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,

Thorax computed tomography findings in patients victims of chest trauma

Directory of Open Access Journals (Sweden)

Francisco Jose Rodrigues de Moura Filho

2015-12-01

Full Text Available Objective: To describe thorax computed tomography findings in patients assisted in the emergency unit of Institute Dr Jose Frota (IJF. Materials and Methods: Descriptive study analyzing 160 consecutive contrast-enhanced thorax computed tomography of patients victims of thoracic trauma admitted to the emergency unit of IJF, between November 1st, 2014 and January 31st, 2015. Results: Abnormal findings were observed in 91,2 % of the patients. Among them, the following findings were most frequently observed: fractures (48%, hemothorax (43%, atelectasis (37%, pneumothorax (26% and lung contusions (17% Rupture of the esophagus was seen in three patients. Conclusion: We recognize that the findings encountered in our study are of similar prevalence to the ones reported in the literature and that CT scan is essencial to quickly diagnose these findings.

Alveolar echinococcosis of the liver - computed tomographic findings

International Nuclear Information System (INIS)

Merkle, E.; Usadel, S.; Vogel, J.; Kern, P.; Friedrich, J.M.; Brambs, H.J.

1995-01-01

In order to ascertain the typical computed tomographic findings of hepatic alveolar echinococcosis, 24 computed tomograms of 19 patients were evaluated. The liver was involved in all cases whereas the diaphragma was infiltrated in 32%, and the retroperioteneal area in 42%. The right liver lobe was affected in 65%. Both before and after intravenous bolus contrast medium administration, the lesions were mainly inhomogeneous and of low density; a masking of the lesions due to the contrast medium administration was not observed; the enhancement pattern was irregular. Calcifications were detected in 96% of the cases, cystic structures in 50%, and cholestasis in 54%. On the basis of the crucial finding of calcifications in combination with the other typical observations, CT seems to be very suitable for the evaluation of hepatic alveolar echinococcosis. (orig.) [de

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

Computational identification of putative cytochrome P450 genes in ...

African Journals Online (AJOL)

In this work, a computational study of expressed sequence tags (ESTs) of soybean was performed by data mining methods and bio-informatics tools and as a result 78 putative P450 genes were identified, including 57 new ones. These genes were classified into five clans and 20 families by sequence similarities and among ...

Acute mediastinitis: multidetector computed tomography findings following cardiac surgery

International Nuclear Information System (INIS)

Macedo, Clarissa Aguiar de; Baena, Marcos Eduardo da Silva; Uezumi, Kiyomi Kato; Castro, Claudio Campi de; Lucarelli, Claudio Luiz; Cerri, Giovanni Guido

2008-01-01

Postoperative mediastinitis is defined as an infection of the organs and tissues in the mediastinal space, with an incidence ranging between 0.4% and 5% of cases. This disease severity varies from infection of superficial tissues in the chest wall to fulminant mediastinitis with sternal involvement. Diagnostic criterion for postoperative detection of acute mediastinitis at computed tomography is the presence of fluid collections and gas in the mediastinal space, which might or might not be associated with peristernal abnormalities such as edema of soft tissues, separation of sternal segments with marginal bone resorption, sclerosis and osteomyelitis. Other associated findings include lymphadenomegaly, pulmonary consolidation and pleural/ pericardial effusion. Some of these findings, such as mediastinal gas and small fluid collections can be typically found in the absence of infection, early in the period following thoracic surgery where the effectiveness of computed tomography is limited. After approximately two weeks, computed tomography achieves almost 100% sensitivity and specificity. Patients with clinical suspicion of mediastinitis should be submitted to computed tomography for investigating the presence of fluid collections to identify the extent and nature of the disease. Multidetector computed tomography allows 3D images reconstruction, contributing particularly to the evaluation of the sternum. (author)

Acute mediastinitis: multidetector computed tomography findings following cardiac surgery

Energy Technology Data Exchange (ETDEWEB)

Macedo, Clarissa Aguiar de [Universidade de Sao Paulo (USP), SP (Brazil). Faculdade de Medicina. Instituto do Coracao (InCor)]. E-mail: clarissaaguiarm@yahoo.com.br; Baena, Marcos Eduardo da Silva [Instituto do Coracao (InCor), Sao Paulo, SP (Brazil). Unit of Ultrasonography; Uezumi, Kiyomi Kato [Instituto do Coracao (InCor), Sao Paulo, SP (Brazil). Unit of Computed Tomography; Castro, Claudio Campi de [Instituto do Coracao (InCor), Sao Paulo, SP (Brazil). Unit of Magnetic Resonance Imaging; Lucarelli, Claudio Luiz [Instituto do Coracao (InCor), Sao Paulo, SP (Brazil). Center of Diagnosis; Cerri, Giovanni Guido [Universidade de Sao Paulo (USP), SP (Brazil). School of Medicine. Dept. of Radiology

2008-07-15

Postoperative mediastinitis is defined as an infection of the organs and tissues in the mediastinal space, with an incidence ranging between 0.4% and 5% of cases. This disease severity varies from infection of superficial tissues in the chest wall to fulminant mediastinitis with sternal involvement. Diagnostic criterion for postoperative detection of acute mediastinitis at computed tomography is the presence of fluid collections and gas in the mediastinal space, which might or might not be associated with peristernal abnormalities such as edema of soft tissues, separation of sternal segments with marginal bone resorption, sclerosis and osteomyelitis. Other associated findings include lymphadenomegaly, pulmonary consolidation and pleural/ pericardial effusion. Some of these findings, such as mediastinal gas and small fluid collections can be typically found in the absence of infection, early in the period following thoracic surgery where the effectiveness of computed tomography is limited. After approximately two weeks, computed tomography achieves almost 100% sensitivity and specificity. Patients with clinical suspicion of mediastinitis should be submitted to computed tomography for investigating the presence of fluid collections to identify the extent and nature of the disease. Multidetector computed tomography allows 3D images reconstruction, contributing particularly to the evaluation of the sternum. (author)

Computed tomographic findings in penetrating peptic ulcer

International Nuclear Information System (INIS)

Madrazo, B.L.; Halpert, R.D.; Sandler, M.A.; Pearlberg, J.L.

1984-01-01

Four cases of peptic ulcer penetrating the head of the pancreas were diagnosed by computed tomography (CT). Findings common to 3 cases included (a) an ulcer crater, (b) a sinus tract, and (c) enlargement of the head of the pancreas. Unlike other modalities, the inherent spatial resolution of CT allows a convenient diagnosis of this important complication of peptic ulcer disease

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.

High-resolution computed tomography findings in pulmonary Langerhans cell histiocytosis

Energy Technology Data Exchange (ETDEWEB)

Rodrigues, Rosana Souza [Universidade Federal do Rio de Janeiro (HUCFF/UFRJ), RJ (Brazil). Hospital Universitario Clementino Fraga Filho. Unit of Radiology; Capone, Domenico; Ferreira Neto, Armando Leao [Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro, RJ (Brazil)

2011-07-15

Objective: The present study was aimed at characterizing main lung changes observed in pulmonary Langerhans cell histiocytosis by means of high-resolution computed tomography. Materials and Methods: High-resolution computed tomography findings in eight patients with proven disease diagnosed by open lung biopsy, immunohistochemistry studies and/or extrapulmonary manifestations were retrospectively evaluated. Results: Small rounded, thin-walled cystic lesions were observed in the lung of all the patients. Nodules with predominantly peripheral distribution over the lung parenchyma were observed in 75% of the patients. The lesions were diffusely distributed, predominantly in the upper and middle lung fields in all of the cases, but involvement of costophrenic angles was observed in 25% of the patients. Conclusion: Comparative analysis of high-resolution computed tomography and chest radiography findings demonstrated that thinwalled cysts and small nodules cannot be satisfactorily evaluated by conventional radiography. Because of its capacity to detect and characterize lung cysts and nodules, high-resolution computed tomography increases the probability of diagnosing pulmonary Langerhans cell histiocytosis. (author)

High-resolution computed tomography and histopathological findings in hypersensitivity pneumonitis: a pictorial essay

Energy Technology Data Exchange (ETDEWEB)

Torres, Pedro Paulo Teixeira e Silva; Moreira, Marise Amaral Reboucas; Silva, Daniela Graner Schuwartz Tannus; Moreira, Maria Auxiliadora do Carmo [Universidade Federal de Goias (UFG), Goiania, GO (Brazil); Gama, Roberta Rodrigues Monteiro da [Hospital do Cancer de Barretos, Barretos, SP (Brazil); Sugita, Denis Masashi, E-mail: pedroptstorres@yahoo.com.br [Anapolis Unievangelica, Anapolis, GO (Brazil)

2016-03-15

Hypersensitivity pneumonitis is a diffuse interstitial and granulomatous lung disease caused by the inhalation of any one of a number of antigens. The objective of this study was to illustrate the spectrum of abnormalities in high-resolution computed tomography and histopathological findings related to hypersensitivity pneumonitis. We retrospectively evaluated patients who had been diagnosed with hypersensitivity pneumonitis (on the basis of clinical-radiological or clinical-radiological-pathological correlations) and had undergone lung biopsy. Hypersensitivity pneumonitis is clinically divided into acute, subacute, and chronic forms; high-resolution computed tomography findings correlate with the time of exposure; and the two occasionally overlap. In the subacute form, centrilobular micronodules, ground glass opacities, and air trapping are characteristic high-resolution computed tomography findings, whereas histopathology shows lymphocytic inflammatory infiltrates, bronchiolitis, variable degrees of organizing pneumonia, and giant cells. In the chronic form, high-resolution computed tomography shows traction bronchiectasis, honeycombing, and lung fibrosis, the last also being seen in the biopsy sample. A definitive diagnosis of hypersensitivity pneumonitis can be made only through a multidisciplinary approach, by correlating clinical findings, exposure history, high-resolution computed tomography findings, and lung biopsy findings. (author)

Designing a parallel evolutionary algorithm for inferring gene networks on the cloud computing environment.

Science.gov (United States)

Lee, Wei-Po; Hsiao, Yu-Ting; Hwang, Wei-Che

2014-01-16

To improve the tedious task of reconstructing gene networks through testing experimentally the possible interactions between genes, it becomes a trend to adopt the automated reverse engineering procedure instead. Some evolutionary algorithms have been suggested for deriving network parameters. However, to infer large networks by the evolutionary algorithm, it is necessary to address two important issues: premature convergence and high computational cost. To tackle the former problem and to enhance the performance of traditional evolutionary algorithms, it is advisable to use parallel model evolutionary algorithms. To overcome the latter and to speed up the computation, it is advocated to adopt the mechanism of cloud computing as a promising solution: most popular is the method of MapReduce programming model, a fault-tolerant framework to implement parallel algorithms for inferring large gene networks. This work presents a practical framework to infer large gene networks, by developing and parallelizing a hybrid GA-PSO optimization method. Our parallel method is extended to work with the Hadoop MapReduce programming model and is executed in different cloud computing environments. To evaluate the proposed approach, we use a well-known open-source software GeneNetWeaver to create several yeast S. cerevisiae sub-networks and use them to produce gene profiles. Experiments have been conducted and the results have been analyzed. They show that our parallel approach can be successfully used to infer networks with desired behaviors and the computation time can be largely reduced. Parallel population-based algorithms can effectively determine network parameters and they perform better than the widely-used sequential algorithms in gene network inference. These parallel algorithms can be distributed to the cloud computing environment to speed up the computation. By coupling the parallel model population-based optimization method and the parallel computational framework, high

Computed tomography findings of malignant pleural mesothelioma

Energy Technology Data Exchange (ETDEWEB)

Shiota, Yutaro; Sato, Toshio; Yamaguchi, Kazuo; Ono, Tetsuya; Kaji, Masaro; Niiya, Harutaka (Kure Kyosai Hospital, Hiroshima (Japan))

1994-04-01

Computed tomography (CT) findings were assessed in 7 patients with malignant mesothelioma. CT findings were also reviewed in 9 patients with lung cancer and pleuritis carcinomatosa and in 11 patients with tuberculous pleuritis. Five patients with malignant mesothelioma underwent CT scans twice, on admission and from 1 to 7 months after admission. Tuberculous pleuritis could be distinguished from pleuritis carcinomatosa and malignant mesothelioma by the presence or absence of pleural nodularity and chest wall invasion. Although it was difficult to identify specific CT features clearly distinguishing malignant mesothelioma from pleuritis carcinomatosa, characteristic findings of malignant mesothelioma appeared to include the rapid development and progression of pleural rind and a tendency to spread directly into the chest wall. We divided the pleural into the four regions; upper anterior, upper posterior, lower anterior and lower posterior regions. Pleural changes were more frequently seen in the lower pleural regions than in the upper pleural regions in malignant mesothelioma. (author).

Computed tomography findings of malignant pleural mesothelioma

International Nuclear Information System (INIS)

Shiota, Yutaro; Sato, Toshio; Yamaguchi, Kazuo; Ono, Tetsuya; Kaji, Masaro; Niiya, Harutaka

1994-01-01

Computed tomography (CT) findings were assessed in 7 patients with malignant mesothelioma. CT findings were also reviewed in 9 patients with lung cancer and pleuritis carcinomatosa and in 11 patients with tuberculous pleuritis. Five patients with malignant mesothelioma underwent CT scans twice, on admission and from 1 to 7 months after admission. Tuberculous pleuritis could be distinguished from pleuritis carcinomatosa and malignant mesothelioma by the presence or absence of pleural nodularity and chest wall invasion. Although it was difficult to identify specific CT features clearly distinguishing malignant mesothelioma from pleuritis carcinomatosa, characteristic findings of malignant mesothelioma appeared to include the rapid development and progression of pleural rind and a tendency to spread directly into the chest wall. We divided the pleural into the four regions; upper anterior, upper posterior, lower anterior and lower posterior regions. Pleural changes were more frequently seen in the lower pleural regions than in the upper pleural regions in malignant mesothelioma. (author)

Computed tomographic findings of intracerebral cysticercosis

Energy Technology Data Exchange (ETDEWEB)

Hong, Jin Kyo; Lee, Sun Wha; Kim, Ho Kyun; Ahn, Chi Yul [School of Medicine, Kyung-Hee University, Seoul (Korea, Republic of)

1980-12-15

Cysticercosis is a parasitic disease in which man serves as the intermediate host of Taenia Solium, the pork tapeworm. The computed tomographic findings of 25 cases of intracerebral cysticercosis proven by pathologic and/or clinical findings during past 2 years were analysed. The results were as follows; 1. The sex was 19 males and 6 females, and 56 percent of the patients were seen in fourth and fifth decades. The most common symptom was epilepsy (72%). 2. The C. T. findings in precontrast study were varied; such as ill defined low density (48%), cystic low density (20%), dilated ventricles (20%), ill defined low density with isodense nodule (18%), cystic low density with isodense mural nodule (12%) and calcification (8%). 3. The areas of involvement were 20 cases (80%) of parenchymal form, 3 cases (12%) of ventricular form and 2 cases (8%) of mixed form. 4. The contrast-enhanced 13 cases were 5 nodular, 5 ring or rim-like and 3 mixed type enhancements, while 12 cases were not enhanced. 5. C.T. scan demonstrated more precise location and extents of cerebral cysticercosis, especially in parenchymal form. It was considered to be important in determination of surgical feasibility and its approach.

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...

Computational Identification of Novel Genes: Current and Future Perspectives.

Science.gov (United States)

Klasberg, Steffen; Bitard-Feildel, Tristan; Mallet, Ludovic

2016-01-01

While it has long been thought that all genomic novelties are derived from the existing material, many genes lacking homology to known genes were found in recent genome projects. Some of these novel genes were proposed to have evolved de novo, ie, out of noncoding sequences, whereas some have been shown to follow a duplication and divergence process. Their discovery called for an extension of the historical hypotheses about gene origination. Besides the theoretical breakthrough, increasing evidence accumulated that novel genes play important roles in evolutionary processes, including adaptation and speciation events. Different techniques are available to identify genes and classify them as novel. Their classification as novel is usually based on their similarity to known genes, or lack thereof, detected by comparative genomics or against databases. Computational approaches are further prime methods that can be based on existing models or leveraging biological evidences from experiments. Identification of novel genes remains however a challenging task. With the constant software and technologies updates, no gold standard, and no available benchmark, evaluation and characterization of genomic novelty is a vibrant field. In this review, the classical and state-of-the-art tools for gene prediction are introduced. The current methods for novel gene detection are presented; the methodological strategies and their limits are discussed along with perspective approaches for further studies.

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...

Lipoid pneumonia in adults: findings on high-resolution computed tomography

International Nuclear Information System (INIS)

Marchiori, Edson; Escuissato, Dante L.; Souza Junior, Arthur Soares; Araujo Neto, Cesar; Nobre, Luiz Felipe; Irion, Klaus L.; Rodrigues, Rosana; Mancano, Alexandre Dias; Capone, Domenico; Fialho, Suzane Mansur; Souza, Carolina Althoff

2007-01-01

Objective: The present study was aimed at describing the findings on high-resolution computed tomography in patients with exogenous lipoid pneumonia secondary to mineral oil aspiration. Materials and methods: Eight adult patients - four men and four women - with mean age of 69.4 years were studied. All of the patients were users of mineral oil for treating intestinal constipation. High-resolution computed tomography studies of these patients were blindly evaluated by two radiologists. Results: Air-space consolidation with areas of fat density and crazy paving pattern were the most frequent findings. The lesions were bilateral in six cases and unilateral in two. Conclusion: Air-space consolidation with areas of fat density, associated with a clinical history of mineral oil ingestion virtually indicates a diagnosis of exogenous lipoid pneumonia. (author)

Lipoid pneumonia in adults: findings on high-resolution computed tomography

Energy Technology Data Exchange (ETDEWEB)

Marchiori, Edson [Universidade Federal Fluminense (UFF), Niteroi, RJ (Brazil). Dept. of Radiology]. E-mail: edmarchiori@gmail.com; Zanetti, Glaucia [Faculdade de Medicina de Petropolis, RJ (Brazil); Escuissato, Dante L. [Universidade Federal do Parana (UFPR), Curitiba, PR (Brazil); Souza Junior, Arthur Soares [Faculdade de Medicina de Sao Jose do Rio Preto (FAMERP), SP (Brazil); Araujo Neto, Cesar [Universidade Federal da Bahia (UFBA), Salvador, BA (Brazil); Nobre, Luiz Felipe [Universidade Federal de Santa Catarina (UFSC), Florianopolis, SC (Brazil); Irion, Klaus L. [The Cardiothoracic Centre NHS Trust, Liverpool (United Kingdom); Rodrigues, Rosana [Universidade Federal do Rio de Janeiro (UFRJ), RJ (Brazil). Hospital Universitario Clementino Fraga Filho (HUCFF); Mancano, Alexandre Dias [Hospital Regional de Taguatinga, Brasilia, DF (Brazil); Capone, Domenico [Universidade Estadual do Rio de Janeiro (UERJ), RJ (Brazil); Fialho, Suzane Mansur [Centro Nuclear da Guanabara, Rio de Janeiro, RJ (Brazil); Souza, Carolina Althoff [University of Ottawa (Canada)

2007-09-15

Objective: The present study was aimed at describing the findings on high-resolution computed tomography in patients with exogenous lipoid pneumonia secondary to mineral oil aspiration. Materials and methods: Eight adult patients - four men and four women - with mean age of 69.4 years were studied. All of the patients were users of mineral oil for treating intestinal constipation. High-resolution computed tomography studies of these patients were blindly evaluated by two radiologists. Results: Air-space consolidation with areas of fat density and crazy paving pattern were the most frequent findings. The lesions were bilateral in six cases and unilateral in two. Conclusion: Air-space consolidation with areas of fat density, associated with a clinical history of mineral oil ingestion virtually indicates a diagnosis of exogenous lipoid pneumonia. (author)

Development of a Computational Steering Framework for High Performance Computing Environments on Blue Gene/P Systems

KAUST Repository

Danani, Bob K.

2012-07-01

Computational steering has revolutionized the traditional workflow in high performance computing (HPC) applications. The standard workflow that consists of preparation of an application’s input, running of a simulation, and visualization of simulation results in a post-processing step is now transformed into a real-time interactive workflow that significantly reduces development and testing time. Computational steering provides the capability to direct or re-direct the progress of a simulation application at run-time. It allows modification of application-defined control parameters at run-time using various user-steering applications. In this project, we propose a computational steering framework for HPC environments that provides an innovative solution and easy-to-use platform, which allows users to connect and interact with running application(s) in real-time. This framework uses RealityGrid as the underlying steering library and adds several enhancements to the library to enable steering support for Blue Gene systems. Included in the scope of this project is the development of a scalable and efficient steering relay server that supports many-to-many connectivity between multiple steered applications and multiple steering clients. Steered applications can range from intermediate simulation and physical modeling applications to complex computational fluid dynamics (CFD) applications or advanced visualization applications. The Blue Gene supercomputer presents special challenges for remote access because the compute nodes reside on private networks. This thesis presents an implemented solution and demonstrates it on representative applications. Thorough implementation details and application enablement steps are also presented in this thesis to encourage direct usage of this framework.

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

Bosniak classification of renal cystic lesions according to multidetector computed tomography findings

International Nuclear Information System (INIS)

Miranda, Christiana Maia Nobre Rocha de; Padilha, Igor Gomes; Farias, Lucas de Padua Gomes de; Rocha, Milzi Sarmento da; Maranhao, Carol Pontes de Miranda; Santos, Carla Jotta Justo dos

2014-01-01

Renal cystic lesions are usually diagnosed in the radiologists' practice and therefore their characterization is crucial to determine the clinical approach to be adopted and prognosis. The Bosniak classification based on computed tomography findings has allowed for standardization and categorization of lesions in increasing order of malignancy (I, II, IIF, III and IV) in a simple and accurate way. The present iconographic essay developed with multidetector computed tomography images of selected cases from the archives of the authors' institution, is aimed at describing imaging findings that can help in the diagnosis of renal cysts. (author)

Renal lymphangiectasia: incidental finding at multislice computed tomography and literature review

Energy Technology Data Exchange (ETDEWEB)

Vasconcelos, Rodrigo Abdalla de; Pereira, Emanuelle Santiago [Hospital de Base do Distrito Federal (HBDF), Brasilia, DF (Brazil); Bauab Junior, Tufik [Instituto de Radiodiagnostico Rio Preto - Ultra-X and Hospital de Base de Faculdade de Medicina de Sao Jose do Rio Preto (Famerp), Sao Jose do Rio Preto, SP (Brazil); Valente, Rodolfo Silva [Hospital Universitario de Brasilia (HUB), Brasilia, DF (Brazil)

2012-05-15

Renal lymphangiectasia is a rare condition characterized by parapyelic and perirenal fluid collections, which may progress from asymptomatic condition to chronic renal failure. The present report describes a case of incidental computed tomography finding of bilateral lymphangiectasia in an asymptomatic patient, as well as the main imaging findings with a comprehensive literature review. (author)

Computed tomography findings in convergent strabismus fixus

International Nuclear Information System (INIS)

Ohta, Michitaka; Iwashige, Hiroyasu; Hayashi, Takao; Maruo, Toshio

1995-01-01

X-ray computed tomography (CT) of the eyeball and orbit revealed the cause of eye movement disorder in convergent strabismus fixus. The findings suggest that the disease can be diagnosed and treated at an early stage. Twelve cases of progressive esotropia with high myopia and 20 cases with normal visual acuity served as subjects in this study. The CT slice was parallel to the German horizontal plane, and the lens and medial and lateral rectus muscles were scanned. The average axial length of the affected eyes was significantly longer than in normal eyes. In progressive esotropia, the characteristic CT findings are an elongated eyeball, mechanical contact between the eyeball and lateral wall of the orbit, and a downward displacement of the lateral rectus muscle. Thus, it is reasonable to conclude that eye movement disorder in convergent strabismus fixus results from weakness of the lateral rectus muscle which has been displaced downward due to compression of the eyeball against the orbital wall. (author)

Normal postperative computed tomography findings after avariety of pancreatic surgeries

Energy Technology Data Exchange (ETDEWEB)

Seo, Ji Won; Hwang, Ho Kyoung; Lee, Min Wook; Kim, Ki Whang; Kang, Chang Moo; Kim, Myeong Jin; Chung, Yong Eun [Yonsei University College of Medicine, Seoul (Korea, Republic of)

2017-04-15

Pancreatic surgery remains the only curative treatment for pancreatic neoplasms, and plays an important role in the management of medically intractable diseases. Since the original Whipple operation in the 20th century, surgical techniques have advanced, resulting in decreased postoperative complications and better clinical outcomes. Normal postoperative imaging findings vary greatly depending on the surgical technique used. Radiologists are required to be familiar with the normal postoperative imaging findings, in order to distinguish from postoperative complications or tumor recurrence. In this study, we briefly review a variety of surgical techniques for the pancreas, and present the normal postoperative computed tomography findings.

Computed tomographic findings in manifesting carriers of Duchenne muscular dystrophy

NARCIS (Netherlands)

de Visser, M.; Verbeeten, B.

1985-01-01

Clinical and computed tomographic (CT) findings in 3 manifesting carriers of Duchenne muscular dystrophy are reported. CT proved to be an important adjunct to the clinical examination: in all our 3 cases a decrease in density was found in various non-paretic muscles

Arranging and finding folders and files on your Windows 7 computer

CERN Document Server

Steps, Studio Visual

2014-01-01

If you have lots of documents on your desk, it may prove to be impossible to find the document you are looking for. In order to easily find certain documents, they are often stored in a filing cabinet and arranged in a logical order. The folders on your computer serve the same purpose. They do not just contain files; they can also contain other folders. You can create an unlimited number of folders, and each folder can contain any number of subfolders and files. You can use Windows Explorer, also called the folder window, to work with the files and folders on your computer. You can copy, delete, move, find, and sort files, among other things. Or you can transfer files and folders to a USB stick, an external hard drive, a CD, DVD or Blu-Ray disk. In this practical guide we will show you how to use the folder window, and help you arrange your own files.

Computational Tools and Algorithms for Designing Customized Synthetic Genes

Energy Technology Data Exchange (ETDEWEB)

Gould, Nathan [Department of Computer Science, The College of New Jersey, Ewing, NJ (United States); Hendy, Oliver [Department of Biology, The College of New Jersey, Ewing, NJ (United States); Papamichail, Dimitris, E-mail: papamicd@tcnj.edu [Department of Computer Science, The College of New Jersey, Ewing, NJ (United States)

2014-10-06

Advances in DNA synthesis have enabled the construction of artificial genes, gene circuits, and genomes of bacterial scale. Freedom in de novo design of synthetic constructs provides significant power in studying the impact of mutations in sequence features, and verifying hypotheses on the functional information that is encoded in nucleic and amino acids. To aid this goal, a large number of software tools of variable sophistication have been implemented, enabling the design of synthetic genes for sequence optimization based on rationally defined properties. The first generation of tools dealt predominantly with singular objectives such as codon usage optimization and unique restriction site incorporation. Recent years have seen the emergence of sequence design tools that aim to evolve sequences toward combinations of objectives. The design of optimal protein-coding sequences adhering to multiple objectives is computationally hard, and most tools rely on heuristics to sample the vast sequence design space. In this review, we study some of the algorithmic issues behind gene optimization and the approaches that different tools have adopted to redesign genes and optimize desired coding features. We utilize test cases to demonstrate the efficiency of each approach, as well as identify their strengths and limitations.

Computational Tools and Algorithms for Designing Customized Synthetic Genes

International Nuclear Information System (INIS)

Gould, Nathan; Hendy, Oliver; Papamichail, Dimitris

2014-01-01

Advances in DNA synthesis have enabled the construction of artificial genes, gene circuits, and genomes of bacterial scale. Freedom in de novo design of synthetic constructs provides significant power in studying the impact of mutations in sequence features, and verifying hypotheses on the functional information that is encoded in nucleic and amino acids. To aid this goal, a large number of software tools of variable sophistication have been implemented, enabling the design of synthetic genes for sequence optimization based on rationally defined properties. The first generation of tools dealt predominantly with singular objectives such as codon usage optimization and unique restriction site incorporation. Recent years have seen the emergence of sequence design tools that aim to evolve sequences toward combinations of objectives. The design of optimal protein-coding sequences adhering to multiple objectives is computationally hard, and most tools rely on heuristics to sample the vast sequence design space. In this review, we study some of the algorithmic issues behind gene optimization and the approaches that different tools have adopted to redesign genes and optimize desired coding features. We utilize test cases to demonstrate the efficiency of each approach, as well as identify their strengths and limitations.

Computed tomographic findings of cerebral paragonimiasis

International Nuclear Information System (INIS)

Sung, Nak Kwan; Nam, Kyung Jin; Park, Churl Min; Eun, Chung Kie; Lee, Sun Wha

1983-01-01

Paragonimiasis is widely distributed in Far East and Southeast Asia, particularly in Korea. The central nervous system is the most frequent location for paragonimiasis outside the lungs. We analyzed the computed tomographic findings of 17 cases which were diagnosed pathologically and clinically as cerebral paragonimiasis. The results were as follows: 1. The ratio of male to female was 10 : 7 and about 88% of cases were under the age of 40 years. 2. The common locations of cerebral paragonimiasis were the occipital (12 cases) and temporal (11 cases) lobes. 3. Precontrast CT findings of cerebral paragonimiasis were low density with calcifications in 6 cases, low and isodensities in 4 cases, mixed densities in 3 cases, only low density in 2 cases and only calcification in 2 cases. Hydrocephalus (7 cases), mass effect (6 cases), atrophic change (6 cases) and cyst formation (3 cases) were associated. 4. The shape of calcifications in CT scan were soap-bubble or ring in 6 cases, nodular or oval in 6 cases, stipple in 4 cases and amorphous conglomerated in 2 cases. 5. The contrast -enhanced 8 cases were 5 ring or rim like, 2 nodular and 1 irregular enhancements, while 9 cases were not enhanced

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

DrugSig: A resource for computational drug repositioning utilizing gene expression signatures.

Directory of Open Access Journals (Sweden)

Hongyu Wu

Full Text Available Computational drug repositioning has been proved as an effective approach to develop new drug uses. However, currently existing strategies strongly rely on drug response gene signatures which scattered in separated or individual experimental data, and resulted in low efficient outputs. So, a fully drug response gene signatures database will be very helpful to these methods. We collected drug response microarray data and annotated related drug and targets information from public databases and scientific literature. By selecting top 500 up-regulated and down-regulated genes as drug signatures, we manually established the DrugSig database. Currently DrugSig contains more than 1300 drugs, 7000 microarray and 800 targets. Moreover, we developed the signature based and target based functions to aid drug repositioning. The constructed database can serve as a resource to quicken computational drug repositioning. Database URL: http://biotechlab.fudan.edu.cn/database/drugsig/.

Computed tomographic findings of progressive supranuclear palsy compared with Parkinson's disease

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Yuki, Nobuhiro; Sato, Shuzo; Yuasa, Tatsuhiko; Ito, Jusuke; Miyatake, Tadashi [Niigata Univ. (Japan). School of Dentistry

1990-10-01

We investigated computed tomographic (CT) films of 4 pathologically documented cases of progressive supranuclear palsy (PSP) in which the clinical presentations were atypical and compared the findings with those of 15 patients with Parkinson's disease (PD). Dilatation of the third ventricle, atrophy of the midbrain tegmentum, and enlargement of the interpeduncular cistern toward the aqueduct were found to be the characteristic findings in PSP. Thus, radiological findings can be useful when the differential diagnosis between PSP and PD is clinically difficult. (author).

Laryngotracheobronchial papillomatosis: findings on computed tomography scans of the chest

International Nuclear Information System (INIS)

Marchiori, Edson; Irion, Klaus Loureiro; Zanetti, Glaucia; Missrie, Israel; Sato, Juliana

2008-01-01

Objectives: To present the findings of computed tomography (CT) scans of the chest in patients with laryngotracheobronchial papillomatosis. Methods: We retrospectively analyzed CT scans of eight patients, five males and three females, ranging from 5 to 18 years of age with a mean age of 10.5 years. Images were independently reviewed by two radiologists. In discrepant cases, a consensus was reached. Results: The most common CT findings were intratracheal polypoid lesions and pulmonary nodules, many of which were cavitated. Conclusions: In patients with laryngotracheobronchial papillomatosis, the most common tomographic finding was the combination of intratracheal polypoid lesions and multiple pulmonary nodules, many of which were cavitated. (author)

Laryngotracheobronchial papillomatosis: findings on computed tomography scans of the chest

Energy Technology Data Exchange (ETDEWEB)

Marchiori, Edson [Universidade Federal Fluminense (UFF), Niteroi, RJ (Brazil). Dept. de Radiologia; Araujo Neto, Cesar de [Universidade Federal da Bahia (UFBA), Salvador, BA (Brazil). Dept. de Radiologia; Meirelles, Gustavo Souza Portes [Universidade Federal de Sao Paulo (UNIFESP-EPM), SP (Brazil); Irion, Klaus Loureiro [The Royal Liverpool University Hospital, Liverpool (United Kingdom); Zanetti, Glaucia [Faculdade de Medicina de Petropolis (FMP), RJ (Brazil); Missrie, Israel [Universidade Federal de Sao Paulo (UNIFESP-EPM), SP (Brazil). Dept. de Diagnostico por Imagem; Sato, Juliana [Universidade Federal de Sao Paulo (UNIFESP-EPM), SP (Brazil). Dept. de Otorrinolaringologia e Cirurgia de Cabeca e Pescoco

2008-12-15

Objectives: To present the findings of computed tomography (CT) scans of the chest in patients with laryngotracheobronchial papillomatosis. Methods: We retrospectively analyzed CT scans of eight patients, five males and three females, ranging from 5 to 18 years of age with a mean age of 10.5 years. Images were independently reviewed by two radiologists. In discrepant cases, a consensus was reached. Results: The most common CT findings were intratracheal polypoid lesions and pulmonary nodules, many of which were cavitated. Conclusions: In patients with laryngotracheobronchial papillomatosis, the most common tomographic finding was the combination of intratracheal polypoid lesions and multiple pulmonary nodules, many of which were cavitated. (author)

Computational prediction and experimental validation of Ciona intestinalis microRNA genes

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Pasquinelli Amy E

2007-11-01

Full Text Available Abstract Background This study reports the first collection of validated microRNA genes in the sea squirt, Ciona intestinalis. MicroRNAs are processed from hairpin precursors to ~22 nucleotide RNAs that base pair to target mRNAs and inhibit expression. As a member of the subphylum Urochordata (Tunicata whose larval form has a notochord, the sea squirt is situated at the emergence of vertebrates, and therefore may provide information about the evolution of molecular regulators of early development. Results In this study, computational methods were used to predict 14 microRNA gene families in Ciona intestinalis. The microRNA prediction algorithm utilizes configurable microRNA sequence conservation and stem-loop specificity parameters, grouping by miRNA family, and phylogenetic conservation to the related species, Ciona savignyi. The expression for 8, out of 9 attempted, of the putative microRNAs in the adult tissue of Ciona intestinalis was validated by Northern blot analyses. Additionally, a target prediction algorithm was implemented, which identified a high confidence list of 240 potential target genes. Over half of the predicted targets can be grouped into the gene ontology categories of metabolism, transport, regulation of transcription, and cell signaling. Conclusion The computational techniques implemented in this study can be applied to other organisms and serve to increase the understanding of the origins of non-coding RNAs, embryological and cellular developmental pathways, and the mechanisms for microRNA-controlled gene regulatory networks.

Ectopic pregnancy: pictorial essay focusing on computed tomography and magnetic resonance imaging findings

International Nuclear Information System (INIS)

Febronio, Eduardo Miguel; Rosas, George de Queiroz; D'Ippolito, Giuseppe

2012-01-01

The objective of the present study is to describe key computed tomography and magnetic resonance imaging findings in patients with acute abdominal pain caused by ectopic pregnancy. For this purpose, two radiologists consensually selected and analyzed computed tomography and magnetic resonance imaging studies performed in female patients with acute abdominal pain caused by proven ectopic pregnancy in the period between January 2010 and December 2011. The imaging diagnosis of ectopic pregnancy is usually obtained by ultrasonography, however, with the increasing use of computed tomography and magnetic resonance imaging in the assessment of patients with acute abdomen of gynecological origin it is necessary that the radiologist becomes familiar with the main findings observed at these diagnostic methods. (author)

Ectopic pregnancy: pictorial essay focusing on computed tomography and magnetic resonance imaging findings

Energy Technology Data Exchange (ETDEWEB)

Febronio, Eduardo Miguel; Rosas, George de Queiroz; D' Ippolito, Giuseppe [Escola Paulista de Medicina - Universidade Federal de Sao Paulo (EPM-Unifesp), Sao Paulo, SP (Brazil). Dept. of Imaging Diagnosis; Cardia, Patricia Prando, E-mail: giuseppe_dr@uol.com.br [Centro Radiologico Campinas, Campinas, SP (Brazil)

2012-09-15

The objective of the present study is to describe key computed tomography and magnetic resonance imaging findings in patients with acute abdominal pain caused by ectopic pregnancy. For this purpose, two radiologists consensually selected and analyzed computed tomography and magnetic resonance imaging studies performed in female patients with acute abdominal pain caused by proven ectopic pregnancy in the period between January 2010 and December 2011. The imaging diagnosis of ectopic pregnancy is usually obtained by ultrasonography, however, with the increasing use of computed tomography and magnetic resonance imaging in the assessment of patients with acute abdomen of gynecological origin it is necessary that the radiologist becomes familiar with the main findings observed at these diagnostic methods. (author)

GENE-counter: a computational pipeline for the analysis of RNA-Seq data for gene expression differences.

Science.gov (United States)

Cumbie, Jason S; Kimbrel, Jeffrey A; Di, Yanming; Schafer, Daniel W; Wilhelm, Larry J; Fox, Samuel E; Sullivan, Christopher M; Curzon, Aron D; Carrington, James C; Mockler, Todd C; Chang, Jeff H

2011-01-01

GENE-counter is a complete Perl-based computational pipeline for analyzing RNA-Sequencing (RNA-Seq) data for differential gene expression. In addition to its use in studying transcriptomes of eukaryotic model organisms, GENE-counter is applicable for prokaryotes and non-model organisms without an available genome reference sequence. For alignments, GENE-counter is configured for CASHX, Bowtie, and BWA, but an end user can use any Sequence Alignment/Map (SAM)-compliant program of preference. To analyze data for differential gene expression, GENE-counter can be run with any one of three statistics packages that are based on variations of the negative binomial distribution. The default method is a new and simple statistical test we developed based on an over-parameterized version of the negative binomial distribution. GENE-counter also includes three different methods for assessing differentially expressed features for enriched gene ontology (GO) terms. Results are transparent and data are systematically stored in a MySQL relational database to facilitate additional analyses as well as quality assessment. We used next generation sequencing to generate a small-scale RNA-Seq dataset derived from the heavily studied defense response of Arabidopsis thaliana and used GENE-counter to process the data. Collectively, the support from analysis of microarrays as well as the observed and substantial overlap in results from each of the three statistics packages demonstrates that GENE-counter is well suited for handling the unique characteristics of small sample sizes and high variability in gene counts.

GENE-counter: a computational pipeline for the analysis of RNA-Seq data for gene expression differences.

Directory of Open Access Journals (Sweden)

Jason S Cumbie

Full Text Available GENE-counter is a complete Perl-based computational pipeline for analyzing RNA-Sequencing (RNA-Seq data for differential gene expression. In addition to its use in studying transcriptomes of eukaryotic model organisms, GENE-counter is applicable for prokaryotes and non-model organisms without an available genome reference sequence. For alignments, GENE-counter is configured for CASHX, Bowtie, and BWA, but an end user can use any Sequence Alignment/Map (SAM-compliant program of preference. To analyze data for differential gene expression, GENE-counter can be run with any one of three statistics packages that are based on variations of the negative binomial distribution. The default method is a new and simple statistical test we developed based on an over-parameterized version of the negative binomial distribution. GENE-counter also includes three different methods for assessing differentially expressed features for enriched gene ontology (GO terms. Results are transparent and data are systematically stored in a MySQL relational database to facilitate additional analyses as well as quality assessment. We used next generation sequencing to generate a small-scale RNA-Seq dataset derived from the heavily studied defense response of Arabidopsis thaliana and used GENE-counter to process the data. Collectively, the support from analysis of microarrays as well as the observed and substantial overlap in results from each of the three statistics packages demonstrates that GENE-counter is well suited for handling the unique characteristics of small sample sizes and high variability in gene counts.

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

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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.

Methanol poisoning: brain computed tomography scan findings in four patients

International Nuclear Information System (INIS)

Patankar, T.; Prasad, S.; Rathod, K.; Bichile, L.; Karnad, D.

1999-01-01

Methanol, through its chief metabolite, formate, causes irreversible neurological damage. Methanol intoxication produces classic neuropathological changes and characteristic imaging findings. Computed tomography was performed on four patients who presented with a history of methanol poisoning. Prominent, hypodense lesions in the lentilform nuclei and peripheral white matter, sometimes with haemorrhage, were the characteristic imaging findings in the present patients. It was noted that the severity and extent of necrosis of the lentilform nuclei do not necessarily correlate with the clinical outcome. Copyright (1999) Blackwell Science Pty Ltd

Pulmonary high-resolution computed tomography findings in nephropathia epidemica

Energy Technology Data Exchange (ETDEWEB)

Paakkala, Antti, E-mail: antti.paakkala@pshp.fi [Medical Imaging Centre, Tampere University Hospital, 33521 Tampere (Finland); Jaervenpaeae, Ritva, E-mail: ritva.jarvenpaa@pshp.fi [Medical Imaging Centre, Tampere University Hospital, 33521 Tampere (Finland); Maekelae, Satu, E-mail: satu.marjo.makela@uta.fi [Department of Internal Medicine, Tampere University Hospital, 33521 Tampere (Finland); Medical School, University of Tampere, 33521 Tampere (Finland); Huhtala, Heini, E-mail: heini.huhtala@uta.fi [School of Public Health, University of Tampere, 33521 Tampere (Finland); Mustonen, Jukka, E-mail: jukka.mustonen@uta.fi [Department of Internal Medicine, Tampere University Hospital, 33521 Tampere (Finland); Medical School, University of Tampere, 33521 Tampere (Finland)

2012-08-15

Purpose: To evaluate lung high-resolution computed tomography (HRCT) findings in patients with Puumala hantavirus-induced nephropathia epidemica (NE), and to determine if these findings correspond to chest radiograph findings. Materials and methods: HRCT findings and clinical course were studied in 13 hospital-treated NE patients. Chest radiograph findings were studied in 12 of them. Results: Twelve patients (92%) showed lung parenchymal abnormalities in HRCT, while only 8 had changes in their chest radiography. Atelectasis, pleural effusion, intralobular and interlobular septal thickening were the most common HRCT findings. Ground-glass opacification (GGO) was seen in 4 and hilar and mediastinal lymphadenopathy in 3 patients. Atelectasis and pleural effusion were also mostly seen in chest radiographs, other findings only in HRCT. Conclusion: Almost every NE patient showed lung parenchymal abnormalities in HRCT. The most common findings of lung involvement in NE can be defined as accumulation of pleural fluid and atelectasis and intralobular and interlobular septal thickening, most profusely in the lower parts of the lung. As a novel finding, lymphadenopathy was seen in a minority, probably related to capillary leakage and overall fluid overload. Pleural effusion is not the prominent feature in other viral pneumonias, whereas intralobular and interlobular septal thickening are characteristic of other viral pulmonary infections as well. Lung parenchymal findings in HRCT can thus be taken not to be disease-specific in NE and HRCT is useful only for scientific purposes.

A new computational method for the detection of horizontal gene transfer events.

Science.gov (United States)

Tsirigos, Aristotelis; Rigoutsos, Isidore

2005-01-01

In recent years, the increase in the amounts of available genomic data has made it easier to appreciate the extent by which organisms increase their genetic diversity through horizontally transferred genetic material. Such transfers have the potential to give rise to extremely dynamic genomes where a significant proportion of their coding DNA has been contributed by external sources. Because of the impact of these horizontal transfers on the ecological and pathogenic character of the recipient organisms, methods are continuously sought that are able to computationally determine which of the genes of a given genome are products of transfer events. In this paper, we introduce and discuss a novel computational method for identifying horizontal transfers that relies on a gene's nucleotide composition and obviates the need for knowledge of codon boundaries. In addition to being applicable to individual genes, the method can be easily extended to the case of clusters of horizontally transferred genes. With the help of an extensive and carefully designed set of experiments on 123 archaeal and bacterial genomes, we demonstrate that the new method exhibits significant improvement in sensitivity when compared to previously published approaches. In fact, it achieves an average relative improvement across genomes of between 11 and 41% compared to the Codon Adaptation Index method in distinguishing native from foreign genes. Our method's horizontal gene transfer predictions for 123 microbial genomes are available online at http://cbcsrv.watson.ibm.com/HGT/.

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.

Computed tomographic findings of cerebral arterial ectasia

International Nuclear Information System (INIS)

Choi, Woo Suk; Ko, Young Ho; Lim, Jae Hoon

1987-01-01

The computed tomographic findings of cerebral arterial ectasia in 8 patients, of which 5 cases were angiographically documented, are reported. The ecstatic arteries, located predominantly in the suprasellar and interpeduncular cisterns, appeared as serpignous, tubular structures on the unenhanced scan. The enhanced CT scan demonstrated dense, sharply defined, homogeneous intraluminal enhancement. Until recently, the diagnosis of cerebral arterial ectasia was usually established by angiography. With introduction of CT it has become possible to noninvasively identify and characterize this vascular disorder and its associated intracranial complications. The vertebrobasilar dolichoectasia may be diagnosed by CT as an extra-axial lesion in the cerebellopontine angle. It enhances in a tubular fashion after intravenous injection of contrast.

Computational Tools and Algorithms for Designing Customized Synthetic Genes

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Nathan eGould

2014-10-01

Full Text Available Advances in DNA synthesis have enabled the construction of artificial genes, gene circuits, and genomes of bacterial scale. Freedom in de-novo design of synthetic constructs provides significant power in studying the impact of mutations in sequence features, and verifying hypotheses on the functional information that is encoded in nucleic and amino acids. To aid this goal, a large number of software tools of variable sophistication have been implemented, enabling the design of synthetic genes for sequence optimization based on rationally defined properties. The first generation of tools dealt predominantly with singular objectives such as codon usage optimization and unique restriction site incorporation. Recent years have seen the emergence of sequence design tools that aim to evolve sequences toward combinations of objectives. The design of optimal protein coding sequences adhering to multiple objectives is computationally hard, and most tools rely on heuristics to sample the vast sequence design space. In this review we study some of the algorithmic issues behind gene optimization and the approaches that different tools have adopted to redesign genes and optimize desired coding features. We utilize test cases to demonstrate the efficiency of each approach, as well as identify their strengths and limitations.

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

A hybrid computational method for the discovery of novel reproduction-related genes.

Science.gov (United States)

Chen, Lei; Chu, Chen; Kong, Xiangyin; Huang, Guohua; Huang, Tao; Cai, Yu-Dong

2015-01-01

Uncovering the molecular mechanisms underlying reproduction is of great importance to infertility treatment and to the generation of healthy offspring. In this study, we discovered novel reproduction-related genes with a hybrid computational method, integrating three different types of method, which offered new clues for further reproduction research. This method was first executed on a weighted graph, constructed based on known protein-protein interactions, to search the shortest paths connecting any two known reproduction-related genes. Genes occurring in these paths were deemed to have a special relationship with reproduction. These newly discovered genes were filtered with a randomization test. Then, the remaining genes were further selected according to their associations with known reproduction-related genes measured by protein-protein interaction score and alignment score obtained by BLAST. The in-depth analysis of the high confidence novel reproduction genes revealed hidden mechanisms of reproduction and provided guidelines for further experimental validations.

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.

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

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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.

Computed tomographic findings in acute superior mesenteric arterial occlusion

International Nuclear Information System (INIS)

Kuwabara, Yoshiyuki; Kataoka, Makoto; Kureyama, Yasuyuki; Iwata, Hiroshi; Kashima, Taketoshi; Sinoda, Noriyuki; Sato, Atsushi; Hattori, Kohji; Masaoka, Akira

1993-01-01

In this study computed tomography (CT) findings were examined in 6 cases of acute superior mesenteric arterial (SMA) occlusion. With simple CT, occluded site of SMA revealed a slightly high density in 2 cases, while no findings were noted in other cases. Slightly dilated multiple loops of the intestine were confirmed in 3 cases, but no particular changes in the intestinal wall were found. As other findings, ascites and air in the portal vein were found in each one case. Contrast enhanced CT was conducted in 2 out of the 6 cases, and occluded site was visualized as spots in one case but no findings were noted in the other. The contrast enhancement effect in vessels in SMA region was examined from its root to the peripheral in this order, and the 2 cases showed common findings that the contrast enhancement effect abruptly disappeared at a point in vessels in SMA region (discontinuance). The point was consistent with the occluded site on angiography. These findings indicate that simple CT alone is difficult to offer correct diagnosis of SMA occlusion, but contrast enhanced CT is able to visualize the SMA occlusion as a discontinuance picture. It is thought that contrast enhanced CT can be a useful procedure for early diagnosis of SMA occlusion. (author)

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

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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

The findings of noninvasive cardiovascular diagnosis with multihelical computed tomography

International Nuclear Information System (INIS)

Fed'kyiv, S.V.

2009-01-01

The patients aged of 25-82 underwent the multihelical computed tomography, 508 of them with coronary artery disease and 109 are under control. The findings of MHCT-analysis of the coronary arteries at their atherosclerotic involvement were presented with the use of quantitative assessment of coronary artery calcinosis according to Agatston's technique and noninvasive MHCT-coronagraphy.

Computer finds ore

Science.gov (United States)

Bell, Peter M.

Artificial intelligence techniques are being used for the first time to evaluate geophysical, geochemical, and geologic data and theory in order to locate ore deposits. After several years of development, an intelligent computer code has been formulated and applied to the Mount Tolman area in Washington state. In a project funded by the United States Geological Survey and the National Science Foundation a set of computer programs, under the general title Prospector, was used successfully to locate a previously unknown ore-grade porphyry molybdenum deposit in the vicinity of Mount Tolman (Science, Sept. 3, 1982).The general area of the deposit had been known to contain exposures of porphyry mineralization. Between 1964 and 1978, exploration surveys had been run by the Bear Creek Mining Company, and later exploration was done in the area by the Amax Corporation. Some of the geophysical data and geochemical and other prospecting surveys were incorporated into the programs, and mine exploration specialists contributed to a set of rules for Prospector. The rules were encoded as ‘inference networks’ to form the ‘expert system’ on which the artificial intelligence codes were based. The molybdenum ore deposit discovered by the test is large, located subsurface, and has an areal extent of more than 18 km2.

Computed tomography findings of early abdominal postoperative complications

International Nuclear Information System (INIS)

Zissin, R.; Osadchy, A.; Gayer, G.

2007-01-01

Various surgical approaches are used for different abdominal pathological conditions. Postoperative complications occur not infrequently and vary according to the type of the surgery and the clinical context. Nowadays, multidetector computed tomography (MDCT) provides superb anatomic detail and diagnostic accuracy for various intraabdominal pathological processes, even if clinically unsuspected, and it thus has become an essential diagnostic tool for evaluating postoperative insults. Other advantages of abdominal MDCT include its accessibility and its speed, which allow scanning of uncooperative, marginally stable patients. Computed tomography (CT)-guided percutaneous (PC) drainage of postoperative collections is another advantage of CT. Therefore, although CT requires transportation of a critically ill, postoperative patient, it is recommended in any suspicious clinical setting because several conditions require prompt management and a correct diagnosis is crucial. In assessing a patient for suspected postoperative complications, several points should be taken into consideration, including the relevant clinical and laboratory data, the surgical findings, the type of the surgery, the time elapsed since surgery, and the operative technique (either open laparotomy of laparoscopic procedure). (author)

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

Computed tomography findings in cases of Minamata disease

International Nuclear Information System (INIS)

Shirakawa, Kenichi; Hirota, Koichi; Tsubaki, Tadao; Tanimura, Kenichi; Yamamoto, Tsuneo.

1979-01-01

Computed tomography (CT) was used to evaluate 57 patients with Minamata disease (methylmercury poisoning); it was proved to be an objective and practical screening procedure. A typical patient who presented an acute onset of concentric constriction of visual fields and cerebellar ataxia showed a low-density area in both occipital regions; cerebellar atrophy and enlarged cerebral cortical sulci. On the other hand, the majority of patients who presented a chronic onset, with only a mild concentric constriction of visual fields, dysdiadochokinesis, and sensory disturbance showed only a questionable or a mild cerebellar atrophy. An enlarged paracerebellar space in mild cerebellar atrophy was easily identified at the pontine angle cistern, the paravermian cistern, and the triangular space of the rectal sinus in the coronal section on an enhanced CT scan. These findings were compatible with pathological findings of mild cases of Minamata disease. The correlation of dysdiadochokinesis with the degree of cerebellar atrophy was demonstrated. (author)

Correlation of computed tomographic and magnetic resonance imaging findings in cerebral infartion

International Nuclear Information System (INIS)

Komatsubara, Chizuko; Chuda, Moriyoshi; Taka, Toshihiko

1989-01-01

We evaluated neurological findings in 75 patients of cerebral infarction, and correlated computed tomographic (CT) and magnetic resonance imaging (MRI) findings. MRI was found to have the advantage when the lesion were multiple, or in the posterior fossa. MRI demonstrates the anatomical details, and lacks the bony artifact, so it is an excellent method for identification of cerebral infarction. (author)

Computed tomography findings after radiofrequency ablation in locally advanced pancreatic cancer

NARCIS (Netherlands)

Rombouts, Steffi J. E.; Derksen, Tyche C.; Nio, Chung Y.; van Hillegersberg, Richard; van Santvoort, Hjalmar C.; Walma, Marieke S.; Molenaar, Izaak Q.; van Leeuwen, Maarten S.

2018-01-01

The purpose of the study was to provide a systematic evaluation of the computed tomography(CT) findings after radiofrequency ablation (RFA) in locally advanced pancreatic cancer(LAPC). Eighteen patients with intra-operative RFA-treated LAPC were included in a prospective case series. All CT-scans

Progress and challenges in the computational prediction of gene function using networks [v1; ref status: indexed, http://f1000r.es/SqmJUM

Directory of Open Access Journals (Sweden)

Paul Pavlidis

2012-09-01

Full Text Available In this opinion piece, we attempt to unify recent arguments we have made that serious confounds affect the use of network data to predict and characterize gene function. The development of computational approaches to determine gene function is a major strand of computational genomics research. However, progress beyond using BLAST to transfer annotations has been surprisingly slow. We have previously argued that a large part of the reported success in using "guilt by association" in network data is due to the tendency of methods to simply assign new functions to already well-annotated genes. While such predictions will tend to be correct, they are generic; it is true, but not very helpful, that a gene with many functions is more likely to have any function. We have also presented evidence that much of the remaining performance in cross-validation cannot be usefully generalized to new predictions, making progressive improvement in analysis difficult to engineer. Here we summarize our findings about how these problems will affect network analysis, discuss some ongoing responses within the field to these issues, and consolidate some recommendations and speculation, which we hope will modestly increase the reliability and specificity of gene function prediction.

