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Sample records for invasion molecular analysis

  1. Unveiling an ancient biological invasion: molecular analysis of an old European alien, the crested porcupine (Hystrix cristata

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    Sbordoni Valerio

    2009-05-01

    Full Text Available Abstract Background Biological invasions can be considered one of the main threats to biodiversity, and the recognition of common ecological and evolutionary features among invaders can help developing a predictive framework to control further invasions. In particular, the analysis of successful invasive species and of their autochthonous source populations by means of genetic, phylogeographic and demographic tools can provide novel insights into the study of biological invasion patterns. Today, long-term dynamics of biological invasions are still poorly understood and need further investigations. Moreover, distribution and molecular data on native populations could contribute to the recognition of common evolutionary features of successful aliens. Results We analyzed 2,195 mitochondrial base pairs, including Cytochrome b, Control Region and rRNA 12S, in 161 Italian and 27 African specimens and assessed the ancient invasive origin of Italian crested porcupine (Hystrix cristata populations from Tunisia. Molecular coalescent-based Bayesian analyses proposed the Roman Age as a putative timeframe of introduction and suggested a retention of genetic diversity during the early phases of colonization. The characterization of the native African genetic background revealed the existence of two differentiated clades: a Mediterranean group and a Sub-Saharan one. Both standard population genetic and advanced molecular demography tools (Bayesian Skyline Plot did not evidence a clear genetic signature of the expected increase in population size after introduction. Along with the genetic diversity retention during the bottlenecked steps of introduction, this finding could be better described by hypothesizing a multi-invasion event. Conclusion Evidences of the ancient anthropogenic invasive origin of the Italian Hystrix cristata populations were clearly shown and the native African genetic background was preliminary described. A more complex pattern than a

  2. Unveiling an ancient biological invasion: molecular analysis of an old European alien, the crested porcupine (Hystrix cristata).

    Science.gov (United States)

    Trucchi, Emiliano; Sbordoni, Valerio

    2009-05-18

    Biological invasions can be considered one of the main threats to biodiversity, and the recognition of common ecological and evolutionary features among invaders can help developing a predictive framework to control further invasions. In particular, the analysis of successful invasive species and of their autochthonous source populations by means of genetic, phylogeographic and demographic tools can provide novel insights into the study of biological invasion patterns. Today, long-term dynamics of biological invasions are still poorly understood and need further investigations. Moreover, distribution and molecular data on native populations could contribute to the recognition of common evolutionary features of successful aliens. We analyzed 2,195 mitochondrial base pairs, including Cytochrome b, Control Region and rRNA 12S, in 161 Italian and 27 African specimens and assessed the ancient invasive origin of Italian crested porcupine (Hystrix cristata) populations from Tunisia. Molecular coalescent-based Bayesian analyses proposed the Roman Age as a putative timeframe of introduction and suggested a retention of genetic diversity during the early phases of colonization. The characterization of the native African genetic background revealed the existence of two differentiated clades: a Mediterranean group and a Sub-Saharan one. Both standard population genetic and advanced molecular demography tools (Bayesian Skyline Plot) did not evidence a clear genetic signature of the expected increase in population size after introduction. Along with the genetic diversity retention during the bottlenecked steps of introduction, this finding could be better described by hypothesizing a multi-invasion event. Evidences of the ancient anthropogenic invasive origin of the Italian Hystrix cristata populations were clearly shown and the native African genetic background was preliminary described. A more complex pattern than a simple demographic exponential growth from a single propagule

  3. Geographic distribution of Staphylococcus aureus causing invasive infections in Europe : A molecular-epidemiological analysis

    NARCIS (Netherlands)

    Grundmann, Hajo; Aanensen, David M; van den Wijngaard, Cees C; Spratt, Brian G; Harmsen, Dag; Friedrich, Alexander W; Tami, Adriana

    Background: Staphylococcus aureus is one of the most important human pathogens and methicillin-resistant variants (MRSAs) are a major cause of hospital and community-acquired infection. We aimed to map the geographic distribution of the dominant clones that cause invasive infections in Europe.

  4. Geographic distribution of Staphylococcus aureus causing invasive infections in Europe: a molecular-epidemiological analysis.

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    Hajo Grundmann

    2010-01-01

    Full Text Available Staphylococcus aureus is one of the most important human pathogens and methicillin-resistant variants (MRSAs are a major cause of hospital and community-acquired infection. We aimed to map the geographic distribution of the dominant clones that cause invasive infections in Europe.In each country, staphylococcal reference laboratories secured the participation of a sufficient number of hospital laboratories to achieve national geo-demographic representation. Participating laboratories collected successive methicillin-susceptible (MSSA and MRSA isolates from patients with invasive S. aureus infection using an agreed protocol. All isolates were sent to the respective national reference laboratories and characterised by quality-controlled sequence typing of the variable region of the staphylococcal spa gene (spa typing, and data were uploaded to a central database. Relevant genetic and phenotypic information was assembled for interactive interrogation by a purpose-built Web-based mapping application. Between September 2006 and February 2007, 357 laboratories serving 450 hospitals in 26 countries collected 2,890 MSSA and MRSA isolates from patients with invasive S. aureus infection. A wide geographical distribution of spa types was found with some prevalent in all European countries. MSSA were more diverse than MRSA. Genetic diversity of MRSA differed considerably between countries with dominant MRSA spa types forming distinctive geographical clusters. We provide evidence that a network approach consisting of decentralised typing and visualisation of aggregated data using an interactive mapping tool can provide important information on the dynamics of MRSA populations such as early signalling of emerging strains, cross border spread, and importation by travel.In contrast to MSSA, MRSA spa types have a predominantly regional distribution in Europe. This finding is indicative of the selection and spread of a limited number of clones within health care

  5. E-cadherin expression phenotypes associated with molecular subtypes in invasive non-lobular breast cancer: evidence from a retrospective study and meta-analysis.

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    Liu, Jiang-Bo; Feng, Chen-Yi; Deng, Miao; Ge, Dong-Feng; Liu, De-Chun; Mi, Jian-Qiang; Feng, Xiao-Shan

    2017-08-01

    This retrospective study and meta-analysis was designed to explore the relationship between E-cadherin (E-cad) expression and the molecular subtypes of invasive non-lobular breast cancer, especially in early-stage invasive ductal carcinoma (IDC). A total of 156 post-operative cases of early-stage IDCs were retrospectively collected for the immunohistochemistry (IHC) detection of E-cad expression. The association of E-cad expression with molecular subtypes of early-stage IDCs was analyzed. A literature search was conducted in March 2016 to retrieve publications on E-cad expression in association with molecular subtypes of invasive non-lobular breast cancer, and a meta-analysis was performed to estimate the relational statistics. E-cad was expressed in 82.7% (129/156) of early-stage IDCs. E-cad expression was closely associated with the molecular types of early-stage IDCs (P cancer (TNBC) than in other molecular subtypes (TNBC vs. luminal A: RR = 3.45, 95% CI = 2.79-4.26; TNBC vs. luminal B: RR = 2.41, 95% CI = 1.49-3.90; TNBC vs. HER2-enriched: RR = 1.95, 95% CI = 1.24-3.07). Early-stage IDCs or invasive non-lobular breast cancers with the TNBC molecular phenotype have a higher risk for the loss of E-cad expression than do tumors with non-TNBC molecular phenotypes, suggesting that E-cad expression phenotypes were closely related to molecular subtypes and further studies are needed to clarify the underlying mechanism.

  6. Integrated molecular analysis of Tamoxifen-resistant invasive lobular breast cancer cells identifies MAPK and GRM/mGluR signaling as therapeutic vulnerabilities.

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    Stires, Hillary; Heckler, Mary M; Fu, Xiaoyong; Li, Zhao; Grasso, Catherine S; Quist, Michael J; Lewis, Joseph A; Klimach, Uwe; Zwart, Alan; Mahajan, Akanksha; Győrffy, Balázs; Cavalli, Luciane R; Riggins, Rebecca B

    2018-08-15

    Invasive lobular breast cancer (ILC) is an understudied malignancy with distinct clinical, pathological, and molecular features that distinguish it from the more common invasive ductal carcinoma (IDC). Mounting evidence suggests that estrogen receptor-alpha positive (ER+) ILC has a poor response to Tamoxifen (TAM), but the mechanistic drivers of this are undefined. In the current work, we comprehensively characterize the SUM44/LCCTam ILC cell model system through integrated analysis of gene expression, copy number, and mutation, with the goal of identifying actionable alterations relevant to clinical ILC that can be co-targeted along with ER to improve treatment outcomes. We show that TAM has several distinct effects on the transcriptome of LCCTam cells, that this resistant cell model has acquired copy number alterations and mutations that impinge on MAPK and metabotropic glutamate receptor (GRM/mGluR) signaling networks, and that pharmacological inhibition of either improves or restores the growth-inhibitory actions of endocrine therapy. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

  7. Molecular analysis of ex-vivo CD133+ GBM cells revealed a common invasive and angiogenic profile but different proliferative signatures among high grade gliomas

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    Garcia Juan L

    2010-08-01

    Full Text Available Abstract Background Gliomas are the most common type of primary brain tumours, and in this group glioblastomas (GBMs are the higher-grade gliomas with fast progression and unfortunate prognosis. Two major aspects of glioma biology that contributes to its awful prognosis are the formation of new blood vessels through the process of angiogenesis and the invasion of glioma cells. Despite of advances, two-year survival for GBM patients with optimal therapy is less than 30%. Even in those patients with low-grade gliomas, that imply a moderately good prognosis, treatment is almost never curative. Recent studies have demonstrated the existence of a small fraction of glioma cells with characteristics of neural stem cells which are able to grow in vitro forming neurospheres and that can be isolated in vivo using surface markers such as CD133. The aim of this study was to define the molecular signature of GBM cells expressing CD133 in comparison with non expressing CD133 cells. This molecular classification could lead to the finding of new potential therapeutic targets for the rationale treatment of high grade GBM. Methods Eight fresh, primary and non cultured GBMs were used in order to study the gene expression signatures from its CD133 positive and negative populations isolated by FACS-sorting. Dataset was generated with Affymetrix U133 Plus 2 arrays and analysed using the software of the Affymetrix Expression Console. In addition, genomic analysis of these tumours was carried out by CGH arrays, FISH studies and MLPA; Results Gene expression analysis of CD133+ vs. CD133- cell population from each tumour showed that CD133+ cells presented common characteristics in all glioblastoma samples (up-regulation of genes involved in angiogenesis, permeability and down-regulation of genes implicated in cell assembly, neural cell organization and neurological disorders. Furthermore, unsupervised clustering of gene expression led us to distinguish between two groups

  8. Molecular and Genetic Determinants of Glioma Cell Invasion

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    Kenta Masui

    2017-12-01

    Full Text Available A diffusely invasive nature is a major obstacle in treating a malignant brain tumor, “diffuse glioma”, which prevents neurooncologists from surgically removing the tumor cells even in combination with chemotherapy and radiation. Recently updated classification of diffuse gliomas based on distinct genetic and epigenetic features has culminated in a multilayered diagnostic approach to combine histologic phenotypes and molecular genotypes in an integrated diagnosis. However, it is still a work in progress to decipher how the genetic aberrations contribute to the aggressive nature of gliomas including their highly invasive capacity. Here we depict a set of recent discoveries involving molecular genetic determinants of the infiltrating nature of glioma cells, especially focusing on genetic mutations in receptor tyrosine kinase pathways and metabolic reprogramming downstream of common cancer mutations. The specific biology of glioma cell invasion provides an opportunity to explore the genotype-phenotype correlation in cancer and develop novel glioma-specific therapeutic strategies for this devastating disease.

  9. Molecular aspects of tumor cell migration and invasion

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    Giuseppina Bozzuto

    2010-03-01

    Full Text Available Cell migration and invasion are crucial steps in many physiological events. However, they are also implicated in the physiopathology of many diseases, such as cancer. To spread through the tissues, tumor cells use mechanisms that involve several molecular actors: adhesion receptor families, receptor tyrosine kinases, cytoskeleton proteins, adapter and signalling proteins interplay in a complex scenario. The balance of cellular signals for proliferation and survival responses also regulates migratory behaviours of tumor cells. To complicate the scene of crime drug resistance players can interfere thus worsening this delicate situation. The complete understanding of this molecular jungle is an impossible mission: some molecular aspects are reviewed in this paper.

  10. The Correlation Between Candida Colonization of Distinct Body Sites and Invasive Candidiasis in Emergency Intensive Care Units: Statistical and Molecular Biological Analysis.

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    Li, Zhen; Jiang, Cen; Dong, Danfeng; Zhang, Lihua; Tian, Yuan; Ni, Qi; Mao, Enqiang; Peng, Yibing

    2016-08-01

    Both statistical and molecular biological methods were used to evaluate the association between Candida colonization of different body sites and invasive candidiasis (IC) and analyse the potential infection sources of IC. Candida surveillance cultures from the urine, sputum, rectum and skin were performed on patients admitted to an emergency intensive care units (EICU) of a tertiary care hospital in Shanghai, China, from February 2014 to January 2015. Specimens were collected once a week at admission and thereafter. The patients' clinical data were collected, and Candida isolates were genotyped using polymorphic microsatellite markers. A total of 111 patients were enrolled. Patients with positive urine (23.3 vs. 2.5 %, p = 0.001) and rectal swab (13.6 vs. 0 %, p = 0.010) cultures were more likely to develop IC. However, the risk for IC was not significantly different among patients with and without respiratory (10.0 vs. 5.8 %, p = 0.503) and skin (33.3 vs. 6.5 %, p = 0.056) colonization. Gene microevolution frequently occurred at rectal swab and urine sites, and IC with possible source of infection was caused by rectal isolates (2/7), urine isolates (4/7) and sputum isolate (1/7).The colonization of gut and urinary tract maybe more relevant indicators of IC, which should be taken into consideration when selecting practical body sites for Candida surveillance cultures.

  11. Molecular genetics and genomics generate new insights into invertebrate pest invasions.

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    Kirk, Heather; Dorn, Silvia; Mazzi, Dominique

    2013-07-01

    Invertebrate pest invasions and outbreaks are associated with high social, economic, and ecological costs, and their significance will intensify with an increasing pressure on agricultural productivity as a result of human population growth and climate change. New molecular genetic and genomic techniques are available and accessible, but have been grossly underutilized in studies of invertebrate pest invasions, despite that they are useful tools for applied pest management and for understanding fundamental features of pest invasions including pest population demographics and adaptation of pests to novel and/or changing environments. Here, we review current applications of molecular genetics and genomics in the study of invertebrate pest invasions and outbreaks, and we highlight shortcomings from the current body of research. We then discuss recent conceptual and methodological advances in the areas of molecular genetics/genomics and data analysis, and we highlight how these advances will further our understanding of the demographic, ecological, and evolutionary features of invertebrate pest invasions. We are now well equipped to use molecular data to understand invertebrate dispersal and adaptation, and this knowledge has valuable applications in agriculture at a time when these are critically required.

  12. Molecular Signature for Lymphatic Invasion Associated with Survival of Epithelial Ovarian Cancer.

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    Paik, E Sun; Choi, Hyun Jin; Kim, Tae-Joong; Lee, Jeong-Won; Kim, Byoung-Gie; Bae, Duk-Soo; Choi, Chel Hun

    2018-04-01

    We aimed to develop molecular classifier that can predict lymphatic invasion and their clinical significance in epithelial ovarian cancer (EOC) patients. We analyzed gene expression (mRNA, methylated DNA) in data from The Cancer Genome Atlas. To identify molecular signatures for lymphatic invasion, we found differentially expressed genes. The performance of classifier was validated by receiver operating characteristics analysis, logistic regression, linear discriminant analysis (LDA), and support vector machine (SVM). We assessed prognostic role of classifier using random survival forest (RSF) model and pathway deregulation score (PDS). For external validation,we analyzed microarray data from 26 EOC samples of Samsung Medical Center and curatedOvarianData database. We identified 21 mRNAs, and seven methylated DNAs from primary EOC tissues that predicted lymphatic invasion and created prognostic models. The classifier predicted lymphatic invasion well, which was validated by logistic regression, LDA, and SVM algorithm (C-index of 0.90, 0.71, and 0.74 for mRNA and C-index of 0.64, 0.68, and 0.69 for DNA methylation). Using RSF model, incorporating molecular data with clinical variables improved prediction of progression-free survival compared with using only clinical variables (p < 0.001 and p=0.008). Similarly, PDS enabled us to classify patients into high-risk and low-risk group, which resulted in survival difference in mRNA profiles (log-rank p-value=0.011). In external validation, gene signature was well correlated with prediction of lymphatic invasion and patients' survival. Molecular signature model predicting lymphatic invasion was well performed and also associated with survival of EOC patients.

  13. A meta-analysis of trait differences between invasive and non-invasive plant species

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    van Kleunen, Mark; Weber, Ewald; Fischer, Markus

    2010-01-01

    A major aim in ecology is identifying determinants of invasiveness. We performed a meta-analysis of 117 field or experimental-garden studies that measured pair-wise trait differences of a total of 125 invasive and 196 non-invasive plant species in the invasive range of the invasive species. We tested whether invasiveness is associated with performance-related traits (physiology, leaf-area allocation, shoot allocation, growth rate, size and fitness), and whether such associations depend on typ...

  14. Comprehensive Molecular Portraits of Invasive Lobular Breast Cancer.

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    Ciriello, Giovanni; Gatza, Michael L; Beck, Andrew H; Wilkerson, Matthew D; Rhie, Suhn K; Pastore, Alessandro; Zhang, Hailei; McLellan, Michael; Yau, Christina; Kandoth, Cyriac; Bowlby, Reanne; Shen, Hui; Hayat, Sikander; Fieldhouse, Robert; Lester, Susan C; Tse, Gary M K; Factor, Rachel E; Collins, Laura C; Allison, Kimberly H; Chen, Yunn-Yi; Jensen, Kristin; Johnson, Nicole B; Oesterreich, Steffi; Mills, Gordon B; Cherniack, Andrew D; Robertson, Gordon; Benz, Christopher; Sander, Chris; Laird, Peter W; Hoadley, Katherine A; King, Tari A; Perou, Charles M

    2015-10-08

    Invasive lobular carcinoma (ILC) is the second most prevalent histologic subtype of invasive breast cancer. Here, we comprehensively profiled 817 breast tumors, including 127 ILC, 490 ductal (IDC), and 88 mixed IDC/ILC. Besides E-cadherin loss, the best known ILC genetic hallmark, we identified mutations targeting PTEN, TBX3, and FOXA1 as ILC enriched features. PTEN loss associated with increased AKT phosphorylation, which was highest in ILC among all breast cancer subtypes. Spatially clustered FOXA1 mutations correlated with increased FOXA1 expression and activity. Conversely, GATA3 mutations and high expression characterized luminal A IDC, suggesting differential modulation of ER activity in ILC and IDC. Proliferation and immune-related signatures determined three ILC transcriptional subtypes associated with survival differences. Mixed IDC/ILC cases were molecularly classified as ILC-like and IDC-like revealing no true hybrid features. This multidimensional molecular atlas sheds new light on the genetic bases of ILC and provides potential clinical options. Copyright © 2015 Elsevier Inc. All rights reserved.

