen. At least, 10 patients(43%) of full term group showed abnormal MRI findings reflecting intrauterine brain damage and all 5 patients of premature group showed isolate periventricular white matter lesions suggesting immaturity of brain. MRI is thought to be very useful in the assessment of brain damage for the patients with cerebral palsy by recognizing the location of the lesion and estimating the time of damage.

  7. 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)

  8. 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]. ...

  9. Imaging findings of avalanche victims

    Energy Technology Data Exchange (ETDEWEB)

    Grosse, Alexandra B.; Grosse, Claudia A.; Anderson, Suzanne [University Hospital of Berne, Inselspital, Department of Diagnostic, Pediatric and Interventional Radiology, Berne (Switzerland); Steinbach, Lynne S. [University of California San Francisco, Department of Radiology, San Francisco, CA (United States); Zimmermann, Heinz [University Hospital of Berne, Inselspital, Department of Trauma and Emergency Medicine, Berne (Switzerland)

    2007-06-15

    Skiing and hiking outside the boundaries remains an attractive wilderness activity despite the danger of avalanches. Avalanches occur on a relatively frequent basis and may be devastating. Musculoskeletal radiologists should be acquainted with these injuries. Fourteen avalanche victims (11 men and 3 women; age range 17-59 years, mean age 37.4 years) were air transported to a high-grade trauma centre over a period of 2 years. Radiographs, CT and MR images were prospectively evaluated by two observers in consensus. Musculoskeletal findings (61%) were more frequent than extraskeletal findings (39%). Fractures were most commonly seen (36.6%), involving the spine (14.6%) more frequently than the extremities (9.8%). Blunt abdominal and thoracic trauma were the most frequent extraskeletal findings. A wide spectrum of injuries can be found in avalanche victims, ranging from extremity fractures to massive polytrauma. Asphyxia remains the main cause of death along with hypoxic brain injury and hypothermia. (orig.)

  10. 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

  11. 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

  12. 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.

  13. 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......Apostolico and Ehrenfeucht defined the notion of a maximal quasiperiodic substring and gave an algorithm that finds all maximal quasiperiodic substrings in a string of length n in time O(n log2 n). In this paper we give an algorithm that finds all maximal quasiperiodic substrings in a string...... in the suffix tree that have a superprimitive path-label....

  14. 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.

  15. Radiologic findings of struma ovarii

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Jong Chul [Chungnam National Univ. School of Medicine, Taejeon (Korea, Republic of); Shin, Hyun Ja [Korea Veterans Hospital, Seoul (Korea, Republic of); Kim, Seung Hyup [Seoul National Univ. College of Medicine, Seoul (Korea, Republic of); Byun, Jae Young [Catholic Univ. College of Medicine, Seoul (Korea, Republic of)

    1997-01-01

    Struma ovarii is ovarian tumor composed solely or predominantly of thyroid tissue or tumor in which hyperthyroidism results from ovarian thyroid tissue, and usually occurs in tandem with cystic teratoma. Ovarian cystic teratoma is radiologically easily diagnosed due to calcification or fat, for example, but the preoperative diagnosis of struma ovarii is often difficult due to rare characteristic features of thyroid tissue. Our purpose was to determine whether there were specific findings of struma ovarii which distinguished it from other ovarian tumors, and this involved analysis of its radiologic findings. Using ultrasonography, computed tomography, and magnetic resonance imaging, preoperative radiologic findings of pathologically-proven struma ovarii in eleven patients were retrospectively evaluated for site, margin, nature (cystic, solid, mixed), contrast enhancement, septa, mural nodule, calcification, fat, and metastasis. These findings were compared with pathologic findings. All eleven tumors were unilateral, ten had smooth tumor margins, seven were mixed cystic and solid tumors (more than 70% of solid components in one tumor), and nine had regular septa. Three of four cystic masses (one unilocular, one bilocular and two multilocular cysts) had mural nodules. Calcifications were found in two tumors, and fat in one. Malignant change or metastasis was not found in any tumor. In one patient with hyperthyroidism due to struma ovarii, symptoms and signs of this subsided after removal of the tumor on salpingo-oophorectomy. Most cases of struma ovarii occurred unilaterally within ovarian teratomas in premenopausal women, and were mixed cystic and solid masses with smooth margins that are commonly enhanced on contrast enhanced scans. In one patient, hyperthyroidism was caused by struma ovarii. There were, however, no specific radiologic findings that were sufficiently typical to suggest the correct preoperative diagnosis of struma ovarii.

  16. Radiologic findings of struma ovarii

    International Nuclear Information System (INIS)

    Kim, Jong Chul; Shin, Hyun Ja; Kim, Seung Hyup; Byun, Jae Young

    1997-01-01

    Struma ovarii is ovarian tumor composed solely or predominantly of thyroid tissue or tumor in which hyperthyroidism results from ovarian thyroid tissue, and usually occurs in tandem with cystic teratoma. Ovarian cystic teratoma is radiologically easily diagnosed due to calcification or fat, for example, but the preoperative diagnosis of struma ovarii is often difficult due to rare characteristic features of thyroid tissue. Our purpose was to determine whether there were specific findings of struma ovarii which distinguished it from other ovarian tumors, and this involved analysis of its radiologic findings. Using ultrasonography, computed tomography, and magnetic resonance imaging, preoperative radiologic findings of pathologically-proven struma ovarii in eleven patients were retrospectively evaluated for site, margin, nature (cystic, solid, mixed), contrast enhancement, septa, mural nodule, calcification, fat, and metastasis. These findings were compared with pathologic findings. All eleven tumors were unilateral, ten had smooth tumor margins, seven were mixed cystic and solid tumors (more than 70% of solid components in one tumor), and nine had regular septa. Three of four cystic masses (one unilocular, one bilocular and two multilocular cysts) had mural nodules. Calcifications were found in two tumors, and fat in one. Malignant change or metastasis was not found in any tumor. In one patient with hyperthyroidism due to struma ovarii, symptoms and signs of this subsided after removal of the tumor on salpingo-oophorectomy. Most cases of struma ovarii occurred unilaterally within ovarian teratomas in premenopausal women, and were mixed cystic and solid masses with smooth margins that are commonly enhanced on contrast enhanced scans. In one patient, hyperthyroidism was caused by struma ovarii. There were, however, no specific radiologic findings that were sufficiently typical to suggest the correct preoperative diagnosis of struma ovarii

  17. CT findings of the thymus

    Energy Technology Data Exchange (ETDEWEB)

    Kang, Eun Young; Kim, Yun Hwan; Seol, Hae Young; Chung, Woun Kyun; Suh, Won Hyuck [Korea University College of Medicine, Seoul (Korea, Republic of)

    1987-02-15

    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.

  18. 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)

  19. Sonographic findings of renal tuberculosis

    International Nuclear Information System (INIS)

    Yoon, Chong Hyun; Lee, Chang Joon; Kim, Seung Hyun

    1990-01-01

    In order to determine sonographic characteristic of renal tuberculosis, we retrospectively collected 27 cases during a 5 year period. Infected kidneys showed large size (52%) and lobulating contour (76%). In 19 cases of increased parenchymal echogenicity, most of them (16 cases) showed decreased parenchymal thickness. We divided hydronephrotic patterns into 4 categories; predominant calyceal dilatation with mild or no pelvic dilatation (67%), focal calyectasis without pelvic dilation (15%), parenchymal cavitation without hydronephrosis (11%) and proportional hydronephrosis with calyceal deformity (7%). Our findings suggest that disproportional hydronephrosis would be the characteristic finding of renal tuberculosis

  20. 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.

  1. Ultrasonographic findings of tuberculous peritonitis

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Dong Ho; Oh, C. H.; Koh, Y. T.; Lim, J. H. [Seoul National University College of Medicine, Seoul (Korea, Republic of)

    1989-12-15

    Sonograms in forty two patients with tuberculous peritonitis of the wet-ascitic type were retrospectively analyzed. The ascites was clear in 24 patients (57%). There were septations, membranes and debris in 6 (14%), floating debris in 5 (12%), mobile strands or membranes in 4 (10%), and fixed septations in three(7%). Other findings were increased hepatic echogenicity, hepatosplenomegaly, pleural effusion, omental cake, thickened mesentery with adherent bowel loops, lymphadenopathy, thickening of the ileal wall, presented in order of frequency. The ultrasonographic findings are not specific for tuberculous peritonitis, but may give profitable information and protect the patient from unnecessary laparotomy

  2. Scintigraphic findings in ankylosing spondylitis

    International Nuclear Information System (INIS)

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

    1977-01-01

    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 percent 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 percent 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

  3. 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.

  4. 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.

  5. 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

  6. 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.

  7. 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.

  8. 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.

  9. Pigmented villonodular synovitis: MR findings

    International Nuclear Information System (INIS)

    Soler, R.; Rivera, E.; Perez Fontan, F.J.; Yebra, T.; Fuente, C. de la

    1994-01-01

    Pigmented villonodular synovitis is an un-common lesion of the synovium that typically involves diffusely the knee. We present the MR findings of two cases involving the knee,one of them diffuse and the other one localized in the supra patellar bursa. (Author)

  10. 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...

  11. 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.”

  12. US findings of tubal pregnancy

    International Nuclear Information System (INIS)

    Lee, Hwa Sung; Kim, Hyun Hee; Jee, Mi Hyun; Kweon, Young Hwa; Oh, Yoon Jin; Hong, Ju Hee; Kim, Soon Yong; Kim, Sang Young

    1994-01-01

    Early diagnosis of ruptured and unruptured tubal pregnancy became more accurate with the introduction of transvaginal sonographic equipment. The management principle of tubal pregnancy might be changed according to the sonographic findings. The purposes of this study were to define the sonographic findings of tubal pregnancy and to determine whether it is possible to differentiate the unruptured tubal pregnancies from the ruptured ones depending on the sonographic findings. The authors investigated the sonographic findings of the surgically confirmed 25 tubal pregnancy patients. There were 22(88%) unruptured and 3(12%) ruptured tubal pregnancies. Unruptured pregnancies showed tubal ring in 8, well defined hematosalpinx in 11, and poorly defined hematosalpinxin 2 patients. Ruptured pregnancies showed tubal sac with irregular margin in 2, and ill-defined hematosalpinx in one patient. In summary, well marginated tubal ring and hematosalpinx suggested unruptured tubal pregnancy, while tubal sac with irregular margin suggested ruptured pregnancy. However, it was difficult to differentiate the unruptured tubal pregnancy from the ruptured one when hematosalpinx was ill-defined

  13. How to Find Bed Bugs

    Science.gov (United States)

    Find and correctly identify an infestation early before it becomes widespread. Look for rusty or reddish stains and pinpoint dark spots on bed sheets or mattresses, and search for bugs near the piping, seams and tags of the mattress and box spring.

  14. 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.)

  15. 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.)

  16. 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 ea...

  17. 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)

  18. Finding Rising and Falling Words

    NARCIS (Netherlands)

    Tjong Kim Sang, E.

    2016-01-01

    We examine two different methods for finding rising words (among which neologisms) and falling words (among which archaisms) in decades of magazine texts (millions of words) and in years of tweets (billions of words): one based on correlation coefficients of relative frequencies and time, and one

  19. 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.

  20. 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

  1. Interesting bone scans - unusual findings

    International Nuclear Information System (INIS)

    Dobson, M.; Wadhwa, S.S.; Mansberg, R.; Fernandes, V.B.

    1997-01-01

    A 59-year-old female with carcinoma of the colon and known liver metastatic disease was referred for bone scan to evaluate for bone metastases. Although no bone metastases were found, there was abnormal uptake noted in the liver corresponding to a metastatic calcified lesion. The only other findings were of degenerative disease in the cervical spine, right shoulder and small joints of the hands. A 69-year-old male with carcinoma of the prostate and right side low back pain was referred for bone scan. No focal abnormalities to suggest metastatic disease were identified; findings within the cervical spine, lumber spine and knees were presumed secondary to degenerative disease. Intermittent pain persisted and the patient was referred for a repeat bone scan six months later. Previous scan findings of degenerative disease and no metastatic disease were confirmed; however, closer inspection revealed an enlarged right kidney with significant retention of tracer in the pelvicalyceal system suggesting possible obstruction. A Retrograde pyelogram was performed, and no obvious obstruction demonstrated. As bone scan findings were very suggestive of obstruction, a DTPA scan with lasix was performed showing a dilated right collecting system with no functional obstruction. Given the degree of dilation, it is possible that the patient experiences intermittent PUJ obstruction causing his symptoms. A 33-year-old male with insulin dependent diabetes mellitus and viral arthritis was referred for a bone scan. A three phase revealed increased uptake in the region of the knee and leR proximal tibia. Delayed whole body images revealed multiple focal areas of osteoblastic activity in the leR tibia. Abnormal uptake was also seen in the upper third of the leR femur. The remainder of the skeletal survey was normal. X-ray correlation of the leR tibia and femoral findings was undertaken. Combinating unilateral changes on bone scan and X-ray although very suggestive of sclerotic polyostotic

  2. CT-findings in ARDS

    Energy Technology Data Exchange (ETDEWEB)

    Stark, P; Greene, R; Kott, M M; Hall, T; Vanderslice, L

    1987-08-01

    The CT features of 28 patients with ARDS are described. Diffuse lung consolidation, multifocal patchy involvement and lobar or segmental disease were observed. Large lung cysts as well as small cysts producing a 'swiss-cheese' appearance of the parenchyma, were detected. These findings were not regularly appreciated on chest radiographs. The overall mortality of our 28 patients was 72.7% (22 out 28). Patients with lung cysts showed a trend toward higher mortality (87.5% or 13 out 16). Other unexpected findings were basilar lung abscesses and an empyema. In 15 out of 28 patients, CT scans provided additional information, not obvious on bedside chest radiographs and led to a change in management in five patients.