Computational design and application of endogenous promoters for transcriptionally targeted gene therapy for rheumatoid arthritis.

NARCIS (Netherlands)

Geurts, J.; Joosten, L.A.B.; Takahashi, N.; Arntz, O.J.; Gluck, A.; Bennink, M.B.; Berg, W.B. van den; Loo, F.A.J. van de

2009-01-01

The promoter regions of genes that are differentially regulated in the synovial membrane during the course of rheumatoid arthritis (RA) represent attractive candidates for application in transcriptionally targeted gene therapy. In this study, we applied an unbiased computational approach to define

Wegener's granulomatosis: chest computed tomography findings; Granulomatose de Wegener: aspectos na tomografia computadorizada de torax

Energy Technology Data Exchange (ETDEWEB)

Monteiro, Evelise de Azevedo; Marchiori, Edson; Martins, Erick Malheiro Leoncio [Universidade Federal Fluminense, Niteroi, RJ (Brazil). Dept. de Radiologia]. E-mail: edmarchiori@zipmail.com.br; Souza Junior, Arthur Soares [Faculdade de Medicina de Sao Jose do Rio Preto (FAMERP), SP (Brazil). Hospital de Base; Cerqueira, Elza Maria F.P. de [Universidade Estadual de Campinas, SP (Brazil). Faculdade de Ciencias Medicas. Dept. de Radiologia; Irion, Klaus L. [Pavilhao Pereira Filho, Porto Alegre, RS (Brazil); Araujo Neto, Cesar de [Bahia Univ., Salvador, BA (Brazil). Dept. de Radiologia; Souza, Rodrigo Azeredo de [Universidade Federal, Rio de Janeiro, RJ (Brazil). Faculdade de Medicina. Dept. de Radiologia

2003-03-01

Wegeners granulomatosis is an inflammatory systemic necrotizing idiopathic vasculitis affecting mainly small vessels. In this paper we analyzed the computed tomography findings of seven patients with Wegeners granulomatosis. The most common findings were masses and nodules (71.4%), areas of ground glass attenuation (57.1%), consolidation (42.8%), halo sign (42.8%), cavitation (42.8%), interlobular septa thickening (14.2%), bronchial wall thickening (14.2%) and pleural effusion (14.2%). Although radiological findings are mostly nonspecific, computed tomography and particularly high-resolution computed tomography are important tools in the evaluation of disease activity when evaluated in association with bronchoscopy findings and clinical data. (author)

Computed tomographic findings of liver injury in adults

International Nuclear Information System (INIS)

Ha, Deok Gi; Lee, Hyeon Kyeong; Lee, Won Jae; Oh, Yeon Hee; Lee, Sung Hee; Yun, Jee Yeong; Lee, Tae Woo; Lee, Sung Woo; Park, Soo Soung

1994-01-01

We studied to compare computed tomographic(CT) findings of liver injury with management method in adults and, moreover, to present the CT basis for the management. We retrospectively reviewed CT scans of 43 adults diagnosed as liver injury during a 66 month period. Thirty-eight patients were hemodynamically stable. Thirty-two of them were managed conservatively, whereas six managed operatively. Five unstable patients underwent emergency operation. We classified CT findings according to the severity of liver injuries(ie, hematoma, laceration, and periportal tracking) and hemoperitoneum, ranging from grade 1 to 5 and from 0 to 3 +. respectively. Thus, we compared the CT classifications with their management(ie, operation rate), especially hemodynamically stable patients. Operation rates of all patients and hemodynamically stable patients were 26% and 16%, respectively. Operation rate at each grade of liver injury was low, especially in hemodynamically stable, despite relatively high operation rate in grade 4. Operation rate of 3+ homoperitoneum was 100%, including hemodynamically stable patients, in contrast to otherwise low operation rate of others. Most liver injury in adults, including grade 4, were managed conservatively, especially hemodynamically stable. Though large amount of hemoperitoneum(ie, 3+) required operation, most hemooperitoeum were managed conservatively. Thus, CT findings of liver injury is helpful in the decision for the management method

Heterogeneous High Throughput Scientific Computing with APM X-Gene and Intel Xeon Phi

CERN Document Server

Abdurachmanov, David; Elmer, Peter; Eulisse, Giulio; Knight, Robert; Muzaffar, Shahzad

2014-01-01

Electrical power requirements will be a constraint on the future growth of Distributed High Throughput Computing (DHTC) as used by High Energy Physics. Performance-per-watt is a critical metric for the evaluation of computer architectures for cost- efficient computing. Additionally, future performance growth will come from heterogeneous, many-core, and high computing density platforms with specialized processors. In this paper, we examine the Intel Xeon Phi Many Integrated Cores (MIC) co-processor and Applied Micro X-Gene ARMv8 64-bit low-power server system-on-a-chip (SoC) solutions for scientific computing applications. We report our experience on software porting, performance and energy efficiency and evaluate the potential for use of such technologies in the context of distributed computing systems such as the Worldwide LHC Computing Grid (WLCG).

Heterogeneous High Throughput Scientific Computing with APM X-Gene and Intel Xeon Phi

Science.gov (United States)

Abdurachmanov, David; Bockelman, Brian; Elmer, Peter; Eulisse, Giulio; Knight, Robert; Muzaffar, Shahzad

2015-05-01

Electrical power requirements will be a constraint on the future growth of Distributed High Throughput Computing (DHTC) as used by High Energy Physics. Performance-per-watt is a critical metric for the evaluation of computer architectures for cost- efficient computing. Additionally, future performance growth will come from heterogeneous, many-core, and high computing density platforms with specialized processors. In this paper, we examine the Intel Xeon Phi Many Integrated Cores (MIC) co-processor and Applied Micro X-Gene ARMv8 64-bit low-power server system-on-a-chip (SoC) solutions for scientific computing applications. We report our experience on software porting, performance and energy efficiency and evaluate the potential for use of such technologies in the context of distributed computing systems such as the Worldwide LHC Computing Grid (WLCG).

Heterogeneous High Throughput Scientific Computing with APM X-Gene and Intel Xeon Phi

International Nuclear Information System (INIS)

Abdurachmanov, David; Bockelman, Brian; Elmer, Peter; Eulisse, Giulio; Muzaffar, Shahzad; Knight, Robert

2015-01-01

Electrical power requirements will be a constraint on the future growth of Distributed High Throughput Computing (DHTC) as used by High Energy Physics. Performance-per-watt is a critical metric for the evaluation of computer architectures for cost- efficient computing. Additionally, future performance growth will come from heterogeneous, many-core, and high computing density platforms with specialized processors. In this paper, we examine the Intel Xeon Phi Many Integrated Cores (MIC) co-processor and Applied Micro X-Gene ARMv8 64-bit low-power server system-on-a-chip (SoC) solutions for scientific computing applications. We report our experience on software porting, performance and energy efficiency and evaluate the potential for use of such technologies in the context of distributed computing systems such as the Worldwide LHC Computing Grid (WLCG). (paper)

Acute pelvic inflammatory disease: pictorial essay focused on computed tomography and magnetic resonance imaging findings

Energy Technology Data Exchange (ETDEWEB)

Febronio, Eduardo Miguel; Rosas, George de Queiroz; D' Ippolito, Giuseppe, E-mail: giuseppe_dr@uol.com.br [Department of Imaging Diagnosis, Escola Paulista de Medicina - Universidade Federal de Sao Paulo (EPMUnifesp), Sao Paulo, SP (Brazil)

2012-11-15

The present study was aimed at describing key computed tomography and magnetic resonance imaging findings in patients with acute abdominal pain derived from pelvic inflammatory disease. Two radiologists consensually selected and analyzed computed tomography and magnetic resonance imaging studies performed between January 2010 and December 2011 in patients with proven pelvic inflammatory disease leading to presentation of acute abdomen. Main findings included presence of intracavitary fluid collections, anomalous enhancement of the pelvic excavation and densification of adnexal fat planes. Pelvic inflammatory disease is one of the leading causes of abdominal pain in women of childbearing age and it has been increasingly been diagnosed by means of computed tomography and magnetic resonance imaging supplementing the role of ultrasonography. It is crucial that radiologists become familiar with the main sectional imaging findings in the diagnosis of this common cause of acute abdomen (author)

Unusual computed tomography findings and complications in acute appendicitis

International Nuclear Information System (INIS)

Palacio, Glaucia Andrade e Silva; D'Ippolito, Giuseppe

2003-01-01

The objective of this article is to describe and illustrate unusual computed tomography (CT) findings in patients with acute appendicitis. We reviewed the charts of 200 patients with clinical suspicion of acute appendicitis who were submitted to abdominal CT before surgery. Patients with unusual presentation or complications were selected for illustrating the main CT findings. Unusual complications of acute appendicitis were related to anomalous position of the appendix, contiguity to intraperitoneal organs such as the liver, gall bladder, annexes and the bladder and continuous use of anti inflammatory or antibiotics during the diagnostic process. We concluded that CT is a useful diagnostic tool in patients with complicated or unusual presentation acute appendicitis. The first step towards diagnosis in these cases i to have in mind the hypothesis of appendicitis in patients with acute abdominal pain. (author)

[The different manifestations of pulmonary aspergillosis: multidetector computed tomography findings].

Science.gov (United States)

Koren Fernández, L; Alonso Charterina, S; Alcalá-Galiano Rubio, A; Sánchez Nistal, M A

2014-01-01

Pulmonary aspergillosis is a fungal infection usually caused by inhaling Aspergillus fumigatus spores. However, when we talk about aspergillosis, we normally refer to the spectrum of clinical and radiological findings that depend directly on the patient's immune status, on the prior existence of lung disease, and on the virulence of the infective organism. There are four types of pulmonary aspergillosis (aspergilloma, allergic bronchopulmonary aspergillosis, chronic necrotizing pulmonary aspergillosis, and invasive aspergillosis), and each type has its own distinct radiologic findings. We review the signs of pulmonary aspergillosis on multidetector computed tomography and we correlate them with patients' symptoms and immune responses. Likewise, we discuss the differential diagnoses. Copyright © 2013 SERAM. Published by Elsevier Espana. All rights reserved.

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

Computed tomographic findings of hepatocellular carcinoma

Energy Technology Data Exchange (ETDEWEB)

Eun, Chung Kie [Kyung Hee University College of Medicine, Seoul (Korea, Republic of)

1982-09-15

It is well known that CT is very useful in the evaluation of hepatocellular carcinoma. The computed tomographic findings of 56 patients diagnosed as hepatocellular carcinoma were reviewed and analyzed. The results were as follows: 1. The male to female ratio was 3 : 1 and the age ranged from 31 to 73 years with average age of 54 years. 2. Alpha-fetoprotein was positive in 19 out of 38 cases (50%). HBsAg was positive in 8 out of 33 cases (24%). 3. All lesions were seen as areas of low density except 1 case (0%) of isodensity, and 40 cases (72%) appeared to be solitary while 15 (26%) were multifocal. The low density was homogenous in 13 cases (24%) and inhomogenous in 42 cases (76%), and 18 cases out of 42 cases inhomogenous low density showed peripheal and/or central nodular enhancement. The additional findings were contour changes in 37 cases (66%), metastasis in 35 cases (63%), splenomegaly in 23 cases (42%) and ascities in 22 cases (39%). 4. In postcontrast scans, 41 cases (80%) out of 51 cases showed the change of density after contrast infusion. The presence and extent of tumors were better seen after contrast infusion in 30 cases (59%), better seen before contrast infusion in 11 cases (21%) and no significant difference before and after contrast infusion in 10 cases (20%). 5. The sites of involved lobe were right lobe in 38 cases (68%), left lobe in 5 cases (9%) and both lobes in 13 cases (23%). 6. 35 cases (63%) showed evidence of metastasis to regional lymph nodes, organ or tissues.

Computed tomographic findings of cerebral paragonimiasis

International Nuclear Information System (INIS)

Bae, Weon Tae; Jung, Min Ki; Kang, Heoung Keun; Chung, Hyon De

1988-01-01

Authors analyzed the computed tomographic (CT) findings of 19 cases pathologically and clinically proven cerebral paragonimiasis that were performed at Chonnam University Hospital from April 1983 through March 1987. The results were as follows: 1. Male to female ratio was 15:4 and the most prevalent age group was 3rd decade (7 cases). The common symptoms were epileptic seizure (16 cases) and headache (12 cases). 2. The multiplicity of cerebral paragonimiasis was 7 of 19 cases and the distributions of lesion were occipital (11 cases), temporal (6 cases), frontal (5 cases) and parietal (5 cases) lobe. 3. The calcification on CT scan were single (7 cases) or multiple (7 cases) and the shape of calcification were nodular (10 cases), soap babble of ring (8 cases), and stippled (6 cases). The pattern of contrast enhancement were ring (5 cases) or nodular (1 case), and along the basal cistern (1 case with arachnoiditis). 4. 12 out of 13 cases, had long clinical symptoms over 3 years with calcifications, could be analyzed according to Valentine's vascular territory; 6 cases in PCA territory, 3 in MCA and 3 in ACA. 5. CT findings were noted according to the duration of symptoms; 5 cases, had symptoms less than 1 year, showed abscess (5 cases) and arachnoiditis (1 case) with brain edema, mass effect, hydrocephalus and contrast enhancement but no calcification in all. One case, had symptom of 1 year and 2 months, showed partially calcified granulomatous lesion with perifocal edema and contrast enhancement, 13 cases, had symptoms over 3 years, showed multiple calcification with brain atrophy (10 cases), but no contrast enhancement in all cases.

Congenital anomalies of the pulmonary arteries: spectrum of findings on computed tomography.

Science.gov (United States)

Bueno, J; Flors, L; Mejía, M

Congenital anomalies of the pulmonary arteries are uncommon. They can occur in isolation or in association with congenital heart defects. Isolated congenital anomalies remain undiscovered until they are reported as incidental findings on imaging tests, usually not until adolescence. We review the embryological development and normal anatomy of the pulmonary arteries as well as the spectrum of computed tomography findings for various congenital anomalies: unilateral interruption of the pulmonary artery, anomalous origin of the left pulmonary artery (pulmonary artery sling), idiopathic aneurysm of the pulmonary artery, and other anomalies associated with congenital heart defects. Congenital anomalies of the pulmonary arteries represent a diagnostic challenge for clinicians and radiologists. Computed tomography is useful for their diagnosis, and general radiologists need to be familiar with their imaging appearance because they are often discovered incidentally. Copyright © 2016 SERAM. Publicado por Elsevier España, S.L.U. All rights reserved.

Neurocysticercosis: Imaging Findings in Computed Tomography. Review of Literature and Two Case Reports

International Nuclear Information System (INIS)

Alejandra Borbon Garzon; Alvaro Jose Perez; Veronica Pinto Schmidt

2008-01-01

Neurocysticercosis is a central nervous system parasitic infection caused by Taenia Solium whose clinical manifestations include seizures in 50-70% of patients, headache, intracranial hypertension and focal neurological deficits. Objective: To review the literature and to present imaging studies of two patients with the disease and classify its findings according to the pathologic stage. Methods: Review of literature and imaging of two patients with parenchymal neurocysticercosis using cranial computed tomography which showed cystic lesions at the gray-white junction associated with ring enhancement and some of them with surrounding edema; besides calcified granulomatous lesions. The documented findings represent the imaging spectrum of different parenchymal stages of neurocysticercosis. Conclusions: The cranial computed tomography is very helpful in diagnosis and monitoring neurocysticercosis.

Incidental findings on cone beam computed tomography scans in cleft lip and palate patients

NARCIS (Netherlands)

Kuijpers, Mette A. R.; Pazera, Andrzej; Admiraal, Ronald J.; Berge, Stefaan J.; Vissink, Arjan; Pazera, Pawel

Cone beam computed tomography (CBCT) is frequently used in treatment planning for alveolar bone grafting (ABG) and orthognathic surgery in patients with cleft lip and palate (CLP). CBCT images may depict coincident findings. The aim of this study was to assess the prevalence of incidental findings

Computed tomography of delayed encephalopathy of acute carbon monoxide poisoning - correlation with clinical findings -

International Nuclear Information System (INIS)

Suh, Chang Hae; Chung, Sung Hoon; Choo, In Wook; Chang, Kee Hyun

1986-01-01

Cerebral computed tomography (CT) findings were described in twenty-six cases with the late sequelae of acute carbon monoxide poisoning and were computed with the neurological symptoms and signs. The CT findings include symmetrical periventricular white matter low density in five cases, globes pallidus low density in six cases, ventricular dilatation in seven cases, ventricular dilatation and sulci widening in three cases, and normal findings in ten cases. Only one case showed low densities in both periventricular white matter and globes pallidus. Late sequelae of the interval from of carbon monoxide poisoning were clinically categorized as cortical dysfunction, parkinsonian feature, and cerebella dysfunction. The severity of the clinical symptoms and signs of neurological sequelae is generally correlated with presence and multiplicity of abnormal brain CT findings. But of fourteen cases showing the parkinsonian feature, only five cases had low density of globes pallidus in brain CT. Another case showing small unilateral low density of globes pallidus had no parkinsonian feature but showed mild cortical dysfunction.

Stratified computed tomography findings improve diagnostic accuracy for appendicitis

Science.gov (United States)

Park, Geon; Lee, Sang Chul; Choi, Byung-Jo; Kim, Say-June

2014-01-01

AIM: To improve the diagnostic accuracy in patients with symptoms and signs of appendicitis, but without confirmative computed tomography (CT) findings. METHODS: We retrospectively reviewed the database of 224 patients who had been operated on for the suspicion of appendicitis, but whose CT findings were negative or equivocal for appendicitis. The patient population was divided into two groups: a pathologically proven appendicitis group (n = 177) and a non-appendicitis group (n = 47). The CT images of these patients were re-evaluated according to the characteristic CT features as described in the literature. The re-evaluations and baseline characteristics of the two groups were compared. RESULTS: The two groups showed significant differences with respect to appendiceal diameter, and the presence of periappendiceal fat stranding and intraluminal air in the appendix. A larger proportion of patients in the appendicitis group showed distended appendices larger than 6.0 mm (66.3% vs 37.0%; P appendicitis group. Furthermore, the presence of two or more of these factors increased the odds ratio to 6.8 times higher than baseline (95%CI: 3.013-15.454; P appendicitis with equivocal CT findings. PMID:25320531

Computed tomography and (18)F-fluorodeoxyglucose positron emission tomography/computed tomography findings in adrenal candidiasis and histoplasmosis: two cases.

Science.gov (United States)

Altinmakas, Emre; Guo, Ming; Kundu, Uma R; Habra, Mouhammed Amir; Ng, Chaan

2015-01-01

We report the contrast-enhanced computed tomography (CT) and (18)F-fluorodeoxyglucose positron emission tomography findings in adrenal histoplasmosis and candidiasis. Both demonstrated bilateral hypermetabolic heterogeneous adrenal masses with limited wash-out on delayed CT. Adrenal candidiasis has not been previously reported, nor have the CT wash-out findings in either infection. The adrenal imaging findings are indistinguishable from malignancy, which is more common; but in this setting, physicians should be alert to the differential diagnosis of fungal infections, since it can be equally deadly. Published by Elsevier Inc.

Non-cardiac findings on coronary computed tomography and magnetic resonance imaging

International Nuclear Information System (INIS)

Dewey, Marc; Schnapauff, Dirk; Teige, Florian; Hamm, Bernd

2007-01-01

Both multislice computed tomography (CT) and magnetic resonance imaging (MRI) are emerging as methods to detect coronary artery stenoses and assess cardiac function and morphology. Non-cardiac structures are also amenable to assessment by these non-invasive tests. We investigated the rate of significant and insignificant non-cardiac findings using CT and MRI. A total of 108 consecutive patients suspected of having coronary artery disease and without contraindications to CT and MRI were included in this study. Significant non-cardiac findings were defined as findings that required additional clinical or radiological follow-up. CT and MR images were read independently in a blinded fashion. CT yielded five significant non-cardiac findings in five patients (5%). These included a pulmonary embolism, large pleural effusions, sarcoid, a large hiatal hernia, and a pulmonary nodule (>1.0 cm). Two of these significant non-cardiac findings were also seen on MRI (pleural effusions and sarcoid, 2%). Insignificant non-cardiac findings were more frequent than significant findings on both CT (n = 11, 10%) and MRI (n = 7, 6%). Incidental non-cardiac findings on CT and MRI of the coronary arteries are common, which is why images should be analyzed by radiologists to ensure that important findings are not missed and unnecessary follow-up examinations are avoided. (orig.)

Non-cardiac findings on coronary computed tomography and magnetic resonance imaging

Energy Technology Data Exchange (ETDEWEB)

Dewey, Marc; Schnapauff, Dirk; Teige, Florian; Hamm, Bernd [Charite-Universitaetsmedizin Berlin, Humboldt-Universitaet zu Berlin, Department of Radiology, Chariteplatz 1, P.O. Box 10098, Berlin (Germany)

2007-08-15

Both multislice computed tomography (CT) and magnetic resonance imaging (MRI) are emerging as methods to detect coronary artery stenoses and assess cardiac function and morphology. Non-cardiac structures are also amenable to assessment by these non-invasive tests. We investigated the rate of significant and insignificant non-cardiac findings using CT and MRI. A total of 108 consecutive patients suspected of having coronary artery disease and without contraindications to CT and MRI were included in this study. Significant non-cardiac findings were defined as findings that required additional clinical or radiological follow-up. CT and MR images were read independently in a blinded fashion. CT yielded five significant non-cardiac findings in five patients (5%). These included a pulmonary embolism, large pleural effusions, sarcoid, a large hiatal hernia, and a pulmonary nodule (>1.0 cm). Two of these significant non-cardiac findings were also seen on MRI (pleural effusions and sarcoid, 2%). Insignificant non-cardiac findings were more frequent than significant findings on both CT (n = 11, 10%) and MRI (n = 7, 6%). Incidental non-cardiac findings on CT and MRI of the coronary arteries are common, which is why images should be analyzed by radiologists to ensure that important findings are not missed and unnecessary follow-up examinations are avoided. (orig.)

Computational fitness landscape for all gene-order permutations of an RNA virus.

Directory of Open Access Journals (Sweden)

Kwang-il Lim

2009-02-01

Full Text Available How does the growth of a virus depend on the linear arrangement of genes in its genome? Answering this question may enhance our basic understanding of virus evolution and advance applications of viruses as live attenuated vaccines, gene-therapy vectors, or anti-tumor therapeutics. We used a mathematical model for vesicular stomatitis virus (VSV, a prototype RNA virus that encodes five genes (N-P-M-G-L, to simulate the intracellular growth of all 120 possible gene-order variants. Simulated yields of virus infection varied by 6,000-fold and were found to be most sensitive to gene-order permutations that increased levels of the L gene transcript or reduced levels of the N gene transcript, the lowest and highest expressed genes of the wild-type virus, respectively. Effects of gene order on virus growth also depended upon the host-cell environment, reflecting different resources for protein synthesis and different cell susceptibilities to infection. Moreover, by computationally deleting intergenic attenuations, which define a key mechanism of transcriptional regulation in VSV, the variation in growth associated with the 120 gene-order variants was drastically narrowed from 6,000- to 20-fold, and many variants produced higher progeny yields than wild-type. These results suggest that regulation by intergenic attenuation preceded or co-evolved with the fixation of the wild type gene order in the evolution of VSV. In summary, our models have begun to reveal how gene functions, gene regulation, and genomic organization of viruses interact with their host environments to define processes of viral growth and evolution.

Computational modeling identifies key gene regulatory interactions underlying phenobarbital-mediated tumor promotion

Science.gov (United States)

Luisier, Raphaëlle; Unterberger, Elif B.; Goodman, Jay I.; Schwarz, Michael; Moggs, Jonathan; Terranova, Rémi; van Nimwegen, Erik

2014-01-01

Gene regulatory interactions underlying the early stages of non-genotoxic carcinogenesis are poorly understood. Here, we have identified key candidate regulators of phenobarbital (PB)-mediated mouse liver tumorigenesis, a well-characterized model of non-genotoxic carcinogenesis, by applying a new computational modeling approach to a comprehensive collection of in vivo gene expression studies. We have combined our previously developed motif activity response analysis (MARA), which models gene expression patterns in terms of computationally predicted transcription factor binding sites with singular value decomposition (SVD) of the inferred motif activities, to disentangle the roles that different transcriptional regulators play in specific biological pathways of tumor promotion. Furthermore, transgenic mouse models enabled us to identify which of these regulatory activities was downstream of constitutive androstane receptor and β-catenin signaling, both crucial components of PB-mediated liver tumorigenesis. We propose novel roles for E2F and ZFP161 in PB-mediated hepatocyte proliferation and suggest that PB-mediated suppression of ESR1 activity contributes to the development of a tumor-prone environment. Our study shows that combining MARA with SVD allows for automated identification of independent transcription regulatory programs within a complex in vivo tissue environment and provides novel mechanistic insights into PB-mediated hepatocarcinogenesis. PMID:24464994

Drowning - post-mortem imaging findings by computed tomography

International Nuclear Information System (INIS)

Christe, Andreas; Aghayev, Emin; Jackowski, Christian; Thali, Michael J.; Vock, Peter

2008-01-01

The aim of this study was to identify the classic autopsy signs of drowning in post-mortem multislice computed tomography (MSCT). Therefore, the post-mortem pre-autopsy MSCT- findings of ten drowning cases were correlated with autopsy and statistically compared with the post-mortem MSCT of 20 non-drowning cases. Fluid in the airways was present in all drowning cases. Central aspiration in either the trachea or the main bronchi was usually observed. Consecutive bronchospasm caused emphysema aquosum. Sixty percent of drowning cases showed a mosaic pattern of the lung parenchyma due to regions of hypo- and hyperperfused lung areas of aspiration. The resorption of fresh water in the lung resulted in hypodensity of the blood representing haemodilution and possible heart failure. Swallowed water distended the stomach and duodenum; and inflow of water filled the paranasal sinuses (100%). All the typical findings of drowning, except Paltau's spots, were detected using post-mortem MSCT, and a good correlation of MSCT and autopsy was found. The advantage of MSCT was the direct detection of bronchospasm, haemodilution and water in the paranasal sinus, which is rather complicated or impossible at the classical autopsy. (orig.)

Computed tomographic findings in children with spastic diplegia

International Nuclear Information System (INIS)

Yokochi, Kenji; Horie, Masayo; Inukai, Kazuhisa; Kito, Hideyuki; Shimabukuro, Satoshi; Kodama, Kazuo.

1989-01-01

Computed tomographic findings of 46 children with spastic diplegia examined at nine months to three years of age corrected for preterm births were analyzed. Both the size of the lateral ventricles measured by the width of the anterior horns, and the volume of the extracerebral low-density areas were enlarged in some patiens. Both enlargements did not, however, correlate to the severity of the motor abnormality in the patients. The low-density areas of the periventricular white matter, especially adjacent to the trigone, were reduced in many children, probably due to the atrophy of the cerebral white matter having periventricular leukomalacia. The anterior expansion of the white matter reduction from the trigone corresponded to the severer motor abnormality in the children with spastic diplegia. (author)

Computed tomography findings of pancreatic metastases from renal cell carcinoma

International Nuclear Information System (INIS)

Prando, Adilson

2008-01-01

Objective: To present computed tomography findings observed in four patients submitted to radical nephrectomy for renal cell carcinoma who developed pancreatic metastases afterwards. Materials and methods: The four patients underwent radical nephrectomy for stage Tz1 (n=2) and stage T3a (n=2) renal cell carcinoma. The mean interval between nephrectomy and detection of pancreatic metastases was eight years. Two asymptomatic patients presented with solitary pancreatic metastases (confined to the pancreas). Two symptomatic patients presented with single and multiple pancreatic metastases, both with tumor recurrence in the contralateral kidney. Results: Computed tomography studies demonstrated pancreatic metastases as solitary (n=2), single (n=1) or multiple (n=1) hypervascular lesions. Partial pancreatectomy was performed in two patients with solitary pancreatic metastases and both are free of disease at four and two years after surgery. Conclusion: Pancreatic metastases from renal cell carcinoma are rare and can occur many years after the primary tumor presentation. Multiple pancreatic metastases and pancreatic metastases associated with tumor recurrence in the contralateral kidney are uncommon. Usually, on computed tomography images pancreatic metastases are visualized as solitary hypervascular lesions, simulating isletcell tumors. Surgical management should be considered for patients with solitary pancreatic lesions. (author)

Computed tomography findings of pancreatic metastases from renal cell carcinoma

Energy Technology Data Exchange (ETDEWEB)

Prando, Adilson [Hospital Vera Cruz, Campinas, SP (Brazil). Dept. of Radiology and Imaging Diagnosis]. E-mail: adilson.prando@gmail.com

2008-07-15

Objective: To present computed tomography findings observed in four patients submitted to radical nephrectomy for renal cell carcinoma who developed pancreatic metastases afterwards. Materials and methods: The four patients underwent radical nephrectomy for stage Tz1 (n=2) and stage T3a (n=2) renal cell carcinoma. The mean interval between nephrectomy and detection of pancreatic metastases was eight years. Two asymptomatic patients presented with solitary pancreatic metastases (confined to the pancreas). Two symptomatic patients presented with single and multiple pancreatic metastases, both with tumor recurrence in the contralateral kidney. Results: Computed tomography studies demonstrated pancreatic metastases as solitary (n=2), single (n=1) or multiple (n=1) hypervascular lesions. Partial pancreatectomy was performed in two patients with solitary pancreatic metastases and both are free of disease at four and two years after surgery. Conclusion: Pancreatic metastases from renal cell carcinoma are rare and can occur many years after the primary tumor presentation. Multiple pancreatic metastases and pancreatic metastases associated with tumor recurrence in the contralateral kidney are uncommon. Usually, on computed tomography images pancreatic metastases are visualized as solitary hypervascular lesions, simulating isletcell tumors. Surgical management should be considered for patients with solitary pancreatic lesions. (author)

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

Computational prediction of miRNA genes from small RNA sequencing data

Directory of Open Access Journals (Sweden)

Wenjing eKang

2015-01-01

Full Text Available Next-generation sequencing now for the first time allows researchers to gauge the depth and variation of entire transcriptomes. However, now as rare transcripts can be detected that are present in cells at single copies, more advanced computational tools are needed to accurately annotate and profile them. miRNAs are 22 nucleotide small RNAs (sRNAs that post-transcriptionally reduce the output of protein coding genes. They have established roles in numerous biological processes, including cancers and other diseases. During miRNA biogenesis, the sRNAs are sequentially cleaved from precursor molecules that have a characteristic hairpin RNA structure. The vast majority of new miRNA genes that are discovered are mined from small RNA sequencing (sRNA-seq, which can detect more than a billion RNAs in a single run. However, given that many of the detected RNAs are degradation products from all types of transcripts, the accurate identification of miRNAs remain a non-trivial computational problem. Here we review the tools available to predict animal miRNAs from sRNA sequencing data. We present tools for generalist and specialist use cases, including prediction from massively pooled data or in species without reference genome. We also present wet-lab methods used to validate predicted miRNAs, and approaches to computationally benchmark prediction accuracy. For each tool, we reference validation experiments and benchmarking efforts. Last, we discuss the future of the field.

A computational procedure for finding multiple solutions of convective heat transfer equations

International Nuclear Information System (INIS)

Mishra, S; DebRoy, T

2005-01-01

In recent years numerical solutions of the convective heat transfer equations have provided significant insight into the complex materials processing operations. However, these computational methods suffer from two major shortcomings. First, these procedures are designed to calculate temperature fields and cooling rates as output and the unidirectional structure of these solutions preclude specification of these variables as input even when their desired values are known. Second, and more important, these procedures cannot determine multiple pathways or multiple sets of input variables to achieve a particular output from the convective heat transfer equations. Here we propose a new method that overcomes the aforementioned shortcomings of the commonly used solutions of the convective heat transfer equations. The procedure combines the conventional numerical solution methods with a real number based genetic algorithm (GA) to achieve bi-directionality, i.e. the ability to calculate the required input variables to achieve a specific output such as temperature field or cooling rate. More important, the ability of the GA to find a population of solutions enables this procedure to search for and find multiple sets of input variables, all of which can lead to the desired specific output. The proposed computational procedure has been applied to convective heat transfer in a liquid layer locally heated on its free surface by an electric arc, where various sets of input variables are computed to achieve a specific fusion zone geometry defined by an equilibrium temperature. Good agreement is achieved between the model predictions and the independent experimental results, indicating significant promise for the application of this procedure in finding multiple solutions of convective heat transfer equations

Large-scale computational drug repositioning to find treatments for rare diseases.

Science.gov (United States)

Govindaraj, Rajiv Gandhi; Naderi, Misagh; Singha, Manali; Lemoine, Jeffrey; Brylinski, Michal

2018-01-01

Rare, or orphan, diseases are conditions afflicting a small subset of people in a population. Although these disorders collectively pose significant health care problems, drug companies require government incentives to develop drugs for rare diseases due to extremely limited individual markets. Computer-aided drug repositioning, i.e., finding new indications for existing drugs, is a cheaper and faster alternative to traditional drug discovery offering a promising venue for orphan drug research. Structure-based matching of drug-binding pockets is among the most promising computational techniques to inform drug repositioning. In order to find new targets for known drugs ultimately leading to drug repositioning, we recently developed e MatchSite, a new computer program to compare drug-binding sites. In this study, e MatchSite is combined with virtual screening to systematically explore opportunities to reposition known drugs to proteins associated with rare diseases. The effectiveness of this integrated approach is demonstrated for a kinase inhibitor, which is a confirmed candidate for repositioning to synapsin Ia. The resulting dataset comprises 31,142 putative drug-target complexes linked to 980 orphan diseases. The modeling accuracy is evaluated against the structural data recently released for tyrosine-protein kinase HCK. To illustrate how potential therapeutics for rare diseases can be identified, we discuss a possibility to repurpose a steroidal aromatase inhibitor to treat Niemann-Pick disease type C. Overall, the exhaustive exploration of the drug repositioning space exposes new opportunities to combat orphan diseases with existing drugs. DrugBank/Orphanet repositioning data are freely available to research community at https://osf.io/qdjup/.

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

High-resolution computed tomography findings in eight patients with hantavirus pulmonary syndrome

Energy Technology Data Exchange (ETDEWEB)

Barbosa, Diego de Lacerda; Hochhegger, Bruno; Souza Junior, Arthur Soares; Zanetti, Glaucia; Escuissato, Dante Luiz; Meirelles, Gustavo de Souza Portes; Funari, Marcelo Buarque de Gusmao; Marchiori, Edson, E-mail: edmarchiori@gmail.com [Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ (Brazil); Santa Casa de Porto Alegre, Porto Alegre, RS (Brazil); Faculdade de Medicina de Sao Jose do Rio Preto (FAMERP), SP (Brazil); Ultra X, Sao Jose do Rio Preto, SP (Brazil); Universidade Federal do Parana (UFPR), Curitiba, PR (Brazil); Universidade Federal de Sao Paulo (UNIFESP), Sao Paulo, SP (Brazil); Grupo Fleury, Sao Paulo, SP (Brazil); Universidade de Sao Paulo (FM/USP), Sao Paulo, SP (Brazil). Faculdade de Medicina

2017-05-15

Objective: The purpose of this study was to describe the high-resolution computed tomography (HRCT) findings in patients with hantavirus pulmonary syndrome (HPS). Materials and Methods: We retrospectively reviewed HRCT findings from eight cases of HPS. All patients were men, aged 19-70 (mean, 41.7) years. Diagnoses were established by serological test (enzyme-linked immunosorbent assay) in all patients. Two chest radiologists analyzed the images and reached decisions by consensus. Results: The predominant HRCT findings were ground-glass opacities (GGOs) and smooth inter- and intralobular septal thickening, found in all eight cases; however, the crazy-paving pattern was found in only three cases. Pleural effusion and peribronchovascular thickening were observed in five patients. The abnormalities were bilateral in all patients. Conclusion: The predominant HRCT findings in patients with HPS were GGOs and smooth inter- and intralobular septal thickening, which probably correlate with the histopathologic findings of pulmonary edema. (author)

High-resolution computed tomography findings in eight patients with hantavirus pulmonary syndrome

International Nuclear Information System (INIS)

Barbosa, Diego de Lacerda; Hochhegger, Bruno; Souza Junior, Arthur Soares; Zanetti, Glaucia; Escuissato, Dante Luiz; Meirelles, Gustavo de Souza Portes; Funari, Marcelo Buarque de Gusmao; Marchiori, Edson; Santa Casa de Porto Alegre, Porto Alegre, RS; Faculdade de Medicina de Sao Jose do Rio Preto; Ultra X, Sao Jose do Rio Preto, SP; Universidade Federal do Parana; Universidade Federal de Sao Paulo; Grupo Fleury, Sao Paulo, SP; Universidade de Sao Paulo

2017-01-01

Objective: The purpose of this study was to describe the high-resolution computed tomography (HRCT) findings in patients with hantavirus pulmonary syndrome (HPS). Materials and Methods: We retrospectively reviewed HRCT findings from eight cases of HPS. All patients were men, aged 19-70 (mean, 41.7) years. Diagnoses were established by serological test (enzyme-linked immunosorbent assay) in all patients. Two chest radiologists analyzed the images and reached decisions by consensus. Results: The predominant HRCT findings were ground-glass opacities (GGOs) and smooth inter- and intralobular septal thickening, found in all eight cases; however, the crazy-paving pattern was found in only three cases. Pleural effusion and peribronchovascular thickening were observed in five patients. The abnormalities were bilateral in all patients. Conclusion: The predominant HRCT findings in patients with HPS were GGOs and smooth inter- and intralobular septal thickening, which probably correlate with the histopathologic findings of pulmonary edema. (author)

Computed tomography findings of paracoccidiodomycosis in musculoskeletal system

Energy Technology Data Exchange (ETDEWEB)

Lima Junior, Francisco Valtenor Araujo; Savarese, Leonor Garbin; Monsignore, Lucas Moretti; Martinez, Roberto; Nogueira-Barbosa, Marcello Henrique, E-mail: fvaltenor@gmail.com [Universidade de Sao Paulo (FM/USP), Ribeirao Preto, SP (Brazil). Fac. de Medicina

2015-01-15

Objective: to evaluate musculoskeletal involvement in paracoccidioidomycosis at computed tomography. Materials and methods: development of a retrospective study based on a review of radiologic and pathologic reports in the institution database. Patients with histopathologically confirmed musculoskeletal paracoccidioidomycosis and submitted to computed tomography were included in the present study. The imaging findings were consensually described by two radiologists. In order to avoid bias in the analysis, one patient with uncountable bone lesions was excluded from the study. Results: a total of seven patients were included in the present study. A total of 18 bone lesions were counted. The study group consisted of 7 patients. A total number of 18 bone lesions were counted. Osteoarticular lesions were the first manifestation of the disease in four patients (57.14%). Bone lesions were multiple in 42.85% of patients. Appendicular and axial skeleton were affected in 85.71% and 42.85% of cases, respectively. Bone involvement was characterized by well-demarcated osteolytic lesions. Marginal osteosclerosis was identified in 72.22% of the lesions, while lamellar periosteal reaction and soft tissue component were present in 5.55% of them. One patient showed multiple small lesions with bone sequestra. Conclusion: paracoccidioidomycosis can be included in the differential diagnosis of either single or multiple osteolytic lesions in young patients even in the absence of a previous diagnosis of pulmonary or visceral paracoccidioidomycosis. (author)

Collaborative Creativity: A Computational Approach: Raw Shaping Form Finding in Higher Education Domain

NARCIS (Netherlands)

Wendrich, Robert E.; Guerrero, J.E.

2013-01-01

This paper examines the conceptual synthesis processes in conjunction with assistive computational support for individual and collaborative interaction. We present findings from two educational design interaction experiments in product creation processing (PCP). We focus on metacognitive aspects of

Computed tomography findings in pancreas divisum

International Nuclear Information System (INIS)

Lindstroem, E.; Ihse, I.

1989-01-01

In 29 patients with abdominal pain the diagnosis of pancreas divisum (PD) was verified by endoscopic retrograde pancreatography (EPR) via both the major and the minor papilla. Computed tomography (CT) was done in all patients to evaluate contour, volume, antero-posterior diameters and attenuation values of the gland in comparison with a normal reference series. Also, the validity of the CT grading of pancreatitis was assessed in comparison with ERP grading. Patients with PD had an increased cranio-caudal diameter of the pancreatic head (p<0.001). Further, the main pancreatic duct was visualized more often in patients with PD (p<0.01), who also had an increasing frequency of pancreatic calcifications (p<0.05). Otherwise there were no differences compared with the normal series. The observed reduction in the volume of the gland in patients with marked pancreatitis at ERP seemingly reflected the severity of inflammation. No cleavage between the dorsal and ventral anlage was identified. CT was found to be too unspecific to be of any use in grading of pancreatitis. In conclusion, CT findings in patients with PD are sparse, unspecific and preferably a reflection of pancreatitis, if present. ERP remains the ''gold standard'' for the diagnosis. (orig.)

Clustering based gene expression feature selection method: A computational approach to enrich the classifier efficiency of differentially expressed genes

KAUST Repository

Abusamra, Heba

2016-07-20

The native nature of high dimension low sample size of gene expression data make the classification task more challenging. Therefore, feature (gene) selection become an apparent need. Selecting a meaningful and relevant genes for classifier not only decrease the computational time and cost, but also improve the classification performance. Among different approaches of feature selection methods, however most of them suffer from several problems such as lack of robustness, validation issues etc. Here, we present a new feature selection technique that takes advantage of clustering both samples and genes. Materials and methods We used leukemia gene expression dataset [1]. The effectiveness of the selected features were evaluated by four different classification methods; support vector machines, k-nearest neighbor, random forest, and linear discriminate analysis. The method evaluate the importance and relevance of each gene cluster by summing the expression level for each gene belongs to this cluster. The gene cluster consider important, if it satisfies conditions depend on thresholds and percentage otherwise eliminated. Results Initial analysis identified 7120 differentially expressed genes of leukemia (Fig. 15a), after applying our feature selection methodology we end up with specific 1117 genes discriminating two classes of leukemia (Fig. 15b). Further applying the same method with more stringent higher positive and lower negative threshold condition, number reduced to 58 genes have be tested to evaluate the effectiveness of the method (Fig. 15c). The results of the four classification methods are summarized in Table 11. Conclusions The feature selection method gave good results with minimum classification error. Our heat-map result shows distinct pattern of refines genes discriminating between two classes of leukemia.

Finding New Math Identities by Computer

Science.gov (United States)

Bailey, David H.; Chancellor, Marisa K. (Technical Monitor)

1996-01-01

Recently a number of interesting new mathematical identities have been discovered by means of numerical searches on high performance computers, using some newly discovered algorithms. These include the following: pi = ((sup oo)(sub k=0))(Sigma) (1 / 16) (sup k) ((4 / 8k+1) - (2 / 8k+4) - (1 / 8k+5) - (1 / 8k+6)) and ((17 pi(exp 4)) / 360) = ((sup oo)(sub k=1))(Sigma) (1 + (1/2) + (1/3) + ... + (1/k))(exp 2) k(exp -2), zeta(3, 1, 3, 1, ..., 3, 1) = (2 pi(exp 4m) / (4m+2)! where m = number of (3,1) pairs. and where zeta(n1,n2,...,nr) = (sub k1 (is greater than) k2 (is greater than) ... (is greater than) kr)(Sigma) (1 / (k1 (sup n1) k2 (sup n2) ... kr (sup nr). The first identity is remarkable in that it permits one to compute the n-th binary or hexadecimal digit of pu directly, without computing any of the previous digits, and without using multiple precision arithmetic. Recently the ten billionth hexadecimal digit of pi was computed using this formula. The third identity has connections to quantum field theory. (The first and second of these been formally established; the third is affirmed by numerical evidence only.) The background and results of this work will be described, including an overview of the algorithms and computer techniques used in these studies.

Characteristic findings of computed tomography in cerebral metastatic malignant melanomas

International Nuclear Information System (INIS)

Kukita, Chikashige; Nose, Tadao; Nakagawa, Kunio; Tomono, Yuji; Enomoto, Takao; Hashikawa, Masanori; Egashira, Taihei; Maki, Yutaka

1986-01-01

Four cases with metastatic cerebral melanoma were studied by means of computed tomography (CT). Two cases were male, and the other two were female, with an average age of 55 years. Their primary lesions were on the chest wall in two cases, around the calcaneus in one, and around the genitalia in one. All cases died within 6 months after the metastatic brain lesions were found. Necropsies were carried out in two cases. CT revealed high-density areas in all cases, and contrast studies showed an enhancement of the lesions, as has previously been reported. On the other hand, autopsied cases revealed neither fresh nor old intratumoral bleedings such as a scattered focus of hemosiderin. These findings suggest that the high-density tumoral shadows in CT are probably not intratumoral bleedings due to a bleeding tendency of the tumors, as some authors have previously supposed. We mentioned some other factors contributing to the high density of the melanoma on computed tomograms. (author)

Semantic Disease Gene Embeddings (SmuDGE): phenotype-based disease gene prioritization without phenotypes

KAUST Repository

AlShahrani, Mona; Hoehndorf, Robert

2018-01-01

In the past years, several methods have been developed to incorporate information about phenotypes into computational disease gene prioritization methods. These methods commonly compute the similarity between a disease's (or patient's) phenotypes and a database of gene-to-phenotype associations to find the phenotypically most similar match. A key limitation of these methods is their reliance on knowledge about phenotypes associated with particular genes which is highly incomplete in humans as well as in many model organisms such as the mouse. Results: We developed SmuDGE, a method that uses feature learning to generate vector-based representations of phenotypes associated with an entity. SmuDGE can be used as a trainable semantic similarity measure to compare two sets of phenotypes (such as between a disease and gene, or a disease and patient). More importantly, SmuDGE can generate phenotype representations for entities that are only indirectly associated with phenotypes through an interaction network; for this purpose, SmuDGE exploits background knowledge in interaction networks comprising of multiple types of interactions. We demonstrate that SmuDGE can match or outperform semantic similarity in phenotype-based disease gene prioritization, and furthermore significantly extends the coverage of phenotype-based methods to all genes in a connected interaction network.

Semantic Disease Gene Embeddings (SmuDGE): phenotype-based disease gene prioritization without phenotypes

KAUST Repository

Alshahrani, Mona

2018-04-30

In the past years, several methods have been developed to incorporate information about phenotypes into computational disease gene prioritization methods. These methods commonly compute the similarity between a disease\\'s (or patient\\'s) phenotypes and a database of gene-to-phenotype associations to find the phenotypically most similar match. A key limitation of these methods is their reliance on knowledge about phenotypes associated with particular genes which is highly incomplete in humans as well as in many model organisms such as the mouse. Results: We developed SmuDGE, a method that uses feature learning to generate vector-based representations of phenotypes associated with an entity. SmuDGE can be used as a trainable semantic similarity measure to compare two sets of phenotypes (such as between a disease and gene, or a disease and patient). More importantly, SmuDGE can generate phenotype representations for entities that are only indirectly associated with phenotypes through an interaction network; for this purpose, SmuDGE exploits background knowledge in interaction networks comprising of multiple types of interactions. We demonstrate that SmuDGE can match or outperform semantic similarity in phenotype-based disease gene prioritization, and furthermore significantly extends the coverage of phenotype-based methods to all genes in a connected interaction network.

Computed tomography findings in patients with H1N1 influenza A infection

Energy Technology Data Exchange (ETDEWEB)

Amorim, Viviane Brandao; Rodrigues, Rosana Souza; Barreto, Miriam Menna; Marchiori, Edson, E-mail: edmarchiori@gmail.com [Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ (Brazil); Zanetti, Glaucia [Faculdade de Medicina de Petropolis (FMP), RJ (Brazil)

2013-09-15

The present study aimed to review high resolution computed tomography findings in patients with H1N1 influenza A infection. The most common tomographic findings include ground-glass opacities, areas of consolidation or a combination of both patterns. Some patients may also present bronchial wall thickening, airspace nodules, crazy-paving pattern, perilobular opacity, air trapping and findings related to organizing pneumonia. These abnormalities are frequently bilateral, with subpleural distribution. Despite their non specificity, it is important to recognize the main tomographic findings in patients affected by H1N1 virus in order to include this possibility in the differential diagnosis, characterize complications and contribute in the follow-up, particularly in cases of severe disease. (author)

Computed tomography findings in patients with H1N1 influenza A infection

International Nuclear Information System (INIS)

Amorim, Viviane Brandao; Rodrigues, Rosana Souza; Barreto, Miriam Menna; Marchiori, Edson; Zanetti, Glaucia

2013-01-01

The present study aimed to review high resolution computed tomography findings in patients with H1N1 influenza A infection. The most common tomographic findings include ground-glass opacities, areas of consolidation or a combination of both patterns. Some patients may also present bronchial wall thickening, airspace nodules, crazy-paving pattern, perilobular opacity, air trapping and findings related to organizing pneumonia. These abnormalities are frequently bilateral, with subpleural distribution. Despite their non specificity, it is important to recognize the main tomographic findings in patients affected by H1N1 virus in order to include this possibility in the differential diagnosis, characterize complications and contribute in the follow-up, particularly in cases of severe disease. (author)

Typical computer tomographic findings in neurofibromatosis

International Nuclear Information System (INIS)

Allgayer, B.; Reiser, M.; Kramann, B.

1984-01-01

Three pateints with neurofibromatosis (Recklinghausen's disease) were examined by computer tomography. In this way, the exact extent and localisation of the neurofibromatous tumours could be demonstrated. In one patient, CT provided evidence of malignant change; this was verified histologically. The appearances of neurofibromatosis associated with elephantiasis is described. In each patient, treatment was significantly influenced by computer tomography. (orig.) [de

Typical computer tomographic findings in neurofibromatosis

Energy Technology Data Exchange (ETDEWEB)

Allgayer, B.; Reiser, M.; Kramann, B.

1984-06-01

Three pateints with neurofibromatosis (Recklinghausen's disease) were examined by computer tomography. In this way, the exact extent and localisation of the neurofibromatous tumours could be demonstrated. In one patient, CT provided evidence of malignant change; this was verified histologically. The appearances of neurofibromatosis associated with elephantiasis is described. In each patient, treatment was significantly influenced by computer tomography.

Brain computed tomographic findings in post-cardiopulmonary resuscitation patients

International Nuclear Information System (INIS)

Ishida, Tsuguharu; Yoshinaga, Kazumasa; Horibe, Takashi; Kokubu, Kiyokazu; Kokura, Yoshihiro; Matsui, Konosuke; Inamoto, Kazuo.

1986-01-01

We retrospectively assessed the brain computed tomographic (CT) findings in 22 post-cardiopulmonary resuscitation (CPR) patients excluding neonatal cases. On the basis of the CT findings, the patients were divided into two groups. Eight patients (36.4 %) had bilateral abnormal lowdensity areas in the basal ganglia (Group I). The remaining 14 patients (63.6 %) had no abnormalities in that area (Group II). In Group I, the incidence of primary cardiac arrest and duration of advanced life support (ALS) was significantly different (p < 0.05) from Group II. Sex, age, duration of basic life support (BLS), time elapsed from initiation of BLS to initial CT and from initiation of ALS to initial CT was not significantly different between the two groups. Outcome was very poor in both groups and no significant difference was noted between them. We conclude that primary cardiac arrest and long duration of ALS were predictors of abnormal bilateral low-density areas in the basal ganglia in post-CPR patients. However, their appearance was not related to outcome. (author)

Spatially Uniform ReliefF (SURF for computationally-efficient filtering of gene-gene interactions

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Greene Casey S

2009-09-01

Full Text Available Abstract Background Genome-wide association studies are becoming the de facto standard in the genetic analysis of common human diseases. Given the complexity and robustness of biological networks such diseases are unlikely to be the result of single points of failure but instead likely arise from the joint failure of two or more interacting components. The hope in genome-wide screens is that these points of failure can be linked to single nucleotide polymorphisms (SNPs which confer disease susceptibility. Detecting interacting variants that lead to disease in the absence of single-gene effects is difficult however, and methods to exhaustively analyze sets of these variants for interactions are combinatorial in nature thus making them computationally infeasible. Efficient algorithms which can detect interacting SNPs are needed. ReliefF is one such promising algorithm, although it has low success rate for noisy datasets when the interaction effect is small. ReliefF has been paired with an iterative approach, Tuned ReliefF (TuRF, which improves the estimation of weights in noisy data but does not fundamentally change the underlying ReliefF algorithm. To improve the sensitivity of studies using these methods to detect small effects we introduce Spatially Uniform ReliefF (SURF. Results SURF's ability to detect interactions in this domain is significantly greater than that of ReliefF. Similarly SURF, in combination with the TuRF strategy significantly outperforms TuRF alone for SNP selection under an epistasis model. It is important to note that this success rate increase does not require an increase in algorithmic complexity and allows for increased success rate, even with the removal of a nuisance parameter from the algorithm. Conclusion Researchers performing genetic association studies and aiming to discover gene-gene interactions associated with increased disease susceptibility should use SURF in place of ReliefF. For instance, SURF should be

Incidental dentomaxillofacial findings on cone beam computed tomography images of Iranian population

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Leila Khojastepour

2014-04-01

Full Text Available BACKGROUND AND AIM: The present study aimed to assess the nature and prevalence of incidental findings in cone beam computed tomography (CBCT images of oral and maxillofacial patients. METHODS: In this cross-sectional study, 773 CBCT samples were retrieved from archives of a private oral and maxillofacial radiology center. Any findings that were not related to the reason of CBCT request was recorded in forms designed originally for this study. RESULTS: 475 patients out of 773 had at least one incidental finding. It composed about 60% of the patients. The largest frequency of incidental findings were cases of periapical lesions. (n = 189, followed by mucous thickening of maxillary sinus (n = 170, retained root (n = 32, impaction and 3rd molar (n = 26. Other incidental findings were torus (n = 25, dental anomalies (n = 13, vertical root fracture (n = 5, intra bony lesion and periapical pathosis (n = 4 and the lowest frequency was sialoliths (n = 1. CONCLUSION: About half of the subjects have had at least one incidental finding, so the precise review of the CBCT images seems to be necessary.