  15. Molecular Landscape of Non-Muscle Invasive Bladder Cancer.

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    Meeks, Joshua J; Lerner, Seth P

    2017-11-13

    In this issue of Cancer Cell, Hurst et al. report an integrated analysis of non-invasive (stage Ta) bladder cancer. Two genomic subtypes are distinguished by chromosome 9q loss, resulting in increased AKT/PI3K/mTOR signaling. Tumors from female patients have a higher frequency of KDM6A mutations. Copyright © 2017 Elsevier Inc. All rights reserved.

  16. Direct-Conversion Molecular Breast Imaging of Invasive Breast Cancer: Imaging Features, Extent of Invasive Disease, and Comparison Between Invasive Ductal and Lobular Histology.

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    Conners, Amy Lynn; Jones, Katie N; Hruska, Carrie B; Geske, Jennifer R; Boughey, Judy C; Rhodes, Deborah J

    2015-09-01

    The purposes of this study were to compare the tumor appearance of invasive breast cancer on direct-conversion molecular breast imaging using a standardized lexicon and to determine how often direct-conversion molecular breast imaging identifies all known invasive tumor foci in the breast, and whether this differs for invasive ductal versus lobular histologic profiles. Patients with prior invasive breast cancer and concurrent direct-conversion molecular breast imaging examinations were retrospectively reviewed. Blinded review of direct-conversion molecular breast imaging examinations was performed by one of two radiologists, according to a validated lexicon. Direct-conversion molecular breast imaging findings were matched with lesions described on the pathology report to exclude benign reasons for direct-conversion molecular breast imaging findings and to document direct-conversion molecular breast imaging-occult tumor foci. Associations between direct-conversion molecular breast imaging findings and tumor histologic profiles were examined using chi-square tests. In 286 patients, 390 invasive tumor foci were present in 294 breasts. A corresponding direct-conversion molecular breast imaging finding was present for 341 of 390 (87%) tumor foci described on the pathology report. Invasive ductal carcinoma (IDC) tumor foci were more likely to be a mass (40% IDC vs 15% invasive lobular carcinoma [ILC]; p < 0.001) and to have marked intensity than were ILC foci (63% IDC vs 32% ILC; p < 0.001). Direct-conversion molecular breast imaging correctly revealed all pathology-proven foci of invasive disease in 79.8% of cases and was more likely to do so for IDC than for ILC (86.1% vs 56.7%; p < 0.0001). Overall, direct-conversion molecular breast imaging showed all known invasive foci in 249 of 286 (87%) patients. Direct-conversion molecular breast imaging features of invasive cancer, including lesion type and intensity, differ by histologic subtype. Direct-conversion molecular

  17. Immunophenotyping invasive breast cancer: paving the road for molecular imaging

    International Nuclear Information System (INIS)

    Vermeulen, Jeroen F; Brussel, Aram SA van; Groep, Petra van der; Morsink, Folkert HM; Bult, Peter; Wall, Elsken van der; Diest, Paul J van

    2012-01-01

    Mammographic population screening in The Netherlands has increased the number of breast cancer patients with small and non-palpable breast tumors. Nevertheless, mammography is not ultimately sensitive and specific for distinct subtypes. Molecular imaging with targeted tracers might increase specificity and sensitivity of detection. Because development of new tracers is labor-intensive and costly, we searched for the smallest panel of tumor membrane markers that would allow detection of the wide spectrum of invasive breast cancers. Tissue microarrays containing 483 invasive breast cancers were stained by immunohistochemistry for a selected set of membrane proteins known to be expressed in breast cancer. The combination of highly tumor-specific markers glucose transporter 1 (GLUT1), epidermal growth factor receptor (EGFR), insulin-like growth factor-1 receptor (IGF1-R), human epidermal growth factor receptor 2 (HER2), hepatocyte growth factor receptor (MET), and carbonic anhydrase 9 (CAIX) 'detected' 45.5% of tumors, especially basal/triple negative and HER2-driven ductal cancers. Addition of markers with a 2-fold tumor-to-normal ratio increased the detection rate to 98%. Including only markers with >3 fold tumor-to-normal ratio (CD44v6) resulted in an 80% detection rate. The detection rate of the panel containing both tumor-specific and less tumor-specific markers was not dependent on age, tumor grade, tumor size, or lymph node status. In search of the minimal panel of targeted probes needed for the highest possible detection rate, we showed that 80% of all breast cancers express at least one of a panel of membrane markers (CD44v6, GLUT1, EGFR, HER2, and IGF1-R) that may therefore be suitable for molecular imaging strategies. This study thereby serves as a starting point for further development of a set of antibody-based optical tracers with a high breast cancer detection rate

  18. Immunophenotyping invasive breast cancer: paving the road for molecular imaging

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    Vermeulen Jeroen F

    2012-06-01

    Full Text Available Abstract Background Mammographic population screening in The Netherlands has increased the number of breast cancer patients with small and non-palpable breast tumors. Nevertheless, mammography is not ultimately sensitive and specific for distinct subtypes. Molecular imaging with targeted tracers might increase specificity and sensitivity of detection. Because development of new tracers is labor-intensive and costly, we searched for the smallest panel of tumor membrane markers that would allow detection of the wide spectrum of invasive breast cancers. Methods Tissue microarrays containing 483 invasive breast cancers were stained by immunohistochemistry for a selected set of membrane proteins known to be expressed in breast cancer. Results The combination of highly tumor-specific markers glucose transporter 1 (GLUT1, epidermal growth factor receptor (EGFR, insulin-like growth factor-1 receptor (IGF1-R, human epidermal growth factor receptor 2 (HER2, hepatocyte growth factor receptor (MET, and carbonic anhydrase 9 (CAIX 'detected' 45.5% of tumors, especially basal/triple negative and HER2-driven ductal cancers. Addition of markers with a 2-fold tumor-to-normal ratio increased the detection rate to 98%. Including only markers with >3 fold tumor-to-normal ratio (CD44v6 resulted in an 80% detection rate. The detection rate of the panel containing both tumor-specific and less tumor-specific markers was not dependent on age, tumor grade, tumor size, or lymph node status. Conclusions In search of the minimal panel of targeted probes needed for the highest possible detection rate, we showed that 80% of all breast cancers express at least one of a panel of membrane markers (CD44v6, GLUT1, EGFR, HER2, and IGF1-R that may therefore be suitable for molecular imaging strategies. This study thereby serves as a starting point for further development of a set of antibody-based optical tracers with a high breast cancer detection rate.

  19. Identification of molecular pathways facilitating glioma cell invasion in situ.

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    Ido Nevo

    Full Text Available Gliomas are mostly incurable secondary to their diffuse infiltrative nature. Thus, specific therapeutic targeting of invasive glioma cells is an attractive concept. As cells exit the tumor mass and infiltrate brain parenchyma, they closely interact with a changing micro-environmental landscape that sustains tumor cell invasion. In this study, we used a unique microarray profiling approach on a human glioma stem cell (GSC xenograft model to explore gene expression changes in situ in Invading Glioma Cells (IGCs compared to tumor core, as well as changes in host cells residing within the infiltrated microenvironment relative to the unaffected cortex. IGCs were found to have reduced expression of genes within the extracellular matrix compartment, and genes involved in cell adhesion, cell polarity and epithelial to mesenchymal transition (EMT processes. The infiltrated microenvironment showed activation of wound repair and tissue remodeling networks. We confirmed by protein analysis the downregulation of EMT and polarity related genes such as CD44 and PARD3 in IGCs, and EFNB3, a tissue-remodeling agent enriched at the infiltrated microenvironment. OLIG2, a proliferation regulator and glioma progenitor cell marker upregulated in IGCs was found to function in enhancing migration and stemness of GSCs. Overall, our results unveiled a more comprehensive picture of the complex and dynamic cell autonomous and tumor-host interactive pathways of glioma invasion than has been previously demonstrated. This suggests targeting of multiple pathways at the junction of invading tumor and microenvironment as a viable option for glioma therapy.

  20. Comprehensive Molecular Characterization of Muscle-Invasive Bladder Cancer.

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    Robertson, A Gordon; Kim, Jaegil; Al-Ahmadie, Hikmat; Bellmunt, Joaquim; Guo, Guangwu; Cherniack, Andrew D; Hinoue, Toshinori; Laird, Peter W; Hoadley, Katherine A; Akbani, Rehan; Castro, Mauro A A; Gibb, Ewan A; Kanchi, Rupa S; Gordenin, Dmitry A; Shukla, Sachet A; Sanchez-Vega, Francisco; Hansel, Donna E; Czerniak, Bogdan A; Reuter, Victor E; Su, Xiaoping; de Sa Carvalho, Benilton; Chagas, Vinicius S; Mungall, Karen L; Sadeghi, Sara; Pedamallu, Chandra Sekhar; Lu, Yiling; Klimczak, Leszek J; Zhang, Jiexin; Choo, Caleb; Ojesina, Akinyemi I; Bullman, Susan; Leraas, Kristen M; Lichtenberg, Tara M; Wu, Catherine J; Schultz, Nicholaus; Getz, Gad; Meyerson, Matthew; Mills, Gordon B; McConkey, David J; Weinstein, John N; Kwiatkowski, David J; Lerner, Seth P

    2017-10-19

    We report a comprehensive analysis of 412 muscle-invasive bladder cancers characterized by multiple TCGA analytical platforms. Fifty-eight genes were significantly mutated, and the overall mutational load was associated with APOBEC-signature mutagenesis. Clustering by mutation signature identified a high-mutation subset with 75% 5-year survival. mRNA expression clustering refined prior clustering analyses and identified a poor-survival "neuronal" subtype in which the majority of tumors lacked small cell or neuroendocrine histology. Clustering by mRNA, long non-coding RNA (lncRNA), and miRNA expression converged to identify subsets with differential epithelial-mesenchymal transition status, carcinoma in situ scores, histologic features, and survival. Our analyses identified 5 expression subtypes that may stratify response to different treatments. Copyright © 2017 Elsevier Inc. All rights reserved.

  1. Molecular analysis of thymoma.

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    Sunil Badve

    Full Text Available Histologic classification of thymomas has significant limitations with respect to both subtype definitions and consistency. In order to better understand the biology of the disease processes, we performed whole genome gene expression analysis. RNA was extracted from fresh frozen tumors from 34 patients with thymomas and followup data was available. Using the Illumina BeadStudio® platform and Human Ref-8 Beadchip, gene expression data was analyzed with Partek Genomics Suite®, and Ingenuity Pathways Analysis (IPA. Unsupervised clustering of gene expression data, representing one of the largest series in literature, resulted in identification of four molecular clusters of tumors (C1-C4, which correlated with histology (P = 0.002. However, neither histology nor clusters correlated with clinical outcomes. Correlation of gene expression data with clinical data showed that a number of genes were associated with either advanced stage at diagnosis or development of recurrence or metastases. The top pathways associated with metastases were amino acid metabolisms, biosynthesis of steroids and glycosphingolipids, cell cycle checkpoint proteins and Notch signaling. The differential expression of some of the top genes related to both metastases and stage was confirmed by RT-PCR in all cases of metastases and matched nonmetastatic cases. A number of potential candidates for therapeutics were also identified.

  2. Comparative proteomic analysis of ductal and lobular invasive breast carcinoma.

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    Oliveira, N C S; Gomig, T H B; Milioli, H H; Cordeiro, F; Costa, G G; Urban, C A; Lima, R S; Cavalli, I J; Ribeiro, E M S F

    2016-04-04

    Breast cancer is the second most common cancer worldwide and the first among women. Invasive ductal carcinoma (IDC) and invasive lobular carcinoma (ILC) are the two major histological subtypes, and the clinical and molecular differences between them justify the search for new markers to distinguish them. As proteomic analysis allows for a powerful and analytical approach to identify potential biomarkers, we performed a comparative analysis of IDC and ILC samples by using two-dimensional electrophoresis and mass spectrometry. Twenty-three spots were identified corresponding to 10 proteins differentially expressed between the two subtypes. ACTB, ACTG, TPM3, TBA1A, TBA1B, VIME, TPIS, PDIA3, PDIA6, and VTDB were upregulated in ductal carcinoma compared to in lobular carcinoma samples. Overall, these 10 proteins have a key role in oncogenesis. Their specific functions and relevance in cancer initiation and progression are further discussed in this study. The identified peptides represent promising biomarkers for the differentiation of ductal and lobular breast cancer subtypes, and for future interventions based on tailored therapy.

  3. Economic Analysis of Biological Invasions in Forests

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    Tomas P. Holmes; Julian Aukema; Jeffrey Englin; Robert G. Haight; Kent Kovacs; Brian Leung

    2014-01-01

    Biological invasions of native forests by nonnative pests result from complex stochastic processes that are difficult to predict. Although economic optimization models describe efficient controls across the stages of an invasion, the ability to calibrate such models is constrained by lack of information on pest population dynamics and consequent economic damages. Here...

  4. Differentiating invasive and pre-invasive lung cancer by quantitative analysis of histopathologic images

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    Zhou, Chuan; Sun, Hongliu; Chan, Heang-Ping; Chughtai, Aamer; Wei, Jun; Hadjiiski, Lubomir; Kazerooni, Ella

    2018-02-01

    We are developing automated radiopathomics method for diagnosis of lung nodule subtypes. In this study, we investigated the feasibility of using quantitative methods to analyze the tumor nuclei and cytoplasm in pathologic wholeslide images for the classification of pathologic subtypes of invasive nodules and pre-invasive nodules. We developed a multiscale blob detection method with watershed transform (MBD-WT) to segment the tumor cells. Pathomic features were extracted to characterize the size, morphology, sharpness, and gray level variation in each segmented nucleus and the heterogeneity patterns of tumor nuclei and cytoplasm. With permission of the National Lung Screening Trial (NLST) project, a data set containing 90 digital haematoxylin and eosin (HE) whole-slide images from 48 cases was used in this study. The 48 cases contain 77 regions of invasive subtypes and 43 regions of pre-invasive subtypes outlined by a pathologist on the HE images using the pathological tumor region description provided by NLST as reference. A logistic regression model (LRM) was built using leave-one-case-out resampling and receiver operating characteristic (ROC) analysis for classification of invasive and pre-invasive subtypes. With 11 selected features, the LRM achieved a test area under the ROC curve (AUC) value of 0.91+/-0.03. The results demonstrated that the pathologic invasiveness of lung adenocarcinomas could be categorized with high accuracy using pathomics analysis.

  5. Urinary high molecular weight matrix metalloproteinases as non-invasive biomarker for detection of bladder cancer

    OpenAIRE

    Mohammed, Mohammed A; Seleim, Manar F; Abdalla, Mohga S; Sharada, Hayat M; Abdel Wahab, Abdel Hady A

    2013-01-01

    Background Matrix Metalloproteinases (MMPs) are key molecules for tumor growth, invasion and metastasis. Over-expression of different MMPs in tumor tissues can disturb the homeostasis and increase the level of various body fluids. Many MMPs including high molecular weights (HMWs) were detected in the urine of prostate and bladder cancer patients. Our aim here is to assess the usefulness of HMW MMPs as non invasive biomarkers in bilharzial bladder cancer in Egyptian patients. Methods The activ...

  6. Molecular Features of Subtype-Specific Progression from Ductal Carcinoma In Situ to Invasive Breast Cancer

    Directory of Open Access Journals (Sweden)

    Robert Lesurf

    2016-07-01

    Full Text Available Breast cancer consists of at least five main molecular “intrinsic” subtypes that are reflected in both pre-invasive and invasive disease. Although previous studies have suggested that many of the molecular features of invasive breast cancer are established early, it is unclear what mechanisms drive progression and whether the mechanisms of progression are dependent or independent of subtype. We have generated mRNA, miRNA, and DNA copy-number profiles from a total of 59 in situ lesions and 85 invasive tumors in order to comprehensively identify those genes, signaling pathways, processes, and cell types that are involved in breast cancer progression. Our work provides evidence that there are molecular features associated with disease progression that are unique to the intrinsic subtypes. We additionally establish subtype-specific signatures that are able to identify a small proportion of pre-invasive tumors with expression profiles that resemble invasive carcinoma, indicating a higher likelihood of future disease progression.

  7. Pushing the envelope in genetic analysis of species invasion

    Science.gov (United States)

    Samuel A. Cushman

    2015-01-01

    How a species spreads once introduced into a new environment is a major question in landscape genetics. When the species in question is a potential disease vector, the findings are important not only for fundamental science, but can impact applied science and public health as well. In this issue of Molecular Ecology Medley et al. (2014) study, the invasion...

  8. A first step in understanding an invasive weed through its genes: an EST analysis of invasive Centaurea maculosa

    Directory of Open Access Journals (Sweden)

    He Ji

    2007-05-01

    Full Text Available Abstract Background The economic and biological implications of plant invasion are overwhelming; however, the processes by which plants become successful invaders are not well understood. Limited genetic resources are available for most invasive and weedy species, making it difficult to study molecular and genetic aspects that may be associated with invasion. Results As an initial step towards understanding the molecular mechanisms by which plants become invasive, we have generated a normalized Expressed Sequence Tag (EST library comprising seven invasive populations of Centaurea maculosa, an invasive aster in North America. Seventy-seven percent of the 4423 unique transcripts showed significant similarity to existing proteins in the NCBI database and could be grouped based on gene ontology assignments. Conclusion The C. maculosa EST library represents an initial step towards looking at gene-specific expression in this species, and will pave the way for creation of other resources such as microarray chips that can help provide a view of global gene expression in invasive C. maculosa and its native counterparts. To our knowledge, this is the first published set of ESTs derived from an invasive weed that will be targeted to study invasive behavior. Understanding the genetic basis of evolution for increased invasiveness in exotic plants is critical to understanding the mechanisms through which exotic invasions occur.

  9. A first step in understanding an invasive weed through its genes: an EST analysis of invasive Centaurea maculosa.

    Science.gov (United States)

    Broz, Amanda K; Broeckling, Corey D; He, Ji; Dai, Xinbin; Zhao, Patrick X; Vivanco, Jorge M

    2007-05-24

    The economic and biological implications of plant invasion are overwhelming; however, the processes by which plants become successful invaders are not well understood. Limited genetic resources are available for most invasive and weedy species, making it difficult to study molecular and genetic aspects that may be associated with invasion. As an initial step towards understanding the molecular mechanisms by which plants become invasive, we have generated a normalized Expressed Sequence Tag (EST) library comprising seven invasive populations of Centaurea maculosa, an invasive aster in North America. Seventy-seven percent of the 4423 unique transcripts showed significant similarity to existing proteins in the NCBI database and could be grouped based on gene ontology assignments. The C. maculosa EST library represents an initial step towards looking at gene-specific expression in this species, and will pave the way for creation of other resources such as microarray chips that can help provide a view of global gene expression in invasive C. maculosa and its native counterparts. To our knowledge, this is the first published set of ESTs derived from an invasive weed that will be targeted to study invasive behavior. Understanding the genetic basis of evolution for increased invasiveness in exotic plants is critical to understanding the mechanisms through which exotic invasions occur.