  3. 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

  4. Imaging Findings of Ulceroglandular Tularemia.

    Science.gov (United States)

    Anand, Neil; Deochand, Osmani; Murphy, Robyn

    2017-01-01

    Francisella tularensis, the causative organism in Tularemia, is a relatively rare disease. There are a few radiological clues to elucidate its presence when suspicion arises. There should be strong consideration for Tularemia in the differential of any patient with its classic symptoms, diffuse cervical lymphadenopathy with evidence of necrosis, and enlarged adenoids. Ultrasound may demonstrate suppurative lymphadenopathy suggestive of infection, as in the case presented. CT often will demonstrate the extent of lymphadenopathy. On chest radiography, tularemia pneumonia is often the presenting finding, which may demonstrate bilateral or lobar infiltrates. Additionally, hilar lymphadenopathy and pleural effusions are often associated findings. Cavitary lesions may be present, which are better delineated on CT scan. We present a case of a 7-year-old male who presented with a painful right-sided palpable neck mass for 9 days, who was diagnosed with Tularemia after numerous admissions.

  5. Gout: radiographic findings mimicking infection

    International Nuclear Information System (INIS)

    Rousseau, I.; Raymond-Tremblay, D.; Cardinal, E.; Beauregard, C.G.; Braunstein, E.M.; Saint-Pierre, A.

    2001-01-01

    Objective: To describe radiographic features of gout that may mimic infection. Design and patients: We report five patients with acute bacterial gout who presented with clinical as well as radiological findings mimicking acute bacterial septic arthritis or osteomyelitis. Three patients had delay in the appropriate treatment with the final diagnosis being established after needle aspiration and identification of urate crystals under polarized light microscopy. Two patients underwent digit amputation for not responding to antibiotic treatment and had histological findings confirming the diagnosis of gout. Conclusion: It is important for the radiologist to be aware of the radiological manifestations of acute gout that can resemble infection in order to avoid inappropriate diagnosis and delay in adequate treatment. The definitive diagnosis should rely on needle aspiration and a specific search for urate crystals. (orig.)

  6. Radiologic findings of hemophilic arthropathy

    Energy Technology Data Exchange (ETDEWEB)

    Jun, Young Hwan; Yeon, Kyung Mo; Kim, Chu Wan [College of Medicine, Seoul National University, Seoul (Korea, Republic of)

    1980-12-15

    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)

  7. 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)

  8. 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

  9. Ultrasonography findings of gastric carcinoma

    Energy Technology Data Exchange (ETDEWEB)

    Chung, Chong Ku; Choi, Ji Bai; Ko, Young Tae; Lim, Jae Hoon; Kim, Soon Young [Kyung Hee University Hospital, Seoul (Korea, Republic of)

    1985-12-15

    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.

  10. 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

  11. 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

  12. Angiographic findings of hepatocellular carcinoma

    Energy Technology Data Exchange (ETDEWEB)

    Han, Man Chung; Cho, Byung Jae; Huh, Seung Jae; Bae, Sang Hoon; Kim, Ung Jin; Kim, Chung Yong; Kim, Noe Kyeong [Yonsei University College of Medicine, Seoul (Korea, Republic of)

    1985-12-15

    From March 1977 to July 1979, 69 cases of angiograms of hepatocellular carcinoma were observed in Seoul National University Hospital. The findings of selective celiac and/or hepatic arteriography in total 69 cases of confirmed hepatocellular carcinoma, with clinical and laboratory findings, were analyzed. The summarized results are as follows; 1. Among 69 cases od hepatoma, 62 were male and 7 were female with sex ratio of 8.9 : 1. Peak incidence is 5th to 7th decades (72.5%). Epigastric pain, indigestion, and palpable mass in right upper quadrant were common symptoms and sign. Laboratory findings showed elevated serum alkaline phosphatase more than 5 Bodansky unit in 75.4%. Alpha-feto protein was positive in 65.2% of all the patients. 2 All 69 cases were classified into 31 cases of massive type, 22 cases of diffuse type, and 16 cases of nodular type, in accordance with angiographic gross anatomy. The frequency of angiographic findings were hypervascularities and tumor vessels (100%), tumor stainings (98.5%), arteriovenous shunt (71.0%), displacement of intrahepatic arteries (66.7%), vascular lakes and channel (59.4%). Encasement of hepatic artery and portal vein regurgitation was respectively 4 cases. Tumor mass in portal vein were 6 cases and tumor mass in hepatic vein was 1 case. 3. Intraarterial infusion of 5-FU was performed in 15 hepatoma patients, and the results were that angiographic improvement was demonstrated in 3 cases, no improvement in 8 cases, and incomplete infusion in 4 cases. 4. The selective celiac and/or hepatic angiograms are excellent diagnostic tools as well as therapeutic management for intraarterial infusion of anticancerous drugs.

  13. 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.

  14. Primary cerebral lymphoma: radiological findings

    International Nuclear Information System (INIS)

    Ruiz, J.C.; Grandse, D.; Equidazu, J.; Elizagaray, E.; Grande, J.; Carrandi, J.

    1990-01-01

    We present four cases of primary cerebral lymphoma in non-immunodepressed adult patients. All cases were dsemonstrated with pathological study. CAT study showed solitary or multiple isodense lesions, which incorporated avidly and homoneneously the contrast. Arteriography performed in three patients and magnetic resonance, performed in one did not help for diagnosis. We also review the radiological findings obtained with different imaging methods, and suggest the criteria which could be useful for early diagnosis (Author)

  15. CT findings following diphenylhydantoin intoxication

    Energy Technology Data Exchange (ETDEWEB)

    Baier, W.K.; Beck, U.; Hirsch, W.

    1985-05-01

    CT findings in three female epileptic patients are presented. The patients were treated with toxic doses of the anticonvulsant diphenylhydantoin, leading to irreversible ataxia of varying severity. CT shows cerebellar atrophy, including discernible sulci, a dilated 4th ventricle, basal cisterns, and subarachnoid space. These effects of severe DPH toxicity are in the differential diagnosis from the ''idiopathic'' and other toxic and systemic atrophies, as well as from the dysontogenetic lesions of the cerebellum.

  16. CT finding of emphysematous gastritis

    Energy Technology Data Exchange (ETDEWEB)

    Ahn, Sang Won; Juhn, Jae Ryang; Cha, Seong Sook; Eun, Tchoong Kie; Chung, Duck Hwan [Inje Medical College Paik HospitalYonsei University College of Medicine, Seoul (Korea, Republic of)

    1988-12-15

    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.

  17. 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.

  18. CT findings following diphenylhydantoin intoxication

    International Nuclear Information System (INIS)

    Baier, W.K.; Beck, U.; Hirsch, W.; Kiel Univ.

    1985-01-01

    CT findings in three female epileptic patients are presented. The patients were treated with toxic doses of the anticonvulsant diphenylhydantoin, leading to irreversible ataxia of varying severity. CT shows cerebellar atrophy, including discernible sulci, a dilated 4th ventricle, basal cisterns, and subarachnoid space. These effects of severe DPH toxicity are in the differential diagnosis from the ''idiopathic'' and other toxic and systemic atrophies, as well as from the dysontogenetic lesions of the cerebellum. (orig.)

  19. Angiographic findings of hepatocellular carcinoma

    International Nuclear Information System (INIS)

    Han, Man Chung; Cho, Byung Jae; Huh, Seung Jae; Bae, Sang Hoon; Kim, Ung Jin; Kim, Chung Yong; Kim, Noe Kyeong

    1985-01-01

    From March 1977 to July 1979, 69 cases of angiograms of hepatocellular carcinoma were observed in Seoul National University Hospital. The findings of selective celiac and/or hepatic arteriography in total 69 cases of confirmed hepatocellular carcinoma, with clinical and laboratory findings, were analyzed. The summarized results are as follows; 1. Among 69 cases od hepatoma, 62 were male and 7 were female with sex ratio of 8.9 : 1. Peak incidence is 5th to 7th decades (72.5%). Epigastric pain, indigestion, and palpable mass in right upper quadrant were common symptoms and sign. Laboratory findings showed elevated serum alkaline phosphatase more than 5 Bodansky unit in 75.4%. Alpha-feto protein was positive in 65.2% of all the patients. 2 All 69 cases were classified into 31 cases of massive type, 22 cases of diffuse type, and 16 cases of nodular type, in accordance with angiographic gross anatomy. The frequency of angiographic findings were hypervascularities and tumor vessels (100%), tumor stainings (98.5%), arteriovenous shunt (71.0%), displacement of intrahepatic arteries (66.7%), vascular lakes and channel (59.4%). Encasement of hepatic artery and portal vein regurgitation was respectively 4 cases. Tumor mass in portal vein were 6 cases and tumor mass in hepatic vein was 1 case. 3. Intraarterial infusion of 5-FU was performed in 15 hepatoma patients, and the results were that angiographic improvement was demonstrated in 3 cases, no improvement in 8 cases, and incomplete infusion in 4 cases. 4. The selective celiac and/or hepatic angiograms are excellent diagnostic tools as well as therapeutic management for intraarterial infusion of anticancerous drugs.

  20. CT findings of peritoneal carcinomatosis

    International Nuclear Information System (INIS)

    Kim, Eun Sook; Park, Mi Sook; Cho, On Koo; Koh, Byung Hee; Kim, Soon Yong

    1989-01-01

    CT findings in 137 patients with peritoneal cacinomatosis were reviewed to determine the CT signs of peritoneal malignancy. CT of the 20 liver cirrhosis and 17 tuberculous peritonitis were also reviewed to define the differential point between benign and malignant peritoneal change. The results were as follows. 1. The most common primary malignancy encountered in peritoneal carcinomatosis was stomach Ca.(50.4%), followed by pancreas Ca, hepatoma, colon Ca. and ovarian Ca. 2. Ascites was the most common CT feature of peritoneal malignancy, present in 99 cases (72.3%). The amount of ascites was voluminous, grade III in 70% of cases and showed high density ascites with average 23 Hounsfield units. 3. Greater omentum involvement was noted in 88 patients, peritoneum in 71 patients and mesentery in 65% patients. There was no correlation of the primary malignancy type with the incidence or pattern of the above mentioned site. 4. Bowel wall thickenings were observed in 51 patients, among which transverse colon was most frequently involved. 5. Mean attenuation value of ascites in liver cirrhosis was 10.7 HU, which was much lower than that of peritoneal carcinomatosis. 6. Even though intraperitoneal findings in Tbc. Peritonitis showed tendency of relatively small amount of ascites with more predominant mesenteric change, but, the findings of high density ascites, change of peritoneum and omentum etc. were very similar to those of peritoneal carcinomatosis. Therefore, based on only intraperitoneal change, differential diagnosis between them was difficult. 7. False negatives in CT diagnosis of peritoneal carcinomatosis occurred in 7 cases. There were tiny nodular changes in intraperitoneal cavity without ascites on operative findings

  1. 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#

  2. Finding two-dimensional peaks

    International Nuclear Information System (INIS)

    Silagadze, Z.K.

    2007-01-01

    Two-dimensional generalization of the original peak finding algorithm suggested earlier is given. The ideology of the algorithm emerged from the well-known quantum mechanical tunneling property which enables small bodies to penetrate through narrow potential barriers. We merge this 'quantum' ideology with the philosophy of Particle Swarm Optimization to get the global optimization algorithm which can be called Quantum Swarm Optimization. The functionality of the newborn algorithm is tested on some benchmark optimization problems

  3. AffyMiner: mining differentially expressed genes and biological knowledge in GeneChip microarray data

    Directory of Open Access Journals (Sweden)

    Xia Yuannan

    2006-12-01

    Full Text Available Abstract Background DNA microarrays are a powerful tool for monitoring the expression of tens of thousands of genes simultaneously. With the advance of microarray technology, the challenge issue becomes how to analyze a large amount of microarray data and make biological sense of them. Affymetrix GeneChips are widely used microarrays, where a variety of statistical algorithms have been explored and used for detecting significant genes in the experiment. These methods rely solely on the quantitative data, i.e., signal intensity; however, qualitative data are also important parameters in detecting differentially expressed genes. Results AffyMiner is a tool developed for detecting differentially expressed genes in Affymetrix GeneChip microarray data and for associating gene annotation and gene ontology information with the genes detected. AffyMiner consists of the functional modules, GeneFinder for detecting significant genes in a treatment versus control experiment and GOTree for mapping genes of interest onto the Gene Ontology (GO space; and interfaces to run Cluster, a program for clustering analysis, and GenMAPP, a program for pathway analysis. AffyMiner has been used for analyzing the GeneChip data and the results were presented in several publications. Conclusion AffyMiner fills an important gap in finding differentially expressed genes in Affymetrix GeneChip microarray data. AffyMiner effectively deals with multiple replicates in the experiment and takes into account both quantitative and qualitative data in identifying significant genes. AffyMiner reduces the time and effort needed to compare data from multiple arrays and to interpret the possible biological implications associated with significant changes in a gene's expression.

  4. Fibrolipomatous hamartoma: MR imaging findings

    International Nuclear Information System (INIS)

    De Maeseneer, M.; Jaovisidha, S.; Lenchik, L.; Witte, D.; Schweitzer, M.E.; Sartoris, D.J.; Resnick, D.