Computed tomography findings in patients less than 20 years old with lymphoma

International Nuclear Information System (INIS)

Borba, Adriana Moreira Viana; Skinner, Luis Flavio

2007-01-01

Objective: To describe the general findings of lymphoma and their histological patterns in patients less than 20 years old. Materials And Methods: Twenty-two cases (16 male and 6 female, mean age 11.5 years) from the digital archive of computed tomography at the Cancer Control Center of Hospital Universitario Pedro Ernesto - Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brazil, were retrospectively analyzed in the period between March 2003 and July 2005. Of these 22 cases, 12 were Hodgkin's and 10 were non-Hodgkin's. Results: Overall, mediastinal lymphadenomegaly was the most frequent finding (59%), with predominance in the Hodgkin's subgroup (75%), followed by hepatosplenomegaly (50%) and cervical and retroperitoneal lymphadenomegaly (27.3%). The Hodgkin's subgroup presented a prevalence of lymphadenopathy, in many lymph node chains, followed by hepatosplenomegaly (50%). One case was found with unilateral tonsillar mass, pulmonary ground-glass opacities, and renal nodules. In the non-Hodgkin's subgroup, the disease was predominantly extranodal, characterized by hepatosplenomegaly (50%), thickening of the intestinal wall (40%), pleural effusion (30%), pulmonary nodule (20%), ascites (10%), pericardial effusion (10%) and mixed bone lesions (10%). Conclusion: Computed tomography is an extremely useful method for detection, staging and follow-up of lymphomas, with alert findings like mediastinal lymphadenopathy, hepatosplenomegaly, unilateral tonsillar mass and thickening of intestinal wall. (author)

Retrospective analysis of whole-body multislice computed tomography findings taken in trauma patients

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Ozlem Bingol

2015-09-01

Full Text Available Objectives: Using whole-body multislice computed tomography (MSCT excessively or with irrelevant indications can be seen in many centers. The aim of this study was to analyze retrospectively the MSCT findings in trauma patients admitted to the emergency department. Methods: Records of the patients who have applied to the emergency department due to blunt trauma in a 12 month period and whose whole body MSCT images have been taken, were evaluated using the “Nucleus Medical Information System”. Results: The most frequent type of trauma was traffic accidents in 61.4%, falling down from the height in 22.4%, and motorcycle accidents in 11.4% of patients. Of the patients, 25.2% were discharged from the emergency, while 73.8% were hospitalized. At least one CT findings associated with trauma was present in 61.4% of our patients. Pathological findings in MSCT were most frequently detected in the head and face (35.3% and thoracic (28.6% regions, respectively. The most common finding in the head and face region was fractures. The most common pathological findings in the thoracic region were pulmonary contusion and rib fractures. A significant relationship was detected between trauma type and spinal MSCT result (p < 0.001. In a large percentage of the patients, MSCT findings were normal in the abdominal region and genitourinary system. Vertebral fractures were most frequently detected in the thoracolumbar region. Conclusions: In our study, our rate of negative CT was found to be 38.6%, which is a higher ratio compared to other studies conducte on this topic. Keywords: Emergency, Trauma, Whole-body multislice computed tomography

Fluorodeoxyglucose positron emission tomography-computed tomography findings in a case of xanthogranulomatous pyelonephritis

Science.gov (United States)

Joshi, Prathamesh; Lele, Vikram; Shah, Hardik

2013-01-01

Xanthogranulomatous pyelonephritis (XGNP) is an uncommon condition characterized by chronic suppurative renal inflammation that leads to progressive parenchymal destruction. This condition can clinically present as recurrent urinary tract infections, flank pain, hematuria, and occasionally sepsis, and weight loss. This condition is usually associated with obstructing renal calculus. We present 18-fluorodeoxyglucose positron emission tomography-computed tomography (18-FDG PET/CT) findings in an elderly male suffering from pyrexia and weight loss and suspected urinary tract infection. PET/CT findings in this case lead to diagnosis of XGNP. This diagnosis should be kept in mind while evaluating similar symptoms and PET/CT scan findings. PMID:24019680

Pulmonary infection caused by Mycobacterium kansasii: findings on computed tomography of the chest

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Mogami, Roberto; Lopes, Agnaldo Jose; Marca, Patricia Gomes Cytrangulo de, E-mail: agnaldolopes.uerj@gmail.com [Universidade do Estado do Rio de Janeiro (UERJ), RJ (Brazil); Goldenberg, Telma; Mello, Fernanda Carvalho de Queiroz [Universidade Federal do Rio de Janeiro (UFRJ), RJ (Brazil)

2016-07-15

Objective: To describe the main tomography findings in patients diagnosed with pulmonary infection caused by Mycobacterium kansasii. Materials and Methods: Retrospective study of computed tomography scans of 19 patients with pulmonary infection by M. kansasii. Results: Of the 19 patients evaluated, 10 (52.6%) were male and 9 (47.4%) were female. The mean age of the patients was 58 years (range, 33-76 years). Computed tomography findings were as follows: architectural distortion, in 17 patients (89.5%); reticular opacities and bronchiectasis, in 16 (84.2%); cavities, in 14 (73.7%); centrilobular nodules, in 13 (68.4%); small consolidations, in 10 (52.6%); atelectasis and large consolidations, in 9 (47.4%); subpleural blebs and emphysema, in 6 (31.6%); and adenopathy, in 1 (5.3%). Conclusion: There was a predominance of cavities, as well as of involvement of the small and large airways. The airway disease was characterized by bronchiectasis and bronchiolitis presenting as centrilobular nodules. (author)

Computed tomography findings mimicking appendicitis as a manifestation of colorectal cancer☆

Science.gov (United States)

Watchorn, Richard E.; Poder, Liina; Wang, Zhen J.; Yeh, Benjamin M.; Webb, Emily M.; Coakley, Fergus V.

2009-01-01

The primary computed tomography (CT) signs of appendicitis can also be seen with other inflammatory or neoplastic processes. We report on two cases in which appendiceal dilatation and peri-appendiceal fluid or stranding were the dominant imaging manifestations of colorectal carcinoma in the ascending colon. This study highlights the need to closely examine the ascending colon in patients with a suspected CT diagnosis of acute appendicitis, since these findings may be secondary to an inconspicuous colorectal carcinoma. PMID:19857802

Isolated submucosal lipomatosis of appendix mimicking acute appendicitis: computed tomography findings

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Şükrü Şanlı

2014-03-01

Full Text Available Acute appendicitis is one of the more common surgical emergencies, and it is one of the most common causes of acute abdominal pain. Intestinal lipomatosis is a rare condition particularly the isolated form of lipomatosis of the appendix which may mimic or present as an acute appendicitis, that frequently requires the surgical exploration.In this paper, we report computed tomography findings of a case wıth isolated form of submucosal lipomatosis of appendix.

Computed tomography findings in patients with mild head trauma

International Nuclear Information System (INIS)

Sanei Taheri, M.; Hemadi, H.; Sajadinasab, M.; Sharifi, G.; Jalali, A. H.; Shakiba, M.

2007-01-01

To determine the frequency of computed tomography (CT) findings in patients with mild head trauma. Patients and Methods: In this cross-sectional study conducted between September 2005 and April 2006, 708 patients with mild head trauma as defined by a Glasgow Coma Score (GCS) of 13-15, were underwent standard clinical examination and cranial CT. Results The mean±SD age of our patients was 26.8±19.03 years (range: 1 month to 89 years). 489 (68.9%) patients were male and 219 (30.8%) were female. GSC was 13 in 1%. 14 in 4.6% and 15 in 94.4% of patients. The most common mechanism of trauma was car accident and falling down, each of which happened for 132 patients (18.6%). The most common findings on CT were subgaleal hematomas in 213(30%) and intracranial lesions were seen in 41 patients(5.8%) :among them 37 were male. Among intracranial lesions, the most common finding was epidural hematoma in 18 patients followed by hemorrhagic contusion in 13 patients. lntracranial lesions were observed in 28.6% of patients with GCS of 13: in 15.25% with GCS of 14 and in 5.1% with GCS of 15 (P=.002). conclusion: Many of patients with GCS equal to 15 after head trauma have considerable intracranial and minor focal neurologic signs revealed by careful physical examination could be a good marker of these lesions

Many unexpected abdominal findings on staging computed tomography in patients with colorectal cancer

DEFF Research Database (Denmark)

Holmsted, Kim; Nørring, Keld; Laustrup, Lene Collatz

2011-01-01

; an issue that was previously studied in relation to CT colonography, but not in relation to staging CT with intravenous contrast in CRC patients. The aim of the present study was to evaluate the number and significance of such unexpected findings on staging CTs in CRC patients.......Computed tomography (CT) was proven to be superior to preoperative abdominal ultrasound in the preoperative setting for detection of hepatic metastases from colorectal cancer (CRC). The higher sensitivity of CT has resulted in a number of unexpected abdominal findings of varying importance...

Misty mesentery: computed tomography findings

International Nuclear Information System (INIS)

Ahualli, Jorge; Mendez Uriburu, Luis; Ravera, Maria L.; Cikman, Pablo

2008-01-01

An alteration in the density of the mesenteric adipose tissue is often the principal clue of underlying mesenteric and bowel disease. The term 'Misty Mesentery' describes the computed tomographic appearance of mesenteric fat infiltrated by inflammatory cells, fluid (edema, lymph, and/or blood), tumor, and fibrosis. (author) [es

Incidental head and neck findings on 18F-fluoro-deoxy-glucose positron emission tomography computed tomography.

Science.gov (United States)

Williams, S P; Kinshuck, A J; Williams, C; Dwivedi, R; Wieshmann, H; Jones, T M

2015-09-01

The overlapping risk factors for lung and head and neck cancer present a definite risk of synchronous malignant pathology. This is the first study to specifically review incidental positron emission tomography computed tomography findings in the head and neck region in lung carcinoma patients. A retrospective review was performed of all lung cancer patients who underwent positron emission tomography computed tomography imaging over a five-year period (January 2008 - December 2012), identified from the Liverpool thoracic multidisciplinary team database. Six hundred and nine patients underwent positron emission tomography computed tomography imaging over this period. In 76 (12.5 per cent) scans, incidental regions of avid 18F-fluoro-deoxy-glucose uptake were reported in the head and neck region. In the 28 patients who were fully investigated, there were 4 incidental findings of malignancy. In lung cancer patients undergoing investigative positron emission tomography computed tomography scanning, a significant number will also present with areas of clinically significant 18F-fluoro-deoxy-glucose uptake in the head and neck region. Of these, at least 5 per cent may have an undiagnosed malignancy.

Computed Tomography Imaging findings in Chemical Warfare Victims with pulmonary Complications

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Zahra Salehinezhad

2013-05-01

Full Text Available Introduction: Data on imaging findings in pulmonary complications of chemical agents is scarce. The current study aimed to evaluate radiological findings of late onset pulmonary complications in chemical warfare victims (CWV and to guide pulmonologists in diagnosis of these subjects. Materials and Methods: Ninety- three male CWV were enrolled in this prospective study, 20-25 years (mean=23 after exposure. Demographic and clinical data were recorded. High resolution computed Tomography (HRCT of the lung was performed during inspiration and expiration and was double reported blindly by two radiologists. Final diagnosis was made according to HRCT findings. The HRCT findings, final diagnosis, and distribution of the abnormalities were compared between subjects whom had been exposed to more complex chemical agents used during the second half of the war and simpler agents during the first half. Results: The most frequent HRCT findings were air trapping (56.7% and mosaic attenuation (35.1%. The distribution of abnormalities was mostly local (79.4% and bilateral (73% especially in lower regions (61.3%. The diagnosed respiratory diseases included bronchiolitis obliterans (43%, chronic obstructive pulmonary disease (COPD (27.9%, asthma (23.6%, bronchiectasis (13.9% and interstitial lung disease (ILD (9.6%. Frequency of subjects involved in the second half of the period of war was more than the first period (P-value < 0.05 but the HRCT findings were similar. Conclusions: Bronchiolitis obliterans with picture of focal bilateral air trapping was the most common finding in CWV but asthma appeared to have become a new problem in these subjects.

Imaging Findings of Sonography and Computed Tomography for a Penile Leiomyosarcoma: A Case Report

International Nuclear Information System (INIS)

Chung, Jin; Chung, Jae Joon; Yu, Jeong Sik; Kim, Joo Hee

2009-01-01

We report the ultrasonographic and computed tomography (CT) findings of a deep type of penile leiomyosarcoma that helped characterize a penile mass along with a review of the published literature. Leiomyosarcoma of the penis is a very rare disease characterized by a lobulated, expansile, soft tissue mass in CT images, with peripheral rim enhancement and internal homogeneous low density. The ultrasonographic findings revealed a lobulated and heterogeneously hypoechoic solid mass at the distal tip of the penis

Imaging Findings of Sonography and Computed Tomography for a Penile Leiomyosarcoma: A Case Report

Energy Technology Data Exchange (ETDEWEB)

Chung, Jin; Chung, Jae Joon; Yu, Jeong Sik; Kim, Joo Hee [Gangnam Severance Hospital, Seoul (Korea, Republic of)

2009-12-15

We report the ultrasonographic and computed tomography (CT) findings of a deep type of penile leiomyosarcoma that helped characterize a penile mass along with a review of the published literature. Leiomyosarcoma of the penis is a very rare disease characterized by a lobulated, expansile, soft tissue mass in CT images, with peripheral rim enhancement and internal homogeneous low density. The ultrasonographic findings revealed a lobulated and heterogeneously hypoechoic solid mass at the distal tip of the penis.

Finding-specific display presets for computed radiography soft-copy reading.

Science.gov (United States)

Andriole, K P; Gould, R G; Webb, W R

1999-05-01

Much work has been done to optimize the display of cross-sectional modality imaging examinations for soft-copy reading (i.e., window/level tissue presets, and format presentations such as tile and stack modes, four-on-one, nine-on-one, etc). Less attention has been paid to the display of digital forms of the conventional projection x-ray. The purpose of this study is to assess the utility of providing presets for computed radiography (CR) soft-copy display, based not on the window/level settings, but on processing applied to the image optimized for visualization of specific findings, pathologies, etc (i.e., pneumothorax, tumor, tube location). It is felt that digital display of CR images based on finding-specific processing presets has the potential to: speed reading of digital projection x-ray examinations on soft copy; improve diagnostic efficacy; standardize display across examination type, clinical scenario, important key findings, and significant negatives; facilitate image comparison; and improve confidence in and acceptance of soft-copy reading. Clinical chest images are acquired using an Agfa-Gevaert (Mortsel, Belgium) ADC 70 CR scanner and Fuji (Stamford, CT) 9000 and AC2 CR scanners. Those demonstrating pertinent findings are transferred over the clinical picture archiving and communications system (PACS) network to a research image processing station (Agfa PS5000), where the optimal image-processing settings per finding, pathologic category, etc, are developed in conjunction with a thoracic radiologist, by manipulating the multiscale image contrast amplification (Agfa MUSICA) algorithm parameters. Soft-copy display of images processed with finding-specific settings are compared with the standard default image presentation for 50 cases of each category. Comparison is scored using a 5-point scale with the positive scale denoting the standard presentation is preferred over the finding-specific processing, the negative scale denoting the finding

Computed tomography (CT) findings in 88 neurofibromatosis 1 (NF1) patients: Prevalence rates and correlations of thoracic findings

International Nuclear Information System (INIS)

Ueda, Ken; Honda, Osamu; Satoh, Yukihisa; Kawai, Misa; Gyobu, Tomoko; Kanazawa, Toru; Hidaka, Shojiro; Yanagawa, Masahiro; Sumikawa, Hiromitsu; Tomiyama, Noriyuki

2015-01-01

Highlights: • Various thoracic CT findings, including cysts, mediastinal masses, etc. were found. • Cysts show upper and peripheral dominant distribution. • The number, size, and distribution of the pulmonary cysts in NF-1 revealed significant correlation. • It is suspected that thoracic CT findings in NF-1 occur independently. - Abstract: Purpose: To evaluate the prevalence rates and the correlations of thoracic computed tomography (CT) findings of neurofibromatosis 1 (NF1) in 88 patients. Materials and methods: Chest CT images of 88 NF1 patients were independently reviewed by three observers, and the CT findings were evaluated. If abnormal findings were present, their number, size, and distribution were recorded. The prevalence rate of each CT finding was calculated, and the correlations between CT findings were analyzed. Results: Of the 88 cases, 13 were positive for cysts, 16 for emphysema, 8 for nodules, 8 for GGNs (ground glass nodules), 13 for mediastinal masses, 20 for scoliosis, 44 for subcutaneous nodules, and 34 for skin nodules. Cysts showed upper and peripheral dominant distributions. Regarding 13 mediastinal masses, 2 were diagnosed as malignant peripheral nerve sheath tumors (MPNSTs), 1 was diagnosed as primary lung cancer, 2 were diagnosed as lateral meningocele, 3 were diagnosed as neurofibromas, and the remaining 7 were considered neurofibromas. There was a significant correlation between the prevalence of subcutaneous nodules and that of skin nodules. Significant positive correlations were also seen between size and number, size and rate of central distribution, and number and rate of central distribution of cysts. Conclusion: Various CT findings were found in NF-1 patients, and the prevalence rates of subcutaneous and skin nodules were higher than other findings. Though the prevalence rates of subcutaneous nodules and skin nodules were significantly correlated, the other CT findings in NF-1 occurred independently. The number, size, and

Computed tomography (CT) findings in 88 neurofibromatosis 1 (NF1) patients: Prevalence rates and correlations of thoracic findings

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Ueda, Ken, E-mail: k-ueda@radiol.med.osaka-u.ac.jp [Department of Radiology, Osaka University Graduate School of Medicine (Japan); Honda, Osamu [Department of Radiology, Osaka University Graduate School of Medicine (Japan); Satoh, Yukihisa [Department of Diagnostic Radiology, Osaka Medical Center for Cancer and Cardiovascular Diseases (Japan); Kawai, Misa; Gyobu, Tomoko; Kanazawa, Toru; Hidaka, Shojiro; Yanagawa, Masahiro [Department of Radiology, Osaka University Graduate School of Medicine (Japan); Sumikawa, Hiromitsu [Department of Diagnostic Radiology, Osaka Rosai Hospital (Japan); Tomiyama, Noriyuki [Department of Radiology, Osaka University Graduate School of Medicine (Japan)

2015-06-15

Highlights: • Various thoracic CT findings, including cysts, mediastinal masses, etc. were found. • Cysts show upper and peripheral dominant distribution. • The number, size, and distribution of the pulmonary cysts in NF-1 revealed significant correlation. • It is suspected that thoracic CT findings in NF-1 occur independently. - Abstract: Purpose: To evaluate the prevalence rates and the correlations of thoracic computed tomography (CT) findings of neurofibromatosis 1 (NF1) in 88 patients. Materials and methods: Chest CT images of 88 NF1 patients were independently reviewed by three observers, and the CT findings were evaluated. If abnormal findings were present, their number, size, and distribution were recorded. The prevalence rate of each CT finding was calculated, and the correlations between CT findings were analyzed. Results: Of the 88 cases, 13 were positive for cysts, 16 for emphysema, 8 for nodules, 8 for GGNs (ground glass nodules), 13 for mediastinal masses, 20 for scoliosis, 44 for subcutaneous nodules, and 34 for skin nodules. Cysts showed upper and peripheral dominant distributions. Regarding 13 mediastinal masses, 2 were diagnosed as malignant peripheral nerve sheath tumors (MPNSTs), 1 was diagnosed as primary lung cancer, 2 were diagnosed as lateral meningocele, 3 were diagnosed as neurofibromas, and the remaining 7 were considered neurofibromas. There was a significant correlation between the prevalence of subcutaneous nodules and that of skin nodules. Significant positive correlations were also seen between size and number, size and rate of central distribution, and number and rate of central distribution of cysts. Conclusion: Various CT findings were found in NF-1 patients, and the prevalence rates of subcutaneous and skin nodules were higher than other findings. Though the prevalence rates of subcutaneous nodules and skin nodules were significantly correlated, the other CT findings in NF-1 occurred independently. The number, size, and

Incidental findings on cone beam computed tomography scans in cleft lip and palate patients

NARCIS (Netherlands)

Kuijpers, M.A.R.; Pazera, A.; Admiraal, R.J.C.; Berge, S.J.; Vissink, A.; Pazera, P.

2014-01-01

OBJECTIVES: Cone beam computed tomography (CBCT) is frequently used in treatment planning for alveolar bone grafting (ABG) and orthognathic surgery in patients with cleft lip and palate (CLP). CBCT images may depict coincident findings. The aim of this study was to assess the prevalence of

Computational prediction of CTCF/cohesin-based intra-TAD loops that insulate chromatin contacts and gene expression in mouse liver.

Science.gov (United States)

Matthews, Bryan J; Waxman, David J

2018-05-14

CTCF and cohesin are key drivers of 3D-nuclear organization, anchoring the megabase-scale Topologically Associating Domains (TADs) that segment the genome. Here, we present and validate a computational method to predict cohesin-and-CTCF binding sites that form intra-TAD DNA loops. The intra-TAD loop anchors identified are structurally indistinguishable from TAD anchors regarding binding partners, sequence conservation, and resistance to cohesin knockdown; further, the intra-TAD loops retain key functional features of TADs, including chromatin contact insulation, blockage of repressive histone mark spread, and ubiquity across tissues. We propose that intra-TAD loops form by the same loop extrusion mechanism as the larger TAD loops, and that their shorter length enables finer regulatory control in restricting enhancer-promoter interactions, which enables selective, high-level expression of gene targets of super-enhancers and genes located within repressive nuclear compartments. These findings elucidate the role of intra-TAD cohesin-and-CTCF binding in nuclear organization associated with widespread insulation of distal enhancer activity. © 2018, Matthews et al.

Elastofibroma dorsi: computed tomography and magnetic resonance findings in two cases

International Nuclear Information System (INIS)

Cano, A.; Bravo, F.; Garrido, J.; Ortega, R.

2001-01-01

The elastofibroma dorse is a benign, nonencapsulated pseudotumor consisting of a proliferation of fibrous tissue and elastic fibers accompanied by fatty tissue. It is usually locate in the scapular region and can be unilateral or bilateral. The computed tomography and magnetic resonance findings are characteristic and, in the proper clinical context, practically pathognomonic: a fat-containing subcapsular mass with an attenuation coefficient and signal intensity similar to those of the adjacent muscles. We report two new cases of elastofibroma dorsi that fulfilled all the clinical and radiologic criteria, enabling the preoperative diagnosis. (Author) 15 refs

Computed tomographic findings of hepatocellular carcinoma

International Nuclear Information System (INIS)

Jo, In Su; Jong, Woo Yung; Lee, Jong Yul; Choi, Han Yong; Kim, Bong Ki

1987-01-01

With Development of Computed Tomography, detection of the Hepatocellular Carcinoma are easily performed and frequently used in the world. During 15 months, from December 1985 to February 1987, 59 patients with hepatocellular carcinoma were evaluated with computed tomography in department of radiology at Wallace Memorial Baptist Hospital. The results were as follow: 1. The most prevalent age group was 5th to 7th decades, male to female ratio was 4.9:1. 2. Classification with incidence of computed tomographic appearance of the hepatocellular carcinoma were solitary type 28 cases (48%), multinodular type 24 cases (40%), and diffuse type 7 cases (12%), Association with liver cirrhosis was noted in 22 cases (38%). 3. Inhomogenous internal consistency of hepatocellular carcinoma due to central necrosis were 35 cases (60%). Portal vein invasion by hepatocellular carcinoma was noted in 15 cases (25%), and particularly most common in diffuse type 4 cases (55%). 4. On precontrast scan, all hepatocellular carcinoma were seen as area of low density except for 3 cases(0.5%) of near isodensity which turned out to be remarkable low density on postcontrast scan. 5. In solitary type, posterior segment of right lobe was most common site of involvement 12 cases (43%). In diffuse type, bilobar involvement was most common, 6 cases (85%)

Computational inference of replication and transcription activator regulator activity in herpesvirus from gene expression data

NARCIS (Netherlands)

Recchia, A.; Wit, E.; Vinciotti, V.; Kellam, P.

One of the main aims of system biology is to understand the structure and dynamics of genomic systems. A computational approach, facilitated by new technologies for high-throughput quantitative experimental data, is put forward to investigate the regulatory system of dynamic interaction among genes

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

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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.

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.

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

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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.)

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.)

Hepatocellular adenoma: findings at state-of-the-art magnetic resonance imaging, ultrasound, computed tomography and pathologic analysis

International Nuclear Information System (INIS)

Hussain, Shahid M.; Bos, Indra C. van den; Dwarkasing, Roy S.; Kuiper, Jan-Willem; Hollander, Jan den

2006-01-01

The purpose of this paper is to describe the most recent concepts and pertinent findings of hepatocellular adenomas, including clinical presentation, gross pathology and histology, pathogenesis and transformation into hepatocellular carcinoma (HCC), and imaging findings at ultrasound (US), computed tomography (CT), and magnetic resonance (MR) imaging. (orig.)

Renal replacement lipomatosis: multidetector-row computed tomography findings in one case

International Nuclear Information System (INIS)

Calisir, C.; Can, C.; Kebapci, M.

2007-01-01

Replacement lipomatosis of the kidney is the result of severe atrophy of the renal parenchyma often caused by chronic calculus disease with secondary marked benign proliferation of fibrofatty tissue replacing atrophied renal parenchyma. Different radiological modalities have been used to illustrate this entity, with magnetic resonance imaging, ultrasound, intravenous pyelogram, and computed tomography (CT) used most frequently. We report multidedector CT (MDCT) findings of replacement lipomatosis in a 50-year-old woman. We think that it accurately provides a complete one-step diagnostic workup and appropriate pre-surgical planning for patients for whom there is a suspicion of replacement lipomatosis

Computational Prediction of MicroRNAs from Toxoplasma gondii Potentially Regulating the Hosts’ Gene Expression

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Müşerref Duygu Saçar

2014-10-01

Full Text Available MicroRNAs (miRNAs were discovered two decades ago, yet there is still a great need for further studies elucidating their genesis and targeting in different phyla. Since experimental discovery and validation of miRNAs is difficult, computational predictions are indispensable and today most computational approaches employ machine learning. Toxoplasma gondii, a parasite residing within the cells of its hosts like human, uses miRNAs for its post-transcriptional gene regulation. It may also regulate its hosts’ gene expression, which has been shown in brain cancer. Since previous studies have shown that overexpressed miRNAs within the host are causal for disease onset, we hypothesized that T. gondii could export miRNAs into its host cell. We computationally predicted all hairpins from the genome of T. gondii and used mouse and human models to filter possible candidates. These were then further compared to known miRNAs in human and rodents and their expression was examined for T. gondii grown in mouse and human hosts, respectively. We found that among the millions of potential hairpins in T. gondii, only a few thousand pass filtering using a human or mouse model and that even fewer of those are expressed. Since they are expressed and differentially expressed in rodents and human, we suggest that there is a chance that T. gondii may export miRNAs into its hosts for direct regulation.

Gene expression prediction by soft integration and the elastic net-best performance of the DREAM3 gene expression challenge.

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Mika Gustafsson

Full Text Available BACKGROUND: To predict gene expressions is an important endeavour within computational systems biology. It can both be a way to explore how drugs affect the system, as well as providing a framework for finding which genes are interrelated in a certain process. A practical problem, however, is how to assess and discriminate among the various algorithms which have been developed for this purpose. Therefore, the DREAM project invited the year 2008 to a challenge for predicting gene expression values, and here we present the algorithm with best performance. METHODOLOGY/PRINCIPAL FINDINGS: We develop an algorithm by exploring various regression schemes with different model selection procedures. It turns out that the most effective scheme is based on least squares, with a penalty term of a recently developed form called the "elastic net". Key components in the algorithm are the integration of expression data from other experimental conditions than those presented for the challenge and the utilization of transcription factor binding data for guiding the inference process towards known interactions. Of importance is also a cross-validation procedure where each form of external data is used only to the extent it increases the expected performance. CONCLUSIONS/SIGNIFICANCE: Our algorithm proves both the possibility to extract information from large-scale expression data concerning prediction of gene levels, as well as the benefits of integrating different data sources for improving the inference. We believe the former is an important message to those still hesitating on the possibilities for computational approaches, while the latter is part of an important way forward for the future development of the field of computational systems biology.

Computational analysis of candidate disease genes and variants for Salt-sensitive hypertension in indigenous Southern Africans

KAUST Repository

Tiffin, Nicki

2010-09-27

Multiple factors underlie susceptibility to essential hypertension, including a significant genetic and ethnic component, and environmental effects. Blood pressure response of hypertensive individuals to salt is heterogeneous, but salt sensitivity appears more prevalent in people of indigenous African origin. The underlying genetics of salt-sensitive hypertension, however, are poorly understood. In this study, computational methods including text- and data-mining have been used to select and prioritize candidate aetiological genes for salt-sensitive hypertension. Additionally, we have compared allele frequencies and copy number variation for single nucleotide polymorphisms in candidate genes between indigenous Southern African and Caucasian populations, with the aim of identifying candidate genes with significant variability between the population groups: identifying genetic variability between population groups can exploit ethnic differences in disease prevalence to aid with prioritisation of good candidate genes. Our top-ranking candidate genes include parathyroid hormone precursor (PTH) and type-1angiotensin II receptor (AGTR1). We propose that the candidate genes identified in this study warrant further investigation as potential aetiological genes for salt-sensitive hypertension. © 2010 Tiffin et al.

Computational integration of homolog and pathway gene module expression reveals general stemness signatures.

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Martina Koeva

Full Text Available The stemness hypothesis states that all stem cells use common mechanisms to regulate self-renewal and multi-lineage potential. However, gene expression meta-analyses at the single gene level have failed to identify a significant number of genes selectively expressed by a broad range of stem cell types. We hypothesized that stemness may be regulated by modules of homologs. While the expression of any single gene within a module may vary from one stem cell type to the next, it is possible that the expression of the module as a whole is required so that the expression of different, yet functionally-synonymous, homologs is needed in different stem cells. Thus, we developed a computational method to test for stem cell-specific gene expression patterns from a comprehensive collection of 49 murine datasets covering 12 different stem cell types. We identified 40 individual genes and 224 stemness modules with reproducible and specific up-regulation across multiple stem cell types. The stemness modules included families regulating chromatin remodeling, DNA repair, and Wnt signaling. Strikingly, the majority of modules represent evolutionarily related homologs. Moreover, a score based on the discovered modules could accurately distinguish stem cell-like populations from other cell types in both normal and cancer tissues. This scoring system revealed that both mouse and human metastatic populations exhibit higher stemness indices than non-metastatic populations, providing further evidence for a stem cell-driven component underlying the transformation to metastatic disease.

Finding Cardiovascular Disease Genes in the Dog

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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

Computational neurogenetic modeling

CERN Document Server

Benuskova, Lubica

2010-01-01

Computational Neurogenetic Modeling is a student text, introducing the scope and problems of a new scientific discipline - Computational Neurogenetic Modeling (CNGM). CNGM is concerned with the study and development of dynamic neuronal models for modeling brain functions with respect to genes and dynamic interactions between genes. These include neural network models and their integration with gene network models. This new area brings together knowledge from various scientific disciplines, such as computer and information science, neuroscience and cognitive science, genetics and molecular biol

bc-GenExMiner 3.0: new mining module computes breast cancer gene expression correlation analyses.

Science.gov (United States)

Jézéquel, Pascal; Frénel, Jean-Sébastien; Campion, Loïc; Guérin-Charbonnel, Catherine; Gouraud, Wilfried; Ricolleau, Gabriel; Campone, Mario

2013-01-01

We recently developed a user-friendly web-based application called bc-GenExMiner (http://bcgenex.centregauducheau.fr), which offered the possibility to evaluate prognostic informativity of genes in breast cancer by means of a 'prognostic module'. In this study, we develop a new module called 'correlation module', which includes three kinds of gene expression correlation analyses. The first one computes correlation coefficient between 2 or more (up to 10) chosen genes. The second one produces two lists of genes that are most correlated (positively and negatively) to a 'tested' gene. A gene ontology (GO) mining function is also proposed to explore GO 'biological process', 'molecular function' and 'cellular component' terms enrichment for the output lists of most correlated genes. The third one explores gene expression correlation between the 15 telomeric and 15 centromeric genes surrounding a 'tested' gene. These correlation analyses can be performed in different groups of patients: all patients (without any subtyping), in molecular subtypes (basal-like, HER2+, luminal A and luminal B) and according to oestrogen receptor status. Validation tests based on published data showed that these automatized analyses lead to results consistent with studies' conclusions. In brief, this new module has been developed to help basic researchers explore molecular mechanisms of breast cancer. DATABASE URL: http://bcgenex.centregauducheau.fr

Collateral findings during computed tomography scan for atrial fibrillation ablation: Let's take a look around.

Science.gov (United States)

Perna, Francesco; Casella, Michela; Narducci, Maria Lucia; Dello Russo, Antonio; Bencardino, Gianluigi; Pontone, Gianluca; Pelargonio, Gemma; Andreini, Daniele; Vitulano, Nicola; Pizzamiglio, Francesca; Conte, Edoardo; Crea, Filippo; Tondo, Claudio

2016-04-26

The growing number of atrial fibrillation catheter ablation procedures warranted the development of advanced cardiac mapping techniques, such as image integration between electroanatomical map and cardiac computed tomography. While scanning the chest before catheter ablation, it is frequent to detect cardiac and extracardiac collateral findings. Most collateral findings are promptly recognized as benign and do not require further attention. However, sometimes clinically relevant collateral findings are detected, which often warrant extra diagnostic examinations or even invasive procedure, and sometimes need to be followed-up over time. Even though reporting and further investigating collateral findings has not shown a clear survival benefit, almost all the working groups providing data on collateral findings reported some collateral findings eventually coming out to be malignancies, sometimes at an early stage. Therefore, there is currently no clear agreement about the right strategy to be followed.

Identifying Pathogenicity Islands in Bacterial Pathogenomics Using Computational Approaches

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Dongsheng Che

2014-01-01

Full Text Available High-throughput sequencing technologies have made it possible to study bacteria through analyzing their genome sequences. For instance, comparative genome sequence analyses can reveal the phenomenon such as gene loss, gene gain, or gene exchange in a genome. By analyzing pathogenic bacterial genomes, we can discover that pathogenic genomic regions in many pathogenic bacteria are horizontally transferred from other bacteria, and these regions are also known as pathogenicity islands (PAIs. PAIs have some detectable properties, such as having different genomic signatures than the rest of the host genomes, and containing mobility genes so that they can be integrated into the host genome. In this review, we will discuss various pathogenicity island-associated features and current computational approaches for the identification of PAIs. Existing pathogenicity island databases and related computational resources will also be discussed, so that researchers may find it to be useful for the studies of bacterial evolution and pathogenicity mechanisms.

Whole body computed tomographic findings of each one case with primary aldosteronism and Cushing syndrome

International Nuclear Information System (INIS)

Kamata, Shuji; Kawamura, Koro; Nakamura, Motoyuki

1980-01-01

We here report each one case with primary aldosteronism (male, 28 years old) and Cushing syndrome (female, 37 years old). Both of the cases showed characteristic clinical signs of hypertension and typical laboratory findings of adreno-hormonal assays. In performance of whole body computed tomography, clear pictures of tumorous adenomas in both cases were taken and the sizes of adenomas in picture were completely same as the masses obtained by the lateral adrenectomies. As a result, the whole body computed tomography is very useful to diagnose the diseases of adrenal adenoma and hyperplasia. (author)

Metastatic pulmonary calcification: high-resolution computed tomography findings in 23 cases

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Luciana Camara Belém

Full Text Available Abstract Objective: The aim of this study was to evaluate the high-resolution computed tomography (HRCT findings in patients diagnosed with metastatic pulmonary calcification (MPC. Materials and Methods: We retrospectively reviewed the HRCT findings from 23 cases of MPC [14 men, 9 women; mean age, 54.3 (range, 26-89 years]. The patients were examined between 2000 and 2014 in nine tertiary hospitals in Brazil, Chile, and Canada. Diagnoses were established by histopathologic study in 18 patients and clinical-radiological correlation in 5 patients. Two chest radiologists analyzed the images and reached decisions by consensus. Results: The predominant HRCT findings were centrilobular ground-glass nodules (n = 14; 60.9%, consolidation with high attenuation (n = 10; 43.5%, small dense nodules (n = 9; 39.1%, peripheral reticular opacities associated with small calcified nodules (n = 5; 21.7%, and ground-glass opacities without centrilobular ground-glass nodular opacity (n = 5; 21.7%. Vascular calcification within the chest wall was found in four cases and pleural effusion was observed in five cases. The abnormalities were bilateral in 21 cases. Conclusion: MPC manifested with three main patterns on HRCT, most commonly centrilobular ground-glass nodules, often containing calcifications, followed by dense consolidation and small solid nodules, most of which were calcified. We also described another pattern of peripheral reticular opacities associated with small calcified nodules. These findings should suggest the diagnosis of MPC in the setting of hypercalcemia.

Metastatic pulmonary calcification: high-resolution computed tomography findings in 23 cases

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Belem, Luciana Camara; Souza, Carolina A.; Souza Junior, Arthur Soares; Escuissato, Dante Luiz; Hochhegger, Bruno; Nobre, Luiz Felipe; Rodrigues, Rosana Souza; Gomes, Antonio Carlos Portugal; Silva, Claudio S.; Guimaraes, Marcos Duarte; Zanetti, Glaucia; Marchiori, Edson, E-mail: edmarchiori@gmail.com [Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ (Brazil); Ottawa Hospital Research Institute, University of Ottawa, (Canada); Faculdade de Medicina de Sao Jose do Rio Preto (FAMERP), SP (Brazil); Ultra X, Sao Jose do Rio Preto, SP (Brazil); Universidade Federal do Parana (UFPR), Curitiba, PR (Brazil); Universidade Federal de Ciencias da Saude de Porto Alegre (UFCSPA), Porto Alegre, RS (Brazil); Universidade Federal de Santa Catarina (UFSC), Florianopolis, SC (Brazil). Hospital Universitario

2017-07-15

Objective: The aim of this study was to evaluate the high-resolution computed tomography (HRCT) findings in patients diagnosed with metastatic pulmonary calcification (MPC). Materials and Methods: We retrospectively reviewed the HRCT findings from 23 cases of MPC [14 men, 9 women; mean age, 54.3 (range, 26-89) years]. The patients were examined between 2000 and 2014 in nine tertiary hospitals in Brazil, Chile, and Canada. Diagnoses were established by histopathologic study in 18 patients and clinical-radiological correlation in 5 patients. Two chest radiologists analyzed the images and reached decisions by consensus. Results: The predominant HRCT findings were centrilobular ground-glass nodules (n = 14; 60.9%), consolidation with high attenuation (n = 10; 43.5%), small dense nodules (n = 9; 39.1%), peripheral reticular opacities associated with small calcified nodules (n = 5; 21.7%), and ground-glass opacities without centrilobular ground-glass nodular opacity (n = 5; 21.7%). Vascular calcification within the chest wall was found in four cases and pleural effusion was observed in five cases. The abnormalities were bilateral in 21 cases. Conclusion: MPC manifested with three main patterns on HRCT, most commonly centrilobular ground-glass nodules, often containing calcifications, followed by dense consolidation and small solid nodules, most of which were calcified. We also described another pattern of peripheral reticular opacities associated with small calcified nodules. These findings should suggest the diagnosis of MPC in the setting of hypercalcemia. (author)

Metastatic pulmonary calcification: high-resolution computed tomography findings in 23 cases

International Nuclear Information System (INIS)

Belem, Luciana Camara; Souza, Carolina A.; Souza Junior, Arthur Soares; Escuissato, Dante Luiz; Hochhegger, Bruno; Nobre, Luiz Felipe; Rodrigues, Rosana Souza; Gomes, Antonio Carlos Portugal; Silva, Claudio S.; Guimaraes, Marcos Duarte; Zanetti, Glaucia; Marchiori, Edson; Ottawa Hospital Research Institute, University of Ottawa,; Faculdade de Medicina de Sao Jose do Rio Preto; Ultra X, Sao Jose do Rio Preto, SP; Universidade Federal do Parana; Universidade Federal de Ciencias da Saude de Porto Alegre; Universidade Federal de Santa Catarina

2017-01-01

Objective: The aim of this study was to evaluate the high-resolution computed tomography (HRCT) findings in patients diagnosed with metastatic pulmonary calcification (MPC). Materials and Methods: We retrospectively reviewed the HRCT findings from 23 cases of MPC [14 men, 9 women; mean age, 54.3 (range, 26-89) years]. The patients were examined between 2000 and 2014 in nine tertiary hospitals in Brazil, Chile, and Canada. Diagnoses were established by histopathologic study in 18 patients and clinical-radiological correlation in 5 patients. Two chest radiologists analyzed the images and reached decisions by consensus. Results: The predominant HRCT findings were centrilobular ground-glass nodules (n = 14; 60.9%), consolidation with high attenuation (n = 10; 43.5%), small dense nodules (n = 9; 39.1%), peripheral reticular opacities associated with small calcified nodules (n = 5; 21.7%), and ground-glass opacities without centrilobular ground-glass nodular opacity (n = 5; 21.7%). Vascular calcification within the chest wall was found in four cases and pleural effusion was observed in five cases. The abnormalities were bilateral in 21 cases. Conclusion: MPC manifested with three main patterns on HRCT, most commonly centrilobular ground-glass nodules, often containing calcifications, followed by dense consolidation and small solid nodules, most of which were calcified. We also described another pattern of peripheral reticular opacities associated with small calcified nodules. These findings should suggest the diagnosis of MPC in the setting of hypercalcemia. (author)

Computed tomography findings examined on an event which would originate chronic subdural hematoma

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Maekawa, Masayoshi; Fukuda, Seisuke; Awaya, Sakae [Mejiro Hospital, Tokyo (Japan); Teramoto, Akira [Nippon Medical School, Tokyo (Japan)

2002-11-01

Computed tomography (CT) findings examined on an event which would originate chronic subdural hematoma (CSDH) in the future are rare. We studied the original events causing CSDH and the following mechanism by which CSDH was originated on the basis of our CT findings examined on the event originating CSDH. Nine patients with traumatic CSDH were reviewed. The patients ranged in age from 48 to 89 years (mean 69.1 years). CT findings examined on the event originating CSDH were analyzed about both extracranial and intracranial lesions. All patients were divided into two groups; non-advanced age (under 70 years, n=5) and advanced age (over 70 years, n=4). All five patients in the non-advanced age group had abnormal findings at least in the extracranial area on CT examined on the event originating CSDH. On the other hand, only one patient had abnormal findings on CT examined on the event originating CSDH in the advanced age group. It is fact that slight head injuries cause CSDH in the advanced age, but it is probably that not slight head injuries such as to reveal abnormal findings at least in the extracranial area on CT cause CSDH in the non-advanced age. (author)

Computed tomography findings examined on an event which would originate chronic subdural hematoma

International Nuclear Information System (INIS)

Maekawa, Masayoshi; Fukuda, Seisuke; Awaya, Sakae; Teramoto, Akira

2002-01-01

Computed tomography (CT) findings examined on an event which would originate chronic subdural hematoma (CSDH) in the future are rare. We studied the original events causing CSDH and the following mechanism by which CSDH was originated on the basis of our CT findings examined on the event originating CSDH. Nine patients with traumatic CSDH were reviewed. The patients ranged in age from 48 to 89 years (mean 69.1 years). CT findings examined on the event originating CSDH were analyzed about both extracranial and intracranial lesions. All patients were divided into two groups; non-advanced age (under 70 years, n=5) and advanced age (over 70 years, n=4). All five patients in the non-advanced age group had abnormal findings at least in the extracranial area on CT examined on the event originating CSDH. On the other hand, only one patient had abnormal findings on CT examined on the event originating CSDH in the advanced age group. It is fact that slight head injuries cause CSDH in the advanced age, but it is probably that not slight head injuries such as to reveal abnormal findings at least in the extracranial area on CT cause CSDH in the non-advanced age. (author)

Computed Tomography Findings in Patients with Seizure Disorder

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Sumnima Acharya

2016-06-01

Full Text Available Introduction: Seizure occurs in up to 10% of the population, whereas epilepsy is a chronic disease characterized by recurrent seizures that may affect up to 2% of the population. Modern neuroimaging is useful in diagnosis of  abnormalities underlying the epilepsies, but the information provided by imaging techniques can also contribute to proper classification of certain epileptic disorders and can delineate the genetics of some underlying syndromes. Neuroimaging is even more important for those patients who have medically intractable seizures. This study was carried out to establish different etiologies of seizures, to correlate the clinical data and radiological findings in cases of seizure, and to identify the common etiologies in different types of seizures. Methods: This was a retrospective hospital-based study conducted in the Department of Radiodiagnosis of Lumbini Medical College Teaching Hospital. Records of patients of past two years, admitted in any department of the hospital with history of seizure disorder and underwent a Computed Tomography  (CT of brain were included. The CT patterns were assessed and the data were tabulated and statistically analyzed. Results: There were a total of 480 cases out of which 263 (55% were male and 217 (45% were female with M:F ratio of 1.2:1. Generalized seizure was more frequent than partial seizure in both gender. In 274 cases of generalized seizures, CT scan findings were abnormal in 151 cases and normal finding observed in 123 cases. In 206 cases of partial seizures, 125 cases were abnormal and 81 having normal CT scan findings. Age wise distribution showed highest number (n=218 of cases in young group (60 yr. The most common cause of seizure  was  calcified granuloma (n=79, 16.5% followed by neurocysticercosis (NCC, n=64, 13%. Diffuse cerebral edema, sub-arachnoid hemorrhage, and hydrocephalus was seen only in lower age group particularly among 1-20 years. Infarct and diffuse cortical

Where we stand, where we are moving: Surveying computational techniques for identifying miRNA genes and uncovering their regulatory role

KAUST Repository

Kleftogiannis, Dimitrios A.; Korfiati, Aigli; Theofilatos, Konstantinos A.; Likothanassis, Spiridon D.; Tsakalidis, Athanasios K.; Mavroudi, Seferina P.

2013-01-01

Traditional biology was forced to restate some of its principles when the microRNA (miRNA) genes and their regulatory role were firstly discovered. Typically, miRNAs are small non-coding RNA molecules which have the ability to bind to the 3'untraslated region (UTR) of their mRNA target genes for cleavage or translational repression. Existing experimental techniques for their identification and the prediction of the target genes share some important limitations such as low coverage, time consuming experiments and high cost reagents. Hence, many computational methods have been proposed for these tasks to overcome these limitations. Recently, many researchers emphasized on the development of computational approaches to predict the participation of miRNA genes in regulatory networks and to analyze their transcription mechanisms. All these approaches have certain advantages and disadvantages which are going to be described in the present survey. Our work is differentiated from existing review papers by updating the methodologies list and emphasizing on the computational issues that arise from the miRNA data analysis. Furthermore, in the present survey, the various miRNA data analysis steps are treated as an integrated procedure whose aims and scope is to uncover the regulatory role and mechanisms of the miRNA genes. This integrated view of the miRNA data analysis steps may be extremely useful for all researchers even if they work on just a single step. © 2013 Elsevier Inc.

Where we stand, where we are moving: Surveying computational techniques for identifying miRNA genes and uncovering their regulatory role

KAUST Repository

Kleftogiannis, Dimitrios A.

2013-06-01

Traditional biology was forced to restate some of its principles when the microRNA (miRNA) genes and their regulatory role were firstly discovered. Typically, miRNAs are small non-coding RNA molecules which have the ability to bind to the 3\\'untraslated region (UTR) of their mRNA target genes for cleavage or translational repression. Existing experimental techniques for their identification and the prediction of the target genes share some important limitations such as low coverage, time consuming experiments and high cost reagents. Hence, many computational methods have been proposed for these tasks to overcome these limitations. Recently, many researchers emphasized on the development of computational approaches to predict the participation of miRNA genes in regulatory networks and to analyze their transcription mechanisms. All these approaches have certain advantages and disadvantages which are going to be described in the present survey. Our work is differentiated from existing review papers by updating the methodologies list and emphasizing on the computational issues that arise from the miRNA data analysis. Furthermore, in the present survey, the various miRNA data analysis steps are treated as an integrated procedure whose aims and scope is to uncover the regulatory role and mechanisms of the miRNA genes. This integrated view of the miRNA data analysis steps may be extremely useful for all researchers even if they work on just a single step. © 2013 Elsevier Inc.

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

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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

FiGS: a filter-based gene selection workbench for microarray data

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Yun Taegyun

2010-01-01

Full Text Available Abstract Background The selection of genes that discriminate disease classes from microarray data is widely used for the identification of diagnostic biomarkers. Although various gene selection methods are currently available and some of them have shown excellent performance, no single method can retain the best performance for all types of microarray datasets. It is desirable to use a comparative approach to find the best gene selection result after rigorous test of different methodological strategies for a given microarray dataset. Results FiGS is a web-based workbench that automatically compares various gene selection procedures and provides the optimal gene selection result for an input microarray dataset. FiGS builds up diverse gene selection procedures by aligning different feature selection techniques and classifiers. In addition to the highly reputed techniques, FiGS diversifies the gene selection procedures by incorporating gene clustering options in the feature selection step and different data pre-processing options in classifier training step. All candidate gene selection procedures are evaluated by the .632+ bootstrap errors and listed with their classification accuracies and selected gene sets. FiGS runs on parallelized computing nodes that capacitate heavy computations. FiGS is freely accessible at http://gexp.kaist.ac.kr/figs. Conclusion FiGS is an web-based application that automates an extensive search for the optimized gene selection analysis for a microarray dataset in a parallel computing environment. FiGS will provide both an efficient and comprehensive means of acquiring optimal gene sets that discriminate disease states from microarray datasets.

Internal carotid arterial occlusion in computed tomography. Correlation of CT and angiographic findings

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Harada, K.; Miura, T.; Nishikubo, Y.; Kawai, R.; Mitomo, M. (Osaka Univ. (Japan). Faculty of Medicine)

1981-09-01

The computed tomographic appearance of internal carotid arterial occlusion was reviewed in 33 patients. In 23 of them, who underwent 4-vessel study, the angiographic and CT findings were compared. Ten patients were disclosed to have watershed infarction by CT. Seven of them had watershed processes in the centrum semiovale which were considered to be terminal infarction. Patients who showed watershed infarction under CT revealed inadequate circle of Willis and well-developed cortical anastomosis under angiography. Unilaterally accentuated cerebral atrophy, which we have called asymmetrical atrophy in this paper, was noted in 10 patients. The findings of asymmetrical cerebral atrophy sometimes resemble the changes secondary to old infarction. However, the changes in the lateral ventricle caused by asymmetrical cerebral atrophy are somewhat different from those resulting from old infarction. The angiographic findings suggested that asymmetrical cerebral atrophy is, in addition to being associated with incomplete circle of Willis, also associated with local circulatory disturbances which further decrease the regional cerebral blood flow in the affected hemisphere.

The Shortlist Method for fast computation of the Earth Mover's Distance and finding optimal solutions to transportation problems.

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Gottschlich, Carsten; Schuhmacher, Dominic

2014-01-01

Finding solutions to the classical transportation problem is of great importance, since this optimization problem arises in many engineering and computer science applications. Especially the Earth Mover's Distance is used in a plethora of applications ranging from content-based image retrieval, shape matching, fingerprint recognition, object tracking and phishing web page detection to computing color differences in linguistics and biology. Our starting point is the well-known revised simplex algorithm, which iteratively improves a feasible solution to optimality. The Shortlist Method that we propose substantially reduces the number of candidates inspected for improving the solution, while at the same time balancing the number of pivots required. Tests on simulated benchmarks demonstrate a considerable reduction in computation time for the new method as compared to the usual revised simplex algorithm implemented with state-of-the-art initialization and pivot strategies. As a consequence, the Shortlist Method facilitates the computation of large scale transportation problems in viable time. In addition we describe a novel method for finding an initial feasible solution which we coin Modified Russell's Method.

Computed tomographic findings of traumatic intracranial lesions

International Nuclear Information System (INIS)

Jeong, Seong Wook; Kim, Il Young; Lee, Byung Ho; Kim, Ki Jeoung; Yoon, Il Gyu

1985-01-01

Traumatic intracranial lesion has been one of the most frequent and serious problem in neurosurgical pathology. Computed tomography made it possible to get prompt diagnosis and surgical intervention of intracranial lesions by its safety, fastness and accuracy. Computed tomographic scan was carried out on 1309 cases at Soonchunhyang Chunan Hospital for 15 months from October 1983 to December 1984. We have reviewed the computed tomographic scans of 264 patients which showed traumatic intracranial lesion. The result were as follows: 1. Head trauma was the most frequent diagnosed disease using computed tomographic scans (57.8%) and among 264 cases the most frequent mode of injury was traffic accident (73.9%). 2. Skull fracture was accompanied in frequency of 69.7% and it was detected in CT in 38.6%: depression fracture was more easily detected in 81%. 3. Conutercoup lesion (9.5%) was usually accompanied with temporal and occipital fracture, and it appeared in lower incidence among pediatric group. 4. Intracranial lesions of all 264 cases were generalized cerebral swelling (24.6%), subdural hematoma (22.3%), epidural hematoma (20.8%), intracerebral hematoma (6.1%), and subarachnoid hemorrhage (3.0%). 5. The shape of hematoma was usually biconvex (92.7%) in acute epidural hematoma and cresentic (100%) in acute subdural hematoma, but the most chronic the case became, they showed planoconvex and bicconvex shapes. 6. Extra-axial hematoma was getting decreased in density as time gone by. 7. Hematoma density was not in direct proportion to serum hemoglobin level as single factor

Computed tomographic findings of traumatic intracranial lesions

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Jeong, Seong Wook; Kim, Il Young; Lee, Byung Ho; Kim, Ki Jeoung; Yoon, Il Gyu [Soonchunhyang University College of Medicine, Seoul (Korea, Republic of)

1985-10-15

Traumatic intracranial lesion has been one of the most frequent and serious problem in neurosurgical pathology. Computed tomography made it possible to get prompt diagnosis and surgical intervention of intracranial lesions by its safety, fastness and accuracy. Computed tomographic scan was carried out on 1309 cases at Soonchunhyang Chunan Hospital for 15 months from October 1983 to December 1984. We have reviewed the computed tomographic scans of 264 patients which showed traumatic intracranial lesion. The result were as follows: 1. Head trauma was the most frequent diagnosed disease using computed tomographic scans (57.8%) and among 264 cases the most frequent mode of injury was traffic accident (73.9%). 2. Skull fracture was accompanied in frequency of 69.7% and it was detected in CT in 38.6%: depression fracture was more easily detected in 81%. 3. Conutercoup lesion (9.5%) was usually accompanied with temporal and occipital fracture, and it appeared in lower incidence among pediatric group. 4. Intracranial lesions of all 264 cases were generalized cerebral swelling (24.6%), subdural hematoma (22.3%), epidural hematoma (20.8%), intracerebral hematoma (6.1%), and subarachnoid hemorrhage (3.0%). 5. The shape of hematoma was usually biconvex (92.7%) in acute epidural hematoma and cresentic (100%) in acute subdural hematoma, but the most chronic the case became, they showed planoconvex and bicconvex shapes. 6. Extra-axial hematoma was getting decreased in density as time gone by. 7. Hematoma density was not in direct proportion to serum hemoglobin level as single factor.

Ground-glass opacity: High-resolution computed tomography and 64-multi-slice computed tomography findings comparison

International Nuclear Information System (INIS)

Sergiacomi, Gianluigi; Ciccio, Carmelo; Boi, Luca; Velari, Luca; Crusco, Sonia; Orlacchio, Antonio; Simonetti, Giovanni

2010-01-01

Objective: Comparative evaluation of ground-glass opacity using conventional high-resolution computed tomography technique and volumetric computed tomography by 64-row multi-slice scanner, verifying advantage of volumetric acquisition and post-processing technique allowed by 64-row CT scanner. Methods: Thirty-four patients, in which was assessed ground-glass opacity pattern by previous high-resolution computed tomography during a clinical-radiological follow-up for their lung disease, were studied by means of 64-row multi-slice computed tomography. Comparative evaluation of image quality was done by both CT modalities. Results: It was reported good inter-observer agreement (k value 0.78-0.90) in detection of ground-glass opacity with high-resolution computed tomography technique and volumetric Computed Tomography acquisition with moderate increasing of intra-observer agreement (k value 0.46) using volumetric computed tomography than high-resolution computed tomography. Conclusions: In our experience, volumetric computed tomography with 64-row scanner shows good accuracy in detection of ground-glass opacity, providing a better spatial and temporal resolution and advanced post-processing technique than high-resolution computed tomography.