  10. Hypoxia-Targeting Fluorescent Nanobodies for Optical Molecular Imaging of Pre-Invasive Breast Cancer

    NARCIS (Netherlands)

    van Brussel, Aram S A; Adams, Arthur; Oliveira, Sabrina; Dorresteijn, Bram; El Khattabi, Mohamed; Vermeulen, J. F.; van der Wall, Elsken; Mali, Willem P Th M; Derksen, Patrick W B; van Diest, Paul J; van Bergen En Henegouwen, Paul M P

    PURPOSE: The aim of this work was to develop a CAIX-specific nanobody conjugated to IRDye800CW for molecular imaging of pre-invasive breast cancer. PROCEDURES: CAIX-specific nanobodies were selected using a modified phage display technology, conjugated site-specifically to IRDye800CW and evaluated

  11. Hypoxia-Targeting Fluorescent Nanobodies for Optical Molecular Imaging of Pre-Invasive Breast Cancer

    NARCIS (Netherlands)

    van Brussel, Aram S A; Adams, Arthur; Oliveira, Sabrina; Dorresteijn, Bram; El Khattabi, Mohamed; Vermeulen, Jeroen F.; van der Wall, Elsken; Mali, W.P.T.M.; Derksen, Patrick W B; van Diest, Paul J.; van Bergen En Henegouwen, Paul M P

    Purpose: The aim of this work was to develop a CAIX-specific nanobody conjugated to IRDye800CW for molecular imaging of pre-invasive breast cancer. Procedures: CAIX-specific nanobodies were selected using a modified phage display technology, conjugated site-specifically to IRDye800CW and evaluated

  12. Molecular basis of mammalian cell invasion by Trypanosoma cruzi

    Directory of Open Access Journals (Sweden)

    Nobuko Yoshida

    2006-03-01

    Full Text Available Establishment of infection by Trypanosoma cruzi, the agent of Chagas' disease, depends on a series of events involving interactions of diverse parasite molecules with host components. Here we focus on the mechanisms of target cell invasion by metacyclic trypomastigotes (MT and mammalian tissue culture trypomastigotes (TCT. During MT or TCT internalization, signal transduction pathways are activated both in the parasite and the target cell, leading to Ca2+ mobilization. For cell adhesion, MT engage surface glycoproteins, such as gp82 and gp35/50, which are Ca2+ signal-inducing molecules. In T. cruzi isolates that enter host cells in gp82-mediated manner, parasite protein tyrosine kinase as well as phospholipase C are activated, and Ca2+ is released from I P3-sensitive stores, whereas in T. cruzi isolates that attach to target cells mainly through gp35/50, the signaling pathway involving adenylate cyclase appears to be stimulated, with Ca2+ release from acidocalciosomes. In addition, T. cruzi isolate-dependent inhibitory signals, mediated by MT-specific gp90, may be triggered both in the host cell and the parasite. The repertoire of TCT molecules implicated in cell invasion includes surface glycoproteins of gp85 family, with members containing binding sites for laminin and cytokeratin 18, enzymes such as cruzipain, trans-sialidase, and an oligopeptidase B that generates a Ca2+-agonist from a precursor molecule.O estabelecimento da infecção por Trypanosoma cruzi, o agente da doença de Chagas, depende de uma série de eventos envolvendo interações de diversas moléculas do parasita com componentes do hospedeiro. Focalizamos aqui os mecanismos de invasão celular por tripomastigotas metacíclicos (TM e por tripomastigotas de cultura de tecido (TCT. Durante a internalização de TM ou TCT, vias de transdução de sinal são ativadas tanto no parasita como na célula alvo, acarretando a mobilização de Ca2+. Para adesão, TM utiliza as glicoprote

  13. Tissue invasion and metastasis: Molecular, biological and clinical perspectives.

    Science.gov (United States)

    Jiang, W G; Sanders, A J; Katoh, M; Ungefroren, H; Gieseler, F; Prince, M; Thompson, S K; Zollo, M; Spano, D; Dhawan, P; Sliva, D; Subbarayan, P R; Sarkar, M; Honoki, K; Fujii, H; Georgakilas, A G; Amedei, A; Niccolai, E; Amin, A; Ashraf, S S; Ye, L; Helferich, W G; Yang, X; Boosani, C S; Guha, G; Ciriolo, M R; Aquilano, K; Chen, S; Azmi, A S; Keith, W N; Bilsland, A; Bhakta, D; Halicka, D; Nowsheen, S; Pantano, F; Santini, D

    2015-12-01

    Cancer is a key health issue across the world, causing substantial patient morbidity and mortality. Patient prognosis is tightly linked with metastatic dissemination of the disease to distant sites, with metastatic diseases accounting for a vast percentage of cancer patient mortality. While advances in this area have been made, the process of cancer metastasis and the factors governing cancer spread and establishment at secondary locations is still poorly understood. The current article summarizes recent progress in this area of research, both in the understanding of the underlying biological processes and in the therapeutic strategies for the management of metastasis. This review lists the disruption of E-cadherin and tight junctions, key signaling pathways, including urokinase type plasminogen activator (uPA), phosphatidylinositol 3-kinase/v-akt murine thymoma viral oncogene (PI3K/AKT), focal adhesion kinase (FAK), β-catenin/zinc finger E-box binding homeobox 1 (ZEB-1) and transforming growth factor beta (TGF-β), together with inactivation of activator protein-1 (AP-1) and suppression of matrix metalloproteinase-9 (MMP-9) activity as key targets and the use of phytochemicals, or natural products, such as those from Agaricus blazei, Albatrellus confluens, Cordyceps militaris, Ganoderma lucidum, Poria cocos and Silybum marianum, together with diet derived fatty acids gamma linolenic acid (GLA) and eicosapentanoic acid (EPA) and inhibitory compounds as useful approaches to target tissue invasion and metastasis as well as other hallmark areas of cancer. Together, these strategies could represent new, inexpensive, low toxicity strategies to aid in the management of cancer metastasis as well as having holistic effects against other cancer hallmarks. Copyright © 2015 Elsevier Ltd. All rights reserved.

  14. A novel minimally-invasive method to sample human endothelial cells for molecular profiling.

    Directory of Open Access Journals (Sweden)

    Stephen W Waldo

    Full Text Available The endothelium is a key mediator of vascular homeostasis and cardiovascular health. Molecular research on the human endothelium may provide insight into the mechanisms underlying cardiovascular disease. Prior methodology used to isolate human endothelial cells has suffered from poor yields and contamination with other cell types. We thus sought to develop a minimally invasive technique to obtain endothelial cells derived from human subjects with higher yields and purity.Nine healthy volunteers underwent endothelial cell harvesting from antecubital veins using guidewires. Fluorescence-activated cell sorting (FACS was subsequently used to purify endothelial cells from contaminating cells using endothelial surface markers (CD34/CD105/CD146 with the concomitant absence of leukocyte and platelet specific markers (CD11b/CD45. Endothelial lineage in the purified cell population was confirmed by expression of endothelial specific genes and microRNA using quantitative polymerase chain reaction (PCR.A median of 4,212 (IQR: 2161-6583 endothelial cells were isolated from each subject. Quantitative PCR demonstrated higher expression of von Willebrand Factor (vWF, P<0.001, nitric oxide synthase 3 (NOS3, P<0.001 and vascular cell adhesion molecule 1 (VCAM-1, P<0.003 in the endothelial population compared to similarly isolated leukocytes. Similarly, the level of endothelial specific microRNA-126 was higher in the purified endothelial cells (P<0.001.This state-of-the-art technique isolates human endothelial cells for molecular analysis in higher purity and greater numbers than previously possible. This approach will expedite research on the molecular mechanisms of human cardiovascular disease, elucidating its pathophysiology and potential therapeutic targets.

  15. Molecular markers in disease detection and follow-up of patients with non-muscle invasive bladder cancer.

    Science.gov (United States)

    Maas, Moritz; Walz, Simon; Stühler, Viktoria; Aufderklamm, Stefan; Rausch, Steffen; Bedke, Jens; Stenzl, Arnulf; Todenhöfer, Tilman

    2018-05-01

    Diagnosis and surveillance of non-muscle invasive bladder cancer (NMIBC) is mainly based on endoscopic bladder evaluation and urine cytology. Several assays for determining additional molecular markers (urine-, tissue- or blood-based) have been developed in recent years but have not been included in clinical guidelines so far. Areas covered: This review gives an update on different molecular markers in the urine and evaluates their role in patients with NMIBC in disease detection and surveillance. Moreover, the potential of recent approaches such as DNA methylation assays, multi-panel RNA gene expression assays and cell-free DNA analysis is assessed. Expert commentary: Most studies on various molecular urine markers have mainly focused on a potential replacement of cystoscopy. New developments in high throughput technologies and urine markers may offer further advantages as they may represent a non-invasive approach for molecular characterization of the disease. This opens new options for individualized surveillance strategies and may help to choose the best therapeutic option. The implementation of these technologies in well-designed clinical trials is essential to further promote the use of urine diagnostics in the management of patients with NMIBC.

  16. Molecular and immunohistochemical profiling of invasive micropapillary carcinoma of the breast

    Directory of Open Access Journals (Sweden)

    Thomas A

    2014-10-01

    Full Text Available Alexandra Thomas,1 Ryan W Askeland,2 Natalya V Guseva,2 Ramakrishna Sompallae,2,3 Deqin Ma2 1Department of Internal Medicine, 2Department of Pathology, 3Bioinformatics Division, Iowa Institute of Human Genetics, University of Iowa Hospitals and Clinics, Iowa City, IA, USABackground: In this study, molecular and immunohistochemical profiling of invasive micropapillary carcinoma of the breast was used to identify potentially useful markers for targeted therapies with a focus on BRAF V600E mutation.Methods: Formalin-fixed, paraffin-embedded tumor blocks from seven patients were identified from the archives at our institution and tumor registry from 1997 to 2012. Massively parallel (Next-generation sequencing was performed using the Ion AmpliSeq™ Cancer Hotspot Panel version 2 (Life Technologies, Carlsbad, CA, USA. Mutation analysis for BRAF V600E was performed using a single nucleotide primer extension assay. Immunohistochemistry studies for estrogen receptor (ER, progesterone receptor (PR, Her2/Neu, phosphatase and tensin homolog (PTEN, and non-metastatic protein 23 homologue 1 (NM23H1 were performed using the same tumor blocks. Staining for ER, PR, and Her2/Neu was scored according to American Society of Clinical Oncology/College of American Pathologists guidelines, and a four-tier system, ie, strong homogenous, heterogeneous, positive with negative foci, reduced in more than 50%, and lost in all or majority was used for PTEN and NM23H1 staining.Results: No pathogenic mutations were identified in the tumors by next-generation sequencing. The lack of BRAF V600E mutation was confirmed by single nucleotide primer extension assay. All tumors were positive for ER and PR, and showed no overexpression of Her2/Neu. Loss of or reduced PTEN expression was observed in six of seven cases and was associated with lymph node metastasis. Reduced NM23H1 expression was observed in three of seven cases, all of which had concurrent PTEN loss.Conclusion: No somatic

  17. Recent advances in high-throughput molecular marker identification for superficial and invasive bladder cancers

    DEFF Research Database (Denmark)

    Andersen, Lars Dyrskjøt; Zieger, Karsten; Ørntoft, Torben Falck

    2007-01-01

    individually contributed to the management of the disease. However, the development of high-throughput techniques for simultaneous assessment of a large number of markers has allowed classification of tumors into clinically relevant molecular subgroups beyond those possible by pathological classification. Here......Bladder cancer is the fifth most common neoplasm in industrialized countries. Due to frequent recurrences of the superficial form of this disease, bladder cancer ranks as one of the most common cancers. Despite the description of a large number of tumor markers for bladder cancers, none have......, we review the recent advances in high-throughput molecular marker identification for superficial and invasive bladder cancers....

  18. ADAM33 gene silencing by promoter hypermethylation as a molecular marker in breast invasive lobular carcinoma

    Directory of Open Access Journals (Sweden)

    de Souza Emanuel M

    2009-03-01

    Full Text Available Abstract Background ADAM33 protein is a member of the family of transmembrane glycoproteins composed of multidomains. ADAM family members have different activities, such as proteolysis and adhesion, making them good candidates to mediate the extracellular matrix remodelling and changes in cellular adhesion that characterise certain pathologies and cancer development. It was reported that one family member, ADAM23, is down-regulated by promoter hypermethylation. This seems to correlate with tumour progression and metastasis in breast cancer. In this study, we explored the involvement of ADAM33, another ADAM family member, in breast cancer. Methods First, we analysed ADAM33 expression in breast tumour cell lines by RT-PCR and western blotting. We also used 5-aza-2'-deoxycytidine (5azadCR treatment and DNA bisulphite sequencing to study the promoter methylation of ADAM33 in breast tumour cell lines. We evaluated ADAM33 methylation in primary tumour samples by methylation specific PCR (MSP. Finally, ADAM33 promoter hypermethylation was correlated with clinicopathological data using the chi-square test and Fisher's exact test. Results The expression analysis of ADAM33 in breast tumour cell lines by RT-PCR revealed gene silencing in 65% of tumour cell lines. The corresponding lack of ADAM33 protein was confirmed by western blotting. We also used 5-aza-2'-deoxycytidine (5-aza-dCR demethylation and bisulphite sequencing methodologies to confirm that gene silencing is due to ADAM33 promoter hypermethylation. Using MSP, we detected ADAM33 promoter hypermethylation in 40% of primary breast tumour samples. The correlation between methylation pattern and patient's clinicopathological data was not significantly associated with histological grade; tumour stage (TNM; tumour size; ER, PR or ERBB2 status; lymph node status; metastasis or recurrence. Methylation frequency in invasive lobular carcinoma (ILC was 76.2% compared with 25.5% in invasive ductal carcinoma

  19. ADAM33 gene silencing by promoter hypermethylation as a molecular marker in breast invasive lobular carcinoma

    International Nuclear Information System (INIS)

    Seniski, Gerusa G; Zanata, Silvio M; Costa, Fabrício F; Klassen, Giseli; Camargo, Anamaria A; Ierardi, Daniela F; Ramos, Edneia AS; Grochoski, Mariana; Ribeiro, Enilze SF; Cavalli, Iglenir J; Pedrosa, Fabio O; Souza, Emanuel M de

    2009-01-01

    ADAM33 protein is a member of the family of transmembrane glycoproteins composed of multidomains. ADAM family members have different activities, such as proteolysis and adhesion, making them good candidates to mediate the extracellular matrix remodelling and changes in cellular adhesion that characterise certain pathologies and cancer development. It was reported that one family member, ADAM23, is down-regulated by promoter hypermethylation. This seems to correlate with tumour progression and metastasis in breast cancer. In this study, we explored the involvement of ADAM33, another ADAM family member, in breast cancer. First, we analysed ADAM33 expression in breast tumour cell lines by RT-PCR and western blotting. We also used 5-aza-2'-deoxycytidine (5azadCR) treatment and DNA bisulphite sequencing to study the promoter methylation of ADAM33 in breast tumour cell lines. We evaluated ADAM33 methylation in primary tumour samples by methylation specific PCR (MSP). Finally, ADAM33 promoter hypermethylation was correlated with clinicopathological data using the chi-square test and Fisher's exact test. The expression analysis of ADAM33 in breast tumour cell lines by RT-PCR revealed gene silencing in 65% of tumour cell lines. The corresponding lack of ADAM33 protein was confirmed by western blotting. We also used 5-aza-2'-deoxycytidine (5-aza-dCR) demethylation and bisulphite sequencing methodologies to confirm that gene silencing is due to ADAM33 promoter hypermethylation. Using MSP, we detected ADAM33 promoter hypermethylation in 40% of primary breast tumour samples. The correlation between methylation pattern and patient's clinicopathological data was not significantly associated with histological grade; tumour stage (TNM); tumour size; ER, PR or ERBB2 status; lymph node status; metastasis or recurrence. Methylation frequency in invasive lobular carcinoma (ILC) was 76.2% compared with 25.5% in invasive ductal carcinoma (IDC), and this difference was

  20. Conformation analysis of trehalose. Molecular dynamics simulation and molecular mechanics

    International Nuclear Information System (INIS)

    Donnamaira, M.C.; Howard, E.I.; Grigera, J.R.

    1992-09-01

    Conformational analysis of the disaccharide trehalose is done by molecular dynamics and molecular mechanics. In spite of the different force fields used in each case, comparison between the molecular dynamics trajectories of the torsional angles of glycosidic linkage and energy conformational map shows a good agreement between both methods. By molecular dynamics it is observed a moderate mobility of the glycosidic linkage. The demands of computer time is comparable in both cases. (author). 6 refs, 4 figs

  1. Comprehensive Molecular Characterization of Muscle-Invasive Bladder Cancer. | Office of Cancer Genomics

    Science.gov (United States)

    We report a comprehensive analysis of 412 muscle-invasive bladder cancers characterized by multiple TCGA analytical platforms. Fifty-eight genes were significantly mutated, and the overall mutational load was associated with APOBEC-signature mutagenesis. Clustering by mutation signature identified a high-mutation subset with 75% 5-year survival.

  2. Tumour-associated endothelial-FAK correlated with molecular sub-type and prognostic factors in invasive breast cancer

    International Nuclear Information System (INIS)

    Alexopoulou, Annika N; Ho-Yen, Colan M; Papalazarou, Vassilis; Elia, George; Jones, J Louise; Hodivala-Dilke, Kairbaan

    2014-01-01

    Breast cancer is a heterogeneous disease that can be classified into one of 4 main molecular sub-types: luminal A, luminal B, Her2 over-expressing and basal-like (BL). These tumour sub-types require different treatments and have different risks of disease progression. BL cancers can be considered a sub-group of Triple negative (TN) cancers since they lack estrogen (ER), progesterone (PR) and Her2 expression. No targeted treatment currently exists for TN/BL cancers. Thus it is important to identify potential therapeutic targets and describe their relationship with established prognostic factors. Focal adhesion kinase (FAK) is upregulated in several human cancers and also plays a functional role in tumour angiogenesis. However, the association between breast cancer sub-types and tumour endothelial-FAK expression is unknown. Using immunofluorescence, we quantified FAK expression in tumour endothelial and tumour cell compartments in 149 invasive breast carcinomas and correlated expression with clinical, pathological and molecular parameters. Low endothelial-FAK expression was independently associated with luminal A tumours at univariate (p < 0.001) and multivariate (p = 0.001) analysis. There was a positive correlation between FAK expression in the vascular and tumour cell compartments (Spearman’s correlation co-efficient = 0.394, p < 0.001). Additionally, endothelial and tumour cell FAK expression were significantly increased in TN tumours (p = 0.043 and p = 0.033 respectively), in tumours with negative ER and PR status, and in high grade tumours at univariate analysis. Our findings establish a relationship between endothelial-FAK expression levels and the molecular sub-type of invasive breast cancer, and suggest that endothelial-FAK expression is potentially more clinically relevant than tumour cell FAK expression in breast cancer

  3. Impact of Molecular Subtypes in Muscle-invasive Bladder Cancer on Predicting Response and Survival after Neoadjuvant Chemotherapy.