    1997-01-01

    Objective. To analyze the MR imaging features of fibrolipomatous hamartoma (FLH) of nerves. Design and patients. MR imaging studies from six patients (three men and three women) were retrospectively reviewed by three musculoskeletal radiologists. In four patients, a biopsy of the nerve lesion was performed. In two patients, biopsy data were unavailable and the diagnosis was based on the clinical history combined with the MR imaging findings. Results and conclusion. MR imaging demonstrated fusiform nerve enlargement that was caused by fatty proliferation and thickening of nerve bundles. Nerve bundles appeared as serpentine tubular structures, hypointense on both T1- and T2-weighted images. The degree of fatty proliferation varied among patients. In addition, significant variation in the distribution of fat along the course of the nerves was noted. In three patients, FLH followed the branching pattern of the nerves, a characteristic pathologic finding. In two patients, intramuscular fat deposition (biceps and tibialis posterior muscles) was present. MR imaging findings of FLH are typical, allowing a confident diagnosis. The variation of fatty proliferation among patients and involved nerves as well as the tendency of the abnormalities to follow the branching pattern of the nerves is well demonstrated with MR imaging. FLH may present as an isolated nerve lesion, may be associated with intramuscular fat deposition, or may occur as a feature of macrodystrophia lipomatosa (MDL). (orig.). With 5 figs., 2 tabs

  5. Ultrasonographic findings of breast lesions

    International Nuclear Information System (INIS)

    Hwang, In Sung; Kim, Yang Soo; Suh, Hyoung Sim

    1990-01-01

    Authors retrospectively analyzed ultrasonographic findings of 61 cases of breast lesions which were proven pathologically at Daerim St. Mary's Hospital from May 1987 to February 1990. The results were as follows : 1. Of all 61 cases, there were 27 fibroadenomas, 13 fibrocystic diseases, 11 carcinomas, 8 abscesses, 1 sclerosing adenosis, and 1 intraductal papilloma. 2. Findings suggesting benignancy were smooth contour, round or oval shape, homogeneously echolucent internal echo, echogenic boundary echo, and posterior enhancement. In the cases of abscess, the findings were rather irregular contour, strong posterior enhancement, and dirty, inhomogeneous internal echo. While irregular and lobulated shape, inhomogeneous and mixed internal echo and pectoral muscle invasion were suggested for malignancy. 3. The sensitivity was 98% and the specificity 58% in benign mass excluding abscesses, 63% and 98% in abscesses, and 55% and 98% in carcinomas. In conclusion, ultrasonography is one of the excellent imaging modality for detecting breast lesions larger than 5 mm in size, but unfortunately some of the malignant tumors simulated benignancy, thus we considered fine needle aspiration biopsy and adjunctive imaging modalities such as film mammography must be followed for better detection of breast cancer

  6. Ultrasonographic findings of breast lesions

    Energy Technology Data Exchange (ETDEWEB)

    Hwang, In Sung; Kim, Yang Soo; Suh, Hyoung Sim [College of Medicine, Daerim St. Mary' s Hospital, Seoul (Korea, Republic of)

    1990-07-15

    Authors retrospectively analyzed ultrasonographic findings of 61 cases of breast lesions which were proven pathologically at Daerim St. Mary's Hospital from May 1987 to February 1990. The results were as follows : 1. Of all 61 cases, there were 27 fibroadenomas, 13 fibrocystic diseases, 11 carcinomas, 8 abscesses, 1 sclerosing adenosis, and 1 intraductal papilloma. 2. Findings suggesting benignancy were smooth contour, round or oval shape, homogeneously echolucent internal echo, echogenic boundary echo, and posterior enhancement. In the cases of abscess, the findings were rather irregular contour, strong posterior enhancement, and dirty, inhomogeneous internal echo. While irregular and lobulated shape, inhomogeneous and mixed internal echo and pectoral muscle invasion were suggested for malignancy. 3. The sensitivity was 98% and the specificity 58% in benign mass excluding abscesses, 63% and 98% in abscesses, and 55% and 98% in carcinomas. In conclusion, ultrasonography is one of the excellent imaging modality for detecting breast lesions larger than 5 mm in size, but unfortunately some of the malignant tumors simulated benignancy, thus we considered fine needle aspiration biopsy and adjunctive imaging modalities such as film mammography must be followed for better detection of breast cancer.

  7. 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

  8. 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

  9. CT findings of thymic tumors

    Energy Technology Data Exchange (ETDEWEB)

    Chung, Ho Son; Lee, Sang Jin; Hwang, Mi Soo; Cho, Kil Ho; Chang, Jae Chun; Park, Bok Hwan [College of Medicine, Yeungnam University, Daegu (Korea, Republic of)

    1991-05-15

    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.

  10. 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)

  11. Aortographic findings of Takayasu's arteritis

    International Nuclear Information System (INIS)

    Han, Man Chung; Chang, Kee Hyun; Kim, Hyo Rin; Choo, Dong Woon

    1973-01-01

    Takayasu's arteritis is a stenosing inflammatory process of unknown etiology affecting not only the aortic arch and its branches, but also the abdominal aorta, its branches and the pulmonary arteries. During the period from August 1971 to August 1973, 9 cases with Takayasu's arteries have been observed in the Seoul National University Hospital. The diagnosis was mainly based upon the aortography, which is the only practical method of delineating the extent and nature of the vascular involvement. The purpose of this paper is describe and analyze the radiographic findings, especially aortographic aspect. The results obtained are as follows: 1. The 9 cases are all female and two thirds are under 30 years of age. Headache, dizziness, absent or weak radial pulse and hypertension are the most common symptoms and signs. The laboratory data are generally unremarkable, except elevation of E.S.R. and gamma globulin fraction on electrophoresis. 2. Conventional roentgenography of the chest may be helpful but not specific in diagnosis of Takayasu's arteritis. 3. The aortographic findings are characteristic and pathognomonic in diagnosis of Takayasu's arteritis. In our cases, the most common findings are stenosis or occlusion of subclavian artery, diffuse narrowing with irregular contour of descending aorta, renal artery involvement, narrowing and aneurysmal dilatation of abdominal aorta, and multiple sites involvement. 4. Therefore, value of total aortography was stressed

  12. MRI findings in bipartite patella

    International Nuclear Information System (INIS)

    Kavanagh, Eoin C.; Zoga, Adam; Omar, Imran; Ford, Stephanie; Eustace, Stephen; Schweitzer, Mark

    2007-01-01

    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.)

  13. Radiologic findings of pulmonary endometriosis

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Seon Bok; Lee, Eil Seong; Jung, Hae Kyoung; Kim, Uk Jung; Yi, Jeong Geun; Kang, Ik Won [Hallym Univ. College of Medicine, Seoul (Korea, Republic of); Kook, Shin Ho [Kangbuk Samsung Hospital, Seoul (Korea, Republic of); Park, Jae Sung [Soonchunhyang Univ. College of Medicine, Seoul (Korea, Republic of); Ryu, Dae Sik [Kangnung Hospital, Kangnung (Korea, Republic of)

    1998-12-01

    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.

  14. Two fundamentally different classes of microbial genes.

    Science.gov (United States)

    Wolf, Yuri I; Makarova, Kira S; Lobkovsky, Alexander E; Koonin, Eugene V

    2016-11-07

    The evolution of bacterial and archaeal genomes is highly dynamic and involves extensive horizontal gene transfer and gene loss 1-4 . Furthermore, many microbial species appear to have open pangenomes, where each newly sequenced genome contains more than 10% ORFans, that is, genes without detectable homologues in other species 5,6 . Here, we report a quantitative analysis of microbial genome evolution by fitting the parameters of a simple, steady-state evolutionary model to the comparative genomic data on the gene content and gene order similarity between archaeal genomes. The results reveal two sharply distinct classes of microbial genes, one of which is characterized by effectively instantaneous gene replacement, and the other consists of genes with finite, distributed replacement rates. These findings imply a conservative estimate of the size of the prokaryotic genomic universe, which appears to consist of at least a billion distinct genes. Furthermore, the same distribution of constraints is shown to govern the evolution of gene complement and gene order, without the need to invoke long-range conservation or the selfish operon concept 7 .

  15. 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.

  16. 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

  17. MR findings of eosinophilic granuloma

    Energy Technology Data Exchange (ETDEWEB)

    Choi, Jong O; Yee, Mi Kyeung; Cho, Kil Ho [Yeungnam Univ. College of Medicine, Kyongsan (Korea, Republic of); Lee, Sung Moon [Keimyung Univ. College of Medicine, Taegu (Korea, Republic of); Lee, Young Hwan [Hyosung Catholic Univ. College of Medicine, Taegu (Korea, Republic of); Suh, Kyung Jin [Suhjoo MR Clinic, Taegu (Korea, Republic of)

    1999-06-01

    To describe the MR findings for the three phases of eosinophilic granuloma, as defined by Mirra's conventional radiographic criteria. Eighteen lesions in 14 patients with proven eosinophilic granuloma were retrospectively analyzed. Among this total, three vertebral lesions were excluded, and the remaining is were classified as early, middle, or late phase on the basis of Mirra's radiographic criteria. For each phase, we compared MR findings with regard to signal intensity, homogeneity, contrast enhancement, perilesional marrow edema, and soft tissue change. For the three vertebral lesions excluded because the application of radiographic criteria was difficult, MR findings for paravertebral soft tissue reaction and degree of cord compression were compared. Of the fifteen cases classified, eight were early phase, five were mid phase, and two were late phase. During each phase, all lesions except one, as seen on T1-weighted images(T1WI), showed iso-signal intensity. On T2WI, all lesions showed high signal intensity. Contrast study demonstrated marked contrast enhancement. Thus, no remarkable differences were found in the signal intensity degree of contrast enhancement of each phase. With regard to heterogeneity, this was demonstrated in most early phase lesions, reflecting necrosis and hemorrhage of those lesions. Soft tissue swelling was more severe during the early phase than the mid or late phase, but marrow edema was similar in each of the three phase. One of three patients with vertebraplana showed para-vertebral soft tissue swelling and cord compression, but this was not seen in the two other cases. For evalvating the extent of eosinophilic granuloma and its relationship with surrounding structures, MRI was superior to conventional radiography. During the early phase of the disease, lesions showed greater inhomogeneity and more aggressive soft tissue reaction than during the mid and late phase.The use of MRI for the evalvation of eosinophilic granuloma

  18. Ultrasonographic findings of breast disease

    International Nuclear Information System (INIS)

    Choi, Kwang Uk; Kim, Sung Eun; Lee, Hee Chung; Shin, Kyung Ja; Kim, Young Chul; Lee, Sang Chun

    1989-01-01

    The authors analyzed ultrasonographic findings of 60 cases of breast lesions which were proven surgically of pathologically at Seoul Red Cross Hospital from September 1986 to February 1989. The results were as follows; 1. There were 30 fibrocystic diseases, 12 fibroadenomas, 8 carcinomas, 3 abscesses, 3 foreign bodies, 2 gynecomastias, 1 intraductal papilloma, 1 malignant cystosarcoma phylloides. 2. Ultrasonography provided accurate information for the size, location, internal structure and relationship between lesion and adjacent structure. 3. Ultrasonography can be used as an adjunct to film mammography in selective patients and useful for guiding fine needle aspiration biopsies

  19. Focal nodular hyperplasia: imaging findings

    Energy Technology Data Exchange (ETDEWEB)

    Kehagias, D.; Moulopoulos, L.; Antoniou, A.; Hatziioannou, A.; Smyrniotis, V.; Trakadas, S.; Lahanis, S.; Vlahos, L. [Dept. of Radiology, University of Athens (Greece)

    2001-02-01

    Focal nodular hyperplasia is an uncommon benign hepatic tumor that continues to pose diagnostic dilemmas. Imaging techniques are of great value in diagnosis of this tumor. In this article we present the US, CT, MR imaging, scintigraphy, and angiography findings. The demonstration of a central vascular scar is very helpful. Although the radiologic features may be diagnostic, many atypical cases must be differentiated from other benign or malignant hepatic tumors. In these cases excisional biopsy and histopathologic examination are necessary to determine a definite diagnosis. (orig.)

  20. Focal nodular hyperplasia: imaging findings

    International Nuclear Information System (INIS)

    Kehagias, D.; Moulopoulos, L.; Antoniou, A.; Hatziioannou, A.; Smyrniotis, V.; Trakadas, S.; Lahanis, S.; Vlahos, L.

    2001-01-01

    Focal nodular hyperplasia is an uncommon benign hepatic tumor that continues to pose diagnostic dilemmas. Imaging techniques are of great value in diagnosis of this tumor. In this article we present the US, CT, MR imaging, scintigraphy, and angiography findings. The demonstration of a central vascular scar is very helpful. Although the radiologic features may be diagnostic, many atypical cases must be differentiated from other benign or malignant hepatic tumors. In these cases excisional biopsy and histopathologic examination are necessary to determine a definite diagnosis. (orig.)

  1. 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

  2. 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.)

  3. 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.)

  4. MR findings of polymyositis / dermatomyositis

    International Nuclear Information System (INIS)

    Lee, Hak Soo; Joo, Kyung Bin; Moon, Won Jin; Lee, Tae Hee; Park, Ki Ho; Park, Dong Woo; Hahm, Chang Kok

    1998-01-01

    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

  5. 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,

  6. Ultrasonographic findings of breast disease

    Energy Technology Data Exchange (ETDEWEB)

    Choi, Kwang Uk; Kim, Sung Eun; Lee, Hee Chung; Shin, Kyung Ja; Kim, Young Chul; Lee, Sang Chun [Seoul Red Cross Hopital, Seoul (Korea, Republic of)

    1989-10-15

    The authors analyzed ultrasonographic findings of 60 cases of breast lesions which were proven surgically of pathologically at Seoul Red Cross Hospital from September 1986 to February 1989. The results were as follows; 1. There were 30 fibrocystic diseases, 12 fibroadenomas, 8 carcinomas, 3 abscesses, 3 foreign bodies, 2 gynecomastias, 1 intraductal papilloma, 1 malignant cystosarcoma phylloides. 2. Ultrasonography provided accurate information for the size, location, internal structure and relationship between lesion and adjacent structure. 3. Ultrasonography can be used as an adjunct to film mammography in selective patients and useful for guiding fine needle aspiration biopsies.