A Computational Gene Expression Score for Predicting Immune Injury in Renal Allografts.

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Tara K Sigdel

Full Text Available Whole genome microarray meta-analyses of 1030 kidney, heart, lung and liver allograft biopsies identified a common immune response module (CRM of 11 genes that define acute rejection (AR across different engrafted tissues. We evaluated if the CRM genes can provide a molecular microscope to quantify graft injury in acute rejection (AR and predict risk of progressive interstitial fibrosis and tubular atrophy (IFTA in histologically normal kidney biopsies.Computational modeling was done on tissue qPCR based gene expression measurements for the 11 CRM genes in 146 independent renal allografts from 122 unique patients with AR (n = 54 and no-AR (n = 92. 24 demographically matched patients with no-AR had 6 and 24 month paired protocol biopsies; all had histologically normal 6 month biopsies, and 12 had evidence of progressive IFTA (pIFTA on their 24 month biopsies. Results were correlated with demographic, clinical and pathology variables.The 11 gene qPCR based tissue CRM score (tCRM was significantly increased in AR (5.68 ± 0.91 when compared to STA (1.29 ± 0.28; p < 0.001 and pIFTA (7.94 ± 2.278 versus 2.28 ± 0.66; p = 0.04, with greatest significance for CXCL9 and CXCL10 in AR (p <0.001 and CD6 (p<0.01, CXCL9 (p<0.05, and LCK (p<0.01 in pIFTA. tCRM was a significant independent correlate of biopsy confirmed AR (p < 0.001; AUC of 0.900; 95% CI = 0.705-903. Gene expression modeling of 6 month biopsies across 7/11 genes (CD6, INPP5D, ISG20, NKG7, PSMB9, RUNX3, and TAP1 significantly (p = 0.037 predicted the development of pIFTA at 24 months.Genome-wide tissue gene expression data mining has supported the development of a tCRM-qPCR based assay for evaluating graft immune inflammation. The tCRM score quantifies injury in AR and stratifies patients at increased risk of future pIFTA prior to any perturbation of graft function or histology.

Computed Tomographic Findings and Mortality in Patients With Pneumomediastinum From Blunt Trauma.

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Lee, Wayne S; Chong, Vincent E; Victorino, Gregory P

2015-08-01

The care of most patients with pneumomediastinum (PNM) due to trauma can be managed conservatively; however, owing to aerodigestive tract injury and other associated injuries, there is a subset of patients with PNM who are at higher risk of mortality but can be difficult to identify. To characterize computed tomographic (CT) findings associated with mortality in patients with PNM due to blunt trauma. A retrospective review of medical records from January 1, 2002, to December 31, 2011, was conducted at a university-based urban trauma center. The patients evaluated were those injured by blunt trauma and found to have PNM on initial chest CT scanning. Data analysis was performed July 2, 2013, to June 18, 2014. In-hospital mortality. During the study period, 3327 patients with blunt trauma underwent chest CT. Of these, 72 patients (2.2%) had PNM. Patients with PNM had higher Injury Severity Scores (P blunt trauma; however, CT findings of posterior PNM, air in all mediastinal compartments, and concurrent hemothorax are associated with increased mortality. These CT findings could be used as a triage tool to alert the trauma surgeon to a potentially lethal injury.

Identifying the impact of G-quadruplexes on Affymetrix 3' arrays using cloud computing.

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Memon, Farhat N; Owen, Anne M; Sanchez-Graillet, Olivia; Upton, Graham J G; Harrison, Andrew P

2010-01-15

A tetramer quadruplex structure is formed by four parallel strands of DNA/ RNA containing runs of guanine. These quadruplexes are able to form because guanine can Hoogsteen hydrogen bond to other guanines, and a tetrad of guanines can form a stable arrangement. Recently we have discovered that probes on Affymetrix GeneChips that contain runs of guanine do not measure gene expression reliably. We associate this finding with the likelihood that quadruplexes are forming on the surface of GeneChips. In order to cope with the rapidly expanding size of GeneChip array datasets in the public domain, we are exploring the use of cloud computing to replicate our experiments on 3' arrays to look at the effect of the location of G-spots (runs of guanines). Cloud computing is a recently introduced high-performance solution that takes advantage of the computational infrastructure of large organisations such as Amazon and Google. We expect that cloud computing will become widely adopted because it enables bioinformaticians to avoid capital expenditure on expensive computing resources and to only pay a cloud computing provider for what is used. Moreover, as well as financial efficiency, cloud computing is an ecologically-friendly technology, it enables efficient data-sharing and we expect it to be faster for development purposes. Here we propose the advantageous use of cloud computing to perform a large data-mining analysis of public domain 3' arrays.

A computational method based on the integration of heterogeneous networks for predicting disease-gene associations.

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Xingli Guo

Full Text Available The identification of disease-causing genes is a fundamental challenge in human health and of great importance in improving medical care, and provides a better understanding of gene functions. Recent computational approaches based on the interactions among human proteins and disease similarities have shown their power in tackling the issue. In this paper, a novel systematic and global method that integrates two heterogeneous networks for prioritizing candidate disease-causing genes is provided, based on the observation that genes causing the same or similar diseases tend to lie close to one another in a network of protein-protein interactions. In this method, the association score function between a query disease and a candidate gene is defined as the weighted sum of all the association scores between similar diseases and neighbouring genes. Moreover, the topological correlation of these two heterogeneous networks can be incorporated into the definition of the score function, and finally an iterative algorithm is designed for this issue. This method was tested with 10-fold cross-validation on all 1,126 diseases that have at least a known causal gene, and it ranked the correct gene as one of the top ten in 622 of all the 1,428 cases, significantly outperforming a state-of-the-art method called PRINCE. The results brought about by this method were applied to study three multi-factorial disorders: breast cancer, Alzheimer disease and diabetes mellitus type 2, and some suggestions of novel causal genes and candidate disease-causing subnetworks were provided for further investigation.

Algebraic model checking for Boolean gene regulatory networks.

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Tran, Quoc-Nam

2011-01-01

We present a computational method in which modular and Groebner bases (GB) computation in Boolean rings are used for solving problems in Boolean gene regulatory networks (BN). In contrast to other known algebraic approaches, the degree of intermediate polynomials during the calculation of Groebner bases using our method will never grow resulting in a significant improvement in running time and memory space consumption. We also show how calculation in temporal logic for model checking can be done by means of our direct and efficient Groebner basis computation in Boolean rings. We present our experimental results in finding attractors and control strategies of Boolean networks to illustrate our theoretical arguments. The results are promising. Our algebraic approach is more efficient than the state-of-the-art model checker NuSMV on BNs. More importantly, our approach finds all solutions for the BN problems.

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...

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

Fournier gangrene: report of three cases, computed tomography imaging findings and literature review

International Nuclear Information System (INIS)

Judici, Paola Lima Pasini; Christofoli, Maria Olivia Jacques de Medeiros; Oliveira, Paulo Cesar Rocha; Teles, Ilailson de Goes; Najjar, Yana Senna Jeronimo

2010-01-01

The authors report three cases of patients with Fournier gangrene. This is a polymicrobial infectious disease that affects the perineum and genitalia, especially in males, whose source is most commonly genitourinary, colorectal or cutaneous and may also not have a clearly defined focus. Potentially lethal, requires immediate clinical and surgical treatment. The purpose of this report is to describe the main findings of imaging on computed tomography in this disease and to briefly review the literature on the subject. (author)

High-resolution computed tomographic findings of Aspergillus infection in lung transplant patients

International Nuclear Information System (INIS)

Gazzoni, Fernando Ferreira; Hochhegger, Bruno; Severo, Luiz Carlos; Marchiori, Edson; Pasqualotto, Alessandro; Sartori, Ana Paula Garcia; Schio, Sadi; Camargo, José

2014-01-01

Objective: The aim of this study was to assess high-resolution computed tomographic (HRCT) findings at presentation in lung transplant patients diagnosed with pulmonary Aspergillus infection. Materials and methods: We retrospectively reviewed HRCT findings from 23 patients diagnosed with pulmonary aspergillosis. Imaging studies were performed 2–5 days after the onset of symptoms. The patient sample comprised 12 men and 11 women aged 22–59 years (mean age, 43.6 years). All patients had dyspnea, tachypnea, and cough. Diagnoses were established with Platelia Aspergillus enzyme immunoassays for galactomannan antigen detection in bronchoalveolar lavage and recovery of symptoms, and HRCT findings after voriconazole treatment. The HRCT scans were reviewed independently by two observers who reached a consensus decision. Results: The main HRCT pattern, found in 65% (n = 15) of patients, was centrilobular tree-in-bud nodules associated with bronchial thickening. This pattern was described in association with areas of consolidation and ground-glass opacities in 13% (n = 3) of patients. Consolidation and ground-glass opacities were the main pattern in 22% (n = 5) of patients. The pattern of large nodules with and without the halo sign was observed in 13% (n = 3) of patients, and were associated with consolidation and ground-glass opacities in one case. Conclusion: The predominant HRCT findings in lung transplant patients with pulmonary aspergillosis were bilateral bronchial wall thickening and centrilobular opacities with the tree-in-bud pattern. Ground-glass opacities and/or bilateral areas of consolidation were also common findings. Pulmonary nodules with the halo sign were found in only 13% of patients

Primary intestinal lymphangiectasia: Multiple detector computed tomography findings after direct lymphangiography.

Science.gov (United States)

Sun, Xiaoli; Shen, Wenbin; Chen, Xiaobai; Wen, Tingguo; Duan, Yongli; Wang, Rengui

2017-10-01

To analyse the findings of multiple detector computed tomography (MDCT) after direct lymphangiography in primary intestinal lymphangiectasia (PIL). Fifty-five patients with PIL were retrospectively reviewed. All patients underwent MDCT after direct lymphangiography. The pathologies of 16 patients were confirmed by surgery and the remaining 39 patients were confirmed by gastroendoscopy and/or capsule endoscopy. After direct lymphangiography, MDCT found intra- and extraintestinal as well as lymphatic vessel abnormalities. Among the intra- and extraintestinal disorders, 49 patients had varying degrees of intestinal dilatation, 46 had small bowel wall thickening, 9 had pleural and pericardial effusions, 21 had ascites, 41 had mesenteric oedema, 20 had mesenteric nodules and 9 had abdominal lymphatic cysts. Features of lymphatic vessel abnormalities included intestinal trunk reflux (43.6%, n = 24), lumbar trunk reflux (89.1%, n = 49), pleural and pulmonary lymph reflux (14.5%, n = 8), pericardial and mediastinal lymph reflux (16.4%, n = 9), mediastinal and pulmonary lymph reflux (18.2%, n = 10), and thoracic duct outlet obstruction (90.9%, n = 50). Multiple detector computed tomography after direct lymphangiography provides a safe and accurate examination method and is an excellent tool for the diagnosis of PIL. © 2017 The Royal Australian and New Zealand College of Radiologists.

Progressive systemic sclerosis: high-resolution computed tomography findings; Esclerose sistemica progressiva: aspectos na tomografia computadorizada de alta resolucao

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Gasparetto, Emerson L.; Pimenta, Rodrigo; Ono, Sergio E.; Escuissato, Dante L. [Parana Univ., Curitiba, PR (Brazil). Hospital de Clinicas. Servico de Radiologia Medica]. E-mail: dante.luiz@onda.com.br; Inoue, Cesar [Parana Univ., Curitiba, PR (Brazil). Faculdade de Medicina

2005-09-15

Objective: To describe the high-resolution computed tomography findings in the lung of patients with systemic sclerosis, independently of the respiratory symptoms. Materials and methods: Seventy-three high-resolution computed tomography scans of 44 patients with clinical diagnosis of systemic sclerosis were reviewed and defined by the consensus of two radiologists. Results: Abnormalities were seen in 91.8% (n = 67) of the scans. The most frequent findings were reticular pattern (90.4%), ground-glass opacities (63%), traction bronchiectasis and bronchiolectasis (56.2%), esophageal dilatation (46.6%), honeycombing pattern (28.8%) and signs of pulmonary hypertension (15.6%). In most cases the lesions were bilateral (89%) and symmetrical (58.5%). The lesions were predominantly located in the basal (91.2%) and peripheral (92.2%) regions. Conclusion: In the majority of the patients, progressive systemic sclerosis can cause pulmonary fibrosis mainly characterized by reticular pattern with basal and peripheral distribution on high-resolution computed tomography. (author)

Computed Tomographic Findings of Acute Carbon Monoxide Posioning

International Nuclear Information System (INIS)

Park, Young Keun; Won, Hee Sun; Lee, Seung Ro; Hahm, Chang Kok

1983-01-01

Carbon monoxide (CO) is a kind of frequent toxic gas around our living lives, for common use of briquets as fuel, and its pathologic effect has been known due to mainly hypoxia and direct cytotoxicity in some part to almost all organs, especially to the brain and heart. Some authors have reported pathologic and anatomic changes of the acute of poisoning, although in a few cases, that bilaterally symmetrical lesions of the globs pallidus or cerebral white matter regarded as typical. After using computed tomography (CT), those findings have been discovered more easily and accurately. Authors analysed CT findings of 32 cases, who had a history of acute CO poisoning and performed CT at Hanyang University Hospital from May 1970 to June 1983. The results were as follows: 1. Of all 32 cases with CT scan, low density lesions were demonstrated in 28 cases (88%) and others were hemorrhage and calcified in 2(6%), respectively. 2. All lesions were seen as bilaterally symmetrical, except 2 cases of hemorrhage and 1 of low density. 3. Of all 28 cases of the low densities, 15 cases(53.6%) were located in the globs pallidus, 10(35.7%) in the cerebral white matter and 3(10.7%) in both of them. 4. Of all 113 cases of the low density lesions in the cerebral white matter, common locations were in the frontal and parietal lobes (65.6%), and more in frontal (40.6%). 5. Of all 113 cases of low density lesions in the cerebral white matter, cases of involving all of the lobes were found in only 4. 6. All of 2 cases of the calcified lesions were seen at both sides of the globs pallidus, symmetrically. 7. All of 2 cases of the hemorrhage were seen at thalamus, ventricles and head of caudate nucleus, and these locations were different from those of the low densities or calcifications.

Computed tomographic findings of skeletal muscles in amyotrophic lateral sclerosis (ALS)

International Nuclear Information System (INIS)

Takahashi, Ryosuke; Imai, Terukuni; Sadashima, Hiromichi; Matsumoto, Sadayuki; Yamamoto, Toru; Kusaka, Hirobumi; Yamasaki, Masahiro; Maya, Kiyomi; Tanabe, Masaya

1989-01-01

We evaluated the Computed Tomographic (CT) findings of skeletal muscles in 12 cases of amyotrophic lateral sclerosis (ALS), 1 case of spinal progressive muscular atrophy (SPMA), and 1 case of Kugelberg-Welander disease. CT examination was performed in the neck, shoulders, abdomen, pelvis, thighs, and lower legs, 15 muscles were selected for evaluation. The following muscles tended to be affected: m. transversospinalis (12 cases were abnormal), m. deltoideus (10), m. subscapularis (10), m. infraspinatus (10), mm. dorsi (12), hamstring muscles (14), m. tibialis anterior (14), and m. triceps surae (14). On the contrary, the following muscles tended to be preserved: m. sternocleidomastoideus (only 7 cases were abnormal), m. psoas major (7), m. gluteus maximus (7), m. rectus femoris (7), m. sartorius (7) and m. gracilis (6). The distribution of the muscles affected showed neither proximal nor distal dominancy. As the disease advanced, however, all the muscles became affected without any severity. CT findings of skeletal muscles in ALS were characterized by muscle atrophy and fat infiltration, which showed a patchy, linear, or moth-eaten appearance. In mildly affected cases, there was muscle atrophy without internal architectual changes. In moderately affected cases, muscle atrophy advanced and internal architectural changes (patchy, linear, and moth-eaten fat infiltration) became evident. In most advanced cases, every muscle showed a ragged appearance because of severe muscle atrophy and internal architectural changes. These findings were well distinguished from those of SPMA, which resembled the CT pattern of primary muscle diseases. (author)

Computed tomographic findings of skeletal muscles in amyotrophic lateral sclerosis (ALS)

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Takahashi, Ryosuke; Imai, Terukuni; Sadashima, Hiromichi; Matsumoto, Sadayuki; Yamamoto, Toru; Kusaka, Hirobumi; Yamasaki, Masahiro; Maya, Kiyomi; Tanabe, Masaya (Kitano Hospital, Osaka (Japan))

1989-04-01

We evaluated the Computed Tomographic (CT) findings of skeletal muscles in 12 cases of amyotrophic lateral sclerosis (ALS), 1 case of spinal progressive muscular atrophy (SPMA), and 1 case of Kugelberg-Welander disease. CT examination was performed in the neck, shoulders, abdomen, pelvis, thighs, and lower legs, 15 muscles were selected for evaluation. The following muscles tended to be affected: m. transversospinalis (12 cases were abnormal), m. deltoideus (10), m. subscapularis (10), m. infraspinatus (10), mm. dorsi (12), hamstring muscles (14), m. tibialis anterior (14), and m. triceps surae (14). On the contrary, the following muscles tended to be preserved: m. sternocleidomastoideus (only 7 cases were abnormal), m. psoas major (7), m. gluteus maximus (7), m. rectus femoris (7), m. sartorius (7) and m. gracilis (6). The distribution of the muscles affected showed neither proximal nor distal dominancy. As the disease advanced, however, all the muscles became affected without any severity. CT findings of skeletal muscles in ALS were characterized by muscle atrophy and fat infiltration, which showed a patchy, linear, or moth-eaten appearance. In mildly affected cases, there was muscle atrophy without internal architectual changes. In moderately affected cases, muscle atrophy advanced and internal architectural changes (patchy, linear, and moth-eaten fat infiltration) became evident. In most advanced cases, every muscle showed a ragged appearance because of severe muscle atrophy and internal architectural changes. These findings were well distinguished from those of SPMA, which resembled the CT pattern of primary muscle diseases. (author).

Computer tomographic findings in alcoholism

Energy Technology Data Exchange (ETDEWEB)

Agnoli, A.L.; Tzavaras, N.; Reisig, L. (Giessen Univ. (Germany, F.R.). Abt. Neuroradiologie)

1980-05-01

The normal variations in the size of the ventricular systems was determined on technically satisfactory computer tomograms in 275 patients who were psychologically and neurologically normal. Ages range from one to 80 years and the data classified in decades. A physiological increase in the width of the ventricular system was found after the 50sup(t)sup(h) year. The normal patients, who acted as a control group, were compared with 65 alcoholics. A significant increase in size (simple variance) was found in alcoholics after the fourth decade, as compared with normals. Correlation between the width of the ventricular system and cerebral function, and between liver damage and the ventricular system could not be established.

Correlation between presumed sinusitis-induced pain and paranasal sinus computed tomographic findings.

Science.gov (United States)

Mudgil, Shikha P; Wise, Scott W; Hopper, Kenneth D; Kasales, Claudia J; Mauger, David; Fornadley, John A

2002-02-01

The correlation between facial and/or head pain in patients clinically suspected of having sinusitis and actual localized findings on sinus computed tomographic (CT) imaging are poorly understood. To prospectively evaluate the relationship of paranasal sinus pain symptoms with CT imaging. Two hundred consecutive patients referred by otolaryngologists and internists for CT of the paranasal sinuses participated by completing a questionnaire immediately before undergoing CT. Three radiologists blinded to the patients' responses scored the degree of air/fluid level, mucosal thickening, bony reaction, and mucus retention cysts using a graded scale of severity (0 to 3 points). The osteomeatal complexes and nasolacrimal ducts were also evaluated for patency. Bivariate analysis was performed to evaluate the relationship between patients' localized symptoms and CT findings in the respective sinus. One hundred sixty-three patients (82%) reported having some form of facial pain or headache. The right temple/forehead was the most frequently reported region of maximal pain. On CT imaging the maxillary sinus was the most frequently involved sinus. Bivariate analysis failed to show any relationship between patient symptoms and findings on CT. Patients with a normal CT reported a mean 5.88 sites of facial or head pain versus 5.45 sites for patients with an abnormal CT. Patient-based responses of sinonasal pain symptoms fail to correlate with findings in the respective sinuses. CT should therefore be reserved for delineating the anatomy and degree of sinus disease before surgical intervention.

Computed tomographic findings and histological findings of an organized chronic subdural hematoma. A case report

Energy Technology Data Exchange (ETDEWEB)

Kamiya, Kazuko; Inagawa, Tetsuji; Nagasako, Ren

1987-08-01

As chronic subdural hematoma can be readily diagnosed by computed tomography (CT) and can be treated, there are no reports in the literature describing the CT findings of an organized chronic subdural hematoma with a long clinical course. The present case was a 53-year-old male who experienced a series of remissions and aggravations of such symptoms as right hemiparesis and consciousness disturbance for about five years. CT showed a crescent lesion in the left frontoparietal region. In the margin, an uneven, high-density area could be observed running in ward, and in the interior, an iso approx. low-density area could be seen, but no evident enhancement could be noted in either area. The patient died of liver cirrhosis, and an autopsy was performed. The hematoma was encapsulated with a very thick and hard membrane, and directly under the capsule the foci of fresh hemorrhage could be seen along the capsule. The interior of the hematoma was almost entirely organized. The clinical features of this case were considered to reflect the remissions and aggravations of symptoms due to repeated hemorrhages of the chronic subdural hematoma over an extended period.

Impacts of Nonsynonymous Single Nucleotide Polymorphisms of Adiponectin Receptor 1 Gene on Corresponding Protein Stability: A Computational Approach

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Md. Abu Saleh

2016-01-01

Full Text Available Despite the reported association of adiponectin receptor 1 (ADIPOR1 gene mutations with vulnerability to several human metabolic diseases, there is lack of computational analysis on the functional and structural impacts of single nucleotide polymorphisms (SNPs of the human ADIPOR1 at protein level. Therefore, sequence- and structure-based computational tools were employed in this study to functionally and structurally characterize the coding nsSNPs of ADIPOR1 gene listed in the dbSNP database. Our in silico analysis by SIFT, nsSNPAnalyzer, PolyPhen-2, Fathmm, I-Mutant 2.0, SNPs&GO, PhD-SNP, PANTHER, and SNPeffect tools identified the nsSNPs with distorting functional impacts, namely, rs765425383 (A348G, rs752071352 (H341Y, rs759555652 (R324L, rs200326086 (L224F, and rs766267373 (L143P from 74 nsSNPs of ADIPOR1 gene. Finally the aforementioned five deleterious nsSNPs were introduced using Swiss-PDB Viewer package within the X-ray crystal structure of ADIPOR1 protein, and changes in free energy for these mutations were computed. Although increased free energy was observed for all the mutants, the nsSNP H341Y caused the highest energy increase amongst all. RMSD and TM scores predicted that mutants were structurally similar to wild type protein. Our analyses suggested that the aforementioned variants especially H341Y could directly or indirectly destabilize the amino acid interactions and hydrogen bonding networks of ADIPOR1.

Approximating the edit distance for genomes with duplicate genes under DCJ, insertion and deletion

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Shao Mingfu

2012-12-01

Full Text Available Abstract Computing the edit distance between two genomes under certain operations is a basic problem in the study of genome evolution. The double-cut-and-join (DCJ model has formed the basis for most algorithmic research on rearrangements over the last few years. The edit distance under the DCJ model can be easily computed for genomes without duplicate genes. In this paper, we study the edit distance for genomes with duplicate genes under a model that includes DCJ operations, insertions and deletions. We prove that computing the edit distance is equivalent to finding the optimal cycle decomposition of the corresponding adjacency graph, and give an approximation algorithm with an approximation ratio of 1.5 + ∈.

Spectrum of fluorodeoxyglucose-positron emission tomography/computed tomography and magnetic resonance imaging findings of ovarian tumors.

Science.gov (United States)

Kitajima, Kazuhiro; Ueno, Yoshiko; Maeda, Tetsuo; Murakami, Koji; Kaji, Yasushi; Kita, Masato; Suzuki, Kayo; Sugimura, Kazuro

2011-11-01

The purpose of this article is to review fluorodeoxyglucose-positron emission tomography/computed tomography (FDG-PET/CT) and magnetic resonance imaging (MRI) findings in a variety of benign, malignant, and borderline malignant ovarian tumors. It is advantageous to become familiar with the wide variety of FDG-PET/CT findings of this entity. Benign ovarian tumors generally have faint uptake, whereas endometriomas, fibromas, and teratomas show mild to moderate uptake. Malignant ovarian tumors generally have intense uptake, whereas tumors with a small solid component often show minimal uptake.

A BAYESIAN NONPARAMETRIC MIXTURE MODEL FOR SELECTING GENES AND GENE SUBNETWORKS.

Science.gov (United States)

Zhao, Yize; Kang, Jian; Yu, Tianwei

2014-06-01

It is very challenging to select informative features from tens of thousands of measured features in high-throughput data analysis. Recently, several parametric/regression models have been developed utilizing the gene network information to select genes or pathways strongly associated with a clinical/biological outcome. Alternatively, in this paper, we propose a nonparametric Bayesian model for gene selection incorporating network information. In addition to identifying genes that have a strong association with a clinical outcome, our model can select genes with particular expressional behavior, in which case the regression models are not directly applicable. We show that our proposed model is equivalent to an infinity mixture model for which we develop a posterior computation algorithm based on Markov chain Monte Carlo (MCMC) methods. We also propose two fast computing algorithms that approximate the posterior simulation with good accuracy but relatively low computational cost. We illustrate our methods on simulation studies and the analysis of Spellman yeast cell cycle microarray data.

Network Expansion and Pathway Enrichment Analysis towards Biologically Significant Findings from Microarrays

Directory of Open Access Journals (Sweden)

Wu Xiaogang

2012-06-01

Full Text Available In many cases, crucial genes show relatively slight changes between groups of samples (e.g. normal vs. disease, and many genes selected from microarray differential analysis by measuring the expression level statistically are also poorly annotated and lack of biological significance. In this paper, we present an innovative approach - network expansion and pathway enrichment analysis (NEPEA for integrative microarray analysis. We assume that organized knowledge will help microarray data analysis in significant ways, and the organized knowledge could be represented as molecular interaction networks or biological pathways. Based on this hypothesis, we develop the NEPEA framework based on network expansion from the human annotated and predicted protein interaction (HAPPI database, and pathway enrichment from the human pathway database (HPD. We use a recently-published microarray dataset (GSE24215 related to insulin resistance and type 2 diabetes (T2D as case study, since this study provided a thorough experimental validation for both genes and pathways identified computationally from classical microarray analysis and pathway analysis. We perform our NEPEA analysis for this dataset based on the results from the classical microarray analysis to identify biologically significant genes and pathways. Our findings are not only consistent with the original findings mostly, but also obtained more supports from other literatures.

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.

Learning Gene Regulatory Networks Computationally from Gene Expression Data Using Weighted Consensus

KAUST Repository

Fujii, Chisato

2015-04-16

Gene regulatory networks analyze the relationships between genes allowing us to un- derstand the gene regulatory interactions in systems biology. Gene expression data from the microarray experiments is used to obtain the gene regulatory networks. How- ever, the microarray data is discrete, noisy and non-linear which makes learning the networks a challenging problem and existing gene network inference methods do not give consistent results. Current state-of-the-art study uses the average-ranking-based consensus method to combine and average the ranked predictions from individual methods. However each individual method has an equal contribution to the consen- sus prediction. We have developed a linear programming-based consensus approach which uses learned weights from linear programming among individual methods such that the methods have di↵erent weights depending on their performance. Our result reveals that assigning di↵erent weights to individual methods rather than giving them equal weights improves the performance of the consensus. The linear programming- based consensus method is evaluated and it had the best performance on in silico and Saccharomyces cerevisiae networks, and the second best on the Escherichia coli network outperformed by Inferelator Pipeline method which gives inconsistent results across a wide range of microarray data sets.

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.

Incidence of pulmonary embolism and other chest findings in younger patients using multidetector computed tomography

International Nuclear Information System (INIS)

Heredia, Vasco; Ramalho, Miguel; Zapparoli, Mauricio; Semelka, Richard C.

2010-01-01

Background: Multidetector computed tomography (MDCT) has become the first-line modality for imaging patients with suspected pulmonary embolism (PE). The disadvantages of MDCT, the use of ionizing radiation and iodinated contrast agents, are a reasonable cause of concern, especially in young patients, and therefore it is critical to understand the likelihood of PE in these patients to evaluate a risk benefit analysis. Purpose: To calculate the incidence of PE and other chest findings on MDCT in a young adult population investigated for PE. Material and Methods: 387 consecutive patients (age 31.5±13.5 years) underwent chest MDCT for clinically suspected PE between January 2004 and August 2006. Incidence of PE and other chest findings were calculated with a confidence interval of 95% using binomial distribution. Results: PE incidence was 5%; negative PE with other chest findings was 60%. In 89% of the patients with other chest findings, these included findings of the pleura and/or lung parenchyma. The main patterns of disease were lung opacification suggesting pneumonia (41%), atelectasis (12.4%), and nodular/mass findings (17.5%). In 34% of the patients, there was no PE and no other findings present. Conclusion: There is a low incidence of PE in young patients imaged for PE with MDCT

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

Electroencephalographic and computed X-ray tomographic findings in 99 Japanese cases of herpes simplex encephalitis

International Nuclear Information System (INIS)

Kamei, Satoshi; Takasu, Toshiaki; Tamura, Masato; Otani, Sugishi.

1988-01-01

This is a retrospective analysis of electroencephalograms (EEG) and computed tomograms (CT) obtained from 99 Japanese patients with herpes simplex encephalitis (HSE). Abnormal findings of EEG were seen in 89 patients (99 %). Focal abnormality, which was frequently detected in the first EEG recording, was seen in 68 patients (76 %). Periodic synchronous discharge was observed in 25 patients (28 %). There were abnormal findings on CT in 88 patients (81 %). Low and high density areas were seen in 64 patients (73 %) and 26 patients (37 %), respectively, with the most frequent site being the temporal lobe. Mass effect was demonstrated in 33 patients (37 %). Electroencephalography detected the abnormal findings earlier than CT during the early stage of HSE in many instances. There was concordance between EEG and CT in the detection of HSE lesions in 45 patients (58 %). (Namekawa, K.)

Clinicopathological and immunohistochemical features of lung invasive mucinous adenocarcinoma based on computed tomography findings

Directory of Open Access Journals (Sweden)

Shimizu K

2016-12-01

Full Text Available Katsuhiko Shimizu, Riki Okita, Shinsuke Saisho, Ai Maeda, Yuji Nojima, Masao Nakata Department of General Thoracic Surgery, Kawasaki Medical School, Kurashiki, Okayama, Japan Background: We performed an analysis to clarify differences in clinicopathological and molecular features of lung invasive mucinous adenocarcinoma (IMA based on computed tomography (CT findings and their impact on prognosis.Patients and methods: On the basis of CT findings, we divided lung IMA into three subtypes: solid, bubbling, and pneumonic. We then investigated differences in clinicopathological characteristics, prognosis, and the expressions of well-identified biomarkers, including cyclooxygenase-2 (Cox-2, excision repair cross-complementation group 1 (ERCC1, ribonucleotide reductase M1 (RRM1, class III beta-tubulin, thymidylate synthase (TS, secreted protein acidic and rich in cysteine (SPARC, programmed cell death-1 ligand-1 (PD-L1, and epidermal growth factor receptor mutation, among the three subtypes.Results: A total of 29 patients with resected lung IMA were analyzed. Compared with the solid or bubbling type, the pneumonic type had a higher proportion of symptoms, a larger tumor size, a higher pathological stage, and a significantly worse prognosis. The immunohistochemical findings tended to show high expression of RRM1, class III beta-tubulin, and Cox-2 in the tumor and of SPARC in the stroma, but not of ERCC1, TS, and PD-L1 in the tumor. None of the biomarkers with high expression levels in the tumor were prognostic biomarkers, but the expression of SPARC in the stroma was correlated with a poor outcome.Conclusion: Clinical and pathological features, in conjunction with molecular data, indicate that IMA should be divided into different subgroups. In our results, the pneumonic type was correlated with a significantly worse outcome. Further studies should be performed to confirm our conclusion and to explore its molecular implications. Keywords: non-small cell

False Computed Tomography Findings in Bilateral Choanal Atresia

Directory of Open Access Journals (Sweden)

Elsheikh, Ezzeddin

2016-01-01

Full Text Available Introduction Choanal atresia (CA is a challenging surgical problem defined as a failure in the development of communication between the nasal cavity and nasopharynx. Objective The objective of this study is to describe computed tomography (CT findings in cases with bilateral choanal atresia. Methods The study involved performing axial and coronal non-contrast CT scanning with 2–3 mm sections on14 neonates that had bilateral CA. We used fiberoptic nasal endoscopy to confirm the diagnosis. We evaluated coronal CT to study the skull base area in such neonates. Results This study included 14 neonates with bilateral CA; with mean age of 7 ± 3.5 days. Mixed atretic plates were found in 12 (85.7% cases while two (14.3% had pure bony atresia. Isolated CA was detected in 9 cases (64.3% and 5 (35.7% cases had associated anomalies. Coronal CT showed soft tissue density in the nasal cavity that appeared to extend through an apparent defect in the nasal roof (cribriform plate, falsely diagnosed by radiologists as associated encephalocele. At the time of surgical repair, all patients showed thick tenacious mucous secretions in both nasal cavities and revealed no encephalocele. Nasal roof remained intact in all cases. Conclusion The thick secretion of bilateral CA could give a false encephalocele appearance on the CT. It is highly recommended to perform proper suction of the nasal cavity of suspected CA cases just before CT scanning.

Computed tomography findings associated with bacteremia in adult patients with a urinary tract infection.

Science.gov (United States)

Yu, T Y; Kim, H R; Hwang, K E; Lee, J-M; Cho, J H; Lee, J H

2016-11-01

The use of computed tomography (CT) in the diagnosis of urinary tract infection (UTI) has rapidly increased recently at acute stage, but the CT findings associated with bacteremia in UTI patients are unknown. 189 UTI patients were enrolled who underwent a CT scan within 24 h after hospital admission. We classified CT findings into eight types: a focal or multifocal wedge-shaped area of hypoperfusion, enlarged kidneys, perinephric fat stranding, ureteritis or pyelitis, complicated renal cyst, renal papillary necrosis, hydronephrosis, and renal and perirenal abscess. A retrospective analysis was conducted to evaluate the CT findings associated with bacteremia. The mean age of these patients was 60 ± 17.2 years, and 93.1 % were women. Concurrent bacteremia was noted in 40.2 % of the patients. Abnormal CT findings were noted in 96.3 % of the patients and 62.4 % had two or more abnormal findings. The most frequent abnormal CT finding was a focal or multifocal wedge-shaped area of hypoperfusion (77.2 %), followed by perinephric fat stranding (29.1 %). Perinephric fat stranding, hydronephrosis, and the presence of two or more abnormal CT findings were significantly associated with bacteremia in patients with community-acquired UTI. In the multivariate logistic regression analysis, age [odds ratio (OR) 1.03; 95 % confidence interval (CI) 1.009-1.062], two or more abnormal CT findings (OR 3.163; 95 % CI 1.334-7.498), and hydronephrosis (OR 13.160; 95 % CI 1.048-165.282) were significantly associated with bacteremia. Physicians should be aware that appropriate early management is necessary to prevent fatality in patients with these CT findings.

High-resolution Computed Tomography Findings of H1N1 Influenza-Associated Pneumonia in Korea

Energy Technology Data Exchange (ETDEWEB)

Lee, Byung Chan; Choi, Song; Kim, Jin Woong; Lim, Hyo Soon [Dept. of Radiology, Chonnam National University Hospital, Chonnam National University School of Medicine, Kwangju (Korea, Republic of); Seon, Hyung Joo; Shin, Sang Soo [Dept. of Radiology, Chonnam National University Hospital, Chonnam National University School of Medicine, Kwangju (Korea, Republic of); Kim, Yun Hyeon; Park, Kyung Hwa [Dept. of Internal Medicine, Chonnam National University Hospital, Chonnam National University School of Medicine, Kwangju (Korea, Republic of)

2011-04-15

To evaluate and compare the high-resolution computed tomography (HRCT) findings of patients with H1N1 influenza-associated pneumonia compared usual community acquired pneumonia (CAP), to determine whether there were any useful common HRCT findings predicting their prognosis. HRCT findings of 31 patients (M:F = 16:15, mean age 42 yrs) with Influenza A (H1N1) infection were retrospectively reviewed for abnormal HRCT findings and compared to HRCT findings of CAP in matched patients. Patients were matched according to age and sex, from 2009 to January 2010. The predominant HRCT findings of pneumonia consisted of areas of consolidation and/or groundglass opacity (GGO) which showed no statistically significant differences when comparing the two groups. However, the abnormalities of H1N1-related pneumonia showed higher bilaterality and multilobar or multisegmental involvement compared with CAP (p < 0.05). Internal low attenuation or air-densities in pulmonary infiltration /or lymphadenopathy was observed only in patients with CAP (p < 0.05). HRCT findings in 8 patients with poor clinical outcome had bilaterality (p=0.015), multilobar, and multisegmental involvement. The predominant HRCT findings of H1N1-related pneumonia were areas of consolidation and/or GGO. In addition, H1N1-related pneumonia showed higher bilaterality or multilobar/multisegmental involvement compared with CAP. The patients who presented bilaterality had a worse clinical outcome.

Computed Tomography Perfusion, Magnetic Resonance Imaging, and Histopathological Findings After Laparoscopic Renal Cryoablation: An In Vivo Pig Model

DEFF Research Database (Denmark)

Nielsen, Tommy Kjærgaard; Østraat, Øyvind; Graumann, Ole

2017-01-01

The present study investigates how computed tomography perfusion scans and magnetic resonance imaging correlates with the histopathological alterations in renal tissue after cryoablation. A total of 15 pigs were subjected to laparoscopic-assisted cryoablation on both kidneys. After intervention...... of follow-up, but on microscopic examination, the urothelium was found to be intact in all cases. In conclusion, cryoablation effectively destroyed renal parenchyma, leaving the urothelium intact. Both computed tomography perfusion and magnetic resonance imaging reflect the microscopic findings...

Head multidetector computed tomography: emergency medicine physicians overestimate the pretest probability and legal risk of significant findings.

Science.gov (United States)

Baskerville, Jerry Ray; Herrick, John

2012-02-01

This study focuses on clinically assigned prospective estimated pretest probability and pretest perception of legal risk as independent variables in the ordering of multidetector computed tomographic (MDCT) head scans. Our primary aim is to measure the association between pretest probability of a significant finding and pretest perception of legal risk. Secondarily, we measure the percentage of MDCT scans that physicians would not order if there was no legal risk. This study is a prospective, cross-sectional, descriptive analysis of patients 18 years and older for whom emergency medicine physicians ordered a head MDCT. We collected a sample of 138 patients subjected to head MDCT scans. The prevalence of a significant finding in our population was 6%, yet the pretest probability expectation of a significant finding was 33%. The legal risk presumed was even more dramatic at 54%. These data support the hypothesis that physicians presume the legal risk to be significantly higher than the risk of a significant finding. A total of 21% or 15% patients (95% confidence interval, ±5.9%) would not have been subjected to MDCT if there was no legal risk. Physicians overestimated the probability that the computed tomographic scan would yield a significant result and indicated an even greater perceived medicolegal risk if the scan was not obtained. Physician test-ordering behavior is complex, and our study queries pertinent aspects of MDCT testing. The magnification of legal risk vs the pretest probability of a significant finding is demonstrated. Physicians significantly overestimated pretest probability of a significant finding on head MDCT scans and presumed legal risk. Copyright © 2012 Elsevier Inc. All rights reserved.

Computed tomographic findings in pancreatic pathology

International Nuclear Information System (INIS)

Frija, J.; Laval-Jeantet, M.; Larde, D.; Mathieu, D.

1986-01-01

Computed tomography (CT) is actually the most suitable examination for the study of the pancreas. The evolution during the life of its thickness is studied. For the same age group pancreas sharpens from the head to the body and the tail. Pancreas progressively sharpens during the life. The comparison of the efficacy of the other imaging modalities is studied. The indications of the radiological examinations of the pancreas are evaluated during acute and chronic pancreatitis, pseudocysts, adenocarcinoma of the pancreas and endocrine tumors of the pancreas [fr

Computed tomography findings of acute gastric volvulus.

Science.gov (United States)

Millet, Ingrid; Orliac, Celine; Alili, Chakib; Guillon, Françoise; Taourel, Patrice

2014-12-01

To assess the diagnostic performance of CT signs of gastric volvulus in both confirmed cases and control subjects. We retrospectively reviewed CT findings in 10 patients with surgically confirmed acute gastric volvulus and 20 control subjects with gastric distension. Two radiologists independently evaluated CT images for risk factors of gastric volvulus, direct findings of gastric volvulus by assessing gastric dilatation, the presence of an antropyloric transition point, the respective position of the different stomach segments and of the greater and lesser curvatures, stenosis of the gastric segments through the oesophageal hiatus and for findings of gastric ischemia. The sensitivity and specificity of each finding were calculated. The most sensitive direct signs of gastric volvulus were an antropyloric transition point without any abnormality at the transition zone and the antrum at the same level or higher than the fundus. The presence of both these two findings as diagnostic criteria of gastric volvulus had 100% sensitivity and specificity for the diagnosis of gastric volvulus. There was no association between CT signs of ischemia and final bowel ischemia at pathology. CT is both highly sensitive and specific for diagnosing acute gastric volvulus. CT is highly reliable for diagnosing acute gastric volvulus with two findings. The two signs are gastropyloric transition zone and abnormal location of the antrum. This allows fast surgical management of this emergency.

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...

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.

Computer-assisted instruction and diagnosis of radiographic findings.

Science.gov (United States)

Harper, D; Butler, C; Hodder, R; Allman, R; Woods, J; Riordan, D

1984-04-01

Recent advances in computer technology, including high bit-density storage, digital imaging, and the ability to interface microprocessors with videodisk, create enormous opportunities in the field of medical education. This program, utilizing a personal computer, videodisk, BASIC language, a linked textfile system, and a triangulation approach to the interpretation of radiographs developed by Dr. W. L. Thompson, can enable the user to engage in a user-friendly, dynamic teaching program in radiology, applicable to various levels of expertise. Advantages include a relatively more compact and inexpensive system with rapid access and ease of revision which requires little instruction to the user.

Computed tomography findings of acute gastric volvulus

Energy Technology Data Exchange (ETDEWEB)

Millet, Ingrid; Orliac, Celine; Alili, Chakib; Taourel, Patrice [Hopital Lapeyronie, Department of Radiology, Montpellier (France); Guillon, Francoise [University Hospital of Montpellier, Department of Surgery, Montpellier (France)

2014-12-15

To assess the diagnostic performance of CT signs of gastric volvulus in both confirmed cases and control subjects. We retrospectively reviewed CT findings in 10 patients with surgically confirmed acute gastric volvulus and 20 control subjects with gastric distension. Two radiologists independently evaluated CT images for risk factors of gastric volvulus, direct findings of gastric volvulus by assessing gastric dilatation, the presence of an antropyloric transition point, the respective position of the different stomach segments and of the greater and lesser curvatures, stenosis of the gastric segments through the oesophageal hiatus and for findings of gastric ischemia. The sensitivity and specificity of each finding were calculated. The most sensitive direct signs of gastric volvulus were an antropyloric transition point without any abnormality at the transition zone and the antrum at the same level or higher than the fundus. The presence of both these two findings as diagnostic criteria of gastric volvulus had 100 % sensitivity and specificity for the diagnosis of gastric volvulus. There was no association between CT signs of ischemia and final bowel ischemia at pathology. CT is both highly sensitive and specific for diagnosing acute gastric volvulus. (orig.)

Computed tomography findings of acute gastric volvulus

International Nuclear Information System (INIS)

Millet, Ingrid; Orliac, Celine; Alili, Chakib; Taourel, Patrice; Guillon, Francoise

2014-01-01

To assess the diagnostic performance of CT signs of gastric volvulus in both confirmed cases and control subjects. We retrospectively reviewed CT findings in 10 patients with surgically confirmed acute gastric volvulus and 20 control subjects with gastric distension. Two radiologists independently evaluated CT images for risk factors of gastric volvulus, direct findings of gastric volvulus by assessing gastric dilatation, the presence of an antropyloric transition point, the respective position of the different stomach segments and of the greater and lesser curvatures, stenosis of the gastric segments through the oesophageal hiatus and for findings of gastric ischemia. The sensitivity and specificity of each finding were calculated. The most sensitive direct signs of gastric volvulus were an antropyloric transition point without any abnormality at the transition zone and the antrum at the same level or higher than the fundus. The presence of both these two findings as diagnostic criteria of gastric volvulus had 100 % sensitivity and specificity for the diagnosis of gastric volvulus. There was no association between CT signs of ischemia and final bowel ischemia at pathology. CT is both highly sensitive and specific for diagnosing acute gastric volvulus. (orig.)

DNA context represents transcription regulation of the gene in mouse embryonic stem cells

Science.gov (United States)

Ha, Misook; Hong, Soondo

2016-04-01

Understanding gene regulatory information in DNA remains a significant challenge in biomedical research. This study presents a computational approach to infer gene regulatory programs from primary DNA sequences. Using DNA around transcription start sites as attributes, our model predicts gene regulation in the gene. We find that H3K27ac around TSS is an informative descriptor of the transcription program in mouse embryonic stem cells. We build a computational model inferring the cell-type-specific H3K27ac signatures in the DNA around TSS. A comparison of embryonic stem cell and liver cell-specific H3K27ac signatures in DNA shows that the H3K27ac signatures in DNA around TSS efficiently distinguish the cell-type specific H3K27ac peaks and the gene regulation. The arrangement of the H3K27ac signatures inferred from the DNA represents the transcription regulation of the gene in mESC. We show that the DNA around transcription start sites is associated with the gene regulatory program by specific interaction with H3K27ac.

HRGFish: A database of hypoxia responsive genes in fishes

Science.gov (United States)

Rashid, Iliyas; Nagpure, Naresh Sahebrao; Srivastava, Prachi; Kumar, Ravindra; Pathak, Ajey Kumar; Singh, Mahender; Kushwaha, Basdeo

2017-02-01

Several studies have highlighted the changes in the gene expression due to the hypoxia response in fishes, but the systematic organization of the information and the analytical platform for such genes are lacking. In the present study, an attempt was made to develop a database of hypoxia responsive genes in fishes (HRGFish), integrated with analytical tools, using LAMPP technology. Genes reported in hypoxia response for fishes were compiled through literature survey and the database presently covers 818 gene sequences and 35 gene types from 38 fishes. The upstream fragments (3,000 bp), covered in this database, enables to compute CG dinucleotides frequencies, motif finding of the hypoxia response element, identification of CpG island and mapping with the reference promoter of zebrafish. The database also includes functional annotation of genes and provides tools for analyzing sequences and designing primers for selected gene fragments. This may be the first database on the hypoxia response genes in fishes that provides a workbench to the scientific community involved in studying the evolution and ecological adaptation of the fish species in relation to hypoxia.

Bronchobiliary fistula after hemihepatectomy: cholangiopancreaticography, computed tomography and magnetic resonance cholangiography findings

International Nuclear Information System (INIS)

Oettl, C.; Schima, W.; Metz-Schimmerl, S.; Fuegger, R.; Mayrhofer, T.; Herold, C.J.

1999-01-01

A bronchobiliary fistula (BBF), which is defined by an abnormal communication between the biliary system and the bronchial tree, is an uncommon complication after hemihepatectomy, trauma, hydatid disease, choledocholithiasis and other causes of biliary obstruction. We report the case of a 56-year-old man with colon cancer, who developed a BBF 2 months after right hemihepatectomy for liver metastases. The findings at endoscopic retrograde cholangiopancreaticography (ERCP), computed tomography (CT) and magnetic resonance cholangiography (MRC) included a stricture of the common bile duct and biliary leakage from the liver resection plane with biliary infiltration of the right lower lobe of the lung. The patient was treated successfully by endoscopic insertion of a biliary plastic stent which bridged the stricture and lead to closure of the fistula

UniGene Tabulator: a full parser for the UniGene format.

Science.gov (United States)

Lenzi, Luca; Frabetti, Flavia; Facchin, Federica; Casadei, Raffaella; Vitale, Lorenza; Canaider, Silvia; Carinci, Paolo; Zannotti, Maria; Strippoli, Pierluigi

2006-10-15

UniGene Tabulator 1.0 provides a solution for full parsing of UniGene flat file format; it implements a structured graphical representation of each data field present in UniGene following import into a common database managing system usable in a personal computer. This database includes related tables for sequence, protein similarity, sequence-tagged site (STS) and transcript map interval (TXMAP) data, plus a summary table where each record represents a UniGene cluster. UniGene Tabulator enables full local management of UniGene data, allowing parsing, querying, indexing, retrieving, exporting and analysis of UniGene data in a relational database form, usable on Macintosh (OS X 10.3.9 or later) and Windows (2000, with service pack 4, XP, with service pack 2 or later) operating systems-based computers. The current release, including both the FileMaker runtime applications, is freely available at http://apollo11.isto.unibo.it/software/

Find - a computer program for peak search in gamma-ray spectra measured with Ge (Li) detectors

International Nuclear Information System (INIS)

Venturini, L.

1988-01-01

The program FIND is a FORTRAN IV computer code for peak search in spectra measured with Ge(Li) detectors. The program gives the position and estimates energy and relative significance for every peak found in the spectrum. The search in done by calculating a negative smoothed second difference of the experimental spectrum, as suggested by Phillips and Marlow (1). (author) [pt

ANATOMICAL VARIATIONS FINDINGS ON CONE BEAM-COMPUTED TOMOGRAPHY IN CLEFT LIP AND PALATE PATIENTS

Directory of Open Access Journals (Sweden)

Yllka DECOLLI

2015-09-01

Full Text Available Introduction: Cone beam computed tomography (CBCT is frequently used in surgery treatment planning in patients with cleft lip and palate (CLP. The aim of this study was to investigate the presence of different anatomical variations of patients with cleft lip and palate using CBCT images. Materials and method: CBCTs taken from consecutive patients (n =25; mean age 10.7±4 years, range 6.5–23 years with a non-syndromic cleft lip and palate (CLP, between June 2014-2015, were systematically evaluated. Sinuses, nasopharynx, oropharynx, hypopharynx, temporo-mandibular joint (TMJ, maxilla and mandible were checked for incidental findings. Results: On 90.1 % of the CBCTs, incidental findings were found. The most prevalent ones were airway/sinus findings (78.1%, followed by dental problems, e.g. missing teeth (54%, nasal septum deviation (93%, middle ear and mastoid opacification, suggestive for otitis media (8% and (chronic mastoiditis (7%, abnormal TMJ anatomy (4.3%. Conclusions: Incidental findings are common on CBCTs in cleft lip and palate patients. Compared with the literature, CLP patients have more dental, nasal and ear problems. The CBCT scan should be reviewed by all specialists in the CLP team, stress being laid on their specific background knowledge concerning symptoms and treatment of these patients.

Association between clinical and cone-beam computed tomography findings in patients with temporomandibular disorders

Directory of Open Access Journals (Sweden)

Mahrokh Imanimoghaddam

2017-08-01

Full Text Available BACKGROUND AND AIM: The aim of this study was to assess the association between the clinical and cone-beam computed tomography (CBCT findings in relation to bony changes in patients with temporomandibular disorders (TMD. METHODS: According to the research diagnostic criteria for temporomandibular disorder (RDC/TMD, forty-one patients with type II TMD (42 TM joints and type III TMD (40 TM joints were recruited for this study. Condylar position and bony changes including flattening, sclerosis, osteophytes, resorption, and erosion of joint were evaluated by CBCT and compared with clinical findings. Data were analyzed by SPSS software. RESULTS: Condylar flattening, sclerosis, resorption, and erosion were not significantly associated with joint/masticatory muscles pain or crepitus sound. The vertical or horizontal position of the condyle showed no significant relationship with the clinical findings. Condylar osteophyte was significantly associated with pain in masticatory muscles and crepitus (P = 0.030 and P = 0.010, respectively. There was no association between the condylar range of motion and pain in joint or masticatory muscles. CONCLUSION: Condylar osteophyte was significantly associated with both masticatory muscles pain and crepitus sound. No significant relationship was found between the other temporomandibular joint (TMJ radiographic and clinical findings in patients with TMD.

Discovering local patterns of co - evolution: computational aspects and biological examples

Directory of Open Access Journals (Sweden)

Tuller Tamir

2010-01-01

Full Text Available Abstract Background Co-evolution is the process in which two (or more sets of orthologs exhibit a similar or correlative pattern of evolution. Co-evolution is a powerful way to learn about the functional interdependencies between sets of genes and cellular functions and to predict physical interactions. More generally, it can be used for answering fundamental questions about the evolution of biological systems. Orthologs that exhibit a strong signal of co-evolution in a certain part of the evolutionary tree may show a mild signal of co-evolution in other branches of the tree. The major reasons for this phenomenon are noise in the biological input, genes that gain or lose functions, and the fact that some measures of co-evolution relate to rare events such as positive selection. Previous publications in the field dealt with the problem of finding sets of genes that co-evolved along an entire underlying phylogenetic tree, without considering the fact that often co-evolution is local. Results In this work, we describe a new set of biological problems that are related to finding patterns of local co-evolution. We discuss their computational complexity and design algorithms for solving them. These algorithms outperform other bi-clustering methods as they are designed specifically for solving the set of problems mentioned above. We use our approach to trace the co-evolution of fungal, eukaryotic, and mammalian genes at high resolution across the different parts of the corresponding phylogenetic trees. Specifically, we discover regions in the fungi tree that are enriched with positive evolution. We show that metabolic genes exhibit a remarkable level of co-evolution and different patterns of co-evolution in various biological datasets. In addition, we find that protein complexes that are related to gene expression exhibit non-homogenous levels of co-evolution across different parts of the fungi evolutionary line. In the case of mammalian evolution

Genes2Networks: connecting lists of gene symbols using mammalian protein interactions databases

Directory of Open Access Journals (Sweden)

Ma'ayan Avi

2007-10-01

Full Text Available Abstract Background In recent years, mammalian protein-protein interaction network databases have been developed. The interactions in these databases are either extracted manually from low-throughput experimental biomedical research literature, extracted automatically from literature using techniques such as natural language processing (NLP, generated experimentally using high-throughput methods such as yeast-2-hybrid screens, or interactions are predicted using an assortment of computational approaches. Genes or proteins identified as significantly changing in proteomic experiments, or identified as susceptibility disease genes in genomic studies, can be placed in the context of protein interaction networks in order to assign these genes and proteins to pathways and protein complexes. Results Genes2Networks is a software system that integrates the content of ten mammalian interaction network datasets. Filtering techniques to prune low-confidence interactions were implemented. Genes2Networks is delivered as a web-based service using AJAX. The system can be used to extract relevant subnetworks created from "seed" lists of human Entrez gene symbols. The output includes a dynamic linkable three color web-based network map, with a statistical analysis report that identifies significant intermediate nodes used to connect the seed list. Conclusion Genes2Networks is powerful web-based software that can help experimental biologists to interpret lists of genes and proteins such as those commonly produced through genomic and proteomic experiments, as well as lists of genes and proteins associated with disease processes. This system can be used to find relationships between genes and proteins from seed lists, and predict additional genes or proteins that may play key roles in common pathways or protein complexes.

