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Sample records for candidate ml tumor

  1. TumorML: Concept and requirements of an in silico cancer modelling markup language.

    Science.gov (United States)

    Johnson, David; Cooper, Jonathan; McKeever, Steve

    2011-01-01

    This paper describes the initial groundwork carried out as part of the European Commission funded Transatlantic Tumor Model Repositories project, to develop a new markup language for computational cancer modelling, TumorML. In this paper we describe the motivations for such a language, arguing that current state-of-the-art biomodelling languages are not suited to the cancer modelling domain. We go on to describe the work that needs to be done to develop TumorML, the conceptual design, and a description of what existing markup languages will be used to compose the language specification.

  2. Transcriptome Analysis of Human Peripheral Blood Mononuclear Cells Exposed to Lassa Virus and to the Attenuated Mopeia/Lassa Reassortant 29 (ML29), a Vaccine Candidate

    Science.gov (United States)

    Zapata, Juan Carlos; Carrion, Ricardo; Patterson, Jean L.; Crasta, Oswald; Zhang, Yan; Mani, Sachin; Jett, Marti; Poonia, Bhawna; Djavani, Mahmoud; White, David M.; Lukashevich, Igor S.; Salvato, Maria S.

    2013-01-01

    Lassa virus (LASV) is the causative agent of Lassa Fever and is responsible for several hundred thousand infections and thousands of deaths annually in West Africa. LASV and the non-pathogenic Mopeia virus (MOPV) are both rodent-borne African arenaviruses. A live attenuated reassortant of MOPV and LASV, designated ML29, protects rodents and primates from LASV challenge and appears to be more attenuated than MOPV. To gain better insight into LASV-induced pathology and mechanism of attenuation we performed gene expression profiling in human peripheral blood mononuclear cells (PBMC) exposed to LASV and the vaccine candidate ML29. PBMC from healthy human subjects were exposed to either LASV or ML29. Although most PBMC are non-permissive for virus replication, they remain susceptible to signal transduction by virus particles. Total RNA was extracted and global gene expression was evaluated during the first 24 hours using high-density microarrays. Results were validated using RT-PCR, flow cytometry and ELISA. LASV and ML29 elicited differential expression of interferon-stimulated genes (ISG), as well as genes involved in apoptosis, NF-kB signaling and the coagulation pathways. These genes could eventually serve as biomarkers to predict disease outcomes. The remarkable differential expression of thrombomodulin, a key regulator of inflammation and coagulation, suggests its involvement with vascular abnormalities and mortality in Lassa fever disease. PMID:24069471

  3. Transcriptome analysis of human peripheral blood mononuclear cells exposed to Lassa virus and to the attenuated Mopeia/Lassa reassortant 29 (ML29, a vaccine candidate.

    Directory of Open Access Journals (Sweden)

    Juan Carlos Zapata

    Full Text Available Lassa virus (LASV is the causative agent of Lassa Fever and is responsible for several hundred thousand infections and thousands of deaths annually in West Africa. LASV and the non-pathogenic Mopeia virus (MOPV are both rodent-borne African arenaviruses. A live attenuated reassortant of MOPV and LASV, designated ML29, protects rodents and primates from LASV challenge and appears to be more attenuated than MOPV. To gain better insight into LASV-induced pathology and mechanism of attenuation we performed gene expression profiling in human peripheral blood mononuclear cells (PBMC exposed to LASV and the vaccine candidate ML29. PBMC from healthy human subjects were exposed to either LASV or ML29. Although most PBMC are non-permissive for virus replication, they remain susceptible to signal transduction by virus particles. Total RNA was extracted and global gene expression was evaluated during the first 24 hours using high-density microarrays. Results were validated using RT-PCR, flow cytometry and ELISA. LASV and ML29 elicited differential expression of interferon-stimulated genes (ISG, as well as genes involved in apoptosis, NF-kB signaling and the coagulation pathways. These genes could eventually serve as biomarkers to predict disease outcomes. The remarkable differential expression of thrombomodulin, a key regulator of inflammation and coagulation, suggests its involvement with vascular abnormalities and mortality in Lassa fever disease.

  4. Gastrointestinal stromal tumors, somatic mutations and candidate genetic risk variants.

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    Katie M O'Brien

    Full Text Available Gastrointestinal stromal tumors (GISTs are rare but treatable soft tissue sarcomas. Nearly all GISTs have somatic mutations in either the KIT or PDGFRA gene, but there are no known inherited genetic risk factors. We assessed the relationship between KIT/PDGFRA mutations and select deletions or single nucleotide polymorphisms (SNPs in 279 participants from a clinical trial of adjuvant imatinib mesylate. Given previous evidence that certain susceptibility loci and carcinogens are associated with characteristic mutations, or "signatures" in other cancers, we hypothesized that the characteristic somatic mutations in the KIT and PDGFRA genes in GIST tumors may similarly be mutational signatures that are causally linked to specific mutagens or susceptibility loci. As previous epidemiologic studies suggest environmental risk factors such as dioxin and radiation exposure may be linked to sarcomas, we chose 208 variants in 39 candidate genes related to DNA repair and dioxin metabolism or response. We calculated adjusted odds ratios (ORs and 95% confidence intervals (CIs for the association between each variant and 7 categories of tumor mutation using logistic regression. We also evaluated gene-level effects using the sequence kernel association test (SKAT. Although none of the association p-values were statistically significant after adjustment for multiple comparisons, SNPs in CYP1B1 were strongly associated with KIT exon 11 codon 557-8 deletions (OR = 1.9, 95% CI: 1.3-2.9 for rs2855658 and OR = 1.8, 95% CI: 1.2-2.7 for rs1056836 and wild type GISTs (OR = 2.7, 95% CI: 1.5-4.8 for rs1800440 and OR = 0.5, 95% CI: 0.3-0.9 for rs1056836. CYP1B1 was also associated with these mutations categories in the SKAT analysis (p = 0.002 and p = 0.003, respectively. Other potential risk variants included GSTM1, RAD23B and ERCC2. This preliminary analysis of inherited genetic risk factors for GIST offers some clues about the disease's genetic

  5. Evaluation of radiolabeled ML04, a putative irreversible inhibitor of epidermal growth factor receptor, as a bioprobe for PET imaging of EGFR-overexpressing tumors

    International Nuclear Information System (INIS)

    Abourbeh, Galith; Dissoki, Samar; Jacobson, Orit; Litchi, Amir; Daniel, Revital Ben; Laki, Desirediu; Levitzki, Alexander; Mishani, Eyal

    2007-01-01

    Overexpression of epidermal growth factor receptor (EGFR) has been implicated in tumor development and malignancy. Evaluating the degree of EGFR expression in tumors could aid in identifying patients for EGFR-targeted therapies and in monitoring treatment. Nevertheless, no currently available assay can reliably quantify receptor content in tumors. Radiolabeled inhibitors of EGFR-TK could be developed as bioprobes for positron emission tomography imaging. Such imaging agents would not only provide a noninvasive quantitative measurement of EGFR content in tumors but also serve as radionuclide carriers for targeted radiotherapy. The potency, reversibility, selectivity and specific binding characteristics of ML04, an alleged irreversible inhibitor of EGFR, were established in vitro. The distribution of the F-18-labeled compound and the extent of EGFR-specific tumor uptake were evaluated in tumor-bearing mice. ML04 demonstrated potent, irreversible and selective inhibition of EGFR, combined with specific binding to the receptor in intact cells. In vivo distribution of the radiolabeled compound revealed tumor/blood and tumor/muscle activity uptake ratios of about 7 and 5, respectively, 3 h following administration of a radiotracer. Nevertheless, only minor EGFR-specific uptake of the compound was detected in these studies, using either EGFR-negative tumors or blocking studies as controls. To improve the in vivo performance of ML04, administration via prolonged intravenous infusion is proposed. Detailed pharmacokinetic characterization of this bioprobe could assist in the development of a kinetic model that would afford accurate measurement of EGFR content in tumors

  6. AZU-1: A Candidate Breast Tumor Suppressor and Biomarker for Tumor Progression

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Huei-Mei; Schmeichel, Karen L; Mian, I. Saira; Lelie`vre, Sophie; Petersen, Ole W; Bissell, Mina J

    2000-02-04

    To identify genes misregulated in the final stages of breast carcinogenesis, we performed differential display to compare the gene expression patterns of the human tumorigenic mammary epithelial cells, HMT-3522-T4-2, with those of their immediate premalignant progenitors, HMT-3522-S2. We identified a novel gene, called anti-zuai-1 (AZU-1), that was abundantly expressed in non- and premalignant cells and tissues but was appreciably reduced in breast tumor cell types and in primary tumors. The AZU-1 gene encodes an acidic 571-amino-acid protein containing at least two structurally distinct domains with potential protein-binding functions: an N-terminal serine and proline-rich domain with a predicted immunoglobulin-like fold and a C-terminal coiled-coil domain. In HMT-3522 cells, the bulk of AZU-1 protein resided in a detergent-extractable cytoplasmic pool and was present at much lower levels in tumorigenic T4-2 cells than in their nonmalignant counterparts. Reversion of the tumorigenic phenotype of T4-2 cells, by means described previously, was accompanied by the up-regulation of AZU-1. In addition, reexpression of AZU-1 in T4-2 cells, using viral vectors, was sufficient to reduce their malignant phenotype substantially, both in culture and in vivo. These results indicate that AZU-1 is a candidate breast tumor suppressor that may exert its effects by promoting correct tissue morphogenesis.

  7. Neuropathological biomarker candidates in brain tumors: key issues for translational efficiency.

    Science.gov (United States)

    Hainfellner, J A; Heinzl, H

    2010-01-01

    Brain tumors comprise a large spectrum of rare malignancies in children and adults that are often associated with severe neurological symptoms and fatal outcome. Neuropathological tumor typing provides both prognostic and predictive tissue information which is the basis for optimal postoperative patient management and therapy. Molecular biomarkers may extend and refine prognostic and predictive information in a brain tumor case, providing more individualized and optimized treatment options. In the recent past a few neuropathological brain tumor biomarkers have translated smoothly into clinical use whereas many candidates show protracted translation. We investigated the causes of protracted translation of candidate brain tumor biomarkers. Considering the research environment from personal, social and systemic perspectives we identified eight determinants of translational success: methodology, funding, statistics, organization, phases of research, cooperation, self-reflection, and scientific progeny. Smoothly translating biomarkers are associated with low degrees of translational complexity whereas biomarkers with protracted translation are associated with high degrees. Key issues for translational efficiency of neuropathological brain tumor biomarker research seem to be related to (i) the strict orientation to the mission of medical research, that is the improval of medical practice as primordial purpose of research, (ii) definition of research priorities according to clinical needs, and (iii) absorption of translational complexities by means of operatively beneficial standards. To this end, concrete actions should comprise adequate scientific education of young investigators, and shaping of integrative diagnostics and therapy research both on the local level and the level of influential international brain tumor research platforms.

  8. Proteomic analysis of cerebrospinal fluid from children with central nervous system tumors identifies candidate proteins relating to tumor metastatic spread.

    Science.gov (United States)

    Spreafico, Filippo; Bongarzone, Italia; Pizzamiglio, Sara; Magni, Ruben; Taverna, Elena; De Bortoli, Maida; Ciniselli, Chiara M; Barzanò, Elena; Biassoni, Veronica; Luchini, Alessandra; Liotta, Lance A; Zhou, Weidong; Signore, Michele; Verderio, Paolo; Massimino, Maura

    2017-07-11

    Central nervous system (CNS) tumors are the most common solid tumors in childhood. Since the sensitivity of combined cerebrospinal fluid (CSF) cytology and radiological neuroimaging in detecting meningeal metastases remains relatively low, we sought to characterize the CSF proteome of patients with CSF tumors to identify biomarkers predictive of metastatic spread. CSF samples from 27 children with brain tumors and 13 controls (extra-CNS non-Hodgkin lymphoma) were processed using core-shell hydrogel nanoparticles, and analyzed with reverse-phase liquid chromatography/electrospray tandem mass spectrometry (LC-MS/MS). Candidate proteins were identified with Fisher's exact test and/or a univariate logistic regression model. Reverse phase protein array (RPPA), Western blot (WB), and ELISA were used in the training set and in an independent set of CFS samples (60 cases, 14 controls) to validate our discovery findings. Among the 558 non-redundant proteins identified by LC-MS/MS, 147 were missing from the CSF database at http://www.biosino.org. Fourteen of the 26 final top-candidate proteins were chosen for validation with WB, RPPA and ELISA methods. Six proteins (type 1 collagen, insulin-like growth factor binding protein 4, procollagen C-endopeptidase enhancer 1, glial cell-line derived neurotrophic factor receptor α2, inter-alpha-trypsin inhibitor heavy chain 4, neural proliferation and differentiation control protein-1) revealed the ability to discriminate metastatic cases from controls. Combining a unique dataset of CSFs from pediatric CNS tumors with a novel enabling nanotechnology led us to identify CSF proteins potentially related to metastatic status.

  9. Biomarkers Discovery for Colorectal Cancer: A Review on Tumor Endothelial Markers as Perspective Candidates

    Directory of Open Access Journals (Sweden)

    Łukasz Pietrzyk

    2016-01-01

    Full Text Available Colorectal cancer (CRC is the third most common cancer in the world. The early detection of CRC, during the promotion/progression stages, is an enormous challenge for a successful outcome and remains a fundamental problem in clinical approach. Despite the continuous advancement in diagnostic and therapeutic methods, there is a need for discovery of sensitive and specific, noninvasive biomarkers. Tumor endothelial markers (TEMs are associated with tumor-specific angiogenesis and are potentially useful to discriminate between tumor and normal endothelium. The most promising TEMs for oncogenic signaling in CRC appeared to be the TEM1, TEM5, TEM7, and TEM8. Overexpression of TEMs especially TEM1, TEM7, and TEM8 in colorectal tumor tissue compared to healthy tissue suggests their role in tumor blood vessels formation. Thus TEMs appear to be perspective candidates for early detection, monitoring, and treatment of CRC patients. This review provides an update on recent data on tumor endothelial markers and their possible use as biomarkers for screening, diagnosis, and therapy of colorectal cancer patients.

  10. Biomarkers Discovery for Colorectal Cancer: A Review on Tumor Endothelial Markers as Perspective Candidates.

    Science.gov (United States)

    Pietrzyk, Łukasz

    2016-01-01

    Colorectal cancer (CRC) is the third most common cancer in the world. The early detection of CRC, during the promotion/progression stages, is an enormous challenge for a successful outcome and remains a fundamental problem in clinical approach. Despite the continuous advancement in diagnostic and therapeutic methods, there is a need for discovery of sensitive and specific, noninvasive biomarkers. Tumor endothelial markers (TEMs) are associated with tumor-specific angiogenesis and are potentially useful to discriminate between tumor and normal endothelium. The most promising TEMs for oncogenic signaling in CRC appeared to be the TEM1, TEM5, TEM7, and TEM8. Overexpression of TEMs especially TEM1, TEM7, and TEM8 in colorectal tumor tissue compared to healthy tissue suggests their role in tumor blood vessels formation. Thus TEMs appear to be perspective candidates for early detection, monitoring, and treatment of CRC patients. This review provides an update on recent data on tumor endothelial markers and their possible use as biomarkers for screening, diagnosis, and therapy of colorectal cancer patients.

  11. NDRG2 is a candidate tumor-suppressor for oral squamous-cell carcinoma

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    Furuta, Hiroshi; Kondo, Yuudai [Division of Oral and Maxillofacial Surgery, Medicine of Sensory and Motor Organs, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki-gun, Miyazaki 889-1692 (Japan); Division of Tumor and Cellular Biochemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki-gun, Miyazaki 889-1692 (Japan); Nakahata, Shingo; Hamasaki, Makoto [Division of Tumor and Cellular Biochemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki-gun, Miyazaki 889-1692 (Japan); Sakoda, Sumio [Division of Oral and Maxillofacial Surgery, Medicine of Sensory and Motor Organs, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki-gun, Miyazaki 889-1692 (Japan); Morishita, Kazuhiro, E-mail: kmorishi@med.miyazaki-u.ac.jp [Division of Tumor and Cellular Biochemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki-gun, Miyazaki 889-1692 (Japan)

    2010-01-22

    Oral cancer is one of the most common cancers worldwide, and squamous-cell carcinoma (OSCC) is the most common phenotype of oral cancer. Although patients with OSCC have poor survival rates and a high incidence of metastasis, the molecular mechanisms of OSCC development have not yet been elucidated. This study investigated whether N-myc downstream-regulated gene 2 (NDRG2) contributes to the carcinogenesis of OSCC, as NDRG2 is reported to be a candidate tumor-suppressor gene in a wide variety of cancers. The down-regulation of NDRG2 mRNA, which was dependent on promoter methylation, was seen in the majority of OSCC cases and in several cases of precancerous leukoplakia with dysplasia. Induction of NDRG2 expression in an HSC-3/OSCC cell line significantly inhibited cell proliferation and decreased colony formation ability on soft agar. The majority of OSCC cell lines showed an activation of PI3K/Akt signaling, and enforced expression of NDRG2 in HSC-3 cells decreased the level of phosphorylated Akt at Serine 473 (p-Akt). Immunohistochemical p-Akt staining was detected in 56.5% of the OSCC tumors, and 80.4% of the tumors were negative for NDRG2 staining. Moreover, positive p-Akt staining was inversely correlated with decreased NDRG2 expression in OSCC tumors with moderate to poor differentiation (p < 0.005). Therefore, NDRG2 is a candidate tumor-suppressor gene for OSCC development and probably contributes to the tumorigenesis of OSCC partly via the modulation of Akt signaling.

  12. Localization of higher grade tumor foci in potential candidates for active surveillance who opt for radical prostatectomy

    Science.gov (United States)

    Hong, Sung Kyu; Eastham, James A.; Fine, Samson W.

    2013-01-01

    Purpose: To investigate actual intraprostatic location of higher graded tumor foci undetected via standard transrectal ultrasound-guided prostate biopsy amongst patients who would be clinically considered appropriate candidates for active surveillance (AS) but underwent radical prostatectomy (RP). Methods: We reviewed entirely-submitted and whole-mounted RP specimens from 169 men who were deemed appropriate for AS clinically, but opted for RP and were found to have higher grade tumors. For each case, tumor nodules were circled and color-coded in a grade-specific manner and digitally scanned to created tumor maps. The locations of tumor foci with Gleason grade ≥4 were stratified by specific sites: anterior, anterolateral, lateral only (not clearly anterior or posterior), posterior, and posterolateral area. Results: Of 169 patients, 86% had clinical stage T1c and 14% T2a. RP Gleason score 7 in all but two men. Higher-grade tumor foci were localized to: anterior (n=66, 39%), anterolateral (n=4, 2%), lateral only (not clearly anterior or posterior) (n=5, 3%), posterior (n=52, 31%), and posterolateral (n=42, 25%) prostate, respectively. Conclusions: Among patients deemed clinically appropriate for AS, higher-grade tumor foci missed by standard prostate biopsies were localized to both the anterior and posterior prostate, without predominance of a particular area. These findings lend additional support to performing repeat standard prostate biopsy in potential candidates for AS and should be considered in efforts to optimize current biopsy strategies for the selection of AS patients. PMID:24392439

  13. Low levels of tumor suppressor candidate 3 predict poor prognosis of patients with hepatocellular carcinoma

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    Sheng XR

    2018-02-01

    Full Text Available Xu-Ren Sheng,1,2,* Song-Ge Xing,2,3,* Run-Dong Wang,2 Kang Chen,2 Wei-Dong Jia1,2 1Department of Liver Surgery, Affiliated Provincial Hospital, Anhui Medical University, 2Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, 3CAS Key Laboratory of Innate Immunity and Chronic Disease, Innovation Center for Cell Signaling Network, School of Life Sciences, University of Science and Technology of China, Hefei, People’s Republic of China *These authors contributed equally to this work Purpose: The tumor suppressor candidate 3 (TUSC3 has been considered to be closely associated with the occurrence, development and invasion of various malignant tumors. However, the expression of TUSC3 in hepatocellular carcinoma (HCC tissues remains ambiguous. The purpose of this research was to investigate the expression of TUSC3 in HCC tissues and analyze the relationship between TUSC3 levels and clinicopathological characteristics and prognosis of HCC patients. Materials and methods: Immunohistochemistry was used to detect the expression of TUSC3 in HCC and the corresponding para-cancerous tissues from 92 samples of HCC patients. mRNA and protein expression levels of TUSC3 were evaluated by quantitative real-time polymerase chain reaction (qRT-PCR and Western blot assays in 25 paired HCC and corresponding adjacent nontumor tissues. Furthermore, statistical analysis was applied to evaluate the correlation between TUSC3 level and the clinicopathological features and prognosis of HCC patients. Results: Immunohistochemical assay indicated that the expression of TUSC3 was significantly lower in HCC tissues when compared with the corresponding para-cancerous tissues (χ2=11.512, P=0.001. The analysis of clinicopathological characteristics showed that low expression of TUSC3 in HCC tissues was significantly associated with Edmondson grade, Barcelona Clinic Liver Cancer stage and tumor size (P=0.008, 0.009 and 0.020, respectively. Univariate analysis showed

  14. Cancer in silico drug discovery: a systems biology tool for identifying candidate drugs to target specific molecular tumor subtypes.

    Science.gov (United States)

    San Lucas, F Anthony; Fowler, Jerry; Chang, Kyle; Kopetz, Scott; Vilar, Eduardo; Scheet, Paul

    2014-12-01

    Large-scale cancer datasets such as The Cancer Genome Atlas (TCGA) allow researchers to profile tumors based on a wide range of clinical and molecular characteristics. Subsequently, TCGA-derived gene expression profiles can be analyzed with the Connectivity Map (CMap) to find candidate drugs to target tumors with specific clinical phenotypes or molecular characteristics. This represents a powerful computational approach for candidate drug identification, but due to the complexity of TCGA and technology differences between CMap and TCGA experiments, such analyses are challenging to conduct and reproduce. We present Cancer in silico Drug Discovery (CiDD; scheet.org/software), a computational drug discovery platform that addresses these challenges. CiDD integrates data from TCGA, CMap, and Cancer Cell Line Encyclopedia (CCLE) to perform computational drug discovery experiments, generating hypotheses for the following three general problems: (i) determining whether specific clinical phenotypes or molecular characteristics are associated with unique gene expression signatures; (ii) finding candidate drugs to repress these expression signatures; and (iii) identifying cell lines that resemble the tumors being studied for subsequent in vitro experiments. The primary input to CiDD is a clinical or molecular characteristic. The output is a biologically annotated list of candidate drugs and a list of cell lines for in vitro experimentation. We applied CiDD to identify candidate drugs to treat colorectal cancers harboring mutations in BRAF. CiDD identified EGFR and proteasome inhibitors, while proposing five cell lines for in vitro testing. CiDD facilitates phenotype-driven, systematic drug discovery based on clinical and molecular data from TCGA. ©2014 American Association for Cancer Research.

  15. Localization of higher grade tumor foci in potential candidates for active surveillance who opt for radical prostatectomy

    Directory of Open Access Journals (Sweden)

    Sung Kyu Hong

    2013-12-01

    Conclusions: Among patients deemed clinically appropriate for AS, higher-grade tumor foci missed by standard prostate biopsies were localized to both the anterior and posterior prostate, without predominance of a particular area. These findings lend additional support to performing repeat standard prostate biopsy in potential candidates for AS and should be considered in efforts to optimize current biopsy strategies for the selection of AS patients.

  16. RED-ML

    DEFF Research Database (Denmark)

    Xiong, Heng; Liu, Dongbing; Li, Qiye

    2017-01-01

    using diverse RNA-seq datasets, we have developed a software tool, RED-ML: RNA Editing Detection based on Machine learning (pronounced as "red ML"). The input to RED-ML can be as simple as a single BAM file, while it can also take advantage of matched genomic variant information when available...... accurately detect novel RNA editing sites without relying on curated RNA editing databases. We have also made this tool freely available via GitHub . We have developed a highly accurate, speedy and general-purpose tool for RNA editing detection using RNA-seq data....... With the availability of RED-ML, it is now possible to conveniently make RNA editing a routine analysis of RNA-seq. We believe this can greatly benefit the RNA editing research community and has profound impact to accelerate our understanding of this intriguing posttranscriptional modification process....

  17. qcML

    DEFF Research Database (Denmark)

    Walzer, Mathias; Pernas, Lucia Espona; Nasso, Sara

    2014-01-01

    provide tools for the calculation of a wide range of quality metrics as well as a database format and interconversion tools, so that existing LIMS systems can easily add relational storage of the quality control data to their existing schema. We here describe the qcML specification, along with possible...... use cases and an illustrative example of the subsequent analysis possibilities. All information about qcML is available at http://code.google.com/p/qcml....

  18. MPS and ML

    Science.gov (United States)

    ... individuals about MPS and ML, the National MPS Society has created a central location for more information on MPS. Click here to go to the MPS Library. Share Tweet Our Mission The National MPS Society exists to cure, support and advocate for MPS ...

  19. CLAS App ML

    NARCIS (Netherlands)

    Maher, Bridget; Hartkopf, Kathleen; Stieger, Lina; Schroeder, Hanna; Sopka, Sasa; Orrego, Carola; Drachsler, Hendrik

    2014-01-01

    This is a multi-language (ML) update of the CLAS App original design by Bridget Maher from the School of Medicine at University College Cork, Ireland. The current version has an improve counting mechanism and has been translated from English to Spanish, Catalan and German languages within the

  20. Frequent silencing of the candidate tumor suppressor TRIM58 by promoter methylation in early-stage lung adenocarcinoma.

    Science.gov (United States)

    Kajiura, Koichiro; Masuda, Kiyoshi; Naruto, Takuya; Kohmoto, Tomohiro; Watabnabe, Miki; Tsuboi, Mitsuhiro; Takizawa, Hiromitsu; Kondo, Kazuya; Tangoku, Akira; Imoto, Issei

    2017-01-10

    In this study, we aimed to identify novel drivers that would be epigenetically altered through aberrant methylation in early-stage lung adenocarcinoma (LADC), regardless of the presence or absence of tobacco smoking-induced epigenetic field defects. Through genome-wide screening for aberrantly methylated CpG islands (CGIs) in 12 clinically uniform, stage-I LADC cases affecting six non-smokers and six smokers, we identified candidate tumor-suppressor genes (TSGs) inactivated by hypermethylation. Through systematic expression analyses of those candidates in panels of additional tumor samples and cell lines treated or not treated with 5-aza-deoxycitidine followed by validation analyses of cancer-specific silencing by CGI hypermethylation using a public database, we identified TRIM58 as the most prominent candidate for TSG. TRIM58 was robustly silenced by hypermethylation even in early-stage primary LADC, and the restoration of TRIM58 expression in LADC cell lines inhibited cell growth in vitro and in vivo in anchorage-dependent and -independent manners. Our findings suggest that aberrant inactivation of TRIM58 consequent to CGI hypermethylation might stimulate the early carcinogenesis of LADC regardless of smoking status; furthermore, TRIM58 methylation might be a possible early diagnostic and epigenetic therapeutic target in LADC.

  1. Genome‐wide DNA methylation analysis identifies MEGF10 as a novel epigenetically repressed candidate tumor suppressor gene in neuroblastoma

    Science.gov (United States)

    Charlet, Jessica; Tomari, Ayumi; Dallosso, Anthony R.; Szemes, Marianna; Kaselova, Martina; Curry, Thomas J.; Almutairi, Bader; Etchevers, Heather C.; McConville, Carmel; Malik, Karim T. A.

    2016-01-01

    Neuroblastoma is a childhood cancer in which many children still have poor outcomes, emphasising the need to better understand its pathogenesis. Despite recent genome‐wide mutation analyses, many primary neuroblastomas do not contain recognizable driver mutations, implicating alternate molecular pathologies such as epigenetic alterations. To discover genes that become epigenetically deregulated during neuroblastoma tumorigenesis, we took the novel approach of comparing neuroblastomas to neural crest precursor cells, using genome‐wide DNA methylation analysis. We identified 93 genes that were significantly differentially methylated of which 26 (28%) were hypermethylated and 67 (72%) were hypomethylated. Concentrating on hypermethylated genes to identify candidate tumor suppressor loci, we found the cell engulfment and adhesion factor gene MEGF10 to be epigenetically repressed by DNA hypermethylation or by H3K27/K9 methylation in neuroblastoma cell lines. MEGF10 showed significantly down‐regulated expression in neuroblastoma tumor samples; furthermore patients with the lowest‐expressing tumors had reduced relapse‐free survival. Our functional studies showed that knock‐down of MEGF10 expression in neuroblastoma cell lines promoted cell growth, consistent with MEGF10 acting as a clinically relevant, epigenetically deregulated neuroblastoma tumor suppressor gene. © 2016 The Authors. Molecular Carcinogenesis Published by Wiley Periodicals, Inc. PMID:27862318

  2. Physical mapping of a commonly deleted region, the site of a candidate tumor suppressor gene, at 12q22 in human male germ cell tumors

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    Murty, V.V.V.S.; Bosl, G.J.; Chaganti, R.S.K. [Memorial Sloan-Kettering Cancer Center, New York, NY (United States)] [and others

    1996-08-01

    A candidate tumor suppressor gene (TSG) site at 12q22 characterized by a high frequency of loss of heterozygosity (LOH) and a homozygous deletion has previously (LOH) and a homozygous deletion has previously been reported in human male germ cell tumors (GCTs). In a detailed deletion mapping analysis of 67 normal-tumor DNAs utilizing 20 polymorphic markers mapped to 12q22-q24, we identified the limits of the minimal region of deletion at 12q22 between D12S377 (priximal) and D12S296 (distal). We have constructed a YAC contig map of a 3-cM region of this band between the proximal marker D12S101 and the distal marker D12S346, which contained the minimal region of deletion in GCTs. The map is composed of 53 overlapping YACs and 3 cosmids onto which 25 polymorphic and nonpolymorphic sequence-tagged sites (STSs) were placed in a unique order. The size of the minimal region of deletion was approximately 2 Mb from overlapping, nonchimeric YACs that spanned the region. We also developed a radiation hybrid (RH) map of the region between D12S101 and D12S346 containing 17 loci. The consensus order developed by RH mapping is in good agreement with the YAC STS-content map order. The RH map estimated the distance between D12S101 and D12S346 to be 246 cR{sub 8000} and the minimal region of deletion to be 141 cR{sub 8000}. In addition, four genes that were previously mapped to 12q22 have been excluded as candidate genes. The leads gained from the deletion mapping and physical maps should expedite the isolation and characterization of the TSG at 12q22. 35 refs., 4 figs., 2 tabs.

  3. Identification of novel candidate target genes in amplicons of Glioblastoma multiforme tumors detected by expression and CGH microarray profiling

    Directory of Open Access Journals (Sweden)

    Hernández-Moneo Jose-Luis

    2006-09-01

    Full Text Available Abstract Background Conventional cytogenetic and comparative genomic hybridization (CGH studies in brain malignancies have shown that glioblastoma multiforme (GBM is characterized by complex structural and numerical alterations. However, the limited resolution of these techniques has precluded the precise identification of detailed specific gene copy number alterations. Results We performed a genome-wide survey of gene copy number changes in 20 primary GBMs by CGH on cDNA microarrays. A novel amplicon at 4p15, and previously uncharacterized amplicons at 13q32-34 and 1q32 were detected and are analyzed here. These amplicons contained amplified genes not previously reported. Other amplified regions containg well-known oncogenes in GBMs were also detected at 7p12 (EGFR, 7q21 (CDK6, 4q12 (PDGFRA, and 12q13-15 (MDM2 and CDK4. In order to identify the putative target genes of the amplifications, and to determine the changes in gene expression levels associated with copy number change events, we carried out parallel gene expression profiling analyses using the same cDNA microarrays. We detected overexpression of the novel amplified genes SLA/LP and STIM2 (4p15, and TNFSF13B and COL4A2 (13q32-34. Some of the candidate target genes of amplification (EGFR, CDK6, MDM2, CDK4, and TNFSF13B were tested in an independent set of 111 primary GBMs by using FISH and immunohistological assays. The novel candidate 13q-amplification target TNFSF13B was amplified in 8% of the tumors, and showed protein expression in 20% of the GBMs. Conclusion This high-resolution analysis allowed us to propose novel candidate target genes such as STIM2 at 4p15, and TNFSF13B or COL4A2 at 13q32-34 that could potentially contribute to the pathogenesis of these tumors and which would require futher investigations. We showed that overexpression of the amplified genes could be attributable to gene dosage and speculate that deregulation of those genes could be important in the development

  4. Analyses of susceptibility to radiation-induced tumors: Prkdc, a candidate modifier of lymphomas

    International Nuclear Information System (INIS)

    Mori, Nobuko; Okumoto, Masaaki; Nakao, Ren

    2003-01-01

    BALB/cHeA (BALB/c) mice are susceptible to radiation-induced lymphomas, while STS/A (STS) mice are resistant. To analyze the difference in susceptibility between these two strains of mice, we have performed 3 independent studies: 1) mapping of apoptosis susceptibility gene Rapopl (chromosome 16) and identification of Prkdc as a candidate modifier of apoptosis as well as lymphomas, 2) analysis of congenic lines for Lyr, a gene responsible for the lymphoma resistance of STS mice on chromosome 4, 3) genetic analyses of lymphoma susceptibility using a backcross [(BALB/c x STS)F 1 x STS]. Analysis of Rapopl congenic lines indicated a minor contribution of the STS allele at the Rapopl (Prkdc) locus to the lymphoma resistance of STS mice. On the other hand, homozygous STS alleles at Lyr had a substantial, but less potent, effect on radiation lymphomagenesis. Furthermore, there was no single marker where the potent resistance of the STS mice was achieved with the homozygous STS alleles. These results suggest potential involvement of another loci in the resistance of STS mice. (author)

  5. Link of the unique oncogenic properties of adenovirus type 9 E4-ORF1 to a select interaction with the candidate tumor suppressor protein ZO-2

    OpenAIRE

    Glaunsinger, Britt A.; Weiss, Robert S.; Lee, Siu Sylvia; Javier, Ronald

    2001-01-01

    Adenovirus type 9 (Ad9) is distinct among human adenoviruses because it elicits solely mammary tumors in animals and its primary oncogenic determinant is the E4 region-encoded ORF1 (E4-ORF1) protein. We report here that the PDZ domain-containing protein ZO-2, which is a candidate tumor suppressor protein, is a cellular target for tumorigenic Ad9 E4-ORF1 but not for non-tumorigenic wild-type E4-ORF1 proteins encoded by adenovirus types 5 and 12. Complex formation was mediated by the C-terminal...

  6. Frequent loss of heterozygosity and altered expression of the candidate tumor suppressor gene 'FAT' in human astrocytic tumors

    International Nuclear Information System (INIS)

    Chosdol, Kunzang; Misra, Anjan; Puri, Sachin; Srivastava, Tapasya; Chattopadhyay, Parthaprasad; Sarkar, Chitra; Mahapatra, Ashok K; Sinha, Subrata

    2009-01-01

    We had earlier used the comparison of RAPD (Random Amplification of Polymorphic DNA) DNA fingerprinting profiles of tumor and corresponding normal DNA to identify genetic alterations in primary human glial tumors. This has the advantage that DNA fingerprinting identifies the genetic alterations in a manner not biased for locus. In this study we used RAPD-PCR to identify novel genomic alterations in the astrocytic tumors of WHO grade II (Low Grade Diffuse Astrocytoma) and WHO Grade IV (Glioblastoma Multiforme). Loss of heterozygosity (LOH) of the altered region was studied by microsatellite and Single Nucleotide Polymorphism (SNP) markers. Expression study of the gene identified at the altered locus was done by semi-quantitative reverse-transcriptase-PCR (RT-PCR). Bands consistently altered in the RAPD profile of tumor DNA in a significant proportion of tumors were identified. One such 500 bp band, that was absent in the RAPD profile of 33% (4/12) of the grade II astrocytic tumors, was selected for further study. Its sequence corresponded with a region of FAT, a putative tumor suppressor gene initially identified in Drosophila. Fifty percent of a set of 40 tumors, both grade II and IV, were shown to have Loss of Heterozygosity (LOH) at this locus by microsatellite (intragenic) and by SNP markers. Semi-quantitative RT-PCR showed low FAT mRNA levels in a major subset of tumors. These results point to a role of the FAT in astrocytic tumorigenesis and demonstrate the use of RAPD analysis in identifying specific alterations in astrocytic tumors

  7. Superconducting magnet for 'ML-100'

    Energy Technology Data Exchange (ETDEWEB)

    Saito, R; Fujinaga, T; Tada, N; Kimura, H

    1974-07-01

    A magneticaly levitated experimental vehicle (Ml-100) was designed and constructed in commemoration of the centenary of the Japanese National Railways. For magnetic levitation the vehicle is provided with two superconducting magnets. In the test operation of the vehicle, these superconducting magnets showed stable performance in levitating vehicle body.

  8. Candidate Tumor-Suppressor Gene DLEC1 Is Frequently Downregulated by Promoter Hypermethylation and Histone Hypoacetylation in Human Epithelial Ovarian Cancer

    Directory of Open Access Journals (Sweden)

    Joseph Kwong

    2006-04-01

    Full Text Available Suppression of ovarian tumor growth by chromosome 3p was demonstrated in a previous study. Deleted in Lung and Esophageal Cancer 1 (DLEC1 on 3p22.3 is a candidate tumor suppressor in lung, esophageal, and renal cancers. The potential involvement of DLEC1 in epithelial ovarian cancer remains unknown. In the present study, DLEC1 downregulation was found in ovarian cancer cell lines and primary ovarian tumors. Focus-expressed DLEC1 in two ovarian cancer cell lines resulted in 41% to 52% inhibition of colony formation. No chromosomal loss of chromosome 3p22.3 in any ovarian cancer cell line or tissue was found. Promoter hypermethylation of DLEC1 was detected in ovarian cancer cell lines with reduced DLEC1 transcripts, whereas methylation was not detected in normal ovarian epithelium and DLEC1-expressing ovarian cancer cell lines. Treatment with demethylating agent enhanced DLEC1 expression in 90% (9 of 10 of ovarian cancer cell lines. DLEC1 promoter methylation was examined in 13 high-grade ovarian tumor tissues with DLEC1 downregulation, in which 54% of the tumors showed DLEC1 methylation. In addition, 80% of ovarian cancer cell lines significantly upregulated DLEC1 transcripts after histone deacetylase inhibitor treatment. Therefore, our results suggested that DLEC1 suppressed the growth of ovarian cancer cells and that its downregulation was closely associated with promoter hypermethylation and histone hypoacetylation.

  9. Genetic mapping in mice identifies DMBT1 as a candidate modifier of mammary tumors and breast cancer risk

    DEFF Research Database (Denmark)

    Blackburn, Anneke C; Hill, Linda Z; Roberts, Amy L

    2007-01-01

    Low-penetrance breast cancer susceptibility alleles seem to play a significant role in breast cancer risk but are difficult to identify in human cohorts. A genetic screen of 176 N2 backcross progeny of two Trp53(+/-) strains, BALB/c and C57BL/6, which differ in their susceptibility to mammary...... tumors, identified a modifier of mammary tumor susceptibility in an approximately 25-Mb interval on mouse chromosome 7 (designated SuprMam1). Relative to heterozygotes, homozygosity for BALB/c alleles of SuprMam1 significantly decreased mammary tumor latency from 70.7 to 61.1 weeks and increased risk...

  10. Reactive Programming in Standard ML

    OpenAIRE

    Pucella, Riccardo

    2004-01-01

    Reactive systems are systems that maintain an ongoing interaction with their environment, activated by receiving input events from the environment and producing output events in response. Modern programming languages designed to program such systems use a paradigm based on the notions of instants and activations. We describe a library for Standard ML that provides basic primitives for programming reactive systems. The library is a low-level system upon which more sophisticated reactive behavi...

  11. Perineural invasion and Gleason 7-10 tumors predict increased failure in prostate cancer patients with pretreatment PSA <10 ng/ml treated with conformal external beam radiation therapy

    International Nuclear Information System (INIS)

    Anderson, Penny R.; Hanlon, Alexandra L.; Patchefsky, Arthur; Al-Saleem, Tahseen; Hanks, Gerald E.

    1998-01-01

    Purpose: It has been well established that prostate cancer patients with pretreatment PSA<10 ng/ml enjoy excellent bNED control when treated with definitive external beam radiation therapy. This report identifies predictors of failure for patients with pretreatment PSA <10 ng/ml. These predictors are then used to define favorable and unfavorable prognostic subgroups of patients for which bNED control is compared. Methods and Materials: Between 3/87 and 11/94, 266 patients with T1-T3NXM0 prostate cancer and pretreatment PSA values <10 ng/ml were treated with definitive external beam radiation therapy. Median central axis dose and median follow-up for the entire group was 72 Gy (63-79 Gy) and 48 months (2-120 months). Predictors of bNED control were evaluated univariately using Kaplan-Meier methodology and the log-rank test and multivariately using Cox proportional hazards modeling. Covariates considered were pretreatment PSA, palpation stage, Gleason score, presence of perineual invasion (PNI) and central axis dose. Independent predictors based on multivariate results were then used to stratify the patients into two prognostic groups for which bNED control was compared. bNED failure is defined as PSA ≥ 1.5 ng/ml and rising on two consecutive determinations. Results: Univariate analysis according to pretreatment and treatment factors for bNED control demonstrates a statistically significant improvement in 5-year bNED control for patients with Gleason score 2-6 vs. 7-10, patients without evidence of perineural invasion (PNI) vs. those with PNI, and patients with palpation stage T1/T2AB vs. T2C/T3. Multivariate analysis demonstrates that Gleason score (p = 0.0496), PNI (p = 0.0008) and palpation stage (p = 0.0153) are significant independent predictors of bNED control. Based on these factors, patients are stratified into a more favorable prognosis group (Gleason 2-6, no PNI, and stage T1/T2AB, n = 172) and a less favorable prognosis group (Gleason 7-10 or PNI or T2C

  12. Styrene-maleic acid-copolymer conjugated zinc protoporphyrin as a candidate drug for tumor-targeted therapy and imaging.

    Science.gov (United States)

    Fang, Jun; Tsukigawa, Kenji; Liao, Long; Yin, Hongzhuan; Eguchi, Kanami; Maeda, Hiroshi

    2016-01-01

    Previous studies indicated the potential of zinc protoporphyrin (ZnPP) as an antitumor agent targeting to the tumor survival factor heme oxygenase-1, and/or for photodynamic therapy (PDT). In this study, to achieve tumor-targeted delivery, styrene-maleic acid-copolymer conjugated ZnPP (SMA-ZnPP) was synthesized via amide bond, which showed good water solubility, having ZnPP loading of 15%. More importantly, it forms micelles in aqueous solution with a mean particle size of 111.6 nm, whereas it has an apparent Mw of 65 kDa. This micelle formation was not detracted by serum albumin, suggesting it is stable in circulation. Further SMA-ZnPP conjugate will behave as an albumin complex in blood with much larger size (235 kDa) by virtue of the albumin binding property of SMA. Consequently, SMA-ZnPP conjugate exhibited prolonged circulating retention and preferential tumor accumulation by taking advantage of enhanced permeability and retention (EPR) effect. Clear tumor imaging was thus achieved by detecting the fluorescence of ZnPP. In addition, the cytotoxicity and PDT effect of SMA-ZnPP conjugate was confirmed in human cervical cancer HeLa cells. Light irradiation remarkably increased the cytotoxicity (IC50, from 33 to 5 μM). These findings may provide new options and knowledge for developing ZnPP based anticancer theranostic drugs.

  13. Systematic identification and validation of candidate genes for detection of circulating tumor cells in peripheral blood specimens of colorectal cancer patients.

    Science.gov (United States)

    Findeisen, Peter; Röckel, Matthias; Nees, Matthias; Röder, Christian; Kienle, Peter; Von Knebel Doeberitz, Magnus; Kalthoff, Holger; Neumaier, Michael

    2008-11-01

    The presence of tumor cells in peripheral blood is being regarded increasingly as a clinically relevant prognostic factor for colorectal cancer patients. Current molecular methods are very sensitive but due to low specificity their diagnostic value is limited. This study was undertaken in order to systematically identify and validate new colorectal cancer (CRC) marker genes for improved detection of minimal residual disease in peripheral blood mononuclear cells of colorectal cancer patients. Marker genes with upregulated gene expression in colorectal cancer tissue and cell lines were identified using microarray experiments and publicly available gene expression data. A systematic iterative approach was used to reduce a set of 346 candidate genes, reportedly associated with CRC to a selection of candidate genes that were then further validated by relative quantitative real-time RT-PCR. Analytical sensitivity of RT-PCR assays was determined by spiking experiments with CRC cells. Diagnostic sensitivity as well as specificity was tested on a control group consisting of 18 CRC patients compared to 12 individuals without malignant disease. From a total of 346-screened genes only serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 5 (SERPINB5) showed significantly elevated transcript levels in peripheral venous blood specimens of tumor patients when compared to the nonmalignant control group. These results were confirmed by analysis of an enlarged collective consisting of 63 CRC patients and 36 control individuals without malignant disease. In conclusion SERPINB5 seems to be a promising marker for detection of circulating tumor cells in peripheral blood of colorectal cancer patients.

  14. Combined use of expression and CGH arrays pinpoints novel candidate genes in Ewing sarcoma family of tumors

    International Nuclear Information System (INIS)

    Savola, Suvi; Knuutila, Sakari; Klami, Arto; Tripathi, Abhishek; Niini, Tarja; Serra, Massimo; Picci, Piero; Kaski, Samuel; Zambelli, Diana; Scotlandi, Katia

    2009-01-01

    Ewing sarcoma family of tumors (ESFT), characterized by t(11;22)(q24;q12), is one of the most common tumors of bone in children and young adults. In addition to EWS/FLI1 gene fusion, copy number changes are known to be significant for the underlying neoplastic development of ESFT and for patient outcome. Our genome-wide high-resolution analysis aspired to pinpoint genomic regions of highest interest and possible target genes in these areas. Array comparative genomic hybridization (CGH) and expression arrays were used to screen for copy number alterations and expression changes in ESFT patient samples. A total of 31 ESFT samples were analyzed by aCGH and in 16 patients DNA and RNA level data, created by expression arrays, was integrated. Time of the follow-up of these patients was 5–192 months. Clinical outcome was statistically evaluated by Kaplan-Meier/Logrank methods and RT-PCR was applied on 42 patient samples to study the gene of the highest interest. Copy number changes were detected in 87% of the cases. The most recurrent copy number changes were gains at 1q, 2, 8, and 12, and losses at 9p and 16q. Cumulative event free survival (ESFT) and overall survival (OS) were significantly better (P < 0.05) for primary tumors with three or less copy number changes than for tumors with higher number of copy number aberrations. In three samples copy number imbalances were detected in chromosomes 11 and 22 affecting the FLI1 and EWSR1 loci, suggesting that an unbalanced t(11;22) and subsequent duplication of the derivative chromosome harboring fusion gene is a common event in ESFT. Further, amplifications on chromosomes 20 and 22 seen in one patient sample suggest a novel translocation type between EWSR1 and an unidentified fusion partner at 20q. In total 20 novel ESFT associated putative oncogenes and tumor suppressor genes were found in the integration analysis of array CGH and expression data. Quantitative RT-PCR to study the expression levels of the most interesting

  15. NBPF1, a tumor suppressor candidate in neuroblastoma, exerts growth inhibitory effects by inducing a G1 cell cycle arrest

    International Nuclear Information System (INIS)

    Andries, Vanessa; Vandepoele, Karl; Staes, Katrien; Berx, Geert; Bogaert, Pieter; Van Isterdael, Gert; Ginneberge, Daisy; Parthoens, Eef; Vandenbussche, Jonathan; Gevaert, Kris; Roy, Frans van

    2015-01-01

    NBPF1 (Neuroblastoma Breakpoint Family, member 1) was originally identified in a neuroblastoma patient on the basis of its disruption by a chromosomal translocation t(1;17)(p36.2;q11.2). Considering this genetic defect and the frequent genomic alterations of the NBPF1 locus in several cancer types, we hypothesized that NBPF1 is a tumor suppressor. Decreased expression of NBPF1 in neuroblastoma cell lines with loss of 1p36 heterozygosity and the marked decrease of anchorage-independent clonal growth of DLD1 colorectal carcinoma cells with induced NBPF1 expression further suggest that NBPF1 functions as tumor suppressor. However, little is known about the mechanisms involved. Expression of NBPF was analyzed in human skin and human cervix by immunohistochemistry. The effects of NBPF1 on the cell cycle were evaluated by flow cytometry. We investigated by real-time quantitative RT-PCR the expression profile of a panel of genes important in cell cycle regulation. Protein levels of CDKN1A-encoded p21 CIP1/WAF1 were determined by western blotting and the importance of p53 was shown by immunofluorescence and by a loss-of-function approach. LC-MS/MS analysis was used to investigate the proteome of DLD1 colon cancer cells with induced NBPF1 expression. Possible biological interactions between the differentially regulated proteins were investigated with the Ingenuity Pathway Analysis tool. We show that NBPF is expressed in the non-proliferative suprabasal layers of squamous stratified epithelia of human skin and cervix. Forced expression of NBPF1 in HEK293T cells resulted in a G1 cell cycle arrest that was accompanied by upregulation of the cyclin-dependent kinase inhibitor p21 CIP1/WAF1 in a p53-dependent manner. Additionally, forced expression of NBPF1 in two p53-mutant neuroblastoma cell lines also resulted in a G1 cell cycle arrest and CDKN1A upregulation. However, CDKN1A upregulation by NBPF1 was not observed in the DLD1 cells, which demonstrates that NBPF1 exerts cell

  16. Psychological consideration in patients with cerebral gliomas candidates for intra-operative radiation therapy based on tumor location.

    Science.gov (United States)

    Seddighi, Afsoun; Akbari, Mohammad Esmaeil; Seddighi, Amir Saied; Nikouei, Amir

    2017-01-01

    Intra-operative Radiation Therapy (IORT) is gaining popularity as an adjuvant option to surgical resection, in treatment of glioblastoma multiforme (GBM) for increasing survival rate, which a highly aggressive cerebral tumor with poor prognosis. Τhe authors plan to investigate the effects of IORT combined with surgical resection on the psychological status of these patients based on tumor location. From December 2013 to February 2017, we have enrolled 109 patients with high grade cerebral gliomas, documented by Magnetic Resonance Spectroscopy (MRS). Patients with previous history of brain surgery or radiation, altered mental status and psychological content and patients diagnosed with metastases were excluded. Demographic data, tumor volume based on pre-operative Magnetic Resonance Imaging (MRI) and psychological status were recorded based on Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition (DSM-IV) criteria. The remaining 56 patients, were equally randomized into conventional (surgical resection-group A), and trial (surgical resection with IORT-group B) who underwent IORT using the 50kV INTRABEAM® system (Carl Zeiss Meditec AG, Germany). Psychological profiles of both groups were re-evaluated in the 3 rd post-operative month. Group A consisted of 18 males and 10 females with mean age of 54.4 years, while group B consisted of 16 males and 12 females with mean age of 57.8 years. Tumor volumetry revealed mean 81.52cc and 82.8cc for group A and B respectively. (P value 0.14) Patients were classified based on glioma location on pre-operative MRI: a) left parietal lobe (6 in group A, 5 in group B); b) left temporal lobe (7 in group A, 5 in group B); c) right parietal lobe (5 in group A, 6 in group B); d) left fronto-temporal lobe (4 in group A, 6 in group B); e) left parieto-temporal lobe (4 in group A, 5 in group B); and, f) right frontal lobe (2 in group A, 1 in group B). Group B received mean 8.05 Gy radiation for mean 11.2 minutes. Post

  17. CDKN1C/p57kip2 is a candidate tumor suppressor gene in human breast cancer

    International Nuclear Information System (INIS)

    Larson, Pamela S; Schlechter, Benjamin L; King, Chia-Lin; Yang, Qiong; Glass, Chelsea N; Mack, Charline; Pistey, Robert; Morenas, Antonio de las; Rosenberg, Carol L

    2008-01-01

    CDKN1C (also known as p57 KIP2 ) is a cyclin-dependent kinase inhibitor previously implicated in several types of human cancer. Its family members (CDKN1A/p21 CIP1 and B/p27 KIP1 ) have been implicated in breast cancer, but information about CDKN1C's role is limited. We hypothesized that decreased CDKN1C may be involved in human breast carcinogenesis in vivo. We determined rates of allele imbalance or loss of heterozygosity (AI/LOH) in CDKN1C, using an intronic polymorphism, and in the surrounding 11p15.5 region in 82 breast cancers. We examined the CDKN1C mRNA level in 10 cancers using quantitative real-time PCR (qPCR), and the CDKN1C protein level in 20 cancers using immunohistochemistry (IHC). All samples were obtained using laser microdissection. Data were analyzed using standard statistical tests. AI/LOH at 11p15.5 occurred in 28/73 (38%) informative cancers, but CDKN1C itself underwent AI/LOH in only 3/16 (19%) cancers (p = ns). In contrast, CDKN1C mRNA levels were reduced in 9/10 (90%) cancers (p < 0.0001), ranging from 2–60% of paired normal epithelium. Similarly, CDKN1C protein staining was seen in 19/20 (95%) cases' normal epithelium but in only 7/14 (50%) cases' CIS (p < 0.004) and 5/18 (28%) cases' IC (p < 0.00003). The reduction appears primarily due to loss of CDKN1C expression from myoepithelial layer cells, which stained intensely in 17/20 (85%) normal lobules, but in 0/14 (0%) CIS (p < 0.00001). In contrast, luminal cells displayed less intense, focal staining fairly consistently across histologies. Decreased CDKN1C was not clearly associated with tumor grade, histology, ER, PR or HER2 status. CDKN1C is expressed in normal epithelium of most breast cancer cases, mainly in the myothepithelial layer. This expression decreases, at both the mRNA and protein level, in the large majority of breast cancers, and does not appear to be mediated by AI/LOH at the gene. Thus, CDKN1C may be a breast cancer tumor suppressor

  18. The Bonding of Pa to d8-ML3 Complexes

    OpenAIRE

    Kang, Sung-Kwon; Albright, Thomas A.; Silvestre, Jerome

    1985-01-01

    Extended Hiickel calculmions were carried out on 171, 'f/ 2, and 'f/3 complexes of P4 to Rh(PH3)2Cl. The 'f/ 1-square planar and an 'f/2 complex with C2v symmetry are the most stable. Geometrical optimizations and a detailed account of the bonding in each have been carried out. d10 'f/1-tetrahedral complexes of P4 are expected to be quite stable. The best candidate for an 'f/3 mode of bonding is the trimer Fe3(C0)9. Alternative complexes at 'f/3 include a d6-ML3 and d4-ML...

  19. Description of the sodium loop ML-3

    International Nuclear Information System (INIS)

    Torre, de la M.; Melches, I; Lapena, J.; Martinez, T.A.; Miguel, de D.; Duran, F.

    1979-01-01

    The sodium loop ML-3 is described. The main objective of this facility is to obtain mechanical property data for LMFBR materials in creep and low cycle fatigue testing in flowing sodium. ML-3 includes 10 test stations for creep and two for fatigue. It is possible to operate simultaneously at three different temperature levels. The maximum operating temperature is 650 deg C at flow velocities up to 5 m/s. The ML-3 loop has been located in a manner that permits the fill/dump tank cover gas and security systems to be shared with an earlier circuit, the ML-1. (author)

  20. Malignant lymphomas (ML and HIV infection in Tanzania

    Directory of Open Access Journals (Sweden)

    Mwakigonja Amos R

    2008-06-01

    Full Text Available Abstract Background HIV infection is reported to be associated with some malignant lymphomas (ML so called AIDS-related lymphomas (ARL, with an aggressive behavior and poor prognosis. The ML frequency, pathogenicity, clinical patterns and possible association with AIDS in Tanzania, are not well documented impeding the development of preventive and therapeutic strategies. Methods Sections of 176 archival formalin-fixed paraffin-embedded biopsies of ML patients at Muhimbili National Hospital (MNH/Muhimbili University of Health and Allied Sciences (MUHAS, Tanzania from 1996–2001 were stained for hematoxylin and eosin and selected (70 cases for expression of pan-leucocytic (CD45, B-cell (CD20, T-cell (CD3, Hodgkin/RS cell (CD30, histiocyte (CD68 and proliferation (Ki-67 antigen markers. Corresponding clinical records were also evaluated. Available sera from 38 ML patients were screened (ELISA for HIV antibodies. Results The proportion of ML out of all diagnosed tumors at MNH during the 6 year period was 4.2% (176/4200 comprising 77.84% non-Hodgkin (NHL including 19.32% Burkitt's (BL and 22.16% Hodgkin's disease (HD. The ML tumors frequency increased from 0.42% (1997 to 0.70% (2001 and 23.7% of tested sera from these patients were HIV positive. The mean age for all ML was 30, age-range 3–91 and peak age was 1–20 years. The male:female ratio was 1.8:1. Supra-diaphragmatic presentation was commonest and histological sub-types were mostly aggressive B-cell lymphomas however, no clear cases of primary effusion lymphoma (PEL and primary central nervous system lymphoma (PCNSL were diagnosed. Conclusion Malignant lymphomas apparently, increased significantly among diagnosed tumors at MNH between 1996 and 2001, predominantly among the young, HIV infected and AIDS patients. The frequent aggressive clinical and histological presentation as well as the dominant B-immunophenotype and the HIV serology indicate a pathogenic association with AIDS. Therefore

  1. Malignant lymphomas (ML) and HIV infection in Tanzania.

    Science.gov (United States)

    Mwakigonja, Amos R; Kaaya, Ephata E; Mgaya, Edward M

    2008-06-10

    HIV infection is reported to be associated with some malignant lymphomas (ML) so called AIDS-related lymphomas (ARL), with an aggressive behavior and poor prognosis. The ML frequency, pathogenicity, clinical patterns and possible association with AIDS in Tanzania, are not well documented impeding the development of preventive and therapeutic strategies. Sections of 176 archival formalin-fixed paraffin-embedded biopsies of ML patients at Muhimbili National Hospital (MNH)/Muhimbili University of Health and Allied Sciences (MUHAS), Tanzania from 1996-2001 were stained for hematoxylin and eosin and selected (70) cases for expression of pan-leucocytic (CD45), B-cell (CD20), T-cell (CD3), Hodgkin/RS cell (CD30), histiocyte (CD68) and proliferation (Ki-67) antigen markers. Corresponding clinical records were also evaluated. Available sera from 38 ML patients were screened (ELISA) for HIV antibodies. The proportion of ML out of all diagnosed tumors at MNH during the 6 year period was 4.2% (176/4200) comprising 77.84% non-Hodgkin (NHL) including 19.32% Burkitt's (BL) and 22.16% Hodgkin's disease (HD). The ML tumors frequency increased from 0.42% (1997) to 0.70% (2001) and 23.7% of tested sera from these patients were HIV positive. The mean age for all ML was 30, age-range 3-91 and peak age was 1-20 years. The male:female ratio was 1.8:1. Supra-diaphragmatic presentation was commonest and histological sub-types were mostly aggressive B-cell lymphomas however, no clear cases of primary effusion lymphoma (PEL) and primary central nervous system lymphoma (PCNSL) were diagnosed. Malignant lymphomas apparently, increased significantly among diagnosed tumors at MNH between 1996 and 2001, predominantly among the young, HIV infected and AIDS patients. The frequent aggressive clinical and histological presentation as well as the dominant B-immunophenotype and the HIV serology indicate a pathogenic association with AIDS. Therefore, routine HIV screening of all malignant lymphoma

  2. ML Arvutite aktsiakapital suurenes / Anne Oja

    Index Scriptorium Estoniae

    Oja, Anne, 1970-

    2006-01-01

    ML Arvutid omanik Aivar Paalberg tõstis aktsiakapitali seniselt 10 miljonilt 24 miljonile eesmärgiga tugevdada oma positsioone Eesti turul ja kasvada kiiremas tempos kui kogu turg. Diagramm: Majandusnäitajad

  3. CellML, SED-ML, and the Physiome Model Repository

    OpenAIRE

    Nickerson, David

    2016-01-01

    Invited presentation delivered at COMBINE 2016.CellML, SED-ML, and the Physiome Model Repository.David Nickerson, Auckland Bioengineering Institute, University of Auckland, New Zealand.CellML is an XML-based protocol for storing and exchanging computer-based mathematical models in an unambiguous, modular, and reusable manner. In addition to introducing CellML, in this presentation I will provide some of physiological examples that have help drive the development and adoption of CellML. I will...

  4. ML Confidential : machine learning on encrypted data

    NARCIS (Netherlands)

    Graepel, T.; Lauter, K.; Naehrig, M.

    2012-01-01

    We demonstrate that by using a recently proposed somewhat homomorphic encryption (SHE) scheme it is possible to delegate the execution of a machine learning (ML) algorithm to a compute service while retaining confidentiality of the training and test data. Since the computational complexity of the

  5. HEP meets ML award talk : XGBoost

    CERN Multimedia

    CERN. Geneva; CHEN, Tianqi

    2015-01-01

    Tianqi Chen and Tong He (team crowwork) have provided very early in the challenge to all participants XGBoost (for eXtreme Gradient Boosted). It is a parallelised software to train boost decision trees, which has been effectively used by many participants to the challenge. For this, they have won the "HEP meets ML" award which is the invitation to CERN happening today.

  6. Identification of Two Candidate Tumor Suppressor Genes on Chromosome 17p13.3: Assessment of Their Roles in Breast and Ovarian Carcinogenesis

    National Research Council Canada - National Science Library

    Godwin, Andrew

    1998-01-01

    .... To date, we have found that: (1) OVCA2 is a new gene residing in a chromosomal region which is frequently lost in breast, brain, colon, ovarian tumors, acute myeloid leukemia and myelodysplastic syndromes, (2...

  7. GeoSciML and EarthResourceML Update, 2012

    Science.gov (United States)

    Richard, S. M.; Commissionthe Management; Application Inte, I.

    2012-12-01

    CGI Interoperability Working Group activities during 2012 include deployment of services using the GeoSciML-Portrayal schema, addition of new vocabularies to support properties added in version 3.0, improvements to server software for deploying services, introduction of EarthResourceML v.2 for mineral resources, and collaboration with the IUSS on a markup language for soils information. GeoSciML and EarthResourceML have been used as the basis for the INSPIRE Geology and Mineral Resources specifications respectively. GeoSciML-Portrayal is an OGC GML simple-feature application schema for presentation of geologic map unit, contact, and shear displacement structure (fault and ductile shear zone) descriptions in web map services. Use of standard vocabularies for geologic age and lithology enables map services using shared legends to achieve visual harmonization of maps provided by different services. New vocabularies have been added to the collection of CGI vocabularies provided to support interoperable GeoSciML services, and can be accessed through http://resource.geosciml.org. Concept URIs can be dereferenced to obtain SKOS rdf or html representations using the SISSVoc vocabulary service. New releases of the FOSS GeoServer application greatly improve support for complex XML feature schemas like GeoSciML, and the ArcGIS for INSPIRE extension implements similar complex feature support for ArcGIS Server. These improved server implementations greatly facilitate deploying GeoSciML services. EarthResourceML v2 adds features for information related to mining activities. SoilML provides an interchange format for soil material, soil profile, and terrain information. Work is underway to add GeoSciML to the portfolio of Open Geospatial Consortium (OGC) specifications.

  8. CytometryML and other data formats

    Science.gov (United States)

    Leif, Robert C.

    2006-02-01

    Cytology automation and research will be enhanced by the creation of a common data format. This data format would provide the pathology and research communities with a uniform way for annotating and exchanging images, flow cytometry, and associated data. This specification and/or standard will include descriptions of the acquisition device, staining, the binary representations of the image and list-mode data, the measurements derived from the image and/or the list-mode data, and descriptors for clinical/pathology and research. An international, vendor-supported, non-proprietary specification will allow pathologists, researchers, and companies to develop and use image capture/analysis software, as well as list-mode analysis software, without worrying about incompatibilities between proprietary vendor formats. Presently, efforts to create specifications and/or descriptions of these formats include the Laboratory Digital Imaging Project (LDIP) Data Exchange Specification; extensions to the Digital Imaging and Communications in Medicine (DICOM); Open Microscopy Environment (OME); Flowcyt, an extension to the present Flow Cytometry Standard (FCS); and CytometryML. The feasibility of creating a common data specification for digital microscopy and flow cytometry in a manner consistent with its use for medical devices and interoperability with both hospital information and picture archiving systems has been demonstrated by the creation of the CytometryML schemas. The feasibility of creating a software system for digital microscopy has been demonstrated by the OME. CytometryML consists of schemas that describe instruments and their measurements. These instruments include digital microscopes and flow cytometers. Optical components including the instruments' excitation and emission parts are described. The description of the measurements made by these instruments includes the tagged molecule, data acquisition subsystem, and the format of the list-mode and/or image data. Many

  9. AllerML: markup language for allergens.

    Science.gov (United States)

    Ivanciuc, Ovidiu; Gendel, Steven M; Power, Trevor D; Schein, Catherine H; Braun, Werner

    2011-06-01

    Many concerns have been raised about the potential allergenicity of novel, recombinant proteins into food crops. Guidelines, proposed by WHO/FAO and EFSA, include the use of bioinformatics screening to assess the risk of potential allergenicity or cross-reactivities of all proteins introduced, for example, to improve nutritional value or promote crop resistance. However, there are no universally accepted standards that can be used to encode data on the biology of allergens to facilitate using data from multiple databases in this screening. Therefore, we developed AllerML a markup language for allergens to assist in the automated exchange of information between databases and in the integration of the bioinformatics tools that are used to investigate allergenicity and cross-reactivity. As proof of concept, AllerML was implemented using the Structural Database of Allergenic Proteins (SDAP; http://fermi.utmb.edu/SDAP/) database. General implementation of AllerML will promote automatic flow of validated data that will aid in allergy research and regulatory analysis. Copyright © 2011 Elsevier Inc. All rights reserved.

  10. OpenML : An R package to connect to the machine learning platform OpenML

    NARCIS (Netherlands)

    Casalicchio, G.; Bossek, J.; Lang, M.; Kirchhoff, D.; Kerschke, P.; Hofner, B.; Seibold, H.; Vanschoren, J.; Bischl, B.

    2017-01-01

    OpenML is an online machine learning platform where researchers can easily share data, machine learning tasks and experiments as well as organize them online to work and collaborate more efficiently. In this paper, we present an R package to interface with the OpenML platform and illustrate its

  11. Using VS30 to Estimate Station ML Adjustments (dML)

    Science.gov (United States)

    Yong, A.; Herrick, J.; Cochran, E. S.; Andrews, J. R.; Yu, E.

    2017-12-01

    Currently, new seismic stations added to a regional seismic network cannot be used to calculate local or Richter magnitude (ML) until a revised region-wide amplitude decay function is developed. The new station must record a minimum number of local and regional events that meet specific amplitude requirements prior to re-calibration of the amplitude decay function. Therefore, there can be significant delay between when a new station starts contributing real-time waveform packets and when the data can be included in magnitude estimation. The station component adjustments (dML; Uhrhammer et al., 2011) are calculated after first inverting for a new regional amplitude decay function, constrained by the sum of dML for long-running stations. Here, we propose a method to calculate an initial dML using known or proxy values of seismic site conditions. For site conditions, we use the time-averaged shear-wave velocity (VS) of the upper 30 m (VS30). We solve for dML as described in Equation (1) by Uhrhammer et al. (2011): ML = log (A) - log A0 (r) + dML, where A is the maximum Wood and Anderson (1925) trace amplitude (mm), r is the distance (km), and dML is the station adjustment. Measured VS30 and estimated dML data are comprised of records from 887 horizontal components (east-west and north-south orientations) from 93 seismic monitoring stations in the California Integrated Seismic Network. VS30 values range from 202 m/s to 1464 m/s and dML range from -1.10 to 0.39. VS30 and dML exhibit a positive correlation coefficient (R = 0.72), indicating that as VS30 increases, dML increases. This implies that greater site amplification (i.e., lower VS30) results in smaller ML. When we restrict VS30 regional network ML estimates immediately without the need to wait until a minimum set of earthquake data has been recorded.

  12. White cell labeling: 20 ML VS 4 ML of blood volume-case reports

    International Nuclear Information System (INIS)

    Imam, S.K.