  7. VLSI structures for track finding

    International Nuclear Information System (INIS)

    Dell'Orso, M.

    1989-01-01

    We discuss the architecture of a device based on the concept of associative memory designed to solve the track finding problem, typical of high energy physics experiments, in a time span of a few microseconds even for very high multiplicity events. This ''machine'' is implemented as a large array of custom VLSI chips. All the chips are equal and each of them stores a number of ''patterns''. All the patterns in all the chips are compared in parallel to the data coming from the detector while the detector is being read out. (orig.)

  8. Acute bowel ischemia: CT findings

    International Nuclear Information System (INIS)

    Angelelli, Giuseppe; Scardapane, Arnaldo; Memeo, Maurizio; Stabile Ianora, Amato Antonio; Rotondo, Antonio

    2004-01-01

    Acute bowel ischemia represents one of the most dramatic abdominal emergencies and, despite the fact it is more and more frequently observed in clinical practice, its mortality rate remains very high. In recent years Computed Tomography (CT) has proved to be a valid diagnostic tool in the evaluation of patients with acute abdominal syndrome and in the visualization of early signs of bowel ischemia. This paper reviews the aetiological and pathophysiological aspects as well as a broad spectrum of CT findings of this clinical condition

  9. 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

  10. 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 ...

  11. 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

  12. Imaging gene expression in gene therapy

    Energy Technology Data Exchange (ETDEWEB)

    Wiebe, Leonard I. [Alberta Univ., Edmonton (Canada). Noujaim Institute for Pharmaceutical Oncology Research

    1997-12-31

    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{sup +}) 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{sup +} gene expression where the H S V-1 t k{sup +} gene serves a reporter or therapeutic function. Animal gene therapy models have been studied using purine-([{sup 18} F]F H P G; [{sup 18} F]-A C V), and pyrimidine- ([{sup 123}/{sup 131} I]I V R F U; [{sup 124}/{sup 131I}]) antiviral nucleosides. Principles of gene therapy and gene therapy imaging will be reviewed and experimental data for [{sup 123}/{sup 131I}]I V R F U imaging with the H S V-1 t k{sup +} reporter gene will be presented

  13. Identifying key genes in rheumatoid arthritis by weighted gene co-expression network analysis.

    Science.gov (United States)

    Ma, Chunhui; Lv, Qi; Teng, Songsong; Yu, Yinxian; Niu, Kerun; Yi, Chengqin

    2017-08-01

    This study aimed to identify rheumatoid arthritis (RA) related genes based on microarray data using the WGCNA (weighted gene co-expression network analysis) method. Two gene expression profile datasets GSE55235 (10 RA samples and 10 healthy controls) and GSE77298 (16 RA samples and seven healthy controls) were downloaded from Gene Expression Omnibus database. Characteristic genes were identified using metaDE package. WGCNA was used to find disease-related networks based on gene expression correlation coefficients, and module significance was defined as the average gene significance of all genes used to assess the correlation between the module and RA status. Genes in the disease-related gene co-expression network were subject to functional annotation and pathway enrichment analysis using Database for Annotation Visualization and Integrated Discovery. Characteristic genes were also mapped to the Connectivity Map to screen small molecules. A total of 599 characteristic genes were identified. For each dataset, characteristic genes in the green, red and turquoise modules were most closely associated with RA, with gene numbers of 54, 43 and 79, respectively. These genes were enriched in totally enriched in 17 Gene Ontology terms, mainly related to immune response (CD97, FYB, CXCL1, IKBKE, CCR1, etc.), inflammatory response (CD97, CXCL1, C3AR1, CCR1, LYZ, etc.) and homeostasis (C3AR1, CCR1, PLN, CCL19, PPT1, etc.). Two small-molecule drugs sanguinarine and papaverine were predicted to have a therapeutic effect against RA. Genes related to immune response, inflammatory response and homeostasis presumably have critical roles in RA pathogenesis. Sanguinarine and papaverine have a potential therapeutic effect against RA. © 2017 Asia Pacific League of Associations for Rheumatology and John Wiley & Sons Australia, Ltd.

  14. Ultrasonographic finding of hepatocellular carcinoma

    Energy Technology Data Exchange (ETDEWEB)

    Ryu, Han Soo; Woo, Seong Ku; Lim, Jae Hoon; Ko, Young Tae; Kim, Ho Kyun; Kim, Soon Yong [Kyung Hee University Hospital, Seoul (Korea, Republic of)

    1983-12-15

    With the development of gray scale ultrasonography, detection and evaluation of hepatic parenchymal disease including space occupying lesion are easily performed and frequently used in the world. Thrity five cases of histopathologically proven and ultrasonographically suggested hepatocellular carcinoma are retrospectively studied. The results were as follows; 1. Ultrasonographic findings of hepatocellular carcinoma show hyperechoic pattern in 22 cases (63%), hypoechoic pattern in 2 cases (6%), and mixed pattern in 11 cases (31%). 2. The margin of tumor is ill-defined in 19 cases (54%) and well defined in16 cases (46%). 3. The size of tumor by sonographic measurement was large than 5 cm in diameter in 33 cases (94%). 4. The number of tumor is solitary in 19 cases and multiple in 16 cases. The sites of involved lobe were right lobe in 22 cases (63%), left lobe in 2 cases (6%), and both lobes in 11 cases (31%). 5. Associated sonographic findings were hepatomegaly with focal contour change in 25 cases (71%), splenomegaly in 16 cases (46%), cirrhosis of liver in 15 cases (43%), ascites in 11 cases (31%) and tumoral thrombosis in portal vein in 8 cases (23%). 6. The sex ratio is 6 : 1 male predominence and the age ranges from 32 to 76 years with highest incidence in 5th and 6th decades.

  15. Hematological findings in Noonan syndrome

    Directory of Open Access Journals (Sweden)

    Bertola Débora R.

    2003-01-01

    Full Text Available OBJECTIVE: Noonan syndrome is a multiple congenital anomaly syndrome, and bleeding diathesis is considered part of the clinical findings. The purpose of this study was to determine the frequency of hemostatic abnormalities in a group of Noonan syndrome patients. METHOD: We studied 30 patients with clinical diagnosis of Noonan syndrome regarding their hemostatic status consisting of bleeding time, prothrombin time, activated partial thromboplastin time and thrombin time tests, a platelet count, and a quantitative determination of factor XI. RESULTS: An abnormal laboratory result was observed in 9 patients (30%. Although coagulation-factor deficiencies, especially factor XI deficiency, were the most common hematological findings, we also observed abnormalities of platelet count and function in our screening. CONCLUSIONS: Hemostatic abnormalities are found with some frequency in Noonan syndrome patients (30% in our sample. Therefore, we emphasize the importance of a more extensive hematological investigation in these patients, especially prior to an invasive procedure, which is required with some frequency in this disorder.

  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. Sonographic findings in Gouty Nephropathy

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Mi Young; Jeon, Woo Ki; Kim, Ho Kyun; Kim, Yong Soo; Han, Chang Yul; Kim, Young Tong; Han, Sung Tag; Lee, Yoon Woo [Inje University College of Medicine, Seoul (Korea, Republic of)

    1994-09-15

    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.

  18. 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.

  19. Electrocardiographic findings related to aging

    Energy Technology Data Exchange (ETDEWEB)

    Ueda, Shoichi; Yano, Katsuhiko

    1962-12-12

    More than 3000 electrocardiographic tracings for the ABCC-JNIH Adult Health Study Sample were studied to detect any specific abnormalities or nonspecific age changes in relation to possible radiation effects upon the cardiovascular system. The 4 comparison groups were studied with respect to the prevalence of electrocardiographic abnormalities and an electrocardiographic aging index which was defined to evaluate physiological change with age. Statistically significant differences were observed in the following aspects: In males aged 50 to 59, the prevalence of major electrocardiographic abnormalities was highest in the group located nearest the hypocenter. This was not observed in other age groups. In females, the prevalence of QRS high voltage was highest in Group 2 but low in Group 1. This trend was consistent in all age groups. These findings were not fully accounted for by differences in blood pressure, heart size, body weight or serum cholesterol values. In the age trend curve of the electrocardiographic aging index, a difference was observed among comparison groups in both sexes. This difference in electrocardiographic aging index is mainly attributed to T/sub I/ amplitude for males and R/sub II/ amplitude and QRS axis for females. Interpretation of these findings is rather difficult since very little has been known about radiation effects upon the cardiovascular system in humans. Further intensive studies are desired on the basis of the clues suggested in this report. 16 references, 3 figures, 31 tables.

  20. Audiological findings in Noonan syndrome.

    Science.gov (United States)

    Tokgoz-Yilmaz, Suna; Turkyilmaz, Meral Didem; Cengiz, Filiz Basak; Sjöstrand, Alev Pektas; Kose, Serdal Kenan; Tekin, Mustafa

    2016-10-01

    The aim of this study was to evaluate audiologic properties of patients with Noonan syndrome and compare these findings with those of unaffected peers. The study included 17 children with Noonan syndrome and 20 typically developing children without Noonan syndrome. Pure tone and speech audiometry, immitancemetric measurement, otoacoustic emissions measurement and auditory brainstem response tests were applied to all (n = 37) children. Hearing thresholds of children with Noonan syndrome were higher (poorer) than those observed unaffected peers, while the hearing sensitivity of the both groups were normal limits (p = 0.013 for right, p = 0.031 for left ear). Transient evoked otoacoustic emissions amplitudes of the children with Noonan syndrome were lower than the children without Noonan syndrome (p = 0.005 for right, p = 0.002 for left ear). Middle ear pressures and auditory brainstem response values were within normal limits and there was no difference between the two groups (p > 0.05). General benefit of the present study is to characterize the audiologic findings of children with Noonan syndrome, which is beneficial in clinics evaluating children with Noonan syndrome. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  1. 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

  2. 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

  3. 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

  4. MR findings of cyclosporine neurotoxicity

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Po Song; Ahn, Kook Jin; Ahn, Bo Young; Jung, Hae An; Kim, Hee Je; Lee, Jae Mun [The Catholic Univ. St Mary' s Hospital, Seoul (Korea, Republic of)

    1998-12-01

    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. Gene doping: gene delivery for olympic victory.

    Science.gov (United States)

    Gould, David

    2013-08-01

    With one recently recommended gene therapy in Europe and a number of other gene therapy treatments now proving effective in clinical trials it is feasible that the same technologies will soon be adopted in the world of sport by unscrupulous athletes and their trainers in so called 'gene doping'. In this article an overview of the successful gene therapy clinical trials is provided and the potential targets for gene doping are highlighted. Depending on whether a doping gene product is secreted from the engineered cells or is retained locally to, or inside engineered cells will, to some extent, determine the likelihood of detection. It is clear that effective gene delivery technologies now exist and it is important that detection and prevention plans are in place. © 2012 The Author. British Journal of Clinical Pharmacology © 2012 The British Pharmacological Society.

  6. Ultrasonographic Findings of Breast Abscess

    Energy Technology Data Exchange (ETDEWEB)

    Shin, Hyeong Cheol; Oh, Ki Keun [Yonsei University College of Medicine, Seoul (Korea, Republic of)

    1995-06-15

    Breast abscess cannot be differentiated from breast malignancy by film mammography. Pain and spread of infection can be developed during film mammography procedure due to compression. However, ultrasonography is known to be an adequate procedure for diagnosis of breast abscesses. Therefore, we performed the present study to document the ultrasonographic findings of breast abscess. We analyzed ultrasonograms of ninexases with surgically proven breast abscesses. All patients were female and their ages ranged from l2 to 56 years(average, 35 years). The lesion was located in the right breast in four cases, and in the left in five cases. On ultrasonography, all lesions were anechoic or low echoic. The lesion showed mixed echogenicityin five cases. Posterior acoustic enhancement was noted in seven cases. Lateral shadowing was seen in four cases.There were skin thickening in five cases and subcutaneous fat obliteration in all cases. Ultrasonography is useful in the diagnosis of breast abscess

  7. Ultrasonographic Findings of Breast Abscess

    International Nuclear Information System (INIS)

    Shin, Hyeong Cheol; Oh, Ki Keun

    1995-01-01

    Breast abscess cannot be differentiated from breast malignancy by film mammography. Pain and spread of infection can be developed during film mammography procedure due to compression. However, ultrasonography is known to be an adequate procedure for diagnosis of breast abscesses. Therefore, we performed the present study to document the ultrasonographic findings of breast abscess. We analyzed ultrasonograms of ninexases with surgically proven breast abscesses. All patients were female and their ages ranged from l2 to 56 years(average, 35 years). The lesion was located in the right breast in four cases, and in the left in five cases. On ultrasonography, all lesions were anechoic or low echoic. The lesion showed mixed echogenicityin five cases. Posterior acoustic enhancement was noted in seven cases. Lateral shadowing was seen in four cases.There were skin thickening in five cases and subcutaneous fat obliteration in all cases. Ultrasonography is useful in the diagnosis of breast abscess

  8. 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.

  9. 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.