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

Paraquat-poisoning in the rabbit lungs: high resolution computed tomographic findings and pathologic correlation

International Nuclear Information System (INIS)

Lee, Kyung Soo; Kim, Eui Han; Lee, Byoung Ho; Kim, Kun Sang

1992-01-01

The authors evaluated high resolution computed tomographic (HRCT) findings of the isolated rabbit lungs with paraquat poisoning, and the findings were correlated with pathologic specimens. The purposes of this study are 1) to obtain the HRCT findings of the normal rabbit lung. 2) to find out if pulmonary pathology can be induced in rabbits by paraquat, and 3) to correlate the HRCT findings to those of pathology. Thirty rabbits were divided into three groups: group I included four control rabbits; group II included 16 rabbits given paraquat intraperitoneally (IP group); and group III included 10 rabbits given paraquat intravenously (IV group). The rabbits were sacrificed seven, 10, and 14 days after injection of various amount of paraquat, and then the lungs were isolated for HRCT and pathologic studies. Gross and microscopic findings of the three groups of control and paraquat-injected rabbit lungs were correlated with HRCT findings. Pulmonary congestion, mild thickening of alveolar walls and septae, and multifocal micro-atelectasis were the man pathologic findings of the lungs in both groups of the rabbits. Pulmonary hemorrhage was noted in five (31%) of 16 rabbits of IP group and three (30%) of 10 IV group. Pulmonary edema was seen in one rabbits (6%) of IP and four (40%) of IV group. Typical pulmonary fibrosis was seen in one rabbit of IP (6%) and IV (10%) group, respectively. There was no correlation between the amount of paraquat and frequency of the pulmonary pathology. Pulmonary fibrosis was seen at least one week after the paraquat injection. On HRCT, pulmonary hemorrhage and edema appeared as diffuse air-space consolidation and pulmonary fibrosis as linear or band-like opacities. However, minimal changes such as mild congestion

Modeling the Activity of Single Genes

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Mjolsness, Eric; Gibson, Michael

1999-01-01

-scale sequencing began with simple organisms, viruses and bacteria, progressed to eukaryotes such as yeast, and more recently (1998) progressed to a multi-cellular animal, the nematode Caenorhabditis elegans. Sequencers have now moved on to the fruit fly Drosophila melanogaster, whose sequence is slated for completion by the end of 1999. The human genome project is expected to determine the complete sequence of all 3 billion bases of human DNA within the next five years. In the wake of genome-scale sequencing, further instrumentation is being developed to assay gene expression and function on a comparably large scale. Much of the work in computational biology focuses on computational tools used in sequencing, finding genes that are related to a particular gene, finding which parts of the DNA code for proteins and which do not, understanding what proteins will be formed from a given length of DNA, predicting how the proteins will fold from a one-dimensional structure into a three dimensional structure, and so on. Much less computational work has been done regarding the function of proteins. One reason for this is that different proteins function very differently, and so work on protein function is very specific to certain classes of proteins. There are, for example, proteins such enzymes that catalyze various intracellular reactions, receptors that respond to extracellular signals and ion channels that regulate the flow of charged particles into and out of the cell. In this chapter, we will consider a particular class of proteins called transcription factors(TFs), which are responsible for regulating when a certain gene is expressed in a certain cell, which cells it is express in, and how much is expressed. Understanding these processes will involve developing a deeper understanding of transcription, translation, and the cellular processes that control those processes. All of these elements fall under the aegis of gene regulation or more narrowly transcriptional regulation. Some of

The importance of biochemical and genetic findings in the diagnosis of atypical Norrie disease.

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Rodríguez-Muñoz, Ana; García-García, Gema; Menor, Francisco; Millán, José M; Tomás-Vila, Miguel; Jaijo, Teresa

2018-01-26

Norrie disease (ND) is a rare X-linked disorder characterized by bilateral congenital blindness. ND is caused by a mutation in the Norrie disease pseudoglioma (NDP) gene, which encodes a 133-amino acid protein called norrin. Intragenic deletions including NDP and adjacent genes have been identified in ND patients with a more severe neurologic phenotype. We report the biochemical, molecular, clinical and radiological features of two unrelated affected males with a deletion including NDP and MAO genes. Biochemical and genetic analyses were performed to understand the atypical phenotype and radiological findings. Biogenic amines in cerebrospinal fluid (CSF) were measured by high-performance liquid chromatography. The coding exons of NDP gene were amplified by polymerase chain reaction. Multiplex ligation-dependent probe amplification and chromosomal microarray were carried out on both affected males. Computed tomography and magnetic resonance imaging were performed on the two patients. In one patient, the serotonin and catecholamine metabolite levels in CSF were virtually undetectable. In both patients, genetic studies revealed microdeletions in the Xp11.3 region, involving the NDP, MAOA and MAOB genes. Radiological examination demonstrated brain and cerebellar atrophy. We suggest that alterations caused by MAO deficit may remain during the first years of life. Clinical phenotype, biochemical findings and neuroimaging can guide the genetic study in patients with atypical ND and help us to a better understanding of this disease.

Computed tomography findings of community-acquired Stenotrophomonas Maltophilia pneumonia in an immunocompetent patient: A case report

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Cha, Yoon Ki; Kim, Jeung Sook; Park, Seong Yeon; Oh, Jin Young; Kwon, Jae Hyun [Dongguk University Ilsan Hospital, Dongguk University College of Medicine, Goyang (Korea, Republic of)

2016-11-15

Stenotrophomonas maltophilia (S. maltophilia) is a rare, but globally emerging gram-negative multiple-drug-resistant organism usually found in a nosocomial setting in immunocompromised patients. To our best knowledge, computed tomography (CT) features of community-acquired S. maltophilia pneumonia have not been previously reported in an immunocompetent patient. Herein, we presented the CT findings of a previous healthy 56-year-old male with S. maltophilia pneumonia.

EXONSAMPLER: a computer program for genome-wide and candidate gene exon sampling for targeted next-generation sequencing.

Science.gov (United States)

Cosart, Ted; Beja-Pereira, Albano; Luikart, Gordon

2014-11-01

The computer program EXONSAMPLER automates the sampling of thousands of exon sequences from publicly available reference genome sequences and gene annotation databases. It was designed to provide exon sequences for the efficient, next-generation gene sequencing method called exon capture. The exon sequences can be sampled by a list of gene name abbreviations (e.g. IFNG, TLR1), or by sampling exons from genes spaced evenly across chromosomes. It provides a list of genomic coordinates (a bed file), as well as a set of sequences in fasta format. User-adjustable parameters for collecting exon sequences include a minimum and maximum acceptable exon length, maximum number of exonic base pairs (bp) to sample per gene, and maximum total bp for the entire collection. It allows for partial sampling of very large exons. It can preferentially sample upstream (5 prime) exons, downstream (3 prime) exons, both external exons, or all internal exons. It is written in the Python programming language using its free libraries. We describe the use of EXONSAMPLER to collect exon sequences from the domestic cow (Bos taurus) genome for the design of an exon-capture microarray to sequence exons from related species, including the zebu cow and wild bison. We collected ~10% of the exome (~3 million bp), including 155 candidate genes, and ~16,000 exons evenly spaced genomewide. We prioritized the collection of 5 prime exons to facilitate discovery and genotyping of SNPs near upstream gene regulatory DNA sequences, which control gene expression and are often under natural selection. © 2014 John Wiley & Sons Ltd.

Rare finding of Eustachian tube calcifications with cone-beam computed tomography.

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Syed, Ali Z; Hawkins, Anna; Alluri, Leela Subashini; Jadallah, Buthainah; Shahid, Kiran; Landers, Michael; Assaf, Hussein M

2017-12-01

Soft tissue calcification is a pathological condition in which calcium and phosphate salts are deposited in the soft tissue organic matrix. This study presents an unusual calcification noted in the cartilaginous portion of the Eustachian tube. A 67-year-old woman presented for dental treatment, specifically for implant placement, and cone-beam computed tomography (CBCT) was performed. The CBCT scan was reviewed by a board-certified oral and maxillofacial radiologist and revealed incidental findings of 2 distinct calcifications in the cartilaginous portion of the Eustachian tube. To the authors' knowledge, no previous study has reported the diagnosis of Eustachian tube calcification using CBCT. This report describes an uncommon variant of Eustachian tube calcification, which has a significant didactic value because such cases are seldom illustrated either in textbooks or in the literature. This case once again underscores the importance of having CBCT scans evaluated by a board-certified oral and maxillofacial radiologist.

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

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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/.

Clinical characteristics and computed tomography findings of pulmonary toxoplasmosis after hematopoietic stem cell transplantation.

Science.gov (United States)

Sumi, Masahiko; Norose, Kazumi; Hikosaka, Kenji; Kaiume, Hiroko; Takeda, Wataru; Kirihara, Takehiko; Kurihara, Taro; Sato, Keijiro; Ueki, Toshimitsu; Hiroshima, Yuki; Kuraishi, Hiroshi; Watanabe, Masahide; Kobayashi, Hikaru

2016-12-01

The prognosis of pulmonary toxoplasmosis, including disseminated toxoplasmosis involving the lungs, following hematopoietic stem cell transplantation (HSCT) is extremely poor due to the difficulties associated with early diagnosis and the rapidly progressive deterioration of multiorgan function. In our institution, we identified nine cases of toxoplasmosis, representing incidences of 2.2 and 19.6 % among all HSCT recipients and seropositive HSCT recipients, respectively. Of the patients with toxoplasmosis, six had pulmonary toxoplasmosis. Chest computed tomography (CT) findings revealed centrilobular, patchy ground-glass opacities (n = 3), diffuse ground-glass opacities (n = 2), ground-glass opacities with septal thickening (n = 1), and marked pleural effusion (n = 1). All cases died, except for one with suspected pulmonary toxoplasmosis who was diagnosed by a polymerase chain reaction assay 2 days after the onset of symptoms. In pulmonary toxoplasmosis, CT findings are non-specific and may mimic pulmonary congestion, atypical pneumonia, viral pneumonitis, and bronchopneumonia. Early diagnosis and treatment is crucial for overcoming this serious infectious complication. Pulmonary toxoplasmosis should be considered during differential diagnosis in a recipient with otherwise unexplained signs of infection and CT findings with ground-glass opacities, regardless of the distribution.

Frequency of abnormal pulmonary computed tomography findings in asylum seeking refugees in Turkey.

Science.gov (United States)

Soydan, Levent; Demir, Ali Aslan; Tunaci, Atadan

2017-03-01

Lungs are particularly vulnerable to both acute infections, including TB, and chronic diseases such as chronic obstructive pulmonary disease, as well as to malignancies, all of which require particular attention during war times in which health conditions are far from optimal. This retrospective cross-sectional study included 1149 refugees that underwent thoracic computed tomography (CT) for respiratory symptoms between March 2013 and February 2015 in Turkey. At least one positive CT finding was seen in 231 (20.1%) of the patients. The most common findings were chronic pulmonary changes (n=197, 17.2%), followed by findings suggestive of infections (n=39, 3.4%), and mass/nodular lesions (n=16, 1.4%). The rates of the lesions suggestive of active TB and malignancy were 1.0% (n=11) and 0.7% (n=8), respectively. Age 55-64 years was an independent significant predictor for any CT lesion, chronic changes, mass lesions, and lesions suggestive of malignancy. Age>65 years was predictive of any CT lesion and chronic changes. The findings of this study indicate the need for implementation of cost-effective screening strategies in refugees, particularly during war times. Screening for TB would improve disease control among both refugees and the host populations. Middle aged and older individuals, in particular, would benefit from more proactive screening tools and strategies for the early diagnosis of pulmonary malignancies and chronic lung diseases. © The Author 2017. Published by Oxford University Press on behalf of Royal Society of Tropical Medicine and Hygiene. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Benign thyroid and neck lesions mimicking malignancy with false positive findings on positron emission tomography-computed tomography

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Yoon, Ye Ri; Kim, Shin Young; Lee, Sang Mi [Soonchunhyang University Cheonan Hospital, Cheonan (Korea, Republic of); Lee, Deuk Young [Dept. of Surgery, Younsei Angelot Women' s Clinic, Cheonan (Korea, Republic of)

2017-02-15

The increasing use of positron emission tomography-computed tomography (PET/CT) has led to the frequent detection of incidental thyroid and neck lesions with increased 18F-deoxyglucose (FDG) uptake. Although lesions with increased FDG uptake are commonly assumed to be malignant, benign lesions may also exhibit increased uptake. The purpose of this pictorial essay is to demonstrate that benign thyroid and neck lesions can produce false-positive findings on PET/CT, and to identify various difficulties in interpretation. It is crucial to be aware that differentiating between benign and malignant lesions is difficult in a considerable proportion of cases, when relying only on PET/CT findings. Correlation of PET/CT findings with additional imaging modalities is essential to avoid misdiagnosis.

Correlations between computed tomography findings and clinical manifestations of Streptococcus pneumoniae pneumonia

International Nuclear Information System (INIS)

Yagihashi, Kunihiro; Kurihara, Yasuyuki; Fujikawa, Atsuko; Matsuoka, Shin; Nakajima, Yasuo

2011-01-01

The aim of this study was to characterize the imaging features and compare computed tomography (CT) findings with clinical features of patients with Streptococcus pneumoniae pneumonia. We retrospectively reviewed 75 patients (44 men, 31 women; mean age 67 years) diagnosed with S. pneumoniae pneumonia who underwent chest CT scanning at our institution between January 2007 and August 2008. Diagnoses were based on detection of the S. pneumoniae antigen in urine. Chest CT scans revealed abnormalities in all patients. The predominant opacity patterns were an airspace pneumonia pattern (48%) and a bronchopneumonia pattern (48%), followed by an interstitial pneumonia pattern (4%). Consolidation was observed most frequently (84%) followed by ground glass opacity (82.7%), bronchial wall thickening (61.3%), and centrilobular nodules (49.3%). Airway dilatation (21.6%), pleural effusion (33.3%), lymphadenopathy (34.8%), and pulmonary emphysema (21.3%) were also observed. Pulmonary emphysema was significantly less frequent in patients with the bronchopneumonia pattern than in those without (p=0.007). The clinical features and CT findings did not differ significantly. CT image analysis showed that patients with S. pneumoniae pneumonia exhibited the bronchopneumonia and airspace pneumonia patterns with equal frequency. Bronchopneumonia pattern was less common in patients with preexisting emphysema. (author)

Imaging findings of Copa syndrome in a 12-year-old boy

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Noorelahi, Razan; Otero, Hansel J. [George Washington University School of Medicine and Health Services, Department of Diagnostic Imaging and Radiology, Children' s National Health System, Washington, DC (United States); Perez, Geovany [George Washington University School of Medicine and Health Sciences, Pulmonary and Sleep Medicine Division, Washington, DC (United States)

2018-02-15

Copa syndrome is a newly described autosomal dominant autoinflammatory disease that presents as pulmonary hemosiderosis and polyarticular arthritis. Twenty-one cases from five families have been reported to date. We present chest computed tomography (CT) and temporomandibular joint magnetic resonance (MR) findings of a 12-year-old boy presenting with dyspnea on exertion, fatigue and clubbing. Additional findings included a restrictive pattern of pulmonary involvement and positive inflammatory markers and autoantibodies. Genetic testing revealed a p.W240R variant of the COPA gene confirming the diagnosis of Copa syndrome. CT of the chest showed a nonspecific interstitial pneumonia pattern distributed mainly in the lower lobes. MR of the temporomandibular joints and follow-up CT three years later are also described. (orig.)

Association between Smoking and the Progression of Computed Tomography Findings in Chronic Pancreatitis.

Science.gov (United States)

Lee, Jeong Woo; Kim, Ho Gak; Lee, Dong Wook; Han, Jimin; Kwon, Hyuk Yong; Seo, Chang Jin; Oh, Ji Hye; Lee, Joo Hyoung; Jung, Jin Tae; Kwon, Joong Goo; Kim, Eun Young

2016-05-23

Smoking and alcohol intake are two wellknown risk factors for chronic pancreatitis. However, there are few studies examining the association between smoking and changes in computed tomography (CT) findings in chronic pancreatitis. The authors evaluated associations between smoking, drinking and the progression of calcification on CT in chronic pancreatitis. In this retrospective study, 59 patients with chronic pancreatitis who had undergone initial and follow-up CT between January 2002 and September 2010 were included. Progression of calcification among CT findings was compared according to the amount of alcohol intake and smoking. The median duration of followup was 51.6 months (range, 17.1 to 112.7 months). At initial CT findings, there was pancreatic calcification in 35 patients (59.3%). In the follow-up CT, progression of calcification was observed in 37 patients (62.7%). Progression of calcification was more common in smokers according to the multivariate analysis (odds ratio [OR], 9.987; p=0.006). The amount of smoking was a significant predictor for progression of calcification in the multivariate analysis (OR, 6.051 in less than 1 pack per day smokers; OR, 36.562 in more than 1 pack per day smokers; p=0.008). Continued smoking accelerates pancreatic calcification, and the amount of smoking is associated with the progression of calcification in chronic pancreatitis.

Swine-origin influenza A viral (H1N1) infection in children. Chest computed tomography findings

International Nuclear Information System (INIS)

Im, Soo-Ah; Kim, Hyo-Lim; Yoon, Jong-seo; Kang, Jin-Han; Lee, Joon-Sung; Chun, Ho-Jong

2011-01-01

The aim of this study was to review the chest computed tomography (CT) findings in children with swine-origin influenza (H1N1) virus (S-OIV) infection. The radiologists retrospectively reviewed chest CT findings in 12 children with S-OIV infection and recorded the following findings: ground-glass opacities (GGO), consolidation, nodules, reticular opacities, peribronchial cuffing, and air trapping; distribution; affected lobes. The presence of pleural effusions, pneumomediastinum, pulmonary interstitial emphysema (PIE), and lymphadenopathy was also recorded. Chest CT revealed GGO (67%), consolidation (67%), nodules (25%), peribronchial cuffing (42%), and air trapping (33%). The distribution of the lesions was random (75%), peribronchial (17%), or subpleural (8%). The lobes affected were the lower (92%), upper (58%), and middle (17%) lobes. There were associated pleural effusions (42%), PIE (42%), pneumomediastinum (33%), and lymphadenopathy (75%). Among five patients with air-leak complications, three had a history of allergies and three required the intensive care unit. Chest CT findings in children with S-OIV infection were peribronchial thickening and a mixture of airspace consolidation and GGO with random distribution and lower lobe predominance. Pleural effusion, lymphadenopathy, PIE, and pneumomediastinum may be associated findings. (author)

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…

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...

Retroperitoneal and pelvic plexiform neurofibromatosis: computed tomography and magnetic resonance findings - case report and review of literature

International Nuclear Information System (INIS)

Cancado, Daniel Dutra; Bahia, Paulo Roberto Valle; Leijoto, Camila Cruz; Carvalho, Carlos Eduardo Souza

2005-01-01

The authors report a case of neurofibromatosis type I, characterized by multiple plexiform neurofibromas in the retroperitoneum and pelvis. Computed tomography showed markedly hypodense lesions involving mainly the psoas and the paravertebral regions, findings which could mimic other diseases such as abscesses and lymphadenopathy. Magnetic resonance imaging was useful to better evaluate the extension and internal structure of the neurofibromas. (author)

Genome-Wide Detection and Analysis of Multifunctional Genes

Science.gov (United States)

Pritykin, Yuri; Ghersi, Dario; Singh, Mona

2015-01-01

Many genes can play a role in multiple biological processes or molecular functions. Identifying multifunctional genes at the genome-wide level and studying their properties can shed light upon the complexity of molecular events that underpin cellular functioning, thereby leading to a better understanding of the functional landscape of the cell. However, to date, genome-wide analysis of multifunctional genes (and the proteins they encode) has been limited. Here we introduce a computational approach that uses known functional annotations to extract genes playing a role in at least two distinct biological processes. We leverage functional genomics data sets for three organisms—H. sapiens, D. melanogaster, and S. cerevisiae—and show that, as compared to other annotated genes, genes involved in multiple biological processes possess distinct physicochemical properties, are more broadly expressed, tend to be more central in protein interaction networks, tend to be more evolutionarily conserved, and are more likely to be essential. We also find that multifunctional genes are significantly more likely to be involved in human disorders. These same features also hold when multifunctionality is defined with respect to molecular functions instead of biological processes. Our analysis uncovers key features about multifunctional genes, and is a step towards a better genome-wide understanding of gene multifunctionality. PMID:26436655

Head and neck: normal variations and benign findings in FDG positron emission tomography/computed tomography imaging.

Science.gov (United States)

Højgaard, Liselotte; Berthelsen, Anne Kiil; Loft, Annika

2014-04-01

Positron emission tomography (PET)/computed tomography with FDG of the head and neck region is mainly used for the diagnosis of head and neck cancer, for staging, treatment evaluation, relapse, and planning of surgery and radio therapy. This article is a practical guide of imaging techniques, including a detailed protocol for FDG PET in head and neck imaging, physiologic findings, and pitfalls in selected case stories. Copyright © 2014 Elsevier Inc. All rights reserved.

Agreement between computed tomography, magnetic resonance imaging, and surgical findings in dogs with degenerative lumbosacral stenosis.

Science.gov (United States)

Suwankong, Niyada; Voorhout, George; Hazewinkel, Herman A W; Meij, Björn P

2006-12-15

To assess the extent of agreement between computed tomography (CT), magnetic resonance imaging (MRI), and surgical findings in dogs with degenerative lumbosacral stenosis. Observational study. 35 dogs with degenerative lumbosacral stenosis. Results of preoperative CT and MRI were compared with surgical findings with respect to degree and location of disk protrusion, position of the dural sac, amount of epidural fat, and swelling of spinal nerve roots. A lumbosacral step was seen on radiographic images from 22 of 32 (69%) dogs, on CT images from 23 of 35 (66%) dogs, and on MR images from 21 of 35 (60%) dogs. Most dogs had slight or moderate disk protrusion that was centrally located. There was substantial or near perfect agreement between CT and MRI findings in regard to degree of disk protrusion (kappa, 0.88), location of disk protrusion (0.63), position of the dural sac (0.89), amount of epidural fat (0.72), and swelling of spinal nerve roots (0.60). The degree of agreement between CT and surgical findings and between MRI and surgical findings was moderate in regard to degree and location of disk protrusion (kappa, 0.44 to 0.56) and swelling of spinal nerve roots (0.40 and 0.50). Results indicate that there is a high degree of agreement between CT and MRI findings in dogs with degenerative lumbosacral stenosis but that the degree of agreement between diagnostic imaging findings and surgical findings is lower.

Thin-section computed tomography findings in 104 immunocompetent patients with adenovirus pneumonia.

Science.gov (United States)

Park, Chan Kue; Kwon, Hoon; Park, Ji Young

2017-08-01

Background To date, there has been no computed tomography (CT) evaluation of adenovirus pneumonia in a large number of immunocompetent patients. Purpose To describe the thin-section CT findings of immunocompetent patients with adenovirus pneumonia. Material and Methods We prospectively enrolled 104 patients with adenovirus pneumonia from a military hospital. CT scans of each patient were retrospectively and independently assessed by two radiologists for the presence of abnormalities, laterality and zonal predominance of the parenchymal abnormalities, and dominant imaging patterns and their anatomic distributions. Results CT findings included consolidation (n = 92), ground-glass opacity (GGO; n = 82), septal thickening (n = 34), nodules (n = 46), bronchial wall thickening (n = 32), pleural effusion (n = 16), and lymphadenopathy (n = 3). Eighty-four patients (81%) exhibited unilateral parenchymal abnormalities and 57 (57%) exhibited lower lung zone abnormalities. The most frequently dominant CT pattern was consolidation with surrounding GGO (n = 50), with subpleural (70%) and peribronchovascular (94%) distributions. Consolidation-the second-most common pattern (n = 33)-also exhibited subpleural (79%) and peribronchovascular (97%) distributions. The dominant nodule pattern (n = 14) exhibited mixed (64%) and peribronchovascular (100%) distributions. A dominant GGO pattern was only observed in four patients; none had central distribution. Conclusion Although the manifestations of adenovirus pneumonia on CT are varied, we found the most frequent pattern was consolidation with or without surrounding GGO, with subpleural and peribronchovascular distributions. Parenchymal abnormalities were predominantly unilateral and located in the lower lung zone. If dominant consolidation findings are present in immunocompetent patients during the early stages, adenovirus pneumonia should be considered.

Pulmonary complications of induction therapy for acute myeloid leukemia in adults. Findings of chest X-rays and computed tomography

International Nuclear Information System (INIS)

Kirchner, J.; Huettmann, C.; Jacobi, V.; Boehme, A.

1998-01-01

To exclude pulmonary complications, 359 chest radiographs and 50 computed tomographs of the lung were performed in 95 patients suffering from acute myeloid leukemia. The radiological findings were registered, described and correlated with clinical findings in the present study on 2395 days of observation. Results: In summary, 52 patients showed alterations of the lung. Pulmonary hyperhydration was seen in 21 cases, bacterial pneumonia was found in 18 cases, invasive pulmonary aspergillosis was documented in 14 cases, and 5 cases of severe haemorrhage were seen. An unexplained pulmonary edema in 13 patients with interstitial and alveolar infiltrates is considered to be a complication of treatment with cytosine-arabinoside. Conclusion: The results demonstrate that chest X-ray and computed tomography have a high impact in detection and treatment of pulmonary complications following intensive chemotherapy. We may expect the development of diffuse opacity following administration of cytosine-arabinoside in medium-sized doses. (orig.) [de

Fat deposition in the urinary bladder wall: Incidental finding on abdominal computed tomography: A case report

Energy Technology Data Exchange (ETDEWEB)

Park, Min Ho; Moon, Sung Kyoung; Ahn, Sung Eun; Park, Seong Jin; Lim, Joo Won; Lee, Dong Ho [Dept. of Radiology, Kyung Hee University Medical Center, Kyung Hee University School of Medicine, Seoul (Korea, Republic of)

2015-02-15

In a computed tomography (CT) scan, fat deposition in the urinary bladder wall is seen as a linear hypoattenuating band surrounded by soft tissue density. It is uncommon, but is often seen in normal cases. However, there is no report of fat deposition in the urinary bladder wall in Korea. The authors encountered a 62-year-old male patient who showed an incidental hypoattenuating band in the urinary bladder wall on abdominal CT. The patient showed no clinical signs related to fat deposition in the urinary bladder wall. When the patient's previous abdominal CT was retrospectively reviewed, the same CT finding was seen. This linear hypoattenuating band within the urinary bladder wall should be considered as a normal CT finding, although it is uncommon.

Computational method for discovery of estrogen responsive genes

DEFF Research Database (Denmark)

Tang, Suisheng; Tan, Sin Lam; Ramadoss, Suresh Kumar

2004-01-01

Estrogen has a profound impact on human physiology and affects numerous genes. The classical estrogen reaction is mediated by its receptors (ERs), which bind to the estrogen response elements (EREs) in target gene's promoter region. Due to tedious and expensive experiments, a limited number of hu...

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.)

Prevalence of extra-cardiac findings on studies of noninvasive coronary angiography multidetector computed tomography 64 rows

International Nuclear Information System (INIS)

Carrascosa, Patricia M.; Capunay, Carlos M.; Deviggiano, A.; Melendez, F.; Carrascosa, Jorge M.; Garcia, M.

2007-01-01

The aim of this paper is to show the importance of evaluating in a full form images obtained from a studio of noninvasive coronary angiography by multidetector computed tomography (AC-TCMD). 90 users of AC-TCMD were evaluated retrospectively conducted between October 2006 and April 2007 with a multidetector tomography of 64-rows(Phillips Medical Systems) . The images were reprocessed with a maximum field of vision and determined the presence of extra-cardiac findings, which were classified according to their impact on the management and treatment of patient at 3 degrees: low, medium and high grade. The studies were assessed jointly by a cardiologist and a radiologist qualified for cardiac and corporal evaluation. Extra-cardiac findings were identified in 58 patients. There were 38 patients with findings of low grade, 31 medium grade and 1 high grade. It was recommended to 16 patients its monitoring by images on reasonable period of time [es

Global discriminative learning for higher-accuracy computational gene prediction.

Directory of Open Access Journals (Sweden)

Axel Bernal

2007-03-01

Full Text Available Most ab initio gene predictors use a probabilistic sequence model, typically a hidden Markov model, to combine separately trained models of genomic signals and content. By combining separate models of relevant genomic features, such gene predictors can exploit small training sets and incomplete annotations, and can be trained fairly efficiently. However, that type of piecewise training does not optimize prediction accuracy and has difficulty in accounting for statistical dependencies among different parts of the gene model. With genomic information being created at an ever-increasing rate, it is worth investigating alternative approaches in which many different types of genomic evidence, with complex statistical dependencies, can be integrated by discriminative learning to maximize annotation accuracy. Among discriminative learning methods, large-margin classifiers have become prominent because of the success of support vector machines (SVM in many classification tasks. We describe CRAIG, a new program for ab initio gene prediction based on a conditional random field model with semi-Markov structure that is trained with an online large-margin algorithm related to multiclass SVMs. Our experiments on benchmark vertebrate datasets and on regions from the ENCODE project show significant improvements in prediction accuracy over published gene predictors that use intrinsic features only, particularly at the gene level and on genes with long introns.

Atypical findings on computed tomography in tuberous sclerosis

International Nuclear Information System (INIS)

Glass, R.B.J.; Mendelsohn, D.B.; Hertzanu, Y.

1984-01-01

In 3 patients with tuberous sclerosis computed tomography showed numerous low-density areas suggestive of brain demyelination. In addition, solitary small subependymal calcifications were noted. These features in an infant or child with unexplained seizures should alert one to the diagnosis of tuberous sclerosis

Research progress in machine learning methods for gene-gene interaction detection.

Science.gov (United States)

Peng, Zhe-Ye; Tang, Zi-Jun; Xie, Min-Zhu

2018-03-20

Complex diseases are results of gene-gene and gene-environment interactions. However, the detection of high-dimensional gene-gene interactions is computationally challenging. In the last two decades, machine-learning approaches have been developed to detect gene-gene interactions with some successes. In this review, we summarize the progress in research on machine learning methods, as applied to gene-gene interaction detection. It systematically examines the principles and limitations of the current machine learning methods used in genome wide association studies (GWAS) to detect gene-gene interactions, such as neural networks (NN), random forest (RF), support vector machines (SVM) and multifactor dimensionality reduction (MDR), and provides some insights on the future research directions in the field.

Computer-Aided College Algebra: Learning Components that Students Find Beneficial

Science.gov (United States)

Aichele, Douglas B.; Francisco, Cynthia; Utley, Juliana; Wescoatt, Benjamin

2011-01-01

A mixed-method study was conducted during the Fall 2008 semester to better understand the experiences of students participating in computer-aided instruction of College Algebra using the software MyMathLab. The learning environment included a computer learning system for the majority of the instruction, a support system via focus groups (weekly…

GENIE: a software package for gene-gene interaction analysis in genetic association studies using multiple GPU or CPU cores

Directory of Open Access Journals (Sweden)

Wang Kai

2011-05-01

Full Text Available Abstract Background Gene-gene interaction in genetic association studies is computationally intensive when a large number of SNPs are involved. Most of the latest Central Processing Units (CPUs have multiple cores, whereas Graphics Processing Units (GPUs also have hundreds of cores and have been recently used to implement faster scientific software. However, currently there are no genetic analysis software packages that allow users to fully utilize the computing power of these multi-core devices for genetic interaction analysis for binary traits. Findings Here we present a novel software package GENIE, which utilizes the power of multiple GPU or CPU processor cores to parallelize the interaction analysis. GENIE reads an entire genetic association study dataset into memory and partitions the dataset into fragments with non-overlapping sets of SNPs. For each fragment, GENIE analyzes: 1 the interaction of SNPs within it in parallel, and 2 the interaction between the SNPs of the current fragment and other fragments in parallel. We tested GENIE on a large-scale candidate gene study on high-density lipoprotein cholesterol. Using an NVIDIA Tesla C1060 graphics card, the GPU mode of GENIE achieves a speedup of 27 times over its single-core CPU mode run. Conclusions GENIE is open-source, economical, user-friendly, and scalable. Since the computing power and memory capacity of graphics cards are increasing rapidly while their cost is going down, we anticipate that GENIE will achieve greater speedups with faster GPU cards. Documentation, source code, and precompiled binaries can be downloaded from http://www.cceb.upenn.edu/~mli/software/GENIE/.

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

Melanotic neuroectodermal tumor of infancy (progonoma): a case report emphasizing the computed tomography findings and literature review

International Nuclear Information System (INIS)

Araujo Junior, Cyrillo Rodrigues de; Carvalho, Tarcisio Nunes; Fraguas Filho, Sergio Roberto; Costa, Marlos Augusto Bitencourt; Borba, Ana Olivia Cardoso; Figueiredo, Sizenildo da Silva; Machado, Marcio Martins; Teixeira, Kim-Ir-Sen Santos

2004-01-01

The melanotic neuroectodermal tumor of infancy, also known as progonoma, is a rare benign disease of neural crest origin that occurs within the first year of life and affects mainly the maxilla. The authors report a case of a 10-month-old child presenting with this uncommon tumor in the maxilla, emphasizing the diagnostic findings on computed tomography, and present a literature review. (author)

GBOOST: a GPU-based tool for detecting gene-gene interactions in genome-wide case control studies.

Science.gov (United States)

Yung, Ling Sing; Yang, Can; Wan, Xiang; Yu, Weichuan

2011-05-01

Collecting millions of genetic variations is feasible with the advanced genotyping technology. With a huge amount of genetic variations data in hand, developing efficient algorithms to carry out the gene-gene interaction analysis in a timely manner has become one of the key problems in genome-wide association studies (GWAS). Boolean operation-based screening and testing (BOOST), a recent work in GWAS, completes gene-gene interaction analysis in 2.5 days on a desktop computer. Compared with central processing units (CPUs), graphic processing units (GPUs) are highly parallel hardware and provide massive computing resources. We are, therefore, motivated to use GPUs to further speed up the analysis of gene-gene interactions. We implement the BOOST method based on a GPU framework and name it GBOOST. GBOOST achieves a 40-fold speedup compared with BOOST. It completes the analysis of Wellcome Trust Case Control Consortium Type 2 Diabetes (WTCCC T2D) genome data within 1.34 h on a desktop computer equipped with Nvidia GeForce GTX 285 display card. GBOOST code is available at http://bioinformatics.ust.hk/BOOST.html#GBOOST.

Computed Tomography findings in Fournier's gangrene

International Nuclear Information System (INIS)

Isusi, M.; Campo, M.; Oleaga, L.; Grande, J.; Grande, D.

2000-01-01

To assess the utility of computed tomography (CT) as an imaging technique in the diagnosis and determination of the extension of Fournier's gangrene (FG). We report the cases of six patients who had been clinically diagnosed as having FG, CT, enhanced by oral and intravenous contrast media, was performed in all the patients. All six patients presented soft tissue masses and gas in the scrotal region, which were also detected in the perineal region in five. In two patients, the gas extended toward anterior abdominal wall and in one of them, it also observed in anterior and posterior para renal space. The major predisposing factors were diabetes and alcoholism and the most common triggering factor was urologic disease. CT confirms the existence of FG and aids in assessing its extension and, in some cases, in identifying the underlying cause. (Author) 15 refs

Computed tomography findings of hepatic veno-occlusive disease caused by Sedum aizoon with histopathological correlation

Energy Technology Data Exchange (ETDEWEB)

Shao, H.; Chen, H. Z., E-mail: chenhz@enzemed.com; Zhu, J. S. [Department of Infectious Diseases, Taizhou Hospital Affiliated to Wenzhou Medical College, Linhai (China); Ruan, B. [State Key Laboratory for Diagnosis and Treatment of Infectious Disease, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou (China); Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou (China); Zhang, Z. Q. [Department of Infectious Disease, Xianju Hospital of Traditional Chinese Medicine, Xianju (China); Lin, X.; Gan, M. F. [Department of Infectious Diseases, Taizhou Hospital Affiliated to Wenzhou Medical College, Linhai (China)

2015-11-23

This study investigated the value of computed tomography (CT) in the diagnosis and treatment of hepatic veno-occlusive disease (HVOD) caused by Sedum aizoon (SA). The clinical manifestations, treatment results, imaging findings, and histological findings of the liver were analyzed in 39 patients with HVOD caused by SA. Hepatomegaly, liver dysfunction, abdominal effusion, and geographic density changes on liver CT scans were found in all 39 patients. The pathological findings of histological liver examination included swelling and point-like necrosis of liver cells, significant expansion and congestion of the sinuses, endothelial swelling, and wall thickening with incomplete lumen occlusion of small liver vessels. CT geographic density changes were confirmed by histological examination of the liver in 18 patients. Sixteen patients with small amounts of ascites that started within 4 weeks of treatment recovered completely or significantly improved after symptomatic and supportive treatment. However, only 43.75% of the patients with larger amounts of ascites improved following symptomatic and supportive treatment. In conclusion, liver CT examination is a valuable, safe, and noninvasive tool for the diagnosis of HVOD caused by SA. In selected cases, liver CT examination may replace liver biopsy and histological analysis.

Spectrum of high resolution computed tomography findings in occupational lung disease: experience in a tertiary care institute.

Science.gov (United States)

Bhawna, Satija; Ojha, U C; Kumar, Sanyal; Gupta, Rajiv; Gothi, Dipti; Pal, R S

2013-01-01

To study the spectrum of high resolution computed tomography (HRCT) findings in occupational lung disease in industrial workers and to assess the utility of International classification of HRCT for occupational and environmental respiratory diseases (ICHOERD). Retrospective analysis of radiological data (radiographs and computed tomography chest scans) gathered over a period of 3 years (January 2010- December 2012) of industrial workers in an organised sector who presented with respiratory complaints. The HRCT findings were evaluated using ICHOERD. There were 5 females and 114 males in the study, with a mean age of 49 years. These workers were exposed to different harmful agents including silica, asbestos, cotton dust, metal dust, iron oxide, organic dust, rubber fumes, plastic fumes, acid fumes, and oil fumes. There were 10 smokers in the study. The radiograph of chest was normal in 53 patients. 46% of these normal patients (21.8% of total) demonstrated positive findings on HRCT. When the radiograph was abnormal, HRCT provided more accurate information and excluded the other diagnosis. The HRCT findings were appropriately described using the ICHOERD. Bronchiectasis was the most common finding (44.5%) with mild central cylindrical bronchiectasis as the most common pattern. Pleural thickening was seen in 41 patients (34.5%). Enlarged hilar or mediastinal lymphnodes were seen in 10 patients (8.4%) with egg-shell calcification in 1 patient exposed to silica. Bronchogenic carcinoma was seen in 1 patient exposed to asbestos. Occupational lung disease is a common work related condition in industrial workers even in the organized sector. Though chest radiograph is the primary diagnostic tool, HRCT is the undisputed Gold Standard for evaluation of these patients. Despite the disadvantage of radiation exposure, low dose CT may serve as an important tool for screening and surveillance. The ICHOERD is a powerful and reliable tool not only for diagnosis, but also for

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.

Integrative Functional Genomics for Systems Genetics in GeneWeaver.org.

Science.gov (United States)

Bubier, Jason A; Langston, Michael A; Baker, Erich J; Chesler, Elissa J

2017-01-01

The abundance of existing functional genomics studies permits an integrative approach to interpreting and resolving the results of diverse systems genetics studies. However, a major challenge lies in assembling and harmonizing heterogeneous data sets across species for facile comparison to the positional candidate genes and coexpression networks that come from systems genetic studies. GeneWeaver is an online database and suite of tools at www.geneweaver.org that allows for fast aggregation and analysis of gene set-centric data. GeneWeaver contains curated experimental data together with resource-level data such as GO annotations, MP annotations, and KEGG pathways, along with persistent stores of user entered data sets. These can be entered directly into GeneWeaver or transferred from widely used resources such as GeneNetwork.org. Data are analyzed using statistical tools and advanced graph algorithms to discover new relations, prioritize candidate genes, and generate function hypotheses. Here we use GeneWeaver to find genes common to multiple gene sets, prioritize candidate genes from a quantitative trait locus, and characterize a set of differentially expressed genes. Coupling a large multispecies repository curated and empirical functional genomics data to fast computational tools allows for the rapid integrative analysis of heterogeneous data for interpreting and extrapolating systems genetics results.

Brain computed tomography findings of schizophrenia, (2)

International Nuclear Information System (INIS)

Fukuhara, Tomokazu; Tanaka, Yuzo; Hazama, Hidebumi

1982-01-01

The relationship between brain CT findings and the total dose of antipsychotic drugs was examined in 47 cases with schizophrenia ranging from 20 to 42 years in age (31 males and 16 females). The methods of Gyldensted et al. and Okamoto et al. were modified for CT measurements. The total dose during the entire course was converted into the dose of chlorpromazine (CPZ) for each case. For comparisons with CT findings, the total dose was classified into three types each for both sexes: ''less than'' 100 g, ''less than'' 500 g and ''more than'' 500 g for the males and ''more than'' 500 g, ''less than'' 1,000 g and ''more than'' 1,000 g for the females. For similar comparisons, the same subjects were matched for the age and sex distinction, and were divided into the ''less than'' and ''more than'' groups for 500 g and 800 g, respectively. In both the matched and non-matched cases, each measurement value of the ventricular system on CT tended to be higher in the ''more than'' groups than in the ''less than'' groups. The relationship between CT findings and the total dose was nogligible. (Chiba, N.)

Retrospective evaluation of thoracic computed tomography findings in dogs naturally infected by Angiostrongylus vasorum.

Science.gov (United States)

Coia, Mark E; Hammond, Gawain; Chan, Daniel; Drees, Randi; Walker, David; Murtagh, Kevin; Stone, Janine; Bexfield, Nicholas; Reeve, Lizzie; Helm, Jenny

2017-09-01

Angiostrongylus vasorum (A. vasorum) is an important emerging disease of canidae. Cardiorespiratory signs are common in affected dogs, therefore thoracic imaging is critical for diagnosing and monitoring disease. Descriptions of thoracic computed tomography (CT) findings in dogs naturally infected with A. vasorum are currently lacking. Aims of this multicenter, retrospective study were to describe thoracic CT findings in a group of dogs with confirmed disease, determine whether any changes were consistent among dogs, and propose standardized terms for describing thoracic CT findings. Nine UK-based referral centers' clinical and imaging databases were searched for dogs that had a confirmed diagnosis of A. vasorum, and had undergone thoracic CT examination. Eighteen dogs, from seven of the centers, fulfilled the inclusion criteria. The lung lobes were divided into the following three zones and the CT changes described in each: pleural (zone 1), subpleural (zone 2), and peribronchovascular (zone 3). The predominent abnormality was increased lung attenuation due to poorly defined ground-glass opacity or consolidation. There were regions of mosaic attenuation due to peripheral bronchiectasis. Nine/18 (50%) dogs showed hyperattenuating nodules of varying sizes with ill-defined margins. The distribution always affected zones 1 and 2 with varied involvement of zone 3; this resulted in clear delineation between zones 2 and 3. Tracheobronchial lymphadenomegaly was frequently noted. Findings were nonspecific and there was considerable overlap with other pulmonary conditions. However, authors recommend that A. vasorum be considered a likely differential diagnosis for dogs with a predominantly peripheral distribution of lung changes. © 2017 American College of Veterinary Radiology.

New Genome Similarity Measures based on Conserved Gene Adjacencies.

Science.gov (United States)

Doerr, Daniel; Kowada, Luis Antonio B; Araujo, Eloi; Deshpande, Shachi; Dantas, Simone; Moret, Bernard M E; Stoye, Jens

2017-06-01

Many important questions in molecular biology, evolution, and biomedicine can be addressed by comparative genomic approaches. One of the basic tasks when comparing genomes is the definition of measures of similarity (or dissimilarity) between two genomes, for example, to elucidate the phylogenetic relationships between species. The power of different genome comparison methods varies with the underlying formal model of a genome. The simplest models impose the strong restriction that each genome under study must contain the same genes, each in exactly one copy. More realistic models allow several copies of a gene in a genome. One speaks of gene families, and comparative genomic methods that allow this kind of input are called gene family-based. The most powerful-but also most complex-models avoid this preprocessing of the input data and instead integrate the family assignment within the comparative analysis. Such methods are called gene family-free. In this article, we study an intermediate approach between family-based and family-free genomic similarity measures. Introducing this simpler model, called gene connections, we focus on the combinatorial aspects of gene family-free genome comparison. While in most cases, the computational costs to the general family-free case are the same, we also find an instance where the gene connections model has lower complexity. Within the gene connections model, we define three variants of genomic similarity measures that have different expression powers. We give polynomial-time algorithms for two of them, while we show NP-hardness for the third, most powerful one. We also generalize the measures and algorithms to make them more robust against recent local disruptions in gene order. Our theoretical findings are supported by experimental results, proving the applicability and performance of our newly defined similarity measures.

Species-independent MicroRNA Gene Discovery

KAUST Repository

Kamanu, Timothy K.

2012-12-01

MicroRNA (miRNA) are a class of small endogenous non-coding RNA that are mainly negative transcriptional and post-transcriptional regulators in both plants and animals. Recent studies have shown that miRNA are involved in different types of cancer and other incurable diseases such as autism and Alzheimer’s. Functional miRNAs are excised from hairpin-like sequences that are known as miRNA genes. There are about 21,000 known miRNA genes, most of which have been determined using experimental methods. miRNA genes are classified into different groups (miRNA families). This study reports about 19,000 unknown miRNA genes in nine species whereby approximately 15,300 predictions were computationally validated to contain at least one experimentally verified functional miRNA product. The predictions are based on a novel computational strategy which relies on miRNA family groupings and exploits the physics and geometry of miRNA genes to unveil the hidden palindromic signals and symmetries in miRNA gene sequences. Unlike conventional computational miRNA gene discovery methods, the algorithm developed here is species-independent: it allows prediction at higher accuracy and resolution from arbitrary RNA/DNA sequences in any species and thus enables examination of repeat-prone genomic regions which are thought to be non-informative or ’junk’ sequences. The information non-redundancy of uni-directional RNA sequences compared to information redundancy of bi-directional DNA is demonstrated, a fact that is overlooked by most pattern discovery algorithms. A novel method for computing upstream and downstream miRNA gene boundaries based on mathematical/statistical functions is suggested, as well as cutoffs for annotation of miRNA genes in different miRNA families. Another tool is proposed to allow hypotheses generation and visualization of data matrices, intra- and inter-species chromosomal distribution of miRNA genes or miRNA families. Our results indicate that: miRNA and mi

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.

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.

Computed tomographic findings and treatment of a bull with pituitary gland abscess.

Science.gov (United States)

Braun, Ueli; Malbon, Alexandra; Kochan, Manon; Riond, Barbara; Janett, Fredi; Iten, Cornelia; Dennler, Matthias

2017-01-13

In cattle, the prognosis of brain abscess is unfavourable and treatment is therefore not recommended. To the knowledge of the authors, there has been no report of successful treatment of a brain abscess in cattle.This report describes the clinical, computed tomographic and postmortem findings in a Holstein-Friesian bull with a hypophyseal abscess. The main clinical findings were generalised ataxia, ptyalism, prolapse of the tongue, dropped jaw, dysphagia, head tilt and unilateral ptosis. Cerebrospinal fluid evaluation revealed 2437 leukocytes/µl and severe pleocytosis. CT examination of the head showed a cavitary lesion consistent with an abscess in the hypophysis. Treatment consisted of gentamicin and flunixin meglumine for 3 days and amoxicillin for 40 days. The neurological signs resolved within 8 days of the start of treatment. The bull was slaughtered 11 months later because of infertility, and a postmortem examination was carried out. Histologically, a mild chronic non suppurative meningoencephalitis restricted to the ventral diencephalon was diagnosed. In addition, there was mild to moderate multifocal chronic lymphoplasmacytic hypophysitis with mild multifocal fibrosis. This case report stresses the significance of CT in confirming the clinical and laboratory diagnosis of central nervous system disorders in cattle and for localising brain lesions. Treatment of the brain abscess resulted, with respect to the central nervous disorder, in a successful outcome and was encouraging considering that most cases have an unfavourable prognosis.

Computer-aided detection of colorectal polyps: can it improve sensitivity of less-experienced readers? Preliminary findings.

Science.gov (United States)

Baker, Mark E; Bogoni, Luca; Obuchowski, Nancy A; Dass, Chandra; Kendzierski, Renee M; Remer, Erick M; Einstein, David M; Cathier, Pascal; Jerebko, Anna; Lakare, Sarang; Blum, Andrew; Caroline, Dina F; Macari, Michael

2007-10-01

To determine whether computer-aided detection (CAD) applied to computed tomographic (CT) colonography can help improve sensitivity of polyp detection by less-experienced radiologist readers, with colonoscopy or consensus used as the reference standard. The release of the CT colonographic studies was approved by the individual institutional review boards of each institution. Institutions from the United States were HIPAA compliant. Written informed consent was waived at all institutions. The CT colonographic studies in 30 patients from six institutions were collected; 24 images depicted at least one confirmed polyp 6 mm or larger (39 total polyps) and six depicted no polyps. By using an investigational software package, seven less-experienced readers from two institutions evaluated the CT colonographic images and marked or scored polyps by using a five-point scale before and after CAD. The time needed to interpret the CT colonographic findings without CAD and then to re-evaluate them with CAD was recorded. For each reader, the McNemar test, adjusted for clustered data, was used to compare sensitivities for readers without and with CAD; a Wilcoxon signed-rank test was used to analyze the number of false-positive results per patient. The average sensitivity of the seven readers for polyp detection was significantly improved with CAD-from 0.810 to 0.908 (P=.0152). The number of false-positive results per patient without and with CAD increased from 0.70 to 0.96 (95% confidence interval for the increase: -0.39, 0.91). The mean total time for the readings was 17 minutes 54 seconds; for interpretation of CT colonographic findings alone, the mean time was 14 minutes 16 seconds; and for review of CAD findings, the mean time was 3 minutes 38 seconds. Results of this feasibility study suggest that CAD for CT colonography significantly improves per-polyp detection for less-experienced readers. Copyright (c) RSNA, 2007.

Comparison between computed tomographic and surgical findings in nine large-breed dogs with lumbosacral stenosis

International Nuclear Information System (INIS)

Jones, J.C.; Sorjonen, D.C.; Simpson, S.T.; Coates, J.R.; Lenz, S.D.; Hathcock, J.T.; Agee, M.W.; Bartels, J.E.

1996-01-01

In a three-year prospective study, computed tomographic (CT) and surgical findings were compared for nine large breed dogs with lumbosacral stenosis. Surgically-excised tissue was examined histologically in seven dogs and additional necropsy evaluation was performed in one dog. The CT abnormalities observed at sites of confirmed cauda equina compression were: loss of epidural fat, increased soft tissue opacity, bulging of the intervertebral disc margin, spondylosis, thecal sac displacement, narrowed intervertebral foramen, narrowed vertebral canal, thickened articular process, articular process subluxation, articular process osteophyte, and telescoped sacral lamina. The CT characteristics of lumbosacral degenerative disease and discospondylitis were similar to those described in humans. In three dogs, CT findings at the site of cauda equina compression were consistent with congenital or developmental spinal stenosis, but the method of surgical exposure precluded confirmation. Epidural fibrosis (eight dogs) and multi-level CT abnormalities (six dogs) were identified but the cause(s) and significance were unknown

Computed tomography and magnetic resonance imaging findings of solitary fibrous tumors in the pelvis: Correlation with histopathological findings

International Nuclear Information System (INIS)

Zhang Weidong; Chen Jianyu; Cao Yun; Liu Qingyu; Luo Rongguang

2011-01-01

Objective: We aimed to analyze the computed tomography (CT) and magnetic resonance imaging (MRI) findings of pelvic solitary fibrous tumors (SFTs) and to improve the diagnostic efficacy for such tumors. Methods: Six cases of pelvic SFTs confirmed by histopathology were analyzed retrospectively. Of the 6 patients, 4 had undergone CT scanning, and 2 had undergone magnetic resonance imaging. All the patients had undergone unenhanced and contrast-enhanced examinations, and 2 had also undergone dynamic CT enhancement examination. Image characteristics such as shape, size, number, edge, attenuation or intensity for each lesion before and after contrast enhancement were analyzed and compared with the pathomorphology of the tumors. Results: All the 6 cases showed oval or rounded and well-defined masses. Unenhanced CT images showed heterogeneous masses with patchy, necrotic foci in 3 cases and homogeneous mass in 1 case. None of the tumors showed calcification. Contrast-enhanced CT images showed marked, heterogeneous enhancement in the first and second cases. Dynamic enhancement scan demonstrated mild homogeneous enhancement in the third case and mild prolonged, delayed enhancement and washout in the fourth case. T1-weighted MR images showed heterogeneous mild hypointense lesion with linear hyperintensity in 1 case, and homogeneous isointensity in the other. T2-weighted images showed heterogeneous mixed intensity in 1 case and mostly hyperintensive lesion with hypointense foci in another case. A case showed marked heterogeneous enhancement and another showed marked homogeneous enhancement on contrast-enhanced T1-weighted images. Conclusion: Radiological findings of pelvic SFTs are variable and nonspecific. However, a well-defined, ovoid or rounded mass with hypointense on MR T2-weighted images and variable enhancement on CT and MR images may suggest the diagnosis of SFTs. Pelvic SFTs should be included in the differential diagnosis of regional tumors.

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.

Operative findings of conductive hearing loss with intact tympanic membrane and normal temporal bone computed tomography.

Science.gov (United States)

Kim, Se-Hyung; Cho, Yang-Sun; Kim, Hye Jeong; Kim, Hyung-Jin

2014-06-01

Despite recent technological advances in diagnostic methods including imaging technology, it is often difficult to establish a preoperative diagnosis of conductive hearing loss (CHL) in patients with an intact tympanic membrane (TM). Especially, in patients with a normal temporal bone computed tomography (TBCT), preoperative diagnosis is more difficult. We investigated middle ear disorders encountered in patients with CHL involving an intact TM and normal TBCT. We also analyzed the surgical results with special reference to the pathology. We reviewed the medical records of 365 patients with intact TM, who underwent exploratory tympanotomy for CHL. Fifty nine patients (67 ears, eight bilateral surgeries) had a normal preoperative TBCT findings reported by neuro-radiologists. Demographic data, otologic history, TM findings, preoperative imaging findings, intraoperative findings, and pre- and postoperative audiologic data were obtained and analyzed. Exploration was performed most frequently in the second and fifth decades. The most common postoperative diagnosis was stapedial fixation with non-progressive hearing loss. The most commonly performed hearing-restoring procedure was stapedotomy with piston wire prosthesis insertion. Various types of hearing-restoring procedures during exploration resulted in effective hearing improvement, especially with better outcome in the ossicular chain fixation group. In patients with CHL who have intact TM and normal TBCT, we should consider an exploratory tympanotomy for exact diagnosis and hearing improvement. Information of the common operative findings from this study may help in preoperative counseling.