    1998-01-01

    Full text: Some times, it becomes difficult to draw 20 mL blood from a patient with bad veins. On two occasions, we could collect only about 4 mL of blood, that too with a great deal of struggle, and then we carried out the routine labelling procedure. A labelling efficiency of 98.2% and 95.6% was achieved. The white cell scan was negative in one patient, but positive in the next one. In a third patient, a comparison of labelling efficiency was done between 5 and 20 mLs of blood volumes separately and the results were found to be identical, 98.5% and 98.4%, respectively. As we have achieved the usual pattern of white cell scan with as low as 4-5 mL of blood, it appears that enough number of white cells is present even in the 4-5 mL of blood that is capable of generating a white cell scan and so, it seems rational to reduce the blood volume from 20 mL to 4 or 5 mL. However, further studies are warranted before adopting this modification. The procedure appears to carry the following advantages: ease of blood collection, handling and re-injection and less risk to the patient

  13. A practical guide to SysML the systems modeling language

    CERN Document Server

    Friendenthal,Sanford; Steiner, Rick

    2009-01-01

    This book is the bestselling, authoritative guide to SysML for systems and software engineers, providing a comprehensive and practical resource for modeling systems with SysML. Fully updated to cover newly released version 1.3, it includes a full description of the modeling language along with a quick reference guide, and shows how an organization or project can transition to model-based systems engineering using SysML, with considerations for processes, methods, tools, and training. Numerous examples help readers understand how SysML can be used in practice, while reference material facilitates studying for the OMG Systems Modeling Professional (OCSMP) Certification Program, designed to test candidates' knowledge of SysML and their ability to use models to represent real-world systems.

  14. International Conference ML4CPS 2016

    CERN Document Server

    Niggemann, Oliver; Kühnert, Christian

    2017-01-01

    The work presents new approaches to Machine Learning for Cyber Physical Systems, experiences and visions. It contains some selected papers from the international Conference ML4CPS – Machine Learning for Cyber Physical Systems, which was held in Karlsruhe, September 29th, 2016. Cyber Physical Systems are characterized by their ability to adapt and to learn: They analyze their environment and, based on observations, they learn patterns, correlations and predictive models. Typical applications are condition monitoring, predictive maintenance, image processing and diagnosis. Machine Learning is the key technology for these developments. The Editors Prof. Dr.-Ing. Jürgen Beyerer is Professor at the Department for Interactive Real-Time Systems at the Karlsruhe Institute of Technology. In addition he manages the Fraunhofer Institute of Optronics, System Technologies and Image Exploitation IOSB. Prof. Dr. Oliver Niggemann is Professor for Embedded Software Engineering. His research interests are in the field of Di...

  15. 64 kDa protein is a candidate for a thyrotropin-releasing hormone receptor in prolactin-producing rat pituitary tumor cells (GH4C1 cells)

    International Nuclear Information System (INIS)

    Wright, M.; Hogset, A.; Alestrom, P.; Gautvik, K.M.

    1988-01-01

    A thyrotropin-releasing hormone (TRH) binding protein of 64 kDa has been identified by covalently crosslinking [ 3 H]TRH to GH4C1 cells by ultraviolet illumination. The crosslinkage of [ 3 H]TRH is UV-dose dependent and is inhibited by an excess of unlabeled TRH. A 64 kDa protein is also detected on immunoblots using an antiserum raised against GH4C1 cell surface epitopes. In a closely related cell line (GH12C1) which does not bind [ 3 H]TRH, the 64 kDa protein cannot be demonstrated by [ 3 H]TRH crosslinking nor by immunoblotting. These findings indicate that the 64 kDa protein is a candidate for a TRH-receptor protein in GH4C1 cells

  16. The Ozobranchus leech is a candidate mechanical vector for the fibropapilloma-associated turtle herpesvirus found latently infecting skin tumors on Hawaiian green turtles (Chelonia mydas)

    International Nuclear Information System (INIS)

    Greenblatt, Rebecca J.; Work, Thierry M.; Balazs, George H.; Sutton, Claudia A.; Casey, Rufina N.; Casey, James W.

    2004-01-01

    Fibropapillomatosis (FP) of marine turtles is a neoplastic disease of ecological concern. A fibropapilloma-associated turtle herpesvirus (FPTHV) is consistently present, usually at loads exceeding one virus copy per tumor cell. DNA from an array of parasites of green turtles (Chelonia mydas) was examined with quantitative PCR (qPCR) to determine whether any carried viral loads are sufficient to implicate them as vectors for FPTHV. Marine leeches (Ozobranchus spp.) were found to carry high viral DNA loads; some samples approached 10 million copies per leech. Isopycnic sucrose density gradient/qPCR analysis confirmed that some of these copies were associated with particles of the density of enveloped viruses. The data implicate the marine leech Ozobranchus as a mechanical vector for FPTHV. Quantitative RT-PCR analysis of FPTHV gene expression indicated that most of the FPTHV copies in a fibropapilloma have restricted DNA polymerase expression, suggestive of latent infection

  17. Machine learning (ML)-guided OPC using basis functions of polar Fourier transform

    Science.gov (United States)

    Choi, Suhyeong; Shim, Seongbo; Shin, Youngsoo

    2016-03-01

    With shrinking feature size, runtime has become a limitation of model-based OPC (MB-OPC). A few machine learning-guided OPC (ML-OPC) have been studied as candidates for next-generation OPC, but they all employ too many parameters (e.g. local densities), which set their own limitations. We propose to use basis functions of polar Fourier transform (PFT) as parameters of ML-OPC. Since PFT functions are orthogonal each other and well reflect light phenomena, the number of parameters can significantly be reduced without loss of OPC accuracy. Experiments demonstrate that our new ML-OPC achieves 80% reduction in OPC time and 35% reduction in the error of predicted mask bias when compared to conventional ML-OPC.

  18. New candidate tumor-suppressor gene KLF6 and its splice variant KLF6 SV2 counterbalancing expression in primary hepatocarcinoma.

    Science.gov (United States)

    Zhenzhen, Zhou; De'an, Tian; Limin, Xia; Wei, Yan; Min, Luo

    2012-01-01

    This study aimed to detect the expression of newly discovered zinc finger transcriptional factor KLF6 and its splice variant KLF6 SV2 in primary hepatocarcinoma (PHC) tissues and hepatoma cell strains, and to evaluate their clinicopathologic relationship with PHC. Wild-type KLF6 and KLF6 SV2 mRNA expression was determined by RTPCR in 27 cases of PHC tissues and cell strains of HepG2, SMMC7721 and LO2. Western blotting and immunohistochemical staining were adopted to detect KLF6 protein expression. Positive area ratio of wild-type KLF6 protein expression and its relationship with clinicopathological parameters of PHC was analyzed. Wild-type KLF6 expression in PHC tissues was lower than that in paracancerous tissues. In contrast, KLF6 SV2 mRNA expression was higher in PHC tissues and hepatoma cell strains (p<0.05). Positive area ratio of wild-type KLF6 protein expression was positively correlated with cellular differentiation degree of PHC (p<0.01), but negatively correlated not only with liver cirrhosis, tumor size and extrahepatic metastases (p<0.01), but also with portal vein thrombus and the number of lymph nodes with metastasis (p<0.05). Wild-type KLF6 deletion and inactivation was involved in the growth, cell differentiation and other physiological processes of PHC. The upregulation of KLF6 splice variant might counterbalance the wildtype KLF6 and contribute to the occurrence and development of PHC.

  19. Impact of ER520, a candidate of selective estrogen receptor modulators, on in vitro cell growth, migration, invasion, angiogenesis and in vivo tumor xenograft of human breast cancer cells.

    Science.gov (United States)

    Wang, Lijun; Wang, Ying; Du, Huaqing; Jiang, Yao; Tang, Zhichao; Liu, Hongyi; Xiang, Hua; Xiao, Hong

    2015-12-01

    ER520, a derivative of indenoisoquinoline, is a patented compound. This study was designed to screen its biological properties and to evaluate its antineoplastic and antiangiogenic effect. Western blot was employed to monitor the ERα and ERβ protein expression in human breast cancer MCF-7 cells and endometrial carcinoma Ishikawa cells. MTT assay was employed to determine cell proliferation. Cell adhesion, scratch and Transwell assay were utilized to estimate the ability of cellular adhesion, migration and invasion. ELISA kit was applied to detect the VEGF products in culture medium. In addition, the inhibitory effect of ER520 on the vessel-like construction of HUVEC cells and the angiogenesis of chicken embryos was investigated. The efficiency of ER520 on tumor growth in nude mice was also assessed. ER520 inhibited the expression of ERα in MCF-7 and Ishikawa cells, while it increased ERβ protein level. ER520 also suppressed the proliferation of MCF-7 and Ishikawa cells. Due to its remarkably negative role in cell adhesion, migration and invasion, ER520 showed a potential ability of inhibiting tumor metastasis. Meanwhile, ER520 reduced the VEGF secretion of MCF-7 and Ishikawa cells, prevented the formation of VEGF-stimulated tubular structure and the cell migration of HUVEC cells, and inhibited the angiogenesis of chicken chorioallantoic membrane. Animal experiment also demonstrated that ER520 could frustrate the in vivo tumor growth and the inhibitory ratio was 48.5 % compared with control group. Our findings indicate that ER520 possesses the competence to be a candidate against breast cancer and angiogenesis.

  20. ML 3.1 developer's guide.

    Energy Technology Data Exchange (ETDEWEB)

    Sala, Marzio; Hu, Jonathan Joseph (Sandia National Laboratories, Livermore, CA); Tuminaro, Raymond Stephen (Sandia National Laboratories, Livermore, CA)

    2004-05-01

    ML development was started in 1997 by Ray Tuminaro and Charles Tong. Currently, there are several full- and part-time developers. The kernel of ML is written in ANSI C, and there is a rich C++ interface for Trilinos users and developers. ML can be customized to run geometric and algebraic multigrid; it can solve a scalar or a vector equation (with constant number of equations per grid node), and it can solve a form of Maxwell's equations. For a general introduction to ML and its applications, we refer to the Users Guide [SHT04], and to the ML web site, http://software.sandia.gov/ml.

  1. Safety, immunogenicity, and efficacy of the ML29 reassortant vaccine for Lassa fever in small non-human primates✩

    Science.gov (United States)

    Lukashevich, Igor S.; Carrion, Ricardo; Salvato, Maria S.; Mansfield, Keith; Brasky, Kathleen; Zapata, Juan; Cairo, Cristiana; Goicochea, Marco; Hoosien, Gia E.; Ticer, Anysha; Bryant, Joseph; Davis, Harry; Hammamieh, Rasha; Mayda, Maria; Jett, Marti; Patterson, Jean

    2008-01-01

    A single injection of ML29 reassortant vaccine for Lassa fever induces low, transient viremia, and low or moderate levels of ML29 replication in tissues of common marmosets depending on the dose of the vaccination. The vaccination elicits specific immune responses and completely protects marmosets against fatal disease by induction of sterilizing cell-mediated immunity. DNA array analysis of human peripheral blood mononuclear cells from healthy donors exposed to ML29 revealed that gene expression patterns in ML29-exposed PBMC and control, media-exposed PBMC, clustered together confirming safety profile of the ML29 in non-human primates. The ML29 reassortant is a promising vaccine candidate for Lassa fever. PMID:18692539

  2. The XBabelPhish MAGE-ML and XML translator.

    Science.gov (United States)

    Maier, Don; Wymore, Farrell; Sherlock, Gavin; Ball, Catherine A

    2008-01-18

    MAGE-ML has been promoted as a standard format for describing microarray experiments and the data they produce. Two characteristics of the MAGE-ML format compromise its use as a universal standard: First, MAGE-ML files are exceptionally large - too large to be easily read by most people, and often too large to be read by most software programs. Second, the MAGE-ML standard permits many ways of representing the same information. As a result, different producers of MAGE-ML create different documents describing the same experiment and its data. Recognizing all the variants is an unwieldy software engineering task, resulting in software packages that can read and process MAGE-ML from some, but not all producers. This Tower of MAGE-ML Babel bars the unencumbered exchange of microarray experiment descriptions couched in MAGE-ML. We have developed XBabelPhish - an XQuery-based technology for translating one MAGE-ML variant into another. XBabelPhish's use is not restricted to translating MAGE-ML documents. It can transform XML files independent of their DTD, XML schema, or semantic content. Moreover, it is designed to work on very large (> 200 Mb.) files, which are common in the world of MAGE-ML. XBabelPhish provides a way to inter-translate MAGE-ML variants for improved interchange of microarray experiment information. More generally, it can be used to transform most XML files, including very large ones that exceed the capacity of most XML tools.

  3. Gating-ML: XML-based gating descriptions in flow cytometry.

    Science.gov (United States)

    Spidlen, Josef; Leif, Robert C; Moore, Wayne; Roederer, Mario; Brinkman, Ryan R

    2008-12-01

    The lack of software interoperability with respect to gating due to lack of a standardized mechanism for data exchange has traditionally been a bottleneck, preventing reproducibility of flow cytometry (FCM) data analysis and the usage of multiple analytical tools. To facilitate interoperability among FCM data analysis tools, members of the International Society for the Advancement of Cytometry (ISAC) Data Standards Task Force (DSTF) have developed an XML-based mechanism to formally describe gates (Gating-ML). Gating-ML, an open specification for encoding gating, data transformations and compensation, has been adopted by the ISAC DSTF as a Candidate Recommendation. Gating-ML can facilitate exchange of gating descriptions the same way that FCS facilitated for exchange of raw FCM data. Its adoption will open new collaborative opportunities as well as possibilities for advanced analyses and methods development. The ISAC DSTF is satisfied that the standard addresses the requirements for a gating exchange standard.

  4. Allelism of Genes in the Ml-a locus

    DEFF Research Database (Denmark)

    Giese, Nanna Henriette; Jensen, Hans Peter; Jørgensen, Jørgen Helms

    1980-01-01

    Seven barley lines or varieties, each with a different gene at the Ml-a locus for resistance to Erysiphe graminis were intercrossed. Progeny testing of the F2s using two different fungal isolates per cross provided evidence that there are two or more loci in the Ml-a region. Apparent recombinants...... were also screened for recombination between the Hor1 and Hor2 loci which are situated either side of the Ml-a locus. The cross between Ricardo and Iso42R (Rupee) yielded one possible recombinant, with Ml-a3 and Ml-a(Rul) in the coupling phase; other recombinants had wild-type genes in the coupling...... phase. Iso20R, derived from Hordeum spontaneum 'H204', carrying Ml-a6, had an additional gene, in close coupling with Ml-a6, tentatively named Ml-aSp2 or Reglv, causing an intermediate infection type with isolate EmA30. It is suggested that Ml-a(Ar) in Emir and Ml-a(Rul), shown to differ from other Ml...

  5. jmzML, an open-source Java API for mzML, the PSI standard for MS data.

    Science.gov (United States)

    Côté, Richard G; Reisinger, Florian; Martens, Lennart

    2010-04-01

    We here present jmzML, a Java API for the Proteomics Standards Initiative mzML data standard. Based on the Java Architecture for XML Binding and XPath-based XML indexer random-access XML parser, jmzML can handle arbitrarily large files in minimal memory, allowing easy and efficient processing of mzML files using the Java programming language. jmzML also automatically resolves internal XML references on-the-fly. The library (which includes a viewer) can be downloaded from http://jmzml.googlecode.com.

  6. ISAC's Gating-ML 2.0 data exchange standard for gating description.

    Science.gov (United States)

    Spidlen, Josef; Moore, Wayne; Brinkman, Ryan R

    2015-07-01

    The lack of software interoperability with respect to gating has traditionally been a bottleneck preventing the use of multiple analytical tools and reproducibility of flow cytometry data analysis by independent parties. To address this issue, ISAC developed Gating-ML, a computer file format to encode and interchange gates. Gating-ML 1.5 was adopted and published as an ISAC Candidate Recommendation in 2008. Feedback during the probationary period from implementors, including major commercial software companies, instrument vendors, and the wider community, has led to a streamlined Gating-ML 2.0. Gating-ML has been significantly simplified and therefore easier to support by software tools. To aid developers, free, open source reference implementations, compliance tests, and detailed examples are provided to stimulate further commercial adoption. ISAC has approved Gating-ML as a standard ready for deployment in the public domain and encourages its support within the community as it is at a mature stage of development having undergone extensive review and testing, under both theoretical and practical conditions. © 2015 International Society for Advancement of Cytometry.

  7. Proceedings ML Family/OCaml Users and Developers workshops

    OpenAIRE

    Kiselyov, Oleg; Garrigue, Jacques

    2015-01-01

    This volume collects the extended versions of selected papers originally presented at the two ACM SIGPLAN workshops: ML Family Workshop 2014 and OCaml 2014. Both were affiliated with ICFP 2014 and took place on two consecutive days, on September 4 and 5, 2014 in Gothenburg, Sweden. The ML Family workshop aims to recognize the entire extended family of ML and ML-like languages: languages that are Higher-order, Typed, Inferred, and Strict. It provides the forum to discuss common issues, both pr...

  8. Glial tumors with neuronal differentiation.

    Science.gov (United States)

    Park, Chul-Kee; Phi, Ji Hoon; Park, Sung-Hye

    2015-01-01

    Immunohistochemical studies for neuronal differentiation in glial tumors revealed subsets of tumors having both characteristics of glial and neuronal lineages. Glial tumors with neuronal differentiation can be observed with diverse phenotypes and histologic grades. The rosette-forming glioneuronal tumor of the fourth ventricle and papillary glioneuronal tumor have been newly classified as distinct disease entities. There are other candidates for classification, such as the glioneuronal tumor without pseudopapillary architecture, glioneuronal tumor with neuropil-like islands, and the malignant glioneuronal tumor. The clinical significance of these previously unclassified tumors should be confirmed. Copyright © 2015 Elsevier Inc. All rights reserved.

  9. ML at ATLAS&CMS : setting the stage

    CERN Multimedia

    CERN. Geneva

    2015-01-01

    In the early days of the LHC the canonical problems of classification and regression were mostly addressed using simple cut-based techniques. Today, ML techniques (some already pioneered in pre-LHC or non collider experiments) play a fundamental role in the toolbox of any experimentalist. The talk will introduce, through a representative collection of examples, the problems addressed with ML techniques at the LHC. The goal of the talk is to set the stage for a constructive discussion with non-HEP ML practitioners, focusing on the specificities of HEP applications.

  10. Model-driven Service Engineering with SoaML

    Science.gov (United States)

    Elvesæter, Brian; Carrez, Cyril; Mohagheghi, Parastoo; Berre, Arne-Jørgen; Johnsen, Svein G.; Solberg, Arnor

    This chapter presents a model-driven service engineering (MDSE) methodology that uses OMG MDA specifications such as BMM, BPMN and SoaML to identify and specify services within a service-oriented architecture. The methodology takes advantage of business modelling practices and provides a guide to service modelling with SoaML. The presentation is case-driven and illuminated using the telecommunication example. The chapter focuses in particular on the use of the SoaML modelling language as a means for expressing service specifications that are aligned with business models and can be realized in different platform technologies.

  11. QuakeML - An XML Schema for Seismology

    Science.gov (United States)

    Wyss, A.; Schorlemmer, D.; Maraini, S.; Baer, M.; Wiemer, S.

    2004-12-01

    We propose an extensible format-definition for seismic data (QuakeML). Sharing data and seismic information efficiently is one of the most important issues for research and observational seismology in the future. The eXtensible Markup Language (XML) is playing an increasingly important role in the exchange of a variety of data. Due to its extensible definition capabilities, its wide acceptance and the existing large number of utilities and libraries for XML, a structured representation of various types of seismological data should in our opinion be developed by defining a 'QuakeML' standard. Here we present the QuakeML definitions for parameter databases and further efforts, e.g. a central QuakeML catalog database and a web portal for exchanging codes and stylesheets.

  12. Preparing for the future: opportunities for ML in ATLAS & CMS

    CERN Multimedia

    CERN. Geneva

    2015-01-01

    ML is an established tool in HEP and there are many examples which demonstrate its importance for the kind of classification and regression problem we have in our field. However, there is also a big potential for future applications in yet untapped areas. I will summarise these opportunities and highlight recent, ongoing and planned studies of novel ML applications in HEP. Certain aspects of the problems we are faced with in HEP are quite unique and represent interesting benchmark problems for the ML community as a whole. Hence, efficient communication and close interaction between the ML and HEP community is expected to lead to promising cross-fertilisation. This talk attempts to serve as a starting point for such a prospective collaboration.

  13. The jmzQuantML programming interface and validator for the mzQuantML data standard.

    Science.gov (United States)

    Qi, Da; Krishna, Ritesh; Jones, Andrew R

    2014-03-01

    The mzQuantML standard from the HUPO Proteomics Standards Initiative has recently been released, capturing quantitative data about peptides and proteins, following analysis of MS data. We present a Java application programming interface (API) for mzQuantML called jmzQuantML. The API provides robust bridges between Java classes and elements in mzQuantML files and allows random access to any part of the file. The API provides read and write capabilities, and is designed to be embedded in other software packages, enabling mzQuantML support to be added to proteomics software tools (http://code.google.com/p/jmzquantml/). The mzQuantML standard is designed around a multilevel validation system to ensure that files are structurally and semantically correct for different proteomics quantitative techniques. In this article, we also describe a Java software tool (http://code.google.com/p/mzquantml-validator/) for validating mzQuantML files, which is a formal part of the data standard. © 2014 The Authors. Proteomics published by Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. WeedML: a Tool for Collaborative Weed Demographic Modeling

    OpenAIRE

    Holst, Niels

    2010-01-01

    WeedML is a proposed standard to formulate models of weed demography, or maybe even complex models in general, that are both transparent and straightforward to re-use as building blocks for new models. The paper describes the design and thoughts behind WeedML which relies on XML and object-oriented systems development. Proof-of-concept software is provided as open-source C++ code and executables that can be downloaded freely.

  15. Aggressiveness of powdery mildew on 'ml-o'- resistant barley

    International Nuclear Information System (INIS)

    Andersen, Lars

    1990-01-01

    The ml-o genes in barley are important sources in breeding for resistance against the barley powdery mildew fungus (Erysiphe graminis). The resistance mechanism is a rapid formation of a large callose containing cell wall apposition at the site of the pathogen's infection attempt. This reduces the chances of infection to almost nil in all epidermal cells, except in the small subsidiary cells, in which appositions are rarely formed. Small mildew colonies from infections in subsidiary cells may be seen on the otherwise resistant leaf. This is described by the infection type 0/(4). Mildew isolate HL 3 selected by SCHWARZBACH has increased aggressiveness. No ml-o-virulent isolates are known. However, ml-o-resistant varieties when grown extensively in Europe, will introduce field selection for mildew pathotypes with aggressiveness or virulence to ml-o resistance. Studies on increased aggressiveness require new methods. The material comprises two powdery mildew isolates: GE 3 without ml-o aggressiveness and the aggressive HL 3/5; and two near-isogenic barley lines in Carlsberg II: Riso 5678(R) with the recessive mutant resistance gene ml-o5 and Riso 5678(S) with the wild-type gene for susceptibility. Latent period and disease efficiency show no significant differences between the two isolates on the susceptible barley line (S) but the isolates differ from each other on the resistant barley line

  16. QuakeML 2.0: Recent developments

    Science.gov (United States)

    Euchner, Fabian; Kästli, Philipp; Heiniger, Lukas; Saul, Joachim; Schorlemmer, Danijel; Clinton, John

    2016-04-01

    QuakeML is a community-backed data model for seismic event parameter description. Its current version 1.2, released in 2013, has become the gold standard for parametric data dissemination at seismological data centers, and has been adopted as an FDSN standard. It is supported by several popular software products and data services, such as FDSN event web services, QuakePy, and SeisComP3. Work on the successor version 2.0 is under way since 2015. The scope of QuakeML has been expanded beyond event parameter description. Thanks to a modular architecture, many thematic packages have been added, which cover peak ground motion, site and station characterization, hydraulic parameters of borehole injection processes, and macroseismics. The first three packages can be considered near final and implementations of program codes and SQL databases are in productive use at various institutions. A public community review process has been initiated in order to turn them into community-approved standards. The most recent addition is a package for single station quake location, which allows a detailed probabilistic description of event parameters recorded at a single station. This package adds some information elements such as angle of incidence, frequency-dependent phase picks, and dispersion relations. The package containing common data types has been extended with a generic type for probability density functions. While on Earth, single station methods are niche applications, they are of prominent interest in planetary seismology, e.g., the NASA InSight mission to Mars. So far, QuakeML is lacking a description of seismic instrumentation (inventory). There are two existing standards of younger age (FDSN StationXML and SeisComP3 Inventory XML). We discuss their respective strengths, differences, and how they could be combined into an inventory package for QuakeML, thus allowing full interoperability with other QuakeML data types. QuakeML is accompanied by QuakePy, a Python package

  17. Citizen Candidates Under Uncertainty

    OpenAIRE

    Eguia, Jon X.

    2005-01-01

    In this paper we make two contributions to the growing literature on "citizen-candidate" models of representative democracy. First, we add uncertainty about the total vote count. We show that in a society with a large electorate, where the outcome of the election is uncertain and where winning candidates receive a large reward from holding office, there will be a two-candidate equilibrium and no equilibria with a single candidate. Second, we introduce a new concept of equilibrium, which we te...

  18. Modelling CRM implementation services with SysML

    OpenAIRE

    Bibiano, Luis H.; Pastor Collado, Juan Antonio; Mayol Sarroca, Enric

    2009-01-01

    CRM information systems are valuable tools for enterprises. But CRM implementation projects are risky and present a high failure rate. In this paper we regard CRM implementation projects as services that could be greatly improved by addressing them in a methodological way that can be designed with the help of tools such as SysML. Here we introduce and comment on our first experience on the use of SysML language, not very well known, for modelling the elements involved in the CRM implementatio...

  19. Absorption kinetics of two highly concentrated preparations of growth hormone: 12 IU/ml compared to 56 IU/ml

    DEFF Research Database (Denmark)

    Laursen, Torben; Susgaard, Søren; Jensen, Flemming Steen

    1994-01-01

    was to compare the relative bioavailability of two highly concentrated (12 IU/ml versus 56 IU/ml) formulations of biosynthetic human growth hormone administered subcutaneously. After pretreatment with growth hormone for at least four weeks, nine growth hormone deficient patients with a mean age of 26.2 years......AbstractSend to: Pharmacol Toxicol. 1994 Jan;74(1):54-7. Absorption kinetics of two highly concentrated preparations of growth hormone: 12 IU/ml compared to 56 IU/ml. Laursen T1, Susgaard S, Jensen FS, Jørgensen JO, Christiansen JS. Author information Abstract The purpose of this study...... (range 17-43) were studied two times in a randomized design, the two studies being separated by at least one week. At the start of each study period (7 p.m.), growth hormone was injected subcutaneously in a dosage of 3 IU/m2. The 12 IU/ml preparation of growth hormone was administered on one occasion...

  20. CytometryML: a markup language for analytical cytology

    Science.gov (United States)

    Leif, Robert C.; Leif, Stephanie H.; Leif, Suzanne B.

    2003-06-01

    Cytometry Markup Language, CytometryML, is a proposed new analytical cytology data standard. CytometryML is a set of XML schemas for encoding both flow cytometry and digital microscopy text based data types. CytometryML schemas reference both DICOM (Digital Imaging and Communications in Medicine) codes and FCS keywords. These schemas provide representations for the keywords in FCS 3.0 and will soon include DICOM microscopic image data. Flow Cytometry Standard (FCS) list-mode has been mapped to the DICOM Waveform Information Object. A preliminary version of a list mode binary data type, which does not presently exist in DICOM, has been designed. This binary type is required to enhance the storage and transmission of flow cytometry and digital microscopy data. Index files based on Waveform indices will be used to rapidly locate the cells present in individual subsets. DICOM has the advantage of employing standard file types, TIF and JPEG, for Digital Microscopy. Using an XML schema based representation means that standard commercial software packages such as Excel and MathCad can be used to analyze, display, and store analytical cytometry data. Furthermore, by providing one standard for both DICOM data and analytical cytology data, it eliminates the need to create and maintain special purpose interfaces for analytical cytology data thereby integrating the data into the larger DICOM and other clinical communities. A draft version of CytometryML is available at www.newportinstruments.com.

  1. Introducing the Collaborative Learning Modeling Language (ColeML)

    DEFF Research Database (Denmark)

    Bundsgaard, Jeppe

    2014-01-01

    in this area, represented by, for example, the Workflow Management Coalition (Hollingsworth, 1995) and the very widespread standard Business Process Modeling and Notation (BPMN), has been criticized on the basis of research in knowledge work processes. Inspiration for ColeML is found in this research area...

  2. Percutaneous CT-guided high-dose brachytherapy (CT-HDRBT) ablation of primary and metastatic lung tumors in nonsurgical candidates; Perkutane CT-gesteuerte Hochdosis-Brachytherapie (CT-HDRBT) von primaeren und metastatischen Lungentumoren in nicht chirurgischen Kandidaten

    Energy Technology Data Exchange (ETDEWEB)

    Collettini, F.; Schnapauff, D.; Poellinger, A.; Denecke, T.; Banzer, J.; Golenia, M.J.; Gebauer, B. [Charite - Universitatesmedizin Berlin (Germany). Inst. fuer Radiologie; Wust, P. [Charite - Universitatesmedizin Berlin (Germany). Klinik fuer Strahlentherapie

    2012-04-15

    To evaluate the safety and efficacy of CT-guided high-dose brachytherapy (CT-HDRBT) ablation of primary and metastatic lung tumors. Between November 2007 and May 2010, all consecutive patients with primary or metastatic lung tumors, unsuitable for surgery, were treated with CT-HDRBT. Imaging follow-up after treatment was performed with contrast-enhanced CT at 6 weeks, 3 months and every 6 months after the procedure. The endpoints of the study were local tumor control and time to progression. The Kaplan-Meier method was used to estimate survival functions and local tumor progression rates. 34 procedures were carried out on 33 lesions in 22 patients. The mean diameter of the tumors was 33.3 mm (SD = 20.4). The first contrast-enhanced CT showed that complete ablation was achieved in all lesions. The mean minimal tumor enclosing dose was 18.9 Gy (SD = 2). Three patients developed a pneumothorax after the procedure. The mean follow-up time was 13.7 (3 - 29) months. 2 of 32 lesions (6.25 %) developed a local tumor progression. 8 patients (36.3 %) developed a distant tumor progression. After 17.7 months, 13 patients were alive and 9 patients had died. CT-HDRBT ablation is a safe and attractive treatment option for patients with lung malignancies and allows targeted destruction of tumor tissue with simultaneous preservation of important lung structures. Furthermore, CT-HDRBT is independent of the size of the lesion and its location within the lung parenchyma. (orig.)

  3. Interoperability between OPC UA and AutomationML

    OpenAIRE

    Henßen, Robert; Schleipen, Miriam

    2014-01-01

    OPC UA (OPC Unified Architecture) is a platform-independent standard series (IEC 62541) [1], [2] for communication of industrial automation devices and systems. The OPC Unified Architecture is an advanced communication technology for process control. Certainly the launching costs for the initial information model are quite high. AutomationML (Automation Markup Language) is an upcoming open standard series (IEC 62714) [3], [4] for describing production plants or plant components. The goal of t...

  4. Ensemble candidate classification for the LOTAAS pulsar survey

    Science.gov (United States)

    Tan, C. M.; Lyon, R. J.; Stappers, B. W.; Cooper, S.; Hessels, J. W. T.; Kondratiev, V. I.; Michilli, D.; Sanidas, S.

    2018-03-01

    One of the biggest challenges arising from modern large-scale pulsar surveys is the number of candidates generated. Here, we implemented several improvements to the machine learning (ML) classifier previously used by the LOFAR Tied-Array All-Sky Survey (LOTAAS) to look for new pulsars via filtering the candidates obtained during periodicity searches. To assist the ML algorithm, we have introduced new features which capture the frequency and time evolution of the signal and improved the signal-to-noise calculation accounting for broad profiles. We enhanced the ML classifier by including a third class characterizing RFI instances, allowing candidates arising from RFI to be isolated, reducing the false positive return rate. We also introduced a new training data set used by the ML algorithm that includes a large sample of pulsars misclassified by the previous classifier. Lastly, we developed an ensemble classifier comprised of five different Decision Trees. Taken together these updates improve the pulsar recall rate by 2.5 per cent, while also improving the ability to identify pulsars with wide pulse profiles, often misclassified by the previous classifier. The new ensemble classifier is also able to reduce the percentage of false positive candidates identified from each LOTAAS pointing from 2.5 per cent (˜500 candidates) to 1.1 per cent (˜220 candidates).

  5. Tissue engineered tumor models.

    Science.gov (United States)

    Ingram, M; Techy, G B; Ward, B R; Imam, S A; Atkinson, R; Ho, H; Taylor, C R

    2010-08-01

    Many research programs use well-characterized tumor cell lines as tumor models for in vitro studies. Because tumor cells grown as three-dimensional (3-D) structures have been shown to behave more like tumors in vivo than do cells growing in monolayer culture, a growing number of investigators now use tumor cell spheroids as models. Single cell type spheroids, however, do not model the stromal-epithelial interactions that have an important role in controlling tumor growth and development in vivo. We describe here a method for generating, reproducibly, more realistic 3-D tumor models that contain both stromal and malignant epithelial cells with an architecture that closely resembles that of tumor microlesions in vivo. Because they are so tissue-like we refer to them as tumor histoids. They can be generated reproducibly in substantial quantities. The bioreactor developed to generate histoid constructs is described and illustrated. It accommodates disposable culture chambers that have filled volumes of either 10 or 64 ml, each culture yielding on the order of 100 or 600 histoid particles, respectively. Each particle is a few tenths of a millimeter in diameter. Examples of histological sections of tumor histoids representing cancers of breast, prostate, colon, pancreas and urinary bladder are presented. Potential applications of tumor histoids include, but are not limited to, use as surrogate tumors for pre-screening anti-solid tumor pharmaceutical agents, as reference specimens for immunostaining in the surgical pathology laboratory and use in studies of invasive properties of cells or other aspects of tumor development and progression. Histoids containing nonmalignant cells also may have potential as "seeds" in tissue engineering. For drug testing, histoids probably will have to meet certain criteria of size and tumor cell content. Using a COPAS Plus flow cytometer, histoids containing fluorescent tumor cells were analyzed successfully and sorted using such criteria.

  6. Adductor Canal Block With 10 mL Versus 30 mL Local Anesthetics and Quadriceps Strength

    DEFF Research Database (Denmark)

    Jæger, Pia; Koscielniak-Nielsen, Zbigniew J; Hilsted, Karen Lisa

    2015-01-01

    weakness. METHODS: We performed a paired, blinded, randomized trial including healthy men. All subjects received bilateral ACBs with ropivacaine 0.1%; 10 mL in 1 leg and 30 mL in the other leg. The primary outcome was the difference in number of subjects with quadriceps strength reduced by more than 25...... of the predefined time points or in sensory block. The only statistically significant difference between volumes was found in the 30-Second Chair Stand Test at 2 hours (P = 0.02), but this difference had disappeared at 4 hours (P = 0.06). CONCLUSIONS: Varying the volume of ropivacaine 0.1% used for ACB between 10...

  7. QualityML: a dictionary for quality metadata encoding

    Science.gov (United States)

    Ninyerola, Miquel; Sevillano, Eva; Serral, Ivette; Pons, Xavier; Zabala, Alaitz; Bastin, Lucy; Masó, Joan

    2014-05-01

    The scenario of rapidly growing geodata catalogues requires tools focused on facilitate users the choice of products. Having quality fields populated in metadata allow the users to rank and then select the best fit-for-purpose products. In this direction, we have developed the QualityML (http://qualityml.geoviqua.org), a dictionary that contains hierarchically structured concepts to precisely define and relate quality levels: from quality classes to quality measurements. Generically, a quality element is the path that goes from the higher level (quality class) to the lowest levels (statistics or quality metrics). This path is used to encode quality of datasets in the corresponding metadata schemas. The benefits of having encoded quality, in the case of data producers, are related with improvements in their product discovery and better transmission of their characteristics. In the case of data users, particularly decision-makers, they would find quality and uncertainty measures to take the best decisions as well as perform dataset intercomparison. Also it allows other components (such as visualization, discovery, or comparison tools) to be quality-aware and interoperable. On one hand, the QualityML is a profile of the ISO geospatial metadata standards providing a set of rules for precisely documenting quality indicator parameters that is structured in 6 levels. On the other hand, QualityML includes semantics and vocabularies for the quality concepts. Whenever possible, if uses statistic expressions from the UncertML dictionary (http://www.uncertml.org) encoding. However it also extends UncertML to provide list of alternative metrics that are commonly used to quantify quality. A specific example, based on a temperature dataset, is shown below. The annual mean temperature map has been validated with independent in-situ measurements to obtain a global error of 0.5 ° C. Level 0: Quality class (e.g., Thematic accuracy) Level 1: Quality indicator (e.g., Quantitative

  8. The observation of soybean yield components in Ml generation

    International Nuclear Information System (INIS)

    Muryono, H.

    1978-01-01

    Some properties of the soybean yield component in Ml generation were investigated. Soybean seed variety of Taichung were irradiated with gamma rays from the cobalt source at the Gamma Atomic Energy Research Centre, Yogyakarta. Seven different doses at 2, 4, 6, 8, 10, 12, and 14 krads were used. Subsequent growth of the irradiated seed was carried out in the field and the ages of flowering, seedling height number of pods, number of fertile and infertile pods and percentage of sterility were recorded. It was found that the significant effect on the above variables was observed due to the gamma radiation doses between 8-12 krads. (author)

  9. TrackML : The High Energy Physics Tracking Challenge

    CERN Multimedia

    CERN. Geneva

    2018-01-01

    We organize on the Kaggle platform a  data science competition to stimulate both the ML and HEP communities to renew core tracking algorithms in preparation of the next generation of particle detectors at the LHC.    In a nutshell : one event has 100.000 3D points  ; how to associate the points onto 10.000 unknown approximately helicoidal trajectories ? avoiding combinatorial explosion ? you have a few seconds. But we do give you 100.000 events to train on. We ran ttbar+200 minimum bias event into ACTS a simplified (yet accurate) simulation of a generic LHC silicon detectors, and wrote out ...

  10. Sodium corrosion tests in the ML 1 circuit

    International Nuclear Information System (INIS)

    Borgstedt, H.U.

    1977-01-01

    In the ML-1 circuit of the 'Juan Vigon' research centre in Madrid, sodium corrosion tests are being carried out on the austenitic steels DIN 1.4970 (X10NiCrMoTiB1515) and DIN 1.4301 (X5CrNi189) at temperatures between 500 and 700 0 C. The exposure time of the samples amounts to 6,000 h by now. Every 1,000 h, the samples were weighed in order to measure corrosion and deposition effects. After 3,000 and 6,000 h, some selected samples were destroyed for inspection. The results are given. (GSC) [de

  11. Bone tumor

    Science.gov (United States)

    Tumor - bone; Bone cancer; Primary bone tumor; Secondary bone tumor; Bone tumor - benign ... The cause of bone tumors is unknown. They often occur in areas of the bone that grow rapidly. Possible causes include: Genetic defects ...

  12. Simple ML Detector for Multiple Antennas Communication System

    Directory of Open Access Journals (Sweden)

    Ahmad Taqwa

    2010-10-01

    Full Text Available In order to support providing broadband wireless communication services against limited and expensive frequency bandwidth, we have to develop a bandwidth efficient system. Therefore, in this paper we propose a closed-loop MIMO (Multiple-Input-Multiple-Output system using ML (Maximum Likelihood detector to optimize capacity and to increase system performance. What is especially exciting about the benefits offered by MIMO is that a high capacity and performance can be attained without additional frequency-spectral resource. The grand scenario of this concept is the attained advantages of transformation matrices having capability to allocate transmitted signals power suit to the channel. Furthermore, product of these matrices forms parallel singular channels. Due to zero inter-channels correlation, thus we can design ML detector to increase the system performance. Finally, computer simulations validates that at 0 dB SNR our system can reach optimal capacity up to 1 bps/Hz and SER up to 0.2 higher than opened-loop MIMO.

  13. Biodegradation of malathion by Bacillus licheniformis strain ML-1

    Directory of Open Access Journals (Sweden)

    Khan Sara

    2016-01-01

    Full Text Available Malathion, a well-known organophosphate pesticide, has been used in agriculture over the last two decades for controlling pests of economically important crops. In the present study, a single bacterium, ML-1, was isolated by soil-enrichment technique and identified as Bacillus licheniformis on the basis of the 16S rRNA technique. The bacterium was grown in carbon-free minimal salt medium (MSM and was found to be very efficient in utilizing malathion as the sole source of carbon. Biodegradation experiments were performed in MSM without carbon source to determine the malathion degradation by the selected strain, and the residues of malathion were determined quantitatively using HPLC techniques. Bacillus licheniformis showed very promising results and efficiently consumed malathion as the sole carbon source via malathion carboxylesterase (MCE, and about 78% malathion was degraded within 5 days. The carboxylesterase activity was determined by using crude extract while using malathion as substrate, and the residues were determined by HPLC. It has been found that the MCE hydrolyzed 87% malathion within 96 h of incubation. Characterization of crude MCE revealed that the enzyme is robust in nature in terms of organic solvents, as it was found to be stable in various concentrations of ethanol and acetonitrile. Similarly, and it can work in a wide pH and temperature range. The results of this study highlighted the potential of Bacillus licheniformis strain ML-1 as a biodegrader that can be used for the bioremediation of malathion-contaminated soil.

  14. RT-06GAMMA KNIFE SURGERY AFTER NAVIGATION-GUIDED ASPIRATION FOR CYSTIC METASTATIC BRAIN TUMORS

    Science.gov (United States)

    Chiba, Yasuyoshi; Mori, Kanji; Toyota, Shingo; Kumagai, Tetsuya; Yamamoto, Shota; Sugano, Hirofumi; Taki, Takuyu

    2014-01-01

    Metastatic brain tumors over 3 cm in diameter (volume of 14.1ml) are generally considered poor candidates for Gamma Knife surgery (GKS). We retrospectively assessed the method and efficacy of GKS for large cystic metastatic brain tumors after navigation-guided aspiration under local anesthesia. From September 2007 to April 2014, 38 cystic metastatic brain tumors in 32 patients (12 males, 20 females; mean age, 63.2 years) were treated at Kansai Rosai Hospital. The patients were performed navigation-guided cyst aspiration under local anesthesia, then at the day or the next day, were performed GKS and usually discharged on the day. The methods for preventing of leptomeningeal dissemination are following: 1) puncture from the place whose cerebral thickness is 1 cm or more; 2) avoidance of Ommaya reservoir implantation; and 3) placement of absorbable gelatin sponge to the tap tract. Tumor volume, including the cystic component, decreased from 25.4 ml (range 8.7-84.7 ml) to 11.4 ml (range 2.9-36.7 ml) following aspiration; the volume reduction was approximately 51.6%. Follow-up periods in the study population ranged from 0 to 24 months (median 3.5 months). The overall median survival was 6.7 months. There was no leptomeningeal dissemination related to the aspiration. One patient experienced radiation necrosis after GKS, one patient experienced re-aspiration by failure of aspiration, and two patients experienced surgical resections and one patient experienced re-aspiration by cyst regrowth after GKS. Long-term hospitalization is not desirable for the patients with brain metastases. In japan, Long-term hospitalization is required for surgical resection or whole brain radiation therapy, but only two days hospitalization is required for GKS after navigation-guided aspiration at our hospital. This GKS after navigation-guided aspiration is more effective and less invasive than surgical resection or whole brain radiation therapy.

  15. [Obesity studies in candidate genes].

    Science.gov (United States)

    Ochoa, María del Carmen; Martí, Amelia; Martínez, J Alfredo

    2004-04-17

    There are more than 430 chromosomic regions with gene variants involved in body weight regulation and obesity development. Polymorphisms in genes related to energy expenditure--uncoupling proteins (UCPs), related to adipogenesis and insulin resistance--hormone-sensitive lipase (HLS), peroxisome proliferator-activated receptor gamma (PPAR gamma), beta adrenergic receptors (ADRB2,3), and alfa tumor necrosis factor (TNF-alpha), and related to food intake--ghrelin (GHRL)--appear to be associated with obesity phenotypes. Obesity risk depends on two factors: a) genetic variants in candidate genes, and b) biographical exposure to environmental risk factors. It is necessary to perform new studies, with appropriate control groups and designs, in order to reach relevant conclusions with regard to gene/environmental (diet, lifestyle) interactions.

  16. Clinical application of l-123 MlBG cardiac imaging

    Energy Technology Data Exchange (ETDEWEB)

    Kang, Do Young [College of Medicine, Donga Univ., Busan (Korea, Republic of)

    2004-10-01

    Cardiac neurotransmission imaging allows in vivo assessment of presynaptic reuptake, neurotransmitter storage and postsynaptic receptors. Among the various neurotransmitter, I-123 MlBG is most available and relatively well-established. Metaiodobenzylguanidine (MIBG) is an analogue of the false neurotransmitter guanethidine. It is taken up to adrenergic neurons by uptake-1 mechanism as same as norepinephrine. As tagged with I-123, it can be used to image sympathetic function in various organs including heart with planar or SPECT techniques. I-123 MIBG imaging has a unique advantage to evaluate myocardial neuronal activity in which the heart has no significant structural abnormality or even no functional derangement measured with other conventional examination. In patients with cardiomyopathy and heart failure, this imaging has most sensitive technique to predict prognosis and treatment response of betablocker or ACE inhibitor. In diabetic patients, it allow very early detection of autonomic neuropathy. In patients with dangerous arrhythmia such as ventricular tachycardia or fibrillation, MIBG imaging may be only an abnormal result among various exams. In patients with ischemic heart disease, sympathetic derangement may be used as the method of risk stratification. In heart transplanted patients, sympathetic reinnervation is well evaluated. Adriamycin-induced cardiotoxicity is detected earlier than ventricular dysfunction with sympathetic dysfunction. Neurodegenerative disorder such as Parkinson's disease or dementia with Lewy bodies has also cardiac sympathetic dysfunction. Noninvasive assessment of cardiac sympathetic nerve activity with l-123 MlBG imaging may be improve understanding of the pathophysiology of cardiac disease and make a contribution to predict survival and therapy efficacy.

  17. Clinical application of l-123 MlBG cardiac imaging

    International Nuclear Information System (INIS)

    Kang, Do Young

    2004-01-01

    Cardiac neurotransmission imaging allows in vivo assessment of presynaptic reuptake, neurotransmitter storage and postsynaptic receptors. Among the various neurotransmitter, I-123 MlBG is most available and relatively well-established. Metaiodobenzylguanidine (MIBG) is an analogue of the false neurotransmitter guanethidine. It is taken up to adrenergic neurons by uptake-1 mechanism as same as norepinephrine. As tagged with I-123, it can be used to image sympathetic function in various organs including heart with planar or SPECT techniques. I-123 MIBG imaging has a unique advantage to evaluate myocardial neuronal activity in which the heart has no significant structural abnormality or even no functional derangement measured with other conventional examination. In patients with cardiomyopathy and heart failure, this imaging has most sensitive technique to predict prognosis and treatment response of betablocker or ACE inhibitor. In diabetic patients, it allow very early detection of autonomic neuropathy. In patients with dangerous arrhythmia such as ventricular tachycardia or fibrillation, MIBG imaging may be only an abnormal result among various exams. In patients with ischemic heart disease, sympathetic derangement may be used as the method of risk stratification. In heart transplanted patients, sympathetic reinnervation is well evaluated. Adriamycin-induced cardiotoxicity is detected earlier than ventricular dysfunction with sympathetic dysfunction. Neurodegenerative disorder such as Parkinson's disease or dementia with Lewy bodies has also cardiac sympathetic dysfunction. Noninvasive assessment of cardiac sympathetic nerve activity with l-123 MlBG imaging may be improve understanding of the pathophysiology of cardiac disease and make a contribution to predict survival and therapy efficacy

  18. Improving Interoperability by Incorporating UnitsML Into Markup Languages.

    Science.gov (United States)

    Celebi, Ismet; Dragoset, Robert A; Olsen, Karen J; Schaefer, Reinhold; Kramer, Gary W

    2010-01-01

    Maintaining the integrity of analytical data over time is a challenge. Years ago, data were recorded on paper that was pasted directly into a laboratory notebook. The digital age has made maintaining the integrity of data harder. Nowadays, digitized analytical data are often separated from information about how the sample was collected and prepared for analysis and how the data were acquired. The data are stored on digital media, while the related information about the data may be written in a paper notebook or stored separately in other digital files. Sometimes the connection between this "scientific meta-data" and the analytical data is lost, rendering the spectrum or chromatogram useless. We have been working with ASTM Subcommittee E13.15 on Analytical Data to create the Analytical Information Markup Language or AnIML-a new way to interchange and store spectroscopy and chromatography data based on XML (Extensible Markup Language). XML is a language for describing what data are by enclosing them in computer-useable tags. Recording the units associated with the analytical data and metadata is an essential issue for any data representation scheme that must be addressed by all domain-specific markup languages. As scientific markup languages proliferate, it is very desirable to have a single scheme for handling units to facilitate moving information between different data domains. At NIST, we have been developing a general markup language just for units that we call UnitsML. This presentation will describe how UnitsML is used and how it is being incorporated into AnIML.

  19. Bone tumors

    International Nuclear Information System (INIS)

    Unni, K.K.

    1988-01-01

    This book contains the proceedings on bone tumors. Topics covered include: Bone tumor imaging: Contribution of CT and MRI, staging of bone tumors, perind cell tumors of bone, and metastatic bone disease

  20. Candidíase em pacientes aidéticos

    Directory of Open Access Journals (Sweden)

    C.E.O.P. Campos

    1992-09-01

    Full Text Available Trinta e cinco aidéticos entre 19 e 55 anos admitidos e tratados de candidíase no Hospital Emílio Ribas, SP, com ELISA positivo para HIV e confirmado pelo Western Blot. Tuberculose em 9 sendo 2 com pericardite; neurotoxoplasmose em 6; neurocriptococose em 5; herpes labial em 4; pneumocistose em 3 e sarcoma de Kaposi em 2, achavam-se associadas. A concentração inibitória mínima 50% (MIC 50% para os azoles foi: ketoconazol= 2,2 µg/ml; itraconazol- 21,0 µg/ml; fluconazol = 19,0 µg/ml. O MIC 50% para ospolienos: nistatina- 50,0 µg/ml; anfotericina B= 0,12 µg/ml e para 5 fluorcitosina= 1,6 µg/ml nas 35 amostras de Candida isoladas. Testes não paramétricos de Siegel revelaram significante identificação (80% das Candida albicans na candidíase, e que a dose de AMB não modificou o número de óbitos, precoce e tardio, ocorridos nesses aidéticos. O uso prévio dos azoles e da nistatina explicaria, talvez, o elevado MIC 50% observado nas amostras de Candida isoladas.

  1. Dark matter candidates

    International Nuclear Information System (INIS)

    Turner, M.S.

    1989-01-01

    One of the simplest, yet most profound, questions we can ask about the Universe is, how much stuff is in it, and further what is that stuff composed of? Needless to say, the answer to this question has very important implications for the evolution of the Universe, determining both the ultimate fate and the course of structure formation. Remarkably, at this late date in the history of the Universe we still do not have a definitive answer to this simplest of questions---although we have some very intriguing clues. It is known with certainty that most of the material in the Universe is dark, and we have the strong suspicion that the dominant component of material in the Cosmos is not baryons, but rather is exotic relic elementary particles left over from the earliest, very hot epoch of the Universe. If true, the Dark Matter question is a most fundamental one facing both particle physics and cosmology. The leading particle dark matter candidates are: the axion, the neutralino, and a light neutrino species. All three candidates are accessible to experimental tests, and experiments are now in progress. In addition, there are several dark horse, long shot, candidates, including the superheavy magnetic monopole and soliton stars. 13 refs

  2. mzML2ISA & nmrML2ISA: generating enriched ISA-Tab metadata files from metabolomics XML data.

    Science.gov (United States)

    Larralde, Martin; Lawson, Thomas N; Weber, Ralf J M; Moreno, Pablo; Haug, Kenneth; Rocca-Serra, Philippe; Viant, Mark R; Steinbeck, Christoph; Salek, Reza M

    2017-08-15

    Submission to the MetaboLights repository for metabolomics data currently places the burden of reporting instrument and acquisition parameters in ISA-Tab format on users, who have to do it manually, a process that is time consuming and prone to user input error. Since the large majority of these parameters are embedded in instrument raw data files, an opportunity exists to capture this metadata more accurately. Here we report a set of Python packages that can automatically generate ISA-Tab metadata file stubs from raw XML metabolomics data files. The parsing packages are separated into mzML2ISA (encompassing mzML and imzML formats) and nmrML2ISA (nmrML format only). Overall, the use of mzML2ISA & nmrML2ISA reduces the time needed to capture metadata substantially (capturing 90% of metadata on assay and sample levels), is much less prone to user input errors, improves compliance with minimum information reporting guidelines and facilitates more finely grained data exploration and querying of datasets. mzML2ISA & nmrML2ISA are available under version 3 of the GNU General Public Licence at https://github.com/ISA-tools. Documentation is available from http://2isa.readthedocs.io/en/latest/. reza.salek@ebi.ac.uk or isatools@googlegroups.com. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

  3. Comparative study of induction of labour with Foley’s catheter inflated to 30 mL versus 60 mL

    OpenAIRE

    Indira I; Latha G; Lakshmi Narayanamma V

    2016-01-01

    Background: The ripeness of the cervix is an important determinant of the success of induction of labour. One of the mechanical methods of cervical ripening is the use of a transcervical Foley catheter. In this study we compared the efficacy in induction of labour of two insufflation volumes of Foley catheter bulb 30 mL and 60mL. Methods: This was a randomized, single-blind study conducted in 100 women, randomly allocated to the 30 mL group (n=50) and 60 mL group (n=50). Foley’s cath...

  4. jqcML: an open-source java API for mass spectrometry quality control data in the qcML format.

    Science.gov (United States)

    Bittremieux, Wout; Kelchtermans, Pieter; Valkenborg, Dirk; Martens, Lennart; Laukens, Kris

    2014-07-03

    The awareness that systematic quality control is an essential factor to enable the growth of proteomics into a mature analytical discipline has increased over the past few years. To this aim, a controlled vocabulary and document structure have recently been proposed by Walzer et al. to store and disseminate quality-control metrics for mass-spectrometry-based proteomics experiments, called qcML. To facilitate the adoption of this standardized quality control routine, we introduce jqcML, a Java application programming interface (API) for the qcML data format. First, jqcML provides a complete object model to represent qcML data. Second, jqcML provides the ability to read, write, and work in a uniform manner with qcML data from different sources, including the XML-based qcML file format and the relational database qcDB. Interaction with the XML-based file format is obtained through the Java Architecture for XML Binding (JAXB), while generic database functionality is obtained by the Java Persistence API (JPA). jqcML is released as open-source software under the permissive Apache 2.0 license and can be downloaded from https://bitbucket.org/proteinspector/jqcml .

  5. Candidíase em pacientes aidéticos

    Directory of Open Access Journals (Sweden)

    C.E.O.P. Campos

    1992-09-01

    Full Text Available Trinta e cinco aidéticos entre 19 e 55 anos admitidos e tratados de candidíase no Hospital Emílio Ribas, SP, com ELISA positivo para HIV e confirmado pelo Western Blot. Tuberculose em 9 sendo 2 com pericardite; neurotoxoplasmose em 6; neurocriptococose em 5; herpes labial em 4; pneumocistose em 3 e sarcoma de Kaposi em 2, achavam-se associadas. A concentração inibitória mínima 50% (MIC 50% para os azoles foi: ketoconazol= 2,2 µg/ml; itraconazol- 21,0 µg/ml; fluconazol = 19,0 µg/ml. O MIC 50% para ospolienos: nistatina- 50,0 µg/ml; anfotericina B= 0,12 µg/ml e para 5 fluorcitosina= 1,6 µg/ml nas 35 amostras de Candida isoladas. Testes não paramétricos de Siegel revelaram significante identificação (80% das Candida albicans na candidíase, e que a dose de AMB não modificou o número de óbitos, precoce e tardio, ocorridos nesses aidéticos. O uso prévio dos azoles e da nistatina explicaria, talvez, o elevado MIC 50% observado nas amostras de Candida isoladas.A total of 35 in patients admitted at Emilio Ribas Hospital - São Paulo, Brazil, with digestive candidiasis and AIDS clinical diagnostic were evaluated 10 month later, being 29 male and 6 female; white outnumbering black with age ranged from 30 to 50 years old. Agar Sabouraud culture and tube germinative tests identified 28 (80% Candida albicans out 35 strains. Minimum inhibitory concentration (MIC 50% was against azoles (ketoconazole= 2.2 µg/ml; itraconazole = 21.0 µg/ml and fluconazole- 19.0 µg/ml; polyenes (ny statine - 50.0 µg/ml and amphotericin B= 0.12 µg/ml and 5 fluorcytosine= 1.6µg/ml. Siegeltests showed significant Candida albicans proportions in strains isolated from 35 AIDS patients. There was no significant relation between AMB dosis and early or late death. Conclusions: candidiasis in AIDS patients showed high MIC 50% to azoles and nystatine and significant Candida albicans proportion in all strains isolated from AIDS patients. Previous amphotericin B

  6. Intra-articular sodium hyaluronate 2 mL versus physiological saline 20 mL versus physiological saline 2 mL for painful knee osteoarthritis: a randomized clinical trial

    DEFF Research Database (Denmark)

    Lundsgaard, C.; Dufour, N.; Fallentin, E.

    2008-01-01

    , Knee Injury and Osteoarthritis Outcome Score (KOOS), Osteoarthritis Research Society International (OARSI) criteria, and global assessment of the patient's condition. Results: The mean age of the patients was 69.4 years; 55% were women. The effects of hyaluronate 2 mL, physiological saline 20 m......Objective: Methodological constraints weaken previous evidence on intra-articular viscosupplementation and physiological saline distention for osteoarthritis. We conducted a randomized, patient- and observer-blind trial to evaluate these interventions in patients with painful knee osteoarthritis....... Methods: We centrally randomized 251 patients with knee ostcoarthritis to four weekly intra-articular injections of sodium hyaluronate 2 mL (Hyalgan(R) 10.3 mg/mL) versus physiological saline 20 mL (distention) versus physiological saline 2 mL (placebo) and followed patients for 26 weeks. Inclusion...

  7. Pulmonary rehabilitation in lung transplant candidates.

    Science.gov (United States)

    Li, Melinda; Mathur, Sunita; Chowdhury, Noori A; Helm, Denise; Singer, Lianne G

    2013-06-01

    While awaiting lung transplantation, candidates may participate in pulmonary rehabilitation to improve their fitness for surgery. However, pulmonary rehabilitation outcomes have not been systematically evaluated in lung transplant candidates. This investigation was a retrospective cohort study of 345 pre-transplant pulmonary rehabilitation participants who received a lung transplant between January 2004 and June 2009 and had available pre-transplant exercise data. Data extracted included: 6-minute walk tests at standard intervals; exercise training details; health-related quality-of-life (HRQL) measures; and early post-transplant outcomes. Paired t-tests were used to examine changes in the 6MW distance (6MWD), exercise training volume and HRQL during the pre-transplant period. We evaluated the association between pre-transplant 6MWD and transplant hospitalization outcomes. The final 6MWD prior to transplantation was only 15 m less than the listing 6MWD (n = 200; p = 0.002). Exercise training volumes increased slightly from the start of the pulmonary rehabilitation program until transplant: treadmill, increase 0.69 ml/kg/min (n = 238; p volumes are well preserved among lung transplant candidates participating in pulmonary rehabilitation, even in the setting of severe, progressive lung disease. Participants with greater exercise capacity prior to transplantation have more favorable early post-transplant outcomes. Copyright © 2013 International Society for Heart and Lung Transplantation. Published by Elsevier Inc. All rights reserved.

  8. Optimized candidal biofilm microtiter assay

    NARCIS (Netherlands)

    Krom, Bastiaan P.; Cohen, Jesse B.; Feser, Gail E. McElhaney; Cihlar, Ronald L.

    Microtiter based candidal biofilm formation is commonly being used. Here we describe the analysis of factors influencing the development of candidal biofilms such as the coating with serum, growth medium and pH. The data reported here show that optimal candidal biofilm formation is obtained when

  9. Experimental rat lung tumor model with intrabronchial tumor cell implantation.

    Science.gov (United States)

    Gomes Neto, Antero; Simão, Antônio Felipe Leite; Miranda, Samuel de Paula; Mourão, Lívia Talita Cajaseiras; Bezerra, Nilfácio Prado; Almeida, Paulo Roberto Carvalho de; Ribeiro, Ronaldo de Albuquerque

    2008-01-01

    The objective of this study was to develop a rat lung tumor model for anticancer drug testing. Sixty-two female Wistar rats weighing 208 +/- 20 g were anesthetized intraperitoneally with 2.5% tribromoethanol (1 ml/100 g live weight), tracheotomized and intubated with an ultrafine catheter for inoculation with Walker's tumor cells. In the first step of the experiment, a technique was established for intrabronchial implantation of 10(5) to 5 x 10(5) tumor cells, and the tumor take rate was determined. The second stage consisted of determining tumor volume, correlating findings from high-resolution computed tomography (HRCT) with findings from necropsia and determining time of survival. The tumor take rate was 94.7% for implants with 4 x 10(5) tumor cells, HRCT and necropsia findings matched closely (r=0.953; p<0.0001), the median time of survival was 11 days, and surgical mortality was 4.8%. The present rat lung tumor model was shown to be feasible: the take rate was high, surgical mortality was negligible and the procedure was simple to perform and easily reproduced. HRCT was found to be a highly accurate tool for tumor diagnosis, localization and measurement and may be recommended for monitoring tumor growth in this model.

  10. The difference of contrast effects of myelography in normal dogs: Comparison of iohexol (180 mgI/ml), iohexol (240 mgI/ml) and iotrolan (240 mgI/ml)

    International Nuclear Information System (INIS)

    Shimizu, J.; Yamada, K.; Kishimoto, M.; Iwasaki, T.; Miyake, Y.

    2008-01-01

    The contrast effects of three different contrast media preparations (iohexol 180 mgI/ml, iohexol 240 mgI/ml and iotrolan 240 mgI/ml) in conventional and CT myelography were compared. Three beagle dogs were used and the study employed a cross-over method (total of 9) for each contrast media. The result of CT myelography showed that the contrast effect of iohexol (180 mgI/ml), which had low viscosity, was highest in cranial sites, and the contrast effect of high-viscosity iotrolan (240 mgI/ml) was highest in caudal sites 5 min after injection of the contrast media preparations. This shows that the diffusion of contrast media preparations in the subarachnoid space is influenced by viscosity. The results of conventional myelography also showed that the diffusion of contrast media preparations is influenced by viscosity. Therefore, it is important to identify the location of spinal lesions in veterinary practice, and low viscosity contrast medium preparation with wide spread contrast effects is considered suitable for myelography

  11. SED-ML web tools: generate, modify and export standard-compliant simulation studies.

    Science.gov (United States)

    Bergmann, Frank T; Nickerson, David; Waltemath, Dagmar; Scharm, Martin

    2017-04-15

    The Simulation Experiment Description Markup Language (SED-ML) is a standardized format for exchanging simulation studies independently of software tools. We present the SED-ML Web Tools, an online application for creating, editing, simulating and validating SED-ML documents. The Web Tools implement all current SED-ML specifications and, thus, support complex modifications and co-simulation of models in SBML and CellML formats. Ultimately, the Web Tools lower the bar on working with SED-ML documents and help users create valid simulation descriptions. http://sysbioapps.dyndns.org/SED-ML_Web_Tools/ . fbergman@caltech.edu . © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  12. Suppression of phase separation in $(AlAs)_{2ML} (InAs)_{2ML}$ superlattices using $Al_{0.48}In_{0.52}$ As monolayer insertions

    CERN Document Server

    Lee, S R; Follstaedt, D M

    2001-01-01

    Al/sub 0.48/In/sub 0.52/As monolayers (ML) are inserted at the binary-compound interfaces of (AlAs)/sub 2/ /sub ML/(InAs)/sub 2/ /sub ML/ short-period superlattices (SPSs) during growth on (001) In P. The insertion of Al/sub 0.48/In/sub 0.52/As interlayers greater than 2 ML thick tends to suppress the phase separation that normally occurs during molecular beam epitaxy of the SPS. The degree of suppression is a sensitive function of both the monolayer-scale thickness, and the intraperiod growth sequence, of the interlayers in the SPS. Given this sensitivity to monolayer-scale variations in the surface-region composition, we propose that cyclical phase transition of the reconstructed surface initiates SPS decomposition. (21 refs).

  13. IrML – a gene encoding a new member of the ML protein family from the hard tick, Ixodes ricinus

    Czech Academy of Sciences Publication Activity Database

    Horáčková, J.; Rudenko, Natalia; Golovchenko, Maryna; Havlíková, S.; Grubhoffer, Libor

    2010-01-01

    Roč. 35, č. 2 (2010), s. 410-418 ISSN 1081-1710 R&D Projects: GA ČR(CZ) GA524/06/1479; GA MŠk(CZ) LC06009 Institutional research plan: CEZ:AV0Z60220518 Keywords : Ixodes ricinus * tick * ML-domain containing protein * in situ hybridization * gene expression * ML (MD-2-related lipid-recognition) domain Subject RIV: GJ - Animal Vermins ; Diseases, Veterinary Medicine Impact factor: 1.256, year: 2010

  14. Sinus Tumors

    Science.gov (United States)

    ... RESOURCES Medical Societies Patient Education About this Website Font Size + - Home > CONDITIONS > Sinus Tumors Adult Sinusitis Pediatric ... and they vary greatly in location, size and type. Care for these tumors is individualized to each ...

  15. Tumors markers

    International Nuclear Information System (INIS)

    Yamaguchi-Mizumoto, N.H.

    1989-01-01

    In order to study blood and cell components alterations (named tumor markers) that may indicate the presence of a tumor, several methods are presented. Aspects as diagnostic, prognostic, therapeutic value and clinical evaluation are discussed. (M.A.C.)

  16. Wilms tumor

    Science.gov (United States)

    ... suggested. Alternative Names Nephroblastoma; Kidney tumor - Wilms Images Kidney anatomy Wilms tumor References Babaian KN, Delacroix SE, Wood CG, Jonasch E. Kidney cancer. In: Skorecki K, Chertow GM, Marsden PA, ...

  17. Spinal tumors

    International Nuclear Information System (INIS)

    Goethem, J.W.M. van; Hauwe, L. van den; Oezsarlak, Oe.; Schepper, A.M.A. de; Parizel, P.M.

    2004-01-01

    Spinal tumors are uncommon lesions but may cause significant morbidity in terms of limb dysfunction. In establishing the differential diagnosis for a spinal lesion, location is the most important feature, but the clinical presentation and the patient's age and gender are also important. Magnetic resonance (MR) imaging plays a central role in the imaging of spinal tumors, easily allowing tumors to be classified as extradural, intradural-extramedullary or intramedullary, which is very useful in tumor characterization. In the evaluation of lesions of the osseous spine both computed tomography (CT) and MR are important. We describe the most common spinal tumors in detail. In general, extradural lesions are the most common with metastasis being the most frequent. Intradural tumors are rare, and the majority is extramedullary, with meningiomas and nerve sheath tumors being the most frequent. Intramedullary tumors are uncommon spinal tumors. Astrocytomas and ependymomas comprise the majority of the intramedullary tumors. The most important tumors are documented with appropriate high quality CT or MR images and the characteristics of these tumors are also summarized in a comprehensive table. Finally we illustrate the use of the new World Health Organization (WHO) classification of neoplasms affecting the central nervous system

  18. Brain Tumors

    Science.gov (United States)

    A brain tumor is a growth of abnormal cells in the tissues of the brain. Brain tumors can be benign, with no cancer cells, ... cancer cells that grow quickly. Some are primary brain tumors, which start in the brain. Others are ...

  19. Urogenital tumors

    Energy Technology Data Exchange (ETDEWEB)

    Weller, R.E.

    1994-03-01

    An overview is provided for veterinary care of urogenital tumors in companion animals, especially the dog. Neoplasms discussed include tumors of the kidney, urinary bladder, prostate, testis, ovary, vagina, vulva and the canine transmissible venereal tumor. Topics addressed include description, diagnosis and treatment.

  20. NASA Engineering and Safety Center (NESC) Enhanced Melamine (ML) Foam Acoustic Test (NEMFAT)

    Science.gov (United States)

    McNelis, Anne M.; Hughes, William O.; McNelis, Mark E.

    2014-01-01

    The NASA Engineering and Safety Center (NESC) funded a proposal to achieve initial basic acoustic characterization of ML (melamine) foam, which could serve as a starting point for a future, more comprehensive acoustic test program for ML foam. A project plan was developed and implemented to obtain acoustic test data for both normal and enhanced ML foam. This project became known as the NESC Enhanced Melamine Foam Acoustic Test (NEMFAT). This document contains the outcome of the NEMFAT project.

  1. A MuDDy Experience-ML Bindings to a BDD Library

    DEFF Research Database (Denmark)

    Larsen, Ken Friis

    2009-01-01

    . This combination of an ML interface to a high-performance C library is surprisingly fruitful. ML allows you to quickly experiment with high-level symbolic algorithms before handing over the grunt work to the C library. I show how, with a relatively little effort, you can make a domain specific language...... for concurrent finite state-machines embedded in Standard ML and then write various custom model-checking algorithms for this domain specific embedded language (DSEL)....