    Science.gov (United States)

    Seiler, Roland; Ashab, Hussam Al Deen; Erho, Nicholas; van Rhijn, Bas W G; Winters, Brian; Douglas, James; Van Kessel, Kim E; Fransen van de Putte, Elisabeth E; Sommerlad, Matthew; Wang, Natalie Q; Choeurng, Voleak; Gibb, Ewan A; Palmer-Aronsten, Beatrix; Lam, Lucia L; Buerki, Christine; Davicioni, Elai; Sjödahl, Gottfrid; Kardos, Jordan; Hoadley, Katherine A; Lerner, Seth P; McConkey, David J; Choi, Woonyoung; Kim, William Y; Kiss, Bernhard; Thalmann, George N; Todenhöfer, Tilman; Crabb, Simon J; North, Scott; Zwarthoff, Ellen C; Boormans, Joost L; Wright, Jonathan; Dall'Era, Marc; van der Heijden, Michiel S; Black, Peter C

    2017-10-01

    An early report on the molecular subtyping of muscle-invasive bladder cancer (MIBC) by gene expression suggested that response to neoadjuvant chemotherapy (NAC) varies by subtype. To investigate the ability of molecular subtypes to predict pathological downstaging and survival after NAC. Whole transcriptome profiling was performed on pre-NAC transurethral resection specimens from 343 patients with MIBC. Samples were classified according to four published molecular subtyping methods. We developed a single-sample genomic subtyping classifier (GSC) to predict consensus subtypes (claudin-low, basal, luminal-infiltrated and luminal) with highest clinical impact in the context of NAC. Overall survival (OS) according to subtype was analyzed and compared with OS in 476 non-NAC cases (published datasets). Gene expression analysis was used to assign subtypes. Receiver-operating characteristics were used to determine the accuracy of GSC. The effect of GSC on survival was estimated by Cox proportional hazard regression models. The models generated subtype calls in expected ratios with high concordance across subtyping methods. GSC was able to predict four consensus molecular subtypes with high accuracy (73%), and clinical significance of the predicted consensus subtypes could be validated in independent NAC and non-NAC datasets. Luminal tumors had the best OS with and without NAC. Claudin-low tumors were associated with poor OS irrespective of treatment regimen. Basal tumors showed the most improvement in OS with NAC compared with surgery alone. The main limitations of our study are its retrospective design and comparison across datasets. Molecular subtyping may have an impact on patient benefit to NAC. If validated in additional studies, our results suggest that patients with basal tumors should be prioritized for NAC. We discovered the first single-sample classifier to subtype MIBC, which may be suitable for integration into routine clinical practice. Different molecular

  4. Prevalence and molecular diversity of invasive Streptococcus dysgalactiae and Streptococcus pyogenes in a German tertiary care medical centre.

    Science.gov (United States)

    Rößler, S; Berner, R; Jacobs, E; Toepfner, N

    2018-05-03

    Prevalence of invasive ß-haemolytic streptococci (BHS) at a tertiary care hospital and molecular diversity of S. pyogenes and S. dysgalactiae was studied. Between 2012 and 2016, all blood culture sets (n = 55,839), CSF (n = 8413) and soft tissue (n = 20,926) samples were analysed for BHS positivity using HYBASE software. Molecular profiles of 99 S. pyogenes and S. dysgalactiae were identified by sequencing of M protein genes (emm types) and multiplex PCR typing of 20 other virulence determinants. Streptococci contributed to 6.2% of blood, 10.7% of CSF and 14.5% of soft tissue isolates, being among the most common invasive isolates. The overall rates of invasive S. pyogenes, S. agalactiae, S. dysgalactiae and S. pneumoniae were 2.4, 4.4, 2.1, and 5.3%. Whereas S. pneumoniae was 1.5% more common in CSF samples, BHS isolates were 2-fold and 11-fold higher in bacteraemia and invasive soft tissue infections. Genetic BHS typing revealed wide molecular diversity of invasive and noninvasive group A and group G BHS, whereas one emm-type (stG62647.0) and no other virulence determinants except scpA were detected in invasive group C BHS. BHS were important invasive pathogens, outpacing S. pneumoniae in bacteraemia and invasive soft tissue infections. The incidence of S. dysgalactiae infections was comparable to that of S. pyogenes even with less diversity of molecular virulence. The results of this study emphasise the need for awareness of BHS invasiveness in humans and the need to develop BHS prevention strategies.

  5. Preoperative core needle biopsy is accurate in determining molecular subtypes in invasive breast cancer

    International Nuclear Information System (INIS)

    Chen, Xiaosong; Yuan, Ying; Fei, Xiaochun; Jin, Xiaolong; Shen, Kunwei; Sun, Long; Mao, Yan; Zhu, Siji; Wu, Jiayi; Huang, Ou; Li, Yafen; Chen, Weiguo; Wang, Jianhua

    2013-01-01

    Estrogen receptor (ER), progesterone receptor (PgR), HER2, and Ki67 have been increasingly evaluated by core needle biopsy (CNB) and are recommended for classifying breast cancer into molecular subtypes. However, the concordance rate between CNB and open excision biopsy (OEB) has not been well documented. Patients with paired CNB and OEB samples from Oct. 2009 to Feb. 2012 in Ruijin Hospital were included. ER, PgR, HER2, and Ki67 were determined by immunohistochemistry (IHC). Patients with HER2 IHC 2+ were further examined by FISH. Cutoff value for Ki67 high expression was 14%. Molecular subtypes were constructed as follows: Luminal A, Luminal B, Triple Negative, and HER2 positive. There were 298 invasive breast cancer patients analyzed. Concordance rates for ER, PgR, and HER2 were 93.6%, 85.9%, and 96.3%, respectively. Ki67 expression was slightly higher in OEB than in CNB samples (29.3% vs. 26.8%, P = 0.046). Good agreement (κ = 0.658) was demonstrated in evaluating molecular subtypes between CNB and OEB, with a concordance rate of 77.2%. We also used a different Ki67 cutoff value (20%) for determining Luminal A and B subtypes in HR (hormone receptor) +/HER2- diseases and the overall concordance rate was 79.2%. However, using a cut-point of Ki67 either 14% or 20% for both specimens, there will be about 14% of HR+/HER2- specimens that are called Luminal A on CNB and Luminal B on OEB. CNB was accurate in determining ER, PgR, and HER2 status as well as non-Luminal molecular subtypes in invasive breast cancer. Ki67 should be retested on OEB samples in HR+/HER2- patients to accurately distinguish Luminal A from B tumors

  6. Cost-effectiveness analysis in minimally invasive spine surgery.

    Science.gov (United States)

    Al-Khouja, Lutfi T; Baron, Eli M; Johnson, J Patrick; Kim, Terrence T; Drazin, Doniel

    2014-06-01

    Medical care has been evolving with the increased influence of a value-based health care system. As a result, more emphasis is being placed on ensuring cost-effectiveness and utility in the services provided to patients. This study looks at this development in respect to minimally invasive spine surgery (MISS) costs. A literature review using PubMed, the Cost-Effectiveness Analysis (CEA) Registry, and the National Health Service Economic Evaluation Database (NHS EED) was performed. Papers were included in the study if they reported costs associated with minimally invasive spine surgery (MISS). If there was no mention of cost, CEA, cost-utility analysis (CUA), quality-adjusted life year (QALY), quality, or outcomes mentioned, then the article was excluded. Fourteen studies reporting costs associated with MISS in 12,425 patients (3675 undergoing minimally invasive procedures and 8750 undergoing open procedures) were identified through PubMed, the CEA Registry, and NHS EED. The percent cost difference between minimally invasive and open approaches ranged from 2.54% to 33.68%-all indicating cost saving with a minimally invasive surgical approach. Average length of stay (LOS) for minimally invasive surgery ranged from 0.93 days to 5.1 days compared with 1.53 days to 12 days for an open approach. All studies reporting EBL reported lower volume loss in an MISS approach (range 10-392.5 ml) than in an open approach (range 55-535.5 ml). There are currently an insufficient number of studies published reporting the costs of MISS. Of the studies published, none have followed a standardized method of reporting and analyzing cost data. Preliminary findings analyzing the 14 studies showed both cost saving and better outcomes in MISS compared with an open approach. However, more Level I CEA/CUA studies including cost/QALY evaluations with specifics of the techniques utilized need to be reported in a standardized manner to make more accurate conclusions on the cost effectiveness of

  7. Molecular diagnostic methods for invasive fungal disease: the horizon draws nearer?

    Science.gov (United States)

    Halliday, C L; Kidd, S E; Sorrell, T C; Chen, S C-A

    2015-04-01

    Rapid, accurate diagnostic laboratory tests are needed to improve clinical outcomes of invasive fungal disease (IFD). Traditional direct microscopy, culture and histological techniques constitute the 'gold standard' against which newer tests are judged. Molecular diagnostic methods, whether broad-range or fungal-specific, have great potential to enhance sensitivity and speed of IFD diagnosis, but have varying specificities. The use of PCR-based assays, DNA sequencing, and other molecular methods including those incorporating proteomic approaches such as matrix-assisted laser desorption ionisation-time of flight mass spectroscopy (MALDI-TOF MS) have shown promising results. These are used mainly to complement conventional methods since they require standardisation before widespread implementation can be recommended. None are incorporated into diagnostic criteria for defining IFD. Commercial assays may assist standardisation. This review provides an update of molecular-based diagnostic approaches applicable to biological specimens and fungal cultures in microbiology laboratories. We focus on the most common pathogens, Candida and Aspergillus, and the mucormycetes. The position of molecular-based approaches in the detection of azole and echinocandin antifungal resistance is also discussed.

  8. [Molecular markers: an important tool in the diagnosis, treatment and epidemiology of invasive aspergillosis].

    Science.gov (United States)

    Frías-de León, María Guadalupe; Acosta-Altamirano, Gustavo; Duarte-Escalante, Esperanza; Martínez-Hernández, José Enrique; Martínez-Rivera, María de Los Ángeles; Reyes-Montes, María Del Rocío

    2014-01-01

    Increase in the incidence of invasive aspergillosis has represented a difficult problem for management of patients with this infection due to its high rate of mortality, limited knowledge concerning its diagnosis, and therapeutic practice. The difficulty in management of patients with aspergillosis initiates with detection of the fungus in the specimens of immunosuppressed patients infected with Aspergillus fumigatus; in addition, difficulty exists in terms of the development of resistance to antifungals as a consequence of their indiscriminate use in prophylactic and therapeutic practice and to ignorance concerning the epidemiological data of aspergillosis. With the aim of resolving these problems, molecular markers is employed at present with specific and accurate results. However, in Mexico, the use of molecular markers has not yet been implemented in the routine of intrahospital laboratories; despite the fact that these molecular markers has been widely referred in the literature, it is necessary for it to validated and standardized to ensure that the results obtained in any laboratory would be reliable and comparable. In the present review, we present an update on the usefulness of molecular markers in accurate identification of A. fumigatus, detection of resistance to antifugal triazoles, and epidemiological studies for establishing the necessary measures for prevention and control of aspergillosis.

  9. Invasive lobular breast cancer: the prognostic impact of histopathological grade, E-cadherin and molecular subtypes.

    Science.gov (United States)

    Engstrøm, Monica J; Opdahl, Signe; Vatten, Lars J; Haugen, Olav A; Bofin, Anna M

    2015-02-01

    The aim of this study was to compare breast cancer specific survival (BCSS) for invasive lobular carcinoma (ILC) and invasive ductal carcinoma (IDC) and, further, to evaluate critically the prognostic value of histopathological grading of ILC and examine E-cadherin as a prognostic marker in ILC. The study comprised 116 lobular and 611 ductal breast carcinomas occurring between 1961 and 2008. All cases had been classified previously according to histopathological type and grade, stained for oestrogen receptor (ER), progesterone receptor (PR), antigen Ki67 (Ki67), epithelial growth factor receptor (EGFR), cytokeratin 5 (CK5) and human epidermal growth factor receptor 2 (HER2) and classified into molecular subtypes. For the present study, immunohistochemical staining for E-cadherin was performed. The Kaplan-Meier method and Cox proportional hazards models were used in the analyses. Grade 2 tumours comprised 85.3% of the lobular tumours and 51.9% of the ductal tumours. BCSS in ILC grade 2 was comparable to that of IDC grade 3. E-cadherin-negative ILC had a poorer prognosis compared to E-cadherin positive ILC and to IDC regardless of E-cadherin status. The implication of histopathological grading may differ in ILC compared to IDC. E-cadherin may be useful in prognostication in ILC and thereby influence the determination of treatment strategies for this group of women. © 2014 The Authors. Histopathology published by John Wiley & Sons Ltd.

  10. Delimiting invasive Myriophyllum aquaticum in Kashmir Himalaya using a molecular phylogenetic approach.

    Science.gov (United States)

    Shah, M A; Ali, M A; Al-Hemaid, F M; Reshi, Z A

    2014-09-12

    Myriophyllum aquaticum (Vell.) Verdc. (family Haloragaceae) is one of the most invasive and destructive South American aquatic plant species and is present in a wide range of geographic regions, including the Kashmir Himalaya. Confusion regarding the taxonomic delimitation of M. aquaticum in the Himalayan region impedes effective and targeted management. Hence, our goal was improve the identification of M. aquaticum for exclusive delimitation from other related species in the study region using a molecular phylogenetic approach. A maximum parsimony tree recovered from phylogenetic analyses of the internal transcribed spacer sequences of nuclear ribosomal DNA was used to authenticate the identification of M. aquaticum. The results of this study can be used for targeted management of this tropical invader into the temperate Kashmir Himalaya.

  11. Total RNA Sequencing Analysis of DCIS Progressing to Invasive Breast Cancer

    Science.gov (United States)

    2017-09-01

    AWARD NUMBER: W81XWH-14-1-0080 TITLE: Total RNA Sequencing Analysis of DCIS Progressing to Invasive Breast Cancer . PRINCIPAL INVESTIGATOR...TITLE AND SUBTITLE Total RNA Sequencing Analysis of DCIS Progressing to Invasive Breast Cancer . 5a. CONTRACT NUMBER 5b. GRANT NUMBER GRANT11489...institutional, NIH-funded study of genetic and epigenetic alterations of pre-invasive DCIS that did or did not progress to invasive breast cancer , with an

  12. RESEARCH NOTE Molecular genetic analysis of consanguineous ...

    Indian Academy of Sciences (India)

    Navya

    Molecular genetic analysis of consanguineous families with primary microcephaly ... Translational Research Institute, Academic Health System, Hamad Medical ..... bridging the gap between homozygosity mapping and deep sequencing.

  13. The genetic and molecular basis of bacterial invasion of epithelial cells

    African Journals Online (AJOL)

    Invasion of epithelial cells was demonstrated to be triggered by invasion plasmid antigens B, C, and D ( IpaB, IpaC and IpaD ) which is accomplished by intracellular spread gene icsA. The invasion of epithelial cells by some individual species of bacteria were also reviewed.Yersinia enterocolitica invasiveness was shown ...

  14. An investigation on non-invasive fungal sinusitis; Molecular identification of etiologic agents

    Directory of Open Access Journals (Sweden)

    Abdolrasoul Mohammadi

    2017-01-01

    Full Text Available Background: Fungal sinusitis is increasing worldwide in the past two decades. It is divided into two types including invasive and noninvasive. Noninvasive types contain allergic fungal sinusitis (AFS and fungus ball. AFS is a hypersensitivity reaction to fungal allergens in the mucosa of the sinonasal tract in atopic individuals. The fungus ball is a different type of noninvasive fungal rhinosinusitis which is delineated as an accumulation of debris and fungal elements inside a paranasal sinus. Fungal sinusitis caused by various fungi such as Aspergillus species, Penicillium, Mucor, Rhizopus, and phaeohyphomycetes. The aim of the present study is to identify fungal species isolated from noninvasive fungal sinusitis by molecular methods. Materials and Methods: During 2015–2016, a total of 100 suspected patients were examined for fungal sinusitis. Functional endoscopic sinus surgery was performed using the Messerklinger technique. Clinical samples were identified by phenotypic and molecular methods. Polymerase chain reaction (PCR sequencing of ITS1-5.8S-ITS2 region and PCR-restriction fragment length polymorphism with Msp I restriction enzyme was performed for molecular identification of molds and yeasts, respectively. Results: Twenty-seven out of 100 suspected cases (27% had fungal sinusitis. Nasal congestion (59% and headache (19% were the most common clinical signs among patients. Fifteen patients (55.5% were male and 12 patients (44.5% were female. Aspergillus flavus was the most prevalent fungal species (26%, followed by Penicillium chrysogenum (18.5% and Candida glabrata species complex (15%. Conclusion: Since clinical manifestations, computed tomography scan, endoscopy, and histopathological findings are very nonspecific in AFS and fungus ball; therefore, molecular investigations are compulsory for precise identification of etiologic agents and appropriate management of these fungal infections.

  15. Fecal Glucocorticoid Analysis: Non-invasive Adrenal Monitoring in Equids.

    Science.gov (United States)

    Yarnell, Kelly; Purcell, Rebecca S; Walker, Susan L

    2016-04-25

    Adrenal activity can be assessed in the equine species by analysis of feces for corticosterone metabolites. During a potentially aversive situation, corticotrophin releasing hormone (CRH) is released from the hypothalamus in the brain. This stimulates the release of adrenocorticotrophic hormone (ACTH) from the pituitary gland, which in turn stimulates release of glucocorticoids from the adrenal gland. In horses the glucocorticoid corticosterone is responsible for several adaptations needed to support equine flight behaviour and subsequent removal from the aversive situation. Corticosterone metabolites can be detected in the feces of horses and assessment offers a non-invasive option to evaluate long term patterns of adrenal activity. Fecal assessment offers advantages over other techniques that monitor adrenal activity including blood plasma and saliva analysis. The non-invasive nature of the method avoids sampling stress which can confound results. It also allows the opportunity for repeated sampling over time and is ideal for studies in free ranging horses. This protocol describes the enzyme linked immunoassay (EIA) used to assess feces for corticosterone, in addition to the associated biochemical validation.

  16. Risk analysis and bioeconomics of invasive species to inform policy and management

    Science.gov (United States)

    David M. Lodge; Paul W. Simonin; Stanley W. Burgiel; Reuben P. Keller; Jonathan M. Bossenbroek; Christopher L. Jerde; Andrew M. Kramer; Edward S. Rutherford; Matthew A. Barnes; Marion E. Wittmann; W. Lindsay Chadderton; Jenny L. Apriesnig; Dmitry Beletsky; Roger M. Cooke; John M. Drake; Scott P. Egan; David C. Finnoff; Crysta A. Gantz; Erin K. Grey; Michael H. Hoff; Jennifer G. Howeth; Richard A. Jensen; Eric R. Larson; Nicholas E. Mandrak; Doran M. Mason; Felix A. Martinez; Tammy J. Newcomb; John D. Rothlisberger; Andrew J. Tucker; Travis W. Warziniack; Hongyan. Zhang

    2016-01-01

    Risk analysis of species invasions links biology and economics, is increasingly mandated by international and national policies, and enables improved management of invasive species. Biological invasions proceed through a series of transition probabilities (i.e., introduction, establishment, spread, and impact), and each of these presents opportunities for...