Single nucleotide polymorphism in transcriptional regulatory regions and expression of environmentally responsive genes

International Nuclear Information System (INIS)

Wang, Xuting; Tomso, Daniel J.; Liu Xuemei; Bell, Douglas A.

2005-01-01

Single nucleotide polymorphisms (SNPs) in the human genome are DNA sequence variations that can alter an individual's response to environmental exposure. SNPs in gene coding regions can lead to changes in the biological properties of the encoded protein. In contrast, SNPs in non-coding gene regulatory regions may affect gene expression levels in an allele-specific manner, and these functional polymorphisms represent an important but relatively unexplored class of genetic variation. The main challenge in analyzing these SNPs is a lack of robust computational and experimental methods. Here, we first outline mechanisms by which genetic variation can impact gene regulation, and review recent findings in this area; then, we describe a methodology for bioinformatic discovery and functional analysis of regulatory SNPs in cis-regulatory regions using the assembled human genome sequence and databases on sequence polymorphism and gene expression. Our method integrates SNP and gene databases and uses a set of computer programs that allow us to: (1) select SNPs, from among the >9 million human SNPs in the NCBI dbSNP database, that are similar to cis-regulatory element (RE) consensus sequences; (2) map the selected dbSNP entries to the human genome assembly in order to identify polymorphic REs near gene start sites; (3) prioritize the candidate polymorphic RE containing genes by searching the existing genotype and gene expression data sets. The applicability of this system has been demonstrated through studies on p53 responsive elements and is being extended to additional pathways and environmentally responsive genes

GeneNotes – A novel information management software for biologists

Directory of Open Access Journals (Sweden)

Wong Wing H

2005-02-01

Full Text Available Abstract Background Collecting and managing information is a challenging task in a genome-wide profiling research project. Most databases and online computational tools require a direct human involvement. Information and computational results are presented in various multimedia formats (e.g., text, image, PDF, word files, etc., many of which cannot be automatically processed by computers in biologically meaningful ways. In addition, the quality of computational results is far from perfect and requires nontrivial manual examination. The timely selection, integration and interpretation of heterogeneous biological information still heavily rely on the sensibility of biologists. Biologists often feel overwhelmed by the huge amount of and the great diversity of distributed heterogeneous biological information. Description We developed an information management application called GeneNotes. GeneNotes is the first application that allows users to collect and manage multimedia biological information about genes/ESTs. GeneNotes provides an integrated environment for users to surf the Internet, collect notes for genes/ESTs, and retrieve notes. GeneNotes is supported by a server that integrates gene annotations from many major databases (e.g., HGNC, MGI, etc.. GeneNotes uses the integrated gene annotations to (a identify genes given various types of gene IDs (e.g., RefSeq ID, GenBank ID, etc., and (b provide quick views of genes. GeneNotes is free for academic usage. The program and the tutorials are available at: http://bayes.fas.harvard.edu/genenotes/. Conclusions GeneNotes provides a novel human-computer interface to assist researchers to collect and manage biological information. It also provides a platform for studying how users behave when they manipulate biological information. The results of such study can lead to innovation of more intelligent human-computer interfaces that greatly shorten the cycle of biology research.

Scimitar syndrome: multi detector computed tomography angiography findings of a case

International Nuclear Information System (INIS)

Aslan, A.; Bozlar, U.; Ors, F.; Tasar, M.

2012-01-01

Full text: Introduction: Scimitar syndrome also known as pulmonary venolobar syndrome is a rare congenital abnormality. This abnormality consists of ipsilateral anomalous pulmonary venous drainage of right lung into the inferior vena cava (IVC), with hypoplasia of the right lung, an anomalous systemic arterial supply from supradiaphragmatic aorta to the right lower lobe and dextrocardia. Objectives and tasks: In this article, we aimed to present multidetector computed tomography (MDCT) angiography findings of a case with scimitar syndrome. Material and methods: 21 year old male with dextrocardia and anomalous curvilinear density in the right lower lobe directed toward the right hemidiaphragm on chest radiography was evaluated with MDCT angiography examination. Results: Dextrocardia and interruption of IVC with azygous continuation was detected in MDCT angiography examination. Vertically directing right superior pulmonary vein was draining to the suprahepatic segment of IVC. Pulmonary sequestration in the right lower lobe taking feeder from celiac trunk was detected. Right pulmonary artery was hypoplastic and bronchial tree was abnormal, manifesting as a mirror image in both lung lobes. Conclusion: MDCT angiography is very successful imaging method in demonstrating the anomalous pulmonary vein and assessing pulmonary arterial and bronchial anomalies

Gorlin-Goltz syndrome: incidental finding on routine ct scan following car accident.

Science.gov (United States)

Kalogeropoulou, Christina; Zampakis, Petros; Kazantzi, Santra; Kraniotis, Pantelis; Mastronikolis, Nicholas S

2009-11-25

Gorlin-Goltz syndrome is a rare hereditary disease. Pathogenesis of the syndrome is attributed to abnormalities in the long arm of chromosome 9 (q22.3-q31) and loss or mutations of human patched gene (PTCH1 gene). Multiple basal cell carcinomas (BCCs), odontogenic keratocysts, skeletal abnormalities, hyperkeratosis of palms and soles, intracranial ectopic calcifications of the falx cerebri and facial dysmorphism are considered the main clinical features. Diagnosis is based upon established major and minor clinical and radiological criteria and ideally confirmed by DNA analysis. Because of the different systems affected, a multidisciplinary approach team of various experts is required for a successful management. We report the case of a 19 year-old female who was involved in a car accident and found to present imaging findings of Gorlin-Goltz syndrome during a routine whole body computed tomography (CT) scan in order to exclude traumatic injuries. Radiologic findings of the syndrome are easily identifiable on CT scans and may prompt to early verification of the disease, which is very important for regular follow-up and better survival rates from the co-existent diseases.

Postmortem computed tomographic (PMCT) findings of pericardial effusion due to acute aortic dissection

International Nuclear Information System (INIS)

Shiotani, Seiji; Watanabe, Ko; Kohno, Mototsugu; Ohashi, Noriyoshi; Nakayama, Hidetsugu; Yamazaki, Kentaro

2004-01-01

The purpose of this study was to describe the appearance of pericardial effusion in deceased acute aortic dissection patients using postmortem computed tomography (PMCT). PMCT examinations were performed within 2 hours of death in 30 patients with pericardial effusion due to aortic dissection who arrived at our hospital in a state of cardiopulmonary arrest. Pericardial effusion in 18 of 30 patients (60%) showed double concentric rings on PMCT with striking differences in density, a low-density outer ring along the pericardium and a high-density inner ring on the epicardial surface (hyperdense armored heart). Pericardial effusion in two patients (7%) showed a high-density fluid level (hypostasis). Pericardial effusion in the remaining 10 patients (33%) showed no such stratification. A ''hyperdense armored heart'' is the most frequently seen PMCT finding in deceased cases of pericardial effusion due to acute aortic dissection. (author)

Efficient strategy for detecting gene × gene joint action and its application in schizophrenia

NARCIS (Netherlands)

Won, Sungho; Kwon, Min-Seok; Mattheisen, Manuel; Park, Suyeon; Park, Changsoon; Kihara, Daisuke; Cichon, Sven; Ophoff, Roel; Nöthen, Markus M.; Rietschel, Marcella; Baur, Max; Uitterlinden, Andre G.; Hofmann, A.; Lange, Christoph; Kahn, René S.; Linszen, Don H.; van Os, Jim; Wiersma, Durk; Bruggeman, Richard; Cahn, Wiepke; de Haan, Lieuwe; Krabbendam, Lydia; Myin-Germeys, Inez

2014-01-01

We propose a new approach to detect gene × gene joint action in genome-wide association studies (GWASs) for case-control designs. This approach offers an exhaustive search for all two-way joint action (including, as a special case, single gene action) that is computationally feasible at the

Abdominal wall hernias: computed tomography findings

International Nuclear Information System (INIS)

D'Ippolito, Giuseppe; Rosas, George de Queiroz; Mota, Marcos Alexandre; Akisue, Sandra R. Tsukada; Galvao Filho, Mario de Melo.

2005-01-01

Abdominal hernias are a common clinical problem Clinical diagnosis of abdominal hernias can sometimes be challenging, particularly in obese patients or patients with previous abdominal surgery. CT scan of the abdomen allows visualization of hernias and their contents and the differentiation from other masses of the abdominal wall such as tumors, hematomas and abscesses. Moreover, CT may identify complications such as incarceration, bowel obstruction, volvulus and strangulation. This study illustrates the CT scan findings observed in different types of abdominal wall hernias. (author)

Hypersensitivity pneumonitis (extrinsic allergic alveolitis): high-resolution computed tomography findings; Pneumonite por hipersensibilidade (alveolite alergica extrinseca): achados na tomografia computadorizada de alta resolucao

Energy Technology Data Exchange (ETDEWEB)

Almeida Junior, Jose Guiomar de; Marchiori, Edson [Universidade Federal Fluminense, Niteroi, RJ (Brazil). Faculdade de Ciencias Medicas. Dept. de Radiologia]. E-mail: edmarchiori@zipmail.com.br; Escuissato, Dante L. [Parana Univ., Curitiba, PR (Brazil). Dept. de Radiologia; Souza Junior, Arthur Soares [Faculdade de Medicina de Sao Jose do Rio Preto (FAMERP), SP (Brazil). Dept. de Radiologia; Gasparetto, Emerson L. [Parana Univ., Curitiba, PR (Brazil). Hospital de Clinicas; Nobre, Luiz Felipe [Santa Catarina Univ., Florianopolis, SC (Brazil); Irion, Klaus L. [Santa Casa de Misericordia de Porto Alegre, RS (Brazil). Pavilhao Pereira Filho. Servico de Radiologia

2003-12-01

Hypersensitivity pneumonitis, or extrinsic allergic alveolitis, is an immunologic disease of the lungs caused by inhaled chemicals or organics allergens. A lymphocytic inflammatory response in the peripheral airways and surrounding interstitial tissue occurs. In this study the high-resolution computed tomography findings of 13 patients with hypersensitivity pneumonitis were analyzed and discussed. The most frequent high-resolution computed tomography findings were: ground-glass opacities (92.3%), centrilobular nodules (38.4%) and air trapping (38.4%). Other findings included bronchiectasis (23.1%), consolidation (23.1%), crazy paving (7.7%), parenchymal bands (15.4%), linear opacities (7.7%), architectural distortion (7.7%), tracheal dilatation (7.7%), intralobular reticulate (7.7%), honeycombing (7.7%), emphysema (7.7%) and atelectasis (7.7%). In two of the 13 patients there was fibrosis (architectural distortion and honeycombing), which represents the chronic phase of the disease. (author)

Stochastic Boolean networks: An efficient approach to modeling gene regulatory networks

Directory of Open Access Journals (Sweden)

Liang Jinghang

2012-08-01

Full Text Available Abstract Background Various computational models have been of interest due to their use in the modelling of gene regulatory networks (GRNs. As a logical model, probabilistic Boolean networks (PBNs consider molecular and genetic noise, so the study of PBNs provides significant insights into the understanding of the dynamics of GRNs. This will ultimately lead to advances in developing therapeutic methods that intervene in the process of disease development and progression. The applications of PBNs, however, are hindered by the complexities involved in the computation of the state transition matrix and the steady-state distribution of a PBN. For a PBN with n genes and N Boolean networks, the complexity to compute the state transition matrix is O(nN22n or O(nN2n for a sparse matrix. Results This paper presents a novel implementation of PBNs based on the notions of stochastic logic and stochastic computation. This stochastic implementation of a PBN is referred to as a stochastic Boolean network (SBN. An SBN provides an accurate and efficient simulation of a PBN without and with random gene perturbation. The state transition matrix is computed in an SBN with a complexity of O(nL2n, where L is a factor related to the stochastic sequence length. Since the minimum sequence length required for obtaining an evaluation accuracy approximately increases in a polynomial order with the number of genes, n, and the number of Boolean networks, N, usually increases exponentially with n, L is typically smaller than N, especially in a network with a large number of genes. Hence, the computational efficiency of an SBN is primarily limited by the number of genes, but not directly by the total possible number of Boolean networks. Furthermore, a time-frame expanded SBN enables an efficient analysis of the steady-state distribution of a PBN. These findings are supported by the simulation results of a simplified p53 network, several randomly generated networks and a

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...

Colocalization of coregulated genes: a steered molecular dynamics study of human chromosome 19.

Directory of Open Access Journals (Sweden)

Marco Di Stefano

Full Text Available The connection between chromatin nuclear organization and gene activity is vividly illustrated by the observation that transcriptional coregulation of certain genes appears to be directly influenced by their spatial proximity. This fact poses the more general question of whether it is at all feasible that the numerous genes that are coregulated on a given chromosome, especially those at large genomic distances, might become proximate inside the nucleus. This problem is studied here using steered molecular dynamics simulations in order to enforce the colocalization of thousands of knowledge-based gene sequences on a model for the gene-rich human chromosome 19. Remarkably, it is found that most (≈ 88% gene pairs can be brought simultaneously into contact. This is made possible by the low degree of intra-chromosome entanglement and the large number of cliques in the gene coregulatory network. A clique is a set of genes coregulated all together as a group. The constrained conformations for the model chromosome 19 are further shown to be organized in spatial macrodomains that are similar to those inferred from recent HiC measurements. The findings indicate that gene coregulation and colocalization are largely compatible and that this relationship can be exploited to draft the overall spatial organization of the chromosome in vivo. The more general validity and implications of these findings could be investigated by applying to other eukaryotic chromosomes the general and transferable computational strategy introduced here.

Spectrum of High Resolution Computed Tomography Findings in Occupational Lung Disease: Experience in a Tertiary Care Institute

Directory of Open Access Journals (Sweden)

Satija Bhawna

2013-01-01

Full Text Available Objective: To study the spectrum of high resolution computed tomography (HRCT findings in occupational lung disease in industrial workers and to assess the utility of International classification of HRCT for occupational and environmental respiratory diseases (ICHOERD. Materials and Methods: Retrospective analysis of radiological data (radiographs and computed tomography chest scans gathered over a period of 3 years (January 2010- December 2012 of industrial workers in an organised sector who presented with respiratory complaints. The HRCT findings were evaluated using ICHOERD. Results: There were 5 females and 114 males in the study, with a mean age of 49 years. These workers were exposed to different harmful agents including silica, asbestos, cotton dust, metal dust, iron oxide, organic dust, rubber fumes, plastic fumes, acid fumes, and oil fumes. There were 10 smokers in the study. The radiograph of chest was normal in 53 patients. 46% of these normal patients (21.8% of total demonstrated positive findings on HRCT. When the radiograph was abnormal, HRCT provided more accurate information and excluded the other diagnosis. The HRCT findings were appropriately described using the ICHOERD. Bronchiectasis was the most common finding (44.5% with mild central cylindrical bronchiectasis as the most common pattern. Pleural thickening was seen in 41 patients (34.5%. Enlarged hilar or mediastinal lymphnodes were seen in 10 patients (8.4% with egg-shell calcification in 1 patient exposed to silica. Bronchogenic carcinoma was seen in 1 patient exposed to asbestos. Conclusions: Occupational lung disease is a common work related condition in industrial workers even in the organized sector. Though chest radiograph is the primary diagnostic tool, HRCT is the undisputed Gold Standard for evaluation of these patients. Despite the disadvantage of radiation exposure, low dose CT may serve as an important tool for screening and surveillance. The ICHOERD is a

Greater power and computational efficiency for kernel-based association testing of sets of genetic variants.

Science.gov (United States)

Lippert, Christoph; Xiang, Jing; Horta, Danilo; Widmer, Christian; Kadie, Carl; Heckerman, David; Listgarten, Jennifer

2014-11-15

Set-based variance component tests have been identified as a way to increase power in association studies by aggregating weak individual effects. However, the choice of test statistic has been largely ignored even though it may play an important role in obtaining optimal power. We compared a standard statistical test-a score test-with a recently developed likelihood ratio (LR) test. Further, when correction for hidden structure is needed, or gene-gene interactions are sought, state-of-the art algorithms for both the score and LR tests can be computationally impractical. Thus we develop new computationally efficient methods. After reviewing theoretical differences in performance between the score and LR tests, we find empirically on real data that the LR test generally has more power. In particular, on 15 of 17 real datasets, the LR test yielded at least as many associations as the score test-up to 23 more associations-whereas the score test yielded at most one more association than the LR test in the two remaining datasets. On synthetic data, we find that the LR test yielded up to 12% more associations, consistent with our results on real data, but also observe a regime of extremely small signal where the score test yielded up to 25% more associations than the LR test, consistent with theory. Finally, our computational speedups now enable (i) efficient LR testing when the background kernel is full rank, and (ii) efficient score testing when the background kernel changes with each test, as for gene-gene interaction tests. The latter yielded a factor of 2000 speedup on a cohort of size 13 500. Software available at http://research.microsoft.com/en-us/um/redmond/projects/MSCompBio/Fastlmm/. heckerma@microsoft.com Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

Extension and optimization of the FIND algorithm: Computing Green’s and less-than Green’s functions

International Nuclear Information System (INIS)

Li, S.; Darve, E.

2012-01-01

Highlights: ► FIND is an algorithm for calculating entries of the inverse of a sparse matrix. ► We extend the algorithm to other matrix inverse related calculations. ► We exploit sparsity and symmetry to improve performance. - Abstract: The FIND algorithm is a fast algorithm designed to calculate certain entries of the inverse of a sparse matrix. Such calculation is critical in many applications, e.g., quantum transport in nano-devices. We extended the algorithm to other matrix inverse related calculations. Those are required for example to calculate the less-than Green’s function and the current density through the device. For a 2D device discretized as an N x × N y mesh, the best known algorithms have a running time of O(N x 3 N y ), whereas FIND only requires O(N x 2 N y ). Even though this complexity has been reduced by an order of magnitude, the matrix inverse calculation is still the most time consuming part in the simulation of transport problems. We could not reduce the order of complexity, but we were able to significantly reduce the constant factor involved in the computation cost. By exploiting the sparsity and symmetry, the size of the problem beyond which FIND is faster than other methods typically decreases from a 130 × 130 2D mesh down to a 40 × 40 mesh. These improvements make the optimized FIND algorithm even more competitive for real-life applications.

Soft-tissue perineurioma of the retroperitoneum in a 63-year-old man, computed tomography and magnetic resonance imaging findings: a case report

Directory of Open Access Journals (Sweden)

Yasumoto Mayumi

2010-08-01

Full Text Available Abstract Introduction Soft-tissue perineuriomas are rare benign peripheral nerve sheath tumors in the subcutis of the extremities and the trunks of young patients. To our knowledge, this the first presentation of the computed tomography and magnetic resonance imaging of a soft-tissue perineurioma in the retroperitoneum with pathologic correlation. Case presentation A 63-year-old Japanese man was referred for assessment of high blood pressure. Abdominal computed tomography and magnetic resonance imaging showed a well-defined, gradually enhancing tumor without focal degeneration or hemorrhage adjacent to the pancreatic body. Tumor excision with distal pancreatectomy and splenectomy was performed, as a malignant tumor of pancreatic origin could not be ruled out. No recurrence has been noted in the 16 months since the operation. Pathologic examination of the tumor revealed a soft-tissue perineurioma of the retroperitoneum. Conclusion Although the definitive diagnosis of soft-tissue perineurioma requires biopsy and immunohistochemical reactivity evaluation, the computed tomography and magnetic resonance imaging findings described in this report suggest inclusion of this rare tumor in the differential diagnosis when such findings occur in the retroperitoneum.

Incorporating modern neuroscience findings to improve brain-computer interfaces: tracking auditory attention.

Science.gov (United States)

Wronkiewicz, Mark; Larson, Eric; Lee, Adrian Kc

2016-10-01

Brain-computer interface (BCI) technology allows users to generate actions based solely on their brain signals. However, current non-invasive BCIs generally classify brain activity recorded from surface electroencephalography (EEG) electrodes, which can hinder the application of findings from modern neuroscience research. In this study, we use source imaging-a neuroimaging technique that projects EEG signals onto the surface of the brain-in a BCI classification framework. This allowed us to incorporate prior research from functional neuroimaging to target activity from a cortical region involved in auditory attention. Classifiers trained to detect attention switches performed better with source imaging projections than with EEG sensor signals. Within source imaging, including subject-specific anatomical MRI information (instead of using a generic head model) further improved classification performance. This source-based strategy also reduced accuracy variability across three dimensionality reduction techniques-a major design choice in most BCIs. Our work shows that source imaging provides clear quantitative and qualitative advantages to BCIs and highlights the value of incorporating modern neuroscience knowledge and methods into BCI systems.

A computational approach to finding novel targets for existing drugs.

Directory of Open Access Journals (Sweden)

Yvonne Y Li

2011-09-01

Full Text Available Repositioning existing drugs for new therapeutic uses is an efficient approach to drug discovery. We have developed a computational drug repositioning pipeline to perform large-scale molecular docking of small molecule drugs against protein drug targets, in order to map the drug-target interaction space and find novel interactions. Our method emphasizes removing false positive interaction predictions using criteria from known interaction docking, consensus scoring, and specificity. In all, our database contains 252 human protein drug targets that we classify as reliable-for-docking as well as 4621 approved and experimental small molecule drugs from DrugBank. These were cross-docked, then filtered through stringent scoring criteria to select top drug-target interactions. In particular, we used MAPK14 and the kinase inhibitor BIM-8 as examples where our stringent thresholds enriched the predicted drug-target interactions with known interactions up to 20 times compared to standard score thresholds. We validated nilotinib as a potent MAPK14 inhibitor in vitro (IC50 40 nM, suggesting a potential use for this drug in treating inflammatory diseases. The published literature indicated experimental evidence for 31 of the top predicted interactions, highlighting the promising nature of our approach. Novel interactions discovered may lead to the drug being repositioned as a therapeutic treatment for its off-target's associated disease, added insight into the drug's mechanism of action, and added insight into the drug's side effects.

[Treatment choice in dacryostenosis based on single-photon emission computed tomography and X-ray computed tomography findings].

Science.gov (United States)

At'kova, E L; Yartsev, V D; Tomashevskiy, I O; Krakhovetskiy, N N

2016-01-01

To develop surgical indications in dacryostenosis within the vertical portion of lacrimal pathways that would consider findings of single-photon emission computed tomography (SPECT) combined with X-ray computed tomography (CT). A total of 96 patients with isolated vertical-portion dacryostenosis (127 cases) were enrolled. The examination included collecting Munk's scores for epiphora, optical coherence tomography of the lower tear meniscus, lacrimal scintigraphy, and SPECT/CT. Group 1 (40 cases) was composed of patients with lacrimal obstruction on CT, group 2 (87 cases) - of those whose lacrimal pathways proved passable. There were also 3 patients (4 cases) from group 1, whose lacrimal pathways, despite being blocked on CT, were still passable on SPECT. Surgeries performed in group 1 were endoscopic endonasal dacryocystorhinostomy (DCR) (36 cases) and pathways recanalization with bicanalicular intubation and balloon dacryoplasty (DCP) (4 cases). In group 2, all patients (87 cases) underwent recanalization with bicanalicular intubation (supplemented with balloon DCP in 32 cases). Surgical results were evaluated 8-12 months after the treatment. In group 2, particular attention was paid to the concordance in locations of dacryostenosis provided by CT and SPECT scans. Favorable outcomes of endoscopic endonasal DCR were obtained in as many as 32 cases from group 1 (88.9%), while in 4 cases (12.1%) the condition relapsed. Of those patients whose stenosis was not complete on SPECT, 3 cases (75.0%) improved, 1 (25.0%) - relapsed. In group 2, favorable outcomes were obtained in 65 cases (74.7%), relapses were 22 (25.3%). A high concordance in stenosis locations by CT and SPECT was noted in 60 cases of those who improved (92.3%) and 3 cases of those who relapsed (13.6%). The value of information provided by SPECT/CT has proved high in patients with nasolacrimal duct stenosis or obstruction. A combined scan allows to establish causal relationships between anatomical changes

Organic Computing

CERN Document Server

Würtz, Rolf P

2008-01-01

Organic Computing is a research field emerging around the conviction that problems of organization in complex systems in computer science, telecommunications, neurobiology, molecular biology, ethology, and possibly even sociology can be tackled scientifically in a unified way. From the computer science point of view, the apparent ease in which living systems solve computationally difficult problems makes it inevitable to adopt strategies observed in nature for creating information processing machinery. In this book, the major ideas behind Organic Computing are delineated, together with a sparse sample of computational projects undertaken in this new field. Biological metaphors include evolution, neural networks, gene-regulatory networks, networks of brain modules, hormone system, insect swarms, and ant colonies. Applications are as diverse as system design, optimization, artificial growth, task allocation, clustering, routing, face recognition, and sign language understanding.

Computational analysis and low-scale constitutive expression of laccases synthetic genes GlLCC1 from Ganoderma lucidum and POXA 1B from Pleurotus ostreatus in Pichia pastoris.

Directory of Open Access Journals (Sweden)

Claudia M Rivera-Hoyos

Full Text Available Lacasses are multicopper oxidases that can catalyze aromatic and non-aromatic compounds concomitantly with reduction of molecular oxygen to water. Fungal laccases have generated a growing interest due to their biotechnological potential applications, such as lignocellulosic material delignification, biopulping and biobleaching, wastewater treatment, and transformation of toxic organic pollutants. In this work we selected fungal genes encoding for laccase enzymes GlLCC1 in Ganoderma lucidum and POXA 1B in Pleurotus ostreatus. These genes were optimized for codon use, GC content, and regions generating secondary structures. Laccase proposed computational models, and their interaction with ABTS [2, 2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid] substrate was evaluated by molecular docking. Synthetic genes were cloned under the control of Pichia pastoris glyceraldehyde-3-phosphate dehydrogenase (GAP constitutive promoter. P. pastoris X-33 was transformed with pGAPZαA-LaccGluc-Stop and pGAPZαA-LaccPost-Stop constructs. Optimization reduced GC content by 47 and 49% for LaccGluc-Stop and LaccPost-Stop genes, respectively. A codon adaptation index of 0.84 was obtained for both genes. 3D structure analysis using SuperPose revealed LaccGluc-Stop is similar to the laccase crystallographic structure 1GYC of Trametes versicolor. Interaction analysis of the 3D models validated through ABTS, demonstrated higher substrate affinity for LaccPost-Stop, in agreement with our experimental results with enzymatic activities of 451.08 ± 6.46 UL-1 compared to activities of 0.13 ± 0.028 UL-1 for LaccGluc-Stop. This study demonstrated that G. lucidum GlLCC1 and P. ostreatus POXA 1B gene optimization resulted in constitutive gene expression under GAP promoter and α-factor leader in P. pastoris. These are important findings in light of recombinant enzyme expression system utility for environmentally friendly designed expression systems, because of the wide range

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 ...

High-resolution computed tomography findings in pulmonary complications after bone marrow transplantation: iconographic essay

International Nuclear Information System (INIS)

Gasparetto, Emerson L.; Ono, Sergio E.; Souza, Carolina A.; Escuissato, Dante L.; Rocha, Gabriela de Melo; Inoue, Cezar; Falavigna, Joao M.; Marchiori, Edson; Universidade Federal, Rio de Janeiro

2005-01-01

Bone marrow transplantation has been the treatment of choice for many hematologic diseases. However, pulmonary complications, which may occur in up to 60% of the patients, are the main cause of treatment failure and may be divided in three phases according to the patient's immunity. In the first phase, up to 30 days after the procedure, there is a predominance of non-infectious complications and fungal pneumonia. Viral infections, mainly by cytomegalovirus, are common in the second phase (up to 100 days after bone marrow transplantation). Finally, in the late phase after bone marrow transplantation, non-infectious complications as bronchiolitis obliterans organizing pneumonia and graft-versus-host disease are most commonly seen. The authors present a pictorial essay of the high-resolution computed tomography findings in patients with pulmonary complications after bone marrow transplantation. (author)

Massively parallel quantum computer simulator

NARCIS (Netherlands)

De Raedt, K.; Michielsen, K.; De Raedt, H.; Trieu, B.; Arnold, G.; Richter, M.; Lippert, Th.; Watanabe, H.; Ito, N.

2007-01-01

We describe portable software to simulate universal quantum computers on massive parallel Computers. We illustrate the use of the simulation software by running various quantum algorithms on different computer architectures, such as a IBM BlueGene/L, a IBM Regatta p690+, a Hitachi SR11000/J1, a Cray

Principles and limitations of computational microRNA gene and target finding

DEFF Research Database (Denmark)

Lindow, Morten; Gorodkin, Jan

2007-01-01

In 2001 there were four PubMed entries matching the word "microRNA" (miRNA). Interestingly, this number has now far exceeded 1300 and is still rapidly increasing. This more than anything demonstrates the extreme attention this field has had within a short period of time. With the large amounts...

Computational analysis of TRAPPC9: candidate gene for autosomal recessive non-syndromic mental retardation.

Science.gov (United States)

Khattak, Naureen Aslam; Mir, Asif

2014-01-01

Mental retardation (MR)/ intellectual disability (ID) is a neuro-developmental disorder characterized by a low intellectual quotient (IQ) and deficits in adaptive behavior related to everyday life tasks such as delayed language acquisition, social skills or self-help skills with onset before age 18. To date, a few genes (PRSS12, CRBN, CC2D1A, GRIK2, TUSC3, TRAPPC9, TECR, ST3GAL3, MED23, MAN1B1, NSUN1) for autosomal-recessive forms of non syndromic MR (NS-ARMR) have been identified and established in various families with ID. The recently reported candidate gene TRAPPC9 was selected for computational analysis to explore its potentially important role in pathology as it is the only gene for ID reported in more than five different familial cases worldwide. YASARA (12.4.1) was utilized to generate three dimensional structures of the candidate gene TRAPPC9. Hybrid structure prediction was employed. Crystal Structure of a Conserved Metalloprotein From Bacillus Cereus (3D19-C) was selected as best suitable template using position-specific iteration-BLAST. Template (3D19-C) parameters were based on E-value, Z-score and resolution and quality score of 0.32, -1.152, 2.30°A and 0.684 respectively. Model reliability showed 93.1% residues placed in the most favored region with 96.684 quality factor, and overall 0.20 G-factor (dihedrals 0.06 and covalent 0.39 respectively). Protein-Protein docking analysis demonstrated that TRAPPC9 showed strong interactions of the amino acid residues S(253), S(251), Y(256), G(243), D(131) with R(105), Q(425), W(226), N(255), S(233), its functional partner 1KBKB. Protein-protein interacting residues could facilitate the exploration of structural and functional outcomes of wild type and mutated TRAPCC9 protein. Actively involved residues can be used to elucidate the binding properties of the protein, and to develop drug therapy for NS-ARMR patients.

Imaging in blunt cardiac injury: Computed tomographic findings in cardiac contusion and associated injuries.

Science.gov (United States)

Hammer, Mark M; Raptis, Demetrios A; Cummings, Kristopher W; Mellnick, Vincent M; Bhalla, Sanjeev; Schuerer, Douglas J; Raptis, Constantine A

2016-05-01

Blunt cardiac injury (BCI) may manifest as cardiac contusion or, more rarely, as pericardial or myocardial rupture. Computed tomography (CT) is performed in the vast majority of blunt trauma patients, but the imaging features of cardiac contusion are not well described. To evaluate CT findings and associated injuries in patients with clinically diagnosed BCI. We identified 42 patients with blunt cardiac injury from our institution's electronic medical record. Clinical parameters, echocardiography results, and laboratory tests were recorded. Two blinded reviewers analyzed chest CTs performed in these patients for myocardial hypoenhancement and associated injuries. CT findings of severe thoracic trauma are commonly present in patients with severe BCI; 82% of patients with ECG, cardiac enzyme, and echocardiographic evidence of BCI had abnormalities of the heart or pericardium on CT; 73% had anterior rib fractures, and 64% had pulmonary contusions. Sternal fractures were only seen in 36% of such patients. However, myocardial hypoenhancement on CT is poorly sensitive for those patients with cardiac contusion: 0% of right ventricular contusions and 22% of left ventricular contusions seen on echocardiography were identified on CT. CT signs of severe thoracic trauma are frequently present in patients with severe BCI and should be regarded as indirect evidence of potential BCI. Direct CT findings of myocardial contusion, i.e. myocardial hypoenhancement, are poorly sensitive and should not be used as a screening tool. However, some left ventricular contusions can be seen on CT, and these patients could undergo echocardiography or cardiac MRI to evaluate for wall motion abnormalities. Copyright © 2015 Elsevier Ltd. All rights reserved.

Computational Aspects of Dam Risk Analysis: Findings and Challenges

Directory of Open Access Journals (Sweden)

Ignacio Escuder-Bueno

2016-09-01

Full Text Available In recent years, risk analysis techniques have proved to be a useful tool to inform dam safety management. This paper summarizes the outcomes of three themes related to dam risk analysis discussed in the Benchmark Workshops organized by the International Commission on Large Dams Technical Committee on “Computational Aspects of Analysis and Design of Dams.” In the 2011 Benchmark Workshop, estimation of the probability of failure of a gravity dam for the sliding failure mode was discussed. Next, in 2013, the discussion focused on the computational challenges of the estimation of consequences in dam risk analysis. Finally, in 2015, the probability of sliding and overtopping in an embankment was analyzed. These Benchmark Workshops have allowed a complete review of numerical aspects for dam risk analysis, showing that risk analysis methods are a very useful tool to analyze the risk of dam systems, including downstream consequence assessments and the uncertainty of structural models.

Chondrosarcoma of the hyoid bone: computed tomography findings

International Nuclear Information System (INIS)

Saez, J.; Gallego, J. a.; Fuster, M. J.

2001-01-01

Chondrosarcoma of the hyoid bone is a rare entity, only 10 cases of which have been reported in the literature to date. the case we present involved a 24-year-old man who complained of progressive adynophagia and a mass in anterior neck. Computed tomography revealed a low-attenuation mas attached to the left horn of the hyoid bone. The lesion was excised and was diagnosed as a grade II chondrosarcoma. The patient remains asymptomatic 10 years after the operation. (Author) 11 refs

Dissociable contribution of prefrontal and striatal dopaminergic genes to learning in economic games.

Science.gov (United States)

Set, Eric; Saez, Ignacio; Zhu, Lusha; Houser, Daniel E; Myung, Noah; Zhong, Songfa; Ebstein, Richard P; Chew, Soo Hong; Hsu, Ming

2014-07-01

Game theory describes strategic interactions where success of players' actions depends on those of coplayers. In humans, substantial progress has been made at the neural level in characterizing the dopaminergic and frontostriatal mechanisms mediating such behavior. Here we combined computational modeling of strategic learning with a pathway approach to characterize association of strategic behavior with variations in the dopamine pathway. Specifically, using gene-set analysis, we systematically examined contribution of different dopamine genes to variation in a multistrategy competitive game captured by (i) the degree players anticipate and respond to actions of others (belief learning) and (ii) the speed with which such adaptations take place (learning rate). We found that variation in genes that primarily regulate prefrontal dopamine clearance--catechol-O-methyl transferase (COMT) and two isoforms of monoamine oxidase--modulated degree of belief learning across individuals. In contrast, we did not find significant association for other genes in the dopamine pathway. Furthermore, variation in genes that primarily regulate striatal dopamine function--dopamine transporter and D2 receptors--was significantly associated with the learning rate. We found that this was also the case with COMT, but not for other dopaminergic genes. Together, these findings highlight dissociable roles of frontostriatal systems in strategic learning and support the notion that genetic variation, organized along specific pathways, forms an important source of variation in complex phenotypes such as strategic behavior.

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.

Bosniak classification of renal cystic lesions according to multidetector computed tomography findings; Classificacao de Bosniak das lesoes cisticas renais segundo achados na tomografia computadorizada multidetectores

Energy Technology Data Exchange (ETDEWEB)

Miranda, Christiana Maia Nobre Rocha de; Padilha, Igor Gomes; Farias, Lucas de Padua Gomes de; Rocha, Milzi Sarmento da, E-mail: maiachristiana@globo.com [Universidade Federal de Alagoas (UFAL), Maceio, AL (Brazil); Maranhao, Carol Pontes de Miranda; Santos, Carla Jotta Justo dos [Clinica de Medicina Nuclear e Radiologia de Maceio (MedRadiUS), Maceio, AL (Brazil)

2014-03-15

Renal cystic lesions are usually diagnosed in the radiologists' practice and therefore their characterization is crucial to determine the clinical approach to be adopted and prognosis. The Bosniak classification based on computed tomography findings has allowed for standardization and categorization of lesions in increasing order of malignancy (I, II, IIF, III and IV) in a simple and accurate way. The present iconographic essay developed with multidetector computed tomography images of selected cases from the archives of the authors' institution, is aimed at describing imaging findings that can help in the diagnosis of renal cysts. (author)

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.

A crossing programme with mutants in peas: Utilization of a gene bank and a computer system

International Nuclear Information System (INIS)

Blixt, S.

1976-01-01

A gene bank for peas was established at Weibullsholm in 1930, comprising about 1500 lines and including a great number of spontaneous and induced mutants. A Wang 2200 computair system is used in the maintenance and utilization of the gene bank information. The system at present provides programs for establishing and maintaining data-files for lines and crosses, statistical programs for linkage calculations, and technical aids in growing and classifying the material. The system is very promising and can be handled without previous experience of computer work. This system is used in the planning of a specific plant breeding project, PMX and search for material to be used in the project. The PMX project as a whole aims at adapting the pea better to monoculture and to a highly mechanized agriculture, as well as at improving its nutritional value. The material used in the project up to now is four modern varieties, two primitive varieties, two cross-recombinants, one ecotype, three spontaneous mutants and five induced mutants. (author)

Computed tomography findings in head trauma in Sokoto (North ...

African Journals Online (AJOL)

This retrospective study was carried out to present the pattern of injuries seen using computed tomography (CT scan) in head injured patients and to highlight the role, played by this modality of investigation in the management of these patients at the department of Radiology, Usman DanFodio University Teaching ...

Radionuclide reporter gene imaging for cardiac gene therapy

International Nuclear Information System (INIS)

Inubushi, Masayuki; Tamaki, Nagara

2007-01-01

In the field of cardiac gene therapy, angiogenic gene therapy has been most extensively investigated. The first clinical trial of cardiac angiogenic gene therapy was reported in 1998, and at the peak, more than 20 clinical trial protocols were under evaluation. However, most trials have ceased owing to the lack of decisive proof of therapeutic effects and the potential risks of viral vectors. In order to further advance cardiac angiogenic gene therapy, remaining open issues need to be resolved: there needs to be improvement of gene transfer methods, regulation of gene expression, development of much safer vectors and optimisation of therapeutic genes. For these purposes, imaging of gene expression in living organisms is of great importance. In radionuclide reporter gene imaging, ''reporter genes'' transferred into cell nuclei encode for a protein that retains a complementary ''reporter probe'' of a positron or single-photon emitter; thus expression of the reporter genes can be imaged with positron emission tomography or single-photon emission computed tomography. Accordingly, in the setting of gene therapy, the location, magnitude and duration of the therapeutic gene co-expression with the reporter genes can be monitored non-invasively. In the near future, gene therapy may evolve into combination therapy with stem/progenitor cell transplantation, so-called cell-based gene therapy or gene-modified cell therapy. Radionuclide reporter gene imaging is now expected to contribute in providing evidence on the usefulness of this novel therapeutic approach, as well as in investigating the molecular mechanisms underlying neovascularisation and safety issues relevant to further progress in conventional gene therapy. (orig.)

Find_tfSBP: find thermodynamics-feasible and smallest balanced pathways with high yield from large-scale metabolic networks.

Science.gov (United States)

Xu, Zixiang; Sun, Jibin; Wu, Qiaqing; Zhu, Dunming

2017-12-11

Biologically meaningful metabolic pathways are important references in the design of industrial bacterium. At present, constraint-based method is the only way to model and simulate a genome-scale metabolic network under steady-state criteria. Due to the inadequate assumption of the relationship in gene-enzyme-reaction as one-to-one unique association, computational difficulty or ignoring the yield from substrate to product, previous pathway finding approaches can't be effectively applied to find out the high yield pathways that are mass balanced in stoichiometry. In addition, the shortest pathways may not be the pathways with high yield. At the same time, a pathway, which exists in stoichiometry, may not be feasible in thermodynamics. By using mixed integer programming strategy, we put forward an algorithm to identify all the smallest balanced pathways which convert the source compound to the target compound in large-scale metabolic networks. The resulting pathways by our method can finely satisfy the stoichiometric constraints and non-decomposability condition. Especially, the functions of high yield and thermodynamics feasibility have been considered in our approach. This tool is tailored to direct the metabolic engineering practice to enlarge the metabolic potentials of industrial strains by integrating the extensive metabolic network information built from systems biology dataset.

Finding the Hook: Computer Science Education in Elementary Contexts

Science.gov (United States)

Ozturk, Zehra; Dooley, Caitlin McMunn; Welch, Meghan

2018-01-01

The purpose of this study was to investigate how elementary teachers with little knowledge of computer science (CS) and project-based learning (PBL) experienced integrating CS through PBL as a part of a standards-based elementary curriculum in Grades 3-5. The researchers used qualitative constant comparison methods on field notes and reflections…

Mutual information and the fidelity of response of gene regulatory models

International Nuclear Information System (INIS)

Tabbaa, Omar P; Jayaprakash, C

2014-01-01

We investigate cellular response to extracellular signals by using information theory techniques motivated by recent experiments. We present results for the steady state of the following gene regulatory models found in both prokaryotic and eukaryotic cells: a linear transcription-translation model and a positive or negative auto-regulatory model. We calculate both the information capacity and the mutual information exactly for simple models and approximately for the full model. We find that (1) small changes in mutual information can lead to potentially important changes in cellular response and (2) there are diminishing returns in the fidelity of response as the mutual information increases. We calculate the information capacity using Gillespie simulations of a model for the TNF-α-NF-κ B network and find good agreement with the measured value for an experimental realization of this network. Our results provide a quantitative understanding of the differences in cellular response when comparing experimentally measured mutual information values of different gene regulatory models. Our calculations demonstrate that Gillespie simulations can be used to compute the mutual information of more complex gene regulatory models, providing a potentially useful tool in synthetic biology. (paper)

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.

Abdominal tuberculosis: a radiological review with emphasis on computed tomography and magnetic resonance imaging findings

Energy Technology Data Exchange (ETDEWEB)

Rocha, Eduardo Lima da; Pedrassa, Bruno Cheregati; Bormann, Renata Lilian; Kierszenbaum, Marcelo Longo; Torres, Lucas Rios; D' Ippolito, Giuseppe, E-mail: giuseppe_dr@uol.com.br [Universidade Federal de Sao Paulo (EPM/UNIFESP), Sao Paulo, SP (Brazil). Escola Paulista de Medicina

2015-05-15

Tuberculosis is a disease whose incidence has increased principally as a consequence of HIV infection and use of immunosuppressive drugs. The abdomen is the most common site of extrapulmonary tuberculosis. It may be confused with several different conditions such as inflammatory bowel disease, cancer and other infectious diseases. Delay in the diagnosis may result in significantly increased morbidity, and therefore an early recognition of the condition is essential for proper treatment. In the present essay, cases with confirmed diagnosis of abdominal tuberculosis were assessed by means of computed tomography and magnetic resonance imaging, demonstrating the involvement of different organs and systems, and presentations which frequently lead radiologists to a diagnostic dilemma. A brief literature review was focused on imaging findings and their respective prevalence. (author)

Post-mortem whole body computed tomography of opioid (heroin and methadone) fatalities: frequent findings and comparison to autopsy

Energy Technology Data Exchange (ETDEWEB)

Winklhofer, Sebastian; Stolzmann, Paul [University of Zurich, Department of Forensic Medicine and Radiology, Institute of Forensic Medicine, Zurich (Switzerland); University Hospital Zurich, Institute of Diagnostic and Interventional Radiology, Zurich (Switzerland); Surer, Eddie; Ampanozi, Garyfalia; Thali, Michael; Schweitzer, Wolf [University of Zurich, Department of Forensic Medicine and Radiology, Institute of Forensic Medicine, Zurich (Switzerland); Ruder, Thomas [University of Zurich, Department of Forensic Medicine and Radiology, Institute of Forensic Medicine, Zurich (Switzerland); University Hospital Bern, Institute of Diagnostic, Interventional and Pediatric Radiology, Bern (Switzerland); Elliott, Marina [Simon Fraser University, Department of Archaeology, Burnaby, BC (Canada); Oestreich, Andrea; Kraemer, Thomas [University of Zurich, Department of Forensic Pharmacology and Toxicology, Institute of Forensic Medicine, Zurich (Switzerland); Alkadhi, Hatem [University Hospital Zurich, Institute of Diagnostic and Interventional Radiology, Zurich (Switzerland)

2014-06-15

To investigate frequent findings in cases of fatal opioid intoxication in whole-body post-mortem computed tomography (PMCT). PMCT of 55 cases in which heroin and/or methadone had been found responsible for death were retrospectively evaluated (study group), and were compared with PMCT images of an age- and sex-matched control group. Imaging results were compared with conventional autopsy. The most common findings in the study group were: pulmonary oedema (95 %), aspiration (66 %), distended urinary bladder (42 %), cerebral oedema (49 %), pulmonary emphysema (38 %) and fatty liver disease (36 %). These PMCT findings occurred significantly more often in the study group than in the control group (p < 0.05). The combination of lung oedema, brain oedema and distended urinary bladder was seen in 26 % of the cases in the study group but never in the control group (0 %). This triad, as indicator of opioid-related deaths, had a specificity of 100 %, as confirmed by autopsy and toxicological analysis. Frequent findings in cases of fatal opioid intoxication were demonstrated. The triad of brain oedema, lung oedema and a distended urinary bladder on PMCT was highly specific for drug-associated cases of death. (orig.)

Post-mortem whole body computed tomography of opioid (heroin and methadone) fatalities: frequent findings and comparison to autopsy

International Nuclear Information System (INIS)

Winklhofer, Sebastian; Stolzmann, Paul; Surer, Eddie; Ampanozi, Garyfalia; Thali, Michael; Schweitzer, Wolf; Ruder, Thomas; Elliott, Marina; Oestreich, Andrea; Kraemer, Thomas; Alkadhi, Hatem

2014-01-01

To investigate frequent findings in cases of fatal opioid intoxication in whole-body post-mortem computed tomography (PMCT). PMCT of 55 cases in which heroin and/or methadone had been found responsible for death were retrospectively evaluated (study group), and were compared with PMCT images of an age- and sex-matched control group. Imaging results were compared with conventional autopsy. The most common findings in the study group were: pulmonary oedema (95 %), aspiration (66 %), distended urinary bladder (42 %), cerebral oedema (49 %), pulmonary emphysema (38 %) and fatty liver disease (36 %). These PMCT findings occurred significantly more often in the study group than in the control group (p < 0.05). The combination of lung oedema, brain oedema and distended urinary bladder was seen in 26 % of the cases in the study group but never in the control group (0 %). This triad, as indicator of opioid-related deaths, had a specificity of 100 %, as confirmed by autopsy and toxicological analysis. Frequent findings in cases of fatal opioid intoxication were demonstrated. The triad of brain oedema, lung oedema and a distended urinary bladder on PMCT was highly specific for drug-associated cases of death. (orig.)

Left anterior descending coronary artery myocardial bridging by multislice computed tomography: Correlation with clinical findings

International Nuclear Information System (INIS)

Jodocy, Daniel; Aglan, Iman; Friedrich, Guy; Mallouhi, Ammar; Pachinger, Otmar; Jaschke, Werner; Feuchtner, Gudrun M.

2010-01-01

Objective: To assess the relationship between left anterior descending (LAD) coronary artery myocardial bridging detected by 64-slice computed tomography (CT) and clinical findings. Methods: 221 consecutive patients were examined with coronary 64-slice CT angiography. 21 patients with coronary stenosis >50% were excluded. The length, depth, and luminal narrowing of LAD myocardial bridges during systole and diastole were measured. CT findings were compared with the treadmill ECG-stress test, and clinical symptoms. Results: Myocardial bridges of the LAD were found in 23% of patients (51/221) (length, 14.9 ± 6.5 mm; depth, 2.6 ± 1.6 mm). A significant difference was noted between the LAD luminal diameter before the intramyocardial course and intramyocardially, for both diastole and systole (p 50% was found in 3/25 (8%). 30/51 (59%) of bridges were 'deep' (>2 mm myocardial depth), 21/51 (41%) were 'superficial'. The prevalence of a positive ECG-stress tests for the anterior myocardial region was significantly higher in patients with LAD myocardial bridges (34/50; 68%) compared to those without (28/144; 19.4%) (p < 0.001). There was no difference between 'superficial' and 'deep' LAD myocardial bridges in regard to a positive treadmill ECG-stress test. Typical angina was rare with 6%. Conclusion: LAD myocardial bridges are common findings and can possibly explain a positive exercise ECG-stress test for anterior myocardial ischemia. Intramyocardial LAD segments show mild-to-moderate luminal narrowing at rest, which is higher during end-systolic phase.

Chest radiography and thoracic computed tomography findings in children who have family members with active pulmonary tuberculosis

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Uzum, Kazim; Karahan, Okkes I.; Dogan, Sukru; Coskun, Abdulhakim; Topcu, Faik

2003-01-01

Objective: The chest radiography and TCT findings in children who had contacted with adult family members with active pulmonary tuberculosis were compared. The contributions of thoracic computed tomography to the diagnosis of tuberculosis were investigated. Methods and material: The children who were 0-16 years old (n=173) and children of families with an adult member which was diagnosed as pulmonary tuberculosis were evaluated. The children were considered in two groups based on the absence (n=125) or presence (n=48) of complaints and/or ambiguous symptoms such as lack of appetite, mild cough, sweating, history of lung infection, low body weight and those with suspicious chest radiography findings (12 cases) were included in this study. Asymptomatic patients (n=125) did not undergo TCT. Patients who had positive PPD skin tests only received isoniazid. If the TCT demonstrated enlarged lymph nodes or parenchymal lesions, minimally active pulmonary tuberculosis was diagnosed and antituberculous treatment was given. Results and discussions: TCT revealed lymph node enlargement or parenchymal lesions in 39 children (81.2%). Of the 12 children whose CXRs revealed suspicious lymph node enlargement and/or infiltration, five had normal findings in TCT whereas the initial findings were confirmed in the remaining seven. These data suggest that there is a correlation between the presence of ambiguous symptoms in exposed children and TCT findings; chest radiography and TCT findings do not yield parallel findings. All the patients who received anti-TB treatment were resolved in the control examinations. Conclusion: In this study there is a correlation between presence of ambiguous symptoms and TCT findings, but the chest radiography and TCT findings do not yield harmony in exposed children with ambiguous symptoms (suspicious tuberculosis cases). These observations should be considered in children with symptoms similar to those of exposed children, but with no definite history of

Simultaneous inference of phenotype-associated genes and relevant tissues from GWAS data via Bayesian integration of multiple tissue-specific gene networks.

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Wu, Mengmeng; Lin, Zhixiang; Ma, Shining; Chen, Ting; Jiang, Rui; Wong, Wing Hung

2017-12-01

Although genome-wide association studies (GWAS) have successfully identified thousands of genomic loci associated with hundreds of complex traits in the past decade, the debate about such problems as missing heritability and weak interpretability has been appealing for effective computational methods to facilitate the advanced analysis of the vast volume of existing and anticipated genetic data. Towards this goal, gene-level integrative GWAS analysis with the assumption that genes associated with a phenotype tend to be enriched in biological gene sets or gene networks has recently attracted much attention, due to such advantages as straightforward interpretation, less multiple testing burdens, and robustness across studies. However, existing methods in this category usually exploit non-tissue-specific gene networks and thus lack the ability to utilize informative tissue-specific characteristics. To overcome this limitation, we proposed a Bayesian approach called SIGNET (Simultaneously Inference of GeNEs and Tissues) to integrate GWAS data and multiple tissue-specific gene networks for the simultaneous inference of phenotype-associated genes and relevant tissues. Through extensive simulation studies, we showed the effectiveness of our method in finding both associated genes and relevant tissues for a phenotype. In applications to real GWAS data of 14 complex phenotypes, we demonstrated the power of our method in both deciphering genetic basis and discovering biological insights of a phenotype. With this understanding, we expect to see SIGNET as a valuable tool for integrative GWAS analysis, thereby boosting the prevention, diagnosis, and treatment of human inherited diseases and eventually facilitating precision medicine.

Predicting Essential Genes and Proteins Based on Machine Learning and Network Topological Features: A Comprehensive Review

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Zhang, Xue; Acencio, Marcio Luis; Lemke, Ney

2016-01-01

Essential proteins/genes are indispensable to the survival or reproduction of an organism, and the deletion of such essential proteins will result in lethality or infertility. The identification of essential genes is very important not only for understanding the minimal requirements for survival of an organism, but also for finding human disease genes and new drug targets. Experimental methods for identifying essential genes are costly, time-consuming, and laborious. With the accumulation of sequenced genomes data and high-throughput experimental data, many computational methods for identifying essential proteins are proposed, which are useful complements to experimental methods. In this review, we show the state-of-the-art methods for identifying essential genes and proteins based on machine learning and network topological features, point out the progress and limitations of current methods, and discuss the challenges and directions for further research. PMID:27014079

Reveal genes functionally associated with ACADS by a network study.

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Chen, Yulong; Su, Zhiguang

2015-09-15

Establishing a systematic network is aimed at finding essential human gene-gene/gene-disease pathway by means of network inter-connecting patterns and functional annotation analysis. In the present study, we have analyzed functional gene interactions of short-chain acyl-coenzyme A dehydrogenase gene (ACADS). ACADS plays a vital role in free fatty acid β-oxidation and regulates energy homeostasis. Modules of highly inter-connected genes in disease-specific ACADS network are derived by integrating gene function and protein interaction data. Among the 8 genes in ACADS web retrieved from both STRING and GeneMANIA, ACADS is effectively conjoined with 4 genes including HAHDA, HADHB, ECHS1 and ACAT1. The functional analysis is done via ontological briefing and candidate disease identification. We observed that the highly efficient-interlinked genes connected with ACADS are HAHDA, HADHB, ECHS1 and ACAT1. Interestingly, the ontological aspect of genes in the ACADS network reveals that ACADS, HAHDA and HADHB play equally vital roles in fatty acid metabolism. The gene ACAT1 together with ACADS indulges in ketone metabolism. Our computational gene web analysis also predicts potential candidate disease recognition, thus indicating the involvement of ACADS, HAHDA, HADHB, ECHS1 and ACAT1 not only with lipid metabolism but also with infant death syndrome, skeletal myopathy, acute hepatic encephalopathy, Reye-like syndrome, episodic ketosis, and metabolic acidosis. The current study presents a comprehensible layout of ACADS network, its functional strategies and candidate disease approach associated with ACADS network. Copyright © 2015 Elsevier B.V. All rights reserved.