  2. Theoretical analysis of hydrogen chemisorption on Pd(111), Re(0001) and PdML/Re(0001), ReML/Pd(111) pseudomorphic overlayers

    DEFF Research Database (Denmark)

    Pallassana, Venkataraman; Neurock, Matthew; Hansen, Lars Bruno

    1999-01-01

    not appear to provide an independent parameter for assessing surface reactivity. The weak chemisorption of hydrogen on the Pd-ML/Re(0001) surface relates to substantial lowering of the d-band center of Pd, when it is pseudomorphically deposited as a monolayer on a Re substrate. [S0163-1829(99)00331-2].......Gradient-corrected density-functional theory (DFT-GGA) periodic slab calculations have been used to analyze the binding of atomic hydrogen on monometallic Pd(111), Re(0001), and bimetallic Pd-mL/Re(0001) [pseudomorphic monolayer of Pd(111) on Re(0001)] and Re-ML/Pd(111) surfaces. The computed...

  3. Tumor immunology

    International Nuclear Information System (INIS)

    Otter, W. den

    1987-01-01

    Tumor immunology, the use of immunological techniques for tumor diagnosis and approaches to immunotherapy of cancer are topics covered in this multi-author volume. Part A, 'Tumor Immunology', deals with present views on tumor-associated antigens, the initiation of immune reactions of tumor cells, effector cell killing, tumor cells and suppression of antitumor immunity, and one chapter dealing with the application of mathematical models in tumor immunology. Part B, 'Tumor Diagnosis and Imaging', concerns the use of markers to locate the tumor in vivo, for the histological diagnosis, and for the monitoring of tumor growth. In Part C, 'Immunotherapy', various experimental approaches to immunotherapy are described, such as the use of monoclonal antibodies to target drugs, the use of interleukin-2 and the use of drugs inhibiting suppression. In the final section, the evaluation, a pathologist and a clinician evaluate the possibilities and limitations of tumor immunology and the extent to which it is useful for diagnosis and therapy. refs.; figs.; tabs

  4. SysML for systems engineering a model-based approach

    CERN Document Server

    Holt, Jon

    2013-01-01

    This new edition of this popular text has been fully updated to reflect SysML 1.3, the latest version of the standard, and the discussion has been extended to show the power of SysML as a tool for systems engineering in an MBSE context.

  5. A SysML Test Model and Test Suite for the ETCS Ceiling Speed Monitor

    DEFF Research Database (Denmark)

    Braunstein, Cécile; Peleska, Jan; Schulze, Uwe

    2014-01-01

    System specification. The model is provided in SysML, and it is equipped with a formal semantics that is consistent with the (semi formal) SysML standard published by the Object Management Group (OMG). The model and its description are publicly available on http://www.mbt-benchmarks.de, a website...

  6. Post-void residual urine under 150 ml does not exclude voiding dysfunction in women

    DEFF Research Database (Denmark)

    Khayyami, Yasmine; Klarskov, Niels; Lose, Gunnar

    2016-01-01

    INTRODUCTION AND HYPOTHESIS: It has been claimed that post-void residual urine (PVR) below 150 ml rules out voiding dysfunction in women with stress urinary incontinence (SUI) and provides license to perform sling surgery. The cut-off of 150 ml seems arbitrary, not evidence-based, and so we sough...

  7. Evaluation of ML-MC as a Depth Discriminant in Yellowstone, USA and Italy

    Science.gov (United States)

    Li, Z.; Koper, K. D.; Burlacu, R.; Sun, D.; D'Amico, S.

    2017-12-01

    Recent work has shown that the difference between two magnitude scales, ML (local Richter magnitude) and MC (coda/duration magnitude), acts as a depth discriminant in Utah. Shallow seismic sources, such as mining induced earthquakes and explosions, have strongly negative ML-MC values, while deeper tectonic earthquakes have ML-MC values near zero. These observations imply that ML-MC might be effective at discriminating small explosions from deeper natural earthquakes at local distances. In this work, we examine seismicity catalogs for the Yellowstone region and Italy to determine if ML-MCacts as a depth discriminant in these regions as well. We identified 4,780 earthquakes that occurred in the Yellowstone region between Sept. 24, 1994 and March 31, 2017 for which both ML and MC were calculated. The ML-MC distribution is well described by a Gaussian function with a mean of 0.102 and a standard deviation of 0.326. We selected a subset of these events with accurate depths and determined mean ML-MC values in various depth bins. An event depth was considered accurate if the formal depth error was less than 2 km and either (1) the nearest station was within one focal depth or (2) the distance to the nearest station was smaller than the bin size. We find that ML-MC decreases as event depths become shallower than about 10 km. Similar to the results for Utah, the decrease is statistically significant and is robust with respect to small changes in bin size and the criteria used to define accurate depths. We used a similar process to evaluate whether ML-MC was a function of source depth for 63,555 earthquakes that occurred between April 16, 2005 and April 30, 2012 in Italy. The ML-MC values in Italy are also well described by a normal distribution, with a mean of -0.477 and standard deviation of 0.315. We again find a statistically significant decrease in ML-MC for shallow earthquakes. In contrast to the Yellowstone results, for Italy ML-MC decreases at a nearly constant rate

  8. The performance review of EEWS(Earthquake Early Warning System) about Gyeongju earthquakes with Ml 5.1 and Ml 5.8 in Korea

    Science.gov (United States)

    Park, Jung-Ho; Chi, Heon-Cheol; Lim, In-Seub; Seong, Yun-Jeong; Park, Jihwan

    2017-04-01

    EEW(Earthquake Early Warning) service to the public has been officially operated by KMA (Korea Meteorological Administration) from 2015 in Korea. For the KMA's official EEW service, KIGAM has adopted ElarmS from UC Berkeley BSL and modified local magnitude relation, 1-D travel time curves and association procedures with real time waveform from about 201 seismic stations of KMA, KIGAM, KINS and KEPRI. There were two moderate size earthquakes with magnitude Ml 5.1 and Ml 5.8 close to Gyeongju city located at the southeastern part of Korea on Sep. 12. 2016. We have checked the performance of EEWS(Earthquake Early Warning System) named as TrigDB by KIGAM reviewing of these two Gyeongju earthquakes. The nearest station to epicenters of two earthquakes Ml 5.1(35.7697 N, 129.1904 E) and Ml 5.8(35.7632 N, 129.1898 E) was MKL which detected P phases in about 2.1 and 3.6 seconds after the origin times respectively. The first events were issued in 6.3 and 7.0 seconds from each origin time. Because of the unstable results on the early steps due to very few stations and unexpected automated analysis, KMA has the policy to wait for more 20 seconds for confirming the reliability. For these events KMA published EEW alarms in about 26 seconds after origin times with M 5.3 and M 5.9 respectively.

  9. jmzIdentML API: A Java interface to the mzIdentML standard for peptide and protein identification data.

    Science.gov (United States)

    Reisinger, Florian; Krishna, Ritesh; Ghali, Fawaz; Ríos, Daniel; Hermjakob, Henning; Vizcaíno, Juan Antonio; Jones, Andrew R

    2012-03-01

    We present a Java application programming interface (API), jmzIdentML, for the Human Proteome Organisation (HUPO) Proteomics Standards Initiative (PSI) mzIdentML standard for peptide and protein identification data. The API combines the power of Java Architecture of XML Binding (JAXB) and an XPath-based random-access indexer to allow a fast and efficient mapping of extensible markup language (XML) elements to Java objects. The internal references in the mzIdentML files are resolved in an on-demand manner, where the whole file is accessed as a random-access swap file, and only the relevant piece of XMLis selected for mapping to its corresponding Java object. The APIis highly efficient in its memory usage and can handle files of arbitrary sizes. The APIfollows the official release of the mzIdentML (version 1.1) specifications and is available in the public domain under a permissive licence at http://www.code.google.com/p/jmzidentml/. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Polymorphic New World monkeys with more than three M/L cone types

    Science.gov (United States)

    Jacobs, Gerald H.; Deegan, Jess F.

    2005-10-01

    Most New World (platyrrhine) monkeys have M/L cone photopigment polymorphisms that map directly into individual variations in visual sensitivity and color vision. We used electroretinogram flicker photometry to examine M/L cone photopigments in the New World monkey Callicebus moloch (the dusky Titi). Like other New World monkeys, this species has an M/L cone photopigment polymorphism that reflects the presence of X-chromosome opsin gene alleles. However, unlike other platyrrhines in which three M/L photopigments are typical, Callicebus has a total of five M/L cone photopigments. The peak sensitivity values for these pigments extend across the range from 530 to 562 nm. The result is an enhanced array of potential color vision phenotypes in this species.

  11. QuakeML: Status of the XML-based Seismological Data Exchange Format

    Science.gov (United States)

    Euchner, Fabian; Schorlemmer, Danijel; Kästli, Philipp; Quakeml Working Group

    2010-05-01

    QuakeML is an XML-based data exchange standard for seismology that is in its fourth year of active community-driven development. The current release (version 1.2) is based on a public Request for Comments process that included contributions from ETH, GFZ, USC, SCEC, USGS, IRIS DMC, EMSC, ORFEUS, GNS, ZAMG, BRGM, Nanometrics, and ISTI. QuakeML has mainly been funded through the EC FP6 infrastructure project NERIES, in which it was endorsed as the preferred data exchange format. Currently, QuakeML services are being installed at several institutions around the globe, including EMSC, ORFEUS, ETH, Geoazur (Europe), NEIC, ANSS, SCEC/SCSN (USA), and GNS Science (New Zealand). Some of these institutions already provide QuakeML earthquake catalog web services. Several implementations of the QuakeML data model have been made. QuakePy, an open-source Python-based seismicity analysis toolkit using the QuakeML data model, is being developed at ETH. QuakePy is part of the software stack used in the Collaboratory for the Study of Earthquake Predictability (CSEP) testing center installations, developed by SCEC. Furthermore, the QuakeML data model is part of the SeisComP3 package from GFZ Potsdam. QuakeML is designed as an umbrella schema under which several sub-packages are collected. The present scope of QuakeML 1.2 covers a basic description of seismic events including picks, arrivals, amplitudes, magnitudes, origins, focal mechanisms, and moment tensors. Work on additional packages (macroseismic information, seismic inventory, and resource metadata) has been started, but is at an early stage. Contributions from the community that help to widen the thematic coverage of QuakeML are highly welcome. Online resources: http://www.quakeml.org, http://www.quakepy.org

  12. Quantitation of circulating tumor cells in blood samples from ovarian and prostate cancer patients using tumor-specific fluorescent ligands.

    Science.gov (United States)

    He, Wei; Kularatne, Sumith A; Kalli, Kimberly R; Prendergast, Franklyn G; Amato, Robert J; Klee, George G; Hartmann, Lynn C; Low, Philip S

    2008-10-15

    Quantitation of circulating tumor cells (CTCs) can provide information on the stage of a malignancy, onset of disease progression and response to therapy. In an effort to more accurately quantitate CTCs, we have synthesized fluorescent conjugates of 2 high-affinity tumor-specific ligands (folate-AlexaFluor 488 and DUPA-FITC) that bind tumor cells >20-fold more efficiently than fluorescent antibodies. Here we determine whether these tumor-specific dyes can be exploited for quantitation of CTCs in peripheral blood samples from cancer patients. A CTC-enriched fraction was isolated from the peripheral blood of ovarian and prostate cancer patients by an optimized density gradient centrifugation protocol and labeled with the aforementioned fluorescent ligands. CTCs were then quantitated by flow cytometry. CTCs were detected in 18 of 20 ovarian cancer patients (mean 222 CTCs/ml; median 15 CTCs/ml; maximum 3,118 CTCs/ml), whereas CTC numbers in 16 gender-matched normal volunteers were negligible (mean 0.4 CTCs/ml; median 0.3 CTCs/ml; maximum 1.5 CTCs/ml; p < 0.001, chi(2)). CTCs were also detected in 10 of 13 prostate cancer patients (mean 26 CTCs/ml, median 14 CTCs/ml, maximum 94 CTCs/ml) but not in 18 gender-matched healthy donors (mean 0.8 CTCs/ml, median 1, maximum 3 CTC/ml; p < 0.0026, chi(2)). Tumor-specific fluorescent antibodies were much less efficient in quantitating CTCs because of their lower CTC labeling efficiency. Use of tumor-specific fluorescent ligands to label CTCs in peripheral blood can provide a simple, accurate and sensitive method for determining the number of cancer cells circulating in the bloodstream.

  13. qcML: an exchange format for quality control metrics from mass spectrometry experiments.

    Science.gov (United States)

    Walzer, Mathias; Pernas, Lucia Espona; Nasso, Sara; Bittremieux, Wout; Nahnsen, Sven; Kelchtermans, Pieter; Pichler, Peter; van den Toorn, Henk W P; Staes, An; Vandenbussche, Jonathan; Mazanek, Michael; Taus, Thomas; Scheltema, Richard A; Kelstrup, Christian D; Gatto, Laurent; van Breukelen, Bas; Aiche, Stephan; Valkenborg, Dirk; Laukens, Kris; Lilley, Kathryn S; Olsen, Jesper V; Heck, Albert J R; Mechtler, Karl; Aebersold, Ruedi; Gevaert, Kris; Vizcaíno, Juan Antonio; Hermjakob, Henning; Kohlbacher, Oliver; Martens, Lennart

    2014-08-01

    Quality control is increasingly recognized as a crucial aspect of mass spectrometry based proteomics. Several recent papers discuss relevant parameters for quality control and present applications to extract these from the instrumental raw data. What has been missing, however, is a standard data exchange format for reporting these performance metrics. We therefore developed the qcML format, an XML-based standard that follows the design principles of the related mzML, mzIdentML, mzQuantML, and TraML standards from the HUPO-PSI (Proteomics Standards Initiative). In addition to the XML format, we also provide tools for the calculation of a wide range of quality metrics as well as a database format and interconversion tools, so that existing LIMS systems can easily add relational storage of the quality control data to their existing schema. We here describe the qcML specification, along with possible use cases and an illustrative example of the subsequent analysis possibilities. All information about qcML is available at http://code.google.com/p/qcml. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

  14. qcML: An Exchange Format for Quality Control Metrics from Mass Spectrometry Experiments*

    Science.gov (United States)

    Walzer, Mathias; Pernas, Lucia Espona; Nasso, Sara; Bittremieux, Wout; Nahnsen, Sven; Kelchtermans, Pieter; Pichler, Peter; van den Toorn, Henk W. P.; Staes, An; Vandenbussche, Jonathan; Mazanek, Michael; Taus, Thomas; Scheltema, Richard A.; Kelstrup, Christian D.; Gatto, Laurent; van Breukelen, Bas; Aiche, Stephan; Valkenborg, Dirk; Laukens, Kris; Lilley, Kathryn S.; Olsen, Jesper V.; Heck, Albert J. R.; Mechtler, Karl; Aebersold, Ruedi; Gevaert, Kris; Vizcaíno, Juan Antonio; Hermjakob, Henning; Kohlbacher, Oliver; Martens, Lennart

    2014-01-01

    Quality control is increasingly recognized as a crucial aspect of mass spectrometry based proteomics. Several recent papers discuss relevant parameters for quality control and present applications to extract these from the instrumental raw data. What has been missing, however, is a standard data exchange format for reporting these performance metrics. We therefore developed the qcML format, an XML-based standard that follows the design principles of the related mzML, mzIdentML, mzQuantML, and TraML standards from the HUPO-PSI (Proteomics Standards Initiative). In addition to the XML format, we also provide tools for the calculation of a wide range of quality metrics as well as a database format and interconversion tools, so that existing LIMS systems can easily add relational storage of the quality control data to their existing schema. We here describe the qcML specification, along with possible use cases and an illustrative example of the subsequent analysis possibilities. All information about qcML is available at http://code.google.com/p/qcml. PMID:24760958

  15. The abstract geometry modeling language (AgML): experience and road map toward eRHIC

    International Nuclear Information System (INIS)

    Webb, Jason; Lauret, Jerome; Perevoztchikov, Victor

    2014-01-01

    The STAR experiment has adopted an Abstract Geometry Modeling Language (AgML) as the primary description of our geometry model. AgML establishes a level of abstraction, decoupling the definition of the detector from the software libraries used to create the concrete geometry model. Thus, AgML allows us to support both our legacy GEANT 3 simulation application and our ROOT/TGeo based reconstruction software from a single source, which is demonstrably self- consistent. While AgML was developed primarily as a tool to migrate away from our legacy FORTRAN-era geometry codes, it also provides a rich syntax geared towards the rapid development of detector models. AgML has been successfully employed by users to quickly develop and integrate the descriptions of several new detectors in the RHIC/STAR experiment including the Forward GEM Tracker (FGT) and Heavy Flavor Tracker (HFT) upgrades installed in STAR for the 2012 and 2013 runs. AgML has furthermore been heavily utilized to study future upgrades to the STAR detector as it prepares for the eRHIC era. With its track record of practical use in a live experiment in mind, we present the status, lessons learned and future of the AgML language as well as our experience in bringing the code into our production and development environments. We will discuss the path toward eRHIC and pushing the current model to accommodate for detector miss-alignment and high precision physics.

  16. pymzML--Python module for high-throughput bioinformatics on mass spectrometry data.

    Science.gov (United States)

    Bald, Till; Barth, Johannes; Niehues, Anna; Specht, Michael; Hippler, Michael; Fufezan, Christian

    2012-04-01

    pymzML is an extension to Python that offers (i) an easy access to mass spectrometry (MS) data that allows the rapid development of tools, (ii) a very fast parser for mzML data, the standard data format in MS and (iii) a set of functions to compare or handle spectra. pymzML requires Python2.6.5+ and is fully compatible with Python3. The module is freely available on http://pymzml.github.com or pypi, is published under LGPL license and requires no additional modules to be installed. christian@fufezan.net.

  17. Rare A2ML1 variants confer susceptibility to otitis media

    Science.gov (United States)

    Santos-Cortez, Regie Lyn P.; Chiong, Charlotte M.; Reyes-Quintos, Ma. Rina T.; Tantoco, Ma. Leah C.; Wang, Xin; Acharya, Anushree; Abbe, Izoduwa; Giese, Arnaud P.; Smith, Joshua D.; Allen, E. Kaitlynn; Li, Biao; Cutiongco-de la Paz, Eva Maria; Garcia, Marieflor Cristy; Llanes, Erasmo Gonzalo D.V.; Labra, Patrick John; Gloria-Cruz, Teresa Luisa I.; Chan, Abner L.; Wang, Gao T.; Daly, Kathleen A.; Shendure, Jay; Bamshad, Michael J.; Nickerson, Deborah A.; Patel, Janak A.; Riazuddin, Saima; Sale, Michele M.; Chonmaitree, Tasnee; Ahmed, Zubair M.; Abes, Generoso T.; Leal, Suzanne M.

    2015-01-01

    A duplication variant within middle-ear-specific gene A2ML1 co-segregates with otitis media in an indigenous Filipino pedigree (LOD score=7.5 at reduced penetrance) and lies within a founder haplotype that is also shared by three otitis-prone European- and Hispanic-American children, but is absent in non-otitis-prone children and >62,000 next-generation sequences. Seven additional A2ML1 variants were identified in six otitis-prone children. Collectively our studies support a role for A2ML1 in the pathophysiology of otitis media. PMID:26121085

  18. cluML: A markup language for clustering and cluster validity assessment of microarray data.

    Science.gov (United States)

    Bolshakova, Nadia; Cunningham, Pádraig

    2005-01-01

    cluML is a new markup language for microarray data clustering and cluster validity assessment. The XML-based format has been designed to address some of the limitations observed in traditional formats, such as inability to store multiple clustering (including biclustering) and validation results within a dataset. cluML is an effective tool to support biomedical knowledge representation in gene expression data analysis. Although cluML was developed for DNA microarray analysis applications, it can be effectively used for the representation of clustering and for the validation of other biomedical and physical data that has no limitations.

  19. Analisis Pengawasan Logistik Produk Aqua Ukuran 330ml Pada CV. Dlu'x Resto Samarinda

    OpenAIRE

    Mardiana, Ali Masuhud, H. Mulyadi Syp

    2016-01-01

    The problem in this research is "Are Determination Against Aqua Products Logistics Control 330ml sizes on CV. DLux Resto has been optimized? "This study aims to determine the amount of inventory on the CV aqua 330ml sizes. Dlu'x Resto in Samarinda.Formulation of the problem in this study is whether the determination of the logistical monitoring product inventory aqua 330ml sizes that have been carried out on the CV. Dlu'x Resto Samarinda already performed optimally.The hypothesis in this stud...

  20. A dual inhibitor of matrix metalloproteinases and a disintegrin and metalloproteinases, [¹⁸F]FB-ML5, as a molecular probe for non-invasive MMP/ADAM-targeted imaging.

    Science.gov (United States)

    Matusiak, Nathalie; Castelli, Riccardo; Tuin, Adriaan W; Overkleeft, Herman S; Wisastra, Rosalina; Dekker, Frank J; Prély, Laurette M; Bischoff, Rainer; Bischoff, Rainer P M; van Waarde, Aren; Dierckx, Rudi A J O; Elsinga, Philip H

    2015-01-01

    Numerous clinical studies have shown a correlation between increased matrix metalloproteinase (MMP)/a disintegrin and metalloproteinase (ADAM) activity and poor outcome of cancer. Various MMP inhibitors (MMPIs) have been developed for therapeutic purposes in oncology. In addition, molecular imaging of MMP/ADAM levels in vivo would allow the diagnosis of tumors. We selected the dual inhibitor of MMPs and ADAMs, ML5, which is a hydroxamate-based inhibitor with affinities for many MMPs and ADAMs. ML5 was radiolabelled with (18)F and the newly obtained radiolabelled inhibitor was evaluated in vitro and in vivo. ML5 was radiolabelled by direct acylation with N-succinimidyl-4-[(18)F]fluorobenzoate ([(18)F]SFB) for PET (positron emission tomography). The resulting radiotracer [(18)F]FB-ML5 was evaluated in vitro in human bronchial epithelium 16HBE cells and breast cancer MCF-7 cells. The non-radioactive probe FB-ML5 and native ML5 were tested in a fluorogenic inhibition assay against MMP-2, -9, -12 and ADAM-17. The in vivo kinetics of [(18)F]FB-ML5 were examined in a HT1080 tumor-bearing mouse model. Specificity of probe binding was examined by co-injection of 0 or 2.5mg/kg ML5. ML5 and FB-ML5 showed high affinity for MMP-2, -9, -12 and ADAM-17; indeed IC50 values were respectively 7.4 ± 2.0, 19.5 ± 2.8, 2.0 ± 0.2 and 5.7 ± 2.2 nM and 12.5 ± 3.1, 31.5 ± 13.7, 138.0 ± 10.9 and 24.7 ± 2.8 nM. Radiochemical yield of HPLC-purified [(18)F]FB-ML5 was 13-16% (corrected for decay). Cellular binding of [(18)F]FB-ML5 was reduced by 36.6% and 27.5% in MCF-7 and 16 HBE cells, respectively, after co-incubation with 10 μM of ML5. In microPET scans, HT1080 tumors exhibited a low and homogeneous uptake of the tracer. Tumors of mice injected with [(18)F]FB-ML5 showed a SUVmean of 0.145 ± 0.064 (n=6) which decreased to 0.041 ± 0.027 (n=6) after target blocking (pFB-ML5 demonstrated rather low binding in ADAM-17 overexpressing cell lines. [(18)F]FB-ML5 uptake showed significant

  1. Lower tidal volume strategy (?3?ml/kg) combined with extracorporeal CO2 removal versus ?conventional? protective ventilation (6?ml/kg) in severe ARDS

    OpenAIRE

    Bein, Thomas; Weber-Carstens, Steffen; Goldmann, Anton; M?ller, Thomas; Staudinger, Thomas; Brederlau, J?rg; Muellenbach, Ralf; Dembinski, Rolf; Graf, Bernhard M.; Wewalka, Marlene; Philipp, Alois; Wernecke, Klaus-Dieter; Lubnow, Matthias; Slutsky, Arthur S.

    2013-01-01

    Background Acute respiratory distress syndrome is characterized by damage to the lung caused by various insults, including ventilation itself, and tidal hyperinflation can lead to ventilator induced lung injury (VILI). We investigated the effects of a low tidal volume (V T) strategy (V T???3?ml/kg/predicted body weight [PBW]) using pumpless extracorporeal lung assist in established ARDS. Methods Seventy-nine patients were enrolled after a ?stabilization period? (24?h with optimized therapy an...

  2. Tumoral tracers

    International Nuclear Information System (INIS)

    Camargo, E.E.

    1979-01-01

    Direct tumor tracers are subdivided in the following categories:metabolite tracers, antitumoral tracers, radioactive proteins and cations. Use of 67 Ga-citrate as a clinically important tumoral tracer is emphasized and gallium-67 whole-body scintigraphy is discussed in detail. (M.A.) [pt

  3. Evaluating the Impact of Design-Driven Requirements Using SysML

    Data.gov (United States)

    National Aeronautics and Space Administration — The proposed research will develop SysML requirements modeling patterns and scripts to automate the evaluation of the impact of design driven requirements....

  4. SED-ED, a workflow editor for computational biology experiments written in SED-ML.

    Science.gov (United States)

    Adams, Richard R

    2012-04-15

    The simulation experiment description markup language (SED-ML) is a new community data standard to encode computational biology experiments in a computer-readable XML format. Its widespread adoption will require the development of software support to work with SED-ML files. Here, we describe a software tool, SED-ED, to view, edit, validate and annotate SED-ML documents while shielding end-users from the underlying XML representation. SED-ED supports modellers who wish to create, understand and further develop a simulation description provided in SED-ML format. SED-ED is available as a standalone Java application, as an Eclipse plug-in and as an SBSI (www.sbsi.ed.ac.uk) plug-in, all under an MIT open-source license. Source code is at https://sed-ed-sedmleditor.googlecode.com/svn. The application itself is available from https://sourceforge.net/projects/jlibsedml/files/SED-ED/.

  5. On the use of successive data in the ML-EM algorithm in Positron Emission Tomography

    Energy Technology Data Exchange (ETDEWEB)

    Desmedt, P; Lemahieu, I [University of Ghent, ELIS Department, SInt-Pietersnieuwstraat 41, B-9000 Gent, (Belgium)

    1994-12-31

    The Maximum Likelihood-Expectation Maximization (ML-EM) algorithm is the most popular statistical reconstruction technique for Positron Emission Tomography (PET). The ML-EM algorithm is however also renowned for its long reconstruction times. An acceleration technique for this algorithm is studied in this paper. The proposed technique starts the ML-EM algorithm before the measurement process is completed. Since the reconstruction is initiated during the scan of the patient, the time elapsed before a reconstruction becomes available is reduced. Experiments with software phantoms indicate that the quality of the reconstructed image using successive data is comparable to the quality of the reconstruction with the normal ML-EM algorithm. (authors). 7 refs, 3 figs.

  6. The enhanced callose deposition in barley with ml-o powdery mildew resistance genes

    DEFF Research Database (Denmark)

    Skou, Jens-Peder

    1985-01-01

    Carborundum treatment of barley leaves induced a callose deposition which was detected as diffuse blotches in the epidermal cells of susceptible barleys and as deeply stained tracks along the scratches in barleys with the ml-o powdery mildew resistance gene. Subsequent inoculation with powdery...... mildew resulted in appositions that enlarged inversely to their size in the respective varieties when inoculated without carborundum treatment. Aphids sucking the leaves resulted in rows of callose containing spots along the anticlinal cell walls. The spots were larger in the ml-o mutant than...... in the mother variety. Callose was deposited in connection with the pleiotropic necrotic spotting in barleys with the ml-o gene. Modification of the necrotic spotting by crossing the ml-o gene into other gene backgrounds did not result in any change in the size of appositions upon inoculation with powdery...

  7. Animal tumors

    International Nuclear Information System (INIS)

    Gillette, E.L.

    1983-01-01

    There are few trained veterinary radiation oncologists and the expense of facilities has limited the extent to which this modality is used. In recent years, a few cobalt teletherapy units and megavoltage x-ray units have been employed in larger veterinary institutions. In addition, some radiation oncologists of human medical institutions are interested and willing to cooperate with veterinarians in the treatment of animal tumors. Carefully designed studies of the response of animal tumors to new modalities serve two valuable purposes. First, these studies may lead to improved tumor control in companion animals. Second, these studies may have important implications to the improvement of therapy of human tumors. Much remains to be learned of animal tumor biology so that appropriate model systems can be described for such studies. Many of the latter studies can be sponsored by agencies interested in the improvement of cancer management

  8. QuakeML: XML for Seismological Data Exchange and Resource Metadata Description

    Science.gov (United States)

    Euchner, F.; Schorlemmer, D.; Becker, J.; Heinloo, A.; Kästli, P.; Saul, J.; Weber, B.; QuakeML Working Group

    2007-12-01

    QuakeML is an XML-based data exchange format for seismology that is under development. Current collaborators are from ETH, GFZ, USC, USGS, IRIS DMC, EMSC, ORFEUS, and ISTI. QuakeML development was motivated by the lack of a widely accepted and well-documented data format that is applicable to a broad range of fields in seismology. The development team brings together expertise from communities dealing with analysis and creation of earthquake catalogs, distribution of seismic bulletins, and real-time processing of seismic data. Efforts to merge QuakeML with existing XML dialects are under way. The first release of QuakeML will cover a basic description of seismic events including picks, arrivals, amplitudes, magnitudes, origins, focal mechanisms, and moment tensors. Further extensions are in progress or planned, e.g., for macroseismic information, location probability density functions, slip distributions, and ground motion information. The QuakeML language definition is supplemented by a concept to provide resource metadata and facilitate metadata exchange between distributed data providers. For that purpose, we introduce unique, location-independent identifiers of seismological resources. As an application of QuakeML, ETH Zurich currently develops a Python-based seismicity analysis toolkit as a contribution to CSEP (Collaboratory for the Study of Earthquake Predictability). We follow a collaborative and transparent development approach along the lines of the procedures of the World Wide Web Consortium (W3C). QuakeML currently is in working draft status. The standard description will be subjected to a public Request for Comments (RFC) process and eventually reach the status of a recommendation. QuakeML can be found at http://www.quakeml.org.

  9. Diguanylate cyclase activity of the Mycobacterium leprae T cell antigen ML1419c.

    Science.gov (United States)

    Rotcheewaphan, Suwatchareeporn; Belisle, John T; Webb, Kristofor J; Kim, Hee-Jin; Spencer, John S; Borlee, Bradley R

    2016-09-01

    The second messenger, bis-(3',5')-cyclic dimeric guanosine monophosphate (cyclic di-GMP), is involved in the control of multiple bacterial phenotypes, including those that impact host-pathogen interactions. Bioinformatics analyses predicted that Mycobacterium leprae, an obligate intracellular bacterium and the causative agent of leprosy, encodes three active diguanylate cyclases. In contrast, the related pathogen Mycobacterium tuberculosis encodes only a single diguanylate cyclase. One of the M. leprae unique diguanylate cyclases (ML1419c) was previously shown to be produced early during the course of leprosy. Thus, functional analysis of ML1419c was performed. The gene encoding ML1419c was cloned and expressed in Pseudomonas aeruginosa PAO1 to allow for assessment of cyclic di-GMP production and cyclic di-GMP-mediated phenotypes. Phenotypic studies revealed that ml1419c expression altered colony morphology, motility and biofilm formation of P. aeruginosa PAO1 in a manner consistent with increased cyclic di-GMP production. Direct measurement of cyclic di-GMP levels by liquid chromatography-mass spectrometry confirmed that ml1419c expression increased cyclic di-GMP production in P. aeruginosa PAO1 cultures in comparison to the vector control. The observed phenotypes and increased levels of cyclic di-GMP detected in P. aeruginosa expressing ml1419c could be abrogated by mutation of the active site in ML1419c. These studies demonstrated that ML1419c of M. leprae functions as diguanylate cyclase to synthesize cyclic di-GMP. Thus, this protein was renamed DgcA (Diguanylate cyclase A). These results also demonstrated the ability to use P. aeruginosa as a heterologous host for characterizing the function of proteins involved in the cyclic di-GMP pathway of a pathogen refractory to in vitro growth, M. leprae.

  10. CytometryML: a data standard which has been designed to interface with other standards

    Science.gov (United States)

    Leif, Robert C.

    2007-02-01

    Because of the differences in the requirements, needs, and past histories including existing standards of the creating organizations, a single encompassing cytology-pathology standard will not, in the near future, replace the multiple existing or under development standards. Except for DICOM and FCS, these standardization efforts are all based on XML. CytometryML is a collection of XML schemas, which are based on the Digital Imaging and Communications in Medicine (DICOM) and Flow Cytometry Standard (FCS) datatypes. The CytometryML schemas contain attributes that link them to the DICOM standard and FCS. Interoperability with DICOM has been facilitated by, wherever reasonable, limiting the difference between CytometryML and the previous standards to syntax. In order to permit the Resource Description Framework, RDF, to reference the CytometryML datatypes, id attributes have been added to many CytometryML elements. The Laboratory Digital Imaging Project (LDIP) Data Exchange Specification and the Flowcyt standards development effort employ RDF syntax. Documentation from DICOM has been reused in CytometryML. The unity of analytical cytology was demonstrated by deriving a microscope type and a flow cytometer type from a generic cytometry instrument type. The feasibility of incorporating the Flowcyt gating schemas into CytometryML has been demonstrated. CytometryML is being extended to include many of the new DICOM Working Group 26 datatypes, which describe patients, specimens, and analytes. In situations where multiple standards are being created, interoperability can be facilitated by employing datatypes based on a common set of semantics and building in links to standards that employ different syntax.

  11. Assembling Components using SysML with Non-Functional Requirements

    OpenAIRE

    Chouali , Samir; Hammad , Ahmed; Mountassir , Hassan

    2013-01-01

    International audience; Non-functional requirements of component based systems are important as their functional requirements, therefore they must be considered in components assembly. These properties are beforehand specified with SysML requirement diagram. We specify component based system architecture with SysML block definition diagram, and component behaviors with sequence diagrams. We propose to specify formally component interfaces with interface automata, obtained from requirement and...

  12. Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language.

    Science.gov (United States)

    Waltemath, Dagmar; Adams, Richard; Bergmann, Frank T; Hucka, Michael; Kolpakov, Fedor; Miller, Andrew K; Moraru, Ion I; Nickerson, David; Sahle, Sven; Snoep, Jacky L; Le Novère, Nicolas

    2011-12-15

    The increasing use of computational simulation experiments to inform modern biological research creates new challenges to annotate, archive, share and reproduce such experiments. The recently published Minimum Information About a Simulation Experiment (MIASE) proposes a minimal set of information that should be provided to allow the reproduction of simulation experiments among users and software tools. In this article, we present the Simulation Experiment Description Markup Language (SED-ML). SED-ML encodes in a computer-readable exchange format the information required by MIASE to enable reproduction of simulation experiments. It has been developed as a community project and it is defined in a detailed technical specification and additionally provides an XML schema. The version of SED-ML described in this publication is Level 1 Version 1. It covers the description of the most frequent type of simulation experiments in the area, namely time course simulations. SED-ML documents specify which models to use in an experiment, modifications to apply on the models before using them, which simulation procedures to run on each model, what analysis results to output, and how the results should be presented. These descriptions are independent of the underlying model implementation. SED-ML is a software-independent format for encoding the description of simulation experiments; it is not specific to particular simulation tools. Here, we demonstrate that with the growing software support for SED-ML we can effectively exchange executable simulation descriptions. With SED-ML, software can exchange simulation experiment descriptions, enabling the validation and reuse of simulation experiments in different tools. Authors of papers reporting simulation experiments can make their simulation protocols available for other scientists to reproduce the results. Because SED-ML is agnostic about exact modeling language(s) used, experiments covering models from different fields of research

  13. Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language

    Science.gov (United States)

    2011-01-01

    Background The increasing use of computational simulation experiments to inform modern biological research creates new challenges to annotate, archive, share and reproduce such experiments. The recently published Minimum Information About a Simulation Experiment (MIASE) proposes a minimal set of information that should be provided to allow the reproduction of simulation experiments among users and software tools. Results In this article, we present the Simulation Experiment Description Markup Language (SED-ML). SED-ML encodes in a computer-readable exchange format the information required by MIASE to enable reproduction of simulation experiments. It has been developed as a community project and it is defined in a detailed technical specification and additionally provides an XML schema. The version of SED-ML described in this publication is Level 1 Version 1. It covers the description of the most frequent type of simulation experiments in the area, namely time course simulations. SED-ML documents specify which models to use in an experiment, modifications to apply on the models before using them, which simulation procedures to run on each model, what analysis results to output, and how the results should be presented. These descriptions are independent of the underlying model implementation. SED-ML is a software-independent format for encoding the description of simulation experiments; it is not specific to particular simulation tools. Here, we demonstrate that with the growing software support for SED-ML we can effectively exchange executable simulation descriptions. Conclusions With SED-ML, software can exchange simulation experiment descriptions, enabling the validation and reuse of simulation experiments in different tools. Authors of papers reporting simulation experiments can make their simulation protocols available for other scientists to reproduce the results. Because SED-ML is agnostic about exact modeling language(s) used, experiments covering models from

  14. Simulation Experiment Description Markup Language (SED-ML Level 1 Version 3 (L1V3

    Directory of Open Access Journals (Sweden)

    Bergmann Frank T.

    2018-03-01

    Full Text Available The creation of computational simulation experiments to inform modern biological research poses challenges to reproduce, annotate, archive, and share such experiments. Efforts such as SBML or CellML standardize the formal representation of computational models in various areas of biology. The Simulation Experiment Description Markup Language (SED-ML describes what procedures the models are subjected to, and the details of those procedures. These standards, together with further COMBINE standards, describe models sufficiently well for the reproduction of simulation studies among users and software tools. The Simulation Experiment Description Markup Language (SED-ML is an XML-based format that encodes, for a given simulation experiment, (i which models to use; (ii which modifications to apply to models before simulation; (iii which simulation procedures to run on each model; (iv how to post-process the data; and (v how these results should be plotted and reported. SED-ML Level 1 Version 1 (L1V1 implemented support for the encoding of basic time course simulations. SED-ML L1V2 added support for more complex types of simulations, specifically repeated tasks and chained simulation procedures. SED-ML L1V3 extends L1V2 by means to describe which datasets and subsets thereof to use within a simulation experiment.

  15. VarioML framework for comprehensive variation data representation and exchange.

    Science.gov (United States)

    Byrne, Myles; Fokkema, Ivo Fac; Lancaster, Owen; Adamusiak, Tomasz; Ahonen-Bishopp, Anni; Atlan, David; Béroud, Christophe; Cornell, Michael; Dalgleish, Raymond; Devereau, Andrew; Patrinos, George P; Swertz, Morris A; Taschner, Peter Em; Thorisson, Gudmundur A; Vihinen, Mauno; Brookes, Anthony J; Muilu, Juha

    2012-10-03

    Sharing of data about variation and the associated phenotypes is a critical need, yet variant information can be arbitrarily complex, making a single standard vocabulary elusive and re-formatting difficult. Complex standards have proven too time-consuming to implement. The GEN2PHEN project addressed these difficulties by developing a comprehensive data model for capturing biomedical observations, Observ-OM, and building the VarioML format around it. VarioML pairs a simplified open specification for describing variants, with a toolkit for adapting the specification into one's own research workflow. Straightforward variant data can be captured, federated, and exchanged with no overhead; more complex data can be described, without loss of compatibility. The open specification enables push-button submission to gene variant databases (LSDBs) e.g., the Leiden Open Variation Database, using the Cafe Variome data publishing service, while VarioML bidirectionally transforms data between XML and web-application code formats, opening up new possibilities for open source web applications building on shared data. A Java implementation toolkit makes VarioML easily integrated into biomedical applications. VarioML is designed primarily for LSDB data submission and transfer scenarios, but can also be used as a standard variation data format for JSON and XML document databases and user interface components. VarioML is a set of tools and practices improving the availability, quality, and comprehensibility of human variation information. It enables researchers, diagnostic laboratories, and clinics to share that information with ease, clarity, and without ambiguity.

  16. WaterML: an XML Language for Communicating Water Observations Data

    Science.gov (United States)

    Maidment, D. R.; Zaslavsky, I.; Valentine, D.

    2007-12-01

    One of the great impediments to the synthesis of water information is the plethora of formats used to publish such data. Each water agency uses its own approach. XML (eXtended Markup Languages) are generalizations of Hypertext Markup Language to communicate specific kinds of information via the internet. WaterML is an XML language for water observations data - streamflow, water quality, groundwater levels, climate, precipitation and aquatic biology data, recorded at fixed, point locations as a function of time. The Hydrologic Information System project of the Consortium of Universities for the Advancement of Hydrologic Science, Inc (CUAHSI) has defined WaterML and prepared a set of web service functions called WaterOneFLow that use WaterML to provide information about observation sites, the variables measured there and the values of those measurments. WaterML has been submitted to the Open GIS Consortium for harmonization with its standards for XML languages. Academic investigators at a number of testbed locations in the WATERS network are providing data in WaterML format using WaterOneFlow web services. The USGS and other federal agencies are also working with CUAHSI to similarly provide access to their data in WaterML through WaterOneFlow services.

  17. Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3).

    Science.gov (United States)

    Bergmann, Frank T; Cooper, Jonathan; König, Matthias; Moraru, Ion; Nickerson, David; Le Novère, Nicolas; Olivier, Brett G; Sahle, Sven; Smith, Lucian; Waltemath, Dagmar

    2018-03-19

    The creation of computational simulation experiments to inform modern biological research poses challenges to reproduce, annotate, archive, and share such experiments. Efforts such as SBML or CellML standardize the formal representation of computational models in various areas of biology. The Simulation Experiment Description Markup Language (SED-ML) describes what procedures the models are subjected to, and the details of those procedures. These standards, together with further COMBINE standards, describe models sufficiently well for the reproduction of simulation studies among users and software tools. The Simulation Experiment Description Markup Language (SED-ML) is an XML-based format that encodes, for a given simulation experiment, (i) which models to use; (ii) which modifications to apply to models before simulation; (iii) which simulation procedures to run on each model; (iv) how to post-process the data; and (v) how these results should be plotted and reported. SED-ML Level 1 Version 1 (L1V1) implemented support for the encoding of basic time course simulations. SED-ML L1V2 added support for more complex types of simulations, specifically repeated tasks and chained simulation procedures. SED-ML L1V3 extends L1V2 by means to describe which datasets and subsets thereof to use within a simulation experiment.

  18. Spectra, chromatograms, Metadata: mzML-the standard data format for mass spectrometer output.

    Science.gov (United States)

    Turewicz, Michael; Deutsch, Eric W

    2011-01-01

    This chapter describes Mass Spectrometry Markup Language (mzML), an XML-based and vendor-neutral standard data format for storage and exchange of mass spectrometer output like raw spectra and peak lists. It is intended to replace its two precursor data formats (mzData and mzXML), which had been developed independently a few years earlier. Hence, with the release of mzML, the problem of having two different formats for the same purposes is solved, and with it the duplicated effort of maintaining and supporting two data formats. The new format has been developed by a broad-based consortium of major instrument vendors, software vendors, and academic researchers under the aegis of the Human Proteome Organisation (HUPO), Proteomics Standards Initiative (PSI), with full participation of the main developers of the precursor formats. This comprehensive approach helped mzML to become a generally accepted standard. Furthermore, the collaborative development insured that mzML has adopted the best features of its precursor formats. In this chapter, we discuss mzML's development history, its design principles and use cases, as well as its main building components. We also present the available documentation, an example file, and validation software for mzML.

  19. An Ontology for State Analysis: Formalizing the Mapping to SysML

    Science.gov (United States)

    Wagner, David A.; Bennett, Matthew B.; Karban, Robert; Rouquette, Nicolas; Jenkins, Steven; Ingham, Michel

    2012-01-01

    State Analysis is a methodology developed over the last decade for architecting, designing and documenting complex control systems. Although it was originally conceived for designing robotic spacecraft, recent applications include the design of control systems for large ground-based telescopes. The European Southern Observatory (ESO) began a project to design the European Extremely Large Telescope (E-ELT), which will require coordinated control of over a thousand articulated mirror segments. The designers are using State Analysis as a methodology and the Systems Modeling Language (SysML) as a modeling and documentation language in this task. To effectively apply the State Analysis methodology in this context it became necessary to provide ontological definitions of the concepts and relations in State Analysis and greater flexibility through a mapping of State Analysis into a practical extension of SysML. The ontology provides the formal basis for verifying compliance with State Analysis semantics including architectural constraints. The SysML extension provides the practical basis for applying the State Analysis methodology with SysML tools. This paper will discuss the method used to develop these formalisms (the ontology), the formalisms themselves, the mapping to SysML and approach to using these formalisms to specify a control system and enforce architectural constraints in a SysML model.

  20. Characteristic mutations found in the ML0411 gene of Mycobacterium leprae isolated in Northeast Asian countries.

    Science.gov (United States)

    Kai, M; Nakata, N; Matsuoka, M; Sekizuka, T; Kuroda, M; Makino, M

    2013-10-01

    Genome analysis of Mycobacterium leprae strain Kyoto-2 in this study revealed characteristic nucleotide substitutions in gene ML0411, compared to the reference genome M. leprae strain TN. The ML0411 gene of Kyoto-2 had six SNPs compared to that of TN. All SNPs in ML0411 were non-synonymous mutations that result in amino acid replacements. In addition, a seventh SNP was found 41 bp upstream of the start codon in the regulatory region. The seven SNP sites in the ML0411 region were investigated by sequencing in 36 M. leprae isolates from the Leprosy Research Center in Japan. The SNP pattern in 14 of the 36 isolates showed similarity to that of Kyoto-2. Determination of the standard SNP types within the 36 stocked isolates revealed that almost all of the Japanese strains belonged to SNP type III, with nucleotide substitutions at position 14676, 164275, and 2935685 of the M. leprae TN genome. The geographical distribution pattern of east Asian M. leprae isolates by discrimination of ML0411 SNPs was investigated and interestingly turned out to be similar to that of tandem repeat numbers of GACATC in the rpoT gene (3 copies or 4 copies), which has been established as a tool for M. leprae genotyping. All seven Korean M. leprae isolates examined in this study, as well as those derived from Honshu Island of Japan, showed 4 copies of the 6-base tandem repeat plus the ML0411 SNPs observed in M. leprae Kyoto-2. They are termed Northeast Asian (NA) strain of M. leprae. On the other hand, many of isolates derived from the Okinawa Islands of Japan and from the Philippines showed 3 copies of the 6-base tandem repeat in addition to the M. leprae TN ML0411 type of SNPs. These results demonstrate the existence of M. leprae strains in Northeast Asian region having characteristic SNP patterns. Copyright © 2013 Elsevier B.V. All rights reserved.

  1. HepML, an XML-based format for describing simulated data in high energy physics

    Science.gov (United States)

    Belov, S.; Dudko, L.; Kekelidze, D.; Sherstnev, A.

    2010-10-01

    In this paper we describe a HepML format and a corresponding C++ library developed for keeping complete description of parton level events in a unified and flexible form. HepML tags contain enough information to understand what kind of physics the simulated events describe and how the events have been prepared. A HepML block can be included into event files in the LHEF format. The structure of the HepML block is described by means of several XML Schemas. The Schemas define necessary information for the HepML block and how this information should be located within the block. The library libhepml is a C++ library intended for parsing and serialization of HepML tags, and representing the HepML block in computer memory. The library is an API for external software. For example, Matrix Element Monte Carlo event generators can use the library for preparing and writing a header of an LHEF file in the form of HepML tags. In turn, Showering and Hadronization event generators can parse the HepML header and get the information in the form of C++ classes. libhepml can be used in C++, C, and Fortran programs. All necessary parts of HepML have been prepared and we present the project to the HEP community. Program summaryProgram title: libhepml Catalogue identifier: AEGL_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGL_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU GPLv3 No. of lines in distributed program, including test data, etc.: 138 866 No. of bytes in distributed program, including test data, etc.: 613 122 Distribution format: tar.gz Programming language: C++, C Computer: PCs and workstations Operating system: Scientific Linux CERN 4/5, Ubuntu 9.10 RAM: 1 073 741 824 bytes (1 Gb) Classification: 6.2, 11.1, 11.2 External routines: Xerces XML library ( http://xerces.apache.org/xerces-c/), Expat XML Parser ( http://expat.sourceforge.net/) Nature of problem: Monte Carlo simulation in high

  2. Pituitary Tumors

    Science.gov (United States)

    ... Association (ABTA) International RadioSurgery Association National Brain Tumor Society National Institute of Child Health and Human Development ... Definition The pituitary is a small, bean-sized gland ...

  3. Hypothalamic tumor

    Science.gov (United States)

    ... in the brain to reduce spinal fluid pressure. Risks of radiation therapy include damage to healthy brain cells when tumor cells are destroyed. Common side effects from chemotherapy include loss of appetite, nausea and vomiting, and fatigue.

  4. GeoSciML version 3: A GML application for geologic information

    Science.gov (United States)

    International Union of Geological Sciences., I. C.; Richard, S. M.

    2011-12-01

    After 2 years of testing and development, XML schema for GeoSciML version 3 are now ready for application deployment. GeoSciML draws from many geoscience data modelling efforts to establish a common suite of feature types to represent information associated with geologic maps (materials, structures, and geologic units) and observations including structure data, samples, and chemical analyses. After extensive testing and use case analysis, in December 2008 the CGI Interoperability Working Group (IWG) released GeoSciML 2.0 as an application schema for basic geological information. GeoSciML 2.0 is in use to deliver geologic data by the OneGeology Europe portal, the Geological Survey of Canada Groundwater Information Network (wet GIN), and the Auscope Mineral Resources portal. GeoSciML to version 3.0 is updated to OGC Geography Markup Language v3.2, re-engineered patterns for association of element values with controlled vocabulary concepts, incorporation of ISO19156 Observation and Measurement constructs for representing numeric and categorical values and for representing analytical data, incorporation of EarthResourceML to represent mineral occurrences and mines, incorporation of the GeoTime model to represent GSSP and stratigraphic time scale, and refactoring of the GeoSciML namespace to follow emerging ISO practices for decoupling of dependencies between standardized namespaces. These changes will make it easier for data providers to link to standard vocabulary and registry services. The depth and breadth of GeoSciML remains largely unchanged, covering the representation of geologic units, earth materials and geologic structures. ISO19156 elements and patterns are used to represent sampling features such as boreholes and rock samples, as well as geochemical and geochronologic measurements. Geologic structures include shear displacement structures (brittle faults and ductile shears), contacts, folds, foliations, lineations and structures with no preferred

  5. Physical Properties of Asteroid (10302) 1989 ML, a Potential Spacecraft Target, from Spitzer Observations

    Science.gov (United States)

    Mueller, Michael; Harris, A. W.

    2006-09-01

    We report on results from recent Spitzer observations of near-Earth asteroid (10302) 1989 ML, which is among the lowest-ranking objects in terms of the specific momentum Δv required to reach it from Earth. It was originally considered as a target for Hayabusa and is now under consideration as a target of the planned ESA mission Don Quijote. Unfortunately, little is known about the physical properties of 1989 ML, in particular its size and albedo are unknown. Its exhibits an X type reflection spectrum, so depending on its albedo, 1989 ML may be an E, M, or P type asteroid. Provisional results from thermal-infrared observations carried out with Spitzer indicate that the albedo of 1989 ML is compatible with an M- or E-type classification. We will discuss our results and their implications for the physical properties and the rotation period of 1989 ML, and its importance as a potential spacecraft target. This work is based on observations made with the Spitzer Space Telescope, which is operated by the Jet Propulsion Laboratory, California Institute of Technology under a contract with NASA.

  6. The additional benefit of the ML Flow test to classify leprosy patients.

    Science.gov (United States)

    Bührer-Sékula, Samira; Illarramendi, Ximena; Teles, Rose B; Penna, Maria Lucia F; Nery, José Augusto C; Sales, Anna Maria; Oskam, Linda; Sampaio, Elizabeth P; Sarno, Euzenir N

    2009-08-01

    The use of the skin lesion counting classification leads to both under and over diagnosis of leprosy in many instances. Thus, there is a need to complement this classification with another simple and robust test for use in the field. Data of 202 untreated leprosy patients diagnosed at FIOCRUZ, Rio de Janeiro, Brazil, was analyzed. There were 90 patients classified as PB and 112 classified as MB according to the reference standard. The BI was positive in 111 (55%) patients and the ML Flow test in 116 (57.4%) patients. The ML Flow test was positive in 95 (86%) of the patients with a positive BI. The lesion counting classification was confirmed by both BI and ML Flow tests in 65% of the 92 patients with 5 or fewer lesions, and in 76% of the 110 patients with 6 or more lesions. The combination of skin lesion counting and the ML Flow test results yielded a sensitivity of 85% and a specificity of 87% for MB classification, and correctly classified 86% of the patients when compared to the standard reference. A considerable proportion of the patients (43.5%) with discordant test results in relation to standard classification was in reaction. The use of any classification system has limitations, especially those that oversimplify a complex disease such as leprosy. In the absence of an experienced dermatologist and slit skin smear, the ML Flow test could be used to improve treatment decisions in field conditions.

  7. The evolution of the CUAHSI Water Markup Language (WaterML)

    Science.gov (United States)

    Zaslavsky, I.; Valentine, D.; Maidment, D.; Tarboton, D. G.; Whiteaker, T.; Hooper, R.; Kirschtel, D.; Rodriguez, M.

    2009-04-01

    The CUAHSI Hydrologic Information System (HIS, his.cuahsi.org) uses web services as the core data exchange mechanism which provides programmatic connection between many heterogeneous sources of hydrologic data and a variety of online and desktop client applications. The service message schema follows the CUAHSI Water Markup Language (WaterML) 1.x specification (see OGC Discussion Paper 07-041r1). Data sources that can be queried via WaterML-compliant water data services include national and international repositories such as USGS NWIS (National Water Information System), USEPA STORET (Storage & Retrieval), USDA SNOTEL (Snowpack Telemetry), NCDC ISH and ISD(Integrated Surface Hourly and Daily Data), MODIS (Moderate Resolution Imaging Spectroradiometer), and DAYMET (Daily Surface Weather Data and Climatological Summaries). Besides government data sources, CUAHSI HIS provides access to a growing number of academic hydrologic observation networks. These networks are registered by researchers associated with 11 hydrologic observatory testbeds around the US, and other research, government and commercial groups wishing to join the emerging CUAHSI Water Data Federation. The Hydrologic Information Server (HIS Server) software stack deployed at NSF-supported hydrologic observatory sites and other universities around the country, supports a hydrologic data publication workflow which includes the following steps: (1) observational data are loaded from static files or streamed from sensors into a local instance of an Observations Data Model (ODM) database; (2) a generic web service template is configured for the new ODM instance to expose the data as a WaterML-compliant water data service, and (3) the new water data service is registered at the HISCentral registry (hiscentral.cuahsi.org), its metadata are harvested and semantically tagged using concepts from a hydrologic ontology. As a result, the new service is indexed in the CUAHSI central metadata catalog, and becomes

  8. Identifying candidate driver genes by integrative ovarian cancer genomics data

    Science.gov (United States)

    Lu, Xinguo; Lu, Jibo

    2017-08-01

    Integrative analysis of molecular mechanics underlying cancer can distinguish interactions that cannot be revealed based on one kind of data for the appropriate diagnosis and treatment of cancer patients. Tumor samples exhibit heterogeneity in omics data, such as somatic mutations, Copy Number Variations CNVs), gene expression profiles and so on. In this paper we combined gene co-expression modules and mutation modulators separately in tumor patients to obtain the candidate driver genes for resistant and sensitive tumor from the heterogeneous data. The final list of modulators identified are well known in biological processes associated with ovarian cancer, such as CCL17, CACTIN, CCL16, CCL22, APOB, KDF1, CCL11, HNF1B, LRG1, MED1 and so on, which can help to facilitate the discovery of biomarkers, molecular diagnostics, and drug discovery.

  9. Serologic follow-up of IgG responses against recombinant mycobacterial proteins ML0405, ML2331 and LID-1 in a leprosy hyperendemic area in Venezuela

    Directory of Open Access Journals (Sweden)

    Elsa Rada

    2012-12-01

    Full Text Available Leprosy is a slowly evolving disease that occurs mainly in adults. In this study, the Mamaría Village, state of Portuguesa was selected because it had one of the highest prevalence rates (13.25% of leprosy cases in 1997. Between 1998-2004, 20.2% of the 89 cases registered in this village were less than 15 years old and 61.8% were males. Pau-cibacillary (PB lesions were the predominant clinical forms identified, although also multibacillary (MB forms were found. Additionally, 76% of the patients were bacteriologically negative. At the time of diagnosis, 75% of the patients presented with grade 0 disabilities, 23% with grade 1 and 2% with grade 2. Serum samples were collected from 18 PB and 15 MB patients, in addition to 14 family contacts, at the beginning and end of treatment. All the groups were re-evaluated during a three-year period (2008-2011. The proteins used for evaluation were ML0405, ML2331 and LID-1. These mycobacterial proteins were highly specific for Mycobacterium leprae and the IgG responses decreased in both MB and PB patients during multidrug treatment. Our results suggest that these antigens could be used as markers for successful treatment of non-reactional lepromatous patients.

  10. A novel engineered VEGF blocker with an excellent pharmacokinetic profile and robust anti-tumor activity

    International Nuclear Information System (INIS)

    Liu, Lily; Yu, Haijia; Huang, Xin; Tan, Hongzhi; Li, Song; Luo, Yan; Zhang, Li; Jiang, Sumei; Jia, Huifeng; Xiong, Yao; Zhang, Ruliang; Huang, Yi; Chu, Charles C; Tian, Wenzhi

    2015-01-01

    Relatively poor penetration and retention in tumor tissue has been documented for large molecule drugs including therapeutic antibodies and recombinant immunoglobulin constant region (Fc)-fusion proteins due to their large size, positive charge, and strong target binding affinity. Therefore, when designing a large molecular drug candidate, smaller size, neutral charge, and optimal affinity should be considered. We engineered a recombinant protein by molecular engineering the second domain of VEGFR1 and a few flanking residues fused with the Fc fragment of human IgG1, which we named HB-002.1. This recombinant protein was extensively characterized both in vitro and in vivo for its target-binding and target-blocking activities, pharmacokinetic profile, angiogenesis inhibition activity, and anti-tumor therapeutic efficacy. HB-002.1 has a molecular weight of ~80 kDa, isoelectric point of ~6.7, and an optimal target binding affinity of <1 nM. The pharmacokinetic profile was excellent with a half-life of 5 days, maximal concentration of 20.27 μg/ml, and area under the curve of 81.46 μg · days/ml. When tested in a transgenic zebrafish embryonic angiogenesis model, dramatic inhibition in angiogenesis was exhibited by a markedly reduced number of subintestinal vessels. When tested for anti-tumor efficacy, HB-002.1 was confirmed in two xenograft tumor models (A549 and Colo-205) to have a robust tumor killing activity, showing a percentage of inhibition over 90% at the dose of 20 mg/kg. Most promisingly, HB-002.1 showed a superior therapeutic efficacy compared to bevacizumab in the A549 xenograft model (tumor inhibition: 84.7% for HB-002.1 versus 67.6% for bevacizumab, P < 0.0001). HB-002.1 is a strong angiogenesis inhibitor that has the potential to be a novel promising drug for angiogenesis-related diseases such as tumor neoplasms and age-related macular degeneration

  11. Integrative analysis to select cancer candidate biomarkers to targeted validation

    Science.gov (United States)

    Heberle, Henry; Domingues, Romênia R.; Granato, Daniela C.; Yokoo, Sami; Canevarolo, Rafael R.; Winck, Flavia V.; Ribeiro, Ana Carolina P.; Brandão, Thaís Bianca; Filgueiras, Paulo R.; Cruz, Karen S. P.; Barbuto, José Alexandre; Poppi, Ronei J.; Minghim, Rosane; Telles, Guilherme P.; Fonseca, Felipe Paiva; Fox, Jay W.; Santos-Silva, Alan R.; Coletta, Ricardo D.; Sherman, Nicholas E.; Paes Leme, Adriana F.

    2015-01-01

    Targeted proteomics has flourished as the method of choice for prospecting for and validating potential candidate biomarkers in many diseases. However, challenges still remain due to the lack of standardized routines that can prioritize a limited number of proteins to be further validated in human samples. To help researchers identify candidate biomarkers that best characterize their samples under study, a well-designed integrative analysis pipeline, comprising MS-based discovery, feature selection methods, clustering techniques, bioinformatic analyses and targeted approaches was performed using discovery-based proteomic data from the secretomes of three classes of human cell lines (carcinoma, melanoma and non-cancerous). Three feature selection algorithms, namely, Beta-binomial, Nearest Shrunken Centroids (NSC), and Support Vector Machine-Recursive Features Elimination (SVM-RFE), indicated a panel of 137 candidate biomarkers for carcinoma and 271 for melanoma, which were differentially abundant between the tumor classes. We further tested the strength of the pipeline in selecting candidate biomarkers by immunoblotting, human tissue microarrays, label-free targeted MS and functional experiments. In conclusion, the proposed integrative analysis was able to pre-qualify and prioritize candidate biomarkers from discovery-based proteomics to targeted MS. PMID:26540631

  12. The WUW ML bundle detector A flow through detector for alpha-emitters

    CERN Document Server

    Wenzel, U; Lochny, M

    1999-01-01

    Using conventional laboratory ware, we designed and manufactured a flow through cell for monitoring alpha-bearing solutions. The cell consists of a bundle of thermoplastic, transparent tubes coated with a thin layer of the meltable scintillator MELTILEX sup T sup M at the inner surface. With appropriate energy windows set, the detector can suppress beta-particles to a great extent due to its geometrical dimensions. For pure alpha-solutions, the detection limits are 5 Bq/ml, for composite nuclide mixtures, the detector is capable to monitor the decontamination of medium active waste (<=10 sup 7 Bq/ml) down to 100 Bq alpha/g solution. At a throughput of 1 ml/s, the pressure build-up amounts to approx 2 bar. We have developed a quality control program to ensure the regularity of the individual bundle loops.

  13. Alkaline protease production from industrial wastes by bacillus subtilis ML-4

    International Nuclear Information System (INIS)

    Sher, M.G.; Nadeem, M.; Syed, Q.; Irfan, M.; Baig, S.

    2010-01-01

    The influence of various culture conditions on protease production by Bacillus subtilis ML-4 was studied in the presence of growth medium containing poultry feed waste (5%), K/sub 2/HPO/sub 4/ (0.3%), CaCl/sub 2/ (0.03%) and MgSO/sub 4/ (0.015%). Maximum protease production (264.25 +- 1.86 U/ml) was observed at initial pH 9 with 3% (v/v) of inoculum size after 48 h of incubation at 37 degree C. The alkaline protease was stable over a broad range of temperature (30 to 60 degree C) and pH (8 to 11). However, maximum activity (155.45 U/ml) was observed at temperature 50 degree C and pH 10. (author)

  14. The gel electrophoresis markup language (GelML) from the Proteomics Standards Initiative.

    Science.gov (United States)

    Gibson, Frank; Hoogland, Christine; Martinez-Bartolomé, Salvador; Medina-Aunon, J Alberto; Albar, Juan Pablo; Babnigg, Gyorgy; Wipat, Anil; Hermjakob, Henning; Almeida, Jonas S; Stanislaus, Romesh; Paton, Norman W; Jones, Andrew R

    2010-09-01

    The Human Proteome Organisation's Proteomics Standards Initiative has developed the GelML (gel electrophoresis markup language) data exchange format for representing gel electrophoresis experiments performed in proteomics investigations. The format closely follows the reporting guidelines for gel electrophoresis, which are part of the Minimum Information About a Proteomics Experiment (MIAPE) set of modules. GelML supports the capture of metadata (such as experimental protocols) and data (such as gel images) resulting from gel electrophoresis so that laboratories can be compliant with the MIAPE Gel Electrophoresis guidelines, while allowing such data sets to be exchanged or downloaded from public repositories. The format is sufficiently flexible to capture data from a broad range of experimental processes, and complements other PSI formats for MS data and the results of protein and peptide identifications to capture entire gel-based proteome workflows. GelML has resulted from the open standardisation process of PSI consisting of both public consultation and anonymous review of the specifications.

  15. HLS4ML: deploying deep learning on FPGAs for L1 trigger and Data Acquisition

    CERN Multimedia

    CERN. Geneva

    2018-01-01

    Machine learning is becoming ubiquitous across HEP. There is great potential to improve trigger and DAQ performances with it. However, the exploration of such techniques within the field in low latency/power FPGAs has just begun. We present HLS4ML, a user-friendly software, based on High-Level Synthesis (HLS), designed to deploy network architectures on FPGAs. As a case study, we use HLS4ML for boosted-jet tagging with deep networks at the LHC. We show how neural networks can be made fit the resources available on modern FPGAs, thanks to network pruning and quantization. We map out resource usage and latency versus network architectures, to identify the typical problem complexity that HLS4ML could deal with. We discuss possible applications in current and future HEP experiments.

  16. Increase of tumor oxygen tension and potentiation of radiation effects using pentoxifylline, vinpocetine and ticlopidine hydrochloride

    International Nuclear Information System (INIS)

    Amano, Morikazu; Monzen, Hajime; Suzuki, Takatoshi; Hasegawa, Takeo

    2004-01-01

    The effects of pentoxifylline (PTX), vinpocetine (VPT) and ticlopidine hydrochloride (TCD), each drug commonly used for vascular disorders in humans, on the pO 2 in SCC-7 (squamous cell carcinoma) tumors of C3H/HeJ mice on the radioresponse of SCC-7 tumors were investigated. When the SCC-7 implanted in the leg of C3H/HeJ mice grew about 100 mm 3 , the effects of PTX, VPT and TCD on the increase oxygen tension in the tumor was determined with polarography. The mice were injected intraperitoneally (ip) with 5 ml/kg PTX, 5 ml/kg VPT, or 10 ml/kg TCD, the tumor pO 2 increased slowly, peaked about 20-50 min postinjection, and returned to its original level in 60-80 min. When the C3H/HeJ mice bearing SCC-7 tumors in the legs were injected ip with 5 ml/kg PTX, 5 ml/kg VPT or 10 ml/kg TCD and tumors were X-irradiated 30 min later, the radiation induced growth delay of the tumor was greater than that caused by X-irradiation alone. The results in the present study, PTX, VPT and TCD increase the tumor pO 2 in rodent tumors strongly suggest that each drug may be useful for increasing the radiosensitivity of human tumor. (author)

  17. Teacher Candidate Selection and Evaluation.

    Science.gov (United States)

    Collins, Mary Lynn; And Others

    Summaries are presented of three papers presented at a summer workshop on Quality Assurance in Teacher Education conducted by the Association of Teacher Educators. The general topic covered by these presentations was teacher candidate selection and evaluation. Papers focused upon the following questions: (1) What entry level criteria should be…

  18. Candidate Prediction Models and Methods

    DEFF Research Database (Denmark)

    Nielsen, Henrik Aalborg; Nielsen, Torben Skov; Madsen, Henrik

    2005-01-01

    This document lists candidate prediction models for Work Package 3 (WP3) of the PSO-project called ``Intelligent wind power prediction systems'' (FU4101). The main focus is on the models transforming numerical weather predictions into predictions of power production. The document also outlines...... the possibilities w.r.t. different numerical weather predictions actually available to the project....

  19. Candidate cave entrances on Mars

    Science.gov (United States)

    Cushing, Glen E.

    2012-01-01

    This paper presents newly discovered candidate cave entrances into Martian near-surface lava tubes, volcano-tectonic fracture systems, and pit craters and describes their characteristics and exploration possibilities. These candidates are all collapse features that occur either intermittently along laterally continuous trench-like depressions or in the floors of sheer-walled atypical pit craters. As viewed from orbit, locations of most candidates are visibly consistent with known terrestrial features such as tube-fed lava flows, volcano-tectonic fractures, and pit craters, each of which forms by mechanisms that can produce caves. Although we cannot determine subsurface extents of the Martian features discussed here, some may continue unimpeded for many kilometers if terrestrial examples are indeed analogous. The features presented here were identified in images acquired by the Mars Odyssey's Thermal Emission Imaging System visible-wavelength camera, and by the Mars Reconnaissance Orbiter's Context Camera. Select candidates have since been targeted by the High-Resolution Imaging Science Experiment. Martian caves are promising potential sites for future human habitation and astrobiology investigations; understanding their characteristics is critical for long-term mission planning and for developing the necessary exploration technologies.