  10. 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)

  11. 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

  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. Primary thyroid lymphoma: CT findings

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Hyo-Cheol; Han, Moon Hee E-mail: hanmh@radcom.snu.ac.kr; Kim, Keon Ha; Jae, Hwan Jun; Lee, Sang Hyun; Kim, Sam Soo; Kim, Kwang Hyun; Chang, Kee-Hyun

    2003-06-01

    Introduction: To evaluate the computed tomographic (CT) findings of primary thyroid lymphoma. Methods and material: The clinicopathological data and CT images of nine patients with primary thyroid lymphoma were retrospectively reviewed. The CT appearances were classified into three types: type 1, a solitary nodule surrounded by normal thyroid tissue; type 2, multiple nodules in the thyroid, and type 3, a homogeneously enlarged both thyroid glands with a reduced attenuation with or without peripheral thin hyperattenuating thyroid tissue. Results: All patients had a rapidly enlarging thyroid mass and coexistent Hashimoto's thyroiditis. One patient showed type 1 pattern, three type 2, and five type 3. Six patients had homogeneous tumor isoattenuating to surrounding muscles. The tumors had a strong tendency to compress normal remnant thyroid and the surrounding structure without invasion. Conclusion: Primary thyroid lymphoma should be included in the differential diagnosis when old female had a homogeneous thyroidal mass isoattenuating to muscles, which does not invade surrounding structures.

  14. Ultrasonographic Findings of Periappendiceal Abscess

    Energy Technology Data Exchange (ETDEWEB)

    Woo, Seong Ku; Sung, Dong Wook; Ko, Young Tae; Lim, Jae Hoon; Kim, Soon Yong [Kyung Hee University Hospital, Seoul (Korea, Republic of)

    1983-09-15

    Although the ultrasonography has been regarded as a important procedure in the diagnosis of intra-abdominal abscess, there were relatively few papers concerning the ultrasonographic findings of perpendicular abscess. Nineteen cases of surgically proven perpendicular abscess caused by perforated appendicitis were studied by ultrasonography at the Kyung Hee University Hospital during last 34 months. The results were as follows: 1. Diagnostic accuracy of the real-time ultrasonography was 94.7% (18/19). There were only one false positive and one false negative. 2. The location of abscesses were; perpendicular 68.4% (13/19), pelvic 21.0% (4/19), sub hepatic 5.3% (1/19) and sub phrenic 5.3% (1/19) in order of frequency. 3. Variable echo-patterns of abscesses was encounted. But irregular, thick walled, posteriorly reinforcing, echo-free or mixed echo-patterns were most common.

  15. 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.)

  16. Characteristic brain MRI findings in ataxia-neuropathy spectrum related to POLG mutation.

    Science.gov (United States)

    Henao, Adriana I; Pira, Sonia; Herrera, Diego A; Vargas, Sergio A; Montoya, Jorge; Castillo, Mauricio

    2016-02-01

    Patients with mutations in the polymerase gamma gene (POLG) may present with progressive ataxia and in such situations neuroimaging findings may suggest the diagnosis. Herein we report a patient with a POLG gene W748S homozygous mutation and characteristic lesions in the thalamus, cerebellum and inferior olivary nucleus seen on magnetic resonance imaging. © The Author(s) 2016.

  17. 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.

  18. Predictions of Gene Family Distributions in Microbial Genomes: Evolution by Gene Duplication and Modification

    International Nuclear Information System (INIS)

    Yanai, Itai; Camacho, Carlos J.; DeLisi, Charles

    2000-01-01

    A universal property of microbial genomes is the considerable fraction of genes that are homologous to other genes within the same genome. The process by which these homologues are generated is not well understood, but sequence analysis of 20 microbial genomes unveils a recurrent distribution of gene family sizes. We show that a simple evolutionary model based on random gene duplication and point mutations fully accounts for these distributions and permits predictions for the number of gene families in genomes not yet complete. Our findings are consistent with the notion that a genome evolves from a set of precursor genes to a mature size by gene duplications and increasing modifications. (c) 2000 The American Physical Society

  19. Predictions of Gene Family Distributions in Microbial Genomes: Evolution by Gene Duplication and Modification

    Energy Technology Data Exchange (ETDEWEB)

    Yanai, Itai; Camacho, Carlos J.; DeLisi, Charles

    2000-09-18

    A universal property of microbial genomes is the considerable fraction of genes that are homologous to other genes within the same genome. The process by which these homologues are generated is not well understood, but sequence analysis of 20 microbial genomes unveils a recurrent distribution of gene family sizes. We show that a simple evolutionary model based on random gene duplication and point mutations fully accounts for these distributions and permits predictions for the number of gene families in genomes not yet complete. Our findings are consistent with the notion that a genome evolves from a set of precursor genes to a mature size by gene duplications and increasing modifications. (c) 2000 The American Physical Society.

  20. 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)

  1. CT findings in epileptic children

    International Nuclear Information System (INIS)

    Koide, Nobuo; Kimura, Shigeru; Watanabe, Jun; Haneda, Satoshi; Takebe, Yukinao

    1981-01-01

    CT findings in 43 children with generalized seizures (grand mal seizures) (GM group) and in 50 children with partial seizures (P group), classified according to clinical seizure type, were studied. 1) CT abnormalities were demonstrated in 19% (8/43) in GM group and in 40% (20/50) in P group, including localized CT abnormalities in 9.3% (4/43) and in 34% (17/50) respectively. CT abnormalities were found more frequently in cases with abnormal past histories and/or mental defects (MD) than in those without them. 2) In P group, localized CT abnormalities and generalized brain atrophy were observed in 13 and 7 cases respectively. In 40 cases with focal epileptic discharges (FED) in EEG, localized CT abnormalities were demonstrated in 23% (9/40). The sites of localized CT abnormalities corresponded in 73% (11/15) to the sites of focal suppression in EEG (i.e., slowing, low amplitude and lazy pattern) regardless of FED. 3) The bicaudate cerebro-ventricular index (B-CVI) in 19 cases in the normal control group over 2 years of age was 10.0 +- 1.2 (mean +- SD). Ventricular narrowing (VN), with B-CVI less than 8.2 (mean - 1.5 SD), was observed in 5, 17 and 27% in control, GM and P groups respectively, indicating more frequently in epileptic children than in normal controls. Seizures were well controlled in 85% (11/13) in VN group and in 70% (26/36) in normal ventricular group. Brain atrophy in CT findings to inspection was ascertained in all cases by measuring B-CVI. (author)

  2. MRI findings of uveal metastases

    International Nuclear Information System (INIS)

    Chen Qinghua; Wang Zhenchang; Xian Junfang; Yan Fei; He Liyan; Tian Qichang; Yang Bentao; Liu Zhonglin

    2007-01-01

    Objective: To evaluate MR imaging findings of uveal metastases. Methods: MR imaging findings of 20 cases with uveal metastases comfirmed by pathology or follow-up were retrospectively analyzed. MR imaging was performed in 20 patients, of which postcontrast T 1 -weighted imaging was performed in 19 patients including dynamic contrast enhancement scanning in four cases. Results: Metastatic tumor was found in the iris and ciliary body in two cases, and in choroid in 18 cases. The tumor demonstrated slightly hypointense signal on T 1 -weighted imaging and isointense signal on T 2 -weighted imaging in two cases, isointense signal on T 1 -weighted imaging and isointense signal on T 2 -weighted imaging in nine cases, isointense signal on T 1 -weighted imaging and slightly hyperintense signal on T 2 -weighted imaging in three cases, isointense signal on T 1 -weighted imaging and slightly hypointense signal on T 2 - weighted imaging in three cases, slightly hyperintense signal on T 1 -weighted imaging and slightly hypointense signal on T 2 -weighted imaging in two cases, and slightly hyperintense signal on T 1 -weighted imaging and slightly hyperintense signal on T 2 -weighted imaging in one case. The tumor appeared as mild thickness of the wall of the globe in eight cases, a crescent mass in three cases, a fusiform mass in seven cases, and a nodule in two cases. Nineteen patients showed moderate or marked enhancement on postcontrast T 1 -weighted imaging. The time-intensity curve of dynamic contrast enhancement in four patients suggested a rapid enhancement and slow washout pattern. Retinal detachment was observed in 11 patients and abnormal signal intensity within the vitreous body was seen in two cases. Conclusion: MRI can display the location, shape, signal characteristics, and enhancement pattern of uveal metastases, contributing to diagnosis and differential diagnosis. (authors)

  3. Specific CT findings of eclampsia

    International Nuclear Information System (INIS)

    Takahashi, Hiroshi; Nakazawa, Shozo; Imaya, Hisatoshi

    1985-01-01

    Two cases of specific computed tomographic (CT) findings of eclampsia were reported. Case 1 was a 25-year-old primipara in the 10th month of pregnancy, and Case 2 was a 36-year-old primipara in the 9th month of pregnancy. Both were brought to our hospital because of attacks of preeclampsia and eclampsia. On admission, they were in a comatose state. Computed tomography (CT) on admission showed low- and high-density areas in the basal ganglia regions in Case 1 and low-density areas in the same regions in Case 2. In Case 1, cerebral angiograms obtained two days after the attack showed diffuse cerebral vasospasms in the anterior and middle cerebral arteries of both sides and the basilar artery. In Case 2, however, cerebral angiograms obtained three days after the attack showed no abnormal findings. The patients were saved by crisis-overcoming emergency treatment and care. The neurological condition gradually improved. Repeated CT three weeks after the onset showed only a slight low-density area and a small high-density area in the left basal ganglia region in Case 1, while the low-density areas in the bilateral basal ganglia regions disappeared in Case 2. Seven weeks after the attack, cerebral angiography was again performed, but the diffuse vasospasms had disappeared. The clinical courses were good, and the patients were discharged about eight weeks after the onset, by which time their consciousness had become clear and the neurological deficits had been well overcome. Cerebrovascular disorders caused by toxemia of pregnancy is rare; when they do occur, the main lesions of the brain are edema, focal ischemia, thrombosis, and hemorrhage. They may be related to cerebral vasospasm, and subsequent ischemic changes are observed at times with eclampsia. (author)

  4. 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.

  5. Integrative characterization of germ cell-specific genes from mouse spermatocyte UniGene library

    Directory of Open Access Journals (Sweden)

    Eddy Edward M

    2007-07-01

    Full Text Available Abstract Background The primary regulator of spermatogenesis, a highly ordered and tightly regulated developmental process, is an intrinsic genetic program involving male germ cell-specific genes. Results We analyzed the mouse spermatocyte UniGene library containing 2155 gene-oriented transcript clusters. We predict that 11% of these genes are testis-specific and systematically identified 24 authentic genes specifically and abundantly expressed in the testis via in silico and in vitro approaches. Northern blot analysis disclosed various transcript characteristics, such as expression level, size and the presence of isoform. Expression analysis revealed developmentally regulated and stage-specific expression patterns in all of the genes. We further analyzed the genes at the protein and cellular levels. Transfection assays performed using GC-2 cells provided information on the cellular characteristics of the gene products. In addition, antibodies were generated against proteins encoded by some of the genes to facilitate their identification and characterization in spermatogenic cells and sperm. Our data suggest that a number of the gene products are implicated in transcriptional regulation, nuclear integrity, sperm structure and motility, and fertilization. In particular, we found for the first time that Mm.333010, predicted to contain a trypsin-like serine protease domain, is a sperm acrosomal protein. Conclusion We identify 24 authentic genes with spermatogenic cell-specific expression, and provide comprehensive information about the genes. Our findings establish a new basis for future investigation into molecular mechanisms underlying male reproduction.

  6. 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...

  7. 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.

  8. Evolution of homeobox genes.

    Science.gov (United States)

    Holland, Peter W H

    2013-01-01

    Many homeobox genes encode transcription factors with regulatory roles in animal and plant development. Homeobox genes are found in almost all eukaryotes, and have diversified into 11 gene classes and over 100 gene families in animal evolution, and 10 to 14 gene classes in plants. The largest group in animals is the ANTP class which includes the well-known Hox genes, plus other genes implicated in development including ParaHox (Cdx, Xlox, Gsx), Evx, Dlx, En, NK4, NK3, Msx, and Nanog. Genomic data suggest that the ANTP class diversified by extensive tandem duplication to generate a large array of genes, including an NK gene cluster and a hypothetical ProtoHox gene cluster that duplicated to generate Hox and ParaHox genes. Expression and functional data suggest that NK, Hox, and ParaHox gene clusters acquired distinct roles in patterning the mesoderm, nervous system, and gut. The PRD class is also diverse and includes Pax2/5/8, Pax3/7, Pax4/6, Gsc, Hesx, Otx, Otp, and Pitx genes. PRD genes are not generally arranged in ancient genomic clusters, although the Dux, Obox, and Rhox gene clusters arose in mammalian evolution as did several non-clustered PRD genes. Tandem duplication and genome duplication expanded the number of homeobox genes, possibly contributing to the evolution of developmental complexity, but homeobox gene loss must not be ignored. Evolutionary changes to homeobox gene expression have also been documented, including Hox gene expression patterns shifting in concert with segmental diversification in vertebrates and crustaceans, and deletion of a Pitx1 gene enhancer in pelvic-reduced sticklebacks. WIREs Dev Biol 2013, 2:31-45. doi: 10.1002/wdev.78 For further resources related to this article, please visit the WIREs website. The author declares that he has no conflicts of interest. Copyright © 2012 Wiley Periodicals, Inc.