  17. Cellular and Molecular Defects Underlying Invasive Fungal Infections—Revelations from Endemic Mycoses

    Directory of Open Access Journals (Sweden)

    Pamela P. Lee

    2017-06-01

    Full Text Available The global burden of fungal diseases has been increasing, as a result of the expanding number of susceptible individuals including people living with human immunodeficiency virus (HIV, hematopoietic stem cell or organ transplant recipients, patients with malignancies or immunological conditions receiving immunosuppressive treatment, premature neonates, and the elderly. Opportunistic fungal pathogens such as Aspergillus, Candida, Cryptococcus, Rhizopus, and Pneumocystis jiroveci are distributed worldwide and constitute the majority of invasive fungal infections (IFIs. Dimorphic fungi such as Histoplasma capsulatum, Coccidioides spp., Paracoccidioides spp., Blastomyces dermatiditis, Sporothrix schenckii, Talaromyces (Penicillium marneffei, and Emmonsia spp. are geographically restricted to their respective habitats and cause endemic mycoses. Disseminated histoplasmosis, coccidioidomycosis, and T. marneffei infection are recognized as acquired immunodeficiency syndrome (AIDS-defining conditions, while the rest also cause high rate of morbidities and mortalities in patients with HIV infection and other immunocompromised conditions. In the past decade, a growing number of monogenic immunodeficiency disorders causing increased susceptibility to fungal infections have been discovered. In particular, defects of the IL-12/IFN-γ pathway and T-helper 17-mediated response are associated with increased susceptibility to endemic mycoses. In this review, we put together the various forms of endemic mycoses on the map and take a journey around the world to examine how cellular and molecular defects of the immune system predispose to invasive endemic fungal infections, including primary immunodeficiencies, individuals with autoantibodies against interferon-γ, and those receiving biologic response modifiers. Though rare, these conditions provide importance insights to host defense mechanisms against endemic fungi, which can only be appreciated in unique

  18. The impact of new trends in POCTs for companion diagnostics, non-invasive testing and molecular diagnostics.

    Science.gov (United States)

    Huckle, David

    2015-06-01

    Point-of-care diagnostics have been slowly developing over several decades and have taken on a new importance in current healthcare delivery for both diagnostics and development of new drugs. Molecular diagnostics have become a key driver of technology change and opened up new areas in companion diagnostics for use alongside pharmaceuticals and in new clinical approaches such as non-invasive testing. Future areas involving smartphone and other information technology advances, together with new developments in molecular biology, microfluidics and surface chemistry are adding to advances in the market. The focus for point-of-care tests with molecular diagnostic technologies is focused on advancing effective applications.

  19. Ecological niche comparison and molecular phylogeny segregate the invasive moss species Campylopus introflexus (Leucobryaceae, Bryophyta) from its closest relatives.

    Science.gov (United States)

    Gama, Renato; Aguirre-Gutiérrez, Jesús; Stech, Michael

    2017-10-01

    The delimitation of the invasive moss species Campylopus introflexus from its closest relative, Campylopus pilifer , has been long debated based on morphology. Previous molecular phylogenetic reconstructions based on the nuclear ribosomal internal transcribed spacers (ITS) 1 and 2 showed that C. pilifer is split into an Old World and a New World lineage, but remained partly inconclusive concerning the relationships between these two clades and C. introflexus . Analyses of an extended ITS dataset displayed statistically supported incongruence between ITS1 and ITS2. ITS1 separates the New World clade of C. pilifer from a clade comprising C. introflexus and the Old World C. pilifer . Ancestral state reconstruction showed that this topology is morphologically supported by differences in the height of the dorsal costal lamellae in leaf cross-section (despite some overlap). ITS2, in contrast, supports the current morphological species concept, i.e., separating C. introflexus from C. pilifer , which is morphologically supported by the orientation of the hyaline hair point at leaf apex as well as costal lamellae height. Re-analysis of published and newly generated plastid atpB-rbcL spacer sequences supported the three ITS lineages. Ecological niche modeling proved a useful approach and showed that all three molecular lineages occupy distinct environmental spaces that are similar, but undoubtedly not equivalent. In line with the ITS1 topology, the C. pilifer lineage from the New World occupies the most distinct environmental niche, whereas the niches of Old World C. pilifer and C. introflexus are very similar. Taking the inferences from ecological niche comparisons, phylogenetics, and morphology together, we conclude that all three molecular lineages represent different taxa that should be recognized as independent species, viz. C. introflexus , C. pilifer (Old World clade), and the reinstated C. lamellatus Mont. (New World clade).

  20. [Triexponential diffusion analysis in invasive ductal carcinoma and fibroadenoma].

    Science.gov (United States)

    Nakagawa, Masayuki; Miyati, Tosiaki; Hayashi, Tatsuya; Kanao, Syotaro; Taniguchi, Masahiro; Higashimura, Kyoji; Toi, Masakazu; Togashi, Kaori

    2014-03-01

    To simultaneously obtain information on diffusion and perfusion in breast lesions by diffusion-weighted magnetic resonance imaging (DWI), we analyzed three diffusion components using a triexponential function. Eighteen subjects [10 with invasive ductal carcinoma (IDC), 8 with fibroadenoma] were evaluated using DWI with multiple b-values. We derived perfusion-related diffusion, fast free diffusion, and slow restricted diffusion coefficients (Dp, Df, Ds) calculated from the triexponential function using the DWI data. Moreover, the triexponential analysis was compared with biexponential and monoexponential analyses. Each diffusion coefficient with a triexponential function was correlated to a relative enhancement ratio (RER) using dynamic contrast-enhanced MRI. In triexponential analysis, Dp and Ds in IDC were significantly higher than those for fibroadenoma. There was no correlation between each diffusion coefficient from the triexponential analysis in any of the groups (Dp, Df, and Ds), but biexponential analysis revealed a positive correlation between each diffusion coefficient in breast lesions. Strong correlations were found between Dp and RERs. Triexponential analysis thus makes it possible to obtain, in noninvasive fashion, more detailed diffusion and perfusion information in breast lesions.

  1. Who cites who in the invasion zoo: insights from an analysis of the most highly cited papers in invasion ecology

    Czech Academy of Sciences Publication Activity Database

    Pyšek, Petr; Richardson, D. M.; Jarošík, Vojtěch

    2006-01-01

    Roč. 78, - (2006), s. 437-468 ISSN 0032-7786 Institutional research plan: CEZ:AV0Z60050516 Keywords : citation analysis * biological invasions * Web of Science Subject RIV: EF - Botanics Impact factor: 2.119, year: 2006

  2. Mycophenolic acid inhibits migration and invasion of gastric cancer cells via multiple molecular pathways.

    Directory of Open Access Journals (Sweden)

    Boying Dun

    Full Text Available Mycophenolic acid (MPA is the metabolized product and active element of mycophenolate mofetil (MMF that has been widely used for the prevention of acute graft rejection. MPA potently inhibits inosine monophosphate dehydrogenase (IMPDH that is up-regulated in many tumors and MPA is known to inhibit cancer cell proliferation as well as fibroblast and endothelial cell migration. In this study, we demonstrated for the first time MPA's antimigratory and anti-invasion abilities of MPA-sensitive AGS (gastric cancer cells. Genome-wide expression analyses using Illumina whole genome microarrays identified 50 genes with ≥2 fold changes and 15 genes with > 4 fold alterations and multiple molecular pathways implicated in cell migration. Real-time RT-PCR analyses of selected genes also confirmed the expression differences. Furthermore, targeted proteomic analyses identified several proteins altered by MPA treatment. Our results indicate that MPA modulates gastric cancer cell migration through down-regulation of a large number of genes (PRKCA, DOCK1, INF2, HSPA5, LRP8 and PDGFRA and proteins (PRKCA, AKT, SRC, CD147 and MMP1 with promigratory functions as well as up-regulation of a number of genes with antimigratory functions (ATF3, SMAD3, CITED2 and CEAMCAM1. However, a few genes that may promote migration (CYR61 and NOS3 were up-regulated. Therefore, MPA's overall antimigratory role on cancer cells reflects a balance between promigratory and antimigratory signals influenced by MPA treatment.

  3. A Preclinical Evaluation of Antrodia camphorata Alcohol Extracts in the Treatment of Non-Small Cell Lung Cancer Using Non-Invasive Molecular Imaging

    Directory of Open Access Journals (Sweden)

    Jeng-Feng Chiou

    2011-01-01

    Full Text Available This study was carried out to provide a platform for the pre-clinical evaluation of anti-cancer properties of a unique CAM (complementary and alternative medicine agent, Antrodia camphorata alcohol extract (ACAE, in a mouse model with the advantageous non-invasive in vivo bioluminescence molecular imaging technology. In vitro analyses on the proliferation, migration/invasion, cell cycle and apoptosis were performed on ACAE-treated non-small cell lung cancer cells, H441GL and control CGL1 cells. In vivo, immune-deficient mice were inoculated subcutaneously with H441GL followed by oral gavages of ACAE. The effect of ACAE on tumor progression was monitored by non-invasive bioluminescence imaging. The proliferation and migration/invasion of H441GL cells were inhibited by ACAE in a dose-dependent manner. In addition, ACAE induced cell cycle arrest at G0/G1 phase and apoptosis in H441GL cells as shown by flow cytometric analysis, Annexin-V immunoflourescence and DNA fragmentation. In vivo bioluminescence imaging revealed that tumorigenesis was significantly retarded by oral treatment of ACAE in a dose-dependent fashion. Based on our experimental data, ACAE contains anti-cancer properties and could be considered as a potential CAM agent in future clinical evaluation.

  4. Tracheostomy and invasive mechanical ventilation in amyotrophic lateral sclerosis: decision-making factors and survival analysis.

    Science.gov (United States)

    Kimura, Fumiharu

    2016-04-28

    Invasive and/or non-invasive mechanical ventilation are most important options of respiratory management in amyotrophic lateral sclerosis. We evaluated the frequency, clinical characteristics, decision-making factors about ventilation and survival analysis of 190 people with amyotrophic lateral sclerosis patients from 1990 until 2013. Thirty-one percentage of patients underwent tracheostomy invasive ventilation with the rate increasing more than the past 20 years. The ratio of tracheostomy invasive ventilation in patients >65 years old was significantly increased after 2000 (25%) as compared to before (10%). After 2010, the standard use of non-invasive ventilation showed a tendency to reduce the frequency of tracheostomy invasive ventilation. Mechanical ventilation prolonged median survival (75 months in tracheostomy invasive ventilation, 43 months in non-invasive ventilation vs natural course, 32 months). The life-extending effects by tracheostomy invasive ventilation were longer in younger patients ≤65 years old at the time of ventilation support than in older patients. Presence of partners and care at home were associated with better survival. Following factors related to the decision to perform tracheostomy invasive ventilation: patients ≤65 years old: greater use of non-invasive ventilation: presence of a spouse: faster tracheostomy: higher progression rate; and preserved motor functions. No patients who underwent tracheostomy invasive ventilation died from a decision to withdraw mechanical ventilation. The present study provides factors related to decision-making process and survival after tracheostomy and help clinicians and family members to expand the knowledge about ventilation.

  5. Wavelet Analysis for Molecular Dynamics

    Science.gov (United States)

    2015-06-01

    Our method takes as input the topology and sparsity of the bonding structure of a molecular system, and returns a hierarchical set of system-specific...problems, such as modeling crack initiation and propagation, or interfacial phenomena. In the present work, we introduce a wavelet-based approach to extend...Several functional forms are common for angle poten- tials complicating not only implementation but also choice of approximation. In all cases, the

  6. Integrative invasion science: model systems, multi-site studies, focused meta-analysis, and invasion syndromes

    Czech Academy of Sciences Publication Activity Database

    Kueffer, C.; Pyšek, Petr; Richardson, D. M.

    2013-01-01

    Roč. 200, č. 3 (2013), s. 615-633 ISSN 1469-8137 R&D Projects: GA ČR(CZ) GAP504/11/1028; GA ČR GA206/09/0563 Institutional support: RVO:67985939 Keywords : model systems * invasion syndromes * multi-site studies Subject RIV: EF - Botanics Impact factor: 6.545, year: 2013

  7. Invasive Group A Streptococcal Disease. National Epidemiology and Genetic Analysis

    NARCIS (Netherlands)

    Vlaminckx, B.J.M.

    2006-01-01

    Infections with group A streptococci (GAS), or S. pyogenes, range from mild and superficial to very severe and lethal invasive disease. In severe invasive GAS infections, hypotension and multiorgan failure may develop rapidly resulting in the development of toxic shock-like syndrome (TSS). In the

  8. Molecular and Microenvironmental Determinants of Glioma Stem-Like Cell Survival and Invasion

    Directory of Open Access Journals (Sweden)

    Alison Roos

    2017-06-01

    Full Text Available Glioblastoma multiforme (GBM is the most frequent primary brain tumor in adults with a 5-year survival rate of 5% despite intensive research efforts. The poor prognosis is due, in part, to aggressive invasion into the surrounding brain parenchyma. Invasion is a complex process mediated by cell-intrinsic pathways, extrinsic microenvironmental cues, and biophysical cues from the peritumoral stromal matrix. Recent data have attributed GBM invasion to the glioma stem-like cell (GSC subpopulation. GSCs are slowly dividing, highly invasive, therapy resistant, and are considered to give rise to tumor recurrence. GSCs are localized in a heterogeneous cellular niche, and cross talk between stromal cells and GSCs cultivates a fertile environment that promotes GSC invasion. Pro-migratory soluble factors from endothelial cells, astrocytes, macrophages, microglia, and non-stem-like tumor cells can stimulate peritumoral invasion of GSCs. Therefore, therapeutic efforts designed to target the invasive GSCs may enhance patient survival. In this review, we summarize the current understanding of extrinsic pathways and major stromal and immune players facilitating GSC maintenance and survival.

  9. Effects of non-invasive neurostimulation on craving: a meta-analysis

    NARCIS (Netherlands)

    Jansen, Jochem M.; Daams, Joost G.; Koeter, Maarten W. J.; Veltman, Dick J.; van den Brink, Wim; Goudriaan, Anna E.

    2013-01-01

    This meta-analysis was conducted to evaluate the available evidence regarding the effects of non-invasive neurostimulation of the dorsolateral prefrontal cortex (DLPFC), on craving in substance dependence and craving for high palatable food. Non-invasive neurostimulation techniques were restricted

  10. Effects of non-invasive neurostimulation on craving: A meta-analysis

    NARCIS (Netherlands)

    Jansen, J.M.; Daams, J.G.; Koeter, M.W.; Veltman, D.J.; van den Brink, W.; Goudriaan, A.E.

    2013-01-01

    This meta-analysis was conducted to evaluate the available evidence regarding the effects of non-invasive neurostimulation of the dorsolateral prefrontal cortex (DLPFC), on craving in substance dependence and craving for high palatable food. Non-invasive neurostimulation techniques were restricted

  11. Analysis of intravesical recurrence after bladder-preserving therapy for muscle-invasive bladder cancer

    International Nuclear Information System (INIS)

    Onozawa, Mizuki; Miyanaga, Naoto; Hinotsu, Shiro

    2012-01-01

    The aim of the present study was to analyze the pattern of recurrences after bladder-preserving therapy for muscle-invasive bladder cancer. The subjects were 77 patients with T2-3N0M0 bladder cancer whose bladder was preserved by intra-arterial chemotherapy and radiation. The patterns of the first recurrences were retrospectively analyzed. With a median follow-up of 38.5 months, 17 patients (22.1%) experienced intravesical recurrence without metastasis, 14 (82.4%) of which were cases of non-muscle-invasive bladder cancer recurrence and 3 (17.6%) of which were muscle-invasive bladder cancer recurrences. Muscle-invasive bladder cancer recurred at the same site as the initial tumor site in all three cases, whereas non-muscle-invasive bladder cancer recurred at different sites in 64% of the patients in that group. The peak hazard of the non-muscle-invasive bladder cancer recurrence was observed at around a year after treatment. Recurrent non-muscle-invasive bladder cancer was of a significantly lower histological grade with lower Ki-67-labeling indices than the initial muscle-invasive bladder cancer. Twelve (85.7%) of 14 patients with non-muscle-invasive bladder cancer recurrence achieved disease-free status. The multivariate analysis revealed that multiplicity, grade and tumor size were significantly correlated with the recurrence (P=0.0001, 0.0442 and 0.0412, respectively). Most of the recurrences after bladder-preserving therapy were cases of non-muscle-invasive bladder cancer. The recurrence pattern and characteristics of the tumors did not differ from those of primary non-muscle-invasive bladder cancer. Patients with high-risk factors would be candidates for prophylactic intravesical therapy for non-muscle-invasive bladder cancer recurrence. (author)

  12. Analysis of microtraces in invasive traumas using SEM/EDS.

    Science.gov (United States)

    Vermeij, E J; Zoon, P D; Chang, S B C G; Keereweer, I; Pieterman, R; Gerretsen, R R R

    2012-01-10

    Scanning electron microscopy in combination with energy-dispersive X-ray spectrometry (SEM/EDS) is a proven forensic tool and has been used to analyze several kinds of trace evidence. A forensic application of SEM/EDS is the examination of morphological characteristics of tool marks that tools and instruments leave on bone. The microtraces that are left behind by these tools and instruments on the bone are, however, often ignored or not noticed at all. In this paper we will describe the use of SEM/EDS for the analysis of microtraces in invasive sharp-force, blunt-force and bone-hacking traumas in bone. This research is part of a larger multi-disciplinary approach in which pathologists, forensic anthropologists, toolmark and microtrace experts work together to link observed injuries to a suspected weapon or, in case of an unknown weapon, to indicate a group of objects that could have been used as a weapon. Although there are a few difficulties one have to consider, the method itself is rather simple and straightforward to apply. A sample of dry and clean bone is placed into the SEM sample chamber and brightness and contrast are set such that bone appears grey, metal appears white and organic material appears black. The sample is then searched manually to find relevant features. Once features are found their elemental composition is measured by an energy dispersive X-ray spectrometer (EDS). This method is illustrated using several cases. It is shown that SEM/EDS analysis of microtraces in bone is a valuable tool to get clues about an unknown weapon and can associate a specific weapon with injuries on the basis of appearance and elemental composition. In particular the separate results from the various disciplines are complementary and may be combined to reach a conclusion with a stronger probative value. This is not only useful in the courtroom but above all in criminal investigations when one have to know for what weapon or object to look for. Copyright © 2011

  13. Assessing stakeholder perspectives on invasive plants to inform risk analysis

    Science.gov (United States)

    Conservation and land management decisions are often based primarily on natural science, but could be more successful if human influences were effectively integrated into decision-making. This is especially true for efforts to manage invasive plants, whose arrival is usually the product of delibera...

  14. Confronting challenges to economic analysis of biological invasions in forests

    Science.gov (United States)

    Thomas P Holmes

    2010-01-01

    Biological invasions of forests by non-indigenous organisms present a complex, persistent, and largely irreversible threat to forest ecosystems around the globe. Rigorous assessments of the economic impacts of introduced species, at a national scale, are needed to provide credible information to policy makers. It is proposed here that microeconomic models of damage due...

  15. Molecular mechanisms responsive to dehydration may impact the invasiveness of perennial weeds under global climate change

    Science.gov (United States)

    Leafy spurge is an invasive perennial weed in the great plains of the US and Canada. The ability of this herbaceous weed to regenerate new shoot growth from an abundance of crown and root buds after severe abiotic stress is critical for survival. Due to its adaptable and aggressive nature, global cl...