  20. QuakeML: status of the XML-based seismological data exchange format

    Directory of Open Access Journals (Sweden)

    Joachim Saul

    2011-04-01

    Full Text Available QuakeML is an XML-based data exchange standard for seismology that is in its fourth year of active community-driven development. Its development was motivated by the need to consolidate existing data formats for applications in statistical seismology, as well as setting a cutting-edge, community-agreed standard to foster interoperability of distributed infrastructures. The current release (version 1.2 is based on a public Request for Comments process and accounts for suggestions and comments provided by a broad international user community. QuakeML is designed as an umbrella schema under which several sub-packages are collected. The present scope of QuakeML 1.2 covers a basic description of seismic events including picks, arrivals, amplitudes, magnitudes, origins, focal mechanisms, and moment tensors. Work on additional packages (macroseismic information, ground motion, seismic inventory, and resource metadata has been started, but is at an early stage. Several applications based on the QuakeML data model have been created so far. Among these are earthquake catalog web services at the European Mediterranean Seismological Centre (EMSC, GNS Science, and the Southern California Earthquake Data Center (SCEDC, and QuakePy, an open-source Python-based seismicity analysis toolkit. Furthermore, QuakeML is being used in the SeisComP3 system from GFZ Potsdam, and in the Collaboratory for the Study of Earthquake Predictability (CSEP testing center installations, developed by Southern California Earthquake Center (SCEC. QuakeML is still under active and dynamic development. Further contributions from the community are crucial to its success and are highly welcome.

  1. VarioML framework for comprehensive variation data representation and exchange

    Directory of Open Access Journals (Sweden)

    Byrne Myles

    2012-10-01

    Full Text Available Abstract Background Sharing of data about variation and the associated phenotypes is a critical need, yet variant information can be arbitrarily complex, making a single standard vocabulary elusive and re-formatting difficult. Complex standards have proven too time-consuming to implement. Results The GEN2PHEN project addressed these difficulties by developing a comprehensive data model for capturing biomedical observations, Observ-OM, and building the VarioML format around it. VarioML pairs a simplified open specification for describing variants, with a toolkit for adapting the specification into one's own research workflow. Straightforward variant data can be captured, federated, and exchanged with no overhead; more complex data can be described, without loss of compatibility. The open specification enables push-button submission to gene variant databases (LSDBs e.g., the Leiden Open Variation Database, using the Cafe Variome data publishing service, while VarioML bidirectionally transforms data between XML and web-application code formats, opening up new possibilities for open source web applications building on shared data. A Java implementation toolkit makes VarioML easily integrated into biomedical applications. VarioML is designed primarily for LSDB data submission and transfer scenarios, but can also be used as a standard variation data format for JSON and XML document databases and user interface components. Conclusions VarioML is a set of tools and practices improving the availability, quality, and comprehensibility of human variation information. It enables researchers, diagnostic laboratories, and clinics to share that information with ease, clarity, and without ambiguity.

  2. imzML: Imaging Mass Spectrometry Markup Language: A common data format for mass spectrometry imaging.

    Science.gov (United States)

    Römpp, Andreas; Schramm, Thorsten; Hester, Alfons; Klinkert, Ivo; Both, Jean-Pierre; Heeren, Ron M A; Stöckli, Markus; Spengler, Bernhard

    2011-01-01

    Imaging mass spectrometry is the method of scanning a sample of interest and generating an "image" of the intensity distribution of a specific analyte. The data sets consist of a large number of mass spectra which are usually acquired with identical settings. Existing data formats are not sufficient to describe an MS imaging experiment completely. The data format imzML was developed to allow the flexible and efficient exchange of MS imaging data between different instruments and data analysis software.For this purpose, the MS imaging data is divided in two separate files. The mass spectral data is stored in a binary file to ensure efficient storage. All metadata (e.g., instrumental parameters, sample details) are stored in an XML file which is based on the standard data format mzML developed by HUPO-PSI. The original mzML controlled vocabulary was extended to include specific parameters of imaging mass spectrometry (such as x/y position and spatial resolution). The two files (XML and binary) are connected by offset values in the XML file and are unambiguously linked by a universally unique identifier. The resulting datasets are comparable in size to the raw data and the separate metadata file allows flexible handling of large datasets.Several imaging MS software tools already support imzML. This allows choosing from a (growing) number of processing tools. One is no longer limited to proprietary software, but is able to use the processing software which is best suited for a specific question or application. On the other hand, measurements from different instruments can be compared within one software application using identical settings for data processing. All necessary information for evaluating and implementing imzML can be found at http://www.imzML.org .

  3. An overview of the CellML API and its implementation

    Directory of Open Access Journals (Sweden)

    Halstead Matt

    2010-04-01

    Full Text Available Abstract Background CellML is an XML based language for representing mathematical models, in a machine-independent form which is suitable for their exchange between different authors, and for archival in a model repository. Allowing for the exchange and archival of models in a computer readable form is a key strategic goal in bioinformatics, because of the associated improvements in scientific record accuracy, the faster iterative process of scientific development, and the ability to combine models into large integrative models. However, for CellML models to be useful, tools which can process them correctly are needed. Due to some of the more complex features present in CellML models, such as imports, developing code ab initio to correctly process models can be an onerous task. For this reason, there is a clear and pressing need for an application programming interface (API, and a good implementation of that API, upon which tools can base their support for CellML. Results We developed an API which allows the information in CellML models to be retrieved and/or modified. We also developed a series of optional extension APIs, for tasks such as simplifying the handling of connections between variables, dealing with physical units, validating models, and translating models into different procedural languages. We have also provided a Free/Open Source implementation of this application programming interface, optimised to achieve good performance. Conclusions Tools have been developed using the API which are mature enough for widespread use. The API has the potential to accelerate the development of additional tools capable of processing CellML, and ultimately lead to an increased level of sharing of mathematical model descriptions.

  4. Tumor Types: Understanding Brain Tumors

    Science.gov (United States)

    ... May cause excessive secretion of hormones Common among men and women in their 50s-80s Accounts for about 13 percent of all brain tumors Symptoms Headache Depression Vision loss Nausea or vomiting Behavioral and cognitive ...

  5. Model-driven development of smart grid services using SoaML

    DEFF Research Database (Denmark)

    Kosek, Anna Magdalena; Gehrke, Oliver

    2014-01-01

    This paper presents a model-driven software devel- opment process which can be applied to the design of smart grid services. The Service Oriented Architecture Modelling Language (SoaML) is used to describe the architecture as well as the roles and interactions between service participants....... The individual modelling steps and an example design of a SoaML model for a voltage control service are presented and explained. Finally, the paper discusses a proof-of-concept implementation of the modelled service in a smart grid testing laboratory....

  6. The analysis results of EEWS(Earthquake Early Warning System) about Iksan(Ml4.3) and Ulsan(Ml5.0) earthquakes in Korea

    Science.gov (United States)

    Park, J. H.; Chi, H. C.; Lim, I. S.; Seong, Y. J.; Pak, J.

    2016-12-01

    EEW(Earthquake Early Warning) service to the public has been officially operated by KMA (Korea Meteorological Administration) from 2015 in Korea. For the KMA's official EEW service, KIGAM has adopted ElarmS from UC Berkeley BSL and modified local magnitude relation, 1-D travel time curves and association procedures with real time waveforms from about 160 seismic stations of KMA and KIGAM. We have checked the performance of EEWS(Earthquake Early Warning System) reviewing two moderate size earthquakes: one is Iksan Eq.(Ml4.3) inside of networks and the other is Ulsan Eq.(Ml5.0) happened at the southern east sea of Korea outside of networks. The first trigger time at NPR station of the Iksan Eq. took 2.3 sec and BUY and JEO2 stations were associated to produce the first event version in 10.07 sec from the origin time respectively. Because the epicentral distance of JEO2 station is about 30 km and the estimated travel time is 6.2 sec, the delay time including transmission and processing is estimated as 3.87 sec with assumption that P wave velocity is 5 km/sec and the focal depth is 8 km. The first magnitude was M4.9 which was a little bigger than Ml4.3 by KIGAM. After adding 3 more triggers of stations (CHO, KMSA, PORA), the estimated magnitude became to M4.6 and the final was settled down to M4.3 with 10 stations. In the case of Ulsan the first trigger time took 11.04 sec and the first alert time with 3 stations in 14.8 sec from the origin time (OT) respectively. The first magnitude was M5.2, however, the difference between the first EEW epicenter and the manual final result was about 63 km due to the poor azimuth coverage outside of seismic network. After 16.2 sec from OT the fourth station YSB was used to update the location near to the manual results within 6 km with magnitude 5.0 and location and magnitude were stable with more stations. Ulsan Eq. was the first case announced to the public by EEWS and the process and result were successful, however, we have to

  7. Tumor immunology.

    Science.gov (United States)

    Mocellin, Simone; Lise, Mario; Nitti, Donato

    2007-01-01

    Advances in tumor immunology are supporting the clinical implementation of several immunological approaches to cancer in the clinical setting. However, the alternate success of current immunotherapeutic regimens underscores the fact that the molecular mechanisms underlying immune-mediated tumor rejection are still poorly understood. Given the complexity of the immune system network and the multidimensionality of tumor/host interactions, the comprehension of tumor immunology might greatly benefit from high-throughput microarray analysis, which can portrait the molecular kinetics of immune response on a genome-wide scale, thus accelerating the discovery pace and ultimately catalyzing the development of new hypotheses in cell biology. Although in its infancy, the implementation of microarray technology in tumor immunology studies has already provided investigators with novel data and intriguing new hypotheses on the molecular cascade leading to an effective immune response against cancer. Although the general principles of microarray-based gene profiling have rapidly spread in the scientific community, the need for mastering this technique to produce meaningful data and correctly interpret the enormous output of information generated by this technology is critical and represents a tremendous challenge for investigators, as outlined in the first section of this book. In the present Chapter, we report on some of the most significant results obtained with the application of DNA microarray in this oncology field.

  8. Pancreatic islet cell tumor

    Science.gov (United States)

    ... cell tumors; Islet of Langerhans tumor; Neuroendocrine tumors; Peptic ulcer - islet cell tumor; Hypoglycemia - islet cell tumor ... stomach acid. Symptoms may include: Abdominal pain Diarrhea ... and small bowel Vomiting blood (occasionally) Glucagonomas make ...

  9. Therapeutic significance of a D-dimer cut-off level of >3 μg/ml in colorectal cancer patients treated with standard chemotherapy plus bevacizumab

    International Nuclear Information System (INIS)

    Mochizuki, Satoshi; Yoshino, Takayuki; Kojima, Takashi

    2010-01-01

    The risk of venous thromboembolism has been reported to increase when receiving bevacizumab. Many cancer patients are reported to have elevated D-dimer levels. It is not clear what D-dimer level might indicate an increased risk of venous thromboembolism in the colorectal cancer patients treated with bevacizumab-containing chemotherapy. The D-dimer levels and any event concurrent with an elevated D-dimer level were evaluated in patients receiving bevacizumab. The D-dimer cut-off level was determined using the receiver-operating characteristic analysis. The selection criteria were as follows: histologically proven metastatic and unresectable colorectal adenocarcinoma; no prior chemotherapy containing bevacizumab; D-dimer test performed repetitively on the baseline and during bevacizumab administration; no venous thromboembolism identified at the baseline; and enhanced computed tomographic scan performed every 2 months. Sixty-nine patients were included. The chemotherapy regimens with bevacizumab included the regimen of 5-fluorouracil, leucovorin and oxaliplatin (FOLFOX), the regimen of 5-fluorouracil, leucovorin and irinotecan (FOLFIRI), and leucovorin-modulated 5-fluorouracil. The median baseline D-dimer level was 1.2 μg/ml. The appropriate D-dimer cut-off level was 3 μg/ml with the negative predictive value of 98% and relative risk of 6.9. Twenty-one of 69 patients showed elevated D-dimer levels of >3 μg/ml, with 11 patients for unknown reasons, 6 with tumor progression, 3 with venous thromboembolism and 1 with sepsis. In the remaining 48 patients whose D-dimer levels were ≤3 μg/ml, only one patient developed a venous thromboembolism. A D-dimer cut-off level of 3 μg/ml might be a useful indicator level to exclude venous thromboembolism or show an increased risk for venous thromboembolism in colorectal cancer patients treated with bevacizumab-containing chemotherapy. (author)

  10. Using SensorML to describe scientific workflows in distributed web service environments

    CSIR Research Space (South Africa)

    Van Zyl, TL

    2009-07-01

    Full Text Available for increased collaboration through workflow sharing. The Sensor Web is an open complex adaptive system the pervades the internet and provides access to sensor resources. One mechanism for describing sensor resources is through the use of Sensor ML. It is shown...

  11. Using SensorML to describe scientific workflows in distributed web service environments

    CSIR Research Space (South Africa)

    Van Zyl, TL

    2009-07-01

    Full Text Available for increased collaboration through workflow sharing. The Sensor Web is an open complex adaptive system the pervades the internet and provides access to sensor resources. One mechanism for describing sensor resources is through the use of SensorML. It is shown...

  12. The uniform order convergence structure on ML ( X ) | van der Walt ...

    African Journals Online (AJOL)

    The uniform convergence space completion of ML(X) is constructed as the space all normal lower semi-continuous functions on X. It is then shown how these results may be applied to solve nonlinear PDEs. In particular, we construct generalized solutions to the Navier-Stokes equations in three spatial dimensions, subject ...

  13. iML1515, a knowledgebase that computes Escherichia coli traits

    DEFF Research Database (Denmark)

    Monk, Jonathan M.; Lloyd, Colton J.; Brunk, Elizabeth

    2017-01-01

    To the Editor: Extracting knowledge from the many types of big data produced by high-throughput methods remains a challenge, even when data are from Escherichia coli, the best characterized bacterial species. Here, we present iML1515, the most complete genome-scale reconstruction of the metabolic...

  14. Physical Properties of Asteroid (10302) 1989 ML, a Potential Spacecraft Target, from Spitzer Observations

    NARCIS (Netherlands)

    Mueller, Michael; Harris, A. W.

    2006-01-01

    We report on results from recent Spitzer observations of near-Earth asteroid (10302) 1989 ML, which is among the lowest-ranking objects in terms of the specific momentum Δv required to reach it from Earth. It was originally considered as a target for Hayabusa and is now under consideration as a

  15. Correlation between ELISA and ML Flow assays applied to 60 Brazilian patients affected by leprosy

    NARCIS (Netherlands)

    Da Silva, Rozana C.; Lyon, Sandra; Lyon, Ana C.; Grossi, Maria A. F.; Lyon, Silvia H.; Bührer-Sékula, Samira; Antunes, Carlos M. F.

    2010-01-01

    Serological tests can be helpful in classifying leprosy patients as having either the paucibacillary or the multibacillary form. The aim of this study was to evaluate the concordance between two serological assays, i.e. ML Flow and ELISA, in a population of leprosy patients in Brazil. The

  16. Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 2.

    Science.gov (United States)

    Bergmann, Frank T; Cooper, Jonathan; Le Novère, Nicolas; Nickerson, David; Waltemath, Dagmar

    2015-09-04

    The number, size and complexity of computational models of biological systems are growing at an ever increasing pace. It is imperative to build on existing studies by reusing and adapting existing models and parts thereof. The description of the structure of models is not sufficient to enable the reproduction of simulation results. One also needs to describe the procedures the models are subjected to, as recommended by the Minimum Information About a Simulation Experiment (MIASE) guidelines. This document presents Level 1 Version 2 of the Simulation Experiment Description Markup Language (SED-ML), a computer-readable format for encoding simulation and analysis experiments to apply to computational models. SED-ML files are encoded in the Extensible Markup Language (XML) and can be used in conjunction with any XML-based model encoding format, such as CellML or SBML. A SED-ML file includes details of which models to use, how to modify them prior to executing a simulation, which simulation and analysis procedures to apply, which results to extract and how to present them. Level 1 Version 2 extends the format by allowing the encoding of repeated and chained procedures.

  17. ML-o-Scope: A Diagnostic Visualization System for Deep Machine Learning Pipelines

    Science.gov (United States)

    2014-05-16

    Huawei , Intel, Microsoft, NetApp, Pivotal, Splunk, Virdata, VMware, WANdisco and Yahoo!. ML-o-scope: a diagnostic visualization system for deep machine...Facebook, GameOnTalis, Guavus, HP, Huawei , Intel, Microsoft, NetApp, Pivotal, Splunk, Virdata, VMware, WANdisco and Yahoo!. References [1] Bruna, J., and

  18. A best-first tree-searching approach for ML decoding in MIMO system

    KAUST Repository

    Shen, Chung-An; Eltawil, Ahmed M.; Mondal, Sudip; Salama, Khaled N.

    2012-01-01

    In MIMO communication systems maximum-likelihood (ML) decoding can be formulated as a tree-searching problem. This paper presents a tree-searching approach that combines the features of classical depth-first and breadth-first approaches to achieve

  19. Imaging of brain tumors

    International Nuclear Information System (INIS)

    Gaensler, E.H.L.

    1995-01-01

    The contents are diagnostic approaches, general features of tumors -hydrocephalus, edema, attenuation and/or intensity value, hemorrhage, fat, contrast enhancement, intra-axial supratentorial tumors - tumors of glial origin, oligodendrogliomas, ependymomas, subependymomas, subependymal giant cell astrocytomas, choroid plexus papilloma; midline tumors - colloid cysts, craniopharyngiomas; pineal region tumors and miscellaneous tumors i.e. primary intracerebral lymphoma, primitive neuroectodermal tumors, hemangioblastomas; extraaxial tumors - meningiomas; nerve sheath tumors -schwannomas, epidermoids, dermoids, lipomas, arachnoid cysts; metastatic tumors (8 refs.)

  20. Imaging of brain tumors

    Energy Technology Data Exchange (ETDEWEB)

    Gaensler, E H.L. [California Univ., San Francisco, CA (United States). Dept. of Radiology

    1996-12-31

    The contents are diagnostic approaches, general features of tumors -hydrocephalus, edema, attenuation and/or intensity value, hemorrhage, fat, contrast enhancement, intra-axial supratentorial tumors - tumors of glial origin, oligodendrogliomas, ependymomas, subependymomas, subependymal giant cell astrocytomas, choroid plexus papilloma; midline tumors - colloid cysts, craniopharyngiomas; pineal region tumors and miscellaneous tumors i.e. primary intracerebral lymphoma, primitive neuroectodermal tumors, hemangioblastomas; extraaxial tumors - meningiomas; nerve sheath tumors -schwannomas, epidermoids, dermoids, lipomas, arachnoid cysts; metastatic tumors (8 refs.).

  1. Targeting Autophagy in the Tumor Stroma to Eradicate Breast Cancer

    Science.gov (United States)

    2013-09-01

    initiated. One potential caveat that has arisen is that fibroblast specific protein (FSP) may be expressed at low levels in late stage PyMT tumor...digestion solution per 5g of tumor tissue) 1.5 mg/ml Collagenase (from 100X stock solution) 125 U/ml Hyaluronidase (from 100X stock solution) MMF media...g. Determine the latency period to the onset of primary tumor formation and metastasis for recipient mice generated in subtask 1f. At selected

  2. Candidate genes in panic disorder

    DEFF Research Database (Denmark)

    Howe, A. S.; Buttenschön, Henriette N; Bani-Fatemi, A.

    2016-01-01

    The utilization of molecular genetics approaches in examination of panic disorder (PD) has implicated several variants as potential susceptibility factors for panicogenesis. However, the identification of robust PD susceptibility genes has been complicated by phenotypic diversity, underpowered...... association studies and ancestry-specific effects. In the present study, we performed a succinct review of case-control association studies published prior to April 2015. Meta-analyses were performed for candidate gene variants examined in at least three studies using the Cochrane Mantel-Haenszel fixed......-effect model. Secondary analyses were also performed to assess the influences of sex, agoraphobia co-morbidity and ancestry-specific effects on panicogenesis. Meta-analyses were performed on 23 variants in 20 PD candidate genes. Significant associations after correction for multiple testing were observed...

  3. Tumor size and prognosis in patients with Wilms tumor

    Directory of Open Access Journals (Sweden)

    Valentina Oliveira Provenzi

    2015-03-01

    Full Text Available OBJECTIVE: Investigate the relationship of the tumor volume after preoperative chemotherapy (TVAPQ and before preoperative chemotherapy (TVBPQ with overall survival at two and at five years, and lifetime. METHODS: Our sample consisted of consecutive patients evaluated in the period from 1989 to 2009 in an Onco-Hematology Service. Clinical, histological and volumetric data were collected from the medical records. For analysis, chi-square, Kaplan-Meier, log-rank and Cox regression tests were used. RESULTS: The sample consisted of 32 patients, 53.1% were male with a median age at diagnosis of 43 months. There was a significant association between TVAPQ>500mL and the difference between the TVBPQ and TVAPQ (p=0.015 and histologic types of risk (p=0.008. It was also verified an association between the difference between the TVBPQ and TVAPQ and the predominant stromal tumor (p=0.037. When assessing the TVAPQ of all patients, without a cutoff, there was an association of the variable with lifetime (p=0.013, i.e., for each increase of 10mL in TVAPQ there was an average increase of 2% in the risk of death. CONCLUSIONS: Although our results indicate that the TVAPQ could be considered alone as a predictor of poor prognosis regardless of the cutoff suggested in the literature, more studies are needed to replace the histology and staging by tumor size as best prognostic variable.

  4. WaterML, an Information Standard for the Exchange of in-situ hydrological observations

    Science.gov (United States)

    Valentine, D.; Taylor, P.; Zaslavsky, I.

    2012-04-01

    The WaterML 2.0 Standards Working Group (SWG), working within the Open Geospatial Consortium (OGC) and in cooperation with the joint OGC-World Meteorological Organization (WMO) Hydrology Domain Working Group (HDWG), has developed an open standard for the exchange of water observation data; WaterML 2.0. The focus of the standard is time-series data, commonly generated from in-situ style monitoring. This is high value data for hydrological applications such as flood forecasting, environmental reporting and supporting hydrological infrastructure (e.g. dams, supply systems), which is commonly exchanged, but a lack of standards inhibits efficient reuse and automation. The process of developing WaterML required doing a harmonization analysis of existing standards to identify overlapping concepts and come to agreement on a harmonized definition. Generally the formats captured similar requirements, all with subtle differences, such as how time-series point metadata was handled. The in-progress standard WaterML 2.0 incorporates the semantics of the hydrologic information: location, procedure, and observations, and is implemented as an application schema of the Geography Markup Language version 3.2.1, making use of the OGC Observations & Measurements standards. WaterML2.0 is designed as an extensible schema to allow encoding of data to be used in a variety of exchange scenarios. Example areas of usage are: exchange of data for operational hydrological monitoring programs; supporting operation of infrastructure (e.g. dams, supply systems); cross-border exchange of observational data; release of data for public dissemination; enhancing disaster management through data exchange; and exchange in support of national reporting The first phase of WaterML2.0 focused on structural definitions allowing for the transfer of time-series, with less work on harmonization of vocabulary items such as quality codes. Vocabularies from various organizations tend to be specific and take time to

  5. Tumor markers as a diagnostic key for hilar Cholangiocarcinoma

    Directory of Open Access Journals (Sweden)

    Juntermanns B

    2010-08-01

    Full Text Available Abstract Objective Hilar cholangiocarcinoma is the fourth most common gastrointestinal malignancy. CA19-9 and CEA are helpful devices in the management of gastrointestinal malignancies and belong to clinical routine in surgical oncology. But the validity of these parameters in terms of tumor extension and prognosis of bile duct malignancies still remains unclear. Methods From 1998 to 2008, we obtained preoperative CA19-9 and CEA serum levels in 136 patients with hilar cholangiocarcinoma. We correlated tumor stage, resectability rate and survival with preoperative CA 19-9 and CEA serum levels. Results CA19-9 (UICC I: 253 ± 561 U/ml; UICC II: 742 ± 1572 U/ml; UICC III: 906 ± 1708 U/ml; UICC IV: 1707 ± 3053 U/ml and CEA levels (UICC I: 2.9 ± 3.8 U/ml; UICC II: 4.6 ± 6.5 U/ml; UICC III: 18.1 ± 29.6 U/ml; UICC IV: 22.7 ± 53.9 U/ml increase significantly with rising tumor stage. Patients with pre operative serum levels of CA19-9 (> 1000 U/ml and CEA (> 14.4 ng/ml showed a significant poorer resectability rate and survival than patients with lower CA19-9 and CEA serum levels respectively. Conclusion CA19-9 and CEA serum levels are associated with the tumor stage. If preoperatively obtained CA19-9 and CEA serum levels are highly elevated patients have an even worse survival and the frequency of irresectability is significantly higher.

  6. Bone tumors

    International Nuclear Information System (INIS)

    Moylan, D.J.; Yelovich, R.M.

    1991-01-01

    Primary bone malignancies are relatively rare with less than 4,000 new cases per year. Multiple myeloma (more correctly a hematologic malignancy) accounts for 40%; osteosarcomas, 28%; chondrosarcomas, 13%; fibrosarcomas arising in bone, 4%; and Ewing's sarcoma, 7%. The authors discuss various treatments for bone tumors, including radiotherapy, chemotherapy and surgery

  7. Wilms Tumor

    Science.gov (United States)

    ... a child's general health and to detect any adverse side effects (such as low red or white blood cell ... medicine needed, which helps reduce long-term side effects. The most common ... can be completely removed by surgery. About 41% of all Wilms tumors are stage ...

  8. Nephrogenic tumors

    International Nuclear Information System (INIS)

    Wiesbauer, P.

    2008-01-01

    Nephroblastomas are the most common malignant renal tumors in childhood. According to the guidelines of the SIOP (Societe Internationale d'Oncologie Pediatrique) and GPOH (Gesellschaft fuer Paediatrische Onkologie und Haematologie) pre-operative chemotherapy can be started without histological confirmation and thus initial imaging studies, in particular ultrasound, play an outstanding role for diagnostic purposes

  9. A best-first tree-searching approach for ML decoding in MIMO system

    KAUST Repository

    Shen, Chung-An

    2012-07-28

    In MIMO communication systems maximum-likelihood (ML) decoding can be formulated as a tree-searching problem. This paper presents a tree-searching approach that combines the features of classical depth-first and breadth-first approaches to achieve close to ML performance while minimizing the number of visited nodes. A detailed outline of the algorithm is given, including the required storage. The effects of storage size on BER performance and complexity in terms of search space are also studied. Our result demonstrates that with a proper choice of storage size the proposed method visits 40% fewer nodes than a sphere decoding algorithm at signal to noise ratio (SNR) = 20dB and by an order of magnitude at 0 dB SNR.

  10. Seismicity Controlled by a Frictional Afterslip During a Small-Magnitude Seismic Sequence (ML Taiwan

    Science.gov (United States)

    Canitano, Alexandre; Godano, Maxime; Hsu, Ya-Ju; Lee, Hsin-Ming; Linde, Alan T.; Sacks, Selwyn

    2018-02-01

    We report evidence for frictional afterslip at shallow depths (about 5 to 7 km) during a small-magnitude seismic sequence (with MLTaiwan. The afterslip, which was recorded by a nearby borehole dilatometer, lasted about a month with a cumulative geodetic moment magnitude of 4.8 ± 0.2. The afterslip comprised two stages and controlled the aftershock sequence. The first postseismic stage, which followed a ML 4.6 earthquake, lasted about 6 h and mostly controlled the ruptures of neighboring asperities (e.g., multiplets) near the hypocenter. Then, a 4 week duration large afterslip event following a ML 4.9 earthquake controlled the rate of aftershocks during its first 2 days through brittle creep. The study presents a rare case of simultaneous seismological and geodetic observations for afterslip following earthquakes with magnitude lower than 5. Furthermore, the geodetic moment of the postseismic phase is at least equivalent to the coseismic moment of the sequence.

  11. Leak Detection and Location of Water Pipes Using Vibration Sensors and Modified ML Prefilter.

    Science.gov (United States)

    Choi, Jihoon; Shin, Joonho; Song, Choonggeun; Han, Suyong; Park, Doo Il

    2017-09-13

    This paper proposes a new leak detection and location method based on vibration sensors and generalised cross-correlation techniques. Considering the estimation errors of the power spectral densities (PSDs) and the cross-spectral density (CSD), the proposed method employs a modified maximum-likelihood (ML) prefilter with a regularisation factor. We derive a theoretical variance of the time difference estimation error through summation in the discrete-frequency domain, and find the optimal regularisation factor that minimises the theoretical variance in practical water pipe channels. The proposed method is compared with conventional correlation-based techniques via numerical simulations using a water pipe channel model, and it is shown through field measurement that the proposed modified ML prefilter outperforms conventional prefilters for the generalised cross-correlation. In addition, we provide a formula to calculate the leak location using the time difference estimate when different types of pipes are connected.

  12. Leak Detection and Location of Water Pipes Using Vibration Sensors and Modified ML Prefilter

    Directory of Open Access Journals (Sweden)

    Jihoon Choi

    2017-09-01

    Full Text Available This paper proposes a new leak detection and location method based on vibration sensors and generalised cross-correlation techniques. Considering the estimation errors of the power spectral densities (PSDs and the cross-spectral density (CSD, the proposed method employs a modified maximum-likelihood (ML prefilter with a regularisation factor. We derive a theoretical variance of the time difference estimation error through summation in the discrete-frequency domain, and find the optimal regularisation factor that minimises the theoretical variance in practical water pipe channels. The proposed method is compared with conventional correlation-based techniques via numerical simulations using a water pipe channel model, and it is shown through field measurement that the proposed modified ML prefilter outperforms conventional prefilters for the generalised cross-correlation. In addition, we provide a formula to calculate the leak location using the time difference estimate when different types of pipes are connected.

  13. Determination of Stress-Corrosion Cracking in Aluminum-Lithium Alloy ML377

    Science.gov (United States)

    Valek, Bryan C.

    1995-01-01

    The use of aluminum-lithium alloys for aerospace applications is currently being studied at NASA Langley Research Center's Metallic Materials Branch. The alloys in question will operate under stress in a corrosive environment. These conditions are ideal for the phenomena of Stress-Corrosion Cracking (SCC) to occur. The test procedure for SCC calls for alternate immersion and breaking load tests. These tests were optimized for the lab equipment and materials available in the Light Alloy lab. Al-Li alloy ML377 specimens were then subjected to alternate immersion and breaking load tests to determine residual strength and resistance to SCC. Corrosion morphology and microstructure were examined under magnification. Data shows that ML377 is highly resistant to stress-corrosion cracking.

  14. QuakeML: status of the XML-based seismological data exchange format

    OpenAIRE

    Joachim Saul; Philipp Kästli; Fabian Euchner; Danijel Schorlemmer

    2011-01-01

    QuakeML is an XML-based data exchange standard for seismology that is in its fourth year of active community-driven development. Its development was motivated by the need to consolidate existing data formats for applications in statistical seismology, as well as setting a cutting-edge, community-agreed standard to foster interoperability of distributed infrastructures. The current release (version 1.2) is based on a public Request for Comments process and accounts for suggestions and comments...

  15. Bitumen and cement solidifications of LL and ML liquid radwaste. The SGN experience

    International Nuclear Information System (INIS)

    Tchemitcheff, E.; Roux, P.

    1993-01-01

    The presentation is focused on the thin-film evaporator technology and the experience gained in the field of the NPPs and research centers on radwaste conditioning. As early as 1970, SGN was licensed by the CEA for the bituminization of LL and ML radwaste. With the support of EDF and COGEMA, SGN has been performing in depth research on cement solidification of borated concentrates and ion exchange resins generated by reactors or reprocessing plant since 1983

  16. Using DSM and MDM Methodologies to Analyze Structural SysML Models

    OpenAIRE

    Maisenbacher, S.;Kernschmidt, Konstantin;Kasperek, Daniel;Vogel-Heuser, B.;Maurer, M.

    2014-01-01

    Matrices and graph-based representations are commonly used visual models of system structures. Depending on the objective of the observer, both representations offer different opportunities and advantages. A standardized graph-based modeling language is SysML, while the design structure matrix (DSM) and the multiple domain matrix (MDM) are typical matrices used during the development of complex systems. Although both modeling techniques are wide spread, up to now they are hardly used conjoint...

  17. Comparison: Mediation Solutions of WSMOLX and WebML/WebRatio

    Science.gov (United States)

    Zaremba, Maciej; Zaharia, Raluca; Turati, Andrea; Brambilla, Marco; Vitvar, Tomas; Ceri, Stefano

    In this chapter we compare the WSMO/WSML/WSMX andWebML/WebRatio approaches to the SWS-Challenge workshop mediation scenario in terms of the utilized underlying technologies and delivered solutions. In the mediation scenario one partner uses Roset-taNet to define its B2B protocol while the other one operates on a proprietary solution. Both teams shown how these partners could be semantically integrated.

  18. Quality control and stability study of 100 mg/ml paracetamol oral drops

    International Nuclear Information System (INIS)

    Garcia Penna, Caridad M.; Montes de Oca Porto, Yanet; Salomon Izquierdo, Suslebys

    2013-01-01

    Paracetamol is an effective analgesic and antipyretic drug of the non-steroidal anti-inflammatory drug group. Paracetamol oral drops are indicated for use in infant population aged up to 5 years to relieve fever, headache, toothache and symptomatic relief of common cold. To validate two analytical methods for the quality control and the stability study and to study the stability of 100 mg/ml Paracetamol oral drops made in Cuba

  19. A SysML-based Integration Framework for the Engineering of Mechatronic Systems

    OpenAIRE

    Chami, Muhammad; Seemüller, Holger; Voos, Holger

    2010-01-01

    The engineering discipline mechatronics is one of the main innovation leader in industry nowadays. With the need for an optimal synergetic integration of the involved disciplines, the engineering process of mechatronic systems is faced with an increasing complexity and the interdisciplinary nature of these systems. New methods and techniques have to be developed to deal with these challenges. This document presents an approach of a SysML-based integration framework that s...

  20. Tumor Volume-Adapted Dosing in Stereotactic Ablative Radiotherapy of Lung Tumors

    Energy Technology Data Exchange (ETDEWEB)

    Trakul, Nicholas; Chang, Christine N.; Harris, Jeremy [Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA (United States); Chapman, Christopher [Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA (United States); University of Michigan School of Medicine, Ann Arbor, MI (United States); Rao, Aarti [Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA (United States); University of California, Davis, School of Medicine, Davis, CA (United States); Shen, John [Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA (United States); University of California, Irvine, School of Medicine, Irvine, CA (United States); Quinlan-Davidson, Sean [Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA (United States); Department of Radiation Oncology, McMaster University, Juravinski Cancer Centre, Hamilton, Ontario (Canada); Filion, Edith J. [Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA (United States); Departement de Medecine, Service de Radio-Oncologie, Centre Hospitalier de l' Universite de Montreal, Montreal, Quebec (Canada); Wakelee, Heather A.; Colevas, A. Dimitrios [Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, CA (United States); Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA (United States); Whyte, Richard I. [Department of Cardiothoracic Surgery, Division of General Thoracic Surgery, Stanford University School of Medicine, Stanford, CA (United States); Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA (United States); and others

    2012-09-01

    Purpose: Current stereotactic ablative radiotherapy (SABR) protocols for lung tumors prescribe a uniform dose regimen irrespective of tumor size. We report the outcomes of a lung tumor volume-adapted SABR dosing strategy. Methods and Materials: We retrospectively reviewed the outcomes in 111 patients with a total of 138 primary or metastatic lung tumors treated by SABR, including local control, regional control, distant metastasis, overall survival, and treatment toxicity. We also performed subset analysis on 83 patients with 97 tumors treated with a volume-adapted dosing strategy in which small tumors (gross tumor volume <12 mL) received single-fraction regimens with biologically effective doses (BED) <100 Gy (total dose, 18-25 Gy) (Group 1), and larger tumors (gross tumor volume {>=}12 mL) received multifraction regimens with BED {>=}100 Gy (total dose, 50-60 Gy in three to four fractions) (Group 2). Results: The median follow-up time was 13.5 months. Local control for Groups 1 and 2 was 91.4% and 92.5%, respectively (p = 0.24) at 12 months. For primary lung tumors only (excluding metastases), local control was 92.6% and 91.7%, respectively (p = 0.58). Regional control, freedom from distant metastasis, and overall survival did not differ significantly between Groups 1 and 2. Rates of radiation pneumonitis, chest wall toxicity, and esophagitis were low in both groups, but all Grade 3 toxicities developed in Group 2 (p = 0.02). Conclusion: A volume-adapted dosing approach for SABR of lung tumors seems to provide excellent local control for both small- and large-volume tumors and may reduce toxicity.

  1. Tumor Volume-Adapted Dosing in Stereotactic Ablative Radiotherapy of Lung Tumors

    International Nuclear Information System (INIS)

    Trakul, Nicholas; Chang, Christine N.; Harris, Jeremy; Chapman, Christopher; Rao, Aarti; Shen, John; Quinlan-Davidson, Sean; Filion, Edith J.; Wakelee, Heather A.; Colevas, A. Dimitrios; Whyte, Richard I.

    2012-01-01

    Purpose: Current stereotactic ablative radiotherapy (SABR) protocols for lung tumors prescribe a uniform dose regimen irrespective of tumor size. We report the outcomes of a lung tumor volume-adapted SABR dosing strategy. Methods and Materials: We retrospectively reviewed the outcomes in 111 patients with a total of 138 primary or metastatic lung tumors treated by SABR, including local control, regional control, distant metastasis, overall survival, and treatment toxicity. We also performed subset analysis on 83 patients with 97 tumors treated with a volume-adapted dosing strategy in which small tumors (gross tumor volume <12 mL) received single-fraction regimens with biologically effective doses (BED) <100 Gy (total dose, 18–25 Gy) (Group 1), and larger tumors (gross tumor volume ≥12 mL) received multifraction regimens with BED ≥100 Gy (total dose, 50–60 Gy in three to four fractions) (Group 2). Results: The median follow-up time was 13.5 months. Local control for Groups 1 and 2 was 91.4% and 92.5%, respectively (p = 0.24) at 12 months. For primary lung tumors only (excluding metastases), local control was 92.6% and 91.7%, respectively (p = 0.58). Regional control, freedom from distant metastasis, and overall survival did not differ significantly between Groups 1 and 2. Rates of radiation pneumonitis, chest wall toxicity, and esophagitis were low in both groups, but all Grade 3 toxicities developed in Group 2 (p = 0.02). Conclusion: A volume-adapted dosing approach for SABR of lung tumors seems to provide excellent local control for both small- and large-volume tumors and may reduce toxicity.

  2. Radioactivity measurement of 18F in 16 ml vials for calibration of radionuclide calibrators

    International Nuclear Information System (INIS)

    Wurdiyanto, Gatot; Marsoem, Pujadi; Candra, Hermawan; Wijono, Paidi

    2012-01-01

    Fluorine-18 is obtained through the reaction 18 O(p, n) 18 F using a cyclotron that is situated in a hospital in Jakarta. Standardization of the 18 F solution is performed by gamma spectrometry using calibration sources of 152 Eu, 60 Co and 137 Cs that have traceability to the International System of units (SI). The activities in the 16 ml vials that were used for calibrating the radionuclide calibrators were between 1 and 2 GBq, with expanded uncertainties of 3.8%. The expanded uncertainty, at a coverage factor of k=2, on the derived calibration factor for the radionuclide calibrator was 6.6%. - Highlights: ► PTKMR–BATAN as a NMI of Indonesia is required to have procedures to calibrate the radionuclide calibrators. ► Standardizations were carried out on a solution of [ 18 F]FDG using gamma spectrometry. ► The volume of 18 F solutions used was 16 ml because this is the volume often used in hospitals. ► The Secondary Standard ionization chamber is a CRC-7BT Capintec radionuclide calibrator. ► A dial setting for 16 ml of [ 18 F]FDG solution in a vial is 443 for the Capintec dose calibrator.

  3. Candidate immune biomarkers for radioimmunotherapy.

    Science.gov (United States)

    Levy, Antonin; Nigro, Giulia; Sansonetti, Philippe J; Deutsch, Eric

    2017-08-01

    Newly available immune checkpoint blockers (ICBs), capable to revert tumor immune tolerance, are revolutionizing the anticancer armamentarium. Recent evidence also established that ionizing radiation (IR) could produce antitumor immune responses, and may as well synergize with ICBs. Multiple radioimmunotherapy combinations are thenceforth currently assessed in early clinical trials. Past examples have highlighted the need for treatment personalization, and there is an unmet need to decipher immunological biomarkers that could allow selecting patients who could benefit from these promising but expensive associations. Recent studies have identified potential predictive and prognostic immune assays at the cellular (tumor microenvironment composition), genomic (mutational/neoantigen load), and peripheral blood levels. Within this review, we collected the available evidence regarding potential personalized immune biomarker-directed radiation therapy strategies that might be used for patient selection in the era of radioimmunotherapy. Copyright © 2017. Published by Elsevier B.V.

  4. Alternative dark matter candidates. Axions

    International Nuclear Information System (INIS)

    Ringwald, Andreas

    2017-01-01

    The axion is arguably one of the best motivated candidates for dark matter. For a decay constant >or similar 10 9 GeV, axions are dominantly produced non-thermally in the early universe and hence are ''cold'', their velocity dispersion being small enough to fit to large scale structure. Moreover, such a large decay constant ensures the stability at cosmological time scales and its behaviour as a collisionless fluid at cosmological length scales. Here, we review the state of the art of axion dark matter predictions and of experimental efforts to search for axion dark matter in laboratory experiments.

  5. Alternative dark matter candidates. Axions

    Energy Technology Data Exchange (ETDEWEB)

    Ringwald, Andreas

    2017-01-15

    The axion is arguably one of the best motivated candidates for dark matter. For a decay constant >or similar 10{sup 9} GeV, axions are dominantly produced non-thermally in the early universe and hence are ''cold'', their velocity dispersion being small enough to fit to large scale structure. Moreover, such a large decay constant ensures the stability at cosmological time scales and its behaviour as a collisionless fluid at cosmological length scales. Here, we review the state of the art of axion dark matter predictions and of experimental efforts to search for axion dark matter in laboratory experiments.

  6. Can tumor uptake Tc-99m MDP

    International Nuclear Information System (INIS)

    Yang, Y.S.F.; Zeng, Z.J.; Yao, Y.M.; Shi, S.M.P.; Shi, S.Z.Y.

    2002-01-01

    Aim: To study a distribution of Tc-99m MDP in mice bearing tumor cell lines. Methods: The uptake of Tc-99m MDP was analyzed in seven human tumor cell lines (SPC-A1 adenocarcinoma of lung cancer, P37 Breast cancer, T24 Bladder cancer, SKOV2 Ovary carcinoma, Hela-229 Cervical carcinoma, Osteosarcoma, A375 Melanoma) and one mouse lung cancer cell line (Lewis). They were transplanted into 13, 4, 5, 5, 4, 5 athymic mice, 6 SCID nude mice and 4 C57 black mice, respectively. Approximately 10(7) cells of each cell line were injected subcutaneously into a right chest of mouse. After 5∼6 weeks, the Tc-99m MDP scintigraphy were determined 5-6 hours after i.v. injection of 74MBq in 0.05ml every mouse. Result: Biodistribution and tumor uptake MDP was different in the various cell types investigated. Region of interests (RIOs) placed on a small part of the tumor and horizontal copied to left chest or spine of mice in Tc-99m MDP imaging and the average count ratio (tumor to background ratio: T/B, tumor to spine ratio: T/NT) in each ROI was calculated. 13 nude mice bearing the adenocarcinoma (SPC-A1) were sacrificed and biodistribution was determined after Tc-99m MDP scintigraphy. Results were expressed as % injected dose/gram (%ID/g), mean±SD. T-ulcer=ulcer of tumor, T-round=surrounding of tumor, T-center=the center of tumor, Thor-sp=thoracic spine, Lum-ver=lumbar vertebra, LN=lymph node. Conclusions: Tumor can uptake Tc-99m MDP including adenocarcinoma. Higher uptake rate in the center tissue of tumor is than other part of tumor. It maybe connected with necrosis or fibrosis of tumor

  7. "Cancer tumor".

    Science.gov (United States)

    Bronshtehn, V. A.

    The title is a phrase borrowed from a speech by a Leningrad pressman, V. E. Lvov, who called upon those attending a theoretical conference on ideological issues in astronomy held by the Leningrad Branch of the All-Union Astronomic and Geodetic Society (13 - 4 December 1948), "to make a more radical emphasis on the negative role of relativistic cosmology which is a cancer tumor disintegrating the contemporary astronomy theory, and a major ideological enemy of a materialist astronomy".

  8. Tumor imaging with monoclonal antibodies

    International Nuclear Information System (INIS)

    Haisma, H.; Hilgers, J.

    1987-01-01

    Many monoclonal antibodies directed against tumor-associated antigens have been identified, but so far none of these are tumor specific. Polyclonal and monoclonal antibodies have been used for imaging of a wide variety of tumors with success. Radiolabeling of antibody is usually done with iodine isotopes of which 123 I is the best candidate for radioimmunodetection purposes. The labeling of antibodies through chelates makes it possible to use metal radioisotopes like 111 In, which is the best radioisotope for imaging with monoclonal antibodies due to its favorable half-life of 2.5 days. Usually imaging cannot be performed within 24 h after injection, but clearance of antibody can be increased by using F(ab) 2 of Fab. Another approach is to clear non-bound antibody by a second antibody, directed against the first. The detection limit of immunoimaging is about 2 cm, but will be improved by tomography or SPECT. There is still a high false positive and false negative rate, which makes it impossible to use radioimmunodetection as the only technique for diagnosis of tumors. In combination with other detection techniques, tumor imaging with monoclonal antibodies can improve diagnosis. 44 refs.; 3 tabs

  9. Novel fusion genes and chimeric transcripts in ependymal tumors

    DEFF Research Database (Denmark)

    Olsen, Thale Kristin; Panagopoulos, Ioannis; Gorunova, Ludmila

    2016-01-01

    with subsequent Sanger sequencing was used to validate the potential fusions. Fluorescent in situ hybridization (FISH) using locus-specific probes was also performed. A total of 841 candidate chimeric transcripts were identified in the 12 tumors, with an average of 49 unique candidate fusions per tumor. After...... infratentorial anaplastic ependymoma. Our previously reported ALK rearrangements and the RELA and YAP1 fusions found in supratentorial ependymomas were until now the only known fusion genes present in ependymal tumors. The chimeric transcripts presented here are the first to be reported in infratentorial...

  10. Understanding Brain Tumors

    Science.gov (United States)

    ... to Know About Brain Tumors . What is a Brain Tumor? A brain tumor is an abnormal growth
 ... Tumors” from Frankly Speaking Frankly Speaking About Cancer: Brain Tumors Download the full book Questions to ask ...

  11. Brain tumor - primary - adults

    Science.gov (United States)

    ... Vestibular schwannoma (acoustic neuroma) - adults; Meningioma - adults; Cancer - brain tumor (adults) ... Primary brain tumors include any tumor that starts in the brain. Primary brain tumors can start from brain cells, ...

  12. Brain tumor - children

    Science.gov (United States)

    ... children; Neuroglioma - children; Oligodendroglioma - children; Meningioma - children; Cancer - brain tumor (children) ... The cause of primary brain tumors is unknown. Primary brain tumors may ... (spread to nearby areas) Cancerous (malignant) Brain tumors ...

  13. Adrenal Gland Tumors: Statistics

    Science.gov (United States)

    ... Gland Tumor: Statistics Request Permissions Adrenal Gland Tumor: Statistics Approved by the Cancer.Net Editorial Board , 03/ ... primary adrenal gland tumor is very uncommon. Exact statistics are not available for this type of tumor ...

  14. 11 CFR 100.154 - Candidate debates.

    Science.gov (United States)

    2010-01-01

    ... 11 Federal Elections 1 2010-01-01 2010-01-01 false Candidate debates. 100.154 Section 100.154 Federal Elections FEDERAL ELECTION COMMISSION GENERAL SCOPE AND DEFINITIONS (2 U.S.C. 431) Exceptions to Expenditures § 100.154 Candidate debates. Funds used to defray costs incurred in staging candidate debates in...

  15. 11 CFR 100.92 - Candidate debates.

    Science.gov (United States)

    2010-01-01

    ... 11 Federal Elections 1 2010-01-01 2010-01-01 false Candidate debates. 100.92 Section 100.92 Federal Elections FEDERAL ELECTION COMMISSION GENERAL SCOPE AND DEFINITIONS (2 U.S.C. 431) Exceptions to Contributions § 100.92 Candidate debates. Funds provided to defray costs incurred in staging candidate debates...

  16. Pediatric brain tumors

    Energy Technology Data Exchange (ETDEWEB)

    Poussaint, Tina Y. [Department of Radiology, Boston, MA (United States); Panigrahy, Ashok [Children' s Hospital of Pittsburgh of University of Pittsburgh Medical Center, Department of Radiology, Pittsburgh, PA (United States); Huisman, Thierry A.G.M. [Charlotte R. Bloomberg Children' s Center, Johns Hopkins Hospital, Division of Pediatric Radiology and Pediatric Neuroradiology, Baltimore, MD (United States)

    2015-09-15

    Among all causes of death in children from solid tumors, pediatric brain tumors are the most common. This article includes an overview of a subset of infratentorial and supratentorial tumors with a focus on tumor imaging features and molecular advances and treatments of these tumors. Key to understanding the imaging features of brain tumors is a firm grasp of other disease processes that can mimic tumor on imaging. We also review imaging features of a common subset of tumor mimics. (orig.)

  17. EnzML: multi-label prediction of enzyme classes using InterPro signatures

    Directory of Open Access Journals (Sweden)

    De Ferrari Luna

    2012-04-01

    Full Text Available Abstract Background Manual annotation of enzymatic functions cannot keep up with automatic genome sequencing. In this work we explore the capacity of InterPro sequence signatures to automatically predict enzymatic function. Results We present EnzML, a multi-label classification method that can efficiently account also for proteins with multiple enzymatic functions: 50,000 in UniProt. EnzML was evaluated using a standard set of 300,747 proteins for which the manually curated Swiss-Prot and KEGG databases have agreeing Enzyme Commission (EC annotations. EnzML achieved more than 98% subset accuracy (exact match of all correct Enzyme Commission classes of a protein for the entire dataset and between 87 and 97% subset accuracy in reannotating eight entire proteomes: human, mouse, rat, mouse-ear cress, fruit fly, the S. pombe yeast, the E. coli bacterium and the M. jannaschii archaebacterium. To understand the role played by the dataset size, we compared the cross-evaluation results of smaller datasets, either constructed at random or from specific taxonomic domains such as archaea, bacteria, fungi, invertebrates, plants and vertebrates. The results were confirmed even when the redundancy in the dataset was reduced using UniRef100, UniRef90 or UniRef50 clusters. Conclusions InterPro signatures are a compact and powerful attribute space for the prediction of enzymatic function. This representation makes multi-label machine learning feasible in reasonable time (30 minutes to train on 300,747 instances with 10,852 attributes and 2,201 class values using the Mulan Binary Relevance Nearest Neighbours algorithm implementation (BR-kNN.

  18. M&C ML: A modeling language for monitoring and control systems

    Energy Technology Data Exchange (ETDEWEB)

    Patwari, Puneet, E-mail: patwari.puneet@tcs.com; Chaudhuri, Subhrojyoti Roy; Natarajan, Swaminathan; Muralikrishna, G

    2016-11-15

    Highlights: • It is challenging to maintain consistency in the current approach to M&C design. • Based on similarity across various projects, it looks ideal to propose a solution at domain level. • Approach to create a DSL for M&C involves viewing a system through lenses of various domains. • M&CML provides a standard vocabulary and the entire process of M&C solution creation domain-aware. • M&CML provides a holistic view of control architecture. • M&CML has support for inherent consistency checks, user assistance and third party support. - Abstract: The use of System Engineering (SE) language such as SysML [1,20] is common within the community of control system designers. However the design handoff to the subsequent phases of the control system development is carried out manually in most cases without much tool support. The approach to agreeing on the control interface between components is a good example where engineers still rely on either manually created Interface Control Documents (ICD) or one off tools implemented by individual projects. Square Kilometer Array (SKA) [2] and International Thermonuclear Experimental Reactor (ITER) [3] are two good examples of such large projects adopting these approaches. This results in non-uniformity in the overall system design since individual groups invent their own vocabulary while using a language like SysML which leads to inconsistencies across the design, interface and realized code. To mitigate this, we propose the development of a Monitoring and Control Modeling Language (M&CML), a domain specific language (DSL) [4,22] for specifying M&C solutions. M&C ML starts with defining a vocabulary borrowing concepts from standard practices used in the control domain and incorporates a language which ensures uniformity and consistency across the M&C design, interfaces and implementation artifacts. In this paper we discuss this language with an analysis of its usage to point out its benefits.

  19. Representing Misalignments of the STAR Geometry Model using AgML

    Science.gov (United States)

    Webb, Jason C.; Lauret, Jérôme; Perevotchikov, Victor; Smirnov, Dmitri; Van Buren, Gene

    2017-10-01

    The STAR Heavy Flavor Tracker (HFT) was designed to provide high-precision tracking for the identification of charmed hadron decays in heavy-ion collisions at RHIC. It consists of three independently mounted subsystems, providing four precision measurements along the track trajectory, with the goal of pointing decay daughters back to vertices displaced by less than 100 microns from the primary event vertex. The ultimate efficiency and resolution of the physics analysis will be driven by the quality of the simulation and reconstruction of events in heavy-ion collisions. In particular, it is important that the geometry model properly accounts for the relative misalignments of the HFT subsystems, along with the alignment of the HFT relative to STARs primary tracking detector, the Time Projection Chamber (TPC). The Abstract Geometry Modeling Language (AgML) provides a single description of the STAR geometry, generating both our simulation (GEANT 3) and reconstruction geometries (ROOT). AgML implements an ideal detector model, while misalignments are stored separately in database tables. These have historically been applied at the hit level. Simulated detector hits are projected from their ideal position along the track’s trajectory, until they intersect the misaligned detector volume, where the struck detector element is calculated for hit digitization. This scheme has worked well as hit errors have been negligible compared with the size of sensitive volumes. The precision and complexity of the HFT detector require us to apply misalignments to the detector volumes themselves. In this paper we summarize the extension of the AgML language and support libraries to enable the static misalignment of our reconstruction and simulation geometries, discussing the design goals, limitations and path to full misalignment support in ROOT/VMC-based simulation.

  20. M&C ML: A modeling language for monitoring and control systems

    International Nuclear Information System (INIS)

    Patwari, Puneet; Chaudhuri, Subhrojyoti Roy; Natarajan, Swaminathan; Muralikrishna, G

    2016-01-01

    Highlights: • It is challenging to maintain consistency in the current approach to M&C design. • Based on similarity across various projects, it looks ideal to propose a solution at domain level. • Approach to create a DSL for M&C involves viewing a system through lenses of various domains. • M&CML provides a standard vocabulary and the entire process of M&C solution creation domain-aware. • M&CML provides a holistic view of control architecture. • M&CML has support for inherent consistency checks, user assistance and third party support. - Abstract: The use of System Engineering (SE) language such as SysML [1,20] is common within the community of control system designers. However the design handoff to the subsequent phases of the control system development is carried out manually in most cases without much tool support. The approach to agreeing on the control interface between components is a good example where engineers still rely on either manually created Interface Control Documents (ICD) or one off tools implemented by individual projects. Square Kilometer Array (SKA) [2] and International Thermonuclear Experimental Reactor (ITER) [3] are two good examples of such large projects adopting these approaches. This results in non-uniformity in the overall system design since individual groups invent their own vocabulary while using a language like SysML which leads to inconsistencies across the design, interface and realized code. To mitigate this, we propose the development of a Monitoring and Control Modeling Language (M&CML), a domain specific language (DSL) [4,22] for specifying M&C solutions. M&C ML starts with defining a vocabulary borrowing concepts from standard practices used in the control domain and incorporates a language which ensures uniformity and consistency across the M&C design, interfaces and implementation artifacts. In this paper we discuss this language with an analysis of its usage to point out its benefits.

  1. ML-Ask: Open Source Affect Analysis Software for Textual Input in Japanese

    Directory of Open Access Journals (Sweden)

    Michal Ptaszynski

    2017-06-01

    Full Text Available We present ML-Ask – the first Open Source Affect Analysis system for textual input in Japanese. ML-Ask analyses the contents of an input (e.g., a sentence and annotates it with information regarding the contained general emotive expressions, specific emotional words, valence-activation dimensions of overall expressed affect, and particular emotion types expressed with their respective expressions. ML-Ask also incorporates the Contextual Valence Shifters model for handling negation in sentences to deal with grammatically expressible shifts in the conveyed valence. The system, designed to work mainly under Linux and MacOS, can be used for research on, or applying the techniques of Affect Analysis within the framework Japanese language. It can also be used as an experimental baseline for specific research in Affect Analysis, and as a practical tool for written contents annotation.   Funding statement: This research has been supported by: a Research Grant from the Nissan Science Foundation (years 2009–2010, The GCOE Program founded by Japan’s Ministry of Education, Culture, Sports, Science and Technology (years 2009–2010, (JSPS KAKENHI Grant-in-Aid for JSPS Fellows (Project Number: 22-00358 (years 2010–2012, (JSPS KAKENHI Grant-in-Aid for Scientific Research (Project Number: 24600001 (years 2012–2015, (JSPS KAKENHI Grant-in-Aid for Research Activity Start-up (Project Number: 25880003 (years 2013–2015, and (JSPS KAKENHI Grant-in-Aid for Encouragement of Young Scientists (B (Project Number: 15K16044 (years 2015-present, project estimated to end in March 2018.

  2. Modeling the Observed Microwave Emission from Shallow Multi-Layer Tundra Snow Using DMRT-ML

    Directory of Open Access Journals (Sweden)

    Nastaran Saberi

    2017-12-01

    Full Text Available The observed brightness temperatures (Tb at 37 GHz from typical moderate density dry snow in mid-latitudes decreases with increasing snow water equivalent (SWE due to volume scattering of the ground emissions by the overlying snow. At a certain point, however, as SWE increases, the emission from the snowpack offsets the scattering of the sub-nivean emission. In tundra snow, the Tb slope reversal occurs at shallower snow thicknesses. While it has been postulated that the inflection point in the seasonal time series of observed Tb V 37 GHz of tundra snow is controlled by the formation of a thick wind slab layer, the simulation of this effect has yet to be confirmed. Therefore, the Dense Media Radiative Transfer Theory for Multi Layered (DMRT-ML snowpack is used to predict the passive microwave response from airborne observations over shallow, dense, slab-layered tundra snow. Airborne radiometer observations coordinated with ground-based in situ snow measurements were acquired in the Canadian high Arctic near Eureka, NT, in April 2011. The DMRT-ML was parameterized with the in situ snow measurements using a two-layer snowpack and run in two configurations: a depth hoar and a wind slab dominated pack. With these two configurations, the calibrated DMRT-ML successfully predicted the Tb V 37 GHz response (R correlation of 0.83 when compared with the observed airborne Tb footprints containing snow pits measurements. Using this calibrated model, the DMRT-ML was applied to the whole study region. At the satellite observation scale, observations from the Advanced Microwave Scanning Radiometer-Earth Observing System (AMSR-E over the study area reflected seasonal differences between Tb V 37 GHz and Tb V 19 GHz that supports the hypothesis of the development of an early season volume scattering depth hoar layer, followed by the growth of the late season emission-dominated wind slab layer. This research highlights the necessity to consider the two

  3. VolcanoGasML: a format to exchange geochemical volcanic gases data

    Directory of Open Access Journals (Sweden)

    Eric Reiter

    2007-01-01

    Full Text Available Chemical analyses of volcanic gases consist of: location of sampling, date of sampling, identification of the sampling, etc. Nowadays, these data are generally represented in different formats. All of these formats are inflexible and machine dependent. XML has become the most important method of transferring data between computers. VolcanoGasML is a new format, based on XML, for the chemical analyses of volcanic gases. Its definition is divided into several layers: the first one describes the general information concerning the sample, the second, which is organized in several sublayers, contains the chemical data.

  4. Pharmacometrics Markup Language (PharmML): Opening New Perspectives for Model Exchange in Drug Development

    Science.gov (United States)

    Swat, MJ; Moodie, S; Wimalaratne, SM; Kristensen, NR; Lavielle, M; Mari, A; Magni, P; Smith, MK; Bizzotto, R; Pasotti, L; Mezzalana, E; Comets, E; Sarr, C; Terranova, N; Blaudez, E; Chan, P; Chard, J; Chatel, K; Chenel, M; Edwards, D; Franklin, C; Giorgino, T; Glont, M; Girard, P; Grenon, P; Harling, K; Hooker, AC; Kaye, R; Keizer, R; Kloft, C; Kok, JN; Kokash, N; Laibe, C; Laveille, C; Lestini, G; Mentré, F; Munafo, A; Nordgren, R; Nyberg, HB; Parra-Guillen, ZP; Plan, E; Ribba, B; Smith, G; Trocóniz, IF; Yvon, F; Milligan, PA; Harnisch, L; Karlsson, M; Hermjakob, H; Le Novère, N

    2015-01-01

    The lack of a common exchange format for mathematical models in pharmacometrics has been a long-standing problem. Such a format has the potential to increase productivity and analysis quality, simplify the handling of complex workflows, ensure reproducibility of research, and facilitate the reuse of existing model resources. Pharmacometrics Markup Language (PharmML), currently under development by the Drug Disease Model Resources (DDMoRe) consortium, is intended to become an exchange standard in pharmacometrics by providing means to encode models, trial designs, and modeling steps. PMID:26225259

  5. PharmML in Action: an Interoperable Language for Modeling and Simulation

    Science.gov (United States)

    Bizzotto, R; Smith, G; Yvon, F; Kristensen, NR; Swat, MJ

    2017-01-01

    PharmML1 is an XML‐based exchange format2, 3, 4 created with a focus on nonlinear mixed‐effect (NLME) models used in pharmacometrics,5, 6 but providing a very general framework that also allows describing mathematical and statistical models such as single‐subject or nonlinear and multivariate regression models. This tutorial provides an overview of the structure of this language, brief suggestions on how to work with it, and use cases demonstrating its power and flexibility. PMID:28575551

  6. Anesthetic success of 1.8ml lidocaine 2% for mandibular tooth extraction. A pilot study

    OpenAIRE

    Pedro Aravena; Nicol Bustos; Andrea Cerón; Viviana Castillo; Claudio González

    2013-01-01

    RESUMEN Objetivo: Determinar el efecto anestésico de un cartucho de 1,8ml de anestesia lidocaína al 2% con epinefrina 1:100.000 en la técnica troncular al nervio alveolar inferior (NAI) para la exodoncia de dientes mandibulares. Material y método: Estudio piloto de carácter analítico. Participaron pacientes voluntarios del servicio Urgencia Dental de Valdivia-Chile con indicación de exodoncia en dientes mandibulares entre Mayo y Julio del año 2010. La técnica anestésica fue realizada por un ...

  7. The carbohydrate sequence markup language (CabosML): an XML description of carbohydrate structures.

    Science.gov (United States)

    Kikuchi, Norihiro; Kameyama, Akihiko; Nakaya, Shuuichi; Ito, Hiromi; Sato, Takashi; Shikanai, Toshihide; Takahashi, Yoriko; Narimatsu, Hisashi

    2005-04-15

    Bioinformatics resources for glycomics are very poor as compared with those for genomics and proteomics. The complexity of carbohydrate sequences makes it difficult to define a common language to represent them, and the development of bioinformatics tools for glycomics has not progressed. In this study, we developed a carbohydrate sequence markup language (CabosML), an XML description of carbohydrate structures. The language definition (XML Schema) and an experimental database of carbohydrate structures using an XML database management system are available at http://www.phoenix.hydra.mki.co.jp/CabosDemo.html kikuchi@hydra.mki.co.jp.

  8. Pharmacometrics Markup Language (PharmML): Opening New Perspectives for Model Exchange in Drug Development.

    Science.gov (United States)

    Swat, M J; Moodie, S; Wimalaratne, S M; Kristensen, N R; Lavielle, M; Mari, A; Magni, P; Smith, M K; Bizzotto, R; Pasotti, L; Mezzalana, E; Comets, E; Sarr, C; Terranova, N; Blaudez, E; Chan, P; Chard, J; Chatel, K; Chenel, M; Edwards, D; Franklin, C; Giorgino, T; Glont, M; Girard, P; Grenon, P; Harling, K; Hooker, A C; Kaye, R; Keizer, R; Kloft, C; Kok, J N; Kokash, N; Laibe, C; Laveille, C; Lestini, G; Mentré, F; Munafo, A; Nordgren, R; Nyberg, H B; Parra-Guillen, Z P; Plan, E; Ribba, B; Smith, G; Trocóniz, I F; Yvon, F; Milligan, P A; Harnisch, L; Karlsson, M; Hermjakob, H; Le Novère, N

    2015-06-01

    The lack of a common exchange format for mathematical models in pharmacometrics has been a long-standing problem. Such a format has the potential to increase productivity and analysis quality, simplify the handling of complex workflows, ensure reproducibility of research, and facilitate the reuse of existing model resources. Pharmacometrics Markup Language (PharmML), currently under development by the Drug Disease Model Resources (DDMoRe) consortium, is intended to become an exchange standard in pharmacometrics by providing means to encode models, trial designs, and modeling steps.

  9. A RuleML Study on Integrating Geographical and Health Information

    DEFF Research Database (Denmark)

    Gao, Sheng; Mioc, Darka; Boley, Harold

    2008-01-01

    To facilitate health surveillance, flexible ways to represent, integrate, and deduce health information become increasingly important. In this paper, an ontology is used to support the semantic definition of spatial, temporal and thematic factors of health information. The ontology is realized...... as an interchangeable RuleML knowledge base, consisting of facts and rules. Rules are also used for integrating geographical and health information. The implemented eHealthGeo system uses the OO jDREW reasoning engine to deduce implicit information such as spatial relationships. The system combines this with spatial...

  10. Post treatment PSA nadirs support continuing dose escalation study in patients with pretreatment PSA levels >10 ng/ml, but not in those with PSA <10 NG/ML

    International Nuclear Information System (INIS)

    Herold, D.H.; Hanlon, A.L.; Movsas, B.; Hanks, G.E.

    1996-01-01

    Purpose: We have recently shown that ICRU reporting point radiation doses above 71 Gy are not associated with improved bNED survival in prostate cancer patients with pretreatment PSA level 20 ng/ml we found a strong correlation between dose and nadir values < 1.0 ng/ml (p=.003) as well as for nadir's < 0.5 ng/ml (p=.04). This dose/nadir effect held at several dose levels, but 74 Gy for nadir values < 1.0 ng/ml and 72 Gy for nadir's < 0.5 ng/ml remained the most significant. 32% of these patients achieved a nadir < 1.0ng/ml and 15% < 0.5ng/ml. Conclusions: This analysis provides strong additional support that patients with pretreatment PSA values of < 10 ng/ml do not benefit from dose escalation beyond an ICRU reporting point dose of 71 Gy. For patients with pretreatment PSA's of 10-19.9 ng/ml there is no dose/nadir response evaluated at a nadir of 1.0 ng/ml; however, there is a borderline effect observed at a nadir of 0.5 ng/ml. Patients with pretreatment PSA's of 20 ng/ml or greater clearly benefit from higher doses as evaluated by PSA nadirs of 1.0 ng/ml, and 0.5 ng/ml. These studies support the continued investigation of dose escalation in treating patients with PSA levels over 10 ng/ml, they do not support continued investigation of dose escalation beyond 71 Gy in patients with pretreatment PSA levels < 10 ng/ml. The failure to demonstrate any dose response for the low PSA group and the finding of only a borderline effect for the intermediate PSA group may be influenced by the relatively small number of patients in our series treated to doses < 70 Gy and the fact that none of our patients were treated to doses below 65.98 Gy. The lower limit of acceptible dose has yet to be defined

  11. Testis tumors

    International Nuclear Information System (INIS)

    White, R.L.; Maier, J.G.

    1987-01-01

    Clinical trials are evaluating new combinations of drugs with the goal of diminishing the toxicity associated with the current regimens while not compromising the chance for cure. The evolution of information and staging studies such as tumor markers, CT scanning and MR scanning has made possible the detection of residual metastatic disease while obviating the need for surgical staging procedures. This has made less treatment possible for a large number of patients. The regularity of follow-up studies has made early detection of recurrences a possibility, so that effective and curative treatment is generally possible

  12. Robotic partial nephrectomy for complex renal tumors: surgical technique.

    Science.gov (United States)

    Rogers, Craig G; Singh, Amar; Blatt, Adam M; Linehan, W Marston; Pinto, Peter A

    2008-03-01

    Laparoscopic partial nephrectomy requires advanced training to accomplish tumor resection and renal reconstruction while minimizing warm ischemia times. Complex renal tumors add an additional challenge to a minimally invasive approach to nephron-sparing surgery. We describe our technique, illustrated with video, of robotic partial nephrectomy for complex renal tumors, including hilar, endophytic, and multiple tumors. Robotic assistance was used to resect 14 tumors in eight patients (mean age: 50.3 yr; range: 30-68 yr). Three patients had hereditary kidney cancer. All patients had complex tumor features, including hilar tumors (n=5), endophytic tumors (n=4), and/or multiple tumors (n=3). Robotic partial nephrectomy procedures were performed successfully without complications. Hilar clamping was used with a mean warm ischemia time of 31 min (range: 24-45 min). Mean blood loss was 230 ml (range: 100-450 ml). Histopathology confirmed clear-cell renal cell carcinoma (n=3), hybrid oncocytic tumor (n=2), chromophobe renal cell carcinoma (n=2), and oncocytoma (n=1). All patients had negative surgical margins. Mean index tumor size was 3.6 cm (range: 2.6-6.4 cm). Mean hospital stay was 2.6 d. At 3-mo follow-up, no patients experienced a statistically significant change in serum creatinine or estimated glomerular filtration rate and there was no evidence of tumor recurrence. Robotic partial nephrectomy is safe and feasible for select patients with complex renal tumors, including hilar, endophytic, and multiple tumors. Robotic assistance may facilitate a minimally invasive, nephron-sparing approach for select patients with complex renal tumors who might otherwise require open surgery or total nephrectomy.

