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Search Results: 1 - 10 of 5564 matches for " Mary Shimoyama "
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Using Multiple Ontologies to Integrate Complex Biological Data
Mary Shimoyama,Victoria Petri,Dean Pasko,Susan Bromberg,Wenhua Wu,Jiali Chen,Nataliya Nenasheva,Anne Kwitek,Simon Twigger,Howard Jacob
Comparative and Functional Genomics , 2005, DOI: 10.1002/cfg.498
Abstract: The strength of the rat as a model organism lies in its utility in pharmacology, biochemistry and physiology research. Data resulting from such studies is difficult to represent in databases and the creation of user-friendly data mining tools has proved difficult. The Rat Genome Database has developed a comprehensive ontology-based data structure and annotation system to integrate physiological data along with environmental and experimental factors, as well as genetic and genomic information. RGD uses multiple ontologies to integrate complex biological information from the molecular level to the whole organism, and to develop data mining and presentation tools. This approach allows RGD to indicate not only the phenotypes seen in a strain but also the specific values under each diet and atmospheric condition, as well as gender differences. Harnessing the power of ontologies in this way allows the user to gather and filter data in a customized fashion, so that a researcher can retrieve all phenotype readings for which a high hypoxia is a factor. Utilizing the same data structure for expression data, pathways and biological processes, RGD will provide a comprehensive research platform which allows users to investigate the conditions under which biological processes are altered and to elucidate the mechanisms of disease.
RGD: A comparative genomics platform
Mary Shimoyama, Jennifer R Smith, Tom Hayman, Stan Laulederkind, Tim Lowry, Rajni Nigam, Victoria Petri, Shur-Jen Wang, Melinda Dwinell, Howard Jacob, RGD Team
Human Genomics , 2011, DOI: 10.1186/1479-7364-5-2-124
Abstract: The Rat Genome Database (RGD) (http://rgd.mcw.edu webcite) is recognised as the premier resource for genetic, genomic and phenotype data for the laboratory rat, Rattus norvegicus. Since 1999, RGD has provided a comprehensive catalogue of genes, quantitative trait loci (QTL) and strains, along with software tools to retrieve and display data of interest to investigators using this organism. The disease focus of these researchers often results in the use of multiple model organisms, in addition to clinical studies, in their efforts to elucidate the mechanisms and underlying genetic factors involved in human disease. To meet the needs of such users, RGD focuses its manual curation efforts on the functional, phenotype and pathway data related to specific disease areas and has integrated human and mouse data to create a comprehensive platform for comparative genomics and genetics. Several of these components are highlighted here.The wealth of data at RGD includes genes and QTLs for rat, human and mouse, as well as polymorphic markers for rat and human (Table 1). Information on inbred, outbred, mutant, congenic, consomic and other types of rat strains is also provided. A team of scientific curators validates the identity of genomic elements, provides official nomenclature and annotates these elements with functional data from published literature [1]. With more than 1.3 million published rat research papers, prioritising data for curation is a vital task, and a project approach has proved effective. Such projects revolve around gene families, molecular pathways, ultra-conserved gene sets and diseases.The disease portals (http://rgd.mcw.edu/wg/portals/ webcite) create a structure for prioritising rat data curation and integrating rat, human and mouse information, and provide a platform for researchers easily to access multiple data types related to a particular disease area (Table 2). RGD currently has portals for cardiovascular and neurological diseases, cancer, diabetes
Anomalous pairing vibration in neutron-rich Sn isotopes beyond the N=82 magic number
Hirotaka Shimoyama,Masayuki Matsuo
Physics , 2011, DOI: 10.1103/PhysRevC.84.044317
Abstract: Two-neutron transfer associated with the pair correlation in superfluid neutron-rich nuclei is studied with focus on low-lying $0^+$ states in Sn isotopes beyond the N=82 magic number. We describe microscopically the two-neutron addition and removal transitions by means of the Skyrme-Hartree-Fock-Bogoliubov mean-field model and the continuum quasiparticle random phase approximation formulated in the coordinate space representation. It is found that the pair transfer strength for the transitions between the ground states becomes significantly large for the isotopes with $A \ge 140$, reflecting very small neutron separation energy and long tails of the weakly bound $3p$ orbits. In $^{132-140}$Sn, a peculiar feature of the pair transfer is seen in transitions to low-lying excited $0^+$ states. They can be regarded as a novel kind of pair vibrational mode which is characterized by an anomalously long tail of the transition density extending to far outside of the nuclear surface, and a large strength comparable to that of the ground-state transitions. The presence of the weakly bound neutron orbits plays a central role for these anomalous behaviors.