  16. Gene expression analysis of early stage endometrial cancersreveals unique transcripts associated with grade and histologybut not depth of invasion

    Directory of Open Access Journals (Sweden)

    John eRisinger

    2013-06-01

    Full Text Available Endometrial cancer is the most common gynecologic malignancy in the United States but it remains poorly understood at the molecular level. This investigation was conducted to specifically assess whether gene expression changes underlie the clinical and pathologic factors traditionally used for determining treatment regimens in women with stage I endometrial cancer. These include the effect of tumor grade, depth of myometrial invasion and histotype. We utilized oligonucleotide microarrays to assess the transcript expression profile in epithelial glandular cells laser microdissected from 79 endometrioid and 12 serous stage I endometrial cancers with a heterogeneous distribution of grade and depth of myometrial invasion, along with 12 normal post-menopausal endometrial samples. Unsupervised multidimensional scaling analyses revealed that serous and endometrioid stage I cancers have similar transcript expression patterns when compared to normal controls where 900 transcripts were identified to be differentially expressed by at least 4-fold (univariate t-test, p <0.001 between the cancers and normal endometrium. This analysis also identified transcript expression differences between serous and endometrioid cancers and tumor grade, but no apparent differences were identified as a function of depth of myometrial invasion. Four genes were validated by quantitative PCR on an independent set of cancer and normal endometrium samples. These findings indicate that unique gene expression profiles are associated with histologic type and grade, but not myometrial invasion among early stage endometrial cancers. These data provide a comprehensive perspective on the molecular alterations associated with stage I endometrial cancer, particularly those subtypes that have the worst prognosis.

  17. Lysiphlebus orientalis (Hymenoptera, Braconidae), a new invasive aphid parasitoid in Europe – evidence from molecular markers

    Czech Academy of Sciences Publication Activity Database

    Petrović, A.; Mitrović, M.; Starý, Petr; Petrović-Obradović, O.; Žikić, V.; Tomanović, Ž.; Vorburger, C.

    2013-01-01

    Roč. 103, č. 4 (2013), s. 451-457 ISSN 0007-4853 Grant - others:Swiss National Science Foundation(CH) IZ73Z0_1_28174; Ministry of Education and Science of the Republic of Serbia(RS) 43001 Institutional research plan: CEZ:AV0Z50070508 Keywords : new invasive species * Serbia * DNA barcoding Subject RIV: EG - Zoology Impact factor: 1.895, year: 2013

  18. Molecular activation analysis for chemical species studies

    International Nuclear Information System (INIS)

    Chai Zhifang; Mao Xueying; Wang Yuqi; Sun Jingxin; Qian Qingfang; Hou Xiaolin; Zhang Peiqun; Chen Chunying; Feng Weiyu; Ding Wenjun; Li Xiaolin; Li Chunsheng; Dai Xiongxin

    2001-01-01

    The Molecular Activation Analysis (MAA) mainly refers to an activation analysis method that is able to provide information about the chemical species of elements in systems of interest, though its exact definition has remained to be assigned. Its development is strongly stimulated by the urgent need to know the chemical species of elements, because the bulk contents or concentrations are often insignificant for judging biological, environmental or geochemical effects of elements. In this paper, the features, methodology and limitation of MAA were outlined. Further, the up-to-date MAA progress made in our laboratory was introduced as well. (author)

  19. Quantitative CT analysis of pulmonary pure ground-glass nodule predicts histological invasiveness

    Energy Technology Data Exchange (ETDEWEB)

    Li, Qiong, E-mail: liqiongsmmu2008@qq.com [Department of Radiology, Changzheng Hospital, Second Military Medical University, NO. 415, Fengyang Road, Shanghai 200003 (China); Fan, Li, E-mail: fanli0930@163.com [Department of Radiology, Changzheng Hospital, Second Military Medical University, NO. 415, Fengyang Road, Shanghai 200003 (China); Cao, En-Tao, E-mail: cet123cs@126.com [Department of Radiology, Suzhou Municipal Hospital (East District), No.16 West Baita Road, Suzhu, Jiangsu Province 215001 (China); Li, Qing-Chu, E-mail: Wudi327@hotmail.com [Department of Radiology, Changzheng Hospital, Second Military Medical University, NO. 415, Fengyang Road, Shanghai 200003 (China); Gu, Ya-Feng, E-mail: 2528473557@qq.com [Department of Radiology, Changzheng Hospital, Second Military Medical University, NO. 415, Fengyang Road, Shanghai 200003 (China); Liu, Shi−Yuan, E-mail: liusy1186@163.com [Department of Radiology, Changzheng Hospital, Second Military Medical University, NO. 415, Fengyang Road, Shanghai 200003 (China)

    2017-04-15

    Objective: To assess whether quantitative computed tomography (CT) can help predict histological invasiveness of pulmonary adenocarcinoma appearing as pure ground glass nodules (pGGNs). Methods: A total of 110 pulmonary pGGNs were retrospectively evaluated, and pathologically classified as pre-invasive lesions, minimally invasive adenocarcinoma (MIA) and invasive pulmonary adenocarcinoma (IPA). Maximum nodule diameters, largest cross-sectional areas, volumes, mean CT values, weights, and CT attenuation values at the 0th,2th,5th, 25th, 50th,75th, 95th, 98th and100th percentiles on histogram, as well as 2th to 98th, 5th to 95th, 25th to 75th,and 0th to 100thslopes, respectively, were compared among the three groups. Results: Of the 110 pGGNs, 50, 28, and 32 were pre-invasive lesions, MIA, and IPA, respectively. Maximum nodule diameters, largest cross-sectional areas, andmass weights were significantly larger in the IPA group than in pre-invasive lesions. The 95th, 98th, 100th percentiles, and 2th to 98th, 25th to 75th, and 0th to 100thslopes were significantly different between pre-invasive lesions and MIA or IPA. Logistic regression analysis showed that the maximum nodule diameter (OR = 1.21, 95%CI: 1.071–1.366, p < 0.01) and 100th percentile on histogram (OR = 1.02, 95%CI: 1.009–1.032, p < 0.001) independently predicted histological invasiveness. Conclusions: Quantitative analysis of CT imaging can predict histological invasiveness of pGGNs, especiallythe maximum nodule diameter and 100th percentile on CT number histogram; this can instruct the long-term follow-up and selective surgical management.

  20. Molecular Testing of Nodules with a Suspicious or Malignant Cytologic Diagnosis in the Setting of Non-Invasive Follicular Thyroid Neoplasm with Papillary-Like Nuclear Features (NIFTP).

    Science.gov (United States)

    Strickland, Kyle C; Eszlinger, Markus; Paschke, Ralf; Angell, Trevor E; Alexander, Erik K; Marqusee, Ellen; Nehs, Matthew A; Jo, Vickie Y; Lowe, Alarice; Vivero, Marina; Hollowell, Monica; Qian, Xiaohua; Wieczorek, Tad; French, Christopher A; Teot, Lisa A; Cibas, Edmund S; Lindeman, Neal I; Krane, Jeffrey F; Barletta, Justine A

    2018-03-01

    Non-invasive follicular thyroid neoplasm with papillary-like nuclear features (NIFTP) is an indolent thyroid tumor characterized by frequent RAS mutations and an absence of the BRAF V600E mutation commonly seen in classical papillary thyroid carcinoma (cPTC). The ability to differentiate potential NIFTP/follicular variant of papillary thyroid carcinoma (FVPTC) from cPTC at the time of fine-needle aspiration (FNA) can facilitate conservative management of NIFTP. The aim of the current study was to investigate how molecular testing may add to cytologic assessment in the pre-operative differentiation of potential NIFTP/FVPTC and cPTC. We had previously evaluated cytologists' ability to prospectively distinguish potential NIFTP/FVPTC from cPTC in a cohort of 56 consecutive FNAs diagnosed as malignant or suspicious for malignancy. We utilized this cohort to perform molecular analysis. Detected molecular abnormalities were stratified into two groups: (1) those supporting malignancy and (2) those supporting a diagnosis of potential NIFTP/FVPTC. The cytologists' characterization of cases and the detected molecular alterations were correlated with the final histologic diagnoses. Molecular testing was performed in 52 (93%) of the 56 cases. For the 37 cases cytologists favored to be cPTC, 31 (84%) had a molecular result that supported malignancy (28 BRAF V600E mutations, 2 NTRK1 fusions, 1 AGK-BRAF fusion). For the 8 cases that were favored to be NIFTP/FVPTC by cytologists, 7 (88%) had a molecular result that supported conservative management (1 NRAS mutation, 6 wild-type result). Seven cases were designated as cytomorphologically indeterminate for NIFTP/FVPTC or cPTC, of which 6 (86%) had a molecular result that would have aided in the pre-operative assessment of potential NIFTP/FVPTC or cPTC/malignancy. These included 3 BRAF V600E mutations in nodules that were cPTC on resection, an HRAS mutation, and a wild-type result in the 2 nodules that were NIFTP, and a TERT promoter

  1. Molecular evidence for Lessepsian invasion of soritids (larger symbiont bearing benthic foraminifera.

    Directory of Open Access Journals (Sweden)

    Gily Merkado

    Full Text Available The Mediterranean Sea is considered as one of the hotspots of marine bioinvasions, largely due to the influx of tropical species migrating through the Suez Canal, so-called Lessepsian migrants. Several cases of Lessepsian migration have been documented recently, however, little is known about the ecological characteristics of the migrating species and their aptitude to colonize the new areas. This study focused on Red Sea soritids, larger symbiont-bearing benthic foraminifera (LBF that are indicative of tropical and subtropical environments and were recently found in the Israeli coast of the Eastern Mediterranean. We combined molecular phylogenetic analyses of soritids and their algal symbionts as well as network analysis of Sorites orbiculus Forskål to compare populations from the Gulf of Elat (northern Red Sea and from a known hotspot in Shikmona (northern Israel that consists of a single population of S. orbiculus. Our phylogenetic analyses show that all specimens found in Shikmona are genetically identical to a population of S. orbiculus living on a similar shallow water pebbles habitat in the Gulf of Elat. Our analyses also show that the symbionts found in Shikmona and Elat soritids belong to the Symbiodinium clade F5, which is common in the Red Sea and also present in the Indian Ocean and Caribbean Sea. Our study therefore provides the first genetic and ecological evidences that indicate that modern population of soritids found on the Mediterranean coast of Israel is probably Lessepsian, and is less likely the descendant of a native ancient Mediterranean species.

  2. Quantitative CT analysis of pulmonary ground-glass opacity nodules for distinguishing invasive adenocarcinoma from non-invasive or minimally invasive adenocarcinoma: the added value of using iodine mapping

    International Nuclear Information System (INIS)

    Son, Ji Ye; Lee, Ho Yun; Kim, Jae-Hun; Lee, Kyung Soo; Han, Joungho; Jeong, Ji Yun; Kwon, O.J.; Shim, Young Mog

    2016-01-01

    To determine whether quantitative analysis of iodine-enhanced images generated from dual-energy CT (DECT) have added value in distinguishing invasive adenocarcinoma from non-invasive or minimally invasive adenocarcinoma (MIA) showing ground-glass nodule (GGN). Thirty-four patients with 39 GGNs were enrolled in this prospective study and underwent DECT followed by complete tumour resection. Various quantitative imaging parameters were assessed, including virtual non-contrast (VNC) imaging and iodine-enhanced imaging. Of all 39 GGNs, four were adenocarcinoma in situ (AIS) (10 %), nine were MIA (23 %), and 26 were invasive adenocarcinoma (67 %). When assessing only VNC imaging, multivariate analysis revealed that mass, uniformity, and size-zone variability were independent predictors of invasive adenocarcinoma (odds ratio [OR] = 19.92, P = 0.02; OR = 0.70, P = 0.01; OR = 16.16, P = 0.04, respectively). After assessing iodine-enhanced imaging with VNC imaging, both mass on the VNC imaging and uniformity on the iodine-enhanced imaging were independent predictors of invasive adenocarcinoma (OR = 5.51, P = 0.04 and OR = 0.67, P < 0.01). The power of diagnosing invasive adenocarcinoma was improved after adding the iodine-enhanced imaging parameters versus VNC imaging alone, from 0.888 to 0.959, respectively (P = 0.029). Quantitative analysis using iodine-enhanced imaging metrics versus VNC imaging metrics alone generated from DECT have added value in distinguishing invasive adenocarcinoma from AIS or MIA. (orig.)

  3. Quantitative CT analysis of pulmonary ground-glass opacity nodules for distinguishing invasive adenocarcinoma from non-invasive or minimally invasive adenocarcinoma: the added value of using iodine mapping

    Energy Technology Data Exchange (ETDEWEB)

    Son, Ji Ye; Lee, Ho Yun; Kim, Jae-Hun; Lee, Kyung Soo [Sungkyunkwan University School of Medicine, Department of Radiology and Center for Imaging Science, Samsung Medical Center, 81 Irwon-Ro, Gangnam-gu, Seoul (Korea, Republic of); Han, Joungho [Sungkyunkwan University School of Medicine, Department of Pathology, Samsung Medical Center, Seoul (Korea, Republic of); Jeong, Ji Yun [Sungkyunkwan University School of Medicine, Department of Pathology, Samsung Medical Center, Seoul (Korea, Republic of); Kyungpook National University Medical Center, Kyungpook National University School of Medicine, Department of Pathology, Daegu (Korea, Republic of); Kwon, O.J. [Sungkyunkwan University School of Medicine, Division of Respiratory and Critical Medicine of the Department of Internal Medicine, Samsung Medical Center, Seoul (Korea, Republic of); Shim, Young Mog [Sungkyunkwan University School of Medicine, Department of Thoracic and Cardiovascular Surgery, Samsung Medical Center, 81 Irwon-Ro, Gangnam-gu, Seoul (Korea, Republic of)

    2016-01-15

    To determine whether quantitative analysis of iodine-enhanced images generated from dual-energy CT (DECT) have added value in distinguishing invasive adenocarcinoma from non-invasive or minimally invasive adenocarcinoma (MIA) showing ground-glass nodule (GGN). Thirty-four patients with 39 GGNs were enrolled in this prospective study and underwent DECT followed by complete tumour resection. Various quantitative imaging parameters were assessed, including virtual non-contrast (VNC) imaging and iodine-enhanced imaging. Of all 39 GGNs, four were adenocarcinoma in situ (AIS) (10 %), nine were MIA (23 %), and 26 were invasive adenocarcinoma (67 %). When assessing only VNC imaging, multivariate analysis revealed that mass, uniformity, and size-zone variability were independent predictors of invasive adenocarcinoma (odds ratio [OR] = 19.92, P = 0.02; OR = 0.70, P = 0.01; OR = 16.16, P = 0.04, respectively). After assessing iodine-enhanced imaging with VNC imaging, both mass on the VNC imaging and uniformity on the iodine-enhanced imaging were independent predictors of invasive adenocarcinoma (OR = 5.51, P = 0.04 and OR = 0.67, P < 0.01). The power of diagnosing invasive adenocarcinoma was improved after adding the iodine-enhanced imaging parameters versus VNC imaging alone, from 0.888 to 0.959, respectively (P = 0.029). Quantitative analysis using iodine-enhanced imaging metrics versus VNC imaging metrics alone generated from DECT have added value in distinguishing invasive adenocarcinoma from AIS or MIA. (orig.)

  4. Identification of Two Distinct Molecular Subtypes of Non-Invasive Follicular Neoplasm with Papillary-Like Nuclear Features by Digital RNA Counting.

    Science.gov (United States)

    Giannini, Riccardo; Ugolini, Clara; Poma, Anello Marcello; Urpì, Maria; Niccoli, Cristina; Elisei, Rossella; Chiarugi, Massimo; Vitti, Paolo; Miccoli, Paolo; Basolo, Fulvio

    2017-10-01

    The follicular variant (FV) of papillary thyroid cancer (PTC) is one of the most common variants of PTC. Clinically, non-infiltrative FVPTC is considered a low-risk variant of PTC, and the non-invasive encapsulated forms of FVPTC represent a group of thyroid tumors with a particularly good prognosis. Consequently, these neoplasms have been very recently reclassified as non-invasive follicular neoplasms with papillary-like nuclear features (NIFTP). From a molecular standpoint, NIFTP appears to be similar to follicular neoplasms. However, only limited data are currently available regarding their gene expression profile. The aim of this study was to identify specific molecular signatures of 26 NIFTPs compared to those of 19 follicular adenomas (FAs) and 18 infiltrative FVPTCs (IFVPTCs). A nanoString custom assay was used to perform mRNA expression analysis. All cases were also genotyped for BRAF, N-, H-, and K-RAS mutations. Samples were grouped on the basis of gene expression profiles by Pearson's correlation and non-negative matrix factorization clustering analysis. Finally, the uncorrelated shrunken centroid machine-learning algorithm was used to classify the samples. The results revealed distinct expression profiles of FAs and IFVPTCs. NIFTP samples can exhibit different expression profiles, more similar to FAs (FA-like) or to IFVPTCs (IFVPTC-like), and these different expression profiles largely depend on the presence of different mutations (RAS or BRAF). In conclusion, although further validation of the model is required by using a larger group of prospective cases, these data reinforce the hypothesis that IFVPTC-like NIFTPs might represent precursors of IFVPTC.

  5. Precision analysis of a multi-slice ultrasound sensor for non-invasive 3D kinematic analysis of knee joints.

    Science.gov (United States)

    Masum, Md Abdullah; Lambert, Andrew J; Pickering, Mark R; Scarvell, J M; Smith, P N

    2012-01-01

    Currently the standard clinical practice for measuring the motion of bones in a knee joint with sufficient precision involves implanting tantalum beads into the bones to act as fiducial markers prior to imaging using X-ray equipment. This procedure is invasive in nature and exposure to ionizing radiation imposes a cancer risk and the patient's movements are confined to a narrow field of view. In this paper, an ultrasound based system for non-invasive kinematic evaluation of knee joints is proposed. The results of an initial analysis show that this system can provide the precision required for non-invasive motion analysis while the patient performs normal physical activities.

  6. A multilocus molecular phylogeny of combtooth blennies (Percomorpha: Blennioidei: Blenniidae): Multiple invasions of intertidal habitats

    KAUST Repository

    Hundt, Peter J.

    2014-01-01

    The combtooth blennies (f. Blenniidae) is a diverse family of primarily marine fishes with approximately 387 species that inhabit subtidal, intertidal, supralittoral habitats in tropical and warm temperate regions throughout the world. The Blenniidae has typically been divided into six groups based on morphological characters: Blenniini, Nemophini, Omobranchini, Phenablenniini, Parablenniini, and Salariini. There is, however, considerable debate over the validity of these groups and their relationships. Since little is known about the relationships in this group, other aspects of their evolutionary history, such as habitat evolution and remain unexplored. Herein, we use Bayesian and maximum likelihood analyses of four nuclear loci (ENC1, myh6, ptr, and tbr1) from 102 species, representing 41 genera, to resolve the phylogeny of the Blenniidae, determine the validity of the previously recognized groupings, and explore the evolution of habitat association using ancestral state reconstruction. Bayesian and maximum likelihood analyses of the resulting 3100. bp of DNA sequence produced nearly identical topologies, and identified many well-supported clades. Of these clades, Nemophini was the only traditionally recognized group strongly supported as monophyletic. This highly resolved and thoroughly sampled blenniid phylogeny provides strong evidence that the traditional rank-based classification does not adequately delimit monophyletic groups with the Blenniidae. This phylogeny redefines the taxonomy of the group and supports the use of 13 unranked clades for the classification of blenniids. Ancestral state reconstructions identified four independent invasions of intertidal habitats within the Blenniidae, and subsequent invasions into supralittoral and freshwater habitats from these groups. The independent invasions of intertidal habitats are likely to have played an important role in the evolutionary history of blennies. © 2013 Elsevier Inc.