  13. Teratoid Wilms′ tumor - A rare renal tumor

    Directory of Open Access Journals (Sweden)

    Biswanath Mukhopadhyay

    2011-01-01

    Full Text Available Teratoid Wilms′ tumor is an extremely rare renal tumor. We report a case of unilateral teratoid Wilms′ tumor in a 4-year-old girl. The patient was admitted with a right-sided abdominal mass. The mass was arising from the right kidney. Radical nephrectomy was done and the patient had an uneventful recovery. Histopathology report showed teratoid Wilms′ tumor.

  14. BER PERFORMANCE COMPARISON OF MIMO SYSTEMS USING OSTBC WITH ZF AND ML DECODING

    Directory of Open Access Journals (Sweden)

    Zenitha Rehman

    2014-12-01

    Full Text Available Multiple Input Multiple Output (MIMO systems with multiple antenna elements at both transmitter and receiver ends are an efficient solution for wireless communication systems. They provide high data rates by exploiting the spatial domain under the constraints of limited bandwidth and transmit power. Space-Time Block Coding (STBC is a MIMO transmit strategy which exploits transmit diversity and provides high reliability. Implementation of orthogonal space-time block codes (OSTBCs for a two transmitter–two receiver system under AWGN (Additive White Gaussian Noise channel and flat fading channel is performed. Alamouti code is employed for the STBC. The modulation techniques used are BPSK, QPSK and 16-QAM. Decoding is done using the Zero Forcing (ZF algorithm and Maximum Likelihood (ML algorithm. The BER Performance of each modulation scheme is compared with the un-coded version of the same. Performance comparison between the two decoding techniques is also done. It is found that ML detection offers a slightly better performance for BPSK and QPSK system than ZF detection.

  15. Experimental and Analytical Studies on Improved Feedforward ML Estimation Based on LS-SVR

    Directory of Open Access Journals (Sweden)

    Xueqian Liu

    2013-01-01

    Full Text Available Maximum likelihood (ML algorithm is the most common and effective parameter estimation method. However, when dealing with small sample and low signal-to-noise ratio (SNR, threshold effects are resulted and estimation performance degrades greatly. It is proved that support vector machine (SVM is suitable for small sample. Consequently, we employ the linear relationship between least squares support vector regression (LS-SVR’s inputs and outputs and regard LS-SVR process as a time-varying linear filter to increase input SNR of received signals and decrease the threshold value of mean square error (MSE curve. Furthermore, it is verified that by taking single-tone sinusoidal frequency estimation, for example, and integrating data analysis and experimental validation, if LS-SVR’s parameters are set appropriately, not only can the LS-SVR process ensure the single-tone sinusoid and additive white Gaussian noise (AWGN channel characteristics of original signals well, but it can also improves the frequency estimation performance. During experimental simulations, LS-SVR process is applied to two common and representative single-tone sinusoidal ML frequency estimation algorithms, the DFT-based frequency-domain periodogram (FDP and phase-based Kay ones. And the threshold values of their MSE curves are decreased by 0.3 dB and 1.2 dB, respectively, which obviously exhibit the advantage of the proposed algorithm.

  16. Isolation of a novel LPS-induced component of the ML superfamily in Ciona intestinalis.

    Science.gov (United States)

    Vizzini, Aiti; Bonura, Angela; Longo, Valeria; Sanfratello, Maria Antonietta; Parrinello, Daniela; Cammarata, Matteo; Colombo, Paolo

    2015-11-01

    ML superfamily represents a group of proteins playing important roles in lipid metabolism and innate immune response. In this study, we report the identification of the first component of the ML superfamily in the invertebrate Ciona intestinalis by means of a subtractive hybridization strategy. Sequence homology and phylogenetic analysis showed that this protein forms a specific clade with vertebrate components of the Niemann-Pick type C2 protein and, for this reason, it has been named Ci-NPC2. The putative Ci-NPC2 is a 150 amino acids long protein with a short signal peptide, seven cysteine residues, three putative lipid binding site and a three-dimensional model showing a characteristic β-strand structure. Gene expression analysis demonstrated that the Ci-NPC2 protein is positively upregulated after LPS inoculum with a peak of expression 1 h after challenge. Finally, in-situ hybridization demonstrated that the Ci-NPC2 protein is preferentially expressed in hemocytes inside the vessel lumen. Copyright © 2015 Elsevier Ltd. All rights reserved.

  17. PepArML: A Meta-Search Peptide Identification Platform for Tandem Mass Spectra.

    Science.gov (United States)

    Edwards, Nathan J

    2013-12-01

    The PepArML meta-search peptide identification platform for tandem mass spectra provides a unified search interface to seven search engines; a robust cluster, grid, and cloud computing scheduler for large-scale searches; and an unsupervised, model-free, machine-learning-based result combiner, which selects the best peptide identification for each spectrum, estimates false-discovery rates, and outputs pepXML format identifications. The meta-search platform supports Mascot; Tandem with native, k-score and s-score scoring; OMSSA; MyriMatch; and InsPecT with MS-GF spectral probability scores—reformatting spectral data and constructing search configurations for each search engine on the fly. The combiner selects the best peptide identification for each spectrum based on search engine results and features that model enzymatic digestion, retention time, precursor isotope clusters, mass accuracy, and proteotypic peptide properties, requiring no prior knowledge of feature utility or weighting. The PepArML meta-search peptide identification platform often identifies two to three times more spectra than individual search engines at 10% FDR.

  18. Radical prostatectomy outcome when performed with PSA above 20 ng/ml.

    LENUS (Irish Health Repository)

    Connolly, S S

    2012-02-01

    Many centres currently do not offer radical prostatectomy (RP) to men with high-risk localised prostate cancer due to concerns regarding poor outcome, despite evidence to the contrary. We identified 18 men undergoing RP with serum PSA >20 ng\\/ml (high-risk by National Comprehensive Cancer Network definition) and minimum follow-up of 12 years (mean 13.5). Mean preoperative PSA was 37.0 ng\\/ml (Range 21.1-94.0). Prostatectomy pathology reported extracapsular disease in 16 (88.9%), positive surgical margins in 15 (83%) and positive pelvic lymph nodes in 5 (27.8%). Overall and cancer-specific survival at 5 and 10-years was 83.3%, 88.2%, 72% and 76.5% respectively. With complete follow-up 11 (61.1%) are alive, and 5 (27.8%) avoided any adjuvant therapy. Complete continence (defined as no involuntary urine leakage and no use of pads) was achieved in 60%, with partial continence in the remainder. We conclude that surgery for this aggressive variant of localised prostate cancer can result in satisfactory outcome.

  19. The ML1Nx2 Phosphatidylinositol 3,5-Bisphosphate Probe Shows Poor Selectivity in Cells.

    Science.gov (United States)

    Hammond, Gerald R V; Takasuga, Shunsuke; Sasaki, Takehiko; Balla, Tamas

    2015-01-01

    Phosphatidylinositol (3,5)-bisphosphate (PtdIns(3,5)P2) is a quantitatively minor phospholipid in eukaryotic cells that plays a fundamental role in regulating endocytic membrane traffic. Despite its clear importance for cellular function and organism physiology, mechanistic details of its biology have so far not been fully elucidated. In part, this is due to a lack of experimental tools that specifically probe for PtdIns(3,5)P2 in cells to unambiguously identify its dynamics and site(s) of action. In this study, we have evaluated a recently reported PtdIns(3,5)P2 biosensor, GFP-ML1Nx2, for its veracity as such a probe. We report that, in live cells, the localization of this biosensor to sub-cellular compartments is largely independent of PtdIns(3,5)P2, as assessed after pharmacological, chemical genetic or genomic interventions that block the lipid's synthesis. We therefore conclude that it is unwise to interpret the localization of ML1Nx2 as a true and unbiased biosensor for PtdIns(3,5)P2.

  20. Anesthetic success of 1.8ml lidocaine 2% for mandibular tooth extraction. A pilot study

    Directory of Open Access Journals (Sweden)

    Pedro Aravena

    2013-04-01

    Full Text Available Aim: To determine the anesthetic effect of a 1.8ml cartridge of anesthetic lidocaine 2% with epinephrine 1:100,000 in inferior alveolar nerve block (NAI for the extraction in mandibular teeth. Material and methods: A pilot study with analitic design. Participating patients of Dental Emergency Service volunteers from Valdivia-Chile for mandibular teeth extractions attending between May and July of 2010. The anesthetic technique was performed by a dentist using only one cartridge of anesthetic to the NAI. After 15 minutes, the effect was considered effective when anesthetic not require reinforcement with additional anesthesia during extraction of teeth. We analyzed the relationship between success anesthetic effect with sex, age, diagnosis of tooth and type and level of pain observed (chi-square and logistic regression, p<0.05. Results: 62 patients were selected, of which only 47(75.8% was achieved anesthetic success. There was no statistical association with sex, age, type or dental diagnosis and perceived pain. Conclusion: Using a 1.8ml cartridge of anesthesia was effective in three of four patients treated by extraction of mandibular teeth. It suggests further research in relation to the clinical effectiveness of other anesthetics with the same dose in NAI.

  1. Tumor Macroenvironment and Metabolism

    OpenAIRE

    Al-Zhoughbi, Wael; Huang, Jianfeng; Paramasivan, Ganapathy S.; Till, Holger; Pichler, Martin; Guertl-Lackner, Barbara; Hoefler, Gerald

    2014-01-01

    In this review we introduce the concept of the tumor macroenvironment and explore it in the context of metabolism. Tumor cells interact with the tumor microenvironment including immune cells. Blood and lymph vessels are the critical components that deliver nutrients to the tumor and also connect the tumor to the macroenvironment. Several factors are then released from the tumor itself but potentially also from the tumor microenvironment, influencing the metabolism of distant tissues and organ...

  2. Design Analysis Method for Multidisciplinary Complex Product using SysML

    Directory of Open Access Journals (Sweden)

    Liu Jihong

    2017-01-01

    Full Text Available In the design of multidisciplinary complex products, model-based systems engineering methods are widely used. However, the methodologies only contain only modeling order and simple analysis steps, and lack integrated design analysis methods supporting the whole process. In order to solve the problem, a conceptual design analysis method with integrating modern design methods has been proposed. First, based on the requirement analysis of the quantization matrix, the user’s needs are quantitatively evaluated and translated to system requirements. Then, by the function decomposition of the function knowledge base, the total function is semi-automatically decomposed into the predefined atomic function. The function is matched into predefined structure through the behaviour layer using function-structure mapping based on the interface matching. Finally based on design structure matrix (DSM, the structure reorganization is completed. The process of analysis is implemented with SysML, and illustrated through an aircraft air conditioning system for the system validation.

  3. Software support for SBGN maps: SBGN-ML and LibSBGN.

    Science.gov (United States)

    van Iersel, Martijn P; Villéger, Alice C; Czauderna, Tobias; Boyd, Sarah E; Bergmann, Frank T; Luna, Augustin; Demir, Emek; Sorokin, Anatoly; Dogrusoz, Ugur; Matsuoka, Yukiko; Funahashi, Akira; Aladjem, Mirit I; Mi, Huaiyu; Moodie, Stuart L; Kitano, Hiroaki; Le Novère, Nicolas; Schreiber, Falk

    2012-08-01

    LibSBGN is a software library for reading, writing and manipulating Systems Biology Graphical Notation (SBGN) maps stored using the recently developed SBGN-ML file format. The library (available in C++ and Java) makes it easy for developers to add SBGN support to their tools, whereas the file format facilitates the exchange of maps between compatible software applications. The library also supports validation of maps, which simplifies the task of ensuring compliance with the detailed SBGN specifications. With this effort we hope to increase the adoption of SBGN in bioinformatics tools, ultimately enabling more researchers to visualize biological knowledge in a precise and unambiguous manner. Milestone 2 was released in December 2011. Source code, example files and binaries are freely available under the terms of either the LGPL v2.1+ or Apache v2.0 open source licenses from http://libsbgn.sourceforge.net. sbgn-libsbgn@lists.sourceforge.net.

  4. Application and performance of an ML-EM algorithm in NEXT

    Science.gov (United States)

    Simón, A.; Lerche, C.; Monrabal, F.; Gómez-Cadenas, J. J.; Álvarez, V.; Azevedo, C. D. R.; Benlloch-Rodríguez, J. M.; Borges, F. I. G. M.; Botas, A.; Cárcel, S.; Carrión, J. V.; Cebrián, S.; Conde, C. A. N.; Díaz, J.; Diesburg, M.; Escada, J.; Esteve, R.; Felkai, R.; Fernandes, L. M. P.; Ferrario, P.; Ferreira, A. L.; Freitas, E. D. C.; Goldschmidt, A.; González-Díaz, D.; Gutiérrez, R. M.; Hauptman, J.; Henriques, C. A. O.; Hernandez, A. I.; Hernando Morata, J. A.; Herrero, V.; Jones, B. J. P.; Labarga, L.; Laing, A.; Lebrun, P.; Liubarsky, I.; López-March, N.; Losada, M.; Martín-Albo, J.; Martínez-Lema, G.; Martínez, A.; McDonald, A. D.; Monteiro, C. M. B.; Mora, F. J.; Moutinho, L. M.; Muñoz Vidal, J.; Musti, M.; Nebot-Guinot, M.; Novella, P.; Nygren, D. R.; Palmeiro, B.; Para, A.; Pérez, J.; Querol, M.; Renner, J.; Ripoll, L.; Rodríguez, J.; Rogers, L.; Santos, F. P.; dos Santos, J. M. F.; Sofka, C.; Sorel, M.; Stiegler, T.; Toledo, J. F.; Torrent, J.; Tsamalaidze, Z.; Veloso, J. F. C. A.; Webb, R.; White, J. T.; Yahlali, N.

    2017-08-01

    The goal of the NEXT experiment is the observation of neutrinoless double beta decay in 136Xe using a gaseous xenon TPC with electroluminescent amplification and specialized photodetector arrays for calorimetry and tracking. The NEXT Collaboration is exploring a number of reconstruction algorithms to exploit the full potential of the detector. This paper describes one of them: the Maximum Likelihood Expectation Maximization (ML-EM) method, a generic iterative algorithm to find maximum-likelihood estimates of parameters that has been applied to solve many different types of complex inverse problems. In particular, we discuss a bi-dimensional version of the method in which the photosensor signals integrated over time are used to reconstruct a transverse projection of the event. First results show that, when applied to detector simulation data, the algorithm achieves nearly optimal energy resolution (better than 0.5% FWHM at the Q value of 136Xe) for events distributed over the full active volume of the TPC.

  5. Using SysML for verification and validation planning on the Large Synoptic Survey Telescope (LSST)

    Science.gov (United States)

    Selvy, Brian M.; Claver, Charles; Angeli, George

    2014-08-01

    This paper provides an overview of the tool, language, and methodology used for Verification and Validation Planning on the Large Synoptic Survey Telescope (LSST) Project. LSST has implemented a Model Based Systems Engineering (MBSE) approach as a means of defining all systems engineering planning and definition activities that have historically been captured in paper documents. Specifically, LSST has adopted the Systems Modeling Language (SysML) standard and is utilizing a software tool called Enterprise Architect, developed by Sparx Systems. Much of the historical use of SysML has focused on the early phases of the project life cycle. Our approach is to extend the advantages of MBSE into later stages of the construction project. This paper details the methodology employed to use the tool to document the verification planning phases, including the extension of the language to accommodate the project's needs. The process includes defining the Verification Plan for each requirement, which in turn consists of a Verification Requirement, Success Criteria, Verification Method(s), Verification Level, and Verification Owner. Each Verification Method for each Requirement is defined as a Verification Activity and mapped into Verification Events, which are collections of activities that can be executed concurrently in an efficient and complementary way. Verification Event dependency and sequences are modeled using Activity Diagrams. The methodology employed also ties in to the Project Management Control System (PMCS), which utilizes Primavera P6 software, mapping each Verification Activity as a step in a planned activity. This approach leads to full traceability from initial Requirement to scheduled, costed, and resource loaded PMCS task-based activities, ensuring all requirements will be verified.

  6. Is a volume of 3.6 mL better than 1.8 mL for inferior alveolar nerve blocks in patients with symptomatic irreversible pulpitis?

    Science.gov (United States)

    Fowler, Sara; Reader, Al

    2013-08-01

    The purpose of this retrospective study was to determine the success of the inferior alveolar nerve (IAN) block using either 3.6 mL or 1.8 mL 2% lidocaine with 1:100,000 epinephrine in patients presenting with symptomatic irreversible pulpitis. As part of 7 previously published studies, 319 emergency patients presenting with symptomatic irreversible pulpitis received either a 1.8-mL volume or 3.6-mL volume of 2% lidocaine with 1:100,000 epinephrine in an IAN block. One hundred ninety patients received a 1.8-mL volume, and 129 received a 3.6-mL volume. Endodontic emergency treatment was completed on each subject. Success was defined as the ability to access and instrument the tooth without pain (visual analog scale score of 0) or mild pain (VAS rating ≤54 mm). Success of the 1.8-mL volume was 28%, and for the 3.6-mL volume it was 39%. There was no statistically significant difference between the 2 volumes. In conclusion, for patients presenting with irreversible pulpitis, success was not significantly different between a 3.6-mL volume and a 1.8-mL volume of 2% lidocaine with 1:100,000 epinephrine. The success rates (28%-39%) with either volume were not high enough to ensure complete pulpal anesthesia. Copyright © 2013 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

  7. BEEF CATTLE MUSCULARITY CANDIDATE GENES

    Directory of Open Access Journals (Sweden)

    Irida Novianti

    2010-04-01

    Full Text Available Muscularity is a potential indicator for the selection of more productive cattle. Mapping quantitative trait loci (QTL for traits related to muscularity is useful to identify the genomic regions where the genes affecting muscularity reside. QTL analysis from a Limousin-Jersey double backcross herd was conducted using QTL Express software with cohort and breed as the fixed effects. Nine QTL suggested to have an association with muscularity were identified on cattle chromosomes BTA 1, 2, 3, 4, 5, 8, 12, 14 and 17. The myostatin gene is located at the centromeric end of chromosome 2 and not surprisingly, the Limousin myostatin F94L variant accounted for the QTL on BTA2. However, when the myostatin F94L genotype was included as an additional fixed effect, the QTL on BTA17 was also no longer significant. This result suggests that there may be gene(s that have epistatic effects with myostatin located on cattle chromosome 17. Based on the position of the QTL in base pairs, all the genes that reside in the region were determined using the Ensembl data base (www.ensembl.org. There were two potential candidate genes residing within these QTL regions were selected. They were Smad nuclear interacting protein 1 (SNIP1 and similar to follistatin-like 5 (FSTL5. (JIIPB 2010 Vol 20 No 1: 1-10

  8. Magnetic Nickel iron Electroformed Trap (MagNET): a master/replica fabrication strategy for ultra-high throughput (>100 mL h−1) immunomagnetic sorting†

    Science.gov (United States)

    Ko, Jina; Yelleswarapu, Venkata; Singh, Anup; Shah, Nishal

    2016-01-01

    Microfluidic devices can sort immunomagnetically labeled cells with sensitivity and specificity much greater than that of conventional methods, primarily because the size of microfluidic channels and micro-scale magnets can be matched to that of individual cells. However, these small feature sizes come at the expense of limited throughput (ϕ 10 mL whole blood. Here, we report a new approach to micromagnetic sorting that can achieve highly specific cell separation in unprocessed complex samples at a throughput (ϕ > 100 mL h−1) 100× greater than that of conventional microfluidics. To achieve this goal, we have devised a new approach to micromagnetic sorting, the magnetic nickel iron electroformed trap (MagNET), which enables high flow rates by having millions of micromagnetic traps operate in parallel. Our design rotates the conventional microfluidic approach by 90° to form magnetic traps at the edges of pores instead of in channels, enabling millions of the magnetic traps to be incorporated into a centimeter sized device. Unlike previous work, where magnetic structures were defined using conventional microfabrication, we take inspiration from soft lithography and create a master from which many replica electroformed magnetic micropore devices can be economically manufactured. These free-standing 12 µm thick permalloy (Ni80Fe20) films contain micropores of arbitrary shape and position, allowing the device to be tailored for maximal capture efficiency and throughput. We demonstrate MagNET's capabilities by fabricating devices with both circular and rectangular pores and use these devices to rapidly (ϕ = 180 mL h−1) and specifically sort rare tumor cells from white blood cells. PMID:27170379

  9. libNeuroML and PyLEMS: using Python to combine procedural and declarative modeling approaches in computational neuroscience.

    Science.gov (United States)

    Vella, Michael; Cannon, Robert C; Crook, Sharon; Davison, Andrew P; Ganapathy, Gautham; Robinson, Hugh P C; Silver, R Angus; Gleeson, Padraig

    2014-01-01

    NeuroML is an XML-based model description language, which provides a powerful common data format for defining and exchanging models of neurons and neuronal networks. In the latest version of NeuroML, the structure and behavior of ion channel, synapse, cell, and network model descriptions are based on underlying definitions provided in LEMS, a domain-independent language for expressing hierarchical mathematical models of physical entities. While declarative approaches for describing models have led to greater exchange of model elements among software tools in computational neuroscience, a frequent criticism of XML-based languages is that they are difficult to work with directly. Here we describe two Application Programming Interfaces (APIs) written in Python (http://www.python.org), which simplify the process of developing and modifying models expressed in NeuroML and LEMS. The libNeuroML API provides a Python object model with a direct mapping to all NeuroML concepts defined by the NeuroML Schema, which facilitates reading and writing the XML equivalents. In addition, it offers a memory-efficient, array-based internal representation, which is useful for handling large-scale connectomics data. The libNeuroML API also includes support for performing common operations that are required when working with NeuroML documents. Access to the LEMS data model is provided by the PyLEMS API, which provides a Python implementation of the LEMS language, including the ability to simulate most models expressed in LEMS. Together, libNeuroML and PyLEMS provide a comprehensive solution for interacting with NeuroML models in a Python environment.

  10. libNeuroML and PyLEMS: using Python to combine imperative and declarative modelling approaches in computational neuroscience

    Directory of Open Access Journals (Sweden)

    Michael eVella

    2014-04-01

    Full Text Available NeuroML is an XML-based model description language, which provides a powerful common data format for defining and exchanging models of neurons and neuronal networks. In the latest version of NeuroML, the structure and behavior of ion channel, synapse, cell,and network model descriptions are based on underlying definitions provided in LEMS, a domain-independent language for expressing hierarchical mathematical models of physical entities. While declarative approaches for describing models have led to greater exchange of model elements among software tools in computational neuroscience, a frequent criticism of XML-based languages is that they are difficult to work with directly. Here we describe two APIs (Application Programming Interfaces written in Python (http://www.python.org, which simplify the process of developing and modifying models expressed in NeuroML and LEMS. The libNeuroML API provides a Python object model with a direct mapping to all NeuroML concepts defined by the NeuroML Schema, which facilitates reading and writing the XML equivalents. In addition, it offers a memory-efficient, array-based internal representation, which is useful for handling large-scale connectomics data. The libNeuroML API also includes support for performing common operations that are required when working with NeuroML documents. Access to the LEMS data model is provided by the PyLEMS API, which provides a Python implementation of the LEMS language, including the ability to simulate most models expressed in LEMS. Together, libNeuroML and PyLEMS provide a comprehensive solution for interacting with NeuroML models in a Python environment.

  11. Successful Multi-Leg Completion of KS-13 ML-1 & Increased Power Generation of Puna Geothermal Venture (PGV), Hawai'i

    Science.gov (United States)

    Drakos, P. S.; Spielman, P.; Peters, B.

    2017-12-01

    Located in the Puna district on the Big Island in Hawaii, Puna Geothermal Venture (PGV) is the only geothermal power plant in the state. PGV is comprised of two air-cooled power plants with a total generating capacity of 38 MW. Commercial operation commenced in 1993 and the project was acquired by Ormat in June 2004. Over the years, generation has increased by upgrading the plant through resource development and with the addition of a bottoming OEC (Ormat Energy Converter) in 2011. The geothermal reservoir at PGV is hosted within a step-over along the axis of the Kilauea Lower East Rift Zone (LERZ). Subsurface permeability at PGV is controlled by sub-vertical and rift-parallel fractures/faults and dike swarms which are the result of active tectonic dilation across the rift and shallow volcanic activity related to Kilauea. At PGV, the location and attitude of these fractures are well constrained at depth by drilling to be orientated at N63°E and dipping at 5° NW. These fractures are aligned en-echelon and form a major left-step along the rift axis which results in a localized zone of enhanced dilation. In 2016, a program was initiated to increase injection capacity and enthalpy in the PGV wellfield. Existing injection well KS-13 was selected as a candidate for re-drill based on a comprehensive resource model and reservoir modeling predictions. KS-13 ML1 was designed as a multi-leg completion from the existing KS-13 well, whereby the final completion is a forked well composed of the original wellbore and the newly completed second wellbore. The target area for the new multi-leg (ML) were large aperture, steeply dipping fractures associated with the 1955 eruptive fissure. Well KS-13 ML1 was drilled using PGV's Rig and a retrievable whipstock to mill a casing exit window. With the original wellbore temporarily plugged, a multi-rate water loss test was performed and an injectivity of 6 gpm/psi was measured. Following the removal of the whipstock ramp and packer from

  12. Human Tumor Antigens Yesterday, Today, and Tomorrow.

    Science.gov (United States)

    Finn, Olivera J

    2017-05-01

    The question of whether human tumors express antigens that can be recognized by the immune system has been answered with a resounding YES. Most were identified through spontaneous antitumor humoral and cellular immune responses found in cancer patients and include peptides, glycopeptides, phosphopeptides, viral peptides, and peptides resulting from common mutations in oncogenes and tumor-suppressor genes, or common gene fusion events. Many have been extensively tested as candidates for anticancer vaccines. More recently, attention has been focused on the potentially large number of unique tumor antigens, mutated neoantigens, that are the predicted products of the numerous mutations revealed by exome sequencing of primary tumors. Only a few have been confirmed as targets of spontaneous immunity and immunosurveillance, and even fewer have been tested in preclinical and clinical settings. The field has been divided for a long time on the relative importance of shared versus mutated antigens in tumor surveillance and as candidates for vaccines. This question will eventually need to be answered in a head to head comparison in well-designed clinical trials. One advantage that shared antigens have over mutated antigens is their potential to be used in vaccines for primary cancer prevention. Cancer Immunol Res; 5(5); 347-54. ©2017 AACR . ©2017 American Association for Cancer Research.

  13. Major obstetric haemorrhage of 2000 ml or greater: a clinical audit.

    Science.gov (United States)

    O'Sullivan, J; Mansfield, R; Talbot, R; Cairns, A E

    2018-05-04

    Haemorrhage remains a leading cause of maternal death. We conducted an audit to identify strategies to improve the management at our local NHS Trust. A data collection form was based on our local guideline. A coded database search was conducted for all deliveries where the estimated blood loss was ≥2000 ml (from June 1 2015 to December 31 2015), returning 68 search results (13.7/1000 births). Fifty-six records were included. Poor compliance (<75%) was seen in some key areas including the major obstetric haemorrhage (MOH) call activation (52%), the presence of an anaesthetic consultant (63%) and tranexamic acid administration (46%). Thirty out of 56 cases (54%) were acutely transfused. Women, who were not transfused acutely, appeared to be more likely to need a secondary transfusion if no MOH call had been activated (9/27 (33%) versus 3/29 (10%), p = .052). A key area for improvement was the activation of MOH calls. Following this audit, we adjusted our guideline to make it more clinically useful and staff training sessions were held, including simulation training. Impact statement What is already known on this subject? A postpartum haemorrhage (PPH) is an obstetric emergency. A structured approach is important to optimise the care of the mothers during this dangerous time, and has been shown to reduce the transfusion requirements. However, clinical practice may not adhere to the guideline recommendations. What the results of this study add? With the objective evidence of increased rates of PPH ≥2000 ml at our institution, our work identifying the flaws in management was a critical component of the work to improve the outcomes. This study gives impetus to find innovative ways to improve adherence to guidelines, and inspired an update of our local guideline to improve the applicability and utility. This project suggests a new marker for the adequacy of an acute management (a requirement for secondary blood transfusion without having received an acute

  14. Pediatric Brain Tumor Foundation

    Science.gov (United States)

    ... navigate their brain tumor diagnosis. WATCH AND SHARE Brain tumors and their treatment can be deadly so ... Pediatric Central Nervous System Cancers Read more >> Pediatric Brain Tumor Foundation 302 Ridgefield Court, Asheville, NC 28806 ...

  15. Brain Tumors (For Parents)

    Science.gov (United States)

    ... Staying Safe Videos for Educators Search English Español Brain Tumors KidsHealth / For Parents / Brain Tumors What's in ... radiation therapy or chemotherapy, or both. Types of Brain Tumors There are many different types of brain ...

  16. Childhood Brain Tumors

    Science.gov (United States)

    Brain tumors are abnormal growths inside the skull. They are among the most common types of childhood ... still be serious. Malignant tumors are cancerous. Childhood brain and spinal cord tumors can cause headaches and ...

  17. Malignant bone tumors

    International Nuclear Information System (INIS)

    Zedgenidze, G.A.; Kishkovskij, A.N.; Elashov, Yu.G.

    1984-01-01

    Clinicoroentgenologic semiotics of malignant bone tumors as well as metastatic bone tumors are presented. Diagnosis of malignant and metastatic bone tumors should be always complex, representing a result of cooperation of a physician, roentgenologist, pathoanatomist

  18. Tumors and Pregnancy

    Science.gov (United States)

    Tumors during pregnancy are rare, but they can happen. Tumors can be either benign or malignant. Benign tumors aren't cancer. Malignant ones are. The most common cancers in pregnancy are breast cancer, cervical cancer, lymphoma, and melanoma. ...

  19. Neuroendocrine Tumor: Statistics

    Science.gov (United States)

    ... Tumor > Neuroendocrine Tumor: Statistics Request Permissions Neuroendocrine Tumor: Statistics Approved by the Cancer.Net Editorial Board , 01/ ... the body. It is important to remember that statistics on the survival rates for people with a ...

  20. Common genetic variations in cell cycle and DNA repair pathways associated with pediatric brain tumor susceptibility

    DEFF Research Database (Denmark)

    Fahmideh, Maral Adel; Lavebratt, Catharina; Schüz, Joachim

    2016-01-01

    Knowledge on the role of genetic polymorphisms in the etiology of pediatric brain tumors (PBTs) is limited. Therefore, we investigated the association between single nucleotide polymorphisms (SNPs), identified by candidate gene-association studies on adult brain tumors, and PBT risk. The study is...... cycle and DNA repair pathways variations associated with susceptibility to adult brain tumors also seem to be associated with PBT risk, suggesting pediatric and adult brain tumors might share similar etiological pathways....

  1. GeoSciML v3.0 - a significant upgrade of the CGI-IUGS geoscience data model

    Science.gov (United States)

    Raymond, O.; Duclaux, G.; Boisvert, E.; Cipolloni, C.; Cox, S.; Laxton, J.; Letourneau, F.; Richard, S.; Ritchie, A.; Sen, M.; Serrano, J.-J.; Simons, B.; Vuollo, J.

    2012-04-01

    GeoSciML version 3.0 (http://www.geosciml.org), released in late 2011, is the latest version of the CGI-IUGS* Interoperability Working Group geoscience data interchange standard. The new version is a significant upgrade and refactoring of GeoSciML v2 which was released in 2008. GeoSciML v3 has already been adopted by several major international interoperability initiatives, including OneGeology, the EU INSPIRE program, and the US Geoscience Information Network, as their standard data exchange format for geoscience data. GeoSciML v3 makes use of recently upgraded versions of several Open Geospatial Consortium (OGC) and ISO data transfer standards, including GML v3.2, SWE Common v2.0, and Observations and Measurements v2 (ISO 19156). The GeoSciML v3 data model has been refactored from a single large application schema with many packages, into a number of smaller, but related, application schema modules with individual namespaces. This refactoring allows the use and future development of modules of GeoSciML (eg; GeologicUnit, GeologicStructure, GeologicAge, Borehole) in smaller, more manageable units. As a result of this refactoring and the integration with new OGC and ISO standards, GeoSciML v3 is not backwardly compatible with previous GeoSciML versions. The scope of GeoSciML has been extended in version 3.0 to include new models for geomorphological data (a Geomorphology application schema), and for geological specimens, geochronological interpretations, and metadata for geochemical and geochronological analyses (a LaboratoryAnalysis-Specimen application schema). In addition, there is better support for borehole data, and the PhysicalProperties model now supports a wider range of petrophysical measurements. The previously used CGI_Value data type has been superseded in favour of externally governed data types provided by OGC's SWE Common v2 and GML v3.2 data standards. The GeoSciML v3 release includes worked examples of best practice in delivering geochemical

  2. Architecting the Human Space Flight Program with Systems Modeling Language (SysML)

    Science.gov (United States)

    Jackson, Maddalena M.; Fernandez, Michela Munoz; McVittie, Thomas I.; Sindiy, Oleg V.

    2012-01-01

    The next generation of missions in NASA's Human Space Flight program focuses on the development and deployment of highly complex systems (e.g., Orion Multi-Purpose Crew Vehicle, Space Launch System, 21st Century Ground System) that will enable astronauts to venture beyond low Earth orbit and explore the moon, near-Earth asteroids, and beyond. Architecting these highly complex system-of-systems requires formal systems engineering techniques for managing the evolution of the technical features in the information exchange domain (e.g., data exchanges, communication networks, ground software) and also, formal correlation of the technical architecture to stakeholders' programmatic concerns (e.g., budget, schedule, risk) and design development (e.g., assumptions, constraints, trades, tracking of unknowns). This paper will describe how the authors have applied System Modeling Language (SysML) to implement model-based systems engineering for managing the description of the End-to-End Information System (EEIS) architecture and associated development activities and ultimately enables stakeholders to understand, reason, and answer questions about the EEIS under design for proposed lunar Exploration Missions 1 and 2 (EM-1 and EM-2).

  3. Specification and Design of Electrical Flight System Architectures with SysML

    Science.gov (United States)

    McKelvin, Mark L., Jr.; Jimenez, Alejandro

    2012-01-01

    Modern space flight systems are required to perform more complex functions than previous generations to support space missions. This demand is driving the trend to deploy more electronics to realize system functionality. The traditional approach for the specification, design, and deployment of electrical system architectures in space flight systems includes the use of informal definitions and descriptions that are often embedded within loosely coupled but highly interdependent design documents. Traditional methods become inefficient to cope with increasing system complexity, evolving requirements, and the ability to meet project budget and time constraints. Thus, there is a need for more rigorous methods to capture the relevant information about the electrical system architecture as the design evolves. In this work, we propose a model-centric approach to support the specification and design of electrical flight system architectures using the System Modeling Language (SysML). In our approach, we develop a domain specific language for specifying electrical system architectures, and we propose a design flow for the specification and design of electrical interfaces. Our approach is applied to a practical flight system.

  4. Implementation of a Goal-Based Systems Engineering Process Using the Systems Modeling Language (SysML)

    Science.gov (United States)

    Breckenridge, Jonathan T.; Johnson, Stephen B.

    2013-01-01

    Building upon the purpose, theoretical approach, and use of a Goal-Function Tree (GFT) being presented by Dr. Stephen B. Johnson, described in a related Infotech 2013 ISHM abstract titled "Goal-Function Tree Modeling for Systems Engineering and Fault Management", this paper will describe the core framework used to implement the GFTbased systems engineering process using the Systems Modeling Language (SysML). These two papers are ideally accepted and presented together in the same Infotech session. Statement of problem: SysML, as a tool, is currently not capable of implementing the theoretical approach described within the "Goal-Function Tree Modeling for Systems Engineering and Fault Management" paper cited above. More generally, SysML's current capabilities to model functional decompositions in the rigorous manner required in the GFT approach are limited. The GFT is a new Model-Based Systems Engineering (MBSE) approach to the development of goals and requirements, functions, and its linkage to design. As a growing standard for systems engineering, it is important to develop methods to implement GFT in SysML. Proposed Method of Solution: Many of the central concepts of the SysML language are needed to implement a GFT for large complex systems. In the implementation of those central concepts, the following will be described in detail: changes to the nominal SysML process, model view definitions and examples, diagram definitions and examples, and detailed SysML construct and stereotype definitions.

  5. 11 CFR 110.13 - Candidate debates.

    Science.gov (United States)

    2010-01-01

    ... debates include at least two candidates; and (2) The staging organization(s) does not structure the... PROHIBITIONS § 110.13 Candidate debates. (a) Staging organizations. (1) Nonprofit organizations described in 26..., subparts D and E. (b) Debate structure. The structure of debates staged in accordance with this section and...

  6. A possible candidate for cold dark matter

    Indian Academy of Sciences (India)

    This additional scalar can be a viable candidate of cold dark matter (CDM) since the stability of is achieved by the application of Z 2 symmetry on . Considering as a possible candidate of CDM, Boltzmann's equation is solved to find the freeze-out temperature and relic density of for Higgs mass 120 GeV in the scalar ...

  7. 76 FR 36130 - Call for Candidates

    Science.gov (United States)

    2011-06-21

    ... financial information in decision-making. The Board meets in Washington, DC, for two days every other month... FEDERAL ACCOUNTING STANDARDS ADVISORY BOARD Call for Candidates AGENCY: Federal Accounting... candidates. Any applicant who provided the Federal Accounting Standards Advisory Board (FASAB or the Board...

  8. Evaluating historical candidate genes for schizophrenia

    DEFF Research Database (Denmark)

    Farrell, M S; Werge, T; Sklar, P

    2015-01-01

    Prior to the genome-wide association era, candidate gene studies were a major approach in schizophrenia genetics. In this invited review, we consider the current status of 25 historical candidate genes for schizophrenia (for example, COMT, DISC1, DTNBP1 and NRG1). The initial study for 24 of thes...

  9. 11 CFR 9003.2 - Candidate certifications.

    Science.gov (United States)

    2010-01-01

    ... funds under 11 CFR 9003.2(c)(3) shall not count against such candidate's $50,000 expenditure limitation... expenditures. (8) Expenditures made using a credit card for which the candidate is jointly or solely liable will count against the limits of this section to the extent that the full amount due, including any...

  10. Peripheral epithelial odontogenic tumor

    International Nuclear Information System (INIS)

    Carzoglio, J.; Tancredi, N.; Capurro, S.; Ravecca, T.; Scarrone, P.

    2006-01-01

    A new case of peripheral epithelial odontogenic tumor (Pindborg tumor) is reported. It is localized in the superior right gingival region, a less frequent site, and has the histopathological features previously reported. Immunochemical studies were performed, revealing a differential positive stain to cytokeratins in tumor cells deeply seated in the tumor mass, probably related to tumoral cell heterogeneity.Interestingly, in this particular case S-100 protein positive reactivity was also detected in arborescent cells intermingled with tumoral cells, resembling Langerhans cells. Even though referred in the literature in central Pindborg tumors, no references were found about their presence in peripheral tumors, like the one that is presented here

  11. Carcinoembryonic antigen radioimmunoassay in hepatic tumor

    International Nuclear Information System (INIS)

    Aburano, Tamio; Tonami, Norihisa; Hisada, Kinichi

    1976-01-01

    Carcinoembryonic antigen (CEA) radioimmunoassay with the sandwich method was performed in addition to both α 1 -fetoprotein (AFP) radioimmunoassay and liver scintigraphy to elevate the diagnostic accuracy of hepatic tumor in nuclear medicine. All of the ten healthy controls and 47 of 52 cases with benign disease showed a CEA titer less than 2.5ng/ml. 78 of 188 cases (41%) of malignant disease showed a titer of over 2.5ng/ml; however most positive cases were metastatic, especially to the liver. In metastatic liver cancer, thirtythree out of 46 cases (72%) showed a strongly positive CEA titer. Over 5ng/ml was taken as the lower limit for predicting metastasis to the liver. On the other hand, in primary liver cancer thirty-two out of 35 cases (91%) showed a strongly positive AFP titer over 200ng/ml, although only one case showed a CEA titer over 5ng/ml. Seven cases (15%) of metastatic liver cancer also showed a strongly positive AFP titer; however six of these positive cases showed a CEA titer over 5ng/ml. In metastatic liver cancer, eleven out of 46 cases (24%) showed no clearcut focal defects on liver scintigram. Nine of these negative cases showed a CEA titer over 5ng/ml, and at subsequent operation metastatic liver lesions were found. The overall diagnostic accuracy for detecting metastatic liver cancer with a combination of both methods was 95%. CEA radioimmunoassay was found to be useful for the elucidation of the nature of focal hepatic lesions in addition to AFP radioimmunoassay, and moreover could be used as an adjunct to liver scintigraphy for the detection of metastatic lesions in the liver. (auth.)

  12. Radiological diagnostics of skeletal tumors

    International Nuclear Information System (INIS)

    Uhl, M.; Herget, G.W.

    2008-01-01

    The book contains contributions concerning the following topics: 1. introduction and fundamentals: WHO classification of bone tumors, imaging diagnostics and their function; localization, typical clinical and radiological criteria, TNM classification and status classification, invasive tumor diagnostics; 2. specific tumor diagnostics: chondrogenic bone tumors, osseous tumors, connective tissue bony tumors, osteoclastoma, osteomyelogenic bone tumors, vascular bone tumors, neurogenic bone tumors, chordoma; adamantinoma of the long tubular bone; tumor-like lesions, bony metastases, bone granulomas, differential diagnostics: tumor-like lesions

  13. MLS/Aura Level 2 Nitric Acid (HNO3) Mixing Ratio V003 (ML2HNO3) at GES DISC

    Data.gov (United States)

    National Aeronautics and Space Administration — ML2HNO3 is the EOS Aura Microwave Limb Sounder (MLS) standard product for nitric acid derived from radiances measured by the 240 GHz radiometer at and below 10 hPa,...

  14. MLS/Aura Level 2 Hypochlorous Acid (HOCl) Mixing Ratio V003 (ML2HOCL) at GES DISC

    Data.gov (United States)

    National Aeronautics and Space Administration — ML2HOCL is the EOS Aura Microwave Limb Sounder (MLS) standard product for hypochlorous acid derived from radiances measured primarily by the 640 GHz radiometer. The...

  15. MLS/Aura Level 2 Nitric Acid (HNO3) Mixing Ratio V004 (ML2HNO3) at GES DISC

    Data.gov (United States)

    National Aeronautics and Space Administration — ML2HNO3 is the EOS Aura Microwave Limb Sounder (MLS) standard product for nitric acid derived from radiances measured by the 240 GHz radiometer at and below 10 hPa,...

  16. AstroML: "better, faster, cheaper" towards state-of-the-art data mining and machine learning

    Science.gov (United States)

    Ivezic, Zeljko; Connolly, Andrew J.; Vanderplas, Jacob

    2015-01-01

    We present AstroML, a Python module for machine learning and data mining built on numpy, scipy, scikit-learn, matplotlib, and astropy, and distributed under an open license. AstroML contains a growing library of statistical and machine learning routines for analyzing astronomical data in Python, loaders for several open astronomical datasets (such as SDSS and other recent major surveys), and a large suite of examples of analyzing and visualizing astronomical datasets. AstroML is especially suitable for introducing undergraduate students to numerical research projects and for graduate students to rapidly undertake cutting-edge research. The long-term goal of astroML is to provide a community repository for fast Python implementations of common tools and routines used for statistical data analysis in astronomy and astrophysics (see http://www.astroml.org).

  17. Candidate genes for cross-resistance against DNA-damaging drugs

    DEFF Research Database (Denmark)

    Wittig, Rainer; Nessling, Michelle; Will, Rainer D

    2002-01-01

    Drug resistance of tumor cells leads to major drawbacks in the treatment of cancer. To identify candidate genes for drug resistance, we compared the expression patterns of the drug-sensitive human malignant melanoma cell line MeWo and three derived sublines with acquired resistance to the DNA...... as several apoptosis-related genes, in particular STK17A and CRYAB. As MPP1 and CRYAB are also among the 14 genes differentially expressed in all three of the drug-resistant sublines, they represent the strongest candidates for resistance against DNA-damaging drugs....

  18. A Study on GPU-based Iterative ML-EM Reconstruction Algorithm for Emission Computed Tomographic Imaging Systems

    Energy Technology Data Exchange (ETDEWEB)

    Ha, Woo Seok; Kim, Soo Mee; Park, Min Jae; Lee, Dong Soo; Lee, Jae Sung [Seoul National University, Seoul (Korea, Republic of)

    2009-10-15

    The maximum likelihood-expectation maximization (ML-EM) is the statistical reconstruction algorithm derived from probabilistic model of the emission and detection processes. Although the ML-EM has many advantages in accuracy and utility, the use of the ML-EM is limited due to the computational burden of iterating processing on a CPU (central processing unit). In this study, we developed a parallel computing technique on GPU (graphic processing unit) for ML-EM algorithm. Using Geforce 9800 GTX+ graphic card and CUDA (compute unified device architecture) the projection and backprojection in ML-EM algorithm were parallelized by NVIDIA's technology. The time delay on computations for projection, errors between measured and estimated data and backprojection in an iteration were measured. Total time included the latency in data transmission between RAM and GPU memory. The total computation time of the CPU- and GPU-based ML-EM with 32 iterations were 3.83 and 0.26 sec, respectively. In this case, the computing speed was improved about 15 times on GPU. When the number of iterations increased into 1024, the CPU- and GPU-based computing took totally 18 min and 8 sec, respectively. The improvement was about 135 times and was caused by delay on CPU-based computing after certain iterations. On the other hand, the GPU-based computation provided very small variation on time delay per iteration due to use of shared memory. The GPU-based parallel computation for ML-EM improved significantly the computing speed and stability. The developed GPU-based ML-EM algorithm could be easily modified for some other imaging geometries

  19. nmrML: A Community Supported Open Data Standard for the Description, Storage, and Exchange of NMR Data.

    Science.gov (United States)

    Schober, Daniel; Jacob, Daniel; Wilson, Michael; Cruz, Joseph A; Marcu, Ana; Grant, Jason R; Moing, Annick; Deborde, Catherine; de Figueiredo, Luis F; Haug, Kenneth; Rocca-Serra, Philippe; Easton, John; Ebbels, Timothy M D; Hao, Jie; Ludwig, Christian; Günther, Ulrich L; Rosato, Antonio; Klein, Matthias S; Lewis, Ian A; Luchinat, Claudio; Jones, Andrew R; Grauslys, Arturas; Larralde, Martin; Yokochi, Masashi; Kobayashi, Naohiro; Porzel, Andrea; Griffin, Julian L; Viant, Mark R; Wishart, David S; Steinbeck, Christoph; Salek, Reza M; Neumann, Steffen

    2018-01-02

    NMR is a widely used analytical technique with a growing number of repositories available. As a result, demands for a vendor-agnostic, open data format for long-term archiving of NMR data have emerged with the aim to ease and encourage sharing, comparison, and reuse of NMR data. Here we present nmrML, an open XML-based exchange and storage format for NMR spectral data. The nmrML format is intended to be fully compatible with existing NMR data for chemical, biochemical, and metabolomics experiments. nmrML can capture raw NMR data, spectral data acquisition parameters, and where available spectral metadata, such as chemical structures associated with spectral assignments. The nmrML format is compatible with pure-compound NMR data for reference spectral libraries as well as NMR data from complex biomixtures, i.e., metabolomics experiments. To facilitate format conversions, we provide nmrML converters for Bruker, JEOL and Agilent/Varian vendor formats. In addition, easy-to-use Web-based spectral viewing, processing, and spectral assignment tools that read and write nmrML have been developed. Software libraries and Web services for data validation are available for tool developers and end-users. The nmrML format has already been adopted for capturing and disseminating NMR data for small molecules by several open source data processing tools and metabolomics reference spectral libraries, e.g., serving as storage format for the MetaboLights data repository. The nmrML open access data standard has been endorsed by the Metabolomics Standards Initiative (MSI), and we here encourage user participation and feedback to increase usability and make it a successful standard.

  20. A Study on GPU-based Iterative ML-EM Reconstruction Algorithm for Emission Computed Tomographic Imaging Systems

    International Nuclear Information System (INIS)

    Ha, Woo Seok; Kim, Soo Mee; Park, Min Jae; Lee, Dong Soo; Lee, Jae Sung

    2009-01-01

    The maximum likelihood-expectation maximization (ML-EM) is the statistical reconstruction algorithm derived from probabilistic model of the emission and detection processes. Although the ML-EM has many advantages in accuracy and utility, the use of the ML-EM is limited due to the computational burden of iterating processing on a CPU (central processing unit). In this study, we developed a parallel computing technique on GPU (graphic processing unit) for ML-EM algorithm. Using Geforce 9800 GTX+ graphic card and CUDA (compute unified device architecture) the projection and backprojection in ML-EM algorithm were parallelized by NVIDIA's technology. The time delay on computations for projection, errors between measured and estimated data and backprojection in an iteration were measured. Total time included the latency in data transmission between RAM and GPU memory. The total computation time of the CPU- and GPU-based ML-EM with 32 iterations were 3.83 and 0.26 sec, respectively. In this case, the computing speed was improved about 15 times on GPU. When the number of iterations increased into 1024, the CPU- and GPU-based computing took totally 18 min and 8 sec, respectively. The improvement was about 135 times and was caused by delay on CPU-based computing after certain iterations. On the other hand, the GPU-based computation provided very small variation on time delay per iteration due to use of shared memory. The GPU-based parallel computation for ML-EM improved significantly the computing speed and stability. The developed GPU-based ML-EM algorithm could be easily modified for some other imaging geometries

  1. ART-ML: a new markup language for modelling and representation of biological processes in cardiovascular diseases.

    Science.gov (United States)

    Karvounis, E C; Exarchos, T P; Fotiou, E; Sakellarios, A I; Iliopoulou, D; Koutsouris, D; Fotiadis, D I

    2013-01-01

    With an ever increasing number of biological models available on the internet, a standardized modelling framework is required to allow information to be accessed and visualized. In this paper we propose a novel Extensible Markup Language (XML) based format called ART-ML that aims at supporting the interoperability and the reuse of models of geometry, blood flow, plaque progression and stent modelling, exported by any cardiovascular disease modelling software. ART-ML has been developed and tested using ARTool. ARTool is a platform for the automatic processing of various image modalities of coronary and carotid arteries. The images and their content are fused to develop morphological models of the arteries in 3D representations. All the above described procedures integrate disparate data formats, protocols and tools. ART-ML proposes a representation way, expanding ARTool, for interpretability of the individual resources, creating a standard unified model for the description of data and, consequently, a format for their exchange and representation that is machine independent. More specifically, ARTool platform incorporates efficient algorithms which are able to perform blood flow simulations and atherosclerotic plaque evolution modelling. Integration of data layers between different modules within ARTool are based upon the interchange of information included in the ART-ML model repository. ART-ML provides a markup representation that enables the representation and management of embedded models within the cardiovascular disease modelling platform, the storage and interchange of well-defined information. The corresponding ART-ML model incorporates all relevant information regarding geometry, blood flow, plaque progression and stent modelling procedures. All created models are stored in a model repository database which is accessible to the research community using efficient web interfaces, enabling the interoperability of any cardiovascular disease modelling software

  2. Irradiation effects on the tumor and adjacent tissues of brain tumor-bearing mice

    International Nuclear Information System (INIS)

    Yoshii, Yoshihiko; Maki, Yutaka; Tsunemoto, Hiroshi; Koike, Sachiko; Furukawa, Shigeo.

    1979-01-01

    C 3 H mice aged 56 - 70 days, weighing 27 - 37 g were used throughout this experiment. A transplantable fibrosarcoma arising spontaneously from C 3 H mice was used. For experiment, 10 4 tumor cells suspended in 0.025 ml of saline solution were injected into the cerebral hemisphere by a 26 gauge needle with a micrometer syringe under nembutal anesthesia. Whole brain irradiation was performed at 7 days after injection of the tumor cells and the radiation doses were 2,000 and 20,000 rads, respectively. The feature of x-rays were 200 kVp, 20 mA, 0.5 mm Cu + 0.5 mm Al filtration and TSD 20 cm. The dose-rate was 340 - 360 R/min. The articles of this study were as follows: a) Determination of LD 50 values for the mice, tumor-bearing in the brain or non-tumor-bearing; and b) Observation of clinical features and gross autopsy findings of the mice following irradiation. The LD 50 values for 2,000 rad irradiation in the tumor-bearing or non-tumor-bearing mice were 10.9 and 11.4 days, respectively. LD 50 values of 3.7 days and 4.3 days were the results for the tumor-bearing and non-tumor-bearing mice irradiated by 20,000 rad, respectively. On the other hand, the LD 50 value for the control group, i.e. non-irradiated mice, was 6.7 days. At postmortem examinations, gastrointestinal bleeding was observed frequently in mice bearing tumor in the brain. Whole brain irradiation is effective to prolong the life of tumor-bearing mice. However, in some instances, deaths have occurred earlier in tumor-bearing mice compared to the control group. (author)

  3. Liver Tumors (For Parents)

    Science.gov (United States)

    ... Staying Safe Videos for Educators Search English Español Liver Tumors KidsHealth / For Parents / Liver Tumors What's in this article? Types of Tumors ... Cancerous) Tumors Symptoms Diagnosis Treatment Coping Print The liver is the body's largest solid organ. Lying next ...

  4. Evaluation of Lethal Giant Larvae as a Schistosomiasis Vaccine Candidate

    Directory of Open Access Journals (Sweden)

    Yufan Cao

    2016-01-01

    Full Text Available Schistosomiasis is a neglected tropical disease of humans, and it is considered to be the second most devastating parasitic disease after malaria. Eggs produced by normally developed female worms are important in the transmission of the parasite, and they responsible for the pathogenesis of schistosomiasis. The tumor suppressor gene lethal giant larvae (lgl has an essential function in establishing apical-basal cell polarity, cell proliferation, differentiation, and tissue organization. In our earlier study, downregulation of the lgl gene induced a significant reduction in the egg hatching rate of Schistosoma japonicum (Sj eggs. In this study, the Sjlgl gene was used as a vaccine candidate against schistosomiasis, and vaccination achieved and maintained a stable reduction of the egg hatching rate, which is consistent with previous studies, in addition to reducing the worm burden and liver egg burden in some trials.

  5. Seismogenic structures of the 2006 ML4.0 Dangan Island earthquake offshore Hong Kong

    Science.gov (United States)

    Xia, Shaohong; Cao, Jinghe; Sun, Jinlong; Lv, Jinshui; Xu, Huilong; Zhang, Xiang; Wan, Kuiyuan; Fan, Chaoyan; Zhou, Pengxiang

    2018-02-01

    The northern margin of the South China Sea, as a typical extensional continental margin, has relatively strong intraplate seismicity. Compared with the active zones of Nanao Island, Yangjiang, and Heyuan, seismicity in the Pearl River Estuary is relatively low. However, a ML4.0 earthquake in 2006 occurred near Dangan Island (DI) offshore Hong Kong, and this site was adjacent to the source of the historical M5.8 earthquake in 1874. To reveal the seismogenic mechanism of intraplate earthquakes in DI, we systematically analyzed the structural characteristics in the source area of the 2006 DI earthquake using integrated 24-channel seismic profiles, onshore-offshore wide-angle seismic tomography, and natural earthquake parameters. We ascertained the locations of NW- and NE-trending faults in the DI sea and found that the NE-trending DI fault mainly dipped southeast at a high angle and cut through the crust with an obvious low-velocity anomaly. The NW-trending fault dipped southwest with a similar high angle. The 2006 DI earthquake was adjacent to the intersection of the NE- and NW-trending faults, which suggested that the intersection of the two faults with different strikes could provide a favorable condition for the generation and triggering of intraplate earthquakes. Crustal velocity model showed that the high-velocity anomaly was imaged in the west of DI, but a distinct entity with low-velocity anomaly in the upper crust and high-velocity anomaly in the lower crust was found in the south of DI. Both the 1874 and 2006 DI earthquakes occurred along the edge of the distinct entity. Two vertical cross-sections nearly perpendicular to the strikes of the intersecting faults revealed good spatial correlations between the 2006 DI earthquake and the low to high speed transition in the distinct entity. This result indicated that the transitional zone might be a weakly structural body that can store strain energy and release it as a brittle failure, resulting in an earthquake

  6. Control de la calidad y estudio de estabilidad del paracetamol gotas orales 100 mg/ml

    Directory of Open Access Journals (Sweden)

    Caridad M García Peña

    2013-03-01

    Full Text Available Introducción: las gotas orales de Paracetamol, están indicadas a la población infantil hasta los 5 años para el alivio de la fiebre, dolor de cabeza, dolores dentales y proporciona alivio sintomático del resfriado común. Objetivo: validar dos métodos analíticos, para el control de la calidad y el estudio de estabilidad y estudiar la estabilidad de las gotas orales de producción nacional. Métodos: para cuantificar el principio activo para el estudio de estabilidad, la separación se realizó a través de una columna cromatográfica Lichrosorb RP - 18 (5µm (250 x 4 mm, con detección ultravioleta a 243 nm, empleando una fase móvil compuesta por Agua destilada: Metanol (3:1. Mientras que el método para el control de la calidad se utilizó un Espectrofotómetro SPECTRONIC GENESYS 2.Para el estudio de estabilidad, se emplearon los métodos de vida de estante (a temperatura inferior a 30 º C y de estabilidad acelerada (40 ± 2ºC mediante cromatografía líquida de alta eficiencia. Resultados: los resultados obtenidos de los parámetros evaluados en las validaciones se encontraron dentro de los límites establecidos. Los resultados del estudio de estabilidad realizado, demuestran que el producto terminado cumplió con las especificaciones de calidad durante el estudio. Conclusiones: los métodos analíticos por espectrofotometría UV y cromatografía líquida de alta resolución, son válidos para el control de la calidad y estudio de estabilidad de las gotas orales de Paracetamol 100 mg/mL, ya que resultaron lineales, precisos, exactos y específicos. Se demostró la estabilidad física, química y microbiológica del producto por espacio de 12 meses a temperatura inferior a 30 ºC, envasados en frascos de vidrio ámbar por 15 mL, boca 18 mm, calidad hidrolítica III. Además se evidenció que el producto es estable durante 30 días después de abierto el frasco.

  7. Endocrine tumors other than thyroid tumors

    International Nuclear Information System (INIS)

    Takeichi, Norio; Dohi, Kiyohiko

    1992-01-01

    This paper discusses the tendency for the occurrence of tumors in the endocrine glands, other than the thyroid gland, in A-bomb survivors using both autopsy and clinical data. ABCC-RERF sample data using 4136 autopsy cases (1961-1977) revealed parathyroid tumors in 13 A-bomb survivors, including 3 with the associated hyperparathyroidism, with the suggestion of dose-dependent increase in the occurrence of tumors. Based on clinical data from Hiroshima University, 7 (46.7%) of 15 parathyroid tumors cases were A-bomb survivors. Data (1974-1987) from the Tumor Registry Committee (TRC) in Hiroshima Prefecture revealed that a relative risk of parathyroid tumors was 5.6 times higher in the entire group of A-bomb survivors and 16.2 times higher in the group of heavily exposed A-bomb survivors, suggesting the dose-dependent increase in their occurrence. Adrenal tumors were detected in 47 of 123 cases from the TRC data, and 15 (31.5%) of these 47 were A-bomb survivors. Particularly, 11 cases of adrenal tumors associated with Cushing syndrome included 6 A-bomb survivors (54.5%). The incidence of multiple endocrine gonadial tumors (MEGT) tended to be higher with increasing exposure doses; and the 1-9 rad group, the 10-99 rad group, and the 100 or more rad group had a risk of developing MEGT of 4.1, 5.7, and 7.1, respectively, relative to both the not-in the city group and the 0 rad group. These findings suggested that there is a correlation between A-bomb radiation and the occurrence of parathyroid tumors (including hyperparathyroidism), adrenal tumors associated with Cushing syndrome and MEGT (especially, the combined thyroid and ovarian tumors and the combined thyroid and parathyroid tumors). (N.K.)

  8. Quantification of gastrointestinal liquid volumes and distribution following a 240 mL dose of water in the fasted state.

    Science.gov (United States)

    Mudie, Deanna M; Murray, Kathryn; Hoad, Caroline L; Pritchard, Susan E; Garnett, Martin C; Amidon, Gordon L; Gowland, Penny A; Spiller, Robin C; Amidon, Gregory E; Marciani, Luca

    2014-09-02

    The rate and extent of drug dissolution and absorption from solid oral dosage forms is highly dependent upon the volumes and distribution of gastric and small intestinal water. However, little is known about the time courses and distribution of water volumes in vivo in an undisturbed gut. Previous imaging studies offered a snapshot of water distribution in fasted humans and showed that water in the small intestine is distributed in small pockets. This study aimed to quantify the volume and number of water pockets in the upper gut of fasted healthy humans following ingestion of a glass of water (240 mL, as recommended for bioavailability/bioequivalence (BA/BE) studies), using recently validated noninvasive magnetic resonance imaging (MRI) methods. Twelve healthy volunteers underwent upper and lower abdominal MRI scans before drinking 240 mL (8 fluid ounces) of water. After ingesting the water, they were scanned at intervals for 2 h. The drink volume, inclusion criteria, and fasting conditions matched the international standards for BA/BE testing in healthy volunteers. The images were processed for gastric and intestinal total water volumes and for the number and volume of separate intestinal water pockets larger than 0.5 mL. The fasted stomach contained 35 ± 7 mL (mean ± SEM) of resting water. Upon drinking, the gastric fluid rose to 242 ± 9 mL. The gastric water volume declined rapidly after that with a half emptying time (T50%) of 13 ± 1 min. The mean gastric volume returned back to baseline 45 min after the drink. The fasted small bowel contained a total volume of 43 ± 14 mL of resting water. Twelve minutes after ingestion of water, small bowel water content rose to a maximum value of 94 ± 24 mL contained within 15 ± 2 pockets of 6 ± 2 mL each. At 45 min, when the glass of water had emptied completely from the stomach, total intestinal water volume was 77 ± 15 mL distributed into 16 ± 3 pockets of 5 ± 1 mL each. MRI provided unprecedented insights into

  9. CT of abdominal tumor

    International Nuclear Information System (INIS)

    Endo, Satoshi; Yamada, Kenji; Ito, Masatoshi; Ito, Hisao; Yamaura, Harutsugu

    1981-01-01

    CT findings in 33 patients who had an abdominal tumor were evaluated. CT revealed a tumor in 31 cases. The organ from which the tumor originated was correctly diagnosed in 18 patients. Whether the tumor was solid or cystic was correctly predicted in 28 patients. The diagnosis malignant or benign nature of tumor was correct, incorrect and impossible, in 23, 3, and five patiens, respectively. (Kondo, M.)

  10. 76 FR 4896 - Call for Candidates

    Science.gov (United States)

    2011-01-27

    ... designated to establish generally accepted accounting principles for federal government entities. Generally, non-federal Board members are selected from the general financial community, the accounting and... FEDERAL ACCOUNTING STANDARDS ADVISORY BOARD Call for Candidates AGENCY: Federal Accounting...

  11. Updated candidate list for engineered barrier materials

    International Nuclear Information System (INIS)

    McCright, R.D.

    1995-10-01

    This report describes candidate materials to be evaluated over the next several years during advanced design phases for the waste package to be used for the underground disposal of high-level radioactive wastes at the Yucca Mountain facility

  12. Characterization of nanoparticles as candidate reference materials

    International Nuclear Information System (INIS)

    Martins Ferreira, E.H.; Robertis, E. de; Landi, S.M.; Gouvea, C.P.; Archanjo, B.S.; Almeida, C.A.; Araujo, J.R. de; Kuznetsov, O.; Achete, C.A.

    2013-01-01

    We report the characterization of three different nanoparticles (silica, silver and multi-walled carbon nanotubes) as candidate reference material. We focus our analysis on the size distribution of those particles as measured by different microscopy techniques. (author)

  13. Indico CONFERENCE: Candidate participant's registration/application

    CERN Multimedia

    CERN. Geneva; Ferreira, Pedro

    2017-01-01

    In this tutorial you are going to learn how to apply as a candidate participant (if the event requires approval from the event manager) or to register (if participation to the event doesn't require approval from an event manager) to the conference using the registration form for the event. You are also going to learn how to approve a candidate participant's application as an event manager.

  14. Do People 'Like' Candidates on Facebook?

    DEFF Research Database (Denmark)

    Nielsen, Rasmus Kleis

    The online popularity of a few exceptional candidates has led many to suggest that social media have given politicians powerful ways of communicating directly with voters. In this paper, we examine whether this is happening on a significant scale and show, based on analysis of 224 candidates....... We therefore suggest that the political implications of social media are generally better understood in terms of facilitating indirect communication and institutional change than in terms of direct communication....

  15. Development of an automated extraction method for liver tumors in three dimensional multiphase multislice CT images

    International Nuclear Information System (INIS)

    Nakagawa, Junya; Shimizu, Akinobu; Kobatake, Hidefumi

    2004-01-01

    This paper proposes a tumor detection method using four phase three dimensional (3D) CT images of livers, i.e. non-contrast, early, portal, and late phase images. The method extracts liver regions from the four phase images and enhances tumors in the livers using a 3D adaptive convergence index filter. Then it detects local maximum points and extracts tumor candidates by a region growing method. Subsequently several features of the candidates are measured and each candidate is classified into true tumor or normal tissue based on Mahalanobis distances. Above processes except liver region extraction are applied to four phase images, independently and four resultant images are integrated into one. We applied the proposed method to 3D abdominal CT images of ten patients obtained with multi-detector row CT scanner and confirmed that tumor detection rate was 100% without false positives, which was quite promising results. (author)

  16. Contrail Cirrus Forecasts for the ML-CIRRUS Experiment and Some Comparison Results

    Science.gov (United States)

    Schumann, Ulrich; Graf, Kaspar; Bugliaro, Luca; Dörnbrack, Andreas; Giez, Andreas; Jurkat, Tina; Kaufmann, Stefan; Krämer, Martina; Minikin, Andreas; Schäfler, Andreas; Voigt, Christiane; Wirth, Martin; Zahn, Andreas; Ziereis, Helmut

    2015-04-01

    Model simulations with the contrail cirrus prediction model CoCiP driven by numerical weather prediction (NWP) data provided from the European Centre for Medium Range Forecasts (ECMWF) and global aircraft waypoint data show a mean computed cover (for optical depth larger than 0.1) of 0.23% globally, and 5.4% over mid Europe (Schumann and Graf, JGR, 2013). The computed mean longwave radiative forcing (RF) reaches 3 W m-2 over mid Europe (10°W-20°E and 40°N-55°N), and 0.13 W m-2 globally. The global net RF is about 40-60% smaller because of compensating shortwave cooling induced by contrails during daytime. The results depend on several model details such as the number of ice particles forming from aircraft soot emissions, the contrail plume dispersion, ice particle sedimentation etc., all influencing contrail life time and their optical properties. The quantitative results depend also strongly on ambient relative humidity, vertical motion and on ice water content of other cirrus predicted by the NWP model. In order to test and possibly improve this and other contrail models, high-quality observations are needed to which multi-parameter model output can be compared. The Mid-Latitude Cirrus Experiment ML-CIRRUS was performed (see C. Voigt et al., this conference) with a suite of in-situ and Lidar instruments for airborne measurements on the research aircraft HALO. Before and during the mission, CoCiP was run daily to provide 3-days forecasts of contrail cover using operational ECMWF forecasts and historical traffic data. CoCiP forecast output was made available in an internet tool twice a day for experiment planning. The one-day and two-day contrail forecasts often showed only small differences. Still, most recent forecasts and detailed satellite observations results were transmitted via satellite link to the crew for onboard campaign optimization. After the campaign, a data base of realistic air traffic data has been setup from various sources, and CoCiP was

  17. A New Way to Confirm Planet Candidates

    Science.gov (United States)

    Kohler, Susanna

    2016-05-01

    What was the big deal behind the Kepler news conference yesterday? Its not just that the number of confirmed planets found by Kepler has more than doubled (though thats certainly exciting news!). Whats especially interesting is the way in which these new planets were confirmed.Number of planet discoveries by year since 1995, including previous non-Kepler discoveries (blue), previous Kepler discoveries (light blue) and the newly validated Kepler planets (orange). [NASA Ames/W. Stenzel; Princeton University/T. Morton]No Need for Follow-UpBefore Kepler, the way we confirmed planet candidates was with follow-up observations. The candidate could be validated either by directly imaging (which is rare) or obtaining a large number radial-velocity measurements of the wobble of the planets host star due to the planets orbit. But once Kepler started producing planet candidates, these approaches to validation became less feasible. A lot of Kepler candidates are small and orbit faint stars, making follow-up observations difficult or impossible.This problem is what inspired the development of whats known as probabilistic validation, an analysis technique that involves assessing the likelihood that the candidates signal is caused by various false-positive scenarios. Using this technique allows astronomers to estimate the likelihood of a candidate signal being a true planet detection; if that likelihood is high enough, the planet candidate can be confirmed without the need for follow-up observations.A breakdown of the catalog of Kepler Objects of Interest. Just over half had previously been identified as false positives or confirmed as candidates. 1284 are newly validated, and another 455 have FPP of1090%. [Morton et al. 2016]Probabilistic validation has been used in the past to confirm individual planet candidates in Kepler data, but now Timothy Morton (Princeton University) and collaborators have taken this to a new level: they developed the first code thats designed to do fully

  18. Activation of Relaxin Family Receptor 1 from different mammalian species by relaxin peptide and small molecule agonist ML290

    Directory of Open Access Journals (Sweden)

    Zaohua eHuang

    2015-08-01

    Full Text Available Relaxin peptide (RLN, which signals through the relaxin family peptide 1 (RXFP1 GPCR receptor, has shown therapeutic effects in an acute heart failure clinical trial. We have identified a small molecule agonist of human RXFP1, ML290; however, it does not activate the mouse receptor. To find a suitable animal model for ML290 testing and to gain mechanistic insights into the interaction of various ligands with RXFP1, we have cloned rhesus macaque, pig, rabbit, and guinea pig RXFP1s and analyzed their activation by RLN and ML290. HEK293T cells expressing macaque or pig RXFP1 responded to relaxin and ML290 treatment as measured by an increase of cAMP production. Guinea pig RXFP1 responded to relaxin but had very low response to ML290 treatment only at highest concentrations used. The rabbit RXFP1 amino acid sequence was the most divergent, with a number of unique substitutions within the ectodomain and the 7-transmembrane domain (7TM. Two splice variants of rabbit RXFP1 derived through alternative splicing of the forth exon were identified. In contrast to the other species, rabbit RXFP1s were activated by ML290, but not with human, pig, mouse, or rabbit relaxins. Using FLAG-tagged constructs, we have shown that both rabbit RXFP1 variants are expressed on the cell surface. No binding of human Eu-labeled relaxin to rabbit RXFP1 was detected, suggesting that in this species RXFP1 might be non-functional. We used chimeric rabbit-human and guinea pig-human constructs to identify regions important for RLN or ML290 receptor activation. Chimeras with the human ectodomain and rabbit 7TM domain were activated by RLN, whereas substitution of part of the guinea pig 7TM domain with the human sequence only partially restored ML290 activation, confirming the allosteric mode of action for the two ligands. Our data demonstrate that macaque and pig models can be used for ML290 testing.