  9. 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

  10. Knowledge translation of research findings

    Directory of Open Access Journals (Sweden)

    Grimshaw Jeremy M

    2012-05-01

    Full Text Available Abstract Background One of the most consistent findings from clinical and health services research is the failure to translate research into practice and policy. As a result of these evidence-practice and policy gaps, patients fail to benefit optimally from advances in healthcare and are exposed to unnecessary risks of iatrogenic harms, and healthcare systems are exposed to unnecessary expenditure resulting in significant opportunity costs. Over the last decade, there has been increasing international policy and research attention on how to reduce the evidence-practice and policy gap. In this paper, we summarise the current concepts and evidence to guide knowledge translation activities, defined as T2 research (the translation of new clinical knowledge into improved health. We structure the article around five key questions: what should be transferred; to whom should research knowledge be transferred; by whom should research knowledge be transferred; how should research knowledge be transferred; and, with what effect should research knowledge be transferred? Discussion We suggest that the basic unit of knowledge translation should usually be up-to-date systematic reviews or other syntheses of research findings. Knowledge translators need to identify the key messages for different target audiences and to fashion these in language and knowledge translation products that are easily assimilated by different audiences. The relative importance of knowledge translation to different target audiences will vary by the type of research and appropriate endpoints of knowledge translation may vary across different stakeholder groups. There are a large number of planned knowledge translation models, derived from different disciplinary, contextual (i.e., setting, and target audience viewpoints. Most of these suggest that planned knowledge translation for healthcare professionals and consumers is more likely to be successful if the choice of knowledge

  11. Knowledge translation of research findings.

    Science.gov (United States)

    Grimshaw, Jeremy M; Eccles, Martin P; Lavis, John N; Hill, Sophie J; Squires, Janet E

    2012-05-31

    One of the most consistent findings from clinical and health services research is the failure to translate research into practice and policy. As a result of these evidence-practice and policy gaps, patients fail to benefit optimally from advances in healthcare and are exposed to unnecessary risks of iatrogenic harms, and healthcare systems are exposed to unnecessary expenditure resulting in significant opportunity costs. Over the last decade, there has been increasing international policy and research attention on how to reduce the evidence-practice and policy gap. In this paper, we summarise the current concepts and evidence to guide knowledge translation activities, defined as T2 research (the translation of new clinical knowledge into improved health). We structure the article around five key questions: what should be transferred; to whom should research knowledge be transferred; by whom should research knowledge be transferred; how should research knowledge be transferred; and, with what effect should research knowledge be transferred? We suggest that the basic unit of knowledge translation should usually be up-to-date systematic reviews or other syntheses of research findings. Knowledge translators need to identify the key messages for different target audiences and to fashion these in language and knowledge translation products that are easily assimilated by different audiences. The relative importance of knowledge translation to different target audiences will vary by the type of research and appropriate endpoints of knowledge translation may vary across different stakeholder groups. There are a large number of planned knowledge translation models, derived from different disciplinary, contextual (i.e., setting), and target audience viewpoints. Most of these suggest that planned knowledge translation for healthcare professionals and consumers is more likely to be successful if the choice of knowledge translation strategy is informed by an assessment of the

  12. 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

  13. 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

  14. 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.

  15. 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...

  16. 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)

  17. 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.

  18. 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)

  19. MR findings in intralabyrinthine schwannomas

    International Nuclear Information System (INIS)

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

    2002-01-01

    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)

  20. 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.

  1. 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.

  2. 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 < 8 min. One patient and three controls had sudden onset of REM sleep in 2/5 and 3/5 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.

  3. 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)

  4. 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.

  5. 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.

  6. CT findings of nasopharyngeal cancer

    International Nuclear Information System (INIS)

    Kim, Kie Hwan; Byun, Hong Sik; Chin, Soo Yil

    1987-01-01

    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

  7. 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)

  8. Gastric traumatic injuries: CT findings

    International Nuclear Information System (INIS)

    Lassandro, Francesco; Romano, Stefania; Rossi, Giovanni; Muto, Roberto; Cappabianca, Salvatore; Grassi, Roberto

    2006-01-01

    Objective: Gastric blunt traumatic injuries are uncommon and their radiological appearance has been infrequently reported in medical literature. These injuries are difficult to diagnose preoperatively, though they require immediate recognition to minimize their otherwise high mortality and morbidity. The aim of our study is to describe the radiological appearance of blunt gastric traumatic injuries. Materials and methods: Retrospective evaluation of a 25 patients series observed between January 1997 and May 2005. Results: We observed rupture of the stomach in 20% of cases, in 44% of cases a partial lesion of the stomach, in one case a necrotic post-traumatic volvulus, five patients (20%) had benign portal pneumatosis, in three patients the stomach was secondarily involved because of a diaphragmatic hernia. The fundus resulted to be the most frequently damaged part of the stomach (80%). Conclusions: Blunt traumatic injuries need a careful and systematic approach given their economical and social relevance. For these reasons uncommon lesions require attention and may be important to search for specific findings of gastric lesions

  9. Gastric traumatic injuries: CT findings

    Energy Technology Data Exchange (ETDEWEB)

    Lassandro, Francesco [Department of Diagnostic Imaging, ' A. Cardarelli' Hospital, I-80131 Naples (Italy)]. E-mail: francesco.lassandro@fastwebnet.it; Romano, Stefania [Department of Diagnostic Imaging, ' A. Cardarelli' Hospital, I-80131 Naples (Italy); Rossi, Giovanni [Department of Radiology, V. Monaldi Hospital, Naples (Italy); Muto, Roberto [Department of Radiology, V. Monaldi Hospital, Naples (Italy); Cappabianca, Salvatore [Magrassi-Lanzara Department, Institute of Radiology, Second University of Naples (Italy); Grassi, Roberto [Magrassi-Lanzara Department, Institute of Radiology, Second University of Naples (Italy)

    2006-09-15

    Objective: Gastric blunt traumatic injuries are uncommon and their radiological appearance has been infrequently reported in medical literature. These injuries are difficult to diagnose preoperatively, though they require immediate recognition to minimize their otherwise high mortality and morbidity. The aim of our study is to describe the radiological appearance of blunt gastric traumatic injuries. Materials and methods: Retrospective evaluation of a 25 patients series observed between January 1997 and May 2005. Results: We observed rupture of the stomach in 20% of cases, in 44% of cases a partial lesion of the stomach, in one case a necrotic post-traumatic volvulus, five patients (20%) had benign portal pneumatosis, in three patients the stomach was secondarily involved because of a diaphragmatic hernia. The fundus resulted to be the most frequently damaged part of the stomach (80%). Conclusions: Blunt traumatic injuries need a careful and systematic approach given their economical and social relevance. For these reasons uncommon lesions require attention and may be important to search for specific findings of gastric lesions.

  10. 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.)

  11. Why is the correlation between gene importance and gene evolutionary rate so weak?

    Science.gov (United States)

    Wang, Zhi; Zhang, Jianzhi

    2009-01-01

    One of the few commonly believed principles of molecular evolution is that functionally more important genes (or DNA sequences) evolve more slowly than less important ones. This principle is widely used by molecular biologists in daily practice. However, recent genomic analysis of a diverse array of organisms found only weak, negative correlations between the evolutionary rate of a gene and its functional importance, typically measured under a single benign lab condition. A frequently suggested cause of the above finding is that gene importance determined in the lab differs from that in an organism's natural environment. Here, we test this hypothesis in yeast using gene importance values experimentally determined in 418 lab conditions or computationally predicted for 10,000 nutritional conditions. In no single condition or combination of conditions did we find a much stronger negative correlation, which is explainable by our subsequent finding that always-essential (enzyme) genes do not evolve significantly more slowly than sometimes-essential or always-nonessential ones. Furthermore, we verified that functional density, approximated by the fraction of amino acid sites within protein domains, is uncorrelated with gene importance. Thus, neither the lab-nature mismatch nor a potentially biased among-gene distribution of functional density explains the observed weakness of the correlation between gene importance and evolutionary rate. We conclude that the weakness is factual, rather than artifactual. In addition to being weakened by population genetic reasons, the correlation is likely to have been further weakened by the presence of multiple nontrivial rate determinants that are independent from gene importance. These findings notwithstanding, we show that the principle of slower evolution of more important genes does have some predictive power when genes with vastly different evolutionary rates are compared, explaining why the principle can be practically useful

  12. 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

  13. CT findings of pancreatic disease

    International Nuclear Information System (INIS)

    Lee, Mi Sook; Park, In Sook; Jeon, Doo Sung; Kim, Hong Soo; Rhee, Hak Song; Won, Jong Jin

    1988-01-01

    CT was found to be a reliable, often specific, and noninvasive method for detecting pancreatic diseases. In a study of pancreatic lesions, 37 cases having satisfactory operative and histological proofs were analyzed by CT at PMC from Jan. 1986 to Oct. 1987. The results were as following: 1. Male:female is 26:11. 2. The incidence of pancreatic disease were as follows: 1) Pancreatic cancer:21 cases (56%) a.Head:12 cases b.Body:4 cases c.Tail:1 case d.Body and tail:1 case e.Uncinate process:2 cases f.Entire pancreas: 1 case 2) Acute pancreatitis: 6 cases (16%) 3) Chronic pancreatitis:5 cases (14%) 3. The characteristic CT findings: 1) 100% of pancreatic head cancer showed focal mass or alteration of pancreatic head contour and biliary tree dilatation, and 33% (7/12) fat line obliteration. 2) All of other pancreatic cancer except head appeared as focal mass or contour alteration and fat line obliteration. 3) Total 6 cases of acute pancreatitis showed that 5 cases diffuse enlargement of pancreas, 3 fluid collection (2 cases:left anterior pararenal and posterior pararenal space and lesser sac, 1 case:only pancreas body) and 1 case abscess formation. 4) Total 5 cases of chronic pancreatitis revealed diffuse enlargement 2 cases and atrophy 1 case, pancreatic ductal dilatation 3 cases, calcification 2 cases, and biliary tree dilatation with CBD tapering appearance 1 case. 5) All cases of pseudocysts were well marginated cystic lesions that located at head in 3 cases and tail 3 cases, and 4 cases were well defined pure cystic masses but 1 case was well capsulated cyst with multiple internal septation

  14. Regional Transmission Projects: Finding Solutions

    Energy Technology Data Exchange (ETDEWEB)

    The Keystone Center

    2005-06-15

    The Keystone Center convened and facilitated a year-long Dialogue on "Regional Transmission Projects: Finding Solutions" to develop recommendations that will help address the difficult and contentious issues related to expansions of regional electric transmission systems that are needed for reliable and economic transmission of power within and across regions. This effort brought together a cross-section of affected stakeholders and thought leaders to address the problem with the collective wisdom of their experience and interests. Transmission owners sat at the table with consumer advocates and environmental organizations. Representatives from regional transmission organizations exchanged ideas with state and federal regulators. Generation developers explored common interests with public power suppliers. Together, the Dialogue participants developed consensus solutions about how to begin unraveling some of the more intractable issues surrounding identification of need, allocation of costs, and reaching consensus on siting issues that can frustrate the development of regional transmission infrastructure. The recommendations fall into three broad categories: 1. Recommendations on appropriate institutional arrangements and processes for achieving regional consensus on the need for new or expanded transmission infrastructure 2. Recommendations on the process for siting of transmission lines 3. Recommendations on the tools needed to support regional planning, cost allocation, and siting efforts. List of Dialogue participants: List of Dialogue Participants: American Electric Power American Transmission Company American Wind Energy Association California ISO Calpine Corporation Cinergy Edison Electric Institute Environmental Defense Federal Energy Regulatory Commission Great River Energy International Transmission Company ISO-New England Iowa Public Utility Board Kanner & Associates Midwest ISO National Association of Regulatory Utility Commissioners National Association

  15. 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.

  16. 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

  17. Post-therapeutic imaging findings

    International Nuclear Information System (INIS)

    Pollice, Saverio; Muto, Mario; Scarabino, Tommaso

    2015-01-01

    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

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

    DEFF Research Database (Denmark)

    Have, Christian Theil; Mørk, Søren

    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...... 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...... and are evaluated by the effect on prediction performance. Since bacterial gene finding to a large extent is a solved problem it forms an ideal proving ground for evaluating the explicit modeling of larger scale gene sequence composition of genomes. We conclude that the sequential composition of gene reading frames...

  19. 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.

  20. The role of gene-gene interaction in the prediction of criminal behavior.

    Science.gov (United States)

    Boutwell, Brian B; Menard, Scott; Barnes, J C; Beaver, Kevin M; Armstrong, Todd A; Boisvert, Danielle

    2014-04-01

    A host of research has examined the possibility that environmental risk factors might condition the influence of genes on various outcomes. Less research, however, has been aimed at exploring the possibility that genetic factors might interact to impact the emergence of human traits. Even fewer studies exist examining the interaction of genes in the prediction of behavioral outcomes. The current study expands this body of research by testing the interaction between genes involved in neural transmission. Our findings suggest that certain dopamine genes interact to increase the odds of criminogenic outcomes in a national sample of Americans. Copyright © 2014 Elsevier Inc. All rights reserved.

  1. Incorporating networks in a probabilistic graphical model to find drivers for complex human diseases.

    Science.gov (United States)

    Mezlini, Aziz M; Goldenberg, Anna

    2017-10-01

    Discovering genetic mechanisms driving complex diseases is a hard problem. Existing methods often lack power to identify the set of responsible genes. Protein-protein interaction networks have been shown to boost power when detecting gene-disease associations. We introduce a Bayesian framework, Conflux, to find disease associated genes from exome sequencing data using networks as a prior. There are two main advantages to using networks within a probabilistic graphical model. First, networks are noisy and incomplete, a substantial impediment to gene discovery. Incorporating networks into the structure of a probabilistic models for gene inference has less impact on the solution than relying on the noisy network structure directly. Second, using a Bayesian framework we can keep track of the uncertainty of each gene being associated with the phenotype rather than returning a fixed list of genes. We first show that using networks clearly improves gene detection compared to individual gene testing. We then show consistently improved performance of Conflux compared to the state-of-the-art diffusion network-based method Hotnet2 and a variety of other network and variant aggregation methods, using randomly generated and literature-reported gene sets. We test Hotnet2 and Conflux on several network configurations to reveal biases and patterns of false positives and false negatives in each case. Our experiments show that our novel Bayesian framework Conflux incorporates many of the advantages of the current state-of-the-art methods, while offering more flexibility and improved power in many gene-disease association scenarios.