Four-Dimensional Planck Scale is Not Universal in Fifth Dimension in Randall-Sundrum Scenario
Takaaki Ozeki,Noriyuki Shimoyama
Physics , 1999, DOI: 10.1143/PTP.103.1227
Abstract: It has recently been proposed that the hierarchy problem can be solved by considering the warped fifth dimension compactified on $S^{1}/Z_{2}$. Many studies in the context have assumed a particular choice for an integration constant $\sigma_{0}$ that appears when one solves the five-dimensional Einstein equation. Since $\sigma_{0}$ is not determined by the boundary condition of the five-dimensional theory, $\sigma_{0}$ may be regarded as a gauge degree of freedom in a sense. To this time, all indications are that the four-dimensional Planck mass depends on $\sigma_{0}$. In this paper, we carefully investigate the properties of the geometry in the Randall-Sundrum model, and consider in which location $y$ the four-dimensional Planck mass is measured. As a result, we find a $\sigma_{0}$-independent relation between the four-dimensional Planck mass $M_{\rm Pl}$ and five- dimensional fundamental mass scale $M$, and remarkably enough, we can take $M$ to TeV region when we consider models with the Standard Model confined on a distant brane. We also confirm that the physical masses on the distant brane do not depend on $\sigma_{0}$ by considering a bulk scalar field as an illustrative example. The resulting mass scale of the Kaluza-Klein modes is on the order of $M$.
Di-neutron correlation in monopole two-neutron transfer modes in Sn isotope chain
Hirotaka Shimoyama,Masayuki Matsuo
Physics , 2013, DOI: 10.1103/PhysRevC.88.054308
Abstract: We study microscopic structures of monopole pair vibrational modes and associated two-neutron transfer amplitudes in neutron-rich Sn isotopes by means of the linear response formalism of the quasiparticle random phase approximation(QRPA). For this purpose we introduce a method to decompose the transfer amplitudes with respect to two-quasiparticle components of the QRPA eigen mode. It is found that pair-addition ibrational modes in neutron-rich $^{132-140}$Sn and the pair rotational modes in $^{142-150}$Sn are commonly characterized by coherent contributions of quasaiparticle states having high orbital angular momenta $l \gesim 5$, which suggests transfer of a spatially correlated neutron pair. The calculation also predicts a high-lying pair vibration, the giant pair vibration, emerging near the one-neutron separation energy in $^{110-130}$Sn, and we find that they have the same di-neutron characters as that of the low-lying pair vibration in $^{132-140}$Sn.
Evaluation of Antibodies Induced by the Injection of Single Capsid Protein or Purified Virus Particle of Coxsackievirus B3 in Mice  [PDF]
Toshiaki Shimoyama, Takumi Kubota, Junsuke Shirai, Rie Watanabe
World Journal of Vaccines (WJV) , 2014, DOI: 10.4236/wjv.2014.44019
Abstract: Four capsid proteins (VP1, VP2, VP3, and VP4) of coxsackievirus B3 (CVB3) were expressed as recombinant proteins in an Escherichia coli expression system and used as antigens for subunit vaccines against CVB3 in ICR mice. Antigens were expressed as thioredoxin-histidine (TrxHis)-tagged protein and purified before immunization. Although all VPs other than VP4 induced anti-CVB3 specific antibodies in mice (detected by ELISA and western blotting), they did not neutralize the infectious CVB3 in a virus neutralization assay. Meanwhile, 2 virus strains were purified from CVB3 virus stock on the basis of their plaque size on HeLa cells. ICR mice were infected with the 2 purified virus strains (S-strain and L-strain) and unpurified virus stock (wild type) to analyze the difference in antibody responses against infections of purified and unpurified virus strains. The reactivity of antisera against each virus strain was tested by ELISA, and the results showed that the inoculation of purified virus strain induced a strong antibody response against the inoculated strain. As a result, the antibody response against wild-type and other virus strains was suppressed. These results suggest using unpurified virus stock as an antigen is advantageous for inducing a broad antibody response in inoculated animals.
The Rat Genome Database Curators: Who, What, Where, Why
Mary Shimoyama ,G. Thomas Hayman,Stanley J. F. Laulederkind,Rajni Nigam,Timothy F. Lowry,Victoria Petri,Jennifer R. Smith,Shur-Jen Wang,Diane H. Munzenmaier,Melinda R. Dwinell,Simon N. Twigger,Howard J. Jacob,the RGD Team
PLOS Computational Biology , 2009, DOI: 10.1371/journal.pcbi.1000582
Abstract:
Successful type-oriented endoscopic resection for gastric carcinoid tumors: A case report
Shouji Shimoyama,Mitsuhiro Fujishiro,Yutaka Takazawa
World Journal of Gastrointestinal Endoscopy , 2010,
Abstract: The standard treatment in Japan for gastric carcinoid has been gastrectomy with lymphadenectomy. This report describes the possibility of endoscopic treatment as an appropriate option for gastric carcinoid fulfilling certain conditions. A 46 year old woman underwent endoscopic mucosal resection for two 3 mm gastric carcinoids. The patient had hypergastrinemia with pernicious anemia and type A chronic atrophic gastritis, suggesting that the tumors were type I in Rindi's classification. Both tumors were located in the mucosal layer with no cellular polymorphism and were chromogranin A positive. Neither tumor recurrence in the stomach nor distant metastases have been documented during the 5 years of follow-up. Although many type I gastric carcinoids may be clinically indolent, reports on successful endoscopic treatment for this carcinoid have been scanty in the literature in Japan, presumably because of the hitherto surgical treatment stance for the disease. This report discusses how the size, number, depth and histological grading of the type I gastric carcinoid could allow the correct identification of a benign or malignant propensity of an individual tumor and how endoscopic resection could be a treatment of choice when these factors render it feasible. This stance could also obviate unnecessary surgical resection for more benign tumors.