  19. Tumor macroenvironment and metabolism.

    Science.gov (United States)

    Al-Zoughbi, Wael; Al-Zhoughbi, Wael; Huang, Jianfeng; Paramasivan, Ganapathy S; Till, Holger; Pichler, Martin; Guertl-Lackner, Barbara; Hoefler, Gerald

    2014-04-01

    In this review we introduce the concept of the tumor macroenvironment and explore it in the context of metabolism. Tumor cells interact with the tumor microenvironment including immune cells. Blood and lymph vessels are the critical components that deliver nutrients to the tumor and also connect the tumor to the macroenvironment. Several factors are then released from the tumor itself but potentially also from the tumor microenvironment, influencing the metabolism of distant tissues and organs. Amino acids, and distinct lipid and lipoprotein species can be essential for further tumor growth. The role of glucose in tumor metabolism has been studied extensively. Cancer-associated cachexia is the most important tumor-associated systemic syndrome and not only affects the quality of life of patients with various malignancies but is estimated to be the cause of death in 15%-20% of all cancer patients. On the other hand, systemic metabolic diseases such as obesity and diabetes are known to influence tumor development. Furthermore, the clinical implications of the tumor macroenvironment are explored in the context of the patient's outcome with special consideration for pediatric tumors. Finally, ways to target the tumor macroenvironment that will provide new approaches for therapeutic concepts are described. Copyright © 2014 Elsevier Inc. All rights reserved.

  20. JELLYFISH GALAXY CANDIDATES AT LOW REDSHIFT

    Energy Technology Data Exchange (ETDEWEB)

    Poggianti, B. M.; Fasano, G.; Omizzolo, A.; Gullieuszik, M.; Bettoni, D.; Paccagnella, A. [INAF-Astronomical Observatory of Padova (Italy); Moretti, A.; D’Onofrio, M. [Physics and Astronomy Department, University of Padova (Italy); Jaffé, Y. L. [Department of Astronomy, Universidad de Concepción, Concepción (Chile); Vulcani, B. [Kavli Institute for the Physics and Mathematics of the universe (WPI), The University of Tokyo Institutes for Advanced Study (UTIAS), the University of Tokyo, Kashiwa, 277-8582 (Japan); Fritz, J. [Centro de Radioastronomía y Astrofísica, CRyA, UNAM, Michoacán (Mexico); Couch, W. [Australian Astronomical Observatory, North Ryde, NSW 1670 (Australia)

    2016-03-15

    Galaxies that are being stripped of their gas can sometimes be recognized from their optical appearance. Extreme examples of stripped galaxies are the so-called “jellyfish galaxies” that exhibit tentacles of debris material with a characteristic jellyfish morphology. We have conducted the first systematic search for galaxies that are being stripped of their gas at low-z (z = 0.04−0.07) in different environments, selecting galaxies with varying degrees of morphological evidence for stripping. We have visually inspected B- and V-band images and identified 344 candidates in 71 galaxy clusters of the OMEGAWINGS+WINGS sample and 75 candidates in groups and lower mass structures in the PM2GC sample. We present the atlas of stripping candidates and a first analysis of their environment and their basic properties, such as morphologies, star formation rates and galaxy stellar masses. Candidates are found in all clusters and at all clustercentric radii, and their number does not correlate with the cluster velocity dispersion σ or X-ray luminosity L{sub X}. Interestingly, convincing cases of candidates are also found in groups and lower mass halos (10{sup 11}−10{sup 14}M{sub ⊙}), although the physical mechanism at work needs to be securely identified. All the candidates are disky, have stellar masses ranging from log M/M{sub ⊙} < 9 to > 11.5 and the majority of them form stars at a rate that is on average a factor of 2 higher (2.5σ) compared to non-stripped galaxies of similar mass. The few post-starburst and passive candidates have weak stripping evidence. We conclude that disturbed morphologies suggestive of stripping phenomena are ubiquitous in clusters and could be present even in groups and low mass halos. Further studies will reveal the physics of the gas stripping and clarify the mechanisms at work.

  1. Fine physical and genetic mapping of powdery mildew resistance gene MlIW172 originating from wild emmer (Triticum dicoccoides.

    Directory of Open Access Journals (Sweden)

    Shuhong Ouyang

    Full Text Available Powdery mildew, caused by Blumeria graminis f. sp. tritici, is one of the most important wheat diseases in the world. In this study, a single dominant powdery mildew resistance gene MlIW172 was identified in the IW172 wild emmer accession and mapped to the distal region of chromosome arm 7AL (bin7AL-16-0.86-0.90 via molecular marker analysis. MlIW172 was closely linked with the RFLP probe Xpsr680-derived STS marker Xmag2185 and the EST markers BE405531 and BE637476. This suggested that MlIW172 might be allelic to the Pm1 locus or a new locus closely linked to Pm1. By screening genomic BAC library of durum wheat cv. Langdon and 7AL-specific BAC library of hexaploid wheat cv. Chinese Spring, and after analyzing genome scaffolds of Triticum urartu containing the marker sequences, additional markers were developed to construct a fine genetic linkage map on the MlIW172 locus region and to delineate the resistance gene within a 0.48 cM interval. Comparative genetics analyses using ESTs and RFLP probe sequences flanking the MlIW172 region against other grass species revealed a general co-linearity in this region with the orthologous genomic regions of rice chromosome 6, Brachypodium chromosome 1, and sorghum chromosome 10. However, orthologous resistance gene-like RGA sequences were only present in wheat and Brachypodium. The BAC contigs and sequence scaffolds that we have developed provide a framework for the physical mapping and map-based cloning of MlIW172.

  2. QuakeML: Recent Development and First Applications of the Community-Created Seismological Data Exchange Standard

    Science.gov (United States)

    Euchner, F.; Schorlemmer, D.; Kästli, P.; Quakeml Group, T

    2008-12-01

    QuakeML is an XML-based exchange format for seismological data which is being developed using a community-driven approach. It covers basic event description, including picks, arrivals, amplitudes, magnitudes, origins, focal mechanisms, and moment tensors. Contributions have been made from ETH, GFZ, USC, SCEC, USGS, IRIS DMC, EMSC, ORFEUS, GNS, ZAMG, BRGM, and ISTI. The current release (Version 1.1, Proposed Recommendation) reflects the results of a public Request for Comments process which has been documented online at http://quakeml.org/RFC_BED_1.0. QuakeML has recently been adopted as a distribution format for earthquake catalogs by GNS Science, New Zealand, and the European-Mediterranean Seismological Centre (EMSC). These institutions provide prototype QuakeML web services. Furthermore, integration of the QuakeML data model in the CSEP (Collaboratory for the Study of Earthquake Predictability, http://www.cseptesting.org) testing center software developed by SCEC is under way. QuakePy is a Python- based seismicity analysis toolkit which is based on the QuakeML data model. Recently, QuakePy has been used to implement the PMC method for calculating network recording completeness (Schorlemmer and Woessner 2008, in press). Completeness results for seismic networks in Southern California and Japan can be retrieved through the CompletenessWeb (http://completenessweb.org). Future QuakeML development will include an extension for macroseismic information. Furthermore, development on seismic inventory information, resource identifiers, and resource metadata is under way. Online resources: http://www.quakeml.org, http://www.quakepy.org

  3. Therapy reduction in patients with Down syndrome and myeloid leukemia: the international ML-DS 2006 trial.

    Science.gov (United States)

    Uffmann, Madita; Rasche, Mareike; Zimmermann, Martin; von Neuhoff, Christine; Creutzig, Ursula; Dworzak, Michael; Scheffers, Lenie; Hasle, Henrik; Zwaan, C Michel; Reinhardt, Dirk; Klusmann, Jan-Henning

    2017-06-22

    Children with myeloid leukemia associated with Down syndrome (ML-DS) have superior outcome compared with non-DS patients, but suffer from higher constitutional cytotoxic drug susceptibility. We analyzed the outcome of 170 pediatric patients with ML-DS enrolled in the prospective, multicenter, open-label, nonrandomized ML-DS 2006 trial by Nordic Society for Pediatric Hematology and Oncology (NOPHO), Dutch Childhood Oncology Group (DCOG), and Acute Myeloid Leukemia-Berlin-Frankfurt-Münster (AML-BFM) study group. Compared with the historical control arm (reduced-intensity protocol for ML-DS patients from the AML-BFM 98 trial), treatment intensity was reduced by lowering the cumulative dose of etoposide (950 to 450 mg/m 2 ) and intrathecal central nervous system prophylaxis while omitting maintenance therapy. Still, 5-year overall survival (89% ± 3% vs 90% ± 4%; P log-rank = .64), event-free survival (EFS; 87% ± 3% vs 89% ± 4%; P log-rank = .71), and cumulative incidence of relapse/nonresponse (CIR/NR; 6% ± 3% vs 6% ± 2%; P Gray = .03) did not significantly differ between the ML-DS 2006 trial and the historical control arm. Poor early treatment response (5-year EFS, 58% ± 16% vs 88% ± 3%; P log rank = .0008) and gain of chromosome 8 (CIR/NR, 16% ± 7% vs 3% ± 2%, P Gray = .02; 5-year EFS, 73% ± 8% vs 91% ± 4%, P log rank = .018) were identified as independent prognostic factors predicting a worse EFS. Five of 7 relapsed patients (71%) with cytogenetic data had trisomy 8. Our study reveals prognostic markers for children with ML-DS and illustrates that reducing therapy did not impair excellent outcome. The trial was registered at EudraCT as #2007-006219-2. © 2017 by The American Society of Hematology.

  4. Characterization of ML0314c of Mycobacterium leprae and deciphering its role in the immune response in leprosy patients.

    Science.gov (United States)

    Kaur, Gurkamajit; Sharma, Aashish; Narang, Tarun; Dogra, Sunil; Kaur, Jagdeep

    2018-02-15

    Mycobacterium leprae has a reduced genome size due to the reductive evolution over a long period of time. Lipid metabolism plays an important role in the life cycle and pathogenesis of this bacterium. In comparison to 26 lip genes (Lip A-Z) of M. tuberculosis, M. leprae retained only three orthologs indicating their importance in its life cycle. ML0314c (LipU) is one of them. It is conserved throughout the mycobacterium species. Bioinformatics analysis showed the presence of an α/β hydrolase fold and 'GXSXG' characteristic of the esterases/lipases. The gene was expressed in E. coli and purified to homogeneity. It showed preference towards short chain esters with pNP-acetate as the preferred substrate. The enzyme showed optimal activity at 45°C and pH8.0. ML0314c protein was stable between temperatures ranging from 20 to 60°C and pH5.0-8.0, i.e., relatively acidic and neutral conditions. The active site residues predicted bioinformatically were confirmed to be Ser168, Glu267, and His297 by site directed mutagenesis. E-serine, DEPC and Tetrahydrolipstatin (THL) completely inhibited the activity of ML0314c. The protein was localized in cell wall and extracellular medium. Several antigenic epitopes were predicted in ML0314c. Protein elicited strong humoral immune response in leprosy patients, whereas, a reduced immune response was observed in the relapsed cases. No humoral response was observed in treatment completed patients. Overexpression of ml0314c in the surrogate host M. smegmatis showed marked difference in the colony morphology and growth rate. In conclusion, ML0314c is a secretary carboxyl esterase that could modulate the immune response in leprosy patients. Copyright © 2017 Elsevier B.V. All rights reserved.

  5. Bronchial carcinoid tumors: A rare malignant tumor

    African Journals Online (AJOL)

    2015-02-03

    Feb 3, 2015 ... Nigerian Journal of Clinical Practice • Sep-Oct 2015 • Vol 18 • Issue 5. Abstract. Bronchial carcinoid tumors (BCTs) are an uncommon group of lung tumors. They commonly affect the young adults and the middle aged, the same age group affected by other more common chronic lung conditions such as ...

  6. Postoperative Urinary Catheterization Thresholds of 500 versus 800 ml after Fast-track Total Hip and Knee Arthroplasty

    DEFF Research Database (Denmark)

    Bjerregaard, Lars Stryhn; Hornum, Ulla Marianne; Troldborg, C.

    2016-01-01

    arthroplasty (THA) and total knee arthroplasty (TKA). METHODS: This was a randomized, controlled, open-label trial that included patients greater than or equal to 18 yr who underwent THA or TKA in three Danish, fast-track, orthopedic departments. Consenting patients were eligible if they were cooperative......BACKGROUND: No evidence-based threshold exists for postoperative urinary bladder catheterization. The authors hypothesized that a catheterization threshold of 800 ml was superior to 500 ml in reducing postoperative urinary catheterization and urological complications after fast-track total hip...

  7. ML-Space: Hybrid Spatial Gillespie and Particle Simulation of Multi-Level Rule-Based Models in Cell Biology.

    Science.gov (United States)

    Bittig, Arne T; Uhrmacher, Adelinde M

    2017-01-01

    Spatio-temporal dynamics of cellular processes can be simulated at different levels of detail, from (deterministic) partial differential equations via the spatial Stochastic Simulation algorithm to tracking Brownian trajectories of individual particles. We present a spatial simulation approach for multi-level rule-based models, which includes dynamically hierarchically nested cellular compartments and entities. Our approach ML-Space combines discrete compartmental dynamics, stochastic spatial approaches in discrete space, and particles moving in continuous space. The rule-based specification language of ML-Space supports concise and compact descriptions of models and to adapt the spatial resolution of models easily.

  8. Transformation of Arden Syntax's medical logic modules into ArdenML for a business rules management system.

    Science.gov (United States)

    Jung, Chai Young; Choi, Jong-Ye; Jeong, Seong Jik; Cho, Kyunghee; Koo, Yong Duk; Bae, Jin Hee; Kim, Sukil

    2016-05-16

    Arden Syntax is a Health Level Seven International (HL7) standard language that is used for representing medical knowledge as logic statements. Arden Syntax Markup Language (ArdenML) is a new representation of Arden Syntax based on XML. Compilers are required to execute medical logic modules (MLMs) in the hospital environment. However, ArdenML may also replace the compiler. The purpose of this study is to demonstrate that MLMs, encoded in ArdenML, can be transformed into a commercial rule engine format through an XSLT stylesheet and made executable in a target system. The target rule engine selected was Blaze Advisor. We developed an XSLT stylesheet to transform MLMs in ArdenML into Structured Rules Language (SRL) in Blaze Advisor, through a comparison of syntax between the two languages. The stylesheet was then refined recursively, by building and applying rules collected from the billing and coding guidelines of the Korean health insurance service. Two nurse coders collected and verified the rules and two information technology (IT) specialists encoded the MLMs and built the XSLT stylesheet. Finally, the stylesheet was validated by importing the MLMs into Blaze Advisor and applying them to claims data. The language comparison revealed that Blaze Advisor requires the declaration of variables with explicit types. We used both integer and real numbers for numeric types in ArdenML. "IF∼THEN" statements and assignment statements in ArdenML become rules in Blaze Advisor. We designed an XSLT stylesheet to solve this issue. In addition, we maintained the order of rule execution in the transformed rules, and added two small programs to support variable declarations and action statements. A total of 1489 rules were reviewed during this study, of which 324 rules were collected. We removed duplicate rules and encoded 241 unique MLMs in ArdenML, which were successfully transformed into SRL and imported to Blaze Advisor via the XSLT stylesheet. When applied to 73

  9. The tumor vasculature is a target for genetic radiotherapy

    International Nuclear Information System (INIS)

    Mauceri, Helena J.; Heimann, Ruth; Seetharam, Saraswathy; Beckett, Michael A.; Weichselbaum, Ralph R.

    1997-01-01

    Purpose: Tumor progression and metastasis require the growth of new capillaries from existing blood vessels. Tumor cells produce both activators and inhibitors of endothelial cell proliferation and migration. Changes in the balance between these regulators appear to govern an angiogenic switch which is activated during tumor development. Tumor necrosis factor-α (TNF-α) has a biphasic role in angiogenesis. It has been demonstrated that relatively low concentrations of TNF induce angiogenesis while high doses inhibit growth of blood vessels. In our previous studies, using the SQ-20B xenograft model system, we demonstrated increased tumor control when a virus containing the radiation-inducible promoter Egr-1 ligated to a cDNa for TNF-α was combined with radiation. The dominant histopathological feature of tumors receiving combined treatment with Ad.Egr-TNF and radiation was intratumoral vascular thrombosis. The present studies examine the role of TNF in tumor progression by investigating the effects of TNF on VEGF (vascular endothelial growth factor) production in vitro and on tumor vessel count in vivo. Methods: SQ-20B tumor cells in serum-free medium were exposed to hrTNF (10 ng/ml) 4 hours prior to a single dose of x-irradiation (10 Gy). 24 hrs. after treatment, the conditioned medium was harvested, centrifuged, diluted 1:10, and assayed for VEGF using a Quantikine TNF ELISA kit. For studies in vivo, female nude mice were injected sc in the right thigh with 10 6 SQ-20B cells. Xenografts were irradiated with four 5 Gy fractions (20 Gy) and injected twice with either Ad.Egr-TNF or Ad.null. Control tumors were injected with buffer. To highlight vessels, sections from paraffin embedded tissue were stained with anti-CD31 antibody using standard immunohistochemical techniques. Areas of high vascular density were identified and five high power fields (400X) were counted. Data are shown as the mean ± S.E.M. for each treatment group. Significance was evaluated using one

  10. PREOPERATIVE ENDOSCOPIC MARKING OF UNPALPABLE COLONIC TUMORS

    Directory of Open Access Journals (Sweden)

    A. L. Goncharov

    2013-01-01

    Full Text Available The identification of small colon lesions is one of the major problems in laparoscopic colonic resection.Research objective: to develop a technique of visualization of small tumors of a colon by preoperative endoscopic marking of a tumor.Materials and methods. In one day prior to operation to the patient after bowel preparation the colonoscopy is carried out. In the planned point near tumor on antimesentery edge the submucous infiltration of marking solution (Micky Sharpz blue tattoo pigment, UK is made. The volume of entered solution of 1–3 ml. In only 5 months of use of a technique preoperative marking to 14 patients with small (the size of 1–3 cm malignant tumors of the left colon is performed.Results. The tattoo mark was well visualized by during operation at 13 of 14 patients. In all cases we recorded no complications. Time of operation with preoperative marking averaged 108 min, that is significantly less in comparison with average time of operation with an intra-operative colonoscopy – 155 min (р < 0.001.Conclusions. The first experience of preoperative endoscopic marking of non palpable small tumors of a colon is encouraging. Performance of a technique wasn't accompanied by complications and allowed to reduce significantly time of operation and to simplify conditions of performance of operation.

  11. Preoperative trans-arterial embolization for spinal tumor: embolization techniques and results

    International Nuclear Information System (INIS)

    Shi Haibin; Xu Daizhe

    2000-01-01

    Objective: To analyze the technique and to evaluate the safety and value of preoperative trans-arterial embolization of hypervascular spinal tumors. Methods: Eighteen patients with hypervascular spinal tumors underwent trans-arterial embolization before surgery. They arose intradural in six patients and extradural in 12. Thirty-one arteries were embolized with polyvinyl alcohol (PVA) particles (150-500 μm), of which 18 with additional pieces of gelatin sponge for proximal pedicular embolization. The criteria for judging the effectiveness of embolization were the completeness of tumor removal and estimated blood loss during surgery. Results: Tumor embolization with total occlusion was obtained in eight patients, second to total in seven, subtotal in one, and partial in two. There were no symptomatic complications associated with embolization. Tumors were totally removed in 17 patients and nearly totally removed in one. The average estimated blood loss during surgery was 1100 ml (range, 200-6000 ml) for all 18 patients, and 1540 ml in patients with extradural tumors. Conclusions: Preoperative embolization of hypervascular spinal tumors is safe and effective. It can make complete resection of a tumor possible and can make an unresectable tumor resectable. Superselection or flow control is necessary to achieve effective devascularization and avoid complications

  12. Scalar tetraquark candidates on the lattice

    International Nuclear Information System (INIS)

    Berlin, Joshua

    2017-01-01

    The topic of this thesis is the investigation of scalar tetraquark candidates from lattice QCD. It is motivated by a previous study originating in the twisted mass collaboration. The initial tetraquark candidate of choice is the a 0 (980), an isovector in the nonet of light scalars (J P =0 + ). This channel is still poorly understood. It displays an inverted mass hierarchy to what is expected from the conventional quark model and the a 0 (980) and f 0 (980) feature a surprising mass degeneracy. For this reasons the a 0 (980) is a long assumed tetraquark candidate in the literature. We follow a methodological approach by studying the sensitivity of the scalar spectrum with fully dynamical quarks to a large basis of two-quark and four-quark creation operators. Ultimately, the candidate has to be identified in the direct vicinity of two two-particles states, which is understandably inevitable for a tetraquark candidate. To succeed in this difficult task two-meson creation operators are essential to employ in this channel. By localized four-quark operators we intend to probe the Hamiltonian on eigenstates with a closely bound four-quark structure.

  13. Scalar tetraquark candidates on the lattice

    Energy Technology Data Exchange (ETDEWEB)

    Berlin, Joshua

    2017-07-01

    The topic of this thesis is the investigation of scalar tetraquark candidates from lattice QCD. It is motivated by a previous study originating in the twisted mass collaboration. The initial tetraquark candidate of choice is the a{sub 0}(980), an isovector in the nonet of light scalars (J{sup P}=0{sup +}). This channel is still poorly understood. It displays an inverted mass hierarchy to what is expected from the conventional quark model and the a{sub 0}(980) and f{sub 0}(980) feature a surprising mass degeneracy. For this reasons the a{sub 0}(980) is a long assumed tetraquark candidate in the literature. We follow a methodological approach by studying the sensitivity of the scalar spectrum with fully dynamical quarks to a large basis of two-quark and four-quark creation operators. Ultimately, the candidate has to be identified in the direct vicinity of two two-particles states, which is understandably inevitable for a tetraquark candidate. To succeed in this difficult task two-meson creation operators are essential to employ in this channel. By localized four-quark operators we intend to probe the Hamiltonian on eigenstates with a closely bound four-quark structure.

  14. Body surface area adapted iopromide 300 mg/ml versus 370 mg/ml contrast medium injection protocol: Influence on quantitative and clinical assessment in combined PET/CT

    Energy Technology Data Exchange (ETDEWEB)

    Verburg, Frederik A., E-mail: fverburg@ukaachen.de [RWTH Aachen University Hospital, Department of Nuclear Medicine, Pauwelsstraße 30, 52074 Aachen (Germany); Maastricht University Medical Center, Department of Nuclear Medicine, P. Debyelaan 25, 6229 HX Maastricht (Netherlands); Apitzsch, Jonas [RWTH Aachen University Hospital, Department of Diagnostic and Interventional Radiology, Pauwelsstraße 30, 52074 Aachen (Germany); Lensing, Carina [RWTH Aachen University Hospital, Department of Nuclear Medicine, Pauwelsstraße 30, 52074 Aachen (Germany); Kuhl, Christiane K. [RWTH Aachen University Hospital, Department of Diagnostic and Interventional Radiology, Pauwelsstraße 30, 52074 Aachen (Germany); Pietsch, Hubertus [Bayer Pharma AG, Müllerstrasse 178, 13353 Berlin (Germany); Mottaghy, Felix M. [RWTH Aachen University Hospital, Department of Nuclear Medicine, Pauwelsstraße 30, 52074 Aachen (Germany); Maastricht University Medical Center, Department of Nuclear Medicine, P. Debyelaan 25, 6229 HX Maastricht (Netherlands); Behrendt, Florian F. [RWTH Aachen University Hospital, Department of Nuclear Medicine, Pauwelsstraße 30, 52074 Aachen (Germany)

    2013-12-01

    Purpose: To investigate the quantitative and qualitative differences between combined positron emission tomography and computed X-ray tomography (PET/CT) enhanced with contrast medium with either an iodine concentration 300 mg/ml or 370 mg/ml. Materials and methods: 120 consecutive patients scheduled for F-18-Fluorodeoxyglucose (FDG) PET/CT were included. The first (second) 60 patients received contrast medium with 300 (370) mg iodine/ml. Intravenous injection protocols were adapted for an identical iodine delivery rate (1.3 mg/s) and body surface area (BSA) adapted iodine dose (22.26 g I/m{sup 2}). Maximum and mean standardized uptake values (SUV{sub max}; SUV{sub mean}) and contrast enhancement (HU) were determined in the ascending aorta, the abdominal aorta, the inferior vena cava, the portal vein, the liver and the right kidney in the venous contrast medium phase. PET data were evaluated visually for the presence of malignancy and image quality. Results: Both media caused significantly higher values for HU, SUV{sub mean} and SUV{sub max} for the enhanced PET/CT than the non-enhanced one (all p < 0.01). There were no significant differences in the degree of increase of HU, SUV{sub mean} and SUV{sub max} between the two contrast media at any anatomic site (all p > 0.05). Visual evaluation of lesions showed no differences between contrast and non-contrast PET/CT or between the two different contrast media (p = 0.77). Conclusion: When using a constant iodine delivery rate and total iodine dose in a BSA adapted injection protocol, there are no quantitative or qualitative differences in either CT or PET between contrast media with an iodine concentration of 300 mg/ml and 370 mg/ml, respectively.

  15. [Isolation and identification of brain tumor stem cells from human brain neuroepithelial tumors].

    Science.gov (United States)

    Fang, Jia-sheng; Deng, Yong-wen; Li, Ming-chu; Chen, Feng-Hua; Wang, Yan-jin; Lu, Ming; Fang, Fang; Wu, Jun; Yang, Zhuan-yi; Zhou, Xang-yang; Wang, Fei; Chen, Cheng

    2007-01-30

    To establish a simplified culture system for the isolation of brain tumor stem cells (BTSCs) from the tumors of human neuroepithelial tissue, to observe the growth and differentiation pattern of BTSCs, and to investigate their expression of the specific markers. Twenty-six patients with brain neuroepithelial tumors underwent tumor resection. Two pieces of tumor tissues were taken from each tumor to be dissociated, triturated into single cells in sterile DMEM-F12 medium, and then filtered. The tumor cells were seeded at a concentration of 200,000 viable cells per mL into serum-free DMEM-F12 medium simply supplemented with B27, human basic fibroblast growth factor (20 microg/L), human epidermal growth factor (20 microg /L), insulin (4 U/L), L-glutamine, penicillin and streptomycin. After the primary brain tumor spheres (BTSs) were generated, they were triturated again and passed in fresh medium. Limiting dilution assay was performed to observe the monoclone formation. 5-bromodeoxyuridine (BrdU) incorporation test was performed to observe the proliferation of the BTS. The BTSCs were cultured in mitogen-free DMEM-F12 medium supplemented with 10% fetal bovine serum to observe their differentiation. Immunocytochemistry was used to examine the expression of CD133 and nestin, specific markers of BTSC, and the rate of CD133 positive cells. Only a minority of subsets of cells from the tumors of neuroepithelial tissue had the capacity to survive, proliferate, and generate free-floating neurosphere-like BTSs in the simplified serum-free medium. These cells attached to the poly-L-lysine coated coverslips in the serum-supplemented medium and differentiated. The BTSCs were CD133 and nestin positive. The rate of CD133 positive cells in the tumor specimens was (21 +/- 6.2)% - (38 +/- 7.0)%. A new simplified culture system for the isolation of BTSCs is established. The tumors of human neuroepithelial tissue contain CD133 and nestin positive tumor stem cells which can be isolated

  16. Children's Brain Tumor Foundation

    Science.gov (United States)

    ... 2 Family Donate Volunteer Justin's Hope Fund Children’s Brain Tumor Foundation, A non-profit organization, was founded ... and the long term outlook for children with brain and spinal cord tumors through research, support, education, ...

  17. Metaphyseal giant cell tumor

    International Nuclear Information System (INIS)

    Pereira, L.F.; Hemais, P.M.P.G.; Aymore, I.L.; Carmo, M.C.R. do; Cunha, M.E.P.R. da; Resende, C.M.C.

    1986-01-01

    Three cases of metaphyseal giant cell tumor are presented. A review of the literature is done, demostrating the lesion is rare and that there are few articles about it. Age incidence and characteristics of the tumor are discussed. (Author) [pt

  18. Testicular germinal tumors

    International Nuclear Information System (INIS)

    Fresco, R.

    2010-01-01

    This work is about diagnosis, treatment and monitoring of testicular germinal tumors. The presumed diagnosis is based in the anamnesis, clinical examination, testicular ultrasound and tumor markers. The definitive diagnosis is obtained through the inguinal radical orchidectomy

  19. Cancer-associated adipocytes promotes breast tumor radioresistance

    Energy Technology Data Exchange (ETDEWEB)

    Bochet, Ludivine; Meulle, Aline [Universite de Toulouse, UPS, F-31077 Toulouse Cedex (France); CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), 205 route de Narbonne, BP 64182, F-31077 Toulouse Cedex (France); Institut National de la Sante et de la Recherche Medicale, INSERM U1048, 1 Avenue du Pr Jean Poulhes, BP 84225, F-31432 Toulouse Cedex (France); Imbert, Sandrine [CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), 205 route de Narbonne, BP 64182, F-31077 Toulouse Cedex (France); Salles, Bernard [Universite de Toulouse, UPS, F-31077 Toulouse Cedex (France); CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), 205 route de Narbonne, BP 64182, F-31077 Toulouse Cedex (France); Valet, Philippe [Universite de Toulouse, UPS, F-31077 Toulouse Cedex (France); Institut National de la Sante et de la Recherche Medicale, INSERM U1048, 1 Avenue du Pr Jean Poulhes, BP 84225, F-31432 Toulouse Cedex (France); Muller, Catherine, E-mail: muller@ipbs.fr [Universite de Toulouse, UPS, F-31077 Toulouse Cedex (France); CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), 205 route de Narbonne, BP 64182, F-31077 Toulouse Cedex (France)

    2011-07-22

    Highlights: {yields} Tumor-surrounding adipocytes contribute to breast cancer progression. {yields} Breast tumor cells previously co-cultivated with mature adipocytes exhibit radioresistance. {yields} Increased in Chk1 phosphorylation is observed in irradiated co-cultivated tumor cells. {yields} IL-6 is over-expressed in tumor cells co-cultivated with adipocytes. {yields} IL-6 exposure confers increased Chk1 phosphorylation and radioresistance in tumor cells. -- Abstract: Mature adipocytes are excellent candidates to influence tumor behavior through heterotypic signaling processes since these cells produce hormones, growth factors, cytokines and other molecules, a heterogeneous group of molecules named adipokines. Using a 2D coculture system, we demonstrate that breast tumor cells previously co-cultivated with mature adipocytes exhibit radioresistance and an earlier and higher increase in the effector kinase Chk1, a phenotype that was associated with decreased cell death as compared to tumor cells grown alone. Interestingly, the adipocytes-induced tumor changes taking place during the coculture time preceding the exposure to IR were sufficient to confer the radioresistant effect. Notorious among the changes brought by adipocytes was the significant increase of IL-6 expression in tumor cells, whose activity may well account for the observed tumor cell protection from IR toxicity. Indeed, our data confirmed the protective role of this cytokine as tumor cells incubated after irradiation with recombinant IL-6 exhibit an increased in Chk1 phosphorylation and a radioresistant phenotype, thus far recapitulating the effects observed in the presence of adipocytes. Our current study sheds light on a new role of tumor-surrounding adipocytes in fostering a radioresistant phenotype in breast tumors, a finding that might have important clinical implications in obese patients that frequently exhibit aggressive diseases.

  20. Application of detecting cerebrospinal fluid circulating tumor cells in the diagnosis of meningeal metastasis of non-small cell lung cancer

    Directory of Open Access Journals (Sweden)

    Rong JIANG

    2014-08-01

    Full Text Available Objective To observe a new technology for the detection and enumeration of cerebrospinal fluid (CSF circulating tumor cells (CTCs in the diagnosis of non-small cell lung cancer (NSCLC with meningeal metastasis (MM.  Methods Five cases of NSCLC with MM that were diagnosed by CSF cytology were selected, and 20 ml CSF samples were obtained by lumbar puncture for every patient. The tumor marker immunostaining-fluorescence in situ hybridization (TM-iFISH technology was adapted to detect enrichment and enumeration of circulating tumor cells in 7.50 ml CSF samples; CSF cytology was checked in 10 ml CSF samples; CSF tumor markers were detected in 2.50 ml CSF samples. All of 5 cases were examined by MRI enhancement scan.  Results TM-iFISH detection found circulating tumor cells numbers ranging 18-1823/7.50 ml. Only 2 cases of patients with CSF cytology examination showed the tumor cells. The results of CSF tumor markers in all samples were higher than normal serum tumor markers detection results. The enhanced MRI scan of 5 cases revealed typical signs of MM.  Conclusions The TM-iFISH test showed certain advantages in the detection of malignant tumor cells in CSF. This technology may be a new method of detection and enumeration of tumor cells in CSF, but more studies are needed to prove its sensitivity and specificity. doi: 10.3969/j.issn.1672-6731.2014.08.011

  1. Developing Potential Candidates of Preclinical Preeclampsia

    Directory of Open Access Journals (Sweden)

    Sandra Founds

    2015-11-01

    Full Text Available The potential for developing molecules of interest in preclinical preeclampsia from candidate genes that were discovered on gene expression microarray analysis has been challenged by limited access to additional first trimester trophoblast and decidual tissues. The question of whether these candidates encode secreted proteins that may be detected in maternal circulation early in pregnancy has been investigated using various proteomic methods. Pilot studies utilizing mass spectrometry based proteomic assays, along with enzyme linked immunosorbent assays (ELISAs, and Western immunoblotting in first trimester samples are reported. The novel targeted mass spectrometry methods led to robust multiple reaction monitoring assays. Despite detection of several candidates in early gestation, challenges persist. Future antibody-based studies may lead to a novel multiplex protein panel for screening or detection to prevent or mitigate preeclampsia.

  2. The Chances of Subsequent Cancer Detection in Patients with a PSA > 20 ng/ml and an Initial Negative Biopsy

    Directory of Open Access Journals (Sweden)

    Nadeem Shaida

    2009-01-01

    Full Text Available Transrectal ultrasound (TRUS–guided prostate biopsy is known to carry a significant false-negative rate, leading some patients to have multiple biopsies. We investigated cancer detection rates in patients with a PSA >20 ng/ml and a negative initial biopsy. We reviewed our database of 2396 TRUS-guided biopsies done between 1997 and 2002 in order to give a follow-up of at least 6 years. PSA, PSA density (PSAD, PSA velocity (PSAV, prostate volume, and DRE findings were analysed in relation to cancer status. Of the patients, 388 (16% had a PSA >20 ng/ml, including 99 (26% with benign biopsies. Of those, 67 were rebiopsied, including 19 (28% with cancer on the first rebiopsy and four (6% on further biopsies. PSAD, DRE, and volume significantly differed between rebiopsied patients with and without cancer (p 20 ng/ml and have an initial negative biopsy have a high chance of malignancy being detected on a second biopsy. However, if a second biopsy is also negative, then the chances of subsequent biopsies showing signs of cancer are very low if the DRE is normal and particularly if the PSAD is >0.35 ng/ml/cm3.

  3. Plane-dependent ML scatter scaling: 3D extension of the 2D simulated single scatter (SSS) estimate

    Science.gov (United States)

    Rezaei, Ahmadreza; Salvo, Koen; Vahle, Thomas; Panin, Vladimir; Casey, Michael; Boada, Fernando; Defrise, Michel; Nuyts, Johan

    2017-08-01

    Scatter correction is typically done using a simulation of the single scatter, which is then scaled to account for multiple scatters and other possible model mismatches. This scaling factor is determined by fitting the simulated scatter sinogram to the measured sinogram, using only counts measured along LORs that do not intersect the patient body, i.e. ‘scatter-tails’. Extending previous work, we propose to scale the scatter with a plane dependent factor, which is determined as an additional unknown in the maximum likelihood (ML) reconstructions, using counts in the entire sinogram rather than only the ‘scatter-tails’. The ML-scaled scatter estimates are validated using a Monte-Carlo simulation of a NEMA-like phantom, a phantom scan with typical contrast ratios of a 68Ga-PSMA scan, and 23 whole-body 18F-FDG patient scans. On average, we observe a 12.2% change in the total amount of tracer activity of the MLEM reconstructions of our whole-body patient database when the proposed ML scatter scales are used. Furthermore, reconstructions using the ML-scaled scatter estimates are found to eliminate the typical ‘halo’ artifacts that are often observed in the vicinity of high focal uptake regions.

  4. Tumor associated osteoclast-like giant cells promote tumor growth and lymphangiogenesis by secreting vascular endothelial growth factor-C

    International Nuclear Information System (INIS)

    Hatano, Yu; Nakahama, Ken-ichi; Isobe, Mitsuaki; Morita, Ikuo

    2014-01-01

    Highlights: • M-CSF and RANKL expressing HeLa cells induced osteoclastogenesis in vitro. • We established OGC-containing tumor model in vivo. • OGC-containing tumor became larger independent of M-CSF or RANKL effect. • VEGF-C secreted from OGCs was a one of candidates for OGC-containing tumor growth. - Abstract: Tumors with osteoclast-like giant cells (OGCs) have been reported in a variety of organs and exert an invasive and prometastatic phenotype, but the functional role of OGCs in the tumor environment has not been fully clarified. We established tumors containing OGCs to clarify the role of OGCs in tumor phenotype. A mixture of HeLa cells expressing macrophage colony-stimulating factor (M-CSF, HeLa-M) and receptor activator of nuclear factor-κB ligand (RANKL, HeLa-R) effectively supported the differentiation of osteoclast-like cells from bone marrow macrophages in vitro. Moreover, a xenograft study showed OGC formation in a tumor composed of HeLa-M and HeLa-R. Surprisingly, the tumors containing OGCs were significantly larger than the tumors without OGCs, although the growth rates were not different in vitro. Histological analysis showed that lymphangiogenesis and macrophage infiltration in the tumor containing OGCs, but not in other tumors were accelerated. According to quantitative PCR analysis, vascular endothelial growth factor (VEGF)-C mRNA expression increased with differentiation of osteoclast-like cells. To investigate whether VEGF-C expression is responsible for tumor growth and macrophage infiltration, HeLa cells overexpressing VEGF-C (HeLa-VC) were established and transplanted into mice. Tumors composed of HeLa-VC mimicked the phenotype of the tumors containing OGCs. Furthermore, the vascular permeability of tumor microvessels also increased in tumors containing OGCs and to some extent in VEGF-C-expressing tumors. These results suggest that macrophage infiltration and vascular permeability are possible mediators in these tumors. These

  5. Tumor interstitial fluid

    DEFF Research Database (Denmark)

    Gromov, Pavel; Gromova, Irina; Olsen, Charlotta J.

    2013-01-01

    Tumor interstitial fluid (TIF) is a proximal fluid that, in addition to the set of blood soluble phase-borne proteins, holds a subset of aberrantly externalized components, mainly proteins, released by tumor cells and tumor microenvironment through various mechanisms, which include classical...

  6. Interaction of Sr-90 with site candidate soil for demonstration disposal facility at Serpong

    Energy Technology Data Exchange (ETDEWEB)

    Setiawan, Budi, E-mail: bravo@batan.go.id [Radwaste Technology Center-National Nuclear Energy Agency, PUSPIPTEK, Serpong-Tangerang 15310 (Indonesia); Mila, Oktri; Safni [Dept. of Chemistry, Fac. of Math. and Nat. Sci., Andalas University, Kampus Limau Manis, Padang-West Sumatra 25163 (Indonesia)

    2014-03-24

    Interaction of radiostrontium (Sr-90) with site candidate soil for demonstration disposal facility to be constructed in the near future at Serpong has been done. This activity is to anticipate the interim storage facility at Serpong nuclear area becomes full off condition, and show to the public how radioactive waste can be well managed with the existing technology. To ensure that the location is save, a reliability study of site candidate soil becomes very importance to be conducted through some experiments consisted some affected parameters such as contact time, effect of ionic strength, and effect of Sr{sup +} ion in solution. Radiostrontium was used as a tracer on the experiments and has role as radionuclide reference in low-level radioactive waste due to its long half-live and it's easy to associate with organism in nature. So, interaction of radiostrontium and soil samples from site becomes important to be studied. Experiment was performed in batch method, and soil sample-solution containing radionuclide was mixed in a 20 ml of PE vial. Ratio of solid: liquid was 10{sup −2} g/ml. Objective of the experiment is to collect the specific characteristics data of radionuclide sorption onto soil from site candidate. Distribution coefficient value was used as indicator where the amount of initial and final activities of radiostrontium in solution was compared. Result showed that equilibrium condition was reached after contact time 10 days with Kd values ranged from 1600-2350 ml/g. Increased in ionic strength in solution made decreased of Kd value into soil sample due to competition of background salt and radiostrontium into soil samples, and increased in Sr ion in solution caused decreased of Kd value in soil sample due to limitation of sorption capacity in soil samples. Fast condition in saturated of metal ion into soil samples was reached due to a simple reaction was occurred.

  7. P18 tumor suppressor gene and progression of oligodendrogliomas to anaplasia.

    Science.gov (United States)

    He, J; Hoang-Xuan, K; Marie, Y; Leuraud, P; Mokhtari, K; Kujas, M; Delattre, J Y; Sanson, M

    2000-09-26

    P18INK4C is a good candidate to be the tumor suppressor gene involved in oligodendrogliomas on 1p32. Loss of heterozygosity on 1p, mutation(s), homozygous deletion(s), and expression of p18 in 30 oligodendroglial tumors were investigated. Loss of heterozygosity on 1p was found in 15 tumors. A p18 mutation was found at an recurrence of an anaplastic oligodendroglioma, but not in the primary, low-grade tumor. No homozygous deletions were found and p18 was expressed in all cases. These results show that p18 alteration is involved in tumor progression in a subset of oligodendrogliomas.

  8. Issue-Advocacy versus Candidate Advertising: Effects on Candidate Preferences and Democratic Process.

    Science.gov (United States)

    Pfau, Michael; Holbert, R. Lance; Szabo, Erin Alison; Kaminski, Kelly

    2002-01-01

    Examines the influence of soft-money-sponsored issue-advocacy advertising in U.S. House and Senate campaigns, comparing its effects against candidate-sponsored positive advertising and contrast advertising on viewers' candidate preferences and on their attitude that reflect democratic values. Reveals no main effects for advertising approach on…

  9. A multicenter evaluation of seven commercial ML-EM algorithms for SPECT image reconstruction using simulation data

    International Nuclear Information System (INIS)

    Matsumoto, Keiichi; Ohnishi, Hideo; Niida, Hideharu; Nishimura, Yoshihiro; Wada, Yasuhiro; Kida, Tetsuo

    2003-01-01

    The maximum likelihood expectation maximization (ML-EM) algorithm has become available as an alternative to filtered back projection in SPECT. The actual physical performance may be different depending on the manufacturer and model, because of differences in computational details. The purpose of this study was to investigate the characteristics of seven different types of ML-EM algorithms using simple simulation data. Seven ML-EM algorithm programs were used: Genie (GE), esoft (Siemens), HARP-III (Hitachi), GMS-5500UI (Toshiba), Pegasys (ADAC), ODYSSEY-FX (Marconi), and Windows-PC (original software). Projection data of a 2-pixel-wide line source in the center of the field of view were simulated without attenuation or scatter. Images were reconstructed with ML-EM by changing the number of iterations from 1 to 45 for each algorithm. Image quality was evaluated after a reconstruction using full width at half maximum (FWHM), full width at tenth maximum (FWTM), and the total counts of the reconstructed images. In the maximum number of iterations, the difference in the FWHM value was up to 1.5 pixels, and that of FWTM, no less than 2.0 pixels. The total counts of the reconstructed images in the initial few iterations were larger or smaller than the converged value depending on the initial values. Our results for the simplest simulation data suggest that each ML-EM algorithm itself provides a simulation image. We should keep in mind which algorithm is being used and its computational details, when physical and clinical usefulness are compared. (author)

  10. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.

    Science.gov (United States)

    Guindon, Stéphane; Dufayard, Jean-François; Lefort, Vincent; Anisimova, Maria; Hordijk, Wim; Gascuel, Olivier

    2010-05-01

    PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm performing nearest neighbor interchanges to improve a reasonable starting tree topology. Since the original publication (Guindon S., Gascuel O. 2003. A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704), PhyML has been widely used (>2500 citations in ISI Web of Science) because of its simplicity and a fair compromise between accuracy and speed. In the meantime, research around PhyML has continued, and this article describes the new algorithms and methods implemented in the program. First, we introduce a new algorithm to search the tree space with user-defined intensity using subtree pruning and regrafting topological moves. The parsimony criterion is used here to filter out the least promising topology modifications with respect to the likelihood function. The analysis of a large collection of real nucleotide and amino acid data sets of various sizes demonstrates the good performance of this method. Second, we describe a new test to assess the support of the data for internal branches of a phylogeny. This approach extends the recently proposed approximate likelihood-ratio test and relies on a nonparametric, Shimodaira-Hasegawa-like procedure. A detailed analysis of real alignments sheds light on the links between this new approach and the more classical nonparametric bootstrap method. Overall, our tests show that the last version (3.0) of PhyML is fast, accurate, stable, and ready to use. A Web server and binary files are available from http://www.atgc-montpellier.fr/phyml/.

  11. PET and endocrine tumors

    International Nuclear Information System (INIS)

    Rigo, P.; Belhocine, T.; Hustinx, R.; Foidart-Willems, J.

    2000-01-01

    The authors review the main indications of PET examination, and specifically of 18 FDG, in the assessment of endocrine tumors: of the thyroid, of the parathyroid, of the adrenal and of the pituitary glands. Neuroendocrine tumors, gastro-entero-pancreatic or carcinoid tumors are also under the scope. Usually, the most differentiated tumors show only poor uptake of the FDG as they have a weak metabolic and proliferative activity. In the assessment of endocrine tumors, FDG-PET should be used only after most specific nuclear examinations been performed. (author)

  12. Tumor penetrating peptides

    Directory of Open Access Journals (Sweden)

    Tambet eTeesalu

    2013-08-01

    Full Text Available Tumor-homing peptides can be used to deliver drugs into tumors. Phage library screening in live mice has recently identified homing peptides that specifically recognize the endothelium of tumor vessels, extravasate, and penetrate deep into the extravascular tumor tissue. The prototypic peptide of this class, iRGD (CRGDKGPDC, contains the integrin-binding RGD motif. RGD mediates tumor homing through binding to αv integrins, which are selectively expressed on various cells in tumors, including tumor endothelial cells. The tumor-penetrating properties of iRGD are mediated by a second sequence motif, R/KXXR/K. This C-end Rule (or CendR motif is active only when the second basic residue is exposed at the C-terminus of the peptide. Proteolytic processing of iRGD in tumors activates the cryptic CendR motif, which then binds to neuropilin-1 activating an endocytic bulk transport pathway through tumor tissue. Phage screening has also yielded tumor-penetrating peptides that function like iRGD in activating the CendR pathway, but bind to a different primary receptor. Moreover, novel tumor-homing peptides can be constructed from tumor-homing motifs, CendR elements and protease cleavage sites. Pathologies other than tumors can be targeted with tissue-penetrating peptides, and the primary receptor can also be a vascular zip code of a normal tissue. The CendR technology provides a solution to a major problem in tumor therapy, poor penetration of drugs into tumors. The tumor-penetrating peptides are capable of taking a payload deep into tumor tissue in mice, and they also penetrate into human tumors ex vivo. Targeting with these peptides specifically increases the accumulation in tumors of a variety of drugs and contrast agents, such as doxorubicin, antibodies and nanoparticle-based compounds. Remarkably the drug to be targeted does not have to be coupled to the peptide; the bulk transport system activated by the peptide sweeps along any compound that is

  13. Can tumor uptake Tc-99m MDP ?

    International Nuclear Information System (INIS)

    Yand Shun, Fang; Yao, Ming; Zeng, Jun; Shi Zhen, Yu; Zhao Lan, Xiang; Dong Qiang, Gang

    2003-01-01

    To explore the mechanism of technetium-99m-methylene diphosphonate (MDP) uptake within tumor through analyze a distribution of Tc-99m MDP in mice bearing tumor cell lines. Methods: The uptake of Tc-99m MDP was analyzed in seven human tumor cell lines ( SPC-A1 adenocarcinoma of lung cancer, Bcap-37 Breast cancer, T-24 Bladder cancer, SKOV3 Ovary carcinoma, Hela-229 Cervical carcinoma, SCI-OS Osteosarcoma, SCI-375 Melanoma) and mouse Lewis lung cancer cell line. They were transplanted into athymic mice, SCID nude mice and C57BL/6 mice, respectively. Approximately 10(6) cells of each cell line were injected subcutaneously into a right chest of mouse. After 4 and 5 weeks, the Tc-99m MDP scintigraphy were determined 6 hours after tail vein injection of 74MBq in 0.05ml every mouse. Result: Biodistribution and tumor uptake MDP was different in the various cell types investigated. According to the Region Ratio program of Siemens Power Macintosh 9500 Computer System, region of interests (RIOs) placed on a small part of the tumor and horizontal copied to left background (T/B) and thoracic spine (T/N) of mice in Tc-99m MDP imaging. The average cpm/pixel ratios were calculated by standardized uptake measure (SUM) and determined the tumor-positive value (T/B) greater than or equal to 1.2. T/B of cell lines were sorted from higher to lower as follows: SCI-OS, Lewis, SKOV3, SCI-375, T-24, SPC-A1, Bcap-37, Hela-229. T/N: SCI-OS, SKOV3, T-24, SCI-375, Lewis, SPC-A1, Bcap-37, Hela-229. The biodistribution data of 99Tcm-MDP in SPC-A1 tumor-bearing BALB/c nude mice were given as ID/g and represent the means D (n=13) in 30 hours after injection of Tc-99m MDP. ID/g of major tissue were sorted from higher to lower as follows: thoracic spine, lumbar, ribs, kidneys, the center of tumor, the ulcer of tumor, the surrounding of tumor, lymph node, blood, lungs, heart, liver. Conclusions: Most of tumor can uptake Tc-99m MDP including human adenocarcinoma. The uptake rate in the center tissue of

  14. Desempenho de idosos brasileiros no teste de deglutição de 100 ml de água Performance of Brazilian elderly on the 100 ml water swallowing test

    Directory of Open Access Journals (Sweden)

    Graziela Maria Martins Moreira

    2012-03-01

    Full Text Available OBJETIVO: Comparar o desempenho de idosos brasileiros, residentes em uma instituição de longa permanência, no teste de deglutição de 100 ml de água com os resultados obtidos em idosos ingleses. MÉTODOS: Dezoito idosos residentes numa instituição de longa permanência, considerados normais para a função de deglutição (13 mulheres e cinco homens, com idade média de 83,46 anos foram solicitados a beber 100 ml de água de um copo plástico, reproduzindo o estudo inglês. O avaliador observou lateralmente o número de goles, tempo gasto e intercorrências, gerando três índices: volume por deglutição (ml, tempo por deglutição (s e capacidade de deglutição (ml/s. RESULTADOS: A capacidade de deglutição para homens foi menor do que a das mulheres, divergindo do estudo original. O tempo médio de cada deglutição e o volume médio por deglutição foi semelhante para ambos os gêneros. CONCLUSÃO: A capacidade de deglutição em idosos é inferior à de adultos normais, indicando lentificação da deglutição. A diferença entre gêneros encontrada no estudo original não foi reproduzida, entretanto nossa amostra foi mais idosa.PURPOSE: To compare the performance of Brazilian elderly patients living in a long-term care facility on the 100 ml water swallowing test with the results obtained with British elderly. METHODS: Eighteen elderly subjects (13 women and five men, mean age 83.46, residents in a long-term care facility and considered normal regarding the swallowing function, were selected to take part in this study. As in a British study, they were laterally observed by the examiner while swallowing 100 ml of water from a plastic cup. The examiner observed the number of sips, the time taken, and complications during the test, which generated the following indices: volume per swallow (ml, time per swallow (s, and swallowing capacity (ml/s. RESULTS: The elderly men had lower swallowing capacity than the women in the research

  15. Optical observations of southern planetary nebula candidates

    NARCIS (Netherlands)

    VandeSteene, GC; Sahu, KC; Pottasch, [No Value

    1996-01-01

    We present H alpha+[NII] images and low resolution spectra of 16 IRAS-selected, southern planetary nebula candidates previously detected in the radio continuum. The H alpha+[NII] images are presented as finding charts. Contour plots are shown for the resolved planetary nebulae. From these images

  16. 47 CFR 73.1942 - Candidate rates.

    Science.gov (United States)

    2010-10-01

    ... Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) BROADCAST RADIO SERVICES RADIO BROADCAST SERVICES Rules Applicable to All Broadcast Stations § 73.1942 Candidate rates. (a) Charges for use of stations... periods. Any station practices offered to commercial advertisers that enhance the value of advertising...

  17. Candidate genes in ocular dominance plasticity

    NARCIS (Netherlands)

    Rietman, M.L.; Sommeijer, J.-P.; Levelt, C.N.; Heimel, J.A.; Brussaard, A.B.; Borst, J.G.G.; Elgersma, Y.; Galjart, N.; van der Horst, G.T.; Pennartz, C.M.; Smit, A.B.; Spruijt, B.M.; Verhage, M.; de Zeeuw, C.I.

    2012-01-01

    Many studies have been devoted to the identification of genes involved in experience-dependent plasticity in the visual cortex. To discover new candidate genes, we have reexamined data from one such study on ocular dominance (OD) plasticity in recombinant inbred BXD mouse strains. We have correlated

  18. Fuzzy Treatment of Candidate Outliers in Measurements

    Directory of Open Access Journals (Sweden)

    Giampaolo E. D'Errico

    2012-01-01

    Full Text Available Robustness against the possible occurrence of outlying observations is critical to the performance of a measurement process. Open questions relevant to statistical testing for candidate outliers are reviewed. A novel fuzzy logic approach is developed and exemplified in a metrology context. A simulation procedure is presented and discussed by comparing fuzzy versus probabilistic models.

  19. Gallium-67 imaging in candidal esophagitis

    International Nuclear Information System (INIS)

    Rundback, J.H.; Goldfarb, C.R.; Ongseng, F.

    1990-01-01

    Ga-67 scanning has been used to evaluate esophageal carcinoma. It has demonstrated candidal infection in other body sites and, in one previous case, in the esophagus. The authors present a case of diffuse esophageal uptake of Ga-67 in esophageal candidiasis

  20. Gallium-67 imaging in candidal esophagitis

    Energy Technology Data Exchange (ETDEWEB)

    Rundback, J.H.; Goldfarb, C.R.; Ongseng, F. (Beth Israel Medical Center, New York, NY (USA))

    1990-01-01

    Ga-67 scanning has been used to evaluate esophageal carcinoma. It has demonstrated candidal infection in other body sites and, in one previous case, in the esophagus. The authors present a case of diffuse esophageal uptake of Ga-67 in esophageal candidiasis.

  1. Towards Treating Chemistry Teacher Candidates as Human

    Science.gov (United States)

    Lewthwaite, Brian Ellis

    2008-01-01

    This research inquiry investigates the factors influencing chemistry teacher candidates' development during their extended practica in the second and final year of an After-Degree Bachelor of Education at a university in central Canada. A variety of data sources are used to identify the risk and protective factors impeding and contributing to the…

  2. Promoting Team Leadership Skills in Doctoral Candidates

    Science.gov (United States)

    Suleiman, Mahmoud; Whetton, Danny

    2014-01-01

    Doctoral programs can serve as an optimal opportunity for candidates to engage in tasks and activities to transform them and their schools. The paradigm shifts in such preparation involve moving from sitting and getting to making and taking. Most importantly, it requires building leadership skills and styles necessary to bring about desired change…

  3. Query by image example: The CANDID approach

    Energy Technology Data Exchange (ETDEWEB)

    Kelly, P.M.; Cannon, M. [Los Alamos National Lab., NM (United States). Computer Research and Applications Group; Hush, D.R. [Univ. of New Mexico, Albuquerque, NM (United States). Dept. of Electrical and Computer Engineering

    1995-02-01

    CANDID (Comparison Algorithm for Navigating Digital Image Databases) was developed to enable content-based retrieval of digital imagery from large databases using a query-by-example methodology. A user provides an example image to the system, and images in the database that are similar to that example are retrieved. The development of CANDID was inspired by the N-gram approach to document fingerprinting, where a ``global signature`` is computed for every document in a database and these signatures are compared to one another to determine the similarity between any two documents. CANDID computes a global signature for every image in a database, where the signature is derived from various image features such as localized texture, shape, or color information. A distance between probability density functions of feature vectors is then used to compare signatures. In this paper, the authors present CANDID and highlight two results from their current research: subtracting a ``background`` signature from every signature in a database in an attempt to improve system performance when using inner-product similarity measures, and visualizing the contribution of individual pixels in the matching process. These ideas are applicable to any histogram-based comparison technique.

  4. Waiting narratives of lung transplant candidates.

    Science.gov (United States)

    Yelle, Maria T; Stevens, Patricia E; Lanuza, Dorothy M

    2013-01-01

    Before 2005, time accrued on the lung transplant waiting list counted towards who was next in line for a donor lung. Then in 2005 the lung allocation scoring system was implemented, which meant the higher the illness severity scores, the higher the priority on the transplant list. Little is known of the lung transplant candidates who were listed before 2005 and were caught in the transition when the lung allocation scoring system was implemented. A narrative analysis was conducted to explore the illness narratives of seven lung transplant candidates between 2006 and 2007. Arthur Kleinman's concept of illness narratives was used as a conceptual framework for this study to give voice to the illness narratives of lung transplant candidates. Results of this study illustrate that lung transplant candidates expressed a need to tell their personal story of waiting and to be heard. Recommendation from this study calls for healthcare providers to create the time to enable illness narratives of the suffering of waiting to be told. Narrative skills of listening to stories of emotional suffering would enhance how healthcare providers could attend to patients' stories and hear what is most meaningful in their lives.

  5. Waiting Narratives of Lung Transplant Candidates

    Directory of Open Access Journals (Sweden)

    Maria T. Yelle

    2013-01-01

    Full Text Available Before 2005, time accrued on the lung transplant waiting list counted towards who was next in line for a donor lung. Then in 2005 the lung allocation scoring system was implemented, which meant the higher the illness severity scores, the higher the priority on the transplant list. Little is known of the lung transplant candidates who were listed before 2005 and were caught in the transition when the lung allocation scoring system was implemented. A narrative analysis was conducted to explore the illness narratives of seven lung transplant candidates between 2006 and 2007. Arthur Kleinman’s concept of illness narratives was used as a conceptual framework for this study to give voice to the illness narratives of lung transplant candidates. Results of this study illustrate that lung transplant candidates expressed a need to tell their personal story of waiting and to be heard. Recommendation from this study calls for healthcare providers to create the time to enable illness narratives of the suffering of waiting to be told. Narrative skills of listening to stories of emotional suffering would enhance how healthcare providers could attend to patients’ stories and hear what is most meaningful in their lives.

  6. Epilepsy and Brain Tumors

    Institute of Scientific and Technical Information of China (English)

    Zhi-yi Sha

    2009-01-01

    @@ Epidemiology It is estimated 61,414 new cases of primary brain tumors are expected to be diagnosed in 2009 in the U.S. The incidence statistic of 61,414 persons diagnosed per year includes both malignant (22,738) and non-malignant (38,677) brain tumors. (Data from American Brain Tumor Association). During the years 2004-2005, approximately 359,000 people in the United States were living with the diagnosis of a primary brain or central nervous system tumor. Specifically, more than 81,000 persons were living with a malignant tumor, more than 267,000 persons with a benign tumor. For every 100,000 people in the United States, approximately 131 are living following the diagnosis of a brain tumor. This represents a prevalence rate of 130.8 per 100,000 person years[1].

  7. Localization of thymosin ß-4 in tumors

    DEFF Research Database (Denmark)

    Larsson, Lars-Inge; Holck, Susanne

    2007-01-01

    carcinomas. The degree of staining of breast cancer cells for thymosin ß-4 correlated neither to histological grade nor to endothelial cell staining. However, therewas a tendency toward correlation (P = 0.07) between staining of endothelial cells and histological grade. Treatment of cultured breast cancer......Overexpression of thymosin ß-4 has been linked to malignant progression but the localization of this polypeptide within tumor is incompletely known. We therefore examined breast cancers for thymosin ß-4 using immunofluorescence. Reactive cells were identified with monoclonal cell marker antibodies...... cells (SK-BR-3) with 1-4 µg thymosin ß-4/mL significantly increased cell numbers, as determined by MTT-assays. These data reveal an unexpected cellular heterogeneity of thymosin ß-4 expression in breast and colonic carcinomas and suggest that local release of this polypeptide in the tumor...

  8. Comparison of fundamental and wideband harmonic contrast imaging of liver tumors.

    Science.gov (United States)

    Forsberg, F; Liu, J B; Chiou, H J; Rawool, N M; Parker, L; Goldberg, B B

    2000-03-01

    Wideband harmonic imaging (with phase inversion for improved tissue suppression) was compared to fundamental imaging in vivo. Four woodchucks with naturally occurring liver tumors were injected with Imagent (Alliance Pharmaceutical Corp., San Diego, CA). Randomized combinations of dose (0.05, 0.2 and 0.4 ml/kg) and acoustic output power (AO; 5, 25 and 63% or MI Siemens Medical Systems, Issaquah, WA). Tumor vascularity, conspicuity and contrast enhancement were rated by three independent observers. Imagent produced marked tumor enhancement and improved depiction of neovascularity at all dosages and AO settings in both modes. Tumor vascularity and enhancement correlated with mode, dose and AO (P < 0.002). Fundamental imaging produced more enhancement (P < 0.05), but tumor vascularity and conspicuity were best appreciated in harmonic mode (P < 0.05). Under the conditions studied here, the best approach was wideband harmonic imaging with 0.2 ml/kg of Imagent at an AO of 25%.

  9. Potentials and limitations of low-concentration contrast medium (150 mg iodine/ml) in CT pulmonary angiography

    International Nuclear Information System (INIS)

    Radon, M.R.; Kaduthodil, M.J.; Jagdish, J.; Matthews, S.; Hill, C.; Bull, M.J.; Morcos, S.K.

    2011-01-01

    Aim: To assess the feasibility of producing diagnostic multidetector computed tomography (MDCT) pulmonary angiography with low iodine concentration contrast media (150 mg iodine/ml) in patients with suspected acute pulmonary embolism. Materials and methods: Ninety-five randomized patients underwent MDCT (64 row) pulmonary angiography with 100 ml iopromide either at low concentration (LC) of 150 mg iodine/ml (n = 45) or high concentration (HC) of 300 mg iodine/ml (n = 50), delivered at the rate of 5 ml/s via a power injector. Two experienced radiologists, blinded to the concentration used, subjectively assessed the diagnostic quality and confidence using a four-point scale [1 = poor (not diagnostic), 2 = satisfactory, 3 = good, 4 = excellent]. Attenuation values (in HU) were measured in the main proximal branches of the pulmonary arteries. Results: The median diagnostic quality score for both observers was 3.5 (interquartile range 3-4) in the HC group and 2.5 (interquartile range 1.5-3) in the LC group (p < 0.01). The median diagnostic confidence score for both observers was 4 (interquartile range 3-4) in the HC group and 3 (interquartile range 1.5-4) in the LC group (p < 0.01). Both observers rated examinations as diagnostic in 69% of cases in the LC group, compared with 96% of cases in the HC group. Good interobserver agreement was found in both groups (K value 0.72 in the LC group and 0.73 in the HC). Obesity, poor scan timing, and dilution by venous return of non-opacified blood were the main reasons for a reduction in diagnostic quality of examinations in the LC group. Conclusion: Despite a 50% reduction of contrast medium dose in comparison to the standard technique, 150 mg iodine/ml can produce diagnostic MDCT pulmonary angiogram studies in the absence of obesity or high cardiac output and hyper-dynamic pulmonary circulation. Reducing the dose of contrast media would minimize the risk of contrast nephropathy in patients at risk of this complication

  10. Behavioral and functional neuroanatomical correlates of anterograde autobiographical memory in isolated retrograde amnesic patient M.L.

    Science.gov (United States)

    Levine, Brian; Svoboda, Eva; Turner, Gary R; Mandic, Marina; Mackey, Allison

    2009-09-01

    Patient M.L. [Levine, B., Black, S. E., Cabeza, R., Sinden, M., Mcintosh, A. R., Toth, J. P., et al. (1998). Episodic memory and the self in a case of isolated retrograde amnesia. Brain, 121, 1951-1973], lost memory for events occurring before his severe traumatic brain injury, yet his anterograde (post-injury) learning and memory appeared intact, a syndrome known as isolated or focal retrograde amnesia. Studies with M.L. demonstrated a dissociation between episodic and semantic memory. His retrograde amnesia was specific to episodic autobiographical memory. Convergent behavioral and functional imaging data suggested that his anterograde memory, while appearing normal, was accomplished with reduced autonoetic awareness (awareness of the self as a continuous entity across time that is a crucial element of episodic memory). While previous research on M.L. focused on anterograde memory of laboratory stimuli, in this study, M.L.'s autobiographical memory for post-injury events or anterograde autobiographical memory was examined using prospective collection of autobiographical events via audio diary with detailed behavioral and functional neuroanatomical analysis. Consistent with his reports of subjective disconnection from post-injury autobiographical events, M.L. assigned fewer "remember" ratings to his autobiographical events than comparison subjects. His generation of event-specific details using the Autobiographical Interview [Levine, B., Svoboda, E., Hay, J., Winocur, G., & Moscovitch, M. (2002). Aging and autobiographical memory: dissociating episodic from semantic retrieval. Psychology and Aging, 17, 677-689] was low, but not significantly so, suggesting that it is possible to generate episodic-like details even when re-experiencing of those details is compromised. While listening to the autobiographical audio diary segments, M.L. showed reduced activation relative to comparison subjects in midline frontal and posterior nodes previously identified as part of the

  11. Targeted Imaging of Tumor-Associated Macrophages by Cyanine 7-Labeled Mannose in Xenograft Tumors

    Directory of Open Access Journals (Sweden)

    Chong Jiang MD

    2017-01-01

    Full Text Available Mannose receptor is considered as a hallmark of M2-oriented tumor-associated macrophages (TAMs, but its utility in TAMs was rarely reported. Therefore, deoxymannose (DM, a high-affinity ligand of mannose receptor, was labeled with near-infrared dye cyanine 7 (Cy7, and its feasibility of targeted imaging on TAMs was evaluated in vitro and in vivo. The Cy7-DM was synthesized, and its binding affinity with induced TAMs in vitro, whole-body imaging in xenograft tumor mouse model in vivo, and the cellular localization in dissected tissues were evaluated. We demonstrated a high uptake of Cy7-DM by induced M2 macrophages and TAMs in tumor tissues. In vivo near-infrared live imaging visualized abundant TAMs in tumor lesions instead of inflammatory sites by Cy7-DM imaging, and the quantity of Cy7-DM signals in tumors was significantly higher than that shown in inflammatory sites from 1 to 8 hours of imaging. Our results suggest that mannose could rapidly and specifically target TAMs and is a promising candidate for targeted diagnosis of tumor with rich TAMs.