  7. New methods for the analysis of invasion processes: multi-criteria evaluation of the invasion of Hydrilla verticillata in Guatemala.

    Science.gov (United States)

    Monterroso, I; Binimelis, R; Rodríguez-Labajos, B

    2011-03-01

    The study described in this article incorporates stakeholders' views on aquatic invasion processes and combines expert analysis with information from field work into an evaluation exercise. Management scenarios are designed based on available technical data and stakeholders' perceptions. These scenarios are evaluated using the Social Multi-Criteria Evaluation framework employing the NAIADE model. Two evaluations are carried out, technical and social. Social acceptance of different management scenarios, distribution of costs and benefits, and attribution of responsibility are discussed. The case study was carried out on Lake Izabal, a body of water connected to the Caribbean Sea in Northeastern Guatemala. In 2000, local fishermen reported the presence of an alien species in the lake, the macrophyte Hydrilla verticillata. Two years later, this alien species was established around the entire lakeshore, damaging the ecosystem, endangering native species and the subsistence of local inhabitants through impacts on transportation, fishing practices, and tourism. Copyright © 2010 Elsevier Ltd. All rights reserved.

  8. Molecular analysis of precursor lesions in familial pancreatic cancer.

    Directory of Open Access Journals (Sweden)

    Tatjana Crnogorac-Jurcevic

    Full Text Available With less than a 5% survival rate pancreatic adenocarcinoma (PDAC is almost uniformly lethal. In order to make a significant impact on survival of patients with this malignancy, it is necessary to diagnose the disease early, when curative surgery is still possible. Detailed knowledge of the natural history of the disease and molecular events leading to its progression is therefore critical.We have analysed the precursor lesions, PanINs, from prophylactic pancreatectomy specimens of patients from four different kindreds with high risk of familial pancreatic cancer who were treated for histologically proven PanIN-2/3. Thus, the material was procured before pancreatic cancer has developed, rather than from PanINs in a tissue field that already contains cancer. Genome-wide transcriptional profiling using such unique specimens was performed. Bulk frozen sections displaying the most extensive but not microdissected PanIN-2/3 lesions were used in order to obtain the holistic view of both the precursor lesions and their microenvironment. A panel of 76 commonly dysregulated genes that underlie neoplastic progression from normal pancreas to PanINs and PDAC were identified. In addition to shared genes some differences between the PanINs of individual families as well as between the PanINs and PDACs were also seen. This was particularly pronounced in the stromal and immune responses.Our comprehensive analysis of precursor lesions without the invasive component provides the definitive molecular proof that PanIN lesions beget cancer from a molecular standpoint. We demonstrate the need for accumulation of transcriptomic changes during the progression of PanIN to PDAC, both in the epithelium and in the surrounding stroma. An identified 76-gene signature of PDAC progression presents a rich candidate pool for the development of early diagnostic and/or surveillance markers as well as potential novel preventive/therapeutic targets for both familial and sporadic

  9. the genetic and molecular basis of bacterial invasion of epithelial cells

    African Journals Online (AJOL)

    DR. AMINU

    The pathogenic species of bacteria are of great medical importance as causative agents of infectious diseases. Moreover, as the condition of human existence have changed, so have the bacterial species that produce diseases. It is against this background that molecular genetics have now entered the field of microbial ...

  10. Molecular characterization of invasive Streptococcus dysgalactiae subsp. equisimilis. Multicenter study: Argentina 2011-2012.

    Science.gov (United States)

    Traverso, Fernando; Blanco, Alejandra; Villalón, Pilar; Beratz, Noelia; Sáez Nieto, Juan Antonio; Lopardo, Horacio

    Streptococcus dysgalactiae subsp. equisimilis (SDSE) has virulence factors similar to those of Streptococcus pyogenes. Therefore, it causes pharyngitis and severe infections indistinguishable from those caused by the classic pathogen. The objectives of this study were: to know the prevalence of SDSE invasive infections in Argentina, to study the genetic diversity, to determine the presence of virulence genes, to study antibiotic susceptibility and to detect antibiotic resistance genes. Conventional methods of identification were used. Antibiotic susceptibility was determined by the disk diffusion and the agar dilution methods and the E-test. Twenty eight centers from 16 Argentinean cities participated in the study. Twenty three isolates (16 group G and 7 group C) were obtained between July 1 2011 and June 30 2012. Two adult patients died (8.7%). Most of the isolates were recovered from blood (60.9%). All isolates carried speJ and ssa genes. stG62647, stG653 and stG840 were the most frequent emm types. Nineteen different PFGE patterns were detected. All isolates were susceptible to penicillin and levofloxacin, 6 (26.1%) showed resistance or reduced susceptibility to erythromycin [1 mef(A), 3 erm(TR), 1 mef(A)+erm(TR) and 1 erm(TR)+erm(B)] and 7 (30.4%) were resistant or exhibited reduced susceptibility to tetracycline [2 tet(M), 5 tet(M)+tet(O)]. The prevalence in Argentina was of at least 23 invasive infections by SDSE. A wide genetic diversity was observed. All isolates carried speJ and ssa genes. Similarly to other studies, macrolide resistance (26.1%) was mainly associated to the MLS B phenotype. Copyright © 2016 Asociación Argentina de Microbiología. Publicado por Elsevier España, S.L.U. All rights reserved.

  11. Quantitative CT analysis of pulmonary ground-glass opacity nodules for distinguishing invasive adenocarcinoma from non-invasive or minimally invasive adenocarcinoma: the added value of using iodine mapping.

    Science.gov (United States)

    Son, Ji Ye; Lee, Ho Yun; Kim, Jae-Hun; Han, Joungho; Jeong, Ji Yun; Lee, Kyung Soo; Kwon, O Jung; Shim, Young Mog

    2016-01-01

    To determine whether quantitative analysis of iodine-enhanced images generated from dual-energy CT (DECT) have added value in distinguishing invasive adenocarcinoma from non-invasive or minimally invasive adenocarcinoma (MIA) showing ground-glass nodule (GGN). Thirty-four patients with 39 GGNs were enrolled in this prospective study and underwent DECT followed by complete tumour resection. Various quantitative imaging parameters were assessed, including virtual non-contrast (VNC) imaging and iodine-enhanced imaging. Of all 39 GGNs, four were adenocarcinoma in situ (AIS) (10 %), nine were MIA (23 %), and 26 were invasive adenocarcinoma (67 %). When assessing only VNC imaging, multivariate analysis revealed that mass, uniformity, and size-zone variability were independent predictors of invasive adenocarcinoma (odds ratio [OR] = 19.92, P = 0.02; OR = 0.70, P = 0.01; OR = 16.16, P = 0.04, respectively). After assessing iodine-enhanced imaging with VNC imaging, both mass on the VNC imaging and uniformity on the iodine-enhanced imaging were independent predictors of invasive adenocarcinoma (OR = 5.51, P = 0.04 and OR = 0.67, P VNC imaging alone, from 0.888 to 0.959, respectively (P = 0.029). Quantitative analysis using iodine-enhanced imaging metrics versus VNC imaging metrics alone generated from DECT have added value in distinguishing invasive adenocarcinoma from AIS or MIA. Quantitative analysis using DECT was used to distinguish invasive adenocarcinoma. Tumour mass and uniformity were independent predictors of invasive adenocarcinoma. Diagnostic performance was improved after adding iodine parameters to VNC parameters.

  12. Molecular DNA Analysis in Forensic Identification.

    Science.gov (United States)

    Dumache, Raluca; Ciocan, Veronica; Muresan, Camelia; Enache, Alexandra

    2016-01-01

    Serological and biochemical identification methods used in forensics have several major disadvantages, such as: long time in processing biological sample and lack of sensitivity and specificity. In the last 30 years, DNA molecular analysis has become an important tool in forensic investigations. DNA profiling is based on the short tandem repeats (STR) and aids in human identification from biological samples. Forensic genetics, can provide information on the events which occurred at the crime scene or to supplement other methods of forensic identification. Currently, the methods used in identification are based on polymerase chain reaction (PCR) analyses. This method analyses the autosomal STRs, the Y-chromosome, and the mitochondrial DNA. Correlation of biological samples present at the crime scene with identification, selection, and the probative value factor is therefore the first aspect to be taken into consideration in the forensic genetic analysis. In the last decade, because of the advances in the field of molecular biology, new biomarkers such as: microRNAs (miR), messenger RNA (mRNA), and DNA methylation have been studied and proposed to be used in the forensic identifications of body fluids.

  13. Analysis of the Trojan Y-Chromosome eradication strategy for an invasive species.

    Science.gov (United States)

    Wang, Xueying; Walton, Jay R; Parshad, Rana D; Storey, Katie; Boggess, May

    2014-06-01

    The Trojan Y-Chromosome (TYC) strategy, an autocidal genetic biocontrol method, has been proposed to eliminate invasive alien species. In this work, we analyze the dynamical system model of the TYC strategy, with the aim of studying the viability of the TYC eradication and control strategy of an invasive species. In particular, because the constant introduction of sex-reversed trojan females for all time is not possible in practice, there arises the question: What happens if this injection is stopped after some time? Can the invasive species recover? To answer that question, we perform a rigorous bifurcation analysis and study the basin of attraction of the recovery state and the extinction state in both the full model and a certain reduced model. In particular, we find a theoretical condition for the eradication strategy to work. Additionally, the consideration of an Allee effect and the possibility of a Turing instability are also studied in this work. Our results show that: (1) with the inclusion of an Allee effect, the number of the invasive females is not required to be very low when the introduction of the sex-reversed trojan females is stopped, and the remaining Trojan Y-Chromosome population is sufficient to induce extinction of the invasive females; (2) incorporating diffusive spatial spread does not produce a Turing instability, which would have suggested that the TYC eradication strategy might be only partially effective, leaving a patchy distribution of the invasive species.

  14. Analysis of Invasion Dynamics of Matrix-Embedded Cells in a Multisample Format.

    Science.gov (United States)

    Van Troys, Marleen; Masuzzo, Paola; Huyck, Lynn; Bakkali, Karima; Waterschoot, Davy; Martens, Lennart; Ampe, Christophe

    2018-01-01

    In vitro tests of cancer cell invasion are the "first line" tools of preclinical researchers for screening the multitude of chemical compounds or cell perturbations that may aid in halting or treating cancer malignancy. In order to have predictive value or to contribute to designing personalized treatment regimes, these tests need to take into account the cancer cell environment and measure effects on invasion in sufficient detail. The in vitro invasion assays presented here are a trade-off between feasibility in a multisample format and mimicking the complexity of the tumor microenvironment. They allow testing multiple samples and conditions in parallel using 3D-matrix-embedded cells and deal with the heterogeneous behavior of an invading cell population in time. We describe the steps to take, the technical problems to tackle and useful software tools for the entire workflow: from the experimental setup to the quantification of the invasive capacity of the cells. The protocol is intended to guide researchers to standardize experimental set-ups and to annotate their invasion experiments in sufficient detail. In addition, it provides options for image processing and a solution for storage, visualization, quantitative analysis, and multisample comparison of acquired cell invasion data.

  15. Analysis of the Trojan Y-Chromosome eradication strategy for an invasive species

    KAUST Repository

    Wang, Xueying

    2013-05-24

    The Trojan Y-Chromosome (TYC) strategy, an autocidal genetic biocontrol method, has been proposed to eliminate invasive alien species. In this work, we analyze the dynamical system model of the TYC strategy, with the aim of studying the viability of the TYC eradication and control strategy of an invasive species. In particular, because the constant introduction of sex-reversed trojan females for all time is not possible in practice, there arises the question: What happens if this injection is stopped after some time? Can the invasive species recover? To answer that question, we perform a rigorous bifurcation analysis and study the basin of attraction of the recovery state and the extinction state in both the full model and a certain reduced model. In particular, we find a theoretical condition for the eradication strategy to work. Additionally, the consideration of an Allee effect and the possibility of a Turing instability are also studied in this work. Our results show that: (1) with the inclusion of an Allee effect, the number of the invasive females is not required to be very low when the introduction of the sex-reversed trojan females is stopped, and the remaining Trojan Y-Chromosome population is sufficient to induce extinction of the invasive females; (2) incorporating diffusive spatial spread does not produce a Turing instability, which would have suggested that the TYC eradication strategy might be only partially effective, leaving a patchy distribution of the invasive species. © 2013 Springer-Verlag Berlin Heidelberg.

  16. Potential problems of removing one invasive species at a time: a meta-analysis of the interactions between invasive vertebrates and unexpected effects of removal programs.

    Science.gov (United States)

    Ballari, Sebastián A; Kuebbing, Sara E; Nuñez, Martin A

    2016-01-01

    Although the co-occurrence of nonnative vertebrates is a ubiquitous global phenomenon, the study of interactions between invaders is poorly represented in the literature. Limited understanding of the interactions between co-occurring vertebrates can be problematic for predicting how the removal of only one invasive-a common management scenario-will affect native communities. We suggest a trophic food web framework for predicting the effects of single-species management on native biodiversity. We used a literature search and meta-analysis to assess current understanding of how the removal of one invasive vertebrate affects native biodiversity relative to when two invasives are present. The majority of studies focused on the removal of carnivores, mainly within aquatic systems, which highlights a critical knowledge gap in our understanding of co-occurring invasive vertebrates. We found that removal of one invasive vertebrate caused a significant negative effect on native species compared to when two invasive vertebrates were present. These unexpected results could arise because of the positioning and hierarchy of the co-occurring invasives in the food web (e.g., carnivore-carnivore or carnivore-herbivore). We consider that there are important knowledge gaps to determinate the effects of multiple co-existing invaders on native ecosystems, and this information could be precious for management.

  17. Time Management in the Operating Room: An Analysis of the Dedicated Minimally Invasive Surgery Suite

    Science.gov (United States)

    Hsiao, Kenneth C.; Machaidze, Zurab

    2004-01-01

    Background: Dedicated minimally invasive surgery suites are available that contain specialized equipment to facilitate endoscopic surgery. Laparoscopy performed in a general operating room is hampered by the multitude of additional equipment that must be transported into the room. The objective of this study was to compare the preparation times between procedures performed in traditional operating rooms versus dedicated minimally invasive surgery suites to see whether operating room efficiency is improved in the specialized room. Methods: The records of 50 patients who underwent laparoscopic procedures between September 2000 and April 2002 were retrospectively reviewed. Twenty-three patients underwent surgery in a general operating room and 18 patients in an minimally invasive surgery suite. Nine patients were excluded because of cystoscopic procedures undergone prior to laparoscopy. Various time points were recorded from which various time intervals were derived, such as preanesthesia time, anesthesia induction time, and total preparation time. A 2-tailed, unpaired Student t test was used for statistical analysis. Results: The mean preanesthesia time was significantly faster in the minimally invasive surgery suite (12.2 minutes) compared with that in the traditional operating room (17.8 minutes) (P=0.013). Mean anesthesia induction time in the minimally invasive surgery suite (47.5 minutes) was similar to time in the traditional operating room (45.7 minutes) (P=0.734). The average total preparation time for the minimally invasive surgery suite (59.6 minutes) was not significantly faster than that in the general operating room (63.5 minutes) (P=0.481). Conclusion: The amount of time that elapses between the patient entering the room and anesthesia induction is statically shorter in a dedicated minimally invasive surgery suite. Laparoscopic surgery is performed more efficiently in a dedicated minimally invasive surgery suite versus a traditional operating room. PMID

  18. Non-invasive Morphological and Elemental Analysis of Ivory Plate for Artworks\

    Czech Academy of Sciences Publication Activity Database

    Tihlaříková, Eva; Neděla, Vilém; Hradilová, J.; Hradil, David

    2017-01-01

    Roč. 23, S1 (2017), s. 1832-1833 ISSN 1431-9276 R&D Projects: GA MŠk(CZ) LO1212; GA MŠk ED0017/01/01; GA ČR(CZ) GA17-25687S Institutional support: RVO:68081731 ; RVO:61388980 Keywords : ESEM * EDS * non-invasive morphological analysis * non-invasive elemental analysis Subject RIV: JA - Electronics ; Optoelectronics, Electrical Engineering; CA - Inorganic Chemistry (UACH-T) OBOR OECD: Microbiology; Inorganic and nuclear chemistry (UACH-T) Impact factor: 1.891, year: 2016

  19. Molecular Composition Analysis of Distant Targets

    Science.gov (United States)

    Hughes, Gary B.; Lubin, Philip

    2017-01-01

    This document is the Final Report for NASA Innovative Advanced Concepts (NIAC) Phase I Grant 15-NIAC16A-0145, titled Molecular Composition Analysis of Distant Targets. The research was focused on developing a system concept for probing the molecular composition of cold solar system targets, such as Asteroids, Comets, Planets and Moons from a distant vantage, for example from a spacecraft that is orbiting the target (Hughes et al., 2015). The orbiting spacecraft is equipped with a high-power laser, which is run by electricity from photovoltaic panels. The laser is directed at a spot on the target. Materials on the surface of the target are heated by the laser beam, and begin to melt and then evaporate, forming a plume of asteroid molecules in front of the heated spot. The heated spot glows, producing blackbody illumination that is visible from the spacecraft, via a path through the evaporated plume. As the blackbody radiation from the heated spot passes through the plume of evaporated material, molecules in the plume absorb radiation in a manner that is specific to the rotational and vibrational characteristics of the specific molecules. A spectrometer aboard the spacecraft is used to observe absorption lines in the blackbody signal. The pattern of absorption can be used to estimate the molecular composition of materials in the plume, which originated on the target. Focusing on a single spot produces a borehole, and shallow subsurface profiling of the targets bulk composition is possible. At the beginning of the Phase I research, the estimated Technology Readiness Level (TRL) of the system was TRL-1. During the Phase I research, an end-to-end theoretical model of the sensor system was developed from first principles. The model includes laser energy and optical propagation, target heating, melting and evaporation of target material, plume density, thermal radiation from the heated spot, molecular cross section of likely asteroid materials, and estimation of the

  20. Molecular epidemiology of Klebsiella pneumoniae invasive infections over a decade at Kilifi County Hospital in Kenya.