  2. 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

  3. Genes with minimal phylogenetic information are problematic for coalescent analyses when gene tree estimation is biased.

    Science.gov (United States)

    Xi, Zhenxiang; Liu, Liang; Davis, Charles C

    2015-11-01

    The development and application of coalescent methods are undergoing rapid changes. One little explored area that bears on the application of gene-tree-based coalescent methods to species tree estimation is gene informativeness. Here, we investigate the accuracy of these coalescent methods when genes have minimal phylogenetic information, including the implementation of the multilocus bootstrap approach. Using simulated DNA sequences, we demonstrate that genes with minimal phylogenetic information can produce unreliable gene trees (i.e., high error in gene tree estimation), which may in turn reduce the accuracy of species tree estimation using gene-tree-based coalescent methods. We demonstrate that this problem can be alleviated by sampling more genes, as is commonly done in large-scale phylogenomic analyses. This applies even when these genes are minimally informative. If gene tree estimation is biased, however, gene-tree-based coalescent analyses will produce inconsistent results, which cannot be remedied by increasing the number of genes. In this case, it is not the gene-tree-based coalescent methods that are flawed, but rather the input data (i.e., estimated gene trees). Along these lines, the commonly used program PhyML has a tendency to infer one particular bifurcating topology even though it is best represented as a polytomy. We additionally corroborate these findings by analyzing the 183-locus mammal data set assembled by McCormack et al. (2012) using ultra-conserved elements (UCEs) and flanking DNA. Lastly, we demonstrate that when employing the multilocus bootstrap approach on this 183-locus data set, there is no strong conflict between species trees estimated from concatenation and gene-tree-based coalescent analyses, as has been previously suggested by Gatesy and Springer (2014). Copyright © 2015 Elsevier Inc. All rights reserved.

  4. Combining gene prediction methods to improve metagenomic gene annotation

    Directory of Open Access Journals (Sweden)

    Rosen Gail L

    2011-01-01

    Full Text Available Abstract Background Traditional gene annotation methods rely on characteristics that may not be available in short reads generated from next generation technology, resulting in suboptimal performance for metagenomic (environmental samples. Therefore, in recent years, new programs have been developed that optimize performance on short reads. In this work, we benchmark three metagenomic gene prediction programs and combine their predictions to improve metagenomic read gene annotation. Results We not only analyze the programs' performance at different read-lengths like similar studies, but also separate different types of reads, including intra- and intergenic regions, for analysis. The main deficiencies are in the algorithms' ability to predict non-coding regions and gene edges, resulting in more false-positives and false-negatives than desired. In fact, the specificities of the algorithms are notably worse than the sensitivities. By combining the programs' predictions, we show significant improvement in specificity at minimal cost to sensitivity, resulting in 4% improvement in accuracy for 100 bp reads with ~1% improvement in accuracy for 200 bp reads and above. To correctly annotate the start and stop of the genes, we find that a consensus of all the predictors performs best for shorter read lengths while a unanimous agreement is better for longer read lengths, boosting annotation accuracy by 1-8%. We also demonstrate use of the classifier combinations on a real dataset. Conclusions To optimize the performance for both prediction and annotation accuracies, we conclude that the consensus of all methods (or a majority vote is the best for reads 400 bp and shorter, while using the intersection of GeneMark and Orphelia predictions is the best for reads 500 bp and longer. We demonstrate that most methods predict over 80% coding (including partially coding reads on a real human gut sample sequenced by Illumina technology.

  5. 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.

  6. 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

  7. 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.

  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)

    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.

  9. Gene doping in sports.

    Science.gov (United States)

    Unal, Mehmet; Ozer Unal, Durisehvar

    2004-01-01

    Gene or cell doping is defined by the World Anti-Doping Agency (WADA) as "the non-therapeutic use of genes, genetic elements and/or cells that have the capacity to enhance athletic performance". New research in genetics and genomics will be used not only to diagnose and treat disease, but also to attempt to enhance human performance. In recent years, gene therapy has shown progress and positive results that have highlighted the potential misuse of this technology and the debate of 'gene doping'. Gene therapies developed for the treatment of diseases such as anaemia (the gene for erythropoietin), muscular dystrophy (the gene for insulin-like growth factor-1) and peripheral vascular diseases (the gene for vascular endothelial growth factor) are potential doping methods. With progress in gene technology, many other genes with this potential will be discovered. For this reason, it is important to develop timely legal regulations and to research the field of gene doping in order to develop methods of detection. To protect the health of athletes and to ensure equal competitive conditions, the International Olympic Committee, WADA and International Sports Federations have accepted performance-enhancing substances and methods as being doping, and have forbidden them. Nevertheless, the desire to win causes athletes to misuse these drugs and methods. This paper reviews the current status of gene doping and candidate performance enhancement genes, and also the use of gene therapy in sports medicine and ethics of genetic enhancement. Copyright 2004 Adis Data Information BV

  10. 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

  11. 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

  12. 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

  13. Arteriogrpahic findings of Buerger's disease

    Energy Technology Data Exchange (ETDEWEB)

    Oh, Ki Kun; Suh, Jung Ho; Park, Chang Yun; Choi, Byung Sook [Yonsei University College of Medicine, Seoul (Korea, Republic of)

    1973-04-15

    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.

  14. 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.

  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. 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

    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...

  17. Symbiotic and nonsymbiotic hemoglobin genes of Casuarina glauca

    DEFF Research Database (Denmark)

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

    1995-01-01

    Frankia. Both the nonsymbiotic and symbiotic genes retained their specific patterns of expression when introduced into the legume Lotus corniculatus. We interpret this finding to mean that the controls of expression of the symbiotic gene in Casuarina must be similar to the controls of expression...... of the leghemoglobin genes that operate in nodules formed during the interaction between rhizobia and legumes. Deletion analyses of the promoters of the Casuarina symbiotic genes delineated a region that contains nodulin motifs identified in legumes; this region is critical for the controlled expression...... 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...

  18. Gastric Cancer Associated Genes Identified by an Integrative Analysis of Gene Expression Data

    Directory of Open Access Journals (Sweden)

    Bing Jiang

    2017-01-01

    Full Text Available Gastric cancer is one of the most severe complex diseases with high morbidity and mortality in the world. The molecular mechanisms and risk factors for this disease are still not clear since the cancer heterogeneity caused by different genetic and environmental factors. With more and more expression data accumulated nowadays, we can perform integrative analysis for these data to understand the complexity of gastric cancer and to identify consensus players for the heterogeneous cancer. In the present work, we screened the published gene expression data and analyzed them with integrative tool, combined with pathway and gene ontology enrichment investigation. We identified several consensus differentially expressed genes and these genes were further confirmed with literature mining; at last, two genes, that is, immunoglobulin J chain and C-X-C motif chemokine ligand 17, were screened as novel gastric cancer associated genes. Experimental validation is proposed to further confirm this finding.

  19. Calcisponges have a ParaHox gene and dynamic expression of dispersed NK homeobox genes.

    Science.gov (United States)

    Fortunato, Sofia A V; Adamski, Marcin; Ramos, Olivia Mendivil; Leininger, Sven; Liu, Jing; Ferrier, David E K; Adamska, Maja

    2014-10-30

    Sponges are simple animals with few cell types, but their genomes paradoxically contain a wide variety of developmental transcription factors, including homeobox genes belonging to the Antennapedia (ANTP) class, which in bilaterians encompass Hox, ParaHox and NK genes. In the genome of the demosponge Amphimedon queenslandica, no Hox or ParaHox genes are present, but NK genes are linked in a tight cluster similar to the NK clusters of bilaterians. It has been proposed that Hox and ParaHox genes originated from NK cluster genes after divergence of sponges from the lineage leading to cnidarians and bilaterians. On the other hand, synteny analysis lends support to the notion that the absence of Hox and ParaHox genes in Amphimedon is a result of secondary loss (the ghost locus hypothesis). Here we analysed complete suites of ANTP-class homeoboxes in two calcareous sponges, Sycon ciliatum and Leucosolenia complicata. Our phylogenetic analyses demonstrate that these calcisponges possess orthologues of bilaterian NK genes (Hex, Hmx and Msx), a varying number of additional NK genes and one ParaHox gene, Cdx. Despite the generation of scaffolds spanning multiple genes, we find no evidence of clustering of Sycon NK genes. All Sycon ANTP-class genes are developmentally expressed, with patterns suggesting their involvement in cell type specification in embryos and adults, metamorphosis and body plan patterning. These results demonstrate that ParaHox genes predate the origin of sponges, thus confirming the ghost locus hypothesis, and highlight the need to analyse the genomes of multiple sponge lineages to obtain a complete picture of the ancestral composition of the first animal genome.

  20. 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.

  1. 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.

  2. 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

  3. 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...

  4. 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

  5. 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)

  6. 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.

  7. Comparative genomic and transcriptomic analysis of selected fatty acid biosynthesis genes and CNL disease resistance genes in oil palm

    Science.gov (United States)

    Rosli, Rozana; Amiruddin, Nadzirah; Ab Halim, Mohd Amin; Chan, Pek-Lan; Chan, Kuang-Lim; Azizi, Norazah; Morris, Priscilla E.; Leslie Low, Eng-Ti; Ong-Abdullah, Meilina; Sambanthamurthi, Ravigadevi; Singh, Rajinder

    2018-01-01

    Comparative genomics and transcriptomic analyses were performed on two agronomically important groups of genes from oil palm versus other major crop species and the model organism, Arabidopsis thaliana. The first analysis was of two gene families with key roles in regulation of oil quality and in particular the accumulation of oleic acid, namely stearoyl ACP desaturases (SAD) and acyl-acyl carrier protein (ACP) thioesterases (FAT). In both cases, these were found to be large gene families with complex expression profiles across a wide range of tissue types and developmental stages. The detailed classification of the oil palm SAD and FAT genes has enabled the updating of the latest version of the oil palm gene model. The second analysis focused on disease resistance (R) genes in order to elucidate possible candidates for breeding of pathogen tolerance/resistance. Ortholog analysis showed that 141 out of the 210 putative oil palm R genes had homologs in banana and rice. These genes formed 37 clusters with 634 orthologous genes. Classification of the 141 oil palm R genes showed that the genes belong to the Kinase (7), CNL (95), MLO-like (8), RLK (3) and Others (28) categories. The CNL R genes formed eight clusters. Expression data for selected R genes also identified potential candidates for breeding of disease resistance traits. Furthermore, these findings can provide information about the species evolution as well as the identification of agronomically important genes in oil palm and other major crops. PMID:29672525

  8. Comparative genomic and transcriptomic analysis of selected fatty acid biosynthesis genes and CNL disease resistance genes in oil palm.

    Science.gov (United States)

    Rosli, Rozana; Amiruddin, Nadzirah; Ab Halim, Mohd Amin; Chan, Pek-Lan; Chan, Kuang-Lim; Azizi, Norazah; Morris, Priscilla E; Leslie Low, Eng-Ti; Ong-Abdullah, Meilina; Sambanthamurthi, Ravigadevi; Singh, Rajinder; Murphy, Denis J

    2018-01-01

    Comparative genomics and transcriptomic analyses were performed on two agronomically important groups of genes from oil palm versus other major crop species and the model organism, Arabidopsis thaliana. The first analysis was of two gene families with key roles in regulation of oil quality and in particular the accumulation of oleic acid, namely stearoyl ACP desaturases (SAD) and acyl-acyl carrier protein (ACP) thioesterases (FAT). In both cases, these were found to be large gene families with complex expression profiles across a wide range of tissue types and developmental stages. The detailed classification of the oil palm SAD and FAT genes has enabled the updating of the latest version of the oil palm gene model. The second analysis focused on disease resistance (R) genes in order to elucidate possible candidates for breeding of pathogen tolerance/resistance. Ortholog analysis showed that 141 out of the 210 putative oil palm R genes had homologs in banana and rice. These genes formed 37 clusters with 634 orthologous genes. Classification of the 141 oil palm R genes showed that the genes belong to the Kinase (7), CNL (95), MLO-like (8), RLK (3) and Others (28) categories. The CNL R genes formed eight clusters. Expression data for selected R genes also identified potential candidates for breeding of disease resistance traits. Furthermore, these findings can provide information about the species evolution as well as the identification of agronomically important genes in oil palm and other major crops.

  9. Analysis of multiplex gene expression maps obtained by voxelation.

    Science.gov (United States)

    An, Li; Xie, Hongbo; Chin, Mark H; Obradovic, Zoran; Smith, Desmond J; Megalooikonomou, Vasileios

    2009-04-29

    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. 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 cortex and corpus callosum. The experimental

  10. 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

  11. 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.

  12. 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.

  13. Gene therapy in periodontics.

    Science.gov (United States)

    Chatterjee, Anirban; Singh, Nidhi; Saluja, Mini

    2013-03-01

    GENES are made of DNA - the code of life. They are made up of two types of base pair from different number of hydrogen bonds AT, GC which can be turned into instruction. Everyone inherits genes from their parents and passes them on in turn to their children. Every person's genes are different, and the changes in sequence determine the inherited differences between each of us. Some changes, usually in a single gene, may cause serious diseases. Gene therapy is 'the use of genes as medicine'. It involves the transfer of a therapeutic or working gene copy into specific cells of an individual in order to repair a faulty gene copy. Thus it 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. It has a promising era in the field of periodontics. Gene therapy has been used as a mode of tissue engineering in periodontics. The tissue engineering approach reconstructs the natural target tissue by combining four elements namely: Scaffold, signaling molecules, cells and blood supply and thus can help in the reconstruction of damaged periodontium including cementum, gingival, periodontal ligament and bone.