  12. Effects of perfluorochemical emulsion on the timing of administration and irradiation in tumor bearing mice

    International Nuclear Information System (INIS)

    Hishikawa-Itoh, Youko; Ayakawa, Yoshio; Miyata, Nobuki

    1988-01-01

    Perfluorochemical content was examined periodically, in blood, tumor and some organs using gas chromatography, after Fluosol-DA saline 20 % (FDAS) was injected into LLC bearing mice. The blood half-life of FDAS in LLC bearing mice was 3.76 hrs (5 ml/kg injection) or 6.15 hrs (20 ml/kg injection) respectively, and FDAS almost disapeared from the blood after about 2 days (5 ml/kg) and 3 days (20 ml/kg) of FDAS-injection. Most of FDAS was accumulated into spleen and the liver. FDAS accumulation into the tumor tissue was 1 ∼ 6 % of injected-FDAS dose and the peak of FDAS accumulation was 1 ∼ 3 days after injection. The timing of FDAS-injection and irradiation in tumor bearing mice determined according to the results above (half-life and accumulation of FDAS in tumor). FDAS (5, 10, 20 ml/kg) was injected to LLC-bearing mice on 3, 2, 1 and 0 day before irradiation and they were irradiated 15 Gray under oxygen-breathing, respectively. FDAS-injected groups before irradiation (3, 2, 1 day before, respectively) showed a tendency of tumor growth delay, but didn't show significant difference as compared with oxygen-breathing group without FDAS, because they had not enough effective FDAS content in the blood. Although the FDAS-injected groups just before irradiation significantly showed the delay of tumor growth. These results demonstrate that oxygen and FDAS existing in the blood injected just before irradiation effectively delay tumor growth in which the lowest effective dose is 5 ml/kg. In the case of clinical application of FDAS, FDAS may be most effective, when administrated just before irradiation in every fractionated irradiation. (author)

  13. A fundamental study of dynamic CT for hemodynamics in experimental hepatic tumors

    International Nuclear Information System (INIS)

    Yamakawa, Fumiko

    1991-01-01

    Dynamic CT was performed using iodamide meglumine (2 ml/kg) to investigate hemodynamics in experimental hepatic tumors, tumor margins and in normal hepatic tissue as well in rabbits with VX 2 -induced hepatic tumors. Peak time (PT) and first moment (M1) were calculated from a time density curve prepared by eight consecutive 3-second scans over a period of 55 seconds. PT and M1 in tumors were significantly shorter than those in tumor margins and normal tissue, but were not influenced by tumor size. PT and M1 in tumor margins and normal tissue became longer with enlargement of the tumor. Ligation of the hepatic artery caused (1) no change in PT or M1 in normal tissue and tumor margins and (2) difficulty in measuring PT and M1 in tumors. Ligation of the portal vein caused (1) difficulty in measuring PT and M1 in normal tissue and tumor margins and (2) no change in PT or M1 in tumors. Pathological studies of specimens taken from each region of interest (ROI) showed that hemodynamics in the tumors reflected tumor-specific vascular structures. (author)

  14. Impact of pneumoperitoneum on tumor growth.

    Science.gov (United States)

    Lécuru, F; Agostini, A; Camatte, S; Robin, F; Aggerbeck, M; Jaïs, J P; Vilde, F; Taurelle, R

    2002-08-01

    To compare intraperitoneal tumor growth after CO2 laparoscopy (L), gasless laparoscopy (GL), midline laparotomy (ML), and general anesthesia (GA) as a control. A prospective randomized trial was carried out in nude rats. A carcinomatosis was obtained by intraperitoneal injection of either one of the two human ovarian cancer cell lines IGR-OV1 or NIH:OVCAR-3. Rats secondly underwent randomly different kind of procedures: CO2 L (8 mmHg, 60 min), GL (traction by a balloon for 60 min), ML (bowel removed and let on a mesh for 60 min), or GA. The rats were finally killed 10 or 35 days after surgery (respectively in IGR-OV1, or NIH:OVCAR-3 models). Tumor growth was assessed by the weight of the omental metastasis and MIB1 immunostaining. Peritoneal dissemination as well as abdominal wall metastases were assessed by pathological examination. Statistical analysis used the chi-square test (or Fisher exact test) and Bonferroni method for multiple comparison between groups. Fifteen rats were included in each group. Mean omental weight was significantly increased after surgery (3.1 to 5.6 g), when compared to control (2.4 g), but no significant difference was recorded between the three surgical accesses. MIB1 immunostaining was poor in the PNP group (37%), whereas it was higher after midline laparotomy (51%), but the difference was not significant (p = 0.07). Similarly, no significant variation was recorded in the NIH:OVCAR-3 model for omental weight or MIB1 staining. CO2 pneumoperitoneum significantly increased right diaphragmatic dome involvement in the NIH:OVCAR-3 model. Abdominal wall metastases were significantly more frequent after surgery when compared to the control group, but no significant difference could be demonstrated between surgical groups in each model. In these solid tumor models, CO2 pneumoperitoneum had no deleterious effect on tumor growth when compared to gasless laparoscopy or midline laparotomy.

  15. Is Diaphragm Motion a Good Surrogate for Liver Tumor Motion?

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Juan [Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina (United States); School of Information Science and Engineering, Shandong University, Jinan, Shandong (China); Cai, Jing [Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina (United States); Wang, Hongjun [School of Information Science and Engineering, Shandong University, Jinan, Shandong (China); Chang, Zheng; Czito, Brian G. [Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina (United States); Bashir, Mustafa R. [Department of Radiology, Duke University Medical Center, Durham, North Carolina (United States); Palta, Manisha [Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina (United States); Yin, Fang-Fang, E-mail: fangfang.yin@duke.edu [Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina (United States)

    2014-11-15

    Purpose: To evaluate the relationship between liver tumor motion and diaphragm motion. Methods and Materials: Fourteen patients with hepatocellular carcinoma (10 of 14) or liver metastases (4 of 14) undergoing radiation therapy were included in this study. All patients underwent single-slice cine–magnetic resonance imaging simulations across the center of the tumor in 3 orthogonal planes. Tumor and diaphragm motion trajectories in the superior–inferior (SI), anterior–posterior (AP), and medial–lateral (ML) directions were obtained using an in-house-developed normalized cross-correlation–based tracking technique. Agreement between the tumor and diaphragm motion was assessed by calculating phase difference percentage, intraclass correlation coefficient, and Bland-Altman analysis (Diff). The distance between the tumor and tracked diaphragm area was analyzed to understand its impact on the correlation between the 2 motions. Results: Of all patients, the mean (±standard deviation) phase difference percentage values were 7.1% ± 1.1%, 4.5% ± 0.5%, and 17.5% ± 4.5% in the SI, AP, and ML directions, respectively. The mean intraclass correlation coefficient values were 0.98 ± 0.02, 0.97 ± 0.02, and 0.08 ± 0.06 in the SI, AP, and ML directions, respectively. The mean Diff values were 2.8 ± 1.4 mm, 2.4 ± 1.1 mm, and 2.2 ± 0.5 mm in the SI, AP, and ML directions, respectively. Tumor and diaphragm motions had high concordance when the distance between the tumor and tracked diaphragm area was small. Conclusions: This study showed that liver tumor motion had good correlation with diaphragm motion in the SI and AP directions, indicating diaphragm motion in the SI and AP directions could potentially be used as a reliable surrogate for liver tumor motion.

  16. Electoral Competition when Candidates are Better Informed than Voters

    DEFF Research Database (Denmark)

    Jensen, Thomas

    candidates are both completely office-motivated but differ in state-dependent quality. Voters have some information about the state but candidates are better informed. If voters' information is unknown to the candidates when they take positions and sufficiently accurate then candidates will, in refined...

  17. ART-ML - a novel XML format for the biological procedures modeling and the representation of blood flow simulation.

    Science.gov (United States)

    Karvounis, E C; Tsakanikas, V D; Fotiou, E; Fotiadis, D I

    2010-01-01

    The paper proposes a novel Extensible Markup Language (XML) based format called ART-ML that aims at supporting the interoperability and the reuse of models of blood flow, mass transport and plaque formation, exported by ARTool. ARTool is a platform for the automatic processing of various image modalities of coronary and carotid arteries. The images and their content are fused to develop morphological models of the arteries in easy to handle 3D representations. The platform incorporates efficient algorithms which are able to perform blood flow simulation. In addition atherosclerotic plaque development is estimated taking into account morphological, flow and genetic factors. ART-ML provides a XML format that enables the representation and management of embedded models within the ARTool platform and the storage and interchange of well-defined information. This approach influences in the model creation, model exchange, model reuse and result evaluation.

  18. Validation by theoretical approach to the experimental estimation of efficiency for gamma spectrometry of gas in 100 ml standard flask

    International Nuclear Information System (INIS)

    Mohan, V.; Chudalayandi, K.; Sundaram, M.; Krishnamony, S.

    1996-01-01

    Estimation of gaseous activity forms an important component of air monitoring at Madras Atomic Power Station (MAPS). The gases of importance are argon 41 an air activation product and fission product noble gas xenon 133. For estimating the concentration, the experimental method is used in which a grab sample is collected in a 100 ml volumetric standard flask. The activity of gas is then computed by gamma spectrometry using a predetermined efficiency estimated experimentally. An attempt is made using theoretical approach to validate the experimental method of efficiency estimation. Two analytical models named relative flux model and absolute activity model were developed independently of each other. Attention is focussed on the efficiencies for 41 Ar and 133 Xe. Results show that the present method of sampling and analysis using 100 ml volumetric flask is adequate and acceptable. (author). 5 refs., 2 tabs

  19. Candidate marketing takes the guessing game out of choosing employers.

    Science.gov (United States)

    Russell, Judith; Havel, Stacey

    2010-01-01

    Candidate marketing builds a foundation for relationships between employers and potential employees. Additionally, candidate marketing differentiates organizations in the marketplace. Organizations using candidate marketing to communicate the employer brand can expect a higher quality of candidates, and new employees are better prepared for the work environment and culture. Today, organizations can use a variety of integrated tools and techniques to communicate and build relationships with candidates. Candidate marketing demonstrates an organization's willingness towards transparency, and ability to invite open conversations between candidates and members of the organizations.

  20. Paediatric cardiac catheterization. Controlled, randomized study of two iodinated contrast media: iopromide 300 and ioxaglate 320 mgI/ml

    International Nuclear Information System (INIS)

    Amiel, M.; Revel, D.

    1989-01-01

    Thirty-one children were included in a prospective randomized trial comparing a new non-ionic contrast medium, iopromide 300 and the ionic low osmolar contrast medium, ioxaglate 320 mgI/ml in pediatric cardiac catheterization. There were fewer adverse effects with iopromide but no statistically significant difference was demonstrated in this small population, with a very low incidence of allergoid reactions; this tendency was confirmed by meta-analysis of the multicentre study [fr

  1. Army Gas-Cooled Reactor Systems Program. The ML-1 analytical design report. Volume IV. Electrical design

    Energy Technology Data Exchange (ETDEWEB)

    None

    1961-10-01

    The analysis preceding and supporting the design of the ML-1--a mobile, low-power, nuclear power plant--is described in sufficient detail for an engineer, not a specialist, to follow the development of the design. Test results and similar data are used to support the calculations whenever possible. Useless repetition of detail is avoided: when the development of several items of equipment, performing a similar function under similar conditions, is described the calculations and derivations are given only once.

  2. ArdenML: The Arden Syntax Markup Language (or Arden Syntax: It's Not Just Text Any More!)

    Science.gov (United States)

    Sailors, R. Matthew

    2001-01-01

    It is no longer necessary to think of Arden Syntax as simply a text-based knowledge base format. The development of ArdenML (Arden Syntax Markup Language), an XML-based markup language allows structured access to most of the maintenance and library categories without the need to write or buy a compiler may lead to the development of simple commercial and freeware tools for processing Arden Syntax Medical Logic Modules (MLMs)

  3. Analysis of a Multilevel Dual Active Bridge (ML-DAB DC-DC Converter Using Symmetric Modulation

    Directory of Open Access Journals (Sweden)

    M. A. Moonem

    2015-04-01

    Full Text Available Dual active bridge (DAB converters have been popular in high voltage, low and medium power DC-DC applications, as well as an intermediate high frequency link in solid state transformers. In this paper, a multilevel DAB (ML-DAB has been proposed in which two active bridges produce two-level (2L-5L, 5L-2L and 3L-5L voltage waveforms across the high frequency transformer. The proposed ML-DAB has the advantage of being used in high step-up/down converters, which deal with higher voltages, as compared to conventional two-level DABs. A three-level neutral point diode clamped (NPC topology has been used in the high voltage bridge, which enables the semiconductor switches to be operated within a higher voltage range without the need for cascaded bridges or multiple two-level DAB converters. A symmetric modulation scheme, based on the least number of angular parameters rather than the duty-ratio, has been proposed for a different combination of bridge voltages. This ML-DAB is also suitable for maximum power point tracking (MPPT control in photovoltaic applications. Steady-state analysis of the converter with symmetric phase-shift modulation is presented and verified using simulation and hardware experiments.

  4. MMP2 and MMP9 participate in S1P-induced invasion of follicular ML-1 thyroid cancer cells.

    Science.gov (United States)

    Kalhori, Veronica; Törnquist, Kid

    2015-03-15

    The bioactive lipid sphingosine-1-phosphate (S1P) has emerged as a potent inducer of cancer cell migration and invasion. Previously, we have shown that S1P induces invasion of ML-1 follicular thyroid cancer cells via S1P receptors 1 and 3 (S1P1,3). Matrix metalloproteinases (MMPs) are zinc-dependent proteolytic enzymes used by cells for degradation of the extracellular matrix during invasion and migration. In the present study, we examined the role of MMP2 and MMP9 for S1P-induced invasion of ML-1 cells, and found that S1P regulates the secretion and activity of MMP2 and MMP9 via S1P1,3. Both pharmacological inhibitors and siRNA knockdown of MMP2 and MMP9 could attenuate S1P-induced invasion. Additionally, we show that calpains and Rac1 mediate S1P-induced secretion of MMP2 and MMP9. In conclusion, MMP2 and MMP9 participate in S1P-evoked follicular ML-1 thyroid cancer cell invasion. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  5. Blind and semi-blind ML detection for space-time block-coded OFDM wireless systems

    KAUST Repository

    Zaib, Alam; Al-Naffouri, Tareq Y.

    2014-01-01

    This paper investigates the joint maximum likelihood (ML) data detection and channel estimation problem for Alamouti space-time block-coded (STBC) orthogonal frequency-division multiplexing (OFDM) wireless systems. The joint ML estimation and data detection is generally considered a hard combinatorial optimization problem. We propose an efficient low-complexity algorithm based on branch-estimate-bound strategy that renders exact joint ML solution. However, the computational complexity of blind algorithm becomes critical at low signal-to-noise ratio (SNR) as the number of OFDM carriers and constellation size are increased especially in multiple-antenna systems. To overcome this problem, a semi-blind algorithm based on a new framework for reducing the complexity is proposed by relying on subcarrier reordering and decoding the carriers with different levels of confidence using a suitable reliability criterion. In addition, it is shown that by utilizing the inherent structure of Alamouti coding, the estimation performance improvement or the complexity reduction can be achieved. The proposed algorithms can reliably track the wireless Rayleigh fading channel without requiring any channel statistics. Simulation results presented against the perfect coherent detection demonstrate the effectiveness of blind and semi-blind algorithms over frequency-selective channels with different fading characteristics.

  6. [Immune system and tumors].

    Science.gov (United States)

    Terme, Magali; Tanchot, Corinne

    2017-02-01

    Despite having been much debated, it is now well established that the immune system plays an essential role in the fight against cancer. In this article, we will highlight the implication of the immune system in the control of tumor growth and describe the major components of the immune system involved in the antitumoral immune response. The immune system, while exerting pressure on tumor cells, also will play a pro-tumoral role by sculpting the immunogenicity of tumors cells as they develop. Finally, we will illustrate the numerous mechanisms of immune suppression that take place within the tumoral microenvironment which allow tumor cells to escape control from the immune system. The increasingly precise knowledge of the brakes to an effective antitumor immune response allows the development of immunotherapy strategies more and more innovating and promising of hope. Copyright © 2016. Published by Elsevier Masson SAS.

  7. Imaging of pancreatic tumors

    International Nuclear Information System (INIS)

    Brambs, Hans-Juergen; Juchems, Markus

    2010-01-01

    Ductal adenocarcinoma is the most frequent solid tumor of the pancreas. This tumor has distinct features including early obstruction of the pancreatic duct, diminished enhancement after administration of contrast material due to desmoplastic growth, high propensity to infiltrate adjacent structures and to metastasize into the liver and the peritoneum. Hormone active endocrine tumors cause specific clinical symptoms. Imaging is aimed at localization of these hypervascular tumors. Non hormone active tumors are most frequently malignant and demonstrate very varying features. Cystic pancreatic tumors are increasingly detected by means of cross sectional imaging. Exact classification can be achieved with knowledge of the macropathology and considering clinical presentation as well as age and gender of the patients. (orig.)

  8. Computerized tomography and staging of bladder tumors

    International Nuclear Information System (INIS)

    Wozniak, A.; Luongo, A.; Nogueira, A.

    1982-01-01

    Computed Tomography (CT) has been employed in 13 patients with bladder tumors; 8 of them subsequently underwent surgery. Concordance between CT and pathological staging ranged in 90% of accurate results. Our data are discussed and compared to those of other authors in the literature. Staging was carried out according to the International Union Against Cancer. CT proved to be very accurate in the assessment of local and regional spread of tumor, limphatic progression and early detection of ureteral obstruction, as well as diagnosis of distant metastasis in selected patients. In poor candidates for surgery CT provided invaluable data to be used for localizing fields of radiation therapy. CT is a very well tolerated procedure, it is therefore suitable in subsequent treatment control. (Author) [pt

  9. Spectroscopic follow up of Kepler planet candidates

    DEFF Research Database (Denmark)

    Latham..[], D. W.; Cochran, W. D.; Marcy, G.W.

    2010-01-01

    Spectroscopic follow-up observations play a crucial role in the confirmation and characterization of transiting planet candidates identified by Kepler. The most challenging part of this work is the determination of radial velocities with a precision approaching 1 m/s in order to derive masses from...... spectroscopic orbits. The most precious resource for this work is HIRES on Keck I, to be joined by HARPS-North on the William Herschel Telescope when that new spectrometer comes on line in two years. Because a large fraction of the planet candidates are in fact stellar systems involving eclipsing stars...... and not planets, our strategy is to start with reconnaissance spectroscopy using smaller telescopes, to sort out and reject as many of the false positives as possible before going to Keck. During the first Kepler observing season in 2009, more than 100 nights of telescope time were allocated for this work, using...

  10. Discriminating dark matter candidates using direct detection

    International Nuclear Information System (INIS)

    Belanger, G.; Nezri, E.; Pukhov, A.

    2009-01-01

    We examine the predictions for both the spin-dependent and spin-independent direct detection rates in a variety of new particle physics models with dark matter candidates. We show that a determination of both spin-independent and spin-dependent amplitudes on protons and neutrons can in principle discriminate different candidates of dark matter up to a few ambiguities. We emphasize the importance of making measurements with different spin-dependent sensitive detector materials and the need for significant improvement of the detector sensitivities. Scenarios where exchange of new colored particles contributes significantly to the elastic scattering cross sections are often the most difficult to identify, the LHC should give an indication whether such scenarios are relevant for direct detection.

  11. Warm Debris Disk Candidates from WISE

    Science.gov (United States)

    Padgett, Deborah; Stapelfeldt, Karl; Liu, Wilson; Leisawitz, David

    2011-01-01

    The Wide Field Infrared Survey Explorer (WISE) has just completed a sensitive all-sky survey in photometric bands at 3.4, 4.6, 12, and 22 microns. We report on a preliminary investigation of main sequence Hipparcos and Tycho catalog stars with 22 micron emission in excess of photospheric levels. This warm excess emission traces material in the circumstellar region likely to host terrestrial planets and is preferentially found in young systems with ages warm debris disk candidates are detected among FGK stars and 150 A stars within 120 pc. We are in the process of obtaining spectra to determine spectral types and activity level of these stars and are using HST, Herschel and Keck to characterize the dust, multiplicity, and substellar companions of these systems. In this contribution, we will discuss source selection methods and individual examples from among the WISE debris disk candidates.

  12. (VI) ML6 Complexes

    African Journals Online (AJOL)

    A geometric analysis revealed that beta-(C-H) and alpha-(C-C) can occupy the seventh and eighth coordination sites in the title Fischer carbene complexes as agostic interactions, which allows classifying the carbene as a η3 ligand in these cases. This theory was supported by the relative energies of the conformers and an ...

  13. Combined Scintigraphy and Tumor Marker Analysis Predicts Unfavorable Histopathology of Neuroblastic Tumors with High Accuracy.

    Directory of Open Access Journals (Sweden)

    Wolfgang Peter Fendler

    Full Text Available Our aim was to improve the prediction of unfavorable histopathology (UH in neuroblastic tumors through combined imaging and biochemical parameters.123I-MIBG SPECT and MRI was performed before surgical resection or biopsy in 47 consecutive pediatric patients with neuroblastic tumor. Semi-quantitative tumor-to-liver count-rate ratio (TLCRR, MRI tumor size and margins, urine catecholamine and NSE blood levels of neuron specific enolase (NSE were recorded. Accuracy of single and combined variables for prediction of UH was tested by ROC analysis with Bonferroni correction.34 of 47 patients had UH based on the International Neuroblastoma Pathology Classification (INPC. TLCRR and serum NSE both predicted UH with moderate accuracy. Optimal cut-off for TLCRR was 2.0, resulting in 68% sensitivity and 100% specificity (AUC-ROC 0.86, p < 0.001. Optimal cut-off for NSE was 25.8 ng/ml, resulting in 74% sensitivity and 85% specificity (AUC-ROC 0.81, p = 0.001. Combination of TLCRR/NSE criteria reduced false negative findings from 11/9 to only five, with improved sensitivity and specificity of 85% (AUC-ROC 0.85, p < 0.001.Strong 123I-MIBG uptake and high serum level of NSE were each predictive of UH. Combined analysis of both parameters improved the prediction of UH in patients with neuroblastic tumor. MRI parameters and urine catecholamine levels did not predict UH.

  14. Candidates for non-baryonic dark matter

    International Nuclear Information System (INIS)

    Fornengo, Nicolao

    2002-01-01

    This report is a brief review of the efforts to explain the nature of non-baryonic dark matter and of the studies devoted to the search for relic particles. Among the different dark matter candidates, special attention is devoted to relic neutralinos, by giving an overview of the recent calculations of its relic abundance and detection rates in a wide variety of supersymmetric schemes

  15. Candidates for non-baryonic dark matter

    OpenAIRE

    Fornengo, Nicolao

    2002-01-01

    This report is a brief review of the efforts to explain the nature of non-baryonic dark matter and of the studies devoted to the search for relic particles. Among the different dark matter candidates, special attention is devoted to relic neutralinos, by giving an overview of the recent calculations of its relic abundance and detection rates in a wide variety of supersymmetric schemes.

  16. Educational intervention for liver transplantation candidates

    OpenAIRE

    Mendes,Karina Dal Sasso; Silva Junior,Orlando de Castro e; Ziviani,Luciana da Costa; Rossin,Fabiana Murad; Zago,Márcia Maria Fontão; Galvão,Cristina Maria

    2013-01-01

    OBJECTIVE: The objective in this study was to analyze candidates' knowledge on the liver transplantation process before and after putting in practice an educational intervention. METHOD: A quasi-experimental, one-group pretest-posttest research design was adopted. The final sample included 15 subjects. Research data were collected between January and March 2010 in three phases, which were: pretest, implementation of the educational intervention (two meetings) and posttest. RESULTS: The result...

  17. Energy Beverage Consumption Among Naval Aviation Candidates.

    Science.gov (United States)

    Sather, Thomas E; Delorey, Donald R

    2016-06-01

    Since the debut of energy beverages, the consumption of energy beverages has been immensely popular with young adults. Research regarding energy beverage consumption has included college students, European Union residents, and U.S. Army military personnel. However, energy beverage consumption among naval aviation candidates in the United States has yet to be examined. The purpose of this study was to assess energy beverage consumption patterns (frequency and volume) among naval aviation candidates, including attitudes and perceptions regarding the benefits and safety of energy beverage consumption. A 44-item survey was used to assess energy beverage consumption patterns of 302 students enrolled in the Aviation Preflight Indoctrination Course at Naval Air Station Pensacola, FL. Results indicated that 79% of participants (N = 239) reported consuming energy beverages within the last year. However, of those who reported consuming energy beverages within the last year, only 36% (N = 85) reported consuming energy beverages within the last 30 d. Additionally, 51% (N = 153) of participants reported no regular energy beverages consumption. The majority of participants consumed energy beverages for mental alertness (67%), mental endurance (37%), and physical endurance (12%). The most reported side effects among participants included increased mental alertness (67%), increased heart rate (53%), and restlessness (41%). Naval aviation candidates appear to use energy drinks as frequently as a college student population, but less frequently than expected for an active duty military population. The findings of this study indicate that naval aviation candidates rarely use energy beverages (less than once per month), but when consumed, they use it for fatigue management.

  18. Reducing stigma and discrimination: Candidate interventions

    OpenAIRE

    Thornicroft, Graham; Brohan, Elaine; Kassam, Aliya; Lewis-Holmes, Elanor

    2008-01-01

    Abstract This paper proposes that stigma in relation to people with mental illness can be understood as a combination of problems of knowledge (ignorance), attitudes (prejudice) and behaviour (discrimination). From a literature review, a series of candidate interventions are identified which may be effective in reducing stigmatisation and discrimination at the following levels: individuals with mental illness and their family members; the workplace; and local, national and international. The ...

  19. Various Approaches for Targeting Quasar Candidates

    Science.gov (United States)

    Zhang, Y.; Zhao, Y.

    2015-09-01

    With the establishment and development of space-based and ground-based observational facilities, the improvement of scientific output of high-cost facilities is still a hot issue for astronomers. The discovery of new and rare quasars attracts much attention. Different methods to select quasar candidates are in bloom. Among them, some are based on color cuts, some are from multiwavelength data, some rely on variability of quasars, some are based on data mining, and some depend on ensemble methods.

  20. Caffeine Consumption Among Naval Aviation Candidates.

    Science.gov (United States)

    Sather, Thomas E; Williams, Ronald D; Delorey, Donald R; Woolsey, Conrad L

    2017-04-01

    Education frequently dictates students need to study for prolonged periods of time to adequately prepare for examinations. This is especially true with aviation preflight indoctrination (API) candidates who have to assimilate large volumes of information in a limited amount of time during API training. The purpose of this study was to assess caffeine consumption patterns (frequency, type, and volume) among naval aviation candidates attending API to determine the most frequently consumed caffeinated beverage and to examine if the consumption of a nonenergy drink caffeinated beverage was related to energy drink consumption. Data were collected by means of an anonymous 44-item survey administered and completed by 302 students enrolled in API at Naval Air Station Pensacola, FL. Results indicated the most frequently consumed caffeinated beverage consumed by API students was coffee (86.4%), with daily coffee consumption being approximately 28% and the most frequent pattern of consumption being 2 cups per day (85%). The least frequently consumed caffeinated beverages reported were energy drinks (52%) and energy shots (29.1%). The present study also found that the consumption patterns (weekly and daily) of caffeinated beverages (coffee and cola) were positively correlated to energy drink consumption patterns. Naval aviation candidates' consumption of caffeinated beverages is comparable to other college and high school cohorts. This study found that coffee and colas were the beverages of choice, with energy drinks and energy shots being the least frequently reported caffeinated beverages used. Additionally, a relationship between the consumption of caffeinated beverages and energy drinks was identified.Sather TE, Williams RD, Delorey DR, Woolsey CL. Caffeine consumption among naval aviation candidates. Aerosp Med Hum Perform. 2017; 88(4):399-405.

  1. Lower tidal volume strategy (≈3 ml/kg) combined with extracorporeal CO2 removal versus 'conventional' protective ventilation (6 ml/kg) in severe ARDS: the prospective randomized Xtravent-study.

    Science.gov (United States)

    Bein, Thomas; Weber-Carstens, Steffen; Goldmann, Anton; Müller, Thomas; Staudinger, Thomas; Brederlau, Jörg; Muellenbach, Ralf; Dembinski, Rolf; Graf, Bernhard M; Wewalka, Marlene; Philipp, Alois; Wernecke, Klaus-Dieter; Lubnow, Matthias; Slutsky, Arthur S

    2013-05-01

    Acute respiratory distress syndrome is characterized by damage to the lung caused by various insults, including ventilation itself, and tidal hyperinflation can lead to ventilator induced lung injury (VILI). We investigated the effects of a low tidal volume (V(T)) strategy (V(T) ≈ 3 ml/kg/predicted body weight [PBW]) using pumpless extracorporeal lung assist in established ARDS. Seventy-nine patients were enrolled after a 'stabilization period' (24 h with optimized therapy and high PEEP). They were randomly assigned to receive a low V(T) ventilation (≈3 ml/kg) combined with extracorporeal CO2 elimination, or to a ARDSNet strategy (≈6 ml/kg) without the extracorporeal device. The primary outcome was the 28-days and 60-days ventilator-free days (VFD). Secondary outcome parameters were respiratory mechanics, gas exchange, analgesic/sedation use, complications and hospital mortality. Ventilation with very low V(T)'s was easy to implement with extracorporeal CO2-removal. VFD's within 60 days were not different between the study group (33.2 ± 20) and the control group (29.2 ± 21, p = 0.469), but in more hypoxemic patients (PaO2/FIO2 ≤150) a post hoc analysis demonstrated significant improved VFD-60 in study patients (40.9 ± 12.8) compared to control (28.2 ± 16.4, p = 0.033). The mortality rate was low (16.5%) and did not differ between groups. The use of very low V(T) combined with extracorporeal CO2 removal has the potential to further reduce VILI compared with a 'normal' lung protective management. Whether this strategy will improve survival in ARDS patients remains to be determined (Clinical trials NCT 00538928).

  2. Determination of hepatocellular carcinoma grade by needle biopsy is unreliable for liver transplant candidate selection.

    Science.gov (United States)

    Court, Colin M; Harlander-Locke, Michael P; Markovic, Daniela; French, Samuel W; Naini, Bita V; Lu, David S; Raman, Steven S; Kaldas, Fady M; Zarrinpar, Ali; Farmer, Douglas G; Finn, Richard S; Sadeghi, Saeed; Tomlinson, James S; Busuttil, Ronald W; Agopian, Vatche G

    2017-09-01

    The objective of this article is to evaluate the utility of preoperative needle biopsy (PNB) grading of hepatocellular carcinoma (HCC) as a biomarker for liver transplantation (LT) candidate selection. Given the prognostic significance of HCC tumor grade, PNB grading has been proposed as a biomarker for LT candidate selection. Clinicopathologic characteristics of HCC LT recipients (1989-2014) with a PNB were analyzed, and the concordance of PNB grade to explant grade and vascular invasion was assessed to determine whether incorporation of PNB grade to accepted transplant criteria improved candidate selection. Of 965 patients undergoing LT for HCC, 234 (24%) underwent PNB at a median of 280 days prior to transplant. Grade by PNB had poor concordance to final explant pathology (κ = 0.22; P = 0.003), and low sensitivity (29%) and positive predictive value (35%) in identifying poorly differentiated tumors. Vascular invasion was predicted by explant pathologic grade (r s = 0.24; P Liver Transplantation 23 1123-1132 2017 AASLD. © 2017 by the American Association for the Study of Liver Diseases.

  3. Central nervous system tumors

    International Nuclear Information System (INIS)

    Curran, W.J. Jr.

    1991-01-01

    Intrinsic tumors of the central nervous system (CNS) pose a particularly challenging problem to practicing oncologists. These tumors rarely metastasize outside the CNS, yet even histologically benign tumors can be life-threatening due to their local invasiveness and strategic location. The surrounding normal tissues of the nervous system is often incapable of full functional regeneration, therefore prohibiting aggressive attempts to use either complete surgical resection or high doses of irradiation. Despite these limitations, notable achievements have recently been recorded in the management of these tumors

  4. Management of CNS tumors

    International Nuclear Information System (INIS)

    Griem, M.L.

    1987-01-01

    The treatment of tumors of the CNS has undergone a number of changes based on the impact of CT. The use of intraoperative US for the establishment of tumor location and tumor histology is demonstrated. MR imaging also is beginning to make an impact on the diagnosis and treatment of tumors of the CNS. Examples of MR images are shown. The authors then discuss the important aspects of tumor histology as it affects management and newer concepts in surgery, radiation, and chemotherapy on tumor treatment. The role of intraoperative placement of radioactive sources, the utilization of heavy particle radiation therapy, and the potential role of other experimental radiation therapy techniques are discussed. The role of hyperfractionated radiation and of neutrons and x-ray in a mixed-beam treatment are discussed in perspective with standard radiation therapy. Current chemotherapy techniques, including intraarterial chemotherapy, are discussed. The complications of radiation therapy alone and in combination with chemotherapy in the management of primary brain tumors, brain metastases, and leukemia are reviewed. A summary of the current management of pituitary tumors, including secreting pituitary adenomas and chromophobe adenomas, are discussed. The treatment with heavy particle radiation, transsphenoidal microsurgical removal, and combined radiotherapeutic and surgical management are considered. Tumor metastasis management of lesions of the brain and spinal cord are considered

  5. Upper gastrointestinal alterations in kidney transplant candidates.

    Science.gov (United States)

    Homse Netto, João Pedro; Pinheiro, João Pedro Sant'Anna; Ferrari, Mariana Lopes; Soares, Mirella Tizziani; Silveira, Rogério Augusto Gomes; Maioli, Mariana Espiga; Delfino, Vinicius Daher Alvares

    2018-05-14

    The incidence of gastrointestinal disorders among patients with chronic kidney disease (CKD) is high, despite the lack of a good correlation between endoscopic findings and symptoms. Many services thus perform upper gastrointestinal (UGI) endoscopy on kidney transplant candidates. This study aims to describe the alterations seen on the upper endoscopies of 96 kidney-transplant candidates seen from 2014 to 2015. Ninety-six CKD patients underwent upper endoscopic examination as part of the preparation to receive kidney grafts. The data collected from the patients' medical records were charted on Microsoft Office Excel 2016 and presented descriptively. Mean values, medians, interquartile ranges and 95% confidence intervals of the clinic and epidemiological variables were calculated. Possible associations between endoscopic findings and infection by H. pylori were studied. Males accounted for 54.17% of the 96 patients included in the study. Median age and time on dialysis were 50 years and 50 months, respectively. The most frequent upper endoscopy finding was enanthematous pangastritis (57.30%), followed by erosive esophagitis (30.20%). Gastric intestinal metaplasia and peptic ulcer were found in 8.33% and 7.30% of the patients, respectively. H. pylori tests were positive in 49 patients, and H. pylori infection was correlated only with non-erosive esophagitis (P = 0.046). Abnormal upper endoscopy findings were detected in all studied patients. This study suggested that upper endoscopy is a valid procedure for kidney transplant candidates. However, prospective studies are needed to shed more light on this matter.

  6. Nuclear safety in EU candidate countries

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2000-10-01

    Nuclear safety in the candidate countries to the European Union is a major issue that needs to be addressed in the framework of the enlargement process. Therefore WENRA members considered it was their duty to offer their technical assistance to their Governments and the European Union Institutions. They decided to express their collective opinion on nuclear safety in those candidate countries having at least one nuclear power plant: Bulgaria, the Czech Republic, Hungary, Lithuania, Romania, Slovakia and Slovenia. The report is structured as follows: A foreword including background information, structure of the report and the methodology used, General conclusions of WENRA members reflecting their collective opinion, For each candidate country, an executive summary, a chapter on the status of the regulatory regime and regulatory body, and a chapter on the nuclear power plant safety status. Two annexes are added to address the generic safety characteristics and safety issues for RBMK and VVER plants. The report does not cover radiation protection and decommissioning issues, while safety aspects of spent fuel and radioactive waste management are only covered as regards on-site provisions. In order to produce this report, WENRA used different means: For the chapters on the regulatory regimes and regulatory bodies, experts from WENRA did the work. For the chapters on nuclear power plant safety status, experts from WENRA and from French and German technical support organisations did the work. Taking into account the contents of these chapters, WENRA has formulated its general conclusions in this report.

  7. Molecular candidates of MTV in air

    Science.gov (United States)

    Dam, Nico; Mirzaei, Mehrnoosh; van de Water, Willem

    2011-11-01

    In molecular tagging velocimetry (MTV), the molecules of a gas are used as flow tracers. These tracers can be produced at will by illumination with a laser which promotes molecules to a long- lived excited state, fuses N2 and N2 to NO, or makes molecules phosphoresce. A while later these tagged molecules can be visualized by laser-induced fluorescence, or by just watching them while they phosphoresce. Candidates for MTV in turbulence research must be arranged in structures narrower than the Kolmogorov scale, which remain narrow as time progresses, and must live longer than the Kolmogorov time. These requirements invalidate many candidates, candidates once deemed successful. They do so in various surprising manners that involve a combination of fluid flow and molecular dynamics. Rather than velocimetry in turbulence, MTV techniques offer a unique view on basic dispersion processes at the smallest scales of turbulence. In this way we have measured the spreading of clouds whose size is a few times the Kolmogorov length and the Batchelor dispersion of objects whose size is inside the inertial range.

  8. Nuclear safety in EU candidate countries

    International Nuclear Information System (INIS)

    2000-10-01

    Nuclear safety in the candidate countries to the European Union is a major issue that needs to be addressed in the framework of the enlargement process. Therefore WENRA members considered it was their duty to offer their technical assistance to their Governments and the European Union Institutions. They decided to express their collective opinion on nuclear safety in those candidate countries having at least one nuclear power plant: Bulgaria, the Czech Republic, Hungary, Lithuania, Romania, Slovakia and Slovenia. The report is structured as follows: A foreword including background information, structure of the report and the methodology used, General conclusions of WENRA members reflecting their collective opinion, For each candidate country, an executive summary, a chapter on the status of the regulatory regime and regulatory body, and a chapter on the nuclear power plant safety status. Two annexes are added to address the generic safety characteristics and safety issues for RBMK and VVER plants. The report does not cover radiation protection and decommissioning issues, while safety aspects of spent fuel and radioactive waste management are only covered as regards on-site provisions. In order to produce this report, WENRA used different means: For the chapters on the regulatory regimes and regulatory bodies, experts from WENRA did the work. For the chapters on nuclear power plant safety status, experts from WENRA and from French and German technical support organisations did the work. Taking into account the contents of these chapters, WENRA has formulated its general conclusions in this report

  9. Studies of testicular function after treatment for testicular tumor, 1

    International Nuclear Information System (INIS)

    Furuhata, Akihiko; Ogawa, Katsuaki; Hosaka, Masahiko; Sugawara, Toshimichi.

    1985-01-01

    Recently, the treatment for testicular tumor has improved. Preservation of testicular function in the treatment of testicular tumor is important, because the majority of the patients are young. We investigated the testicular function of patients with testicular tumor before, during and after treatment. As a part of this study, the fertility of patients with testicular tumor before and after treatment was evaluated. 1. Fourteen of 78 married patients (18 %) showed sterility for two or more years before treatment. 2. When semen was examined in 31 patients before treatment, only seven patients (23 %) showed normal sperm counts of more than 40 x 10 6 /ml, and 19 (61.3 %) showed oligospermia or azoospermia with sperm counts of less than 10 x 10 6 /ml. 3. Of 20 patients who underwent retroperitoneal lymphnode dissection, 15 developed ejaculation deficiency. Four other patients also developed ejaculation deficiency but recovered, and three of them rendered their wives pregnant. 4. Of 23 patients given radiotherapy, nine produced children both before and after treatment, nine produced children before treatment but showed sterility after treatment, and five showed sterility both before and after treatment. 5. Examination of semen was performed in 17 patients given radiotherapy and in five given chemotherapy. Many patients developed oligospermia or azoospermia after the treatments, but revealed a tendency to recover with time. Based on the results mentioned above, it is inferred that the ability to produce sperm in patients with testicular tumor after treatment decreases but the decrease tends to recover to normal with time. (author)

  10. Tumor carcinoide apendicular Appendiceal carcinoid tumor

    Directory of Open Access Journals (Sweden)

    Julio Vázquez Palanco

    2008-12-01

    Full Text Available El objetivo de este trabajo fue dar a conocer un interesante caso de tumor carcinoide que se presentó con cuadro clínico de apendicitis aguda. El paciente fue un varón de 8 años de edad, al cual se realizó apendicectomía a causa de una apendicitis aguda. El resultado anatomopatológico confirmó un tumor de células endocrinas (argentafinoma, tumor carcinoide en el tercio distal del órgano, que infiltraba hasta la serosa, y apendicitis aguda supurada. El paciente fue enviado a un servicio de oncohematología para tratamiento oncoespecífico. Por lo inusual de estos tumores en edades tempranas y por lo que puede representar para el niño una conducta no consecuente, decidimos presentar este caso a la comunidad científica nacional e internacional. Es extremadamente importante el seguimiento de los pacientes con apendicitis aguda y de las conclusiones del examen histológico, por lo que puede representar para el niño una conducta inadecuada en una situación como esta.The objective of this paper was to make known an interesting case of carcinoid tumor that presented a clinical picture of acute appendicitis.The patient was an eight-year-old boy that underwent appendectomy due to an acute appendicitis. The anatomopathological report confirmed an endocrine cell tumor (argentaffinoma, carcinoid tumor in the distal third of the organ that infiltrated up to the serosa, and acute suppurative appendicitis. The patient was referred to an oncohematology service for oncospecific treatment. As it is a rare tumor at early ages, and taking into account what a inconsequent behavior may represent for the child, it was decided to present this case to the national and international scientific community. The follow-up of the patients with acute appendicitis and of the conclusions of the histological examination is extremely important considering what an inadequate conduct may represent for the child in a situation like this.

  11. Investigation of the Candidate Tumor Suppressor Gene prk in Prostate Cancer

    National Research Council Canada - National Science Library

    Dai, Wei

    2002-01-01

    .... We have proposed to characterize the genetic and epigenetic basis of aberrant PLK3 transcripts detected in prostate cancer, their prevalence and possible clinical relevance, to test the functional...

  12. Identification of Novel Candidate Tumor Suppressor Genes Using C. elegans as a Model

    National Research Council Canada - National Science Library

    Sternberg, Paul

    1999-01-01

    Molecular genetic analysis of the model organism Caenorhabditis elegans was used to identify and study mechanisms of action of negative regulators of tyrosine kinase/RAS mediated signal transduction...

  13. Identification of Novel Candidate Tumor Suppressor Genes Using C. elegans as a Model

    National Research Council Canada - National Science Library

    Sternberg, Paul

    1998-01-01

    Molecular genetic analysis of the model organism Caenorhabditis elegans was used to identify and study mechanisms of action of negative regulators of tyrosine kinase/RAS mediated signal transduction...

  14. An exceptional collision tumor: gastric calcified stromal tumor and ...

    African Journals Online (AJOL)

    The authors report an exceptional case of collision tumor comprised of a gastric calcified stromal tumor and a pancreatic adenocarcinoma. The pancreatic tumor was detected fortuitously on the histological exam of resection specimen. Key words: Collision tumor, stromal tumor, adenocarcinoma ...

  15. Pituitary gland tumors

    International Nuclear Information System (INIS)

    Jesser, J.; Schlamp, K.; Bendszus, M.

    2014-01-01

    This article gives an overview of the most common tumors of the pituitary gland and the differential diagnostics with special emphasis on radiological diagnostic criteria. A selective search of the literature in PubMed was carried out. Pituitary adenomas constitute 10-15 % of all intracranial tumors and are the most common tumors of the sellar region. Tumors smaller than 1 cm in diameter are called microadenomas while those larger than 1 cm in diameter are called macroadenomas. Approximately 65 % of pituitary gland adenomas secrete hormones whereby approximately 50 % secrete prolactin, 10 % secrete growth hormone (somatotropin) and 6 % secrete corticotropin. Other tumors located in the sella turcica can also cause endocrinological symptoms, such as an oversecretion of pituitary hormone or pituitary insufficiency by impinging on the pituitary gland or its stalk. When tumors spread into the space cranial to the sella turcica, they can impinge on the optic chiasm and cause visual disorders. A common differential diagnosis of a sellar tumor is a craniopharyngeoma. In children up to 10 % of all intracranial tumors are craniopharyngeomas. Other differential diagnoses for sellar tumors are metastases, meningiomas, epidermoids and in rare cases astrocytomas, germinomas or Rathke cleft cysts As these tumors are located in an anatomically complex region of the skull base and are often very small, a highly focused imaging protocol is required. The currently favored modality is magnetic resonance imaging (MRI) with the administration of a contrast agent. The sellar region should be mapped in thin slices. In cases of suspected microadenoma the imaging protocol should also contain a sequence with dynamic contrast administration in order to assess the specific enhancement characteristics of the tumor and the pituitary gland. (orig.) [de

  16. [Pituitary gland tumors].

    Science.gov (United States)

    Jesser, J; Schlamp, K; Bendszus, M

    2014-10-01

    This article gives an overview of the most common tumors of the pituitary gland and the differential diagnostics with special emphasis on radiological diagnostic criteria. A selective search of the literature in PubMed was carried out. Pituitary adenomas constitute 10-15% of all intracranial tumors and are the most common tumors of the sellar region. Tumors smaller than 1 cm in diameter are called microadenomas while those larger than 1 cm in diameter are called macroadenomas. Approximately 65% of pituitary gland adenomas secrete hormones whereby approximately 50% secrete prolactin, 10% secrete growth hormone (somatotropin) and 6% secrete corticotropin. Other tumors located in the sella turcica can also cause endocrinological symptoms, such as an oversecretion of pituitary hormone or pituitary insufficiency by impinging on the pituitary gland or its stalk. When tumors spread into the space cranial to the sella turcica, they can impinge on the optic chiasm and cause visual disorders. A common differential diagnosis of a sellar tumor is a craniopharyngeoma. In children up to 10% of all intracranial tumors are craniopharyngeomas. Other differential diagnoses for sellar tumors are metastases, meningiomas, epidermoids and in rare cases astrocytomas, germinomas or Rathke cleft cysts As these tumors are located in an anatomically complex region of the skull base and are often very small, a highly focused imaging protocol is required. The currently favored modality is magnetic resonance imaging (MRI) with the administration of a contrast agent. The sellar region should be mapped in thin slices. In cases of suspected microadenoma the imaging protocol should also contain a sequence with dynamic contrast administration in order to assess the specific enhancement characteristics of the tumor and the pituitary gland.

  17. Buckyballs meet Viral Nanoparticles – Candidates for Biomedicine

    Science.gov (United States)

    Steinmetz, Nicole F.; Hong, Vu; Spoerke, Erik D.; Lu, Ping; Breitenkamp, Kurt; Finn, M.G.; Manchester, Marianne

    2009-01-01

    Fullerenes such as C60 show promise as functional components in several emerging technologies. For biomedical applications, C60 has been used in gene- and drug-delivery vectors, as imaging agents, and as photosensitizers in cancer therapy. A major drawback of C60 for bioapplications is its insolubility in water. To overcome this limitation, we covalently attached C60 derivatives to Cowpea mosaic virus and bacteriophage Qβ virus-like particles, as examples of naturally occurring viral nanoparticle (VNP) structures that have been shown to be promising candidates for biomedicine. Two different labeling strategies were employed, giving rise to water-soluble and stable VNP-C60 and VNP-PEG-C60 conjugates. Samples were characterized using a combination of transmission electron microscopy, scanning transmission electron microscopy (STEM), gel electrophoresis, size-exclusion chromatography, dynamic light scattering, and western blotting. “Click” chemistry bioconjugation using a PEG-modified propargyl-O-PEG-C60 derivative gave rise to high loadings of fullerene on the VNP surface, indicated by the imaging of individual C60 units by STEM. The cellular uptake of dye-labeled VNP-PEG-C60 complexes in a human cancer cell line was found by confocal microscopy to be robust, showing that cell internalization was not inhibited by the attached C60 units. These results open the door for the development of novel therapeutic devices with potential applications in photo-activated tumor therapy. PMID:19904938

  18. Comparison in myelography between iodixanol 270 and 320 mgI/ml and iotrolan 300 mgI/ml: a multicentre, randomised, parallel-group, double-blind, phase III trial

    International Nuclear Information System (INIS)

    Palmers, Yvan; Kuhn, Fritz-Peter; Petersen, Dirk; De Greef, Danielle

    2002-01-01

    The objective of the trial was to compare the safety and efficacy of the non-ionic, dimeric, isotonic contrast medium iodixanol (Visipaque 270 and 320 mgI/ml) with those of iotrolan (Isovist 300 mgI/ml) in myelography. After lumbar or cervical puncture, 315 patients were examined in a multicentre, double-blind, randomised, comparative myelography study. Image quality, changes in vital signs, immediate and delayed adverse events were registered. There was a tendency for better images with iodixanol 320 than with iodixanol 270 and iotrolan 300, but the overall quality was good or excellent with all products. The frequency of patients reporting adverse events and headache varied much across centres, but there was no statistically significant difference between the contrast media. The incidence of events was higher after lumbar puncture than after cervical puncture, in women rather than in men, and after puncture with a 22-gauge (G) bevel-tipped needle compared with a 24 G Sprotte needle. The frequency of headache did not correlate with the absence of pathology. The higher iodine concentration in iodixanol 320 could be an advantage for film quality. When compared with iotrolan 300, iodixanol 320 and 270 give similar incidences of adverse events, including headache. (orig.)

  19. Stage T1-2 prostate cancer with pretreatment PSA 10 ng/ml or less: radiotherapy or surgery?

    International Nuclear Information System (INIS)

    Keyser, Douglas; Kupelian, Patrick; Zippe, Craig; Klein, Eric

    1996-01-01

    Purpose: Presently, patients with pretreatment PSA levels ≤10 ng/ml constitute the majority of cases presenting for definitive treatment. Our aim was to determine whether the type of treatment (radiotherapy versus surgery) affected biochemical failure rates in this group of patients. This study is based on 389 patients treated at a single institution. Material and Methods: The charts of all patients treated with either radiotherapy or prostatectomy alone between 1987 and 1993 were reviewed (n=811). Patients with clinical stage T1 or T2 disease, and a pretreatment PSA level (iPSA) of 10.0 or less were analyzed (n=389). Two hundred forty nine (64%) received radical prostatectomy and 140 (36%) received radiotherapy (median dose 66.6 Gy). Pretreatment patient characteristics including clinical stage, biopsy Gleason score (GS) and iPSA level were not significantly different between the radiation and surgery groups (Table 1). The patients treated with radiation were significantly older (median age 70 years vs. 64 years, p<0.05). A total of 37% of the prostatectomy patients had a positive margin. The median follow-up time was 33 months; 1458 follow-up PSA levels were available for analysis. Biochemical failure was defined as a rise in PSA level of 1.0 ng/ml above the nadir PSA level in radiotherapy cases, or any value above 0.2 ng/ml in the prostatectomy cases. Results: The overall 5 year actuarial biochemical relapse free survival (bRFS) rate was 70%. The 5-year bRFS rates for prostatectomy and radiotherapy were identical (70%) (Fig.1). The significant factors affecting bRFS rates were iPSA level (≤4 vs. 4-10 ng/ml) and Gleason score (≤6 vs. ≥7) (Table 2). The 5-year bRFS rates of patients with iPSA ≤4 vs. iPSA 4-10 ng/ml were 92% vs. 61% respectively, p<0.01. The 5-year clinical relapse free survival was 93%. All clinical failures were preceded by biochemical failure. Patients with positive surgical margins did significantly worse than those with negative

  20. Chemical Preparation Laboratory IND Candidate Compounds.

    Science.gov (United States)

    1986-01-21

    and final products unreported in the chemical literature were fully characterized by elemental and spectral analyses. 3 V% TABLE OF CONTENTS Page I...resulting crystalline material was filtered and washed with water to yield 2.0 g. An additional 0.2 g of the product was recovered from the above filtrate... mercaptopurine (Tri-C- acetvlthioinosine) (3): To a well stirred mixture of 2 (93.0 g, 0.236 mol) and pyridine (3570 mL), phosphorus pentasulfide (220.0 g, 0.49

  1. Multi-slice CT three dimensional volume measurement of tumors and livers in hepatocellular carcinoma

    International Nuclear Information System (INIS)

    Yu Yuanlong; Li Liangcai; Tang Binghang; Hu Zemin

    2004-01-01

    Objective: To examine the accuracy of multi-slice CT (MSCT) three dimensional (3D) volume measurement of tumors and livers in hepatocellular carcinoma cases by using immersion method as the standard. Methods: (1) The volume of 25 porkling livers was measured using immersion method in experiment group in vitro. Then the models were built according to Matsumoto's method and CT scanning and special software were used to measure the volume of the livers. (2) The volume of the tumors in 25 cases of hepatocellular carcinoma was measured using diameter measurement method and special volume measurement software (tissue measurements). Two tumors of them were measured respectively using MSCT 3D measurement, diameter measurement before the operation and immersion method after the operation. The data of the two groups were examined using pairing t test. Results: (1) The volume range of 25 porkling livers was 68.50-1150.10 ml using immersion method and 69.78-1069.97 ml using MSCT 3D measurement. There was no significant difference of the data in these two groups using t-test (t=1.427, P>0.05). (2) The volume range of 25 hepatocellular tumors was 395.16-2747.7 ml using diameter measurement and 203.10-1463.19 ml using MSCT 3D measurement before the operation. There was significant difference of the data in these two groups using t-test (t=7.689, P<0.001). In 2 ablated tumors, 1 case's volume was (21.75±0.60) ml using MSCT 3D measurement and 33.73 ml using diameter measurement before the operation and 21.50 ml using immersion measurement after the operation. The other case's volume was (696.13±5.30) ml using MSCT 3D measurement and 1323.51 ml using diameter measurement before the operation and 685.50 ml using immersion measurement after the operation. Conclusion: MSCT 3D volume measurement can accurately measure the volume of tumor and liver and has important clinical application value. There is no significant difference between MSCT 3D volume measurement and immersion method

  2. SysML Model of the Pick and Place Unit for Papyrus UML: Scenario Sc4b

    OpenAIRE

    Vogel-Heuser, Birgit; Folmer, Jens; Legat, Christoph

    2014-01-01

    The Pick and Place Unit (PPU) is a bench-scale lab demonstrator which is open to the research community to investigate a variety of different topics. To conduct research on the evolution of production automation systems, a variety of different manifestations of the PPU (referred to as scenarios) were developed. A documentation of the PPU and its scenarios is publicly available at www.ppu-demonstrator.org. In this zipped file, a SysML model consisting of state charts and block definition diagr...

  3. The Quest for the 1p36 Tumor Suppressor

    Science.gov (United States)

    Bagchi, Anindya; Mills, Alea A.

    2010-01-01

    Genomic analyses of late-stage human cancers have uncovered deletions encompassing 1p36, thereby providing an extensive body of literature supporting the idea that a potent tumor suppressor resides in this interval. Although a number of genes have been proposed as 1p36 candidate tumor suppressors, convincing evidence that their encoded products protect from cancer has been scanty. A recent functional study identified CHD5 as a novel tumor suppressor mapping to 1p36. Here we discuss evidence supporting CHD5’s tumor suppressive role. Together, these findings suggest that strategies designed to enhance CHD5 activity could provide novel approaches for treating a broad range of human malignancies. PMID:18413720

  4. Ewing tumors in infants

    NARCIS (Netherlands)

    van den Berg, Henk; Dirksen, Uta; Ranft, Andreas; Jürgens, Heribert

    2008-01-01

    Malignancies in infancy are extremely rare. Ewing tumors are hardly ever noted in these children. Since it is generally assumed that malignancies in infancy have an extremely poor outcome, we wanted to investigate whether this was also the case in Ewing tumors. We identified in the Munster data

  5. GASTROENTEROPANCREATIC NEUROENDOCRINE TUMORS ...

    African Journals Online (AJOL)

    Pavel M.E., Baum U., Hahn E.G., Hensen J. Doxorubucin and streptozocin after failed biotherapy of Neuroendocrine tumors. Int J. Gastrointest Cancer 2005; 35 179-185. 33. Yao J.C., Phan A., Hoff P.M., et al. Targeting vas- cular endothelial growth factor in advanced carci- noid tumors: a random assignment phase II study.

  6. Atypically localized glomus tumors

    Directory of Open Access Journals (Sweden)

    Meric Ugurlar

    2016-12-01

    Conclusion: When a painful mass is found in the body, glomus tumors should be kept in mind. The consideration of symptoms, including pain, temperature sensitivity, point tenderness, and discoloration, common characteristics of glomus tumors, may aid diagnosis. [Hand Microsurg 2016; 5(3.000: 112-117

  7. Renal inflammatory myofibroblastic tumor

    DEFF Research Database (Denmark)

    Heerwagen, S T; Jensen, C; Bagi, P

    2007-01-01

    Renal inflammatory myofibroblastic tumor (IMT) is a rare soft-tissue tumor of controversial etiology with a potential for local recurrence after incomplete surgical resection. The radiological findings in renal IMT are not well described. We report two cases in adults with a renal mass treated...

  8. Pseudoanaplastic tumors of bone

    Energy Technology Data Exchange (ETDEWEB)

    Bahk, Won-Jong [Uijongbu St. Mary Hospital, The Catholic University of Korea, Department of Orthopaedic Surgery, Gyunggido, 480-821 (Korea); Mirra, Joseph M. [Orthopaedic Hospital, Orthopedic Oncology, Los Angeles, California (United States)

    2004-11-01

    To discuss the concept of pseudoanaplastic tumors of bone, which pathologically show hyperchromatism and marked pleomorphism with quite enlarged, pleomorphic nuclei, but with no to extremely rare, typical mitoses, and to propose guidelines for their diagnosis. From a database of 4,262 bone tumors covering from 1971 to 2001, 15 cases of pseudoanaplastic bone tumors (0.35% of total) were retrieved for clinical, radiographic and pathologic review. Postoperative follow-up after surgical treatment was at least 3 years and a maximum of 7 years. There were eight male and seven female patients. Their ages ranged from 10 to 64 years with average of 29.7 years. Pathologic diagnoses of pseudoanaplastic variants of benign bone tumors included: osteoblastoma (4 cases), giant cell tumor (4 cases), chondromyxoid fibroma (3 cases), fibrous dysplasia (2 cases), fibrous cortical defect (1 case) and aneurysmal bone cyst (1 case). Radiography of all cases showed features of a benign bone lesion. Six cases, one case each of osteoblastoma, fibrous dysplasia, aneurysmal bone cyst, chondromyxoid fibroma, giant cell tumor and osteoblastoma, were initially misdiagnosed as osteosarcoma. The remaining cases were referred for a second opinion to rule out sarcoma. Despite the presence of significant cytologic aberrations, none of our cases showed malignant behavior following simple curettage or removal of bony lesions. Our observation justifies the concept of pseudoanaplasia in some benign bone tumors as in benign soft tissue tumors, especially in their late evolutionary stage when bizarre cytologic alterations strongly mimic a sarcoma. (orig.)

  9. Vanishing tumor in pregnancy

    Directory of Open Access Journals (Sweden)

    M V Vimal

    2012-01-01

    Full Text Available A patient with microprolactinoma, who had two successful pregnancies, is described for management issues. First pregnancy was uneventful. During the second pregnancy, the tumor enlarged to macroprolactinoma with headache and blurring of vision which was managed successfully with bromocriptine. Post delivery, complete disappearance of the tumor was documented.

  10. Vanishing tumor in pregnancy

    Science.gov (United States)

    Vimal, M. V.; Budyal, Sweta; Kasliwal, Rajeev; Jagtap, Varsha S.; Lila, Anurag R.; Bandgar, Tushar; Menon, Padmavathy; Shah, Nalini S.

    2012-01-01

    A patient with microprolactinoma, who had two successful pregnancies, is described for management issues. First pregnancy was uneventful. During the second pregnancy, the tumor enlarged to macroprolactinoma with headache and blurring of vision which was managed successfully with bromocriptine. Post delivery, complete disappearance of the tumor was documented. PMID:23226664

  11. Biotechnical paving of recombinant enterocin A as the candidate of anti-Listeria agent.

    Science.gov (United States)

    Hu, Xiaoyuan; Mao, Ruoyu; Zhang, Yong; Teng, Da; Wang, Xiumin; Xi, Di; Huang, Jianzhong; Wang, Jianhua

    2014-08-28

    Enterocin A is a classic IIa bacteriocin isolated firstly from Enterococcus faecium CTC492 with selective antimicrobial activity against Listeria strains. However, the application of enterocin A as an anti-Listeria agent has been limited due to its very low native yield. The present work describes high production of enterocin A through codon optimization strategy and its character study. The gene sequence of enterocin A was optimized based on preferential codon usage in Pichia pastoris to increase its expression efficiency. The highest anti-Listeria activity reached 51,200 AU/ml from 180 mg/l of total protein after 24 h of induction in a 5-L fermenter. Recombinant enterocin A (rEntA), purified by gel filtration chromatography, showed very strong activity against Listeria ivanovii ATCC 19119 with a low MIC of 20 ng/ml. In addition, the rEntA killed over 99% of tested L. ivanovii ATCC19119 within 4 h when exposed to 4 × MIC (80 ng/ml). Moreover, it showed high stability under a wide pH range (2-10) and maintained full activity after 1 h of treatment at 80°C within a pH range of 2-8. Its antimicrobial activity was enhanced at 25 and 50 mM NaCl, while 100-400 mM NaCl had little effect on the bactericidal ability of rEntA. The EntA was successfully expressed in P. pastoris, and this feasible system could pave the pre-industrial technological path of rEntA as a competent candidate as an anti-Listeria agent. Furthermore, it showed high stability under wide ranges of conditions, which could be potential as the new candidate of anti-Listeria agent.

  12. Tumorous interstitial lung disease

    International Nuclear Information System (INIS)

    Dinkel, E.; Meyer, E.; Mundinger, A.; Helwig, A.; Blum, U.; Wuertemberger, G.

    1990-01-01

    The radiological findings in pulmonary lymphangitic carcinomatosis and in leukemic pulmonary infiltrates mirror the tumor-dependent monomorphic interstitial pathology of lung parenchyma. It is a proven fact that pulmonary lymphangitic carcinomatosis is caused by hematogenous tumor embolization to the lungs; pathogenesis by contiguous lymphangitic spread is the exception. High-resolution CT performed as a supplement to the radiological work-up improves the sensitivity for pulmonary infiltrates in general and thus makes the differential diagnosis decided easier. Radiological criteria cannot discriminate the different forms of leukemia. Plain chest X-ray allows the diagnosis of pulmonary involvement in leukemia due to tumorous infiltrates and of tumor- or therapy-induced complications. It is essential that the radiological findings be interpreted with reference to the stage of tumor disease and the clinical parameters to make the radiological differential diagnosis of opportunistic infections more reliable. (orig.) [de

  13. Tumors of peripheral nerves

    International Nuclear Information System (INIS)

    Ho, Michael; Lutz, Amelie M.

    2017-01-01

    Differentiation between malignant and benign tumors of peripheral nerves in the early stages is challenging; however, due to the unfavorable prognosis of malignant tumors early identification is required. To show the possibilities for detection, differential diagnosis and clinical management of peripheral nerve tumors by imaging appearance in magnetic resonance (MR) neurography. Review of current literature available in PubMed and MEDLINE, supplemented by the authors' own observations in clinical practice. Although not pathognomonic, several imaging features have been reported for a differentiation between distinct peripheral nerve tumors. The use of MR neurography enables detection and initial differential diagnosis in tumors of peripheral nerves. Furthermore, it plays an important role in clinical follow-up, targeted biopsy and surgical planning. (orig.) [de

  14. Wilm's tumor in adulthood

    International Nuclear Information System (INIS)

    Matveev, B.P.; Bukharkin, B.V.; Gotsadze, D.T.

    1984-01-01

    Wilms' tumor occurs extremely rarely in adults. There is no consensus in the literature on the problems of clinical manifestations, diagnosis and treatment of the diseasa. Ten adult patients (aged 16-29) with Wilms' tumor formed the study group. They made up 0.9 per cent of the total number of kidney tumor patients. The peculiarities of the clinical course that distinguish adult nephroblastoma from renal cancer and Wilms' tumor of the infancy were analysed. The latent period appeared to be long. Problems of diagnosis are discussed. Angiography proved to be of the highest diagnostic value. Complex treatment including transperitoneal nephrectory, radiation and chemotherapy was carried out in 7 cases, palliative radiation treatmenchemotherapy andn 3. Unlike pediatric nephroblastomt - i Wilms' tumor in adults was resistant to radiation. Treatment results still remained unsatisfactory: 6 patients died 7-19 months after the beginning of treatment

  15. Radiotherapy of pineal tumors

    International Nuclear Information System (INIS)

    Danoff, B.; Sheline, G.E.

    1984-01-01

    Radiotherapy has universally been used in the treatment of pineal tumors and suprasellar germinomas. Recently however, major technical advances related to the use of the operating microscope and development of microsurgical techniques have prompted a renewed interest in the direct surgical approach for biopsy and/or excision. This interest has resulted in a controversy regarding the role of surgery prior to radiotherapy. Because of the heterogeneity of tumors occurring in the pineal region (i.e., germ cell tumors, pineal parenchymal tumors, glial tumors, and cysts) and their differing biological behavior, controversy also surrounds aspects of radiotherapy such as: the optimal radiation dose, the volume to be irradiated, and indications for prophylactic spinal irradiation. A review of the available data is presented in an attempt to answer these questions

  16. Molecular characterization of radon-induced rat lung tumors

    International Nuclear Information System (INIS)

    Guillet Bastide, K.

    2008-11-01

    The radon gas is a well known lung carcinogenic factor in human at high doses but the cancer risk at low doses is not established. Indeed, epidemiological studies at low doses are difficult to conduct because of the human exposure to other lung carcinogenic factors. These data underlined the necessity to conduct experiments on lung tumors developed on animal model. The aim of this work was to characterize rat lung tumors by working on a series of radon-induced tumors that included adenocarcinomas (A.C.), squamous cell carcinomas (S.C.C.) and adeno-squamous carcinomas (A.S.C.), that are mixed tumors with both A.C. and S.C.C. cellular components. A C.G.H. analysis of the three types of tumors allowed us to define chromosomal recurrent unbalances and to target candidate genes potentially implicated in lung carcinogenesis, as p16Ink4a, p19Arf, Rb1, K-Ras or c-Myc. A more precise analysis of the p16Ink4a/Cdk4/Rb1 and p19Arf/Mdm2/Tp53 pathways was performed and indicated that the Rb1 pathway was frequently inactivated through an absence of p16 Ink4a protein expression, indicating that it has a major role in rat lung carcinogenesis. Finally, a comparative transcriptomic analysis of the three types of tumors allowed us to show for the first time that the complex tumors A.S.C. have a transcriptomic profile in accordance with their mixed nature but that they also display their own expression profiles specificities. This work allowed us to find molecular characteristics common to murine and human lung tumors, indicating that the model of lung tumors in rat is pertinent to search for radiation-induced lung tumors specificities and to help for a better molecular identification of this type of tumors in human. (author)

  17. Parallel evolution of tumor subclones mimics diversity between tumors

    DEFF Research Database (Denmark)

    Martinez, Pierre; Birkbak, Nicolai Juul; Gerlinger, Marco

    2013-01-01

    Intratumor heterogeneity (ITH) may foster tumor adaptation and compromise the efficacy of personalized medicines approaches. The scale of heterogeneity within a tumor (intratumor heterogeneity) relative to genetic differences between tumors (intertumor heterogeneity) is unknown. To address this, ...