Computed tomographic findings of intrahepatic peripheral cholangiocarcinoma

International Nuclear Information System (INIS)

Woo, Seong Ku; Suh, Soo Jhi; Kim, Ho Joon; Chun, Byung Hee

1986-01-01

Cholangiocarcinoma is synonymous with bile duct carcinoma, and can originate in a small intrahepatic bile duct (peripheral type), a major intrahepatic duct including the hepatic hills, an extrahepatic duct, or near the papilla of Vater (central type). In a sense bile duct carcinoma of the peripheral type is cholangiocarcinoma of the liver; it has the same gross configuration as hepatocellular carcinoma, resulting in difficulty to differentiate on the CT. The authors studied CT findings of 14 cases of pathologically proven peripheral type cholangiocarcinoma of the liver during the last 4 years. The results were as follows: 1. Of 14 cases, 8 were female and 6 were male, and the age ranged from 5th to 7th decades. 2. Preoperative clinical diagnosis were as follows: hepatoma 8 cases, abscess 5 cases and metastasis 1 case in order of frequency. 3. Diagnosis were confirmed by hepatic lobectomy in 7 cases, wedge resection in 5 cases and needle biopsy in 2 case. 4. Laboratory findings were not specific, but there were only 2 cases with elevated alpha-fetoprotein level. 5. Associated diseases were gallstones in 1 case, intrahepatic duct stones in 1 case, extrahepatic duct stones in 2 cases, acute or chronic cholecystitis in 5 cases and CS in 3 cases. 6. Angiographic and scintigraphic findings were helpful in differential diagnosis from hepatoma but ultrasonography was non-specific. 7. The number of tumor were solitary in 12 cases and multiple in 2 cases. Among solitary cases, the site of involvement of the liver were right lobe in 8 cases and left lobe in 4 cases. 8. Common CT features of the intrahepatic peripheral cholangiocinoma of the liver were irregular, inhomogeneous, occasionally peripherally enhancing, low density liver mass, frequently accompanied by diffuse or segmental dilatation of the intrahepatic bile duct. If there were normal alpha fetoprotein level, positive skin and/or stool examination for CS and diffuse or segmental dilatation of the intrahepatic duct

Fluorodeoxyglucose positron emission tomography/computed tomography findings in a patient with cerebellar mutism after operation in posterior fossa

Directory of Open Access Journals (Sweden)

Gonca Kara Gedik

2017-03-01

Full Text Available Cerebellar mutism is a transient period of speechlessness that evolves after posterior fossa surgery in children. Although direct cerebellar and brain stem injury and supratentorial dysfunction have been implicated in the mediation of mutism, the pathophysiological mechanisms involved in the evolution of this kind of mutism remain unclear. Magnetic resonance imaging revealed dentatothalamocortical tract injuries and single photon emission computed tomography showed cerebellar and cerebral hypoperfusion in patients with cerebellar mutism. However, findings with 18F-fluorodeoxyglucose positron emission tomography/computed tomography (FDG PET/CT in this group of patients have not been documented previously. In this clinical case, we report a patient who experienced cerebellar mutism after undergoing a posterior fossa surgery. Right cerebellar and left frontal lobe hypometabolism was shown using FDG PET/CT. The FDG metabolism of both the cerebellum and the frontal lobe returned to normal levels after the resolution of the mutism symptoms.

Computed tomography (CT) findings of the pleural metastasis effusion: the examination of 100 patients

International Nuclear Information System (INIS)

Arenas, J. J.; Alonso, S.; Gil, S.; Fernandez, F.; Lloret, M.

1999-01-01

To evaluate the computed tomography (CT) findings in a series of 100 pleural metastasis effusions. A retrospective study was carried out that consisted of assessing the CT images of 100 malignant pleural metastasis effusions, evaluating the amount of the effusion, its distribution, the presence of swelling or nodules in the different pleural surfaces, the existence and the characteristics of the extrapleural fat and the changes in other locations different to the pleural cavity, mainly the mediastinum and the pulmonary parenchyma. The effusion was located in 12 patients. The amount of the effusion was slight in 14% and massive in 10% of the sick patients. Pleural nodules were detected in 19% of the studies, in all those that affected the costal parental pleura, being less frequent in the other pleural surfaces. The costal parental pleura was swollen in 43% of the sick patients. 52 sick patients did not have any swelling nor pleural nodules, with the pleural effusion being the only sign of pleural metastasis. Changes in the rest of the thorax were frequent in relation to the malignant illness that causes the effusion and appeared in 67% of the sick patients. The patients with pleural effusions of malignant etiology showed variable CT findings, that in general were non-specific, and in almost half the cases no pleural changes can be seen apart from the effusion. (Author) 13 refs

Biomarker Identification for Prostate Cancer and Lymph Node Metastasis from Microarray Data and Protein Interaction Network Using Gene Prioritization Method

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Carlos Roberto Arias

2012-01-01

Full Text Available Finding a genetic disease-related gene is not a trivial task. Therefore, computational methods are needed to present clues to the biomedical community to explore genes that are more likely to be related to a specific disease as biomarker. We present biomarker identification problem using gene prioritization method called gene prioritization from microarray data based on shortest paths, extended with structural and biological properties and edge flux using voting scheme (GP-MIDAS-VXEF. The method is based on finding relevant interactions on protein interaction networks, then scoring the genes using shortest paths and topological analysis, integrating the results using a voting scheme and a biological boosting. We applied two experiments, one is prostate primary and normal samples and the other is prostate primary tumor with and without lymph nodes metastasis. We used 137 truly prostate cancer genes as benchmark. In the first experiment, GP-MIDAS-VXEF outperforms all the other state-of-the-art methods in the benchmark by retrieving the truest related genes from the candidate set in the top 50 scores found. We applied the same technique to infer the significant biomarkers in prostate cancer with lymph nodes metastasis which is not established well.

Brain computed tomography findings of aged schizophrenics

International Nuclear Information System (INIS)

Oomori, Masao; Koshino, Yoshifumi; Murata, Tetsuhito; Murata, Ichirou; Tani, Kazuhiko; Horie, Tan; Isaki, Kiminori

1992-01-01

Brain CT was performed in a total of 30 aged schizophrenic patients, consisting of 20 with no history of psychosurgery (lobotomy) and the other 10 lobotomized patients. The CT findings were compared with those from healthy aged persons. The group of schizophrenic patients had marked atrophy of the frontal lobe and dilatated Sylvian fissure as compared with the control group. There was no significant difference in ventricular factors between the two groups. These findings may have implications for the different mechanisms of the occurrence of atrophied brain surface and enlarged ventricle. The cerebral cortex involved in the occurrence of schizophrenia may be affected by aging-related cerebral atrophy, in addition to the morphological changes due to schizophrenia. Thus, schizophrenic cerebral atrophy was more noticeable than physiological aging-related atrophy. However, enlargement of the ventricle in the schizophrenic group progressed with aging in the same manner as that in the normal group. In comparing schizophrenic patients with or without a history of lobotomy, atrophy of the brain surface and enlargement of the ventricle were more marked in the lobotomized patients than the non-lobotomized patients. This confirmed that lobotomy, as well as surgical scar, is involved in the morphology of schizophrenic brain. (N.K.)

Exploring Valid Reference Genes for Quantitative Real-time PCR Analysis in Plutella xylostella (Lepidoptera: Plutellidae)

Science.gov (United States)

Fu, Wei; Xie, Wen; Zhang, Zhuo; Wang, Shaoli; Wu, Qingjun; Liu, Yong; Zhou, Xiaomao; Zhou, Xuguo; Zhang, Youjun

2013-01-01

Abstract: Quantitative real-time PCR (qRT-PCR), a primary tool in gene expression analysis, requires an appropriate normalization strategy to control for variation among samples. The best option is to compare the mRNA level of a target gene with that of reference gene(s) whose expression level is stable across various experimental conditions. In this study, expression profiles of eight candidate reference genes from the diamondback moth, Plutella xylostella, were evaluated under diverse experimental conditions. RefFinder, a web-based analysis tool, integrates four major computational programs including geNorm, Normfinder, BestKeeper, and the comparative ΔCt method to comprehensively rank the tested candidate genes. Elongation factor 1 (EF1) was the most suited reference gene for the biotic factors (development stage, tissue, and strain). In contrast, although appropriate reference gene(s) do exist for several abiotic factors (temperature, photoperiod, insecticide, and mechanical injury), we were not able to identify a single universal reference gene. Nevertheless, a suite of candidate reference genes were specifically recommended for selected experimental conditions. Our finding is the first step toward establishing a standardized qRT-PCR analysis of this agriculturally important insect pest. PMID:23983612

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

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.

Computed tomographic findings in progressive supranuclear palsy

Energy Technology Data Exchange (ETDEWEB)

Saitoh, H; Yoshii, F; Shinohara, Y

1987-03-01

CT findings of 6 patients with progressive supranuclear palsy (PSP) are described, with emphasis on their supratentorial changes in comparison with those of control subjects and patients with Parkinson's disease (PD). As estimated from CT films, the lateral ventricles, third ventricle and prepontine cistern were significantly enlarged in PSP patients compared with both controls and PD patients. It is suggested that the patients with PSP have not only infratentorial but also supratentorial lesions.

Identifying and Analyzing Novel Epilepsy-Related Genes Using Random Walk with Restart Algorithm

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Wei Guo

2017-01-01

Full Text Available As a pathological condition, epilepsy is caused by abnormal neuronal discharge in brain which will temporarily disrupt the cerebral functions. Epilepsy is a chronic disease which occurs in all ages and would seriously affect patients’ personal lives. Thus, it is highly required to develop effective medicines or instruments to treat the disease. Identifying epilepsy-related genes is essential in order to understand and treat the disease because the corresponding proteins encoded by the epilepsy-related genes are candidates of the potential drug targets. In this study, a pioneering computational workflow was proposed to predict novel epilepsy-related genes using the random walk with restart (RWR algorithm. As reported in the literature RWR algorithm often produces a number of false positive genes, and in this study a permutation test and functional association tests were implemented to filter the genes identified by RWR algorithm, which greatly reduce the number of suspected genes and result in only thirty-three novel epilepsy genes. Finally, these novel genes were analyzed based upon some recently published literatures. Our findings implicate that all novel genes were closely related to epilepsy. It is believed that the proposed workflow can also be applied to identify genes related to other diseases and deepen our understanding of the mechanisms of these diseases.

Meta-analysis of differentiating mouse embryonic stem cell gene expression kinetics reveals early change of a small gene set.

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Clive H Glover

2006-11-01

Full Text Available Stem cell differentiation involves critical changes in gene expression. Identification of these should provide endpoints useful for optimizing stem cell propagation as well as potential clues about mechanisms governing stem cell maintenance. Here we describe the results of a new meta-analysis methodology applied to multiple gene expression datasets from three mouse embryonic stem cell (ESC lines obtained at specific time points during the course of their differentiation into various lineages. We developed methods to identify genes with expression changes that correlated with the altered frequency of functionally defined, undifferentiated ESC in culture. In each dataset, we computed a novel statistical confidence measure for every gene which captured the certainty that a particular gene exhibited an expression pattern of interest within that dataset. This permitted a joint analysis of the datasets, despite the different experimental designs. Using a ranking scheme that favored genes exhibiting patterns of interest, we focused on the top 88 genes whose expression was consistently changed when ESC were induced to differentiate. Seven of these (103728_at, 8430410A17Rik, Klf2, Nr0b1, Sox2, Tcl1, and Zfp42 showed a rapid decrease in expression concurrent with a decrease in frequency of undifferentiated cells and remained predictive when evaluated in additional maintenance and differentiating protocols. Through a novel meta-analysis, this study identifies a small set of genes whose expression is useful for identifying changes in stem cell frequencies in cultures of mouse ESC. The methods and findings have broader applicability to understanding the regulation of self-renewal of other stem cell types.

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.

Computational and Organotypic Modeling of Microcephaly ...

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Microcephaly is associated with reduced cortical surface area and ventricular dilations. Many genetic and environmental factors precipitate this malformation, including prenatal alcohol exposure and maternal Zika infection. This complexity motivates the engineering of computational and experimental models to probe the underlying molecular targets, cellular consequences, and biological processes. We describe an Adverse Outcome Pathway (AOP) framework for microcephaly derived from literature on all gene-, chemical-, or viral- effects and brain development. Overlap with NTDs is likely, although the AOP connections identified here focused on microcephaly as the adverse outcome. A query of the Mammalian Phenotype Browser database for ‘microcephaly’ (MP:0000433) returned 85 gene associations; several function in microtubule assembly and centrosome cycle regulated by (microcephalin, MCPH1), a gene for primary microcephaly in humans. The developing ventricular zone is the likely target. In this zone, neuroprogenitor cells (NPCs) self-replicate during the 1st trimester setting brain size, followed by neural differentiation of the neocortex. Recent studies with human NPCs confirmed infectivity with Zika virions invoking critical cell loss (apoptosis) of precursor NPCs; similar findings have been shown with fetal alcohol or methylmercury exposure in rodent studies, leading to mathematical models of NPC dynamics in size determination of the ventricular zone. A key event

Postoperative computed tomography and low-field magnetic resonance imaging findings in dogs with degenerative lumbosacral stenosis treated by dorsal laminectomy.

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Rapp, Martin; Ley, Charles J; Hansson, Kerstin; Sjöström, Lennart

2017-03-20

To describe postoperative computed tomography (CT) and magnetic resonance imaging (MRI) findings in dogs with degenerative lumbosacral stenosis (DLSS) treated by dorsal laminectomy and partial discectomy. Prospective clinical case study of dogs diagnosed with and treated for DLSS. Surgical and clinical findings were described. Computed tomography and low field MRI findings pre- and postoperatively were described and graded. Clinical, CT and MRI examinations were performed four to 18 months after surgery. Eleven of 13 dogs were clinically improved and two dogs had unchanged clinical status postoperatively despite imaging signs of neural compression. Vacuum phenomenon, spondylosis, sclerosis of the seventh lumbar (L7) and first sacral (S1) vertebrae endplates and lumbosacral intervertebral joint osteoarthritis became more frequent in postoperative CT images. Postoperative MRI showed mild disc extrusions in five cases, and in all cases contrast enhancing non-discal tissue was present. All cases showed contrast enhancement of the L7 spinal nerves both pre- and postoperatively and seven had contrast enhancement of the lumbosacral intervertebral joints and paraspinal tissue postoperatively. Articular process fractures or fissures were noted in four dogs. The study indicates that imaging signs of neural compression are common after DLSS surgery, even in dogs that have clinical improvement. Contrast enhancement of spinal nerves and soft tissues around the region of disc herniation is common both pre- and postoperatively and thus are unreliable criteria for identifying complications of the DLSS surgery.

Acute Knee Trauma: Analysis of Multidetector Computed Tomography Findings and Comparison with Conventional Radiography

International Nuclear Information System (INIS)

Mustonen, A.O.T.; Kiuru, M.J.

2005-01-01

Purpose: To evaluate the multidetector computed tomography (MDCT) findings of acute knee trauma and to compare radiography with MDCT in patients referred ta level 1 trauma center. Material and Methods: During a 5-year period, a total of 415 MDCT examinations were performed on 409 patients with acute knee trauma to reveal complex fracture anatomy or rule out a fracture. MDCT and primary radiographs were re-evaluated with respect to fracture location and trauma mechanism. Tibial plateau fractures were further analyzed depending on anatomical location: anterior-medial, anterior-lateral, posterior-lateral, and posterior-medial regions. Maximal depression of the tibial articular surface was measured. Findings on the primary knee radiographs were compared with MDCT findings. Results: Of the 409 patients, 356 (87%) had a knee fracture. A total of 451 fractures were found in all anatomic regions: distal femur ( n = 49), proximal tibia ( n 307), patella ( n = 23), and proximal fibula ( n = 72). Primary radiographs were available in 316 (76%) cases. Of these, 225 (71%) had MDCT in order to reveal the fracture anatomy better, and 91 (29%) had a subsequent MDCT after negative plain radiographs. Overall sensitivity of radiography was 83%, while negative predictive value was 49%. On radiography, tibial plateau articular depression was underestimated in all regions except when the fracture consisted of the whole half of the anterior or posterior plateau. The three main injury mechanisms were traffic accident, a simple fall, and sport. In 49 cases (15%), primary radiographs were suboptimal due to positioning. Conclusion: In severely injured patients, diagnostically sufficient radiographs are difficult to obtain, and therefore a negative radiograph is not reliable in ruling out a fracture. In these patients, MDCT is a fast and accurate examination and is also recommended in patients with tibial plateau fractures or complex knee injuries in order to evaluate the fracture adequately

Computational methods to dissect cis-regulatory transcriptional ...

Indian Academy of Sciences (India)

The formation of diverse cell types from an invariant set of genes is governed by biochemical and molecular processes that regulate gene activity. A complete understanding of the regulatory mechanisms of gene expression is the major function of genomics. Computational genomics is a rapidly emerging area for ...

Computed tomographic findings of early subacute sclerosing panencephalitis

International Nuclear Information System (INIS)

Pedersen, H.; Wulff, C.H.; Rigshospitalet, Copenhagen

1982-01-01

Computed tomography of the brain (CT) was carried out at the early stages of subacute sclerosing panencephalitis (SSPE) in three children. The lateral ventricles were very small and the hemispheric sulci and interhemispheric fissures were not visible in all three patients in contrast to severe atrophy found at a later stage in one patient. The early CT abnormalities were revealed at the same time as the titres of measles antibodies in blood and cerebrospinal fluid were elevated, and the characteristic periodic complexes in the electroencephalogram established the diagnosis of SSPE. The CT changes indicating brain swelling reflect the reactive changes of this slow virus infection. (orig.)

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.

Dissecting Time- from Tumor-Related Gene Expression Variability in Bilateral Breast Cancer

Directory of Open Access Journals (Sweden)

Maurizio Callari

2018-01-01

Full Text Available Metachronous (MBC and synchronous bilateral breast tumors (SBC are mostly distinct primaries, whereas paired primaries and their local recurrences (LRC share a common origin. Intra-pair gene expression variability in MBC, SBC, and LRC derives from time/tumor microenvironment-related and tumor genetic background-related factors and pairs represents an ideal model for trying to dissect tumor-related from microenvironment-related variability. Pairs of tumors derived from women with SBC (n = 18, MBC (n = 11, and LRC (n = 10 undergoing local-regional treatment were profiled for gene expression; similarity between pairs was measured using an intraclass correlation coefficient (ICC computed for each gene and compared using analysis of variance (ANOVA. When considering biologically unselected genes, the highest correlations were found for primaries and paired LRC, and the lowest for MBC pairs. By instead limiting the analysis to the breast cancer intrinsic genes, correlations between primaries and paired LRC were enhanced, while lower similarities were observed for SBC and MBC. Focusing on stromal-related genes, the ICC values decreased for MBC and were significantly different from SBC. These findings indicate that it is possible to dissect intra-pair gene expression variability into components that are associated with genetic origin or with time and microenvironment by using specific gene subsets.

Unusual computed tomography findings and complications in acute appendicitis; Aspectos tomograficos incomuns da apendicite aguda e suas complicacoes

Energy Technology Data Exchange (ETDEWEB)

Palacio, Glaucia Andrade e Silva; D' Ippolito, Giuseppe [Hospital Sao Luiz, Sao Paulo, SP (Brazil). Setor de Diagnostico por Imagem]. E-mail: glauciapalacio@uol.com.br; Bianco, Fabio Davolio [Hospital Sao Luiz, Sao Paulo, SP (Brazil). Setor de Tomografia Computadorizada e Ressonancia Magnetica; Domenicis Junior, Osvaldo de [CURA Imagem e Diagnostico, Sao Paulo, SP (Brazil)

2003-07-01

The objective of this article is to describe and illustrate unusual computed tomography (CT) findings in patients with acute appendicitis. We reviewed the charts of 200 patients with clinical suspicion of acute appendicitis who were submitted to abdominal CT before surgery. Patients with unusual presentation or complications were selected for illustrating the main CT findings. Unusual complications of acute appendicitis were related to anomalous position of the appendix, contiguity to intraperitoneal organs such as the liver, gall bladder, annexes and the bladder and continuous use of anti inflammatory or antibiotics during the diagnostic process. We concluded that CT is a useful diagnostic tool in patients with complicated or unusual presentation acute appendicitis. The first step towards diagnosis in these cases i to have in mind the hypothesis of appendicitis in patients with acute abdominal pain. (author)

320-row detector computed tomography angiography findings of a case with multiple

International Nuclear Information System (INIS)

Akay, S.; Bozlar, U.; Demirkol, S.; Tasar, M.

2012-01-01

Full text: Introduction: Computed tomography angiography (CTA) with three-dimensional imaging capability is a very reliable imaging modality for the evaluation of the coronary arteries. Objectives and tasks: To discuss the 320-row detector CTA findings of a case with multiple coronary artery course anomaly. Materials and methods: A 46-year-old man with palpitation, admitted to Cardiology department of our hospital. On electrocardiography, polymorphic ventricular early beats were observed. The patient was referred to Radiology department for CTA examination in terms of probable coronary artery anomaly. Results: On CTA, left main coronary artery was short. The bridging causes nearly 75% luminal stenosis was observed in the middle part of left descending artery. Circumflex artery was continuing as the first obtuse margin and this branch was separating to four branches in the middle part. They were coursing subepicardially in the middle and distal part. Right main coronary artery has also subepicardial course in its middle and distal part. Conclusion: Myocardial bridging is not a rare situation in routine clinical practice. But bridging in all of the three coronary arteries is very uncommon. Multidetector CTA is an effective and non-invasive imaging modality for understanding the normal anatomy and detecting the congenital anomalies of the coronary arteries

Intrinsic noise of microRNA-regulated genes and the ceRNA hypothesis.

Directory of Open Access Journals (Sweden)

Javad Noorbakhsh

Full Text Available MicroRNAs are small noncoding RNAs that regulate genes post-transciptionally by binding and degrading target eukaryotic mRNAs. We use a quantitative model to study gene regulation by inhibitory microRNAs and compare it to gene regulation by prokaryotic small non-coding RNAs (sRNAs. Our model uses a combination of analytic techniques as well as computational simulations to calculate the mean-expression and noise profiles of genes regulated by both microRNAs and sRNAs. We find that despite very different molecular machinery and modes of action (catalytic vs stoichiometric, the mean expression levels and noise profiles of microRNA-regulated genes are almost identical to genes regulated by prokaryotic sRNAs. This behavior is extremely robust and persists across a wide range of biologically relevant parameters. We extend our model to study crosstalk between multiple mRNAs that are regulated by a single microRNA and show that noise is a sensitive measure of microRNA-mediated interaction between mRNAs. We conclude by discussing possible experimental strategies for uncovering the microRNA-mRNA interactions and testing the competing endogenous RNA (ceRNA hypothesis.

Pulmonary arteriovenous malformations in hereditary haemorrhagic telangiectasia. Correlations between computed tomography findings and cerebral complications

Energy Technology Data Exchange (ETDEWEB)

Etievant, Johan; Si-Mohamed, Salim; Vinurel, Nicolas; Revel, Didier [Hospices Civils de Lyon, Hopital Cardiologique Louis Pradel, Departement d' Imagerie Cardiaque et Thoracique, Diagnostique et Interventionnelle, Bron (France); Universite Claude Bernard Lyon 1, Villeurbanne (France); Dupuis-Girod, Sophie [Hospices Civils de Lyon, Hopital Femme-Mere-Enfant, Service de Genetique, Centre de Reference pour la maladie de Rendu-Osler, Lyon (France); Decullier, Evelyne [Universite Claude Bernard Lyon 1, Villeurbanne (France); Hospices Civils de Lyon, Pole Information Medicale Evaluation Recherche, Lyon (France); Gamondes, Delphine [Hospices Civils de Lyon, Hopital Cardiologique Louis Pradel, Departement d' Imagerie Cardiaque et Thoracique, Diagnostique et Interventionnelle, Bron (France); Khouatra, Chahera [Hospices Civils de Lyon, Hopital Cardiologique Louis Pradel, Service de pneumologie - Centre des Maladies Orphelines Pulmonaires, Lyon (France); Cottin, Vincent [Universite Claude Bernard Lyon 1, Villeurbanne (France); Hospices Civils de Lyon, Hopital Cardiologique Louis Pradel, Service de pneumologie - Centre des Maladies Orphelines Pulmonaires, Lyon (France)

2018-03-15

Computed tomography (CT) is the modality of choice to characterise pulmonary arteriovenous malformations (PAVMs) in patients with hereditary haemorrhagic telangiectasia (HHT). Our objective was to determine if CT findings were associated with frequency of brain abscess and ischaemic stroke. This retrospective study included patients with HHT-related PAVMs. CT results, i.e. PAVM presentation (unique, multiple, disseminated or diffuse), the number of PAVMs and the largest feeding artery size, were correlated to prevalence of ischaemic stroke and brain abscess. All CTs were reviewed in consensus by two radiologists. Of 170 patients, 73 patients had unique (42.9 %), 49 multiple (28.8 %), 36 disseminated (21.2 %) and 12 diffuse (7.1 %) PAVMs. Fifteen patients presented with brain abscess; 26 patients presented with ischaemic stroke. The number of PAVMs was significantly correlated with brain abscess (11.5 vs. 6.2, respectively; p=0.025). The mean diameter of the largest feeding artery was significantly correlated with ischaemic stroke frequency (4.9 vs. 3.2 mm, respectively; p=0.0098). The number of PAVMs correlated significantly with risk of brain abscess, and a larger feeding artery significantly with more ischaemic strokes. These findings can lead to a better recognition and management of the PAVMs at risk of cerebral complications. (orig.)

HMM-Based Gene Annotation Methods

Energy Technology Data Exchange (ETDEWEB)

Haussler, David; Hughey, Richard; Karplus, Keven

1999-09-20

Development of new statistical methods and computational tools to identify genes in human genomic DNA, and to provide clues to their functions by identifying features such as transcription factor binding sites, tissue, specific expression and splicing patterns, and remove homologies at the protein level with genes of known function.

A Poisson Log-Normal Model for Constructing Gene Covariation Network Using RNA-seq Data.

Science.gov (United States)

Choi, Yoonha; Coram, Marc; Peng, Jie; Tang, Hua

2017-07-01

Constructing expression networks using transcriptomic data is an effective approach for studying gene regulation. A popular approach for constructing such a network is based on the Gaussian graphical model (GGM), in which an edge between a pair of genes indicates that the expression levels of these two genes are conditionally dependent, given the expression levels of all other genes. However, GGMs are not appropriate for non-Gaussian data, such as those generated in RNA-seq experiments. We propose a novel statistical framework that maximizes a penalized likelihood, in which the observed count data follow a Poisson log-normal distribution. To overcome the computational challenges, we use Laplace's method to approximate the likelihood and its gradients, and apply the alternating directions method of multipliers to find the penalized maximum likelihood estimates. The proposed method is evaluated and compared with GGMs using both simulated and real RNA-seq data. The proposed method shows improved performance in detecting edges that represent covarying pairs of genes, particularly for edges connecting low-abundant genes and edges around regulatory hubs.

Computational Intelligence, Cyber Security and Computational Models

CERN Document Server

Anitha, R; Lekshmi, R; Kumar, M; Bonato, Anthony; Graña, Manuel

2014-01-01

This book contains cutting-edge research material presented by researchers, engineers, developers, and practitioners from academia and industry at the International Conference on Computational Intelligence, Cyber Security and Computational Models (ICC3) organized by PSG College of Technology, Coimbatore, India during December 19–21, 2013. The materials in the book include theory and applications for design, analysis, and modeling of computational intelligence and security. The book will be useful material for students, researchers, professionals, and academicians. It will help in understanding current research trends and findings and future scope of research in computational intelligence, cyber security, and computational models.

Explorations in computing an introduction to computer science

CERN Document Server

Conery, John S

2010-01-01

Introduction Computation The Limits of Computation Algorithms A Laboratory for Computational ExperimentsThe Ruby WorkbenchIntroducing Ruby and the RubyLabs environment for computational experimentsInteractive Ruby Numbers Variables Methods RubyLabs The Sieve of EratosthenesAn algorithm for finding prime numbersThe Sieve Algorithm The mod Operator Containers Iterators Boolean Values and the delete if Method Exploring the Algorithm The sieve Method A Better Sieve Experiments with the Sieve A Journey of a Thousand MilesIteration as a strategy for solving computational problemsSearching and Sortin

Computer tomography findings and causes of unilateral exophthalmos

International Nuclear Information System (INIS)

Chen Fangni; Xie Sumin; Tang Haiyong

2010-01-01

Objective: To evaluate the common cause of unilateral exophthalmos and CT findings. Methods: The CT manifestations of 267 cases of unilateral exophthalmos were reviewed. 41 cases were confirmed by surgery and pathology. 68 cases were confirmed by biopsy. Diagnosis was made in 158 cases on the basis of typical history, laboratory findings and response to treatment. Results: The lesions were intraocular (10 cases), intraorbital (230) and periorbital lesions (27). The most common causes of unilateral exophthalmos included inflammatory pseudotumor (67 cases), pleomorphic adenoma or carcinoma of lachrymal gland (44), cavernous angioma (22), carotid cavernous fistula (20) and varices (18). The CT appearances were exophthalmos, intraocular or periorbital tumor, extraocular muscle hypertrophy. The contrast enhancement was variable without enhancement in necrotic areas. Conclusion: CT scan is valuable for diagnosis and displaying the structural change of unilateral exophthalmos. (authors)

Hepatocellular carcinoma with bile duct involvement : computed Tomographic (CT) findings

International Nuclear Information System (INIS)

Lee, Joon Woo; Han, Joon Koo; Kim, Tae Kyoung; And others

2000-01-01

To describe the radiologic features of computed tomography (CT) in hepatocellular carcinoma (HCC) with bile duct involvement. We retrospectively analyzed the two phase spiral CT findings of 31 patients in whom HCC with bile duct invasion (n=3D28) or compression (n=3D3), was diagnosed. Eight of these underwent follow up CT after transarterial chemoembolization. We analyzed the size, type, location, enhancement pattern, and lipiodol retention of parenchymal and intraductal masses, as well as their lymphadenopathy. In all patients with bile duct invasion, single or multiple masses were demonstrated in the bile ducts. Intraductal masses showed the same enhancement characteristics as the parenchymal mass (kappa 0.550, p less than 0.001), and were contiguous to this mass. In 14 of 28 patients, intraductal masses filled the peripheral intrahepatic bile ducts and extended to the common bile ducts. In the other 14, the parenchymal mass extended to the area of the porta hepatis and then directly invaded the large ducts. In nine of the 28 patients, there was a hypoattenuated cleft between the intraductal mass and ductal wall. In six, a parenchymal mass was not apparent (n=3D2), or was smaller than 2cm (n=3D4). In five of eight patients (62.5%), follow-up CT after transarterial chemoembolization showed compact or partial lipiodol retention within the intraductal mass. In patients with bile duct compression, perihilar lymph nodes were noted along with the dilated intrahepatic duct but no intra ductal mass was demonstrated in the duct. Hepatocellular carcinomas cause bile duct dilatation either by direct invasion or by extrinsic compression of the bile duct with surrounding enlarged nodes. For the diagnosis of this condition, CT is helpful. (author)

Incidental Cardiac Findings on Thoracic Imaging.

LENUS (Irish Health Repository)

Kok, Hong Kuan

2013-02-07

The cardiac structures are well seen on nongated thoracic computed tomography studies in the investigation and follow-up of cardiopulmonary disease. A wide variety of findings can be incidentally picked up on careful evaluation of the pericardium, cardiac chambers, valves, and great vessels. Some of these findings may represent benign variants, whereas others may have more profound clinical importance. Furthermore, the expansion of interventional and surgical practice has led to the development and placement of new cardiac stents, implantable pacemaker devices, and prosthetic valves with which the practicing radiologist should be familiar. We present a collection of common incidental cardiac findings that can be readily identified on thoracic computed tomography studies and briefly discuss their clinical relevance.

Comparative phyloinformatics of virus genes at micro and macro levels in a distributed computing environment.

Science.gov (United States)

Singh, Dadabhai T; Trehan, Rahul; Schmidt, Bertil; Bretschneider, Timo

2008-01-01

Preparedness for a possible global pandemic caused by viruses such as the highly pathogenic influenza A subtype H5N1 has become a global priority. In particular, it is critical to monitor the appearance of any new emerging subtypes. Comparative phyloinformatics can be used to monitor, analyze, and possibly predict the evolution of viruses. However, in order to utilize the full functionality of available analysis packages for large-scale phyloinformatics studies, a team of computer scientists, biostatisticians and virologists is needed--a requirement which cannot be fulfilled in many cases. Furthermore, the time complexities of many algorithms involved leads to prohibitive runtimes on sequential computer platforms. This has so far hindered the use of comparative phyloinformatics as a commonly applied tool in this area. In this paper the graphical-oriented workflow design system called Quascade and its efficient usage for comparative phyloinformatics are presented. In particular, we focus on how this task can be effectively performed in a distributed computing environment. As a proof of concept, the designed workflows are used for the phylogenetic analysis of neuraminidase of H5N1 isolates (micro level) and influenza viruses (macro level). The results of this paper are hence twofold. Firstly, this paper demonstrates the usefulness of a graphical user interface system to design and execute complex distributed workflows for large-scale phyloinformatics studies of virus genes. Secondly, the analysis of neuraminidase on different levels of complexity provides valuable insights of this virus's tendency for geographical based clustering in the phylogenetic tree and also shows the importance of glycan sites in its molecular evolution. The current study demonstrates the efficiency and utility of workflow systems providing a biologist friendly approach to complex biological dataset analysis using high performance computing. In particular, the utility of the platform Quascade

Transcriptional control in the segmentation gene network of Drosophila.

Directory of Open Access Journals (Sweden)

Mark D Schroeder

2004-09-01

Full Text Available The segmentation gene network of Drosophila consists of maternal and zygotic factors that generate, by transcriptional (cross- regulation, expression patterns of increasing complexity along the anterior-posterior axis of the embryo. Using known binding site information for maternal and zygotic gap transcription factors, the computer algorithm Ahab recovers known segmentation control elements (modules with excellent success and predicts many novel modules within the network and genome-wide. We show that novel module predictions are highly enriched in the network and typically clustered proximal to the promoter, not only upstream, but also in intronic space and downstream. When placed upstream of a reporter gene, they consistently drive patterned blastoderm expression, in most cases faithfully producing one or more pattern elements of the endogenous gene. Moreover, we demonstrate for the entire set of known and newly validated modules that Ahab's prediction of binding sites correlates well with the expression patterns produced by the modules, revealing basic rules governing their composition. Specifically, we show that maternal factors consistently act as activators and that gap factors act as repressors, except for the bimodal factor Hunchback. Our data suggest a simple context-dependent rule for its switch from repressive to activating function. Overall, the composition of modules appears well fitted to the spatiotemporal distribution of their positive and negative input factors. Finally, by comparing Ahab predictions with different categories of transcription factor input, we confirm the global regulatory structure of the segmentation gene network, but find odd skipped behaving like a primary pair-rule gene. The study expands our knowledge of the segmentation gene network by increasing the number of experimentally tested modules by 50%. For the first time, the entire set of validated modules is analyzed for binding site composition under a

Dynamic computed tomography findings of atypical pulmonary hamartoma and it's pathologic correlations: A case report

Energy Technology Data Exchange (ETDEWEB)

Hong, Seung Baek; Jeong Yeon Joo Lee, Gee Won; Kim, Yeong Dae; Ahn, Hyo Yeong; Lee, Chang Hoon; Kim, Ah Rong; Lee, Ji Won [Medical Research Institute, Pusan National University Hospital, Busan (Korea, Republic of)

2016-04-15

We present the dynamic contrast-enhanced computed tomography (CT) findings of atypical pulmonary hamartoma with a rare histologic pattern in a 20-year-old male. CT showed a 3.4 cm lobulated mass with a 'tip of the iceberg' appearance in the medium bronchus of the right lower lobe. Dynamic contrast-enhanced CT demonstrated a heterogeneously and persistently enhancing mass. The CT Hounsfield unit (HU) measurements were: 17 HU pre-contrast, 32 HU at 1 minute, 44 HU at 2 minutes, 51 HU at 4 minutes, and 64 HU at 15 minutes. Pathologic examination after video-assisted thoracoscopic surgery disclosed a pulmonary hamartoma with a predominant fibroblastic component.

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

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...

Meta-analysis of Cancer Gene Profiling Data.

Science.gov (United States)

Roy, Janine; Winter, Christof; Schroeder, Michael

2016-01-01

The simultaneous measurement of thousands of genes gives the opportunity to personalize and improve cancer therapy. In addition, the integration of meta-data such as protein-protein interaction (PPI) information into the analyses helps in the identification and prioritization of genes from these screens. Here, we describe a computational approach that identifies genes prognostic for outcome by combining gene profiling data from any source with a network of known relationships between genes.

Computational Science at the Argonne Leadership Computing Facility

Science.gov (United States)

Romero, Nichols

2014-03-01

The goal of the Argonne Leadership Computing Facility (ALCF) is to extend the frontiers of science by solving problems that require innovative approaches and the largest-scale computing systems. ALCF's most powerful computer - Mira, an IBM Blue Gene/Q system - has nearly one million cores. How does one program such systems? What software tools are available? Which scientific and engineering applications are able to utilize such levels of parallelism? This talk will address these questions and describe a sampling of projects that are using ALCF systems in their research, including ones in nanoscience, materials science, and chemistry. Finally, the ways to gain access to ALCF resources will be presented. This research used resources of the Argonne Leadership Computing Facility at Argonne National Laboratory, which is supported by the Office of Science of the U.S. Department of Energy under contract DE-AC02-06CH11357.

Spiral computed tomography during arterial portography of the liver: correlations between radiological and intraoperative findings and evaluation of operability

International Nuclear Information System (INIS)

Layer, G.; Runge, I.; Conrad, R.; Pauleit, D.; Jaeger, U.; Schild, H.H.; Gallkowski, U.; Wolff, M.; Hirner, A.

1999-01-01

Purpose: To evaluate the accuracy of spiral computed tomography during arterial portography (SCTAP) in the detection, localization, and resectablility of liver tumors in a correlative study between radiology and intraoperative findings. Method and Materials: Retrospectively, SCTAP images of 168 consecutive patients before liver tumor resection were analyzed. The SCTAP studies (100 ml Iopromid 300 by automated injector with a flow of 3 ml/s; slice thickness, table feed and reconstruction index 5 mm each; scan-delay 30 s; 120 kV; 250 mAs) were evaluated for the detection, localization, and resectability of focal liver lesions by three experienced radiologists in consensus and were correlated with histopathological and intraoperative findings where available (59/168). Results: The sensitivity of SCTAP for the detection of liver tumors was 91% for all lesions and 84% for lesions [de

Inferring biological functions of guanylyl cyclases with computational methods

KAUST Repository

Alquraishi, May Majed; Meier, Stuart Kurt

2013-01-01

A number of studies have shown that functionally related genes are often co-expressed and that computational based co-expression analysis can be used to accurately identify functional relationships between genes and by inference, their encoded proteins. Here we describe how a computational based co-expression analysis can be used to link the function of a specific gene of interest to a defined cellular response. Using a worked example we demonstrate how this methodology is used to link the function of the Arabidopsis Wall-Associated Kinase-Like 10 gene, which encodes a functional guanylyl cyclase, to host responses to pathogens. © Springer Science+Business Media New York 2013.

Inferring biological functions of guanylyl cyclases with computational methods

KAUST Repository

Alquraishi, May Majed

2013-09-03

A number of studies have shown that functionally related genes are often co-expressed and that computational based co-expression analysis can be used to accurately identify functional relationships between genes and by inference, their encoded proteins. Here we describe how a computational based co-expression analysis can be used to link the function of a specific gene of interest to a defined cellular response. Using a worked example we demonstrate how this methodology is used to link the function of the Arabidopsis Wall-Associated Kinase-Like 10 gene, which encodes a functional guanylyl cyclase, to host responses to pathogens. © Springer Science+Business Media New York 2013.

Differences in clinical features and computed tomographic findings between embolic and non-embolic acute ischemic stroke. A quantitative differential diagnosis

International Nuclear Information System (INIS)

Takano, Kentaro; Yamaguchi, Takenori; Minematsu, Kazuo; Sawada, Tohru; Omae, Teruo

1998-01-01

A diagnosis based on the presumed mechanism of stroke onset is useful for management strategies in acute ischemic stroke. Ninety-two patients with embolic (cardiac or artery-to-artery) and 107 with non-embolic (thrombotic or hemodynamic) stroke were diagnosed on strict cerebral angiographic criteria alone. To clearly discriminate between these two groups, the neurological and computed tomographic (CT) findings were then compared. Rapidity of onset, vomiting, urinary incontinence, level of consciousness, cervical bruit, anisocoria, tongue deviation, sensory disturbance, and CT findings (location of hypodense area, findings of brain edema and hemorrhagic transformation) were discriminatory factors between the two groups (p<0.01). According to these 11 items, we prepared a numerical table for quantitative differential diagnosis. A diagnostic accuracy of 98.9% for embolic and 87.9% for non-embolic stroke in internal verification, and 90.0% and 82.9%, respectively, in external verification was observed. The differences in clinical features and CT findings between embolic and non-embolic stroke may reflect the pathophysiological mechanisms of the occlusive process of cerebral artery as well as the extent and severity of ischemia. (author)

Differences in clinical features and computed tomographic findings between embolic and non-embolic acute ischemic stroke. A quantitative differential diagnosis

Energy Technology Data Exchange (ETDEWEB)

Takano, Kentaro; Yamaguchi, Takenori; Minematsu, Kazuo; Sawada, Tohru; Omae, Teruo [National Cardiovascular Center, Suita, Osaka (Japan)

1998-02-01

A diagnosis based on the presumed mechanism of stroke onset is useful for management strategies in acute ischemic stroke. Ninety-two patients with embolic (cardiac or artery-to-artery) and 107 with non-embolic (thrombotic or hemodynamic) stroke were diagnosed on strict cerebral angiographic criteria alone. To clearly discriminate between these two groups, the neurological and computed tomographic (CT) findings were then compared. Rapidity of onset, vomiting, urinary incontinence, level of consciousness, cervical bruit, anisocoria, tongue deviation, sensory disturbance, and CT findings (location of hypodense area, findings of brain edema and hemorrhagic transformation) were discriminatory factors between the two groups (p<0.01). According to these 11 items, we prepared a numerical table for quantitative differential diagnosis. A diagnostic accuracy of 98.9% for embolic and 87.9% for non-embolic stroke in internal verification, and 90.0% and 82.9%, respectively, in external verification was observed. The differences in clinical features and CT findings between embolic and non-embolic stroke may reflect the pathophysiological mechanisms of the occlusive process of cerebral artery as well as the extent and severity of ischemia. (author)

Temporal bone trauma and complications: computed tomography findings

Energy Technology Data Exchange (ETDEWEB)

Costa, Ana Maria Doffemond; Gaiotti, Juliana Oggioni; Couto, Caroline Laurita Batista; Gomes, Natalia Delage; Diniz, Renata Lopes Furletti Caldeira; Motta, Emilia Guerra Pinto Coelho, E-mail: anadoffemond@yahoo.com.br [Hospital Mater Dei, Belo Horizonte, MG (Brazil). Unit of Radiology and Imaging Diagnosis

2013-03-15

Most temporal bone fractures result from high-energy blunt head trauma, and are frequently related to other skull fractures or to polytrauma. Fractures and displacements of ossicular chain in the middle ear represent some of the main complications of temporal bone injury, and hence they will be more deeply approached in the present article. Other types of injuries include labyrinthine fractures, dural fistula, facial nerve paralysis and extension into the carotid canal. Computed tomography plays a fundamental role in the initial evaluation of polytrauma patients, as it can help to identify important structural injuries that may lead to severe complications such as sensorineural hearing loss, conductive hearing loss, dizziness and balance dysfunction, perilymphatic fistulas, facial nerve paralysis, vascular injury and others. (author)

Temporal bone trauma and complications: computed tomography findings

International Nuclear Information System (INIS)

Costa, Ana Maria Doffemond; Gaiotti, Juliana Oggioni; Couto, Caroline Laurita Batista; Gomes, Natalia Delage; Diniz, Renata Lopes Furletti Caldeira; Motta, Emilia Guerra Pinto Coelho

2013-01-01

Most temporal bone fractures result from high-energy blunt head trauma, and are frequently related to other skull fractures or to polytrauma. Fractures and displacements of ossicular chain in the middle ear represent some of the main complications of temporal bone injury, and hence they will be more deeply approached in the present article. Other types of injuries include labyrinthine fractures, dural fistula, facial nerve paralysis and extension into the carotid canal. Computed tomography plays a fundamental role in the initial evaluation of polytrauma patients, as it can help to identify important structural injuries that may lead to severe complications such as sensorineural hearing loss, conductive hearing loss, dizziness and balance dysfunction, perilymphatic fistulas, facial nerve paralysis, vascular injury and others. (author)

Left anterior descending coronary artery myocardial bridging by multislice computed tomography: Correlation with clinical findings

Energy Technology Data Exchange (ETDEWEB)

Jodocy, Daniel; Aglan, Iman [Clinical Department of Radiology II, Innsbruck Medical University, Innsbruck (Austria); Friedrich, Guy [Clinical Department of Cardiology, Innsbruck Medical University, Innsbruck (Austria); Mallouhi, Ammar [Clinical Department of Radiology II, Innsbruck Medical University, Innsbruck (Austria); Pachinger, Otmar [Clinical Department of Radiology II, Innsbruck Medical University, Innsbruck (Austria); Clinical Department of Cardiology, Innsbruck Medical University, Innsbruck (Austria); Jaschke, Werner [Clinical Department of Radiology II, Innsbruck Medical University, Innsbruck (Austria); Feuchtner, Gudrun M. [Clinical Department of Radiology II, Innsbruck Medical University, Innsbruck (Austria)], E-mail: gudrun.feuchtner@i-med.ac.at

2010-01-15

Objective: To assess the relationship between left anterior descending (LAD) coronary artery myocardial bridging detected by 64-slice computed tomography (CT) and clinical findings. Methods: 221 consecutive patients were examined with coronary 64-slice CT angiography. 21 patients with coronary stenosis >50% were excluded. The length, depth, and luminal narrowing of LAD myocardial bridges during systole and diastole were measured. CT findings were compared with the treadmill ECG-stress test, and clinical symptoms. Results: Myocardial bridges of the LAD were found in 23% of patients (51/221) (length, 14.9 {+-} 6.5 mm; depth, 2.6 {+-} 1.6 mm). A significant difference was noted between the LAD luminal diameter before the intramyocardial course and intramyocardially, for both diastole and systole (p < 0.001); with a higher diameter reduction of 27% for end-systole compared to end-diastole with 15% (p = 0.006). Systolic LAD intramyocardial luminal narrowing >50% was found in 3/25 (8%). 30/51 (59%) of bridges were 'deep' (>2 mm myocardial depth), 21/51 (41%) were 'superficial'. The prevalence of a positive ECG-stress tests for the anterior myocardial region was significantly higher in patients with LAD myocardial bridges (34/50; 68%) compared to those without (28/144; 19.4%) (p < 0.001). There was no difference between 'superficial' and 'deep' LAD myocardial bridges in regard to a positive treadmill ECG-stress test. Typical angina was rare with 6%. Conclusion: LAD myocardial bridges are common findings and can possibly explain a positive exercise ECG-stress test for anterior myocardial ischemia. Intramyocardial LAD segments show mild-to-moderate luminal narrowing at rest, which is higher during end-systolic phase.

Dynamic enhanced computed tomographic findings of a perirenal capillary hemangioma

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Lee, Jung Min; Kim, Sang Won; Kim, Hyun Cheol; Yang, Dal Mo; Ryu, Jung Kyu; Lim, Sung Jig [Kyung Hee University Hospital at Gangdong, Seoul (Korea, Republic of)

2016-05-15

Hemangiomas are benign mesenchymal neoplasms that rarely occur in the kidney and perirenal space. Perirenal hemangiomas can mimic the appearance of exophytic renal cell carcinoma or various retroperitoneal tumors. We report a case of perirenal hemangioma detected by dynamic enhanced computed tomography in a 43-year-old female.

Synthetic analog computation in living cells.

Science.gov (United States)

Daniel, Ramiz; Rubens, Jacob R; Sarpeshkar, Rahul; Lu, Timothy K

2013-05-30

A central goal of synthetic biology is to achieve multi-signal integration and processing in living cells for diagnostic, therapeutic and biotechnology applications. Digital logic has been used to build small-scale circuits, but other frameworks may be needed for efficient computation in the resource-limited environments of cells. Here we demonstrate that synthetic analog gene circuits can be engineered to execute sophisticated computational functions in living cells using just three transcription factors. Such synthetic analog gene circuits exploit feedback to implement logarithmically linear sensing, addition, ratiometric and power-law computations. The circuits exhibit Weber's law behaviour as in natural biological systems, operate over a wide dynamic range of up to four orders of magnitude and can be designed to have tunable transfer functions. Our circuits can be composed to implement higher-order functions that are well described by both intricate biochemical models and simple mathematical functions. By exploiting analog building-block functions that are already naturally present in cells, this approach efficiently implements arithmetic operations and complex functions in the logarithmic domain. Such circuits may lead to new applications for synthetic biology and biotechnology that require complex computations with limited parts, need wide-dynamic-range biosensing or would benefit from the fine control of gene expression.

Functionally enigmatic genes: a case study of the brain ignorome.

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Ashutosh K Pandey

Full Text Available What proportion of genes with intense and selective expression in specific tissues, cells, or systems are still almost completely uncharacterized with respect to biological function? In what ways do these functionally enigmatic genes differ from well-studied genes? To address these two questions, we devised a computational approach that defines so-called ignoromes. As proof of principle, we extracted and analyzed a large subset of genes with intense and selective expression in brain. We find that publications associated with this set are highly skewed--the top 5% of genes absorb 70% of the relevant literature. In contrast, approximately 20% of genes have essentially no neuroscience literature. Analysis of the ignorome over the past decade demonstrates that it is stubbornly persistent, and the rapid expansion of the neuroscience literature has not had the expected effect on numbers of these genes. Surprisingly, ignorome genes do not differ from well-studied genes in terms of connectivity in coexpression networks. Nor do they differ with respect to numbers of orthologs, paralogs, or protein domains. The major distinguishing characteristic between these sets of genes is date of discovery, early discovery being associated with greater research momentum--a genomic bandwagon effect. Finally we ask to what extent massive genomic, imaging, and phenotype data sets can be used to provide high-throughput functional annotation for an entire ignorome. In a majority of cases we have been able to extract and add significant information for these neglected genes. In several cases--ELMOD1, TMEM88B, and DZANK1--we have exploited sequence polymorphisms, large phenome data sets, and reverse genetic methods to evaluate the function of ignorome genes.

Functionally enigmatic genes: a case study of the brain ignorome.

Science.gov (United States)

Pandey, Ashutosh K; Lu, Lu; Wang, Xusheng; Homayouni, Ramin; Williams, Robert W

2014-01-01

What proportion of genes with intense and selective expression in specific tissues, cells, or systems are still almost completely uncharacterized with respect to biological function? In what ways do these functionally enigmatic genes differ from well-studied genes? To address these two questions, we devised a computational approach that defines so-called ignoromes. As proof of principle, we extracted and analyzed a large subset of genes with intense and selective expression in brain. We find that publications associated with this set are highly skewed--the top 5% of genes absorb 70% of the relevant literature. In contrast, approximately 20% of genes have essentially no neuroscience literature. Analysis of the ignorome over the past decade demonstrates that it is stubbornly persistent, and the rapid expansion of the neuroscience literature has not had the expected effect on numbers of these genes. Surprisingly, ignorome genes do not differ from well-studied genes in terms of connectivity in coexpression networks. Nor do they differ with respect to numbers of orthologs, paralogs, or protein domains. The major distinguishing characteristic between these sets of genes is date of discovery, early discovery being associated with greater research momentum--a genomic bandwagon effect. Finally we ask to what extent massive genomic, imaging, and phenotype data sets can be used to provide high-throughput functional annotation for an entire ignorome. In a majority of cases we have been able to extract and add significant information for these neglected genes. In several cases--ELMOD1, TMEM88B, and DZANK1--we have exploited sequence polymorphisms, large phenome data sets, and reverse genetic methods to evaluate the function of ignorome genes.

Inferring the gene network underlying the branching of tomato inflorescence.

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Laura Astola

Full Text Available The architecture of tomato inflorescence strongly affects flower production and subsequent crop yield. To understand the genetic activities involved, insight into the underlying network of genes that initiate and control the sympodial growth in the tomato is essential. In this paper, we show how the structure of this network can be derived from available data of the expressions of the involved genes. Our approach starts from employing biological expert knowledge to select the most probable gene candidates behind branching behavior. To find how these genes interact, we develop a stepwise procedure for computational inference of the network structure. Our data consists of expression levels from primary shoot meristems, measured at different developmental stages on three different genotypes of tomato. With the network inferred by our algorithm, we can explain the dynamics corresponding to all three genotypes simultaneously, despite their apparent dissimilarities. We also correctly predict the chronological order of expression peaks for the main hubs in the network. Based on the inferred network, using optimal experimental design criteria, we are able to suggest an informative set of experiments for further investigation of the mechanisms underlying branching behavior.

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

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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.

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

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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.

Multidetector computed tomography has replaced conventional intravenous excretory urography in imaging of the kidneys: A scoping review of multidetector computed tomography findings in renal tuberculosis

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Ntombizakhona B.A. Mthalane

2018-02-01

Full Text Available Background: Tuberculosis (TB is a worldwide infectious disease burden, especially in non-developed countries, with increased morbidity and mortality among human immunodeficiency virus (HIV-infected patients. Extrapulmonary TB is rare and renal TB is one of the commonest manifestations. The end result of renal TB is end-stage renal disease; however, this can be avoided if the diagnosis is made early. The diagnosis of renal TB is challenging because of the non-specific presentation and low sensitivity of clinical tests. Although the sequel of TB infection in the kidney causes varying manifestations depending on the stage of the disease, multidetector computed tomography (MDCT is capable of demonstrating early findings. We performed a 20-year scoping review of MDCT findings in renal TB to promote awareness. Aim: To identify specific MDCT imaging characteristics of renal TB, promote early diagnosis and increase awareness of the typical imaging features. Methods and material: We searched published and unpublished literature from 1997 to 2017 using a combination of search terms on electronic databases. We followed the Joanna Briggs Institute guidelines. Results: A total of 150 articles were identified, of which 145 were found through electronic search engines and 5 were obtained from grey literature. Seventy-nine articles that fulfilled our inclusion criteria were reviewed. These included original research, case reports, literature review, organisational reports and grey literature. Conclusion: Multidetector computed tomography can reproduce images comparable with intravenous excretory urography; together with advantages of being able to better assess the renal parenchyma and surrounding spaces, it is important in suggesting the diagnosis of renal TB and clinicians should consider including MDCT when investigating patients with recurrent urinary tract infection not responding to usual antimicrobial therapy.