Enhanced Disinfection Effect of a Compound Disinfectant against Bovine Herpes Virus Type 1 at Low Temperature  [PDF]
Makoto Nagai, Ryoji Kamimura, Reiji Seki, Toshiaki Shimoyama, Takumi Kubota, Junsuke Shirai
Open Journal of Veterinary Medicine (OJVM) , 2013, DOI: 10.4236/ojvm.2013.35039
Abstract:

A compound disinfectant, which consisted of didecyldimethylammonium chloride (DDAC), ortho-dichlorobenzene (1,2-dichlorobenzene, ODB), and chlorocresol (4-chloro-3-methylphenol, CC), and its component chemicals were individually tested for effectiveness against bovine herpes virus type 1 (BHV-1). DDAC, DDAC+ODB, DDAC+CC, and DDAC+ODB+CC showed effectiveness against BHV-1 at room temperature. However, ODB, CC, and ODB+CC showed no virucidal effects. The effects of all disinfectants tested were decreased at low temperature. DDAC showed disinfectant effects at a dilution of 1/800 and DDAC+ODB, DDAC+CC, and DDAC+ODB+CC at dilutions of 1/800 and 1/1600 at low temperature in the presence of 2% fetal bovine serum (FBS) but ODB, CC, and ODB+CC showed no virucidal effects. At low temperature and in the presence of 10% FBS, DDAC, DDAC+ODB, and DDAC+CC showed disinfectant effects at dilutions of 1/800, whereas ODB, CC, and ODB+CC showed no virucidal effects. DDAC+ ODB+CC was more effective (at 1/800 and 1/1600) than the other disinfectants under these conditions. In conclusion, a combination of three disinfectant components (DDAC+ODB+CC), enhanced the disinfectant effects at low temperature and in organic matter contamination.

Surgeon-Operated In-Office Ultrasonography for the Diagnosis of Rotator Cuff Tears: A Comparison with Magnetic Resonance Imaging  [PDF]
Tsutomu Kobayashi, Atsushi Yamamoto, Hitoshi Shitara, Tsuyoshi Ichinose, Eiji Takasawa, Daisuke Shimoyama, Toshihisa Osawa, Kenji Takagishi
Surgical Science (SS) , 2013, DOI: 10.4236/ss.2013.49A002
Abstract:

Objective: Few investigators have evaluated whether ultrasonography operated by a surgeon during a patient’s clinic visit is capable of obtaining a similar degree of accuracy as magnetic resonance imaging in regard to the diagnosis of rotator cuff tears and lesions of the biceps tendon. The purpose of this study was to clarify the accuracy of in-office ultrasonography for the diagnosis of rotator cuff tears in comparison to magnetic resonance imaging. Methods: One hundred and three patients (105 shoulders) with a clinical diagnosis of impingement and suspected rotator cuff tear, who subsequently underwent arthroscopic surgery were retrospectively enrolled in this study, including 7 males with 89 shoulders, and 33 females with 33 shoulders, and their mean age was 60.9 years (range, 30 to 83 years). The subjects were examined using ultrasonography and magnetic resonance imaging within three months pre-operatively per normal practice of the outpatient clinic. The two modalities were then compared to the reference standard, arthroscopic findings. Results: Intra-operatively, 79 full-thickness and 15 partial-thickness rotator cuff tears were found. The agreement between ultrasonography and magnetic resonance imaging for diagnosis of rotator cuff tears was statistically good; observed degree of agreement was 87% with Kappa coefficient of 0.73. Ultrasonography showed a sensitivity of 94% and a specificity of 100% for full-thickness tears, and a sensitivity of 80% and a specificity of 91% for partial-thickness tears. The agreement of the two modalities for diagnosis of lesions of the biceps tendon was also good; observed degree of agreement was 93% with Kappa coefficient of 0.76. In addition, ultrasonography showed comparable accuracy for classifying the size of rotator cuff tears to that of magnetic resonance imaging. Conclusion: Surgeon-operated in-office ultrasonography is an appropriate technique for the assessment of rotator cuff tears with a comparable sensitivity and specificity to that of magnetic resonance imaging.

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