  18. Reducing stigma and discrimination: Candidate interventions

    Directory of Open Access Journals (Sweden)

    Kassam Aliya

    2008-04-01

    Full Text Available Abstract This paper proposes that stigma in relation to people with mental illness can be understood as a combination of problems of knowledge (ignorance, attitudes (prejudice and behaviour (discrimination. From a literature review, a series of candidate interventions are identified which may be effective in reducing stigmatisation and discrimination at the following levels: individuals with mental illness and their family members; the workplace; and local, national and international. The strongest evidence for effective interventions at present is for (i direct social contact with people with mental illness at the individual level, and (ii social marketing at the population level.

  19. Processability analysis of candidate waste forms

    International Nuclear Information System (INIS)

    Gould, T.H. Jr.; Dunson, J.B. Jr.; Eisenberg, A.M.; Haight, H.G. Jr.; Mello, V.E.; Schuyler, R.L. III.

    1982-01-01

    A quantitative merit evaluation, or processability analysis, was performed to assess the relative difficulty of remote processing of Savannah River Plant high-level wastes for seven alternative waste form candidates. The reference borosilicate glass process was rated as the simplest, followed by FUETAP concrete, glass marbles in a lead matrix, high-silica glass, crystalline ceramics (SYNROC-D and tailored ceramics), and coated ceramic particles. Cost estimates for the borosilicate glass, high-silica glass, and ceramic waste form processing facilities are also reported

  20. Blend Analysis of HATNet Transit Candidates

    Directory of Open Access Journals (Sweden)

    Bakos G.Á.

    2011-02-01

    Full Text Available Candidate transiting planet systems discovered by wide-field groundbased surveys must go through an intensive follow-up procedure to distinguish the true transiting planets from the much more common false positives. Especially pernicious are configurations of three or more stars which produce radial velocity and light curves that are similar to those of single stars transited by a planet. In this contribution we describe the methods used by the HATNet team to reject these blends, giving a few illustrative examples.

  1. Reducing stigma and discrimination: Candidate interventions.

    Science.gov (United States)

    Thornicroft, Graham; Brohan, Elaine; Kassam, Aliya; Lewis-Holmes, Elanor

    2008-04-13

    This paper proposes that stigma in relation to people with mental illness can be understood as a combination of problems of knowledge (ignorance), attitudes (prejudice) and behaviour (discrimination). From a literature review, a series of candidate interventions are identified which may be effective in reducing stigmatisation and discrimination at the following levels: individuals with mental illness and their family members; the workplace; and local, national and international. The strongest evidence for effective interventions at present is for (i) direct social contact with people with mental illness at the individual level, and (ii) social marketing at the population level.

  2. Geoscience Training for NASA Astronaut Candidates

    Science.gov (United States)

    Young, K. E.; Evans, C. A.; Bleacher, J. E.; Graff, T. G.; Zeigler, R.

    2017-01-01

    After being selected to the astronaut office, crewmembers go through an initial two year training flow, astronaut candidacy, where they learn the basic skills necessary for spaceflight. While the bulk of astronaut candidate training currently centers on the multiple subjects required for ISS operations (EVA skills, Russian language, ISS systems, etc.), training also includes geoscience training designed to train crewmembers in Earth observations, teach astronauts about other planetary systems, and provide field training designed to investigate field operations and boost team skills. This training goes back to Apollo training and has evolved to support ISS operations and future exploration missions.

  3. Comparing CT perfusion with oxygen partial pressure in a rabbit VX2 soft-tissue tumor model.

    Science.gov (United States)

    Sun, Chang-Jin; Li, Chao; Lv, Hai-Bo; Zhao, Cong; Yu, Jin-Ming; Wang, Guang-Hui; Luo, Yun-Xiu; Li, Yan; Xiao, Mingyong; Yin, Jun; Lang, Jin-Yi

    2014-01-01

    The aim of this study was to evaluate the oxygen partial pressure of the rabbit model of the VX2 tumor using a 64-slice perfusion CT and to compare the results with that obtained using the oxygen microelectrode method. Perfusion CT was performed for 45 successfully constructed rabbit models of a VX2 brain tumor. The perfusion values of the brain tumor region of interest, the blood volume (BV), the time to peak (TTP) and the peak enhancement intensity (PEI) were measured. The results were compared with the partial pressure of oxygen (PO2) of that region of interest obtained using the oxygen microelectrode method. The perfusion values of the brain tumor region of interest in 45 successfully constructed rabbit models of a VX2 brain tumor ranged from 1.3-127.0 (average, 21.1 ± 26.7 ml/min/ml); BV ranged from 1.2-53.5 ml/100g (average, 22.2 ± 13.7 ml/100g); PEI ranged from 8.7-124.6 HU (average, 43.5 ± 28.7 HU); and TTP ranged from 8.2-62.3 s (average, 38.8 ± 14.8 s). The PO2 in the corresponding region ranged from 0.14-47 mmHg (average, 16 ± 14.8 mmHg). The perfusion CT positively correlated with the tumor PO2, which can be used for evaluating the tumor hypoxia in clinical practice.

  4. Salivary agglutinin/DMBT1SAG expression is up-regulated in the presence of salivary gland tumors

    DEFF Research Database (Denmark)

    Bikker, F J; van der Wal, J E; Ligtenberg, A J M

    2004-01-01

    Salivary agglutinin (SAG) is encoded by the gene Deleted in Malignant Brain Tumors 1 (DMBT1) and represents the salivary variant of DMBT1 (DMBT1(SAG)). While SAG is a bona fide anti-caries factor, DMBT1 was proposed as a candidate tumor-suppressor for brain, digestive tract, and lung cancer. Thou...

  5. Tumor control probability after a radiation of animal tumors

    International Nuclear Information System (INIS)

    Urano, Muneyasu; Ando, Koichi; Koike, Sachiko; Nesumi, Naofumi

    1975-01-01

    Tumor control and regrowth probability of animal tumors irradiated with a single x-ray dose were determined, using a spontaneous C3H mouse mammary carcinoma. Cellular radiation sensitivity of tumor cells and tumor control probability of the tumor were examined by the TD 50 and TCD 50 assays respectively. Tumor growth kinetics were measured by counting the percentage of labelled mitosis and by measuring the growth curve. A mathematical analysis of tumor control probability was made from these results. A formula proposed, accounted for cell population kinetics or division probability model, cell sensitivity to radiation and number of tumor cells. (auth.)

  6. The Tumor Macroenvironment: Cancer-Promoting Networks Beyond Tumor Beds.

    Science.gov (United States)

    Rutkowski, Melanie R; Svoronos, Nikolaos; Perales-Puchalt, Alfredo; Conejo-Garcia, Jose R

    2015-01-01

    During tumor progression, alterations within the systemic tumor environment, or macroenvironment, result in the promotion of tumor growth, tumor invasion to distal organs, and eventual metastatic disease. Distally produced hormones, commensal microbiota residing within mucosal surfaces, myeloid cells and even the bone marrow impact the systemic immune system, tumor growth, and metastatic spread. Understanding the reciprocal interactions between the cells and soluble factors within the macroenvironment and the primary tumor will enable the design of specific therapies that have the potential to prevent dissemination and metastatic spread. This chapter will summarize recent findings detailing how the primary tumor and systemic tumor macroenvironment coordinate malignant progression. © 2015 Elsevier Inc. All rights reserved.

  7. Increased Plasma Colloid Osmotic Pressure Facilitates the Uptake of Therapeutic Macromolecules in a Xenograft Tumor Model

    Directory of Open Access Journals (Sweden)

    Matthias Hofmann

    2009-08-01

    Full Text Available Elevated tumor interstitial fluid pressure (TIFP is a characteristic of most solid tumors. Clinically, TIFP may hamper the uptake of chemotherapeutic drugs into the tumor tissue reducing their therapeutic efficacy. In this study, a means of modulating TIFP to increase the flux of macromolecules into tumor tissue is presented, which is based on the rationale that elevated plasma colloid osmotic pressure (COP pulls water from tumor interstitium lowering the TIFP. Concentrated human serum albumin: (20% HSA, used as an agent to enhance COP, reduced the TIFP time-dependently from 8 to 2 mm Hg in human tumor xenograft models bearing A431 epidermoid vulva carcinomas. To evaluate whether this reduction facilitates the uptake of macromolecules, the intratumoral distribution of fluorescently conjugated dextrans (2.5 mg/ml and cetuximab (2.0 mg/ml was probed using novel time domain nearinfrared fluorescence imaging. This method permitted discrimination and semiquantification of tumor-accumulated conjugate from background and unspecific probe fluorescence. The coadministration of 20% HSA together with either dextrans or cetuximab was found to lower the TIFP significantly and increase the concentration of the substances within the tumor tissue in comparison to control tumors. Furthermore, combined administration of 20%HSA plus cetuximab reduced the tumor growth significantly in comparison to standard cetuximab treatment. These data demonstrate that increased COP lowers the TIFP within hours and increases the uptake of therapeutic macromolecules into the tumor interstitium leading to reduced tumor growth. This model represents a novel approach to facilitate the delivery of therapeutics into tumor tissue, particularly monoclonal antibodies.

  8. Regional cerebral blood flow in the patient with brain tumor

    International Nuclear Information System (INIS)

    Tsuchida, Shohei

    1993-01-01

    Regional cerebral blood flow (rCBF) was measured with xenon-enhanced CT (Xe-CT) in 21 cases of intracranial tumors (13 meningiomas, 5 gliomas, 3 metastatic brain tumors). Peritumoral edema was graded as mild, moderate or severe based on the extent of edema on CT and MRI. According to intratumoral blood flow distribution patterns, three patterns were classified as central type with relatively high blood flow at the center of the tumor, homogeneous type with an almost homogeneous blood flow distribution, and marginal type with relatively high blood flow at the periphery of the tumor. High grade astrocytoma and metastatic brain tumor showed marginal type blood flow and moderate or severe edema except in one case. Five meningiomas with severe peritumoral edema revealed marginal type blood flow and four with mild peritumoral edema showed central type blood flow, except for one case. No correlation was found between the extent of peritumoral edema and histological subtype, tumor size, location, duration of clinical history, vascularization on angiogram, and mean blood flow in the tumor. These results suggest that blood flow distribution patterns within the tumor may affect the extension of peritumoral edema. Pre- and postoperative rCBFs were evaluated with Xe-CT and IMP-SPECT in 7 cases, mean rCBF of peritumoral edema was 6.2 ml/100 g/min preoperatively, and discrepancy between rCBF on Xe-CT and that on IMP-SPECT was shown in the remote cortical region ipsilateral to the tumor. Postoperative rCBF revealed an improved blood flow in both adjacent and remote areas, suggesting that the decreased blood flow associated with brain tumors might be relieved after surgery. (author) 53 refs

  9. ML-7 amplifies the quinocetone-induced cell death through akt and MAPK-mediated apoptosis on HepG2 cell line.

    Science.gov (United States)

    Zhou, Yan; Zhang, Shen; Deng, Sijun; Dai, Chongshan; Tang, Shusheng; Yang, Xiayun; Li, Daowen; Zhao, Kena; Xiao, Xilong

    2016-01-01

    The study aims at evaluating the combination of the quinocetone and the ML-7 in preclinical hepatocellular carcinoma models. To this end, the effect of quinocetone and ML-7 on apoptosis induction and signaling pathways was analyzed on HepG2 cell lines. Here, we report that ML-7, in a nontoxic concentration, sensitized the HepG2 cells to quinocetone-induced cytotoxicity. Also, ML-7 profoundly enhances quinocetone-induced apoptosis in HepG2 cell line. Mechanistic investigations revealed that ML-7 and quinocetone act in concert to trigger the cleavage of caspase-8 as well as Bax/Bcl-2 ratio up-regulation and subsequent cleavage of Bid, capsases-9 and -3. Importantly, ML-7 weakened the quinocetone-induced Akt pathway activation, but strengthened the phosphorylation of p-38, ERK and JNK. Further treatment of Akt activator and p-38 inhibitor almost completely abolished the ML-7/quinocetone-induced apoptosis. In contrast, the ERK and JNK inhibitor aggravated the ML-7/quinocetone-induced apoptosis, indicating that the synergism critically depended on p-38 phosphorylation and HepG2 cells provoke Akt, ERK and JNK signaling pathways to against apoptosis. In conclusion, the rational combination of quinocetone and ML-7 presents a promising approach to trigger apoptosis in hepatocellular carcinoma, which warrants further investigation.

  10. Radiofrequency Ablation of Lung Tumors

    Science.gov (United States)

    ... News Physician Resources Professions Site Index A-Z Radiofrequency Ablation (RFA) / Microwave Ablation (MWA) of Lung Tumors ... and Microwave Ablation of Lung Tumors? What are Radiofrequency and Microwave Ablation of Lung Tumors? Radiofrequency ablation, ...

  11. Candidate luminal B breast cancer genes identified by genome, gene expression and DNA methylation profiling.

    Directory of Open Access Journals (Sweden)

    Stéphanie Cornen

    Full Text Available Breast cancers (BCs of the luminal B subtype are estrogen receptor-positive (ER+, highly proliferative, resistant to standard therapies and have a poor prognosis. To better understand this subtype we compared DNA copy number aberrations (CNAs, DNA promoter methylation, gene expression profiles, and somatic mutations in nine selected genes, in 32 luminal B tumors with those observed in 156 BCs of the other molecular subtypes. Frequent CNAs included 8p11-p12 and 11q13.1-q13.2 amplifications, 7q11.22-q34, 8q21.12-q24.23, 12p12.3-p13.1, 12q13.11-q24.11, 14q21.1-q23.1, 17q11.1-q25.1, 20q11.23-q13.33 gains and 6q14.1-q24.2, 9p21.3-p24,3, 9q21.2, 18p11.31-p11.32 losses. A total of 237 and 101 luminal B-specific candidate oncogenes and tumor suppressor genes (TSGs presented a deregulated expression in relation with their CNAs, including 11 genes previously reported associated with endocrine resistance. Interestingly, 88% of the potential TSGs are located within chromosome arm 6q, and seven candidate oncogenes are potential therapeutic targets. A total of 100 candidate oncogenes were validated in a public series of 5,765 BCs and the overexpression of 67 of these was associated with poor survival in luminal tumors. Twenty-four genes presented a deregulated expression in relation with a high DNA methylation level. FOXO3, PIK3CA and TP53 were the most frequent mutated genes among the nine tested. In a meta-analysis of next-generation sequencing data in 875 BCs, KCNB2 mutations were associated with luminal B cases while candidate TSGs MDN1 (6q15 and UTRN (6q24, were mutated in this subtype. In conclusion, we have reported luminal B candidate genes that may play a role in the development and/or hormone resistance of this aggressive subtype.

  12. The PCa Tumor Microenvironment.

    Science.gov (United States)

    Sottnik, Joseph L; Zhang, Jian; Macoska, Jill A; Keller, Evan T

    2011-12-01

    The tumor microenvironment (TME) is a very complex niche that consists of multiple cell types, supportive matrix and soluble factors. Cells in the TME consist of both host cells that are present at tumor site at the onset of tumor growth and cells that are recruited in either response to tumor- or host-derived factors. PCa (PCa) thrives on crosstalk between tumor cells and the TME. Crosstalk results in an orchestrated evolution of both the tumor and microenvironment as the tumor progresses. The TME reacts to PCa-produced soluble factors as well as direct interaction with PCa cells. In return, the TME produces soluble factors, structural support and direct contact interactions that influence the establishment and progression of PCa. In this review, we focus on the host side of the equation to provide a foundation for understanding how different aspects of the TME contribute to PCa progression. We discuss immune effector cells, specialized niches, such as the vascular and bone marrow, and several key protein factors that mediate host effects on PCa. This discussion highlights the concept that the TME offers a potentially very fertile target for PCa therapy.

  13. Epilepsy and brain tumors

    Science.gov (United States)

    ENGLOT, DARIO J.; CHANG, EDWARD F.; VECHT, CHARLES J.

    2016-01-01

    Seizures are common in patients with brain tumors, and epilepsy can significantly impact patient quality of life. Therefore, a thorough understanding of rates and predictors of seizures, and the likelihood of seizure freedom after resection, is critical in the treatment of brain tumors. Among all tumor types, seizures are most common with glioneuronal tumors (70–80%), particularly in patients with frontotemporal or insular lesions. Seizures are also common in individuals with glioma, with the highest rates of epilepsy (60–75%) observed in patients with low-grade gliomas located in superficial cortical or insular regions. Approximately 20–50% of patients with meningioma and 20–35% of those with brain metastases also suffer from seizures. After tumor resection, approximately 60–90% are rendered seizure-free, with most favorable seizure outcomes seen in individuals with glioneuronal tumors. Gross total resection, earlier surgical therapy, and a lack of generalized seizures are common predictors of a favorable seizure outcome. With regard to anticonvulsant medication selection, evidence-based guidelines for the treatment of focal epilepsy should be followed, and individual patient factors should also be considered, including patient age, sex, organ dysfunction, comorbidity, or cotherapy. As concomitant chemotherapy commonly forms an essential part of glioma treatment, enzyme-inducing anticonvulsants should be avoided when possible. Seizure freedom is the ultimate goal in the treatment of brain tumor patients with epilepsy, given the adverse effects of seizures on quality of life. PMID:26948360

  14. CNS tumors: postoperative evaluation

    International Nuclear Information System (INIS)

    Dayanir, Y.

    2012-01-01

    Full text: Imaging assessment of brain tumors following surgery is complex and depends upon several factors, including the location of the tumor, the surgical procedure and the disease process for which it was performed. Depending upon these factors, one or a combination of complementary imaging modalities may be required to demonstrate any clinically relevant situation, to assist the surgeon in deciding if repeat surgery is necessary. Conventional magnetic resonance imaging (MRI) can show the shape, size, signal intensity, and enhancement of a brain tumor. It has been widely used to diagnose and differentiate brain tumors and to assess the surgery outcomes. Longitudinal MRI scans have also been applied for the assessment of treatment and response to surgery. The newly developed MRI techniques, including diffusion weighted imaging (DWI), perfusion weighted imaging (PWI) and magnetic resonance spectroscopy (MRS), have the potential to provide the molecular, functional and metabolic information of preoperative and postoperative brain tumors. Postoperative diffusion and perfusion magnetic resonance imaging are especially useful in predicting early functional recovery from new deficits after brain tumor surgery.This lecture will stress the principles, applications, and pitfalls of conventional as well as newly developing functional imaging techniques following operation of brain tumors

  15. Vascular thermal adaptation in tumors and normal tissue in rats

    International Nuclear Information System (INIS)

    Nah, Byung Sik; Choi, Ihl-Bohng; Oh, Won Young; Osborn, James L.; Song, Chang W.

    1996-01-01

    Purpose: The vascular thermal adaptation in the R3230 adenocarcinoma, skin and muscle in the legs of Fischer rats was studied. Methods and Materials: The legs of Fischer rats bearing the R3230 AC adenocarcinoma (subcutaneously) were heated once or twice with a water bath, and the blood flow in the tumor, skin and muscle of the legs was measured with the radioactive microsphere method. Results: The blood flow in control R3230 AC tumors was 23.9 ml/100 g/min. The tumor blood flow increased about 1.5 times in 30 min and then markedly decreased upon heating at 44.5 deg. C for 90 min. In the tumors preheated 16 h earlier at 42.5 deg. C for 60 min, reheating at 44.5 deg. C increased the tumor blood flow by 2.5-fold in 30 min. Contrary to the decline in blood flow following an initial increase during the 44.5 deg. C heating without preheating, the tumor blood flow remained elevated throughout the 90 min reheating at 44.5 deg. C. These results indicated that thermal adaptation or thermotolerance developed in the tumor vasculatures after the preheating at 42.5 deg. C for 60 min. The magnitude of vascular thermal adaptation in the tumors 24 h and 48 h after the preheating, as judged from the changes in blood flow, were smaller than that 16 h after the preheating. Heating at 42.5 deg. C for 60 min induced vascular thermal adaptation also in the skin and muscle, which peaked in 48 h and 24 h, respectively, after the heating. Conclusion: Heating at 42.5 deg. C for 1 h induced vascular thermal adaptation in the R3230 AC tumor, skin, and muscle of rats that peaked 16-48 h after the heating. When the tumor blood vessels were thermally adapted, the tumor blood flow increased upon heating at temperatures that would otherwise reduce the tumor blood flow. Such an increase in tumor blood flow may hinder raising the tumor temperature while it may increase tumor oxygenation.

  16. Antitumor effect of Ganoderma lucidum : Cytotoxicity and Tumor Growth Delay(1)

    Energy Technology Data Exchange (ETDEWEB)

    Kwon, Hyoung Cheol; Kim, Jung Soo [Chonbuk National University College of Medicine, Chonju (Korea, Republic of); Choi, Dong Seong [Chonju Woosuck Univ., Chonju (Korea, Republic of); Song, Chang Won [Univ. of Minnesota Medical School, Minneapolis (United States)

    1994-10-15

    Purpose: To investigate the effect of aqueous extract of Ganoderma lucidum(G.I.) on the survival of tumor cells in vitro and on the growth of tumors in vivo. Materials and Methods: Dried G.I. was made into powder, extracted with distilled water, filtered and diluted from a maximum concentration of 100 mg/ml in sequence. The cytotoxicity of G.O. in vitro was evaluated from its ability to reduce the clonogenicity of SCK tumor cells. For the tumor growth delay study, about 2x10{sup 5} of SCK tumor cells were subcutaneously inoculated in the legs of A/J mice. The first experimental group of mice were injected i.p. with 0.2ml of 250 mg/kg of G/I. From the first day after tumor inoculation for 10 days. The second experimental group of mice were injected i.p. with 0.2ml of 250 mg/kg of G.I. either once a day for 10 days or twice a day for 5 days beginning from the 7th day after tumor inoculation. Results: 1. Cytotoxicity in vitro; survival fraction, as judged from the curve, at G.I. concentration of 0.5, 1,5,10,25,50 and 100 mg/ml were 1.0, 0.74{+-}0.03, 0.18{+-}0.03, 0.15{+-}0.02, 0.006{+-}0.002, 0.015 and 0.0015, respectively. 2. Tumor growth delay in vivo; a) the time required for the mean tumor volume to grow to 1,000mm{sup 3} was 11 days in the control group and 14 days in the experimental group. b) the time required for tumor volume to increase 4 times was 11 days in the control group while it was 10.5 and 12 days in the groups injected with G.I. once a day and twice a day from the 7th day after tumor inoculation respectively. Conclusion: Aqueous extracts of G.I. showed a marked cytotoxicity on the SCK mammary cells in vitro. Tumor growth delay was statistically significant when G.I. injection was started soon after tumor inoculation, but it was not significant when injection was started after the tumors were firmly established.

  17. Antitumor effect of Ganoderma lucidum : Cytotoxicity and Tumor Growth Delay(1)

    International Nuclear Information System (INIS)

    Kwon, Hyoung Cheol; Kim, Jung Soo; Choi, Dong Seong; Song, Chang Won

    1994-01-01

    Purpose: To investigate the effect of aqueous extract of Ganoderma lucidum(G.I.) on the survival of tumor cells in vitro and on the growth of tumors in vivo. Materials and Methods: Dried G.I. was made into powder, extracted with distilled water, filtered and diluted from a maximum concentration of 100 mg/ml in sequence. The cytotoxicity of G.O. in vitro was evaluated from its ability to reduce the clonogenicity of SCK tumor cells. For the tumor growth delay study, about 2x10 5 of SCK tumor cells were subcutaneously inoculated in the legs of A/J mice. The first experimental group of mice were injected i.p. with 0.2ml of 250 mg/kg of G/I. From the first day after tumor inoculation for 10 days. The second experimental group of mice were injected i.p. with 0.2ml of 250 mg/kg of G.I. either once a day for 10 days or twice a day for 5 days beginning from the 7th day after tumor inoculation. Results: 1. Cytotoxicity in vitro; survival fraction, as judged from the curve, at G.I. concentration of 0.5, 1,5,10,25,50 and 100 mg/ml were 1.0, 0.74±0.03, 0.18±0.03, 0.15±0.02, 0.006±0.002, 0.015 and 0.0015, respectively. 2. Tumor growth delay in vivo; a) the time required for the mean tumor volume to grow to 1,000mm 3 was 11 days in the control group and 14 days in the experimental group. b) the time required for tumor volume to increase 4 times was 11 days in the control group while it was 10.5 and 12 days in the groups injected with G.I. once a day and twice a day from the 7th day after tumor inoculation respectively. Conclusion: Aqueous extracts of G.I. showed a marked cytotoxicity on the SCK mammary cells in vitro. Tumor growth delay was statistically significant when G.I. injection was started soon after tumor inoculation, but it was not significant when injection was started after the tumors were firmly established

  18. Criteria for candidate species for aquaculture

    Energy Technology Data Exchange (ETDEWEB)

    Webber, H H; Riordan, P F

    1976-01-01

    The nature of the animal taxa that are the most probable candidates for an intensive, commercial aquatic animal husbandry industry is considered. A characterization is presented of those biological criteria that lend the species the necessary physiological and genetic malleability to be adapted and molded into a domesticated race. The animal cultivated must be amenable to intensive management in high-density confinements such as those now being engineered for high-yield aquaculture. Attributes considered are discussed in the context of the various aquacultural ecosystems in which the specific biotype is expected to achieve satisfactory growth and survival. Correlative with bionomic criteria, economic requirements are posed and evaluated in an effort to define a socially and financially profitable agribusiness system. Investment requirements and operating costs are considered in terms of expected returns. However, since production alone is insufficient to sustain an enterprise - i.e., the product must be sold - production costs must be judged against market values. Therefore, ultimate use or consumer acceptance criteria are incorporated into the list of essential requirements for a candidate species for aquafarming.

  19. Elemental abundances of solar sibling candidates

    International Nuclear Information System (INIS)

    Ramírez, I.; Lambert, D. L.; Endl, M.; Cochran, W. D.; MacQueen, P. J.; Bajkova, A. T.; Bobylev, V. V.; Roederer, I. U.; Wittenmyer, R. A.

    2014-01-01

    Dynamical information along with survey data on metallicity and in some cases age have been used recently by some authors to search for candidates of stars that were born in the cluster where the Sun formed. We have acquired high-resolution, high signal-to-noise ratio spectra for 30 of these objects to determine, using detailed elemental abundance analysis, if they could be true solar siblings. Only two of the candidates are found to have solar chemical composition. Updated modeling of the stars' past orbits in a realistic Galactic potential reveals that one of them, HD 162826, satisfies both chemical and dynamical conditions for being a sibling of the Sun. Measurements of rare-element abundances for this star further confirm its solar composition, with the only possible exception of Sm. Analysis of long-term high-precision radial velocity data rules out the presence of hot Jupiters and confirms that this star is not in a binary system. We find that chemical tagging does not necessarily benefit from studying as many elements as possible but instead from identifying and carefully measuring the abundances of those elements that show large star-to-star scatter at a given metallicity. Future searches employing data products from ongoing massive astrometric and spectroscopic surveys can be optimized by acknowledging this fact.

  20. Advanced Vaccine Candidates for Lassa Fever

    Directory of Open Access Journals (Sweden)

    Igor S. Lukashevich

    2012-10-01

    Full Text Available Lassa virus (LASV is the most prominent human pathogen of the Arenaviridae. The virus is transmitted to humans by a rodent reservoir, Mastomys natalensis, and is capable of causing lethal Lassa Fever (LF. LASV has the highest human impact of any of the viral hemorrhagic fevers (with the exception of Dengue Fever with an estimated several hundred thousand infections annually, resulting in thousands of deaths in Western Africa. The sizeable disease burden, numerous imported cases of LF in non-endemic countries, and the possibility that LASV can be used as an agent of biological warfare make a strong case for vaccine development. Presently there is no licensed vaccine against LF or approved treatment. Recently, several promising vaccine candidates have been developed which can potentially target different groups at risk. The purpose of this manuscript is to review the LASV pathogenesis and immune mechanisms involved in protection. The current status of pre-clinical development of the advanced vaccine candidates that have been tested in non-human primates will be discussed. Major scientific, manufacturing, and regulatory challenges will also be considered.

  1. Tumor cell surface proteins

    International Nuclear Information System (INIS)

    Kennel, S.J.; Braslawsky, G.R.; Flynn, K.; Foote, L.J.; Friedman, E.; Hotchkiss, J.A.; Huang, A.H.L.; Lankford, P.K.

    1982-01-01

    Cell surface proteins mediate interaction between cells and their environment. Unique tumor cell surface proteins are being identified and quantified in several tumor systems to address the following questions: (i) how do tumor-specific proteins arise during cell transformation; (ii) can these proteins be used as markers of tumor cell distribution in vivo; (iii) can cytotoxic drugs be targeted specifically to tumor cells using antibody; and (iv) can solid state radioimmunoassay of these proteins provide a means to quantify transformation frequencies. A tumor surface protein of 180,000 M/sub r/ (TSP-180) has been identified on cells of several lung carcinomas of BALB/c mice. TSP-180 was not detected on normal lung tissue, embryonic tissue, or other epithelial or sarcoma tumors, but it was found on lung carcinomas of other strains of mice. Considerable amino acid sequence homology exists among TSP-180's from several cell sources, indicating that TSP-180 synthesis is directed by normal cellular genes although it is not expressed in normal cells. The regulation of synthesis of TSP-180 and its relationship to normal cell surface proteins are being studied. Monoclonal antibodies (MoAb) to TSP-180 have been developed. The antibodies have been used in immunoaffinity chromatography to isolate TSP-180 from tumor cell sources. This purified tumor antigen was used to immunize rats. Antibody produced by these animals reacted at different sites (epitopes) on the TSP-180 molecule than did the original MoAb. These sera and MoAb from these animals are being used to identify normal cell components related to the TSP-180 molecule

  2. Central nervous system tumors

    International Nuclear Information System (INIS)

    Gavin, P.R.; Fike, J.R.; Hoopes, P.J.

    1995-01-01

    Central nervous system (CNS) tumors are relatively common in veterinary medicine, with most diagnoses occurring in the canine and feline species. Numerous tumor types from various cells or origins have been identified with the most common tumors being meningiomas and glial cell tumors. Radiation therapy is often used as an aid to control the clinical signs associated with these neoplasms. In general, these tumors have a very low metastatic potential, such that local control offers substantial benefit. Experience in veterinary radiation oncology would indicate that many patients benefit from radiation treatment. Current practice indicates the need for computed tomography or magnetic resonance imaging studies. These highly beneficial studies are used for diagnosis, treatment planning, and to monitor treatment response. Improvements in treatment planning and radiation delivered to the tumor, while sparing the normal tissues, should improve local control and decrease potential radiation related problems to the CNS. When possible, multiple fractions of 3 Gy or less should be used. The tolerance dose to the normal tissue with this fractionation schedule is 50 to 55 Gy. The most common and serious complications of radiation for CNS tumors is delayed radiation myelopathy and necrosis. Medical management of the patient during radiation therapy requires careful attention to anesthetic protocols, and medications to reduce intracranial pressure that is often elevated in these patients. Canine brain tumors have served as an experimental model to test numerous new treatments. Increased availability of advanced imaging modalities has spawned increased detection of these neoplasms. Early detection of these tumors with appropriate aggressive therapy should prove beneficial to many patients

  3. WE-G-18C-06: Is Diaphragm Motion a Good Surrogate for Liver Tumor Motion?

    Energy Technology Data Exchange (ETDEWEB)

    Yang, J [Department of Radiation Oncology, Duke University Medical Center, Durham, NC (United States); School of Information Science and Engineering, Shandong University, Jinan, Shandong (China); Cai, J; Zheng, C; Czito, B; Palta, M; Yin, F [Department of Radiation Oncology, Duke University Medical Center, Durham, NC (United States); Wang, H [School of Information Science and Engineering, Shandong University, Jinan, Shandong (China); Bashir, M [Department of Radiology, Duke University Medical Center, Durham, NC (United States)

    2014-06-15

    Purpose: To investigate whether diaphragm motion is a good surrogate for liver tumor motion by comparing their motion trajectories obtained from cine-MRI. Methods: Fourteen patients with hepatocellular carcinoma (10/14) or liver metastases (4/14) undergoing radiation therapy were included in this study. All patients underwent single-slice 2D cine-MRI simulations across the center of the tumor in three orthogonal planes. Tumor and diaphragm motion trajectories in the superior-inferior (SI), anteriorposterior (AP), and medial-lateral (ML) directions were obtained using the normalized cross-correlation based tracking technique. Agreement between tumor and diaphragm motions was assessed by calculating the phase difference percentage (PDP), intra-class correlation coefficient (ICC), Bland-Altman analysis (Diffs) and paired t-test. The distance (D) between tumor and tracked diaphragm area was analyzed to understand its impact on the correlation between tumor and diaphragm motions. Results: Of all patients, the means (±standard deviations) of PDP were 7.1 (±1.1)%, 4.5 (±0.5)% and 17.5 (±4.5)% in the SI, AP and ML directions, respectively. The means of ICC were 0.98 (±0.02), 0.97 (±0.02), and 0.08 (±0.06) in the SI, AP and ML directions, respectively. The Diffs were 2.8 (±1.4) mm, 2.4 (±1.1) mm, and 2.2 (±0.5) mm in the SI, AP and ML directions, respectively. The p-values derived from the paired t-test were < 0.02 in SI and AP directions, whereas were > 0.58 in ML direction primarily due to the small motion in ML direction. Tumor and diaphragmatic motion had high concordance when the distance between the tumor and tracked diaphragm areas was small. Conclusion: Preliminary results showed that liver tumor motion had good correlations with diaphragm motion in the SI and AP directions, indicating diaphragm motion in the SI and AP directions could potentially be a reliable surrogate for liver tumor motion. NIH (1R21CA165384-01A1), Golfers Against Cancer (GAC

  4. Stochastic models for tumoral growth

    OpenAIRE

    Escudero, Carlos

    2006-01-01

    Strong experimental evidence has indicated that tumor growth belongs to the molecular beam epitaxy universality class. This type of growth is characterized by the constraint of cell proliferation to the tumor border, and surface diffusion of cells at the growing edge. Tumor growth is thus conceived as a competition for space between the tumor and the host, and cell diffusion at the tumor border is an optimal strategy adopted for minimizing the pressure and helping tumor development. Two stoch...

  5. Tumores del timo y cirugía Tumors of thymus and surgery

    Directory of Open Access Journals (Sweden)

    Miguel Ángel Martín González

    2011-09-01

    Full Text Available Introducción: los tumores del timo constituyen menos del 1 % de todas las neoplasias, y es la cirugía el tratamiento de elección. Objetivos: conocer el tipo de tratamiento quirúrgico y la magnitud de la resección, así como la relación con el tamaño del tumor, el sangrado, el tiempo quirúrgico, la morbilidad y la mortalidad. Métodos: se realizó un estudio prospectivo en 22 pacientes con tumor mediastinal, que tuvieron criterios de cirugía durante el ingreso en los servicios de neurología o cirugía general del hospital "Hermanos Ameijeiras", desde enero de 2007 hasta febrero de 2009. Los resultados se presentan en por cientos y se empleó el chi cuadrado en la relación de variables. Resultados: 12 fueron del sexo femenino (54,5 %. El tratamiento más empleado fue la esternotomía total en 9 pacientes (40,9 %, el tiempo quirúrgico varió de 50 a 260 min con mediana de 127,5, mientras el sangrado por encima de 100 mL estuvo asociado a un tiempo quirúrgico de 61 a 180 min (p= 0,036. Se complicaron 11 pacientes (50 % y hubo 1 fallecido (4,5 %. El tamaño del tumor varió de 3,5 a 20 cm. El paciente con tumor neuroendocrino recidivó a los 10 meses, mientras los pacientes con timomas no muestran hasta la fecha recidiva local ni se ha comprobado actividad metastásica. Conclusión: la cirugía constituye el paso más importante en el tratamiento de los tumores mediastinales, y se logra, en la gran mayoría, la resección completa, a pesar del tamaño y la relación con estructuras vecinas.Introduction: the tumors of thymus account for less than 1 % of all neoplasms and the choice treatment is the surgery. Objectives: to know the type of surgical treatment and the magnitude of resection, as well as the relationship with the tumor size, bleeding, surgical time and morbidity and mortality. Methods: a prospective study was conducted in 20 patients presenting with mediastinum tumor with surgery criteria over the admission in the services of

  6. Uterine mesenchymal tumors

    Directory of Open Access Journals (Sweden)

    Nikhil A Sangle

    2011-01-01

    Full Text Available Uterine mesenchymal tumors are a heterogeneous group of neoplasms that can frequently be diagnostically challenging. Differentiation between the benign and malignant counterparts of mesenchymal tumors is significant due to differences in clinical outcome, and the role of the surgical pathologist in making this distinction (especially in the difficult cases cannot be underestimated. Although immunohistochemical stains are supportive toward establishing a final diagnosis, the morphologic features trump all the other ancillary techniques for this group of neoplasms. This review therefore emphasizes the key morphologic features required to diagnose and distinguish uterine mesenchymal tumors from their mimics, with a brief description of the relevant immunohistochemical features.

  7. Targeting the tumor microenvironment

    Energy Technology Data Exchange (ETDEWEB)

    Kenny, P.A.; Lee, G.Y.; Bissell, M.J.

    2006-11-07

    Despite some notable successes cancer remains, for the most part, a seemingly intractable problem. There is, however, a growing appreciation that targeting the tumor epithelium in isolation is not sufficient as there is an intricate mutually sustaining synergy between the tumor epithelial cells and their surrounding stroma. As the details of this dialogue emerge, new therapeutic targets have been proposed. The FDA has already approved drugs targeting microenvironmental components such as VEGF and aromatase and many more agents are in the pipeline. In this article, we describe some of the 'druggable' targets and processes within the tumor microenvironment and review the approaches being taken to disrupt these interactions.

  8. Assisted editing od SensorML with EDI. A bottom-up scenario towards the definition of sensor profiles.

    Science.gov (United States)

    Oggioni, Alessandro; Tagliolato, Paolo; Fugazza, Cristiano; Bastianini, Mauro; Pavesi, Fabio; Pepe, Monica; Menegon, Stefano; Basoni, Anna; Carrara, Paola

    2015-04-01

    Sensor observation systems for environmental data have become increasingly important in the last years. The EGU's Informatics in Oceanography and Ocean Science track stressed the importance of management tools and solutions for marine infrastructures. We think that full interoperability among sensor systems is still an open issue and that the solution to this involves providing appropriate metadata. Several open source applications implement the SWE specification and, particularly, the Sensor Observation Services (SOS) standard. These applications allow for the exchange of data and metadata in XML format between computer systems. However, there is a lack of metadata editing tools supporting end users in this activity. Generally speaking, it is hard for users to provide sensor metadata in the SensorML format without dedicated tools. In particular, such a tool should ease metadata editing by providing, for standard sensors, all the invariant information to be included in sensor metadata, thus allowing the user to concentrate on the metadata items that are related to the specific deployment. RITMARE, the Italian flagship project on marine research, envisages a subproject, SP7, for the set-up of the project's spatial data infrastructure. SP7 developed EDI, a general purpose, template-driven metadata editor that is composed of a backend web service and an HTML5/javascript client. EDI can be customized for managing the creation of generic metadata encoded as XML. Once tailored to a specific metadata format, EDI presents the users a web form with advanced auto completion and validation capabilities. In the case of sensor metadata (SensorML versions 1.0.1 and 2.0), the EDI client is instructed to send an "insert sensor" request to an SOS endpoint in order to save the metadata in an SOS server. In the first phase of project RITMARE, EDI has been used to simplify the creation from scratch of SensorML metadata by the involved researchers and data managers. An interesting by

  9. Rupture Speed and Dynamic Frictional Processes for the 1995 ML4.1 Shacheng, Hebei, China, Earthquake Sequence

    Science.gov (United States)

    Liu, B.; Shi, B.

    2010-12-01

    An earthquake with ML4.1 occurred at Shacheng, Hebei, China, on July 20, 1995, followed by 28 aftershocks with 0.9≤ML≤4.0 (Chen et al, 2005). According to ZÚÑIGA (1993), for the 1995 ML4.1 Shacheng earthquake sequence, the main shock is corresponding to undershoot, while aftershocks should match overshoot. With the suggestion that the dynamic rupture processes of the overshoot aftershocks could be related to the crack (sub-fault) extension inside the main fault. After main shock, the local stresses concentration inside the fault may play a dominant role in sustain the crack extending. Therefore, the main energy dissipation mechanism should be the aftershocks fracturing process associated with the crack extending. We derived minimum radiation energy criterion (MREC) following variational principle (Kanamori and Rivera, 2004)(ES/M0')min≧[3M0/(ɛπμR3)](v/β)3, where ES and M0' are radiated energy and seismic moment gained from observation, μ is the modulus of fault rigidity, ɛ is the parameter of ɛ=M0'/M0,M0 is seismic moment and R is rupture size on the fault, v and β are rupture speed and S-wave speed. From II and III crack extending model, we attempt to reconcile a uniform expression for calculate seismic radiation efficiency ηG, which can be used to restrict the upper limit efficiency and avoid the non-physics phenomenon that radiation efficiency is larger than 1. In ML 4.1 Shacheng earthquake sequence, the rupture speed of the main shock was about 0.86 of S-wave speed β according to MREC, closing to the Rayleigh wave speed, while the rupture speeds of the remained 28 aftershocks ranged from 0.05β to 0.55β. The rupture speed was 0.9β, and most of the aftershocks are no more than 0.35β using II and III crack extending model. In addition, the seismic radiation efficiencies for this earthquake sequence were: for the most aftershocks, the radiation efficiencies were less than 10%, inferring a low seismic efficiency, whereas the radiation efficiency

  10. Cytolysin a expressing E. coli a promising candidate for imageable therapeutic probe

    International Nuclear Information System (INIS)

    Nguyen, Vu Hong; Phan, Thuy Xuan; Hong, Yeoung Jin; Min, Jung Joon

    2007-01-01

    Using bacteria for cancer treatment has a long history. Discovery of optical reporter genes consisting of fluorescent and luminescent protein facilitates the monitor of bacteria in vivo, non-invasively and repeatedly. E. coli, the natural enteric bacteria possessing capacity of tumor-targeting ability, seems to be suitable candidate for cancer treatment. In this study, we established the strain light-emitting E. coli for diagnostic purpose and Cytolysin A (Cly A) expressing E. coli for therapeutic purpose. E. coli (MG1655, wild type strain) was transformed plasmid pUC19 carrying lux gene to create the light expressing bacteria and test the tumor targeting-capacity by injecting the bacteria into CT26-tumor bearing mice via tail vein. On the other hand, for therapeutic purpose, plasmid containing Cly A gene, which is encoded for a pore-forming protein toxin, was introduced into E. coli. The toxicity of Cly A was evaluated in vitro by inoculating the bacteria with various cultured cancer cell lines. On the other hand, to test the therapeutic effect, the bacteria were injected intratumorally and intravenously into s.c.CT26-bearing as well as CT26-lung metastasized Balb/c mice. In vivo imaging data showed that the E. coli strains selectively located in the tumor. The in vitro result showed that the number of death cells were significantly higher in the samples containing E. coli expressing Cly A (E. coli Cly A) compared with the samples containing wild type strain. The growth of tumors was repressed in mice injected with either E. coli Cly A (significantly) or wild type E. coli (mildly), while tumors in no treatment group still grew fast. Furthermore, the tumors inoculated with E. coli cly A were necrotized but not with wild type E. coli. In the CT26-lung metastasized mouse model, the life span of mice was elongated when inject E. coli and longer in the group injected with E. coli cly A. Cly A expressing E. coli can become an effective candidate for imageable

  11. Political Candidate Campaign Advertising: A Selected Review of the Literature.

    Science.gov (United States)

    Hellweg, Susan A.

    This paper provides a selected review of political candidate campaign advertising studies from the political science, mass communication, advertising, and political communication literature. The paper examines the literature in terms of research pertaining to (1) candidate advertising content (commercials for male versus female candidates and for…

  12. Evaluation of candidate geomagnetic field models for IGRF-11

    DEFF Research Database (Denmark)

    Finlay, Chris; Maus, S.; Beggan, C. D.

    2010-01-01

    variations between candidates originate. A retrospective analysis of IGRF-10 main field candidates for epoch 2005.0 and predictive secular variation candidates for 2005.0–2010.0 using the new IGRF-11 models as a reference is also reported. The high quality and consistency of main field models derived using...

  13. Views on Values Education: From Teacher Candidates to Experienced Teachers

    Science.gov (United States)

    Iscan, Canay Demirhan

    2015-01-01

    This study aimed to identify the views of experienced class teachers and class teacher candidates on values education. It conducted standard open-ended interviews with experienced class teachers and teacher candidates. The study group comprised 9 experienced class teachers from different socio-economic levels and 9 teacher candidates with…

  14. Opinions of the Geography Teacher Candidates toward Mind Maps

    Science.gov (United States)

    Seyihoglu, Aysegul

    2013-01-01

    The purpose of this study is to reveal the opinions of the teacher candidates about mind mapping technique used in Geography education of undergraduate program. In this study, the qualitative research techniques were used. The study group consists of 55 teacher candidates. The teacher candidates have been asked for their opinions about the process…

  15. Cognitive Styles in Admission Procedures for Assessing Candidates of Architecture

    Science.gov (United States)

    Casakin, Hernan; Gigi, Ariela

    2016-01-01

    Cognitive style has a strong predictive power in academic and professional success. This study investigated the cognitive profile of candidates studying architecture. Specifically, it explored the relation between visual and verbal cognitive styles, and the performance of candidates in admission procedures. The cognitive styles of candidates who…

  16. Changing Perceptions of Teacher Candidates in High-Needs Schools

    Science.gov (United States)

    DeJarnette, Nancy K.

    2016-01-01

    Candidates enter teacher education programs with established beliefs about diversity and urban education. These belief systems impact decisions that teacher candidates make both now and in the future. Providing opportunities for candidates to spend quality time in an urban Professional Development School (PDS) setting with the support and guidance…

  17. Tumor-Associated Macrophages and Neutrophils in Tumor Microenvironment

    Directory of Open Access Journals (Sweden)

    Jaehong Kim

    2016-01-01

    Full Text Available Distinct tumor microenvironment forms in each progression step of cancer and has diverse capacities to induce both adverse and beneficial consequences for tumorigenesis. It is now known that immune cells can be activated to favor tumor growth and progression, most probably influenced by the tumor microenvironment. Tumor-associated macrophages and tumor-associated neutrophils can exert protumoral functions, enhancing tumor cell invasion and metastasis, angiogenesis, and extracellular matrix remodeling, while inhibiting the antitumoral immune surveillance. Considering that neutrophils in inflammatory environments recruit macrophages and that recruited macrophages affect neutrophil functions, there may be various degrees of interaction between tumor-associated macrophages and tumor-associated neutrophils. Platelets also play an important role in the recruitment and regulation of monocytic and granulocytic cells in the tumor tissues, suggesting that platelet function may be essential for generation of tumor-associated macrophages and tumor-associated neutrophils. In this review, we will explore the biology of tumor-associated macrophages and tumor-associated neutrophils and their possible interactions in the tumor microenvironment. Special attention will be given to the recruitment and activation of these tumor-associated cells and to the roles they play in maintenance of the tumor microenvironment and progression of tumors.

  18. Plasma soluble podoplanin is a novel marker for the diagnosis of tumor occurrence and metastasis.

    Science.gov (United States)

    Zhao, Xingpeng; Pan, Yanfang; Ren, Weihua; Shen, Fei; Xu, Mengqiao; Yu, Min; Fu, Jianxin; Xia, Lijun; Ruan, Changgeng; Zhao, Yiming

    2018-02-01

    Podoplanin (PDPN) is expressed on many tumors and is involved in tumor metastasis. The objective of the present study was to develop an ELISA for determining soluble PDPN (sPDPN) levels as a potential novel tumor marker in plasma of patients with cancers for detection of tumor occurrence and metastasis. Mouse monoclonal antibodies (mAb) against human PDPN were developed and characterized. Two anti-PDPN mAb, SZ-163 and SZ-168, were used in a sandwich ELISA to detect plasma sPDPN in patients with cancers and in normal individuals. The levels of sPDPN were detected in patients with adenocarcinoma (87 cases, 31.09 ± 5.48 ng/ml), squamous cell carcinoma (86 cases, 6.91 ± 0.59 ng/ml), lung cancer (45 cases, 26.10 ± 7.62 ng/ml), gastric cancer (38 cases, 23.71 ± 6.90 ng/ml) and rectal cancer (27 cases, 32.98 ± 9.88 ng/ml), which were significantly higher than those in normal individuals (99 cases, 1.31 ± 0.13 ng/ml) (P < .0001). Moreover, the sPDPN levels in patients with metastatic cancers were higher (192 cases, 30.35 ± 3.63 ng/ml) than those in non-metastatic cancer patients (92 cases, 6.28 ± 0.77 ng/ml) (P < .0001). The post-treatment sPDPN levels of cancer patients (n = 156) (4.47 ± 0.35 ng/ml) were significantly lower compared with those seen pre-treatment (n = 128) (43.74 ± 4.97 ng/ml) (P < .0001). These results showed that an ELISA method was successfully established for quantitation of plasma sPDPN and plasma sPDPN levels correlate significantly with tumor occurrence and metastasis. © 2017 The Authors. Cancer Science published by John Wiley & Sons Australia, Ltd on behalf of Japanese Cancer Association.

  19. Proceedings of the 15. annual British Columbia MEND ML/ARD workshop : the management of tailings and tailings impoundments

    International Nuclear Information System (INIS)

    2009-02-01

    This Mine Environment Neutral Drainage (MEND) workshop was held to promote the exchange of information and ideas on environmental protection and reclamation associated with mining. The workshop covered a broad spectrum of reclamation issues and the key environmental challenges facing the mining industry, such as acid mine drainage (AMD) control, and metal leaching and acid rock drainage (ML/ARD). The theme for the 2008 workshop was the management of tailings and tailings impoundments. Topics of discussion included hydrogeology and geochemistry; tailings disposal; mitigation; closure plans; and postclosure performance. The emphasis was on full-scale case studies, practical constraints and sustaining successful disposal strategies and remediation. The session on tailings management reviewed overarching policies and practices; methods of subaerial tailings disposal and case studies of tailings management; and detailed investigations of geochemical properties and processes. The conference featured 22 presentations, of which 4 have been catalogued separately for inclusion in this database. refs., tabs., figs

  20. Primary standards for measuring flow rates from 100 nl/min to 1 ml/min - gravimetric principle.

    Science.gov (United States)

    Bissig, Hugo; Petter, Harm Tido; Lucas, Peter; Batista, Elsa; Filipe, Eduarda; Almeida, Nelson; Ribeiro, Luis Filipe; Gala, João; Martins, Rui; Savanier, Benoit; Ogheard, Florestan; Niemann, Anders Koustrup; Lötters, Joost; Sparreboom, Wouter

    2015-08-01

    Microflow and nanoflow rate calibrations are important in several applications such as liquid chromatography, (scaled-down) process technology, and special health-care applications. However, traceability in the microflow and nanoflow range does not go below 16 μl/min in Europe. Furthermore, the European metrology organization EURAMET did not yet validate this traceability by means of an intercomparison between different National Metrology Institutes (NMIs). The NMIs METAS, Centre Technique des Industries Aérauliques et Thermiques, IPQ, Danish Technological Institute, and VSL have therefore developed and validated primary standards to cover the flow rate range from 0.1 μl/min to at least 1 ml/min. In this article, we describe the different designs and methods of the primary standards of the gravimetric principle and the results obtained at the intercomparison for the upper flow rate range for the various NMIs and Bronkhorst High-Tech, the manufacturer of the transfer standards used.

  1. The hazard map of ML6.6 0206 Meinong earthquake near Guanmiao and its Neotectonic implication

    Science.gov (United States)

    Chung, L. H.; Shyu, J. B. H.; Huang, M. H.; Yang, K. M.; Le Beon, M.; Lee, Y. H.; Chuang, R.; Yi, D.

    2016-12-01

    The serious damage was occurred in SW Taiwan by ML 6.6 0206 Meinong earthquake. Based on InSAR result, 10 cm oval-raised surface deformation is 15 km away from its epicenter, and two obviously N-S trend sharp phase change nearby Guanmiao area. Our field investigation shows bulling damage and surface fracture are high related with the two sharp phase change. Here, we perform the detailed shallow underground geometry by using reflection seismic data, geologic data, and field hazard investigation. This N-S trend surface deformation may be induced by local shallow folding, while the huge uplift west of Guanmiao may be related with pure shear deformation of thick clayey Gutingkeng (GTK) Formation. Our results imply that not only a moderate lower crustal earthquake can trigger active structure at shallower depth, but also those minor shallow active structures are occurred serious damage and surface deformation.

  2. Expression of the p16{sup INK4a} tumor suppressor gene in rodent lung tumors

    Energy Technology Data Exchange (ETDEWEB)

    Swafford, D.S.; Tesfaigzi, J.; Belinsky, S.A.

    1995-12-01

    Aberrations on the short arm of chromosome 9 are among the earliest genetic changes in human cancer. p16{sup INK4a} is a candidate tumor suppressor gene that lies within human 9p21, a chromosome region associated with frequent loss of heterozygosity in human lung tumors. The p16{sup INK4a} protein functions as an inhibitor of cyclin D{sub 1}-dependent kinases that phosphorylate the retinoblastoma (Rb) tumor suppressor gene product enabling cell-cycle progression. Thus, overexpression of cyclin D{sub 1}, mutation of cyclin-dependent kinase genes, or loss of p16{sup INK4a} function, can all result in functional inactivation of Rb. Inactivation of Rb by mutation or deletion can result in an increase in p16{sup INK4a} transcription, suggesting that an increased p16{sup INK4a} expression in a tumor cell signals dysfunction of the pathway. The p16{sup (INK4a)} gene, unlike some tumor suppressor genes, is rarely inactivated by mutation. Instead, the expression of this gene is suppressed in some human cancers by hypermethylation of the CpG island within the first exon or by homozygous deletion: 686. Chromosome losses have been observed at 9p21 syntenic loci in tumors of the mouse and rat, two species often used as animal models for pulmonary carcinogenesis. Expression of p16{sup INK4a} is lost in some mouse tumor cell lines, often due to homozygous deletion. These observations indicate that p16{sup INK4a} dysfunction may play a role in the development of neoplasia in rodents as well as humans. The purpose of the current investigation was to define the extent to which p16{sup INK4a} dysfunction contributes to the development of rodent lung tumors and to determine the mechanism of inactivation of the gene. There is no evidence to suggest a loss of function of the p16{sup INK4a} tumor suppressor gene in these primary murine lung tumors by mutation, deletion, or methylation.

  3. Benign Liver Tumors

    Science.gov (United States)

    ... Legacy Society Make Gifts of Stock Donate Your Car Personal Fundraising Partnership & Support Share Your Story Spread the Word Give While You Shop Contact Us Donate Now Benign Liver Tumors Back ...

  4. Overview of Heart Tumors

    Science.gov (United States)

    ... Tumors By Siddique A. Abbasi, MD, MSc, Assistant Professor of Medicine, Warren Alpert Medical School of Brown University; Attending Cardiologist, Director of Heart Failure, and Director of Cardiac MRI, Providence VA Medical ...

  5. Renal tumors in infancy

    International Nuclear Information System (INIS)

    Lucaya, J.; Garcia, P.

    1997-01-01

    The classification of childhood renal masses in updated, including the clinical signs and imaging techniques currently employed to confirm their presence and type them. Several bening and malignant childhood tumors are described in substantial detail. (Author) 24 refs

  6. Radioimmunoassays for tumor diagnosis

    International Nuclear Information System (INIS)

    Dressler, J.

    1983-01-01

    Aside from imaging techniques several (radio-)immunological analyses are used for tumor diagnosis. Oncofetal antigens, for instance the carcinoembryonic antigen (CEA) and alpha-fetoprotein (AFP), have become the most important substances for many malignancies. However, nearly all of the so-called tumor markers are not suitable for early diagnosis or screening either because of low sensitivity or low tumor specifity. On the other hand follow-up measurements give a very sensitive index of the success of treatment and may indicate tumor progression when other signs are still not present. In some carcinomas and under some clinical circumstances tumorspecific markers are available and mandatory for detection and/or staging: AFP in hepatoma, acid phosphatase in metastasizing carcinoma of the prostate and serum thyreoglobulin in differentiated thyroid cancer. (orig.) [de

  7. GASTROINTESTINAL STROMAL TUMOR (GIST

    Directory of Open Access Journals (Sweden)

    Luigi eTornillo

    2014-11-01

    Full Text Available Gastrointestinal stromal tumors are the most frequent mesenchymal tumors of the gastrointestinal tract. The discovery that these tumors, formerly thought of smooth muscle origin, are indeed better characterized by specific activating mutation in genes coding for the receptor tyrosine kinases CKIT and PDGFRA and that these mutations are strongly predictive for the response to targeted therapy with receptor tyrosine kinase inhibitors has made GISTs the typical example of the integration of basic molecular knowledge in the daily clinical activity. The information on the mutational status of these tumors is essential to predict (and subsequently to plan the therapy. As resistant cases are frequently wild-type, other possible oncogenic events, defining other entities, have been discovered (e.g. succinil dehydrogenase mutation/dysregulation, insuline growth factor expression, mutations in the RAS-RAF-MAPK pathway. The classification of disease must nowadays rely on the integration of the clinico-morphological characteristics with the molecular data.

  8. Allogeneic tumor cell vaccines

    Science.gov (United States)

    Srivatsan, Sanjay; Patel, Jaina M; Bozeman, Erica N; Imasuen, Imade E; He, Sara; Daniels, Danielle; Selvaraj, Periasamy

    2014-01-01

    The high mortality rate associated with cancer and its resistance to conventional treatments such as radiation and chemotherapy has led to the investigation of a variety of anti-cancer immunotherapies. The development of novel immunotherapies has been bolstered by the discovery of tumor-associated antigens (TAAs), through gene sequencing and proteomics. One such immunotherapy employs established allogeneic human cancer cell lines to induce antitumor immunity in patients through TAA presentation. Allogeneic cancer immunotherapies are desirable in a clinical setting due to their ease of production and availability. This review aims to summarize clinical trials of allogeneic tumor immunotherapies in various cancer types. To date, clinical trials have shown limited success due potentially to extensive degrees of inter- and intra-tumoral heterogeneity found among cancer patients. However, these clinical results provide guidance for the rational design and creation of more effective allogeneic tumor immunotherapies for use as monotherapies or in combination with other therapies. PMID:24064957

  9. Multiple Primary Tumors

    African Journals Online (AJOL)

    2017-12-05

    Dec 5, 2017 ... Multiple primary tumors occur in clinical practice causing diagnostic dilemma. It is not very .... was estrogen receptor negative, progesterone receptor negative, and ... cervical, ovarian, and urinary bladder cancers. Multiple.

  10. Pituitary Tumors: Condition Information

    Science.gov (United States)

    ... hormones. They can press on or damage the pituitary gland and prevent it from secreting adequate levels of hormones. National Institute of Neurological Disorders and Stroke. (2010). NINDS pituitary tumors information page . ...

  11. Relationship between candidate communication ability and oral certification examination scores.

    Science.gov (United States)

    Lunz, Mary E; Bashook, Philip G

    2008-12-01

    Structured case-based oral examinations are widely used in medical certifying examinations in the USA. These orals assess the candidate's decision-making skills using real or realistic patient cases. Frequently mentioned but not empirically evaluated is the potential bias introduced by the candidate's communication ability. This study aimed to assess the relationship between candidate communication ability and medical certification oral examination scores. Non-doctor communication observers rated a random sample of 90 candidates on communication ability during a medical oral certification examination. The multi-facet Rasch model was used to analyse the communication survey and the oral examination data. The multi-facet model accounts for observer and examiner severity bias. anova was used to measure differences in communication ability between passing and failing candidates and candidates grouped by level of communication ability. Pearson's correlations were used to compare candidate communication ability and oral certification examination performance. Candidate separation reliability values for the communication survey and the oral examination were 0.85 and 0.97, respectively, suggesting accurate candidate measurement. The correlation between communication scores and oral examination scores was 0.10. No significant difference was found between passing and failing candidates for measured communication ability. When candidates were grouped by high, moderate and low communication ability, there was no significant difference in their oral certification examination performance. Candidates' communication ability has little relationship to candidate performance on high-stakes, case-based oral examinations. Examiners for this certifying examination focused on assessing candidate decision-making ability and were not influenced by candidate communication ability.

  12. Radiotherapy combined with Tegafur (FT-207s) for brain tumors

    International Nuclear Information System (INIS)

    Aoki, Yoshiro

    1981-01-01

    5-Fluorouracil (5-FU) has anti-tumor effects as an anti-metabolite, but it cannot pass the Blood-Brain-Barrier (BBB). FT-207 a masked-compound of 5-FU, is easily lipid soluble and is able to pass the BBB. Twenty eight patients of primary brain tumor and 8 patients of metastatic brain tumor were treated with irradiation combined with 750 mg of FT-207 suppository. Twenty four patients of primary brain tumor were treated only with irradiation as control. The mean survival time was 20.4 +- 11.8 months for the combined therapy group and 17.6 +- 8.6 months for the control. The concentration of FT-207 and 5-FU in serum and in cerebrospinal fluid (CSF) was investigated after administration of 750 mg of FT-207 suppository per annum. The maximum concentration of FT-207 and of 5-FU in serum was 20.4 +- 11.8 mcg/ml and 0.06 +- 0.02 mcg/ml, respectively. There were observed several side effects, such as anorexia, nausea, exanthema and etc. These side effects were not so great as to interrupt the therapy at the dose level of 750 mg of FT-207. However, at the dose of 1500 mg, one case showed disturbance of consciousness, to which attention should be called. (author)

  13. Rrp1b, a new candidate susceptibility gene for breast cancer progression and metastasis.

    Directory of Open Access Journals (Sweden)

    Nigel P S Crawford

    2007-11-01

    Full Text Available A novel candidate metastasis modifier, ribosomal RNA processing 1 homolog B (Rrp1b, was identified through two independent approaches. First, yeast two-hybrid, immunoprecipitation, and functional assays demonstrated a physical and functional interaction between Rrp1b and the previous identified metastasis modifier Sipa1. In parallel, using mouse and human metastasis gene expression data it was observed that extracellular matrix (ECM genes are common components of metastasis predictive signatures, suggesting that ECM genes are either important markers or causal factors in metastasis. To investigate the relationship between ECM genes and poor prognosis in breast cancer, expression quantitative trait locus analysis of polyoma middle-T transgene-induced mammary tumor was performed. ECM gene expression was found to be consistently associated with Rrp1b expression. In vitro expression of Rrp1b significantly altered ECM gene expression, tumor growth, and dissemination in metastasis assays. Furthermore, a gene signature induced by ectopic expression of Rrp1b in tumor cells predicted survival in a human breast cancer gene expression dataset. Finally, constitutional polymorphism within RRP1B was found to be significantly associated with tumor progression in two independent breast cancer cohorts. These data suggest that RRP1B may be a novel susceptibility gene for breast cancer progression and metastasis.

  14. What Do Teacher Candidates Think about the Teaching Education? The Example of Social Studies Teacher Candidates

    Science.gov (United States)

    Tonga, Deniz

    2016-01-01

    In this research, it is aimed to reveal the opinions and observations of social studies teacher candidate about the courses they have taken during their 4-year university education. The focus group interview was used as the data collecting tool, and the content analyses were performed on the data obtained. The criterion sampling approach was used…

  15. Antibody tumor penetration

    Science.gov (United States)

    Thurber, Greg M.; Schmidt, Michael M.; Wittrup, K. Dane

    2009-01-01

    Antibodies have proven to be effective agents in cancer imaging and therapy. One of the major challenges still facing the field is the heterogeneous distribution of these agents in tumors when administered systemically. Large regions of untargeted cells can therefore escape therapy and potentially select for more resistant cells. We present here a summary of theoretical and experimental approaches to analyze and improve antibody penetration in tumor tissue. PMID:18541331

  16. Pituitary tumors containing cholecystokinin

    DEFF Research Database (Denmark)

    Rehfeld, J F; Lindholm, J; Andersen, B N

    1987-01-01

    We found small amounts of cholecystokinin in the normal human adenohypophysis and therefore examined pituitary tumors from 87 patients with acromegaly, Cushing's disease, Nelson's syndrome, prolactinoma, or inactive pituitary adenomas. Five adenomas associated with Nelson's syndrome contained......'s disease and 7 acromegaly with adenomas containing ACTH. The cholecystokinin peptides from the tumors were smaller and less sulfated than cholecystokinin from normal pituitary glands. We conclude that ACTH-producing pituitary cells may also produce an altered form of cholecystokinin....

  17. Perlecan and tumor angiogenesis

    DEFF Research Database (Denmark)

    Jiang, Xinnong; Couchman, John R

    2003-01-01

    Perlecan is a major heparan sulfate proteoglycan (HSPG) of basement membranes (BMs) and connective tissues. The core protein of perlecan is divided into five domains based on sequence homology to other known proteins. Commonly, the N-terminal domain I of mammalian perlecan is substituted with thr...... have unwanted promoting effects on tumor cell proliferation and tumor angiogenesis. Understanding of these attributes at the molecular level may offer opportunities for therapeutic intervention....

  18. Adrenocortical tumors in children

    Directory of Open Access Journals (Sweden)

    R.C. Ribeiro

    2000-10-01

    Full Text Available Childhood adrenocortical tumors (ACT are rare. In the USA, only about 25 new cases occur each year. In Southern Brazil, however, approximately 10 times that many cases are diagnosed each year. Most cases occur in the contiguous states of São Paulo and Paraná. The cause of this higher rate has not been identified. Familial genetic predisposition to cancer (p53 mutations and selected genetic syndromes (Beckwith-Wiedemann syndrome have been associated with childhood ACT in general but not with the Brazilian counterpart. Most of the affected children are young girls with classic endocrine syndromes (virilizing and/or Cushing. Levels of urinary 17-ketosteroids and plasma dehydroepiandrosterone sulfate (DHEA-S, which are abnormal in approximately 90% of the cases, provide the pivotal clue to a diagnosis of ACT. Typical imaging findings of pediatric ACT consist of a large, well-defined suprarenal tumor containing calcifications with a thin capsule and central necrosis or hemorrhage. The pathologic classification of pediatric ACT is troublesome. Even an experienced pathologist can find it difficult to differentiate carcinoma from adenoma. Surgery is the single most important procedure in the successful treatment of ACT. The role of chemotherapy in the management of childhood ACT has not been established although occasional tumors are responsive to mitotane or cisplatin-containing regimens. Because of the heterogeneity and rarity of the disease, prognostic factors have been difficult to establish in pediatric ACT. Patients with incomplete tumor resection or with metastatic disease at diagnosis have a dismal prognosis. In patients with localized and completely resected tumors, the size of the tumor has predictive value. Patients with large tumors have a much higher relapse rate than those with small tumors.

  19. Neuroendocrine tumors and smoking

    Directory of Open Access Journals (Sweden)

    Tanja Miličević

    2016-12-01

    Full Text Available Neuroendocrine cells are dispersed around the body and can be found within the gastrointestinal system, lungs, larynx, thymus, thyroid, adrenal, gonads, skin and other tissues. These cells form the so-called ''diffuse neuroendocrine system'' and tumors arising from them are defined as neuroendocrine tumors (NETs. The traditional classification of NETs based on their embryonic origin includes foregut tumors (lung, thymus, stomach, pancreas and duodenum, midgut tumors (beyond the ligament of Treitz of the duodenum to the proximal transverse colon and hindgut tumors (distal colon and rectum. NETs at each site are biologically and clinically distinct from their counterparts at other sites. Symptoms in patients with early disease are often insidious in onset, leading to a delay in diagnosis. The majority of these tumors are thus diagnosed at a stage at which the only curative treatment, radical surgical intervention, is no longer an option. Due to the increasing incidence and mortality, many studies have been conducted in order to identify risk factors for the development of NETs. Still, little is known especially when it comes to preventable risk factors such as smoking. This review will focus on smoking and its contribution to the development of different subtypes of NETs.

  20. Developing a Valid Version of an Inventory to Measure Anger in Mexican Adolescents of Middle School Level: The ML-STAXI-MS

    Science.gov (United States)

    Alcázar-Olán, Raúl J.; Deffenbacher, Jerry L.; Escamilla-Tecalco, Héctor

    2016-01-01

    The goals were to develop a valid version of the Multicultural Latin American Inventory of Anger Expression and Hostility (ML-STAXI) for middle school Mexican youth (ML-STAXI-MS) and to test a new Questionnaire about Anger Expression with Physical Aggression (QAEPA). Five hundred and four adolescents (258 males, 246 females); (M[subscript age] =…