  14. 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.

  15. 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)

  16. 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.

  17. Clock gene modulates roles of OXTR and AVPR1b genes in prosociality.

    Directory of Open Access Journals (Sweden)

    Haipeng Ci

    Full Text Available BACKGROUND: The arginine vasopressin receptor (AVPR and oxytocin receptor (OXTR genes have been demonstrated to contribute to prosocial behavior. Recent research has focused on the manner by which these simple receptor genes influence prosociality, particularly with regard to the AVP system, which is modulated by the clock gene. The clock gene is responsible for regulating the human biological clock, affecting sleep, emotion and behavior. The current study examined in detail whether the influences of the OXTR and AVPR1b genes on prosociality are dependent on the clock gene. METHODOLOGY/PRINCIPAL FINDINGS: This study assessed interactions between the clock gene (rs1801260, rs6832769 and the OXTR (rs1042778, rs237887 and AVPR1b (rs28373064 genes in association with individual differences in prosociality in healthy male Chinese subjects (n = 436. The Prosocial Tendencies Measure (PTM-R was used to assess prosociality. Participants carrying both the GG/GA variant of AVPR1b rs28373064 and the AA variant of clock rs6832769 showed the highest scores on the Emotional PTM. Carriers of both the T allele of OXTR rs1042778 and the C allele of clock rs1801260 showed the lowest total PTM scores compared with the other groups. CONCLUSIONS: The observed interaction effects provide converging evidence that the clock gene and OXT/AVP systems are intertwined and contribute to human prosociality.

  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. 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. ...

  20. 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 ...

  1. Computed tomographic findings of intracranial gliosis

    International Nuclear Information System (INIS)

    Weisberg, L.

    1981-01-01

    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. (orig.)

  2. CT findings of diffuse malignant leptomeningeal melanoma

    Energy Technology Data Exchange (ETDEWEB)

    Fujii, Katsuro; Sahashi, Ko; Takahashi, Akira; Nakagawa, Hiroshi [Aichi Medical Univ., Aichi (Japan); Sumi, Yasuhiko

    1982-04-01

    This was a case of malignant melanoma which spreaded diffusely in the meninges. The diagnosis was established by cytology of the cerebrospinal fluid. The CT images, cerebral angiographic findings and pathological findings by autopsy were presented.

  3. 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.

  4. beta. -Amyloid gene dosage in Alzheimer's disease

    Energy Technology Data Exchange (ETDEWEB)

    Murdoch, G H; Manuelidis, L; Kim, J H; Manuelidis, E E

    1988-01-11

    The 4-5 kd amyloid ..beta..-peptide is a major constituent of the characteristic amyloid plaque of Alzheimer's disease. It has been reported that some cases of sporatic Alzheimer's disease are associated with at least a partial duplication of chromosome 21 containing the gene corresponding to the 695 residue precursor of this peptide. To contribute to an understanding of the frequency to such a duplication event in the overall Alzheimer's population, the authors have determined the gene dosage of the ..beta..-amyloid gene in this collection of cases. All cases had a clinical diagnosis of Alzheimer's confirmed neuropathologically. Each Alzheimer's case had an apparent normal diploid ..beta..-amyloid gene dosage, while control Down's cases had the expected triploid dosage. Thus partial duplication of chromosome 21 may be a rare finding in Alzheimer's disease. Similar conclusions were just reported in several studies of the Harvard Alzheimer collection.

  5. 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...

  6. Cerebral computerized tomography findings in AIDS patients

    International Nuclear Information System (INIS)

    Hol, P.K.; Dunlop, O.

    1997-01-01

    A cerebral CT was performed in 82 of 525 AIDS patients, with positive findings in 46 cases. These findings included cerebral atrophy in 28 cases, pathological demyelinisation in two, progressive multifocal leukoencephalopathy in one, toxoplasmoses in 11, lymphomas in seven, infarction in one and one subdural haematoma. The radiological findings are correlated to pathology and clinical symptoms. The authors point out the importance of these findings for correct interpretation of the CT scans. 11 refs., 7 figs., 2 tabs

  7. Inferring Drosophila gap gene regulatory network: Pattern analysis of simulated gene expression profiles and stability analysis

    OpenAIRE

    Fomekong-Nanfack, Y.; Postma, M.; Kaandorp, J.A.

    2009-01-01

    Abstract Background Inference of gene regulatory networks (GRNs) requires accurate data, a method to simulate the expression patterns and an efficient optimization algorithm to estimate the unknown parameters. Using this approach it is possible to obtain alternative circuits without making any a priori assumptions about the interactions, which all simulate the observed patterns. It is important to analyze the properties of the circuits. Findings We have analyzed the simulated gene expression ...

  8. Paralogous Genes as a Tool to Study the Regulation of Gene Expression

    DEFF Research Database (Denmark)

    Hoffmann, Robert D

    The genomes of plants are marked by reoccurring events of whole-genome duplication. These events are major contributors to speciation and provide the genetic material for organisms to evolve ever greater complexity. Duplicated genes, referred to as paralogs, may be retained because they acquired...... regions. These results suggest that a concurrent purifying selection acts on coding and non-coding sequences of paralogous genes in A. thaliana. Mutational analyses of the promoters from a paralogous gene pair were performed in transgenic A. thaliana plants. The results revealed a 170-bp long DNA sequence...... that forms a bifunctional cis-regulatory module; it represses gene expression in the sporophyte while activating it in pollen. This finding is important for many aspects of gene regulation and the transcriptional changes underlying gametophyte development. In conclusion, the presented thesis suggests that...

  9. No Evidence That Schizophrenia Candidate Genes Are More Associated With Schizophrenia Than Noncandidate Genes.

    Science.gov (United States)

    Johnson, Emma C; Border, Richard; Melroy-Greif, Whitney E; de Leeuw, Christiaan A; Ehringer, Marissa A; Keller, Matthew C

    2017-11-15

    A recent analysis of 25 historical candidate gene polymorphisms for schizophrenia in the largest genome-wide association study conducted to date suggested that these commonly studied variants were no more associated with the disorder than would be expected by chance. However, the same study identified other variants within those candidate genes that demonstrated genome-wide significant associations with schizophrenia. As such, it is possible that variants within historic schizophrenia candidate genes are associated with schizophrenia at levels above those expected by chance, even if the most-studied specific polymorphisms are not. The present study used association statistics from the largest schizophrenia genome-wide association study conducted to date as input to a gene set analysis to investigate whether variants within schizophrenia candidate genes are enriched for association with schizophrenia. As a group, variants in the most-studied candidate genes were no more associated with schizophrenia than were variants in control sets of noncandidate genes. While a small subset of candidate genes did appear to be significantly associated with schizophrenia, these genes were not particularly noteworthy given the large number of more strongly associated noncandidate genes. The history of schizophrenia research should serve as a cautionary tale to candidate gene investigators examining other phenotypes: our findings indicate that the most investigated candidate gene hypotheses of schizophrenia are not well supported by genome-wide association studies, and it is likely that this will be the case for other complex traits as well. Copyright © 2017 Society of Biological Psychiatry. Published by Elsevier Inc. All rights reserved.

  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. Tandemly Arrayed Genes in Vertebrate Genomes

    Directory of Open Access Journals (Sweden)

    Deng Pan

    2008-01-01

    Full Text Available Tandemly arrayed genes (TAGs are duplicated genes that are linked as neighbors on a chromosome, many of which have important physiological and biochemical functions. Here we performed a survey of these genes in 11 available vertebrate genomes. TAGs account for an average of about 14% of all genes in these vertebrate genomes, and about 25% of all duplications. The majority of TAGs (72–94% have parallel transcription orientation (i.e., they are encoded on the same strand in contrast to the genome, which has about 50% of its genes in parallel transcription orientation. The majority of tandem arrays have only two members. In all species, the proportion of genes that belong to TAGs tends to be higher in large gene families than in small ones; together with our recent finding that tandem duplication played a more important role than retroposition in large families, this fact suggests that among all types of duplication mechanisms, tandem duplication is the predominant mechanism of duplication, especially in large families. Finally, several species have a higher proportion of large tandem arrays that are species-specific than random expectation.

  12. 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...

  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. History of gene therapy.

    Science.gov (United States)

    Wirth, Thomas; Parker, Nigel; Ylä-Herttuala, Seppo

    2013-08-10

    Two decades after the initial gene therapy trials and more than 1700 approved clinical trials worldwide we not only have gained much new information and knowledge regarding gene therapy in general, but also learned to understand the concern that has persisted in society. Despite the setbacks gene therapy has faced, success stories have increasingly emerged. Examples for these are the positive recommendation for a gene therapy product (Glybera) by the EMA for approval in the European Union and the positive trials for the treatment of ADA deficiency, SCID-X1 and adrenoleukodystrophy. Nevertheless, our knowledge continues to grow and during the course of time more safety data has become available that helps us to develop better gene therapy approaches. Also, with the increased understanding of molecular medicine, we have been able to develop more specific and efficient gene transfer vectors which are now producing clinical results. In this review, we will take a historical view and highlight some of the milestones that had an important impact on the development of gene therapy. We will also discuss briefly the safety and ethical aspects of gene therapy and address some concerns that have been connected with gene therapy as an important therapeutic modality. Copyright © 2013 Elsevier B.V. All rights reserved.

  15. Refining discordant gene trees.

    Science.gov (United States)

    Górecki, Pawel; Eulenstein, Oliver

    2014-01-01

    Evolutionary studies are complicated by discordance between gene trees and the species tree in which they evolved. Dealing with discordant trees often relies on comparison costs between gene and species trees, including the well-established Robinson-Foulds, gene duplication, and deep coalescence costs. While these costs have provided credible results for binary rooted gene trees, corresponding cost definitions for non-binary unrooted gene trees, which are frequently occurring in practice, are challenged by biological realism. We propose a natural extension of the well-established costs for comparing unrooted and non-binary gene trees with rooted binary species trees using a binary refinement model. For the duplication cost we describe an efficient algorithm that is based on a linear time reduction and also computes an optimal rooted binary refinement of the given gene tree. Finally, we show that similar reductions lead to solutions for computing the deep coalescence and the Robinson-Foulds costs. Our binary refinement of Robinson-Foulds, gene duplication, and deep coalescence costs for unrooted and non-binary gene trees together with the linear time reductions provided here for computing these costs significantly extends the range of trees that can be incorporated into approaches dealing with discordance.

  16. Flies selected for longevity retain a young gene expression profile

    DEFF Research Database (Denmark)

    Sarup, Pernille Merete; Sørensen, Peter; Loeschcke, Volker

    2011-01-01

      We investigated correlated responses in the transcriptomes of longevity-selected lines of Drosophila melanogaster to identify pathways that affect life span in metazoan systems. We evaluated the gene expression profile in young, middle-aged, and old male flies, finding that 530 genes were...

  17. Evaluating codon bias perspective in barbiturase gene using ...

    African Journals Online (AJOL)

    Abdullah

    2014-01-08

    Jan 8, 2014 ... along with codon usage was done to reveal dynamics of gene evolution and expression ... analysis is a potent approach for detecting mutations, selection methods and finding rationale of biased and unbiased gene changes and hence, evolutionary ... in the perception of the molecular basics plus potential.

  18. 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 ...

  19. A Regulatory Network Analysis of Orphan Genes in Arabidopsis Thaliana

    Science.gov (United States)

    Singh, Pramesh; Chen, Tianlong; Arendsee, Zebulun; Wurtele, Eve S.; Bassler, Kevin E.

    Orphan genes, which are genes unique to each particular species, have recently drawn significant attention for their potential usefulness for organismal robustness. Their origin and regulatory interaction patterns remain largely undiscovered. Recently, methods that use the context likelihood of relatedness to infer a network followed by modularity maximizing community detection algorithms on the inferred network to find the functional structure of regulatory networks were shown to be effective. We apply improved versions of these methods to gene expression data from Arabidopsis thaliana, identify groups (clusters) of interacting genes with related patterns of expression and analyze the structure within those groups. Focusing on clusters that contain orphan genes, we compare the identified clusters to gene ontology (GO) terms, regulons, and pathway designations and analyze their hierarchical structure. We predict new regulatory interactions and unravel the structure of the regulatory interaction patterns of orphan genes. Work supported by the NSF through Grants DMR-1507371 and IOS-1546858.

  20. Structure and chromosomal localization of the human renal kallikrein gene

    International Nuclear Information System (INIS)

    Evans, B.A.; Yun, Z.X.; Close, J.A.

    1988-01-01

    Glandular kallikreins are a family of proteases encoded by a variable number of genes in different mammalian species. In all species examined, however, one particular kallikrein is functionally conserved in its capacity to release the vasoactive peptide, Lys-bradykinin, from low molecular weight kininogen. This kallikrein is found in the kidney, pancreas, and salivary gland, showing a unique pattern of tissue-specific expression relative to other members of the family. The authors have isolated a genomic clone carrying the human renal kallikrein gene and compared the nucleotide sequence of its promoter region with those of the mouse renal kallikrein gene and another mouse kallikrein gene expressed in a distinct cell type. They find four sequence elements conserved between renal kallikrein genes from the two species. They have also shown that the human gene is localized to 19q13, a position analogous to that of the kallikrein gene family on mouse chromosome 7