Differentiation of benign and malignant lung lesions: Dual-Energy Computed Tomography findings

International Nuclear Information System (INIS)

González-Pérez, Víctor; Arana, Estanislao; Barrios, María; Bartrés, Albert; Cruz, Julia; Montero, Rafael; González, Manuel; Deltoro, Carlos; Martínez-Pérez, Encarnación; De Aguiar-Quevedo, Karol; Arrarás, Miguel

2016-01-01

Purpose: To determine whether parameters generated by Dual-Energy Computed Tomography (DECT) can distinguish malignant from benign lung lesions. Methods: A prospective review of 125 patients with 126 lung lesions (23 benign and 103 malignant) who underwent lung DECT during arterial phase. All lesions were confirmed by tissue sampling. A radiologist semi-automatically contoured lesions and placed regions of interest (ROIs) in paravertebral muscle (PVM) for normalization. Variables related to absorption in Hounsfield units (HU), effective atomic number (Z eff ), iodine concentration (ρ I ) and spectral CT curves were assessed. Receiver operating characteristic (ROC) curves were generated to calculate sensitivity and specificity as predictors of malignancy. Multivariate logistic regression analysis was performed. Results: Reproducibility of measures normalized with PVM was poor. Bivariate analysis showed minimum Z eff and normalized mean Z eff to be statistically significant (p = 0.001), with area under the curve (AUC) values: 0.66 (CI 95% 0.54–0.80) and 0.72 (CI 95%, 0.60–0.84), respectively. Logistic regression models showed no differences between raw and normalized measurements. In both models, minimum HU (OR: 0.9) and size (OR: 0.1) were predictive of benign lesions. Conclusions: A quantitative approach to DECT using raw measurements is simpler than logistic regression models. Normalization to PVM was not clinically reliable due to its poor reproducibility. Further studies are needed to confirm our findings.

Differentiation of benign and malignant lung lesions: Dual-Energy Computed Tomography findings.

Science.gov (United States)

González-Pérez, Víctor; Arana, Estanislao; Barrios, María; Bartrés, Albert; Cruz, Julia; Montero, Rafael; González, Manuel; Deltoro, Carlos; Martínez-Pérez, Encarnación; De Aguiar-Quevedo, Karol; Arrarás, Miguel

2016-10-01

To determine whether parameters generated by Dual-Energy Computed Tomography (DECT) can distinguish malignant from benign lung lesions. A prospective review of 125 patients with 126 lung lesions (23 benign and 103 malignant) who underwent lung DECT during arterial phase. All lesions were confirmed by tissue sampling. A radiologist semi-automatically contoured lesions and placed regions of interest (ROIs) in paravertebral muscle (PVM) for normalization. Variables related to absorption in Hounsfield units (HU), effective atomic number (Zeff), iodine concentration (ρI) and spectral CT curves were assessed. Receiver operating characteristic (ROC) curves were generated to calculate sensitivity and specificity as predictors of malignancy. Multivariate logistic regression analysis was performed. Reproducibility of measures normalized with PVM was poor. Bivariate analysis showed minimum Zeff and normalized mean Zeff to be statistically significant (p=0.001), with area under the curve (AUC) values: 0.66 (CI 95% 0.54-0.80) and 0.72 (CI 95%, 0.60-0.84), respectively. Logistic regression models showed no differences between raw and normalized measurements. In both models, minimum HU (OR: 0.9) and size (OR: 0.1) were predictive of benign lesions. A quantitative approach to DECT using raw measurements is simpler than logistic regression models. Normalization to PVM was not clinically reliable due to its poor reproducibility. Further studies are needed to confirm our findings. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Computed tomographic findings of intramural hematoma

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Park, Chan Hoon; Kim, Hong; Woo, Seong Ku; Suh, Soo Jhi [Keimyung University School of Medicine, Taegu (Korea, Republic of)

1990-10-15

The CT findings of eleven patients with intramural hematoma of the gastrointestinal tract are presented. The most frequent site of intramural hematoma was duodenum(7/11). followed jejunum(2/11), ascending colon(2/11), stomach(1/11), and rectum(1/11). Blunt abdominal trauma was the prime etiologic factor(7/11). others included pancreatitis, iatrogenic and unknown. Intramural hematoma showed three patterns of CT characteristics: intramural mass(8/11), thickened bowel wall(1/11), and both(2/11). There were variable attenuation value of 10 cases of intramural mass; homogenous hyperdensity or hypodensity in each 3 cases, inhomogeneous or mixed density in 4 cases. Also there were peripheral lucent halo(1/10), pseudocapsule or dense rim(5/10), crescentic hyperdensity(2/10) and central hyperdense area(4/10). Associated CT features were hemoperitoneum(4), mesenteric infiltration, fatty liver, pancreatic confusion, and chronic pancreatitis. CT is the most accurate method in establishing the diagnosis or intramural hematoma, evaluating the extent of bleeding and its effect on adjacent organs, demonstrating regression after treatment, and detecting associating injury.

Computed tomographic findings of intramural hematoma

International Nuclear Information System (INIS)

Park, Chan Hoon; Kim, Hong; Woo, Seong Ku; Suh, Soo Jhi

1990-01-01

The CT findings of eleven patients with intramural hematoma of the gastrointestinal tract are presented. The most frequent site of intramural hematoma was duodenum(7/11). followed jejunum(2/11), ascending colon(2/11), stomach(1/11), and rectum(1/11). Blunt abdominal trauma was the prime etiologic factor(7/11). others included pancreatitis, iatrogenic and unknown. Intramural hematoma showed three patterns of CT characteristics: intramural mass(8/11), thickened bowel wall(1/11), and both(2/11). There were variable attenuation value of 10 cases of intramural mass; homogenous hyperdensity or hypodensity in each 3 cases, inhomogeneous or mixed density in 4 cases. Also there were peripheral lucent halo(1/10), pseudocapsule or dense rim(5/10), crescentic hyperdensity(2/10) and central hyperdense area(4/10). Associated CT features were hemoperitoneum(4), mesenteric infiltration, fatty liver, pancreatic confusion, and chronic pancreatitis. CT is the most accurate method in establishing the diagnosis or intramural hematoma, evaluating the extent of bleeding and its effect on adjacent organs, demonstrating regression after treatment, and detecting associating injury

Comparison of the multidetector-row computed tomography findings of IgG4-related sclerosing cholangitis and extrahepatic cholangiocarcinoma

International Nuclear Information System (INIS)

Yata, M.; Suzuki, K.; Furuhashi, N.; Kawakami, K.; Kawai, Y.; Naganawa, S.

2016-01-01

Aim: To compare the multidetector-row computed tomography (MDCT) findings of IgG4-related sclerosing cholangitis (IgG4-SC) and extrahepatic cholangiocarcinoma (EH-CCA). Materials and methods: Two radiologists who had no knowledge of the patients' clinical information retrospectively evaluated the CT findings of patients with IgG4-SC (n=33) and EH-CCA (n=39) on a consensus basis. Another radiologist measured the biliary lesions. IgG4-SC was diagnosed using the Japan Biliary Association criteria (2012) or the Mayo Clinic's HISORt criteria. EH-CCA was diagnosed based on surgical findings. Results: Compared with EH-CCA, IgG4-SC exhibited the following findings significantly more frequently: (a) wall thickening alone, (b) concentric wall thickening, (c) smooth inner margins, (d) homogeneous attenuation in the arterial phase, (e) a lesion involving the intrapancreatic bile duct, (f) smooth outer margins, (g) fully visible lumen, (h) a funnel-shaped proximal bile duct, (i) skip lesions, and (j) abnormal pancreatic findings. Conversely, (k) dual-layered attenuation in all phases was significantly more common in EH-CCA. The specificity values of parameters (e–k) were >80%. Regarding dimensions, (l) the biliary lesions were longer in IgG4-SC than in EH-CCA. (m) The diameters of the dilated proximal common bile duct and (n) the dilated proximal intrahepatic bile duct were smaller in IgG4-SC than in EH-CCA. Conclusion: A number of CT findings are useful for differentiating between IgG4-SC and EH-CCA. CT findings (e–k) are particularly useful for this purpose. - Highlights: • Some CT findings are useful for differentiating between IgG4-SC and EH-CCA. • Homogeneous attenuation in all phases was more common in IgG4-SC than in EH-CCA. • Abnormal pancreatic findings showed high sensitivity and specificity values. • Dual-layered attenuation in all phases was more common in EH-CCA than in IgG4-SC.

A review for detecting gene-gene interactions using machine learning methods in genetic epidemiology.

Science.gov (United States)

Koo, Ching Lee; Liew, Mei Jing; Mohamad, Mohd Saberi; Salleh, Abdul Hakim Mohamed

2013-01-01

Recently, the greatest statistical computational challenge in genetic epidemiology is to identify and characterize the genes that interact with other genes and environment factors that bring the effect on complex multifactorial disease. These gene-gene interactions are also denoted as epitasis in which this phenomenon cannot be solved by traditional statistical method due to the high dimensionality of the data and the occurrence of multiple polymorphism. Hence, there are several machine learning methods to solve such problems by identifying such susceptibility gene which are neural networks (NNs), support vector machine (SVM), and random forests (RFs) in such common and multifactorial disease. This paper gives an overview on machine learning methods, describing the methodology of each machine learning methods and its application in detecting gene-gene and gene-environment interactions. Lastly, this paper discussed each machine learning method and presents the strengths and weaknesses of each machine learning method in detecting gene-gene interactions in complex human disease.

A Review for Detecting Gene-Gene Interactions Using Machine Learning Methods in Genetic Epidemiology

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Ching Lee Koo

2013-01-01

Full Text Available Recently, the greatest statistical computational challenge in genetic epidemiology is to identify and characterize the genes that interact with other genes and environment factors that bring the effect on complex multifactorial disease. These gene-gene interactions are also denoted as epitasis in which this phenomenon cannot be solved by traditional statistical method due to the high dimensionality of the data and the occurrence of multiple polymorphism. Hence, there are several machine learning methods to solve such problems by identifying such susceptibility gene which are neural networks (NNs, support vector machine (SVM, and random forests (RFs in such common and multifactorial disease. This paper gives an overview on machine learning methods, describing the methodology of each machine learning methods and its application in detecting gene-gene and gene-environment interactions. Lastly, this paper discussed each machine learning method and presents the strengths and weaknesses of each machine learning method in detecting gene-gene interactions in complex human disease.

High-resolution computed tomography findings from adult patients with Influenza A (H1N1) virus-associated pneumonia

International Nuclear Information System (INIS)

Marchiori, Edson; Zanetti, Glaucia; Hochhegger, Bruno; Rodrigues, Rosana Souza; Fontes, Cristina Asvolinsque Pantaleao; Nobre, Luiz Felipe; Dias Mancano, Alexandre; Meirelles, Gustavo; Irion, Klaus Loureiro

2010-01-01

Objective: The aim of this study was to assess the high-resolution computed tomography (HRCT) findings at presentation in patients diagnosed with Influenza A (H1N1) virus-associated pneumonia. Materials and methods: We reviewed the HRCT findings from 20 patients diagnosed with Influenza A (H1N1) and compared their HRCT scans with chest radiographs, obtained on the same day. The imaging studies were obtained 4-9 days after the onset of symptoms. The patients included 11 men and 9 women (ages 24-62 years; mean 42.7 years). All patients had a body temperature greater than 100.4 deg. F (>38 deg. C), tachypnea, and cough. Other common symptoms included diarrhea (60%) and sore throat (30%). The radiographs and HRCT scans were reviewed independently by two observers who reached a consensus decision. Results: The predominant HRCT findings consisted of bilateral ground-glass opacities (n = 12), bilateral areas of consolidation (n = 2), or a mixed bilateral pattern of ground-glass opacities and areas of consolidation (n = 6). The abnormalities were bilateral in all of the 20 patients, had a predominantly sub-pleural distribution in 13 patients, and had a random distribution in the remaining 7 patients. The predominant radiographic findings were consolidations. Normal radiographs were found in 4 out of the 20 patients. Conclusion: HRCT may reveal parenchymal abnormalities in patients with Influenza A (H1N1) infection who have normal findings on radiographs. The predominant HRCT findings were bilateral, peripheral, ground-glass opacities and/or bilateral areas of consolidation. The patients who presented consolidations had more severe clinical course.

High-resolution computed tomography findings from adult patients with Influenza A (H1N1) virus-associated pneumonia

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Marchiori, Edson [Fluminense Federal University, Rio de Janeiro (Brazil); Federal University of Rio de Janeiro, Rio de Janeiro (Brazil)], E-mail: edmarchiori@gmail.com; Zanetti, Glaucia [Federal University of Rio de Janeiro, Rio de Janeiro (Brazil)], E-mail: glauciazanetti@gmail.com; Hochhegger, Bruno [Federal University of Rio de Janeiro, Rio de Janeiro (Brazil)], E-mail: brunohochhegger@gmail.com; Rodrigues, Rosana Souza [Federal University of Rio de Janeiro, Rio de Janeiro (Brazil); D' OR Institute for Research and Education, Rio de Janeiro (Brazil)], E-mail: rosana.souzarodrigues@gmail.com; Fontes, Cristina Asvolinsque Pantaleao [Fluminense Federal University, Rio de Janeiro (Brazil)], E-mail: cristinasvolinsque@gmail.com; Nobre, Luiz Felipe [Santa Catarina Federal University, Florianopolis (Brazil)], E-mail: luizfelipenobresc@gmail.com; Dias Mancano, Alexandre [Anchieta Hospital, Taguatinga, DF (Brazil)], E-mail: alex.manzano1@gmail.com; Meirelles, Gustavo [Sao Paulo Federal University, Sao Paulo (Brazil)], E-mail: gmeirelles@gmail.com; Irion, Klaus Loureiro [Liverpool Heart and Chest Hospital NHS Trust, Liverpool (United Kingdom); Royal Liverpool and Broadgreen University Hospital NHS, Liverpool (United Kingdom)], E-mail: klaus.irion@btinternet.com

2010-04-15

Objective: The aim of this study was to assess the high-resolution computed tomography (HRCT) findings at presentation in patients diagnosed with Influenza A (H1N1) virus-associated pneumonia. Materials and methods: We reviewed the HRCT findings from 20 patients diagnosed with Influenza A (H1N1) and compared their HRCT scans with chest radiographs, obtained on the same day. The imaging studies were obtained 4-9 days after the onset of symptoms. The patients included 11 men and 9 women (ages 24-62 years; mean 42.7 years). All patients had a body temperature greater than 100.4 deg. F (>38 deg. C), tachypnea, and cough. Other common symptoms included diarrhea (60%) and sore throat (30%). The radiographs and HRCT scans were reviewed independently by two observers who reached a consensus decision. Results: The predominant HRCT findings consisted of bilateral ground-glass opacities (n = 12), bilateral areas of consolidation (n = 2), or a mixed bilateral pattern of ground-glass opacities and areas of consolidation (n = 6). The abnormalities were bilateral in all of the 20 patients, had a predominantly sub-pleural distribution in 13 patients, and had a random distribution in the remaining 7 patients. The predominant radiographic findings were consolidations. Normal radiographs were found in 4 out of the 20 patients. Conclusion: HRCT may reveal parenchymal abnormalities in patients with Influenza A (H1N1) infection who have normal findings on radiographs. The predominant HRCT findings were bilateral, peripheral, ground-glass opacities and/or bilateral areas of consolidation. The patients who presented consolidations had more severe clinical course.

Echocardiographic and non-gated computed tomographic findings of intrapericardial tumor and mediastinal tumor adjacent to the heart

International Nuclear Information System (INIS)

Ueda, Minoru; Yamada, Nobuyuki; Saito, Daiji; Haraoka, Shoichi; Tanetani, Setsuro.

1981-01-01

Echocardiographic and computed tomographic findings of a case of intrapericardial tumor are reported, and two other cases of mediastinal tumor are presented in a discussion of the differential diagnosis of intrapericardial from mediastinal tumors. Case report: A 7-year-old male complained of cough and dyspnea. Cardiomegaly had been pointed out at a mass X-ray examination about a month prior to the admission. Two-dimensional echocardiography revealed a massive anterior pericardial effusion and a fist-sized tumor with cystic structure. The tumor pushed the heart backward at the level of the aortic root. Non-gated computed tomography of the chest disclosed the size and location of the tumor, but failed to clarify the internal structure. The patient underwent successful removal of a tumor, 12 x 10 x 8 cm in size and 350 g in weight, originating from the left atrial wall. Histologically, the tumor was a fibrosarcomatous mesothelioma. Usually, an intrapericardial tumor is easily suspected by echocardiography by the presence of pericardial effusion, although there have been a few reports of intrapericardial tumors without pericardial effusion. Echocardiographic diagnosis of the intrapericardial tumor is difficult in such cases. Identification of the pericardium is necessary to diagnose whether a tumor is intra- or extrapericardial. This identification, however, is not always easy by echocardiography when the ultrasonic beams become tangent to the pericardium. The pericardium between the tumor and the heart could not be identified by echocardiography in our two cases of mediastinal tumor. Computed tomography is helpful in diagnosing the size and location of a mediastinal tumor. (author)

Functioning Mediastinal Paraganglioma Associated with a Germline Mutation of von Hippel-Lindau Gene

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Thibault Bahougne

2018-05-01

Full Text Available We report the case of a 21-year old woman presenting with high blood pressure and raised normetanephrine levels. Indium-111-pentetreotide single photon-emission computed tomography with computed tomography (SPECT/CT and 2-deoxy-2-[fluorine-18]fluoro-d-glucose (FDG positron emission tomography/computed tomography (PET/CT imaging showing isolated tracer-uptake by a 2 cm tumor close to the costovertebral angle of the third thoracic vertebra. Thoracic surgery led to normalization of normetanephrine levels. Histological findings were consistent with the presence of a paraganglioma. Mutations in SDHA, SDHB, SDHC, SDHD, RET, SDHAF2, TMEM127, MAX, NF1, FH, MDH2, and EPAS1 were absent, but a heterozygous missense mutation, c.311G > T, was found in exon 1 of the von Hippel-Lindau gene, VHL, resulting in a glycine to valine substitution in the VHL protein at position 104, p.Gly104Val. This same mutation was found in both the mother and the 17-year old sister in whom a small retinal hemangioblastoma was also found. We diagnose an unusual functional mediastinal paraganglioma in this young patient with a germline VHL gene mutation, a mutation previously described as inducing polycythemia and/or pheochromocytoma but not paraganglioma or retinal hemangioblastoma.

Using computers to enable self-management of aphasia therapy exercises for word finding: the patient and carer perspective.

Science.gov (United States)

Palmer, Rebecca; Enderby, Pam; Paterson, Gail

2013-01-01

Speech and language therapy (SLT) for aphasia can be difficult to access in the later stages of stroke recovery, despite evidence of continued improvement with sufficient therapeutic intensity. Computerized aphasia therapy has been reported to be useful for independent language practice, providing new opportunities for continued rehabilitation. The success of this option depends on its acceptability to patients and carers. To investigate factors that affect the acceptability of independent home computerized aphasia therapy practice. An acceptability study of computerized therapy was carried out alongside a pilot randomized controlled trial of computer aphasia therapy versus usual care for people more than 6 months post-stroke. Following language assessment and computer exercise prescription by a speech and language therapist, participants practised three times a week for 5 months at home with monthly volunteer support. Semi-structured interviews were conducted with 14 participants who received the intervention and ten carers (n = 24). Questions from a topic guide were presented and answered using picture, gesture and written support. Interviews were audio recorded, transcribed verbatim and analysed thematically. Three research SLTs identified and cross-checked themes and subthemes emerging from the data. The key themes that emerged were benefits and disadvantages of computerized aphasia therapy, need for help and support, and comparisons with face-to-face therapy. The independence, flexibility and repetition afforded by the computer was viewed as beneficial and the personalized exercises motivated participants to practise. Participants and carers perceived improvements in word-finding and confidence-talking. Computer practice could cause fatigue and interference with other commitments. Support from carers or volunteers for motivation and technical assistance was seen as important. Although some participants preferred face-to-face therapy, using a computer for

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

Pulmonary malaria: high-resolution computed tomography findings - a case report

International Nuclear Information System (INIS)

Rodrigues, Rosana; Souza, Daniel Andrade Tinoco de; Marchiori, Edson

2004-01-01

We report the case of a 38-year-old man with pulmonary malaria. High-resolution computed tomography showed thickening of the peribronchovascular interstitium and interlobular septa, areas of consolidation and ground glass attenuation and bilateral pleural effusion suggesting pulmonary edema. The patient recovered well after receiving specific treatment and was discharged after 11 days of hospitalization. (author)

Middle east respiratory syndrome-corona virus infection: A case report of sieral computed tomographic findings in a young male patient

Energy Technology Data Exchange (ETDEWEB)

Choi, Won Jin; Lee, Ki Nam; Kang, Eun Ju; Lee, Hyuck [Dong A University Hospital, Busan (Korea, Republic of)

2016-02-15

Radiologic findings of Middle East respiratory syndrome (MERS), a novel coronavirus infection, have been rarely reported. We report a 30-year-old male presented with fever, abdominal pain, and diarrhea, who was diagnosed with MERS. A chest computed tomographic scan revealed rapidly developed multifocal nodular consolidations with ground-glass opacity halo and mixed consolidation, mainly in the dependent and peripheral areas. After treatment, follow-up imaging showed that these abnormalities markedly decreased but fibrotic changes developed.

MAGMA: generalized gene-set analysis of GWAS data.

Science.gov (United States)

de Leeuw, Christiaan A; Mooij, Joris M; Heskes, Tom; Posthuma, Danielle

2015-04-01

By aggregating data for complex traits in a biologically meaningful way, gene and gene-set analysis constitute a valuable addition to single-marker analysis. However, although various methods for gene and gene-set analysis currently exist, they generally suffer from a number of issues. Statistical power for most methods is strongly affected by linkage disequilibrium between markers, multi-marker associations are often hard to detect, and the reliance on permutation to compute p-values tends to make the analysis computationally very expensive. To address these issues we have developed MAGMA, a novel tool for gene and gene-set analysis. The gene analysis is based on a multiple regression model, to provide better statistical performance. The gene-set analysis is built as a separate layer around the gene analysis for additional flexibility. This gene-set analysis also uses a regression structure to allow generalization to analysis of continuous properties of genes and simultaneous analysis of multiple gene sets and other gene properties. Simulations and an analysis of Crohn's Disease data are used to evaluate the performance of MAGMA and to compare it to a number of other gene and gene-set analysis tools. The results show that MAGMA has significantly more power than other tools for both the gene and the gene-set analysis, identifying more genes and gene sets associated with Crohn's Disease while maintaining a correct type 1 error rate. Moreover, the MAGMA analysis of the Crohn's Disease data was found to be considerably faster as well.

Lipoid pneumonia: computed tomography findings - a case report

International Nuclear Information System (INIS)

Farias, Janos; Martins, Erick Malheiro Leoncio; Pozes, Aline Serfaty; Marchiori, Edson

2004-01-01

The authors report a case of lipoid pneumonia in an 80 year old man with chronic constipation in regular use of mineral oil as a laxative. According to his family, he experienced coughing episodes when he took his medication. He also presented dyspnoea at rest and diminished consciousness levels. Chest radiographs showed a consolidation area in the posterior segment of right upper lobe, which did not change on successive exams. High resolution computed tomography demonstrated low-density consolidation with negative Hounsfield units (-29 to -83 UH) and ground-glass opacities in the right upper lobe and inferior lobes. These opacities predominated in the posterior regions of the lungs. The diagnosis was confirmed by the presence of oil material on bronchoalveolar washing. The patient was advised to discontinue the ingestion of mineral oil and did not return for follow-up. (author)

Genes2WordCloud: a quick way to identify biological themes from gene lists and free text.

Science.gov (United States)

Baroukh, Caroline; Jenkins, Sherry L; Dannenfelser, Ruth; Ma'ayan, Avi

2011-10-13

Word-clouds recently emerged on the web as a solution for quickly summarizing text by maximizing the display of most relevant terms about a specific topic in the minimum amount of space. As biologists are faced with the daunting amount of new research data commonly presented in textual formats, word-clouds can be used to summarize and represent biological and/or biomedical content for various applications. Genes2WordCloud is a web application that enables users to quickly identify biological themes from gene lists and research relevant text by constructing and displaying word-clouds. It provides users with several different options and ideas for the sources that can be used to generate a word-cloud. Different options for rendering and coloring the word-clouds give users the flexibility to quickly generate customized word-clouds of their choice. Genes2WordCloud is a word-cloud generator and a word-cloud viewer that is based on WordCram implemented using Java, Processing, AJAX, mySQL, and PHP. Text is fetched from several sources and then processed to extract the most relevant terms with their computed weights based on word frequencies. Genes2WordCloud is freely available for use online; it is open source software and is available for installation on any web-site along with supporting documentation at http://www.maayanlab.net/G2W. Genes2WordCloud provides a useful way to summarize and visualize large amounts of textual biological data or to find biological themes from several different sources. The open source availability of the software enables users to implement customized word-clouds on their own web-sites and desktop applications.

Natural computation meta-heuristics for the in silico optimization of microbial strains

DEFF Research Database (Denmark)

Rocha, Miguel; Maia, Paulo; Mendes, Rui

2008-01-01

natural evolution. Results: This work reports on improved EAs, as well as novel Simulated Annealing ( SA) algorithms to address the task of in silico metabolic engineering. Both approaches use a variable size set-based representation, thereby allowing the automatic finding of the best number of gene...... deletions necessary for achieving a given productivity goal. The work presents extensive computational experiments, involving four case studies that consider the production of succinic and lactic acid as the targets, by using S. cerevisiae and E. coli as model organisms. The proposed algorithms are able...

Halo sign nodules in angio invasive pulmonary aspergillosis: correlation of high-resolution computed tomography findings with anatomopathology; Nodulos com sinal do halo na aspergilose pulmonar angioinvasiva: correlacao da tomografia computadorizada de alta resolucao com a anatomopatologia

Energy Technology Data Exchange (ETDEWEB)

Marchiori, Edson [Universidade Federal Fluminense, Niteroi, RJ (Brazil). Dept. de Radiologia; Valiante, Paulo Marcos [Universidade Federal, Rio de Janeiro, RJ (Brazil). Dept. de Patologia; Souza Junior, Arthur Soares [Faculdade de Medicina de Sao Jose do Rio Preto (FAMERP), SP (Brazil). Disciplina de Radiologia

2002-08-01

The aim of this study was to correlate the early findings observed on high-resolution computed tomography with anatomopathology results of patients with angio invasive aspergillosis. The authors studied two patients with leukemia. The nodules seen on high-resolution computed tomography corresponded to areas of hemorrhagic infarction, necrotic coagulation and fungal hyphae infiltration whereas ground glass halo corresponded to intra alveolar hemorrhage. Nodules with halo sign were closely correlated with anatomopathology findings. We concluded that the anatomopathology findings can clearly explain the image features of the lesions observed on high-resolution computed tomography. (author)

Correctness of multi-detector-row computed tomography for diagnosing mechanical prosthetic heart valve disorders using operative findings as a gold standard

Energy Technology Data Exchange (ETDEWEB)

Tsai, I.Chen [Taichung Veterans General Hospital, Department of Radiology, Taichung (China); Institute of Clinical Medicine and Faculty of Medicine, National Yang-Ming University, Taipei (China); Lin, Yung-Kai; Chang, Yen; Wang, Chung-Chi; Hsieh, Shih-Rong; Wei, Hao-Ji; Tsai, Hung-Wen [Taichung Veterans General Hospital, Section of Cardiovascular Surgery, Cardiovascular Center, Taichung (China); Fu, Yun-Ching; Jan, Sheng-Ling [Institute of Clinical Medicine and Faculty of Medicine, National Yang-Ming University, Taipei (China); Taichung Veterans General Hospital, Section of Pediatric Cardiology, Department of Pediatrics, Taichung (China); Wang, Kuo-Yang [Taichung Veterans General Hospital, Section of General Cardiology, Cardiovascular Center, Taichung (China); Chung-Shan Medical University, Department of Medicine, Taichung (China); Chen, Min-Chi; Chen, Clayton Chi-Chang [Taichung Veterans General Hospital, Department of Radiology, Taichung (China); Central Taiwan University of Science and Technology, Department of Radiological Technology, Taichung (China)

2009-04-15

The purpose was to compare the findings of multi-detector computed tomography (MDCT) in prosthetic valve disorders using the operative findings as a gold standard. In a 3-year period, we prospectively enrolled 25 patients with 31 prosthetic heart valves. MDCT and transthoracic echocardiography (TTE) were done to evaluate pannus formation, prosthetic valve dysfunction, suture loosening (paravalvular leak) and pseudoaneurysm formation. Patients indicated for surgery received an operation within 1 week. The MDCT findings were compared with the operative findings. One patient with a Bjoerk-Shiley valve could not be evaluated by MDCT due to a severe beam-hardening artifact; thus, the exclusion rate for MDCT was 3.2% (1/31). Prosthetic valve disorders were suspected in 12 patients by either MDCT or TTE. Six patients received an operation that included three redo aortic valve replacements, two redo mitral replacements and one Amplatzer ductal occluder occlusion of a mitral paravalvular leak. The concordance of MDCT for diagnosing and localizing prosthetic valve disorders and the surgical findings was 100%. Except for images impaired by severe beam-hardening artifacts, MDCT provides excellent delineation of prosthetic valve disorders. (orig.)

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.

Differentiation of benign and malignant lung lesions: Dual-Energy Computed Tomography findings

Energy Technology Data Exchange (ETDEWEB)

González-Pérez, Víctor [Dept Radiophysics, Foundation IVO, Valencia (Spain); Arana, Estanislao, E-mail: aranae@uv.es [Dept Radiology, Foundation IVO, Valencia (Spain); Barrios, María [Dept Radiology, Foundation IVO, Valencia (Spain); Bartrés, Albert [Dept Radiophysics, Foundation IVO, Valencia (Spain); Cruz, Julia [Dept Pathology, Foundation IVO, Valencia (Spain); Montero, Rafael [GE Healthcare Diagnostic Imaging, Iberia (Spain); González, Manuel; Deltoro, Carlos [Dept Radiology, Foundation IVO, Valencia (Spain); Martínez-Pérez, Encarnación [Dept Pneumology, Foundation IVO, Valencia (Spain); De Aguiar-Quevedo, Karol; Arrarás, Miguel [Dept Thoracic Surgery, Foundation IVO, Valencia (Spain)

2016-10-15

Purpose: To determine whether parameters generated by Dual-Energy Computed Tomography (DECT) can distinguish malignant from benign lung lesions. Methods: A prospective review of 125 patients with 126 lung lesions (23 benign and 103 malignant) who underwent lung DECT during arterial phase. All lesions were confirmed by tissue sampling. A radiologist semi-automatically contoured lesions and placed regions of interest (ROIs) in paravertebral muscle (PVM) for normalization. Variables related to absorption in Hounsfield units (HU), effective atomic number (Z{sub eff}), iodine concentration (ρ{sub I}) and spectral CT curves were assessed. Receiver operating characteristic (ROC) curves were generated to calculate sensitivity and specificity as predictors of malignancy. Multivariate logistic regression analysis was performed. Results: Reproducibility of measures normalized with PVM was poor. Bivariate analysis showed minimum Z{sub eff} and normalized mean Z{sub eff} to be statistically significant (p = 0.001), with area under the curve (AUC) values: 0.66 (CI 95% 0.54–0.80) and 0.72 (CI 95%, 0.60–0.84), respectively. Logistic regression models showed no differences between raw and normalized measurements. In both models, minimum HU (OR: 0.9) and size (OR: 0.1) were predictive of benign lesions. Conclusions: A quantitative approach to DECT using raw measurements is simpler than logistic regression models. Normalization to PVM was not clinically reliable due to its poor reproducibility. Further studies are needed to confirm our findings.

Perirolandic hypoperfusion on single-photon emission computed tomography in term infants with perinatal asphyxia: comparison with MRI and clinical findings

Energy Technology Data Exchange (ETDEWEB)

Yoon, C.S.; Kim, D.I.; Lee, S.; Yoon, P.H.; Jeon, T.J.; Lee, J.D. [Department of Diagnostic Radiology, Yonsei University College of Medicine, Seoul (Korea); Ryu, Y.H. [Department of Diagnostic Radiology, Yonsei University College of Medicine, Seoul (Korea); Department of Nuclear Medicine, Ghil Medical Center, Gachon Medical School, Inchon (Korea); Park, C.I. [Department of Rehabilitation Medicine, Yonsei University College of Medicine, Seoul (Korea)

2000-12-01

We describe the findings on single-photon emission computed tomography (SPECT) in patients with perinatal asphyxia at term, with perirolandic cortico-subcortical changes on MRI, and to correlate them with clinical features. SPECT of 7 patients was obtained after injection of 185-370 MBq of Tc-99m-ECD (ethyl cysteinate dimer). The patients had spastic quadriplegia (7/7) with perinatal asphyxia (6/7) at term (7/7). The results were correlated with the MRI findings. Hypoperfusion of the perirolandic cortex was clearly seen on SPECT in all patients, even in two with subtle changes on MRI. SPECT demonstrated a more extensive area of involvement than MRI, notably in the cerebellum (in 4), the thalamus (in 7) and basal ganglia (in 5), where MRI failed to show any abnormalities. (orig.)

Perirolandic hypoperfusion on single-photon emission computed tomography in term infants with perinatal asphyxia: comparison with MRI and clinical findings

International Nuclear Information System (INIS)

Yoon, C.S.; Kim, D.I.; Lee, S.; Yoon, P.H.; Jeon, T.J.; Lee, J.D.; Ryu, Y.H.; Park, C.I.

2000-01-01

We describe the findings on single-photon emission computed tomography (SPECT) in patients with perinatal asphyxia at term, with perirolandic cortico-subcortical changes on MRI, and to correlate them with clinical features. SPECT of 7 patients was obtained after injection of 185-370 MBq of Tc-99m-ECD (ethyl cysteinate dimer). The patients had spastic quadriplegia (7/7) with perinatal asphyxia (6/7) at term (7/7). The results were correlated with the MRI findings. Hypoperfusion of the perirolandic cortex was clearly seen on SPECT in all patients, even in two with subtle changes on MRI. SPECT demonstrated a more extensive area of involvement than MRI, notably in the cerebellum (in 4), the thalamus (in 7) and basal ganglia (in 5), where MRI failed to show any abnormalities. (orig.)

Promoter Analysis Reveals Globally Differential Regulation of Human Long Non-Coding RNA and Protein-Coding Genes

KAUST Repository

Alam, Tanvir

2014-10-02

Transcriptional regulation of protein-coding genes is increasingly well-understood on a global scale, yet no comparable information exists for long non-coding RNA (lncRNA) genes, which were recently recognized to be as numerous as protein-coding genes in mammalian genomes. We performed a genome-wide comparative analysis of the promoters of human lncRNA and protein-coding genes, finding global differences in specific genetic and epigenetic features relevant to transcriptional regulation. These two groups of genes are hence subject to separate transcriptional regulatory programs, including distinct transcription factor (TF) proteins that significantly favor lncRNA, rather than coding-gene, promoters. We report a specific signature of promoter-proximal transcriptional regulation of lncRNA genes, including several distinct transcription factor binding sites (TFBS). Experimental DNase I hypersensitive site profiles are consistent with active configurations of these lncRNA TFBS sets in diverse human cell types. TFBS ChIP-seq datasets confirm the binding events that we predicted using computational approaches for a subset of factors. For several TFs known to be directly regulated by lncRNAs, we find that their putative TFBSs are enriched at lncRNA promoters, suggesting that the TFs and the lncRNAs may participate in a bidirectional feedback loop regulatory network. Accordingly, cells may be able to modulate lncRNA expression levels independently of mRNA levels via distinct regulatory pathways. Our results also raise the possibility that, given the historical reliance on protein-coding gene catalogs to define the chromatin states of active promoters, a revision of these chromatin signature profiles to incorporate expressed lncRNA genes is warranted in the future.

Value of multislice computed tomography angiography of the thorax in preparation for catheter ablation for the treatment of atrial fibrillation: The impact of unexpected cardiac and extracardiac findings on patient care

Energy Technology Data Exchange (ETDEWEB)

Wissner, Erik; Wellnitz, Clinton V.; Srivathsan, Komandoor; Scott, Luis R. [Mayo Clinic Arizona - Mayo Clinic Hospital, Cardiovascular Diseases, 5777 East Mayo Boulevard, Phoenix, AZ 85054 (United States); Altemose, Gregory T. [Mayo Clinic Arizona - Mayo Clinic Hospital, Cardiovascular Diseases, 5777 East Mayo Boulevard, Phoenix, AZ 85054 (United States)], E-mail: altemose.gregory@mayo.edu

2009-11-15

Objective: In patients referred for catheter ablation for the treatment of atrial fibrillation, multislice computed tomography angiography of the thorax is routinely performed to assess pulmonary vein anatomy. We sought to investigate the incidence of unexpected cardiac and extracardiac findings in this select patient population and to establish how these findings influence subsequent patient care. Methods: Ninety-five patients (mean age 62 {+-} 10 years, 35% female) referred to our institution for ablation therapy for atrial fibrillation between July 2003 and October 2007 underwent multislice computed tomography angiography of the thorax. Radiologists interpreted all images. Need for additional testing, consultation and eventual diagnosis were assessed by electronic record review. Results: A total of 83 (5 cardiac, 78 extracardiac) unexpected findings were observed in 50/95 (53%) of patients. The findings prompted 23 additional tests (5 cardiac, 18 noncardiac) in 15/95 (16%) of patients and 8 subsequent referrals in 7/95 (7%) patients. In 6 patients the findings significantly altered future patient care and resulted in postponement of ablation therapy in 4 patients. In 2 patients, extracardiac findings (pulmonary emboli and adenocarcinoma of the lung) were of potentially life-saving consequence. Conclusions: In patients undergoing multislice computed tomography angiography of the thorax in anticipation of planned catheter ablation therapy for the treatment of atrial fibrillation, unexpected findings are common and of potentially significant value. In comparison, there is a higher prevalence of unexpected extracardiac, rather than cardiac findings. Further investigation of these findings may lead to postponement of ablation therapy, but may also be of potentially lifesaving consequence.

Value of multislice computed tomography angiography of the thorax in preparation for catheter ablation for the treatment of atrial fibrillation: The impact of unexpected cardiac and extracardiac findings on patient care

International Nuclear Information System (INIS)

Wissner, Erik; Wellnitz, Clinton V.; Srivathsan, Komandoor; Scott, Luis R.; Altemose, Gregory T.

2009-01-01

Objective: In patients referred for catheter ablation for the treatment of atrial fibrillation, multislice computed tomography angiography of the thorax is routinely performed to assess pulmonary vein anatomy. We sought to investigate the incidence of unexpected cardiac and extracardiac findings in this select patient population and to establish how these findings influence subsequent patient care. Methods: Ninety-five patients (mean age 62 ± 10 years, 35% female) referred to our institution for ablation therapy for atrial fibrillation between July 2003 and October 2007 underwent multislice computed tomography angiography of the thorax. Radiologists interpreted all images. Need for additional testing, consultation and eventual diagnosis were assessed by electronic record review. Results: A total of 83 (5 cardiac, 78 extracardiac) unexpected findings were observed in 50/95 (53%) of patients. The findings prompted 23 additional tests (5 cardiac, 18 noncardiac) in 15/95 (16%) of patients and 8 subsequent referrals in 7/95 (7%) patients. In 6 patients the findings significantly altered future patient care and resulted in postponement of ablation therapy in 4 patients. In 2 patients, extracardiac findings (pulmonary emboli and adenocarcinoma of the lung) were of potentially life-saving consequence. Conclusions: In patients undergoing multislice computed tomography angiography of the thorax in anticipation of planned catheter ablation therapy for the treatment of atrial fibrillation, unexpected findings are common and of potentially significant value. In comparison, there is a higher prevalence of unexpected extracardiac, rather than cardiac findings. Further investigation of these findings may lead to postponement of ablation therapy, but may also be of potentially lifesaving consequence.

Gene expression inference with deep learning.

Science.gov (United States)

Chen, Yifei; Li, Yi; Narayan, Rajiv; Subramanian, Aravind; Xie, Xiaohui

2016-06-15

Large-scale gene expression profiling has been widely used to characterize cellular states in response to various disease conditions, genetic perturbations, etc. Although the cost of whole-genome expression profiles has been dropping steadily, generating a compendium of expression profiling over thousands of samples is still very expensive. Recognizing that gene expressions are often highly correlated, researchers from the NIH LINCS program have developed a cost-effective strategy of profiling only ∼1000 carefully selected landmark genes and relying on computational methods to infer the expression of remaining target genes. However, the computational approach adopted by the LINCS program is currently based on linear regression (LR), limiting its accuracy since it does not capture complex nonlinear relationship between expressions of genes. We present a deep learning method (abbreviated as D-GEX) to infer the expression of target genes from the expression of landmark genes. We used the microarray-based Gene Expression Omnibus dataset, consisting of 111K expression profiles, to train our model and compare its performance to those from other methods. In terms of mean absolute error averaged across all genes, deep learning significantly outperforms LR with 15.33% relative improvement. A gene-wise comparative analysis shows that deep learning achieves lower error than LR in 99.97% of the target genes. We also tested the performance of our learned model on an independent RNA-Seq-based GTEx dataset, which consists of 2921 expression profiles. Deep learning still outperforms LR with 6.57% relative improvement, and achieves lower error in 81.31% of the target genes. D-GEX is available at https://github.com/uci-cbcl/D-GEX CONTACT: xhx@ics.uci.edu 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.

Synthetic RNAs for Gene Regulation: Design Principles and Computational Tools

International Nuclear Information System (INIS)

Laganà, Alessandro; Shasha, Dennis; Croce, Carlo Maria

2014-01-01

The use of synthetic non-coding RNAs for post-transcriptional regulation of gene expression has not only become a standard laboratory tool for gene functional studies but it has also opened up new perspectives in the design of new and potentially promising therapeutic strategies. Bioinformatics has provided researchers with a variety of tools for the design, the analysis, and the evaluation of RNAi agents such as small-interfering RNA (siRNA), short-hairpin RNA (shRNA), artificial microRNA (a-miR), and microRNA sponges. More recently, a new system for genome engineering based on the bacterial CRISPR-Cas9 system (Clustered Regularly Interspaced Short Palindromic Repeats), was shown to have the potential to also regulate gene expression at both transcriptional and post-transcriptional level in a more specific way. In this mini review, we present RNAi and CRISPRi design principles and discuss the advantages and limitations of the current design approaches.

Synthetic RNAs for Gene Regulation: Design Principles and Computational Tools

Energy Technology Data Exchange (ETDEWEB)

Laganà, Alessandro [Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH (United States); Shasha, Dennis [Courant Institute of Mathematical Sciences, New York University, New York, NY (United States); Croce, Carlo Maria [Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH (United States)

2014-12-11

The use of synthetic non-coding RNAs for post-transcriptional regulation of gene expression has not only become a standard laboratory tool for gene functional studies but it has also opened up new perspectives in the design of new and potentially promising therapeutic strategies. Bioinformatics has provided researchers with a variety of tools for the design, the analysis, and the evaluation of RNAi agents such as small-interfering RNA (siRNA), short-hairpin RNA (shRNA), artificial microRNA (a-miR), and microRNA sponges. More recently, a new system for genome engineering based on the bacterial CRISPR-Cas9 system (Clustered Regularly Interspaced Short Palindromic Repeats), was shown to have the potential to also regulate gene expression at both transcriptional and post-transcriptional level in a more specific way. In this mini review, we present RNAi and CRISPRi design principles and discuss the advantages and limitations of the current design approaches.

Gene Circuit Analysis of the Terminal Gap Gene huckebein

Science.gov (United States)

Ashyraliyev, Maksat; Siggens, Ken; Janssens, Hilde; Blom, Joke; Akam, Michael; Jaeger, Johannes

2009-01-01

The early embryo of Drosophila melanogaster provides a powerful model system to study the role of genes in pattern formation. The gap gene network constitutes the first zygotic regulatory tier in the hierarchy of the segmentation genes involved in specifying the position of body segments. Here, we use an integrative, systems-level approach to investigate the regulatory effect of the terminal gap gene huckebein (hkb) on gap gene expression. We present quantitative expression data for the Hkb protein, which enable us to include hkb in gap gene circuit models. Gap gene circuits are mathematical models of gene networks used as computational tools to extract regulatory information from spatial expression data. This is achieved by fitting the model to gap gene expression patterns, in order to obtain estimates for regulatory parameters which predict a specific network topology. We show how considering variability in the data combined with analysis of parameter determinability significantly improves the biological relevance and consistency of the approach. Our models are in agreement with earlier results, which they extend in two important respects: First, we show that Hkb is involved in the regulation of the posterior hunchback (hb) domain, but does not have any other essential function. Specifically, Hkb is required for the anterior shift in the posterior border of this domain, which is now reproduced correctly in our models. Second, gap gene circuits presented here are able to reproduce mutants of terminal gap genes, while previously published models were unable to reproduce any null mutants correctly. As a consequence, our models now capture the expression dynamics of all posterior gap genes and some variational properties of the system correctly. This is an important step towards a better, quantitative understanding of the developmental and evolutionary dynamics of the gap gene network. PMID:19876378

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.)

Perihepatitis associated with systemic lupus erythematosus: computed tomography findings

International Nuclear Information System (INIS)

Schoenwaelder, M.; Stuckey, S.L.

2005-01-01

The imaging findings of a 29-year-old woman with known systemic lupus erythematosus, and a clinical presentation and CT appearances consistent with perihepatitis are presented Copyright (2005) Blackwell Publishing Asia Pty Ltd

Tuberculosis of the Parotid Gland: Computed Tomographic Findings

International Nuclear Information System (INIS)

Wei, Y.; Xiao, J.; Pui, M.H.; Gong, Q.

2008-01-01

Background: Tuberculosis (TB) of the parotid gland is rare, even in endemic regions. Approximately 100 cases have been reported in the English literature. The computed tomographic (CT) features, however, have seldom been studied. Purpose: To determine the diagnostic CT features of tuberculosis of the parotid gland. Material and Methods: CT studies of four histologically proven cases of tuberculosis of the parotid gland were retrospectively reviewed. Results: A total of 15 enlarged lymph nodes were found in the superficial lobes of the parotid glands. The nodes were arranged linearly within the gland. Enhancement patterns included homogeneous enhancement (9/15, 60%), homogeneous enhancement with eccentric microcysts (3/15, 20%), and thick-walled rim enhancement with central lucency (3/15, 20%). Thickened adjacent fascial plane and platysma were seen in two patients. Ipsilateral cervical lymphadenopathy was seen in all patients. Conclusion: In patients presenting with unilateral parotid nodules, TB should be considered when linearly arranged enhancing nodules are demonstrated in the superficial lobes of the glands on CT scan

Visual gene developer: a fully programmable bioinformatics software for synthetic gene optimization

Directory of Open Access Journals (Sweden)

McDonald Karen

2011-08-01

Full Text Available Abstract Background Direct gene synthesis is becoming more popular owing to decreases in gene synthesis pricing. Compared with using natural genes, gene synthesis provides a good opportunity to optimize gene sequence for specific applications. In order to facilitate gene optimization, we have developed a stand-alone software called Visual Gene Developer. Results The software not only provides general functions for gene analysis and optimization along with an interactive user-friendly interface, but also includes unique features such as programming capability, dedicated mRNA secondary structure prediction, artificial neural network modeling, network & multi-threaded computing, and user-accessible programming modules. The software allows a user to analyze and optimize a sequence using main menu functions or specialized module windows. Alternatively, gene optimization can be initiated by designing a gene construct and configuring an optimization strategy. A user can choose several predefined or user-defined algorithms to design a complicated strategy. The software provides expandable functionality as platform software supporting module development using popular script languages such as VBScript and JScript in the software programming environment. Conclusion Visual Gene Developer is useful for both researchers who want to quickly analyze and optimize genes, and those who are interested in developing and testing new algorithms in bioinformatics. The software is available for free download at http://www.visualgenedeveloper.net.

Inferring Gene Regulatory Networks Using Conditional Regulation Pattern to Guide Candidate Genes.

Directory of Open Access Journals (Sweden)

Fei Xiao

Full Text Available Combining path consistency (PC algorithms with conditional mutual information (CMI are widely used in reconstruction of gene regulatory networks. CMI has many advantages over Pearson correlation coefficient in measuring non-linear dependence to infer gene regulatory networks. It can also discriminate the direct regulations from indirect ones. However, it is still a challenge to select the conditional genes in an optimal way, which affects the performance and computation complexity of the PC algorithm. In this study, we develop a novel conditional mutual information-based algorithm, namely RPNI (Regulation Pattern based Network Inference, to infer gene regulatory networks. For conditional gene selection, we define the co-regulation pattern, indirect-regulation pattern and mixture-regulation pattern as three candidate patterns to guide the selection of candidate genes. To demonstrate the potential of our algorithm, we apply it to gene expression data from DREAM challenge. Experimental results show that RPNI outperforms existing conditional mutual information-based methods in both accuracy and time complexity for different sizes of gene samples. Furthermore, the robustness of our algorithm is demonstrated by noisy interference analysis using different types of noise.

SIGNATURE: A workbench for gene expression signature analysis

Directory of Open Access Journals (Sweden)

Chang Jeffrey T

2011-11-01

Full Text Available Abstract Background The biological phenotype of a cell, such as a characteristic visual image or behavior, reflects activities derived from the expression of collections of genes. As such, an ability to measure the expression of these genes provides an opportunity to develop more precise and varied sets of phenotypes. However, to use this approach requires computational methods that are difficult to implement and apply, and thus there is a critical need for intelligent software tools that can reduce the technical burden of the analysis. Tools for gene expression analyses are unusually difficult to implement in a user-friendly way because their application requires a combination of biological data curation, statistical computational methods, and database expertise. Results We have developed SIGNATURE, a web-based resource that simplifies gene expression signature analysis by providing software, data, and protocols to perform the analysis successfully. This resource uses Bayesian methods for processing gene expression data coupled with a curated database of gene expression signatures, all carried out within a GenePattern web interface for easy use and access. Conclusions SIGNATURE is available for public use at http://genepattern.genome.duke.edu/signature/.

Methods for monitoring multiple gene expression

Energy Technology Data Exchange (ETDEWEB)

Berka, Randy [Davis, CA; Bachkirova, Elena [Davis, CA; Rey, Michael [Davis, CA

2012-05-01

The present invention relates to methods for monitoring differential expression of a plurality of genes in a first filamentous fungal cell relative to expression of the same genes in one or more second filamentous fungal cells using microarrays containing Trichoderma reesei ESTs or SSH clones, or a combination thereof. The present invention also relates to computer readable media and substrates containing such array features for monitoring expression of a plurality of genes in filamentous fungal cells.

Methods for monitoring multiple gene expression

Energy Technology Data Exchange (ETDEWEB)

Berka, Randy; Bachkirova, Elena; Rey, Michael

2013-10-01

The present invention relates to methods for monitoring differential expression of a plurality of genes in a first filamentous fungal cell relative to expression of the same genes in one or more second filamentous fungal cells using microarrays containing Trichoderma reesei ESTs or SSH clones, or a combination thereof. The present invention also relates to computer readable media and substrates containing such array features for monitoring expression of a plurality of genes in filamentous fungal cells.

Computational characteristics of valproic acid binding to histone deacetylase

International Nuclear Information System (INIS)

Abou-Zeid, Laila A.; El-Mowafy, Abdalla M.; Eikel, D.; Nau, H.; El-Mazar, M.

2007-01-01

Recently, the anticpileptic drug valproic acid (VPA) has also demonstrated efficacy in the management of cancer and bipolar disorders. These actions are largely mediated by inhibition of the HDAC enzyme/induction of certain genes. Relative to other HDAC inhibitors such as trichostatin-A (TSA), VPA offers higher selectivity on cancer cells with virtually no detrimental effects on normal cells. The molecular underpinnings of these biological profiles for VPA remain undefined. We currently propose for an attempt to identify differences in the binding of VPA and TSA to HDAC. In this paper, conformational changes and energy calculations have derived. VPA had to accomplish conformational changes in its structure for best accommodation at the HDAC binding site. Energy computations showed that VPA has a lower binding affinitythan TSA (-53.80 vs. -66.30 Kcal/mol). These findings demonstrate that VPA binding to HDAC confers catalytic, conformational and computational characteristics that are distinct from those of TSA. These findings of VPA are consistent with a moderate inhibition of HDAC, a low toxicity on normal cells, and a higher selectivity on cancer cells than TSA. Accordingly, these newly identified binding properties of VPA can state a framework strategy for the rational design of VPA-related anticancer drugs with superior cytodifferentiating-and/or safety-profiles. (author)

ConGEMs: Condensed Gene Co-Expression Module Discovery Through Rule-Based Clustering and Its Application to Carcinogenesis

Directory of Open Access Journals (Sweden)

Saurav Mallik

2017-12-01

Full Text Available For transcriptomic analysis, there are numerous microarray-based genomic data, especially those generated for cancer research. The typical analysis measures the difference between a cancer sample-group and a matched control group for each transcript or gene. Association rule mining is used to discover interesting item sets through rule-based methodology. Thus, it has advantages to find causal effect relationships between the transcripts. In this work, we introduce two new rule-based similarity measures—weighted rank-based Jaccard and Cosine measures—and then propose a novel computational framework to detect condensed gene co-expression modules ( C o n G E M s through the association rule-based learning system and the weighted similarity scores. In practice, the list of evolved condensed markers that consists of both singular and complex markers in nature depends on the corresponding condensed gene sets in either antecedent or consequent of the rules of the resultant modules. In our evaluation, these markers could be supported by literature evidence, KEGG (Kyoto Encyclopedia of Genes and Genomes pathway and Gene Ontology annotations. Specifically, we preliminarily identified differentially expressed genes using an empirical Bayes test. A recently developed algorithm—RANWAR—was then utilized to determine the association rules from these genes. Based on that, we computed the integrated similarity scores of these rule-based similarity measures between each rule-pair, and the resultant scores were used for clustering to identify the co-expressed rule-modules. We applied our method to a gene expression dataset for lung squamous cell carcinoma and a genome methylation dataset for uterine cervical carcinogenesis. Our proposed module discovery method produced better results than the traditional gene-module discovery measures. In summary, our proposed rule-based method is useful for exploring biomarker modules from transcriptomic data.

ConGEMs: Condensed Gene Co-Expression Module Discovery Through Rule-Based Clustering and Its Application to Carcinogenesis.

Science.gov (United States)

Mallik, Saurav; Zhao, Zhongming

2017-12-28

For transcriptomic analysis, there are numerous microarray-based genomic data, especially those generated for cancer research. The typical analysis measures the difference between a cancer sample-group and a matched control group for each transcript or gene. Association rule mining is used to discover interesting item sets through rule-based methodology. Thus, it has advantages to find causal effect relationships between the transcripts. In this work, we introduce two new rule-based similarity measures-weighted rank-based Jaccard and Cosine measures-and then propose a novel computational framework to detect condensed gene co-expression modules ( C o n G E M s) through the association rule-based learning system and the weighted similarity scores. In practice, the list of evolved condensed markers that consists of both singular and complex markers in nature depends on the corresponding condensed gene sets in either antecedent or consequent of the rules of the resultant modules. In our evaluation, these markers could be supported by literature evidence, KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway and Gene Ontology annotations. Specifically, we preliminarily identified differentially expressed genes using an empirical Bayes test. A recently developed algorithm-RANWAR-was then utilized to determine the association rules from these genes. Based on that, we computed the integrated similarity scores of these rule-based similarity measures between each rule-pair, and the resultant scores were used for clustering to identify the co-expressed rule-modules. We applied our method to a gene expression dataset for lung squamous cell carcinoma and a genome methylation dataset for uterine cervical carcinogenesis. Our proposed module discovery method produced better results than the traditional gene-module discovery measures. In summary, our proposed rule-based method is useful for exploring biomarker modules from transcriptomic data.