    Science.gov (United States)

    Henson, Sonal P; Boinett, Christine J; Ellington, Matthew J; Kagia, Ngure; Mwarumba, Salim; Nyongesa, Sammy; Mturi, Neema; Kariuki, Samuel; Scott, J Anthony G; Thomson, Nicholas R; Morpeth, Susan C

    2017-10-01

    Multidrug resistant (MDR) Klebsiella pneumoniae is a common cause of nosocomial infections worldwide. Recent years have seen an explosion of resistance to extended-spectrum β-lactamases (ESBLs) and emergence of carbapenem resistance. Here, we examine 198 invasive K. pneumoniae isolates collected from over a decade in Kilifi County Hospital (KCH) in Kenya. We observe a significant increase in MDR K. pneumoniae isolates, particularly to third generation cephalosporins conferred by ESBLs. Using whole-genome sequences, we describe the population structure and the distribution of antimicrobial resistance genes within it. More than half of the isolates examined in this study were ESBL-positive, encoding CTX-M-15, SHV-2, SHV-12 and SHV-27, and 79% were MDR conferring resistance to at least three antimicrobial classes. Although no isolates in our dataset were found to be resistant to carbapenems we did find a plasmid with the genetic architecture of a known New Delhi metallo-β-lactamase-1 (NDM)-carrying plasmid in 25 isolates. In the absence of carbapenem use in KCH and because of the instability of the NDM-1 gene in the plasmid, the NDM-1 gene has been lost in these isolates. Our data suggests that isolates that encode NDM-1 could be present in the population; should carbapenems be introduced as treatment in public hospitals in Kenya, resistance is likely to ensue rapidly. Copyright © 2017 The Authors. Published by Elsevier GmbH.. All rights reserved.

  1. Multicenter evaluation of molecular and culture-dependent diagnostics for Shigella species and Entero-invasive Escherichia coli in the Netherlands.

    Science.gov (United States)

    van den Beld, Maaike J C; Friedrich, Alexander W; van Zanten, Evert; Reubsaet, Frans A G; Kooistra-Smid, Mirjam A M D; Rossen, John W A

    2016-12-01

    An inter-laboratory collaborative trial for the evaluation of diagnostics for detection and identification of Shigella species and Entero-invasive Escherichia coli (EIEC) was performed. Sixteen Medical Microbiological Laboratories (MMLs) participated. MMLs were interviewed about their diagnostic methods and a sample panel, consisting of DNA-extracts and spiked stool samples with different concentrations of Shigella flexneri, was provided to each MML. The results of the trial showed an enormous variety in culture-dependent and molecular diagnostic techniques currently used among MMLs. Despite the various molecular procedures, 15 out of 16 MMLs were able to detect Shigella species or EIEC in all the samples provided, showing that the diversity of methods has no effect on the qualitative detection of Shigella flexneri. In contrast to semi quantitative analysis, the minimum and maximum values per sample differed by approximately five threshold cycles (Ct-value) between the MMLs included in the study. This indicates that defining a uniform Ct-value cut-off for notification to health authorities is not advisable. Copyright © 2016 Elsevier B.V. All rights reserved.

  2. Effects of anion size and concentration on electrolyte invasion into molecular-sized nanopores

    International Nuclear Information System (INIS)

    Liu Ling; Chen Xi; Kim, Taewan; Han Aijie; Qiao Yu

    2010-01-01

    When an electrolyte solution is pressurized into a molecular-sized nanopore, oppositely charged ions are strongly inclined to aggregate, which effectively reduces the ion solubility to zero. Inside the restrictive confinement, a unique quasi-periodic structure is formed where the paired ion couples are periodically separated by a number of water molecules. As the anion size or ion concentration varies, the geometrical characteristics of the confined ion structure would change considerably, leading to a significant variation in the transport pressure. Both experimental and simulation results indicate that, contradictory to the prediction of conventional theory, infiltration pressure decreases as the anions become larger.

  3. Classical and molecular cytogenetics of Khawia sinensis (Cestoda: Caryophyllidea), invasive parasite of carp, Cyprinus carpio

    Czech Academy of Sciences Publication Activity Database

    Orosová, Martina; Oros, A. M.

    2012-01-01

    Roč. 110, č. 5 (2012), s. 1397-1944 ISSN 0932-0113 R&D Projects: GA MŠk LC522; GA ČR GA524/08/0885 Institutional research plan: CEZ:AV0Z60220518 Keywords : TAPEWORMS PLATYHELMINTHES * RIBOSOMAL DNA * CHROMOSOMES * EVOLUTION * FISH * RDNA * PSEUDOPHYLLIDEA * LOCATION * GENES * DIFFERENTIATION Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.852, year: 2012 http://link.springer.com/content/pdf/10.1007%2Fs00436-011-2720-x

  4. Non-small cell lung cancer: Whole-lesion histogram analysis of the apparent diffusion coefficient for assessment of tumor grade, lymphovascular invasion and pleural invasion.

    Science.gov (United States)

    Tsuchiya, Naoko; Doai, Mariko; Usuda, Katsuo; Uramoto, Hidetaka; Tonami, Hisao

    2017-01-01

    Investigating the diagnostic accuracy of histogram analyses of apparent diffusion coefficient (ADC) values for determining non-small cell lung cancer (NSCLC) tumor grades, lymphovascular invasion, and pleural invasion. We studied 60 surgically diagnosed NSCLC patients. Diffusion-weighted imaging (DWI) was performed in the axial plane using a navigator-triggered single-shot, echo-planar imaging sequence with prospective acquisition correction. The ADC maps were generated, and we placed a volume-of-interest on the tumor to construct the whole-lesion histogram. Using the histogram, we calculated the mean, 5th, 10th, 25th, 50th, 75th, 90th, and 95th percentiles of ADC, skewness, and kurtosis. Histogram parameters were correlated with tumor grade, lymphovascular invasion, and pleural invasion. We performed a receiver operating characteristics (ROC) analysis to assess the diagnostic performance of histogram parameters for distinguishing different pathologic features. The ADC mean, 10th, 25th, 50th, 75th, 90th, and 95th percentiles showed significant differences among the tumor grades. The ADC mean, 25th, 50th, 75th, 90th, and 95th percentiles were significant histogram parameters between high- and low-grade tumors. The ROC analysis between high- and low-grade tumors showed that the 95th percentile ADC achieved the highest area under curve (AUC) at 0.74. Lymphovascular invasion was associated with the ADC mean, 50th, 75th, 90th, and 95th percentiles, skewness, and kurtosis. Kurtosis achieved the highest AUC at 0.809. Pleural invasion was only associated with skewness, with the AUC of 0.648. ADC histogram analyses on the basis of the entire tumor volume are able to stratify NSCLCs' tumor grade, lymphovascular invasion and pleural invasion.

  5. Using non-invasive molecular spectroscopic techniques to detect unique aspects of protein Amide functional groups and chemical properties of modeled forage from different sourced-origins.

    Science.gov (United States)

    Ji, Cuiying; Zhang, Xuewei; Yu, Peiqiang

    2016-03-05

    The non-invasive molecular spectroscopic technique-FT/IR is capable to detect the molecular structure spectral features that are associated with biological, nutritional and biodegradation functions. However, to date, few researches have been conducted to use these non-invasive molecular spectroscopic techniques to study forage internal protein structures associated with biodegradation and biological functions. The objectives of this study were to detect unique aspects and association of protein Amide functional groups in terms of protein Amide I and II spectral profiles and chemical properties in the alfalfa forage (Medicago sativa L.) from different sourced-origins. In this study, alfalfa hay with two different origins was used as modeled forage for molecular structure and chemical property study. In each forage origin, five to seven sources were analyzed. The molecular spectral profiles were determined using FT/IR non-invasive molecular spectroscopy. The parameters of protein spectral profiles included functional groups of Amide I, Amide II and Amide I to II ratio. The results show that the modeled forage Amide I and Amide II were centered at 1653 cm(-1) and 1545 cm(-1), respectively. The Amide I spectral height and area intensities were from 0.02 to 0.03 and 2.67 to 3.36 AI, respectively. The Amide II spectral height and area intensities were from 0.01 to 0.02 and 0.71 to 0.93 AI, respectively. The Amide I to II spectral peak height and area ratios were from 1.86 to 1.88 and 3.68 to 3.79, respectively. Our results show that the non-invasive molecular spectroscopic techniques are capable to detect forage internal protein structure features which are associated with forage chemical properties. Copyright © 2015 Elsevier B.V. All rights reserved.

  6. Molecular activation analysis for chemical speciation studies

    International Nuclear Information System (INIS)

    Chai-Chifang

    1998-01-01

    The term of Molecular Activation Analysis (MAA) refers to an activation analysis method that is able to provide information about the chemical species of elements in system of interests, though its definition has remained to be assigned. Its development is strongly stimulated by the urgent need to know the chemical species of elements, because the total concentrations are often without any meaning when assessing health or environmental risks of trace elements.In practice, the MAA is a combination of conventional instrumental or radiochemical activation analysis and physical, chemical or biochemical separation techniques. The MAA is able to play a particular role in speciation studies. However, the critical point in the MAA is that it is not permitted to change the primitive chemical species of elements in systems, or the change has to be under control; in the meantime it is not allowed to form the 'new artifact' originally not present in systems. Some practical examples of MAA for chemical species research performed recently in our laboratory will be presented as follows: Chemical species of platinum group elements in sediment; Chemical species of iodine in marine algae; Chemical species of mercury in human tissues; Chemical species of selenium in corn; Chemical species of rare earth elements in natural plant, etc. The merits and limitations of MAA will be described as well. (author)

  7. Invasive plants found in east Texas forests, 2009 forest inventory and analysis factsheet

    Science.gov (United States)

    Sonja N. Oswalt; Christopher M. Oswalt

    2011-01-01

    This science update provides information on the presence and cover of nonnative invasive plants found in forests of the eastern region of the State of Texas based on an annual inventory conducted by the Forest Inventory and Analysis (FIA) Program at the Southern Research Station of the U.S. Department of Agriculture Forest Service in cooperation with the Texas Forest...

  8. Hyperspectral Time Series Analysis of Native and Invasive Species in Hawaiian Rainforests

    Directory of Open Access Journals (Sweden)

    Gregory P. Asner

    2012-08-01

    Full Text Available The unique ecosystems of the Hawaiian Islands are progressively being threatened following the introduction of exotic species. Operational implementation of remote sensing for the detection, mapping and monitoring of these biological invasions is currently hampered by a lack of knowledge on the spectral separability between native and invasive species. We used spaceborne imaging spectroscopy to analyze the seasonal dynamics of the canopy hyperspectral reflectance properties of four tree species: (i Metrosideros polymorpha, a keystone native Hawaiian species; (ii Acacia koa, a native Hawaiian nitrogen fixer; (iii the highly invasive Psidium cattleianum; and (iv Morella faya, a highly invasive nitrogen fixer. The species specific separability of the reflectance and derivative-reflectance signatures extracted from an Earth Observing-1 Hyperion time series, composed of 22 cloud-free images spanning a period of four years and was quantitatively evaluated using the Separability Index (SI. The analysis revealed that the Hawaiian native trees were universally unique from the invasive trees in their near-infrared-1 (700–1,250 nm reflectance (0.4 > SI > 1.4. Due to its higher leaf area index, invasive trees generally had a higher near-infrared reflectance. To a lesser extent, it could also be demonstrated that nitrogen-fixing trees were spectrally unique from non-fixing trees. The higher leaf nitrogen content of nitrogen-fixing trees was expressed through slightly increased separabilities in visible and shortwave-infrared reflectance wavebands (SI = 0.4. We also found phenology to be key to spectral separability analysis. As such, it was shown that the spectral separability in the near-infrared-1 reflectance between the native and invasive species groups was more expressed in summer (SI > 0.7 than in winter (SI < 0.7. The lowest separability was observed for March-July (SI < 0.3. This could be explained by the

  9. Potential problems of removing one invasive species at a time: a meta-analysis of the interactions between invasive vertebrates and unexpected effects of removal programs

    Directory of Open Access Journals (Sweden)

    Sebastián A. Ballari

    2016-06-01

    Full Text Available Although the co-occurrence of nonnative vertebrates is a ubiquitous global phenomenon, the study of interactions between invaders is poorly represented in the literature. Limited understanding of the interactions between co-occurring vertebrates can be problematic for predicting how the removal of only one invasive—a common management scenario—will affect native communities. We suggest a trophic food web framework for predicting the effects of single-species management on native biodiversity. We used a literature search and meta-analysis to assess current understanding of how the removal of one invasive vertebrate affects native biodiversity relative to when two invasives are present. The majority of studies focused on the removal of carnivores, mainly within aquatic systems, which highlights a critical knowledge gap in our understanding of co-occurring invasive vertebrates. We found that removal of one invasive vertebrate caused a significant negative effect on native species compared to when two invasive vertebrates were present. These unexpected results could arise because of the positioning and hierarchy of the co-occurring invasives in the food web (e.g., carnivore–carnivore or carnivore–herbivore. We consider that there are important knowledge gaps to determinate the effects of multiple co-existing invaders on native ecosystems, and this information could be precious for management.

  10. Molecular cytogenetic analysis of human blastocysts andcytotrophoblasts by multi-color FISH and Spectra Imaging analyses

    Energy Technology Data Exchange (ETDEWEB)

    Weier, Jingly F.; Ferlatte, Christy; Baumgartner, Adolf; Jung,Christine J.; Nguyen, Ha-Nam; Chu, Lisa W.; Pedersen, Roger A.; Fisher,Susan J.; Weier, Heinz-Ulrich G.

    2006-02-08

    Numerical chromosome aberrations in gametes typically lead to failed fertilization, spontaneous abortion or a chromosomally abnormal fetus. By means of preimplantation genetic diagnosis (PGD), we now can screen human embryos in vitro for aneuploidy before transferring the embryos to the uterus. PGD allows us to select unaffected embryos for transfer and increases the implantation rate in in vitro fertilization programs. Molecular cytogenetic analyses using multi-color fluorescence in situ hybridization (FISH) of blastomeres have become the major tool for preimplantation genetic screening of aneuploidy. However, current FISH technology can test for only a small number of chromosome abnormalities and hitherto failed to increase the pregnancy rates as expected. We are in the process of developing technologies to score all 24 chromosomes in single cells within a 3 day time limit, which we believe is vital to the clinical setting. Also, human placental cytotrophoblasts (CTBs) at the fetal-maternal interface acquire aneuploidies as they differentiate to an invasive phenotype. About 20-50% of invasive CTB cells from uncomplicated pregnancies were found aneuploidy, suggesting that the acquisition of aneuploidy is an important component of normal placentation, perhaps limiting the proliferative and invasive potential of CTBs. Since most invasive CTBs are interphase cells and possess extreme heterogeneity, we applied multi-color FISH and repeated hybridizations to investigate individual CTBs. In summary, this study demonstrates the strength of Spectral Imaging analysis and repeated hybridizations, which provides a basis for full karyotype analysis of single interphase cells.

  11. Assessing invasion process through pathway and vector analysis: case of saltcedar (Tamarix spp.

    Directory of Open Access Journals (Sweden)

    Evangelina Natale

    2012-12-01

    Full Text Available Biological invasions are one of the most pervasive environmental threats to native ecosystems worldwide. The spontaneous spread ofsaltcedar is a particular threat to biodiversity conservation in arid and semiarid environments. In Argentina, three species belonging to this genus have been recognized as invaders. The aim of the present study was to identify main dispersal vectors and pathways to refine risk analysis and increase our ability to predict new areas at risk of Tamarix establishment. We surveyed and categorized 223 populations, 39% as invasive, 26% as established, 21% as contained and 14% as detected in nature. Dispersion of saltcedar was found to be associated with watercourses and human-driven disturbances; in addition roads were found to be relevant for the introduction of propagules in newenvironments. Considering the potential impact of saltcedar invasion and that it is an easily wind-dispersed invasive, it is necessary toimplement strategies to monitor dispersal pathways and take actions to eliminate invasion foci, particularly in vulnerable and highconservation value areas.

  12. An ounce of prevention or a pound of cure: bioeconomic risk analysis of invasive species.

    Science.gov (United States)

    Leung, Brian; Lodge, David M; Finnoff, David; Shogren, Jason F; Lewis, Mark A; Lamberti, Gary

    2002-12-07

    Numbers of non-indigenous species--species introduced from elsewhere - are increasing rapidly worldwide, causing both environmental and economic damage. Rigorous quantitative risk-analysis frameworks, however, for invasive species are lacking. We need to evaluate the risks posed by invasive species and quantify the relative merits of different management strategies (e.g. allocation of resources between prevention and control). We present a quantitative bioeconomic modelling framework to analyse risks from non-indigenous species to economic activity and the environment. The model identifies the optimal allocation of resources to prevention versus control, acceptable invasion risks and consequences of invasion to optimal investments (e.g. labour and capital). We apply the model to zebra mussels (Dreissena polymorpha), and show that society could benefit by spending up to US$324 000 year(-1) to prevent invasions into a single lake with a power plant. By contrast, the US Fish and Wildlife Service spent US$825 000 in 2001 to manage all aquatic invaders in all US lakes. Thus, greater investment in prevention is warranted.

  13. Biodiversity of Soil Microbial Communities Following Woody Plant Invasion of Grassland: An Assessment Using Molecular Methods

    Science.gov (United States)

    Kantola, I. B.; Gentry, T. J.; Filley, T. R.; Boutton, T. W.

    2012-12-01

    Woody plants have encroached into grasslands, savannas, and other grass-dominated ecosystems throughout the world during the last century. This dramatic vegetation change is likely driven by livestock grazing, altered fire frequencies, elevated atmospheric CO2 concentrations, and/or changes in atmospheric deposition patterns. Woody invasion often results in significant changes in ecosystem function, including alterations in above- and belowground primary productivity, soil C, N, and P storage and turnover, and the size and activity of the soil microbial biomass pool. The purpose of this study was to examine the relationships and interactions between plant communities and soil microbial communities in the Rio Grande Plains region of southern Texas where grasslands have been largely replaced by woodlands. Research was conducted along a successional chronosequence representing the stages of woody plant encroachment from open grassland to closed-canopy woodland. To characterize soil microbial community composition, soil samples (0-7.5 cm) were collected in remnant grasslands (representing time 0) and near the centers of woody plant clusters, groves, and drainage woodlands ranging in age from 10 to 130 yrs. Ages of woody plant stands were determined by dendrochronology. Community DNA was extracted from each soil sample with a MoBio PowerMax Soil DNA isolation kit. The DNA concentrations were quantified on a NanoDrop ND-1000 spectrophotometer and diluted to a standard concentration. Pyrosequencing was performed by the Research and Testing Laboratory (Lubbock, TX) according to Roche 454 Titanium chemistry protocols. Samples were amplified with primers 27F and 519R for bacteria, and primers ITS1F and ITS4 for fungi. Sequences were aligned using BioEdit and the RDP Pipeline and analyzed in MOTHUR. Non-metric multidimensional scaling of the operational taxonomic units identified by pyrosequencing revealed that both bacterial and fungal community composition were

  14. Molecular analysis of waxy mutants in rice

    International Nuclear Information System (INIS)

    Yatou, O.; Amano, E.

    1990-01-01

    Full text: The 'waxy' gene is a structural gene coding a glycosyl transferase which synthesises amylose in the endosperm tissue. 'Non-waxy' rice cultivars have an active gene and their amylose content is 18-25% depending upon gene performance and modifier genes. In 'waxy' rice, no amylose is found because the enzyme is absent. In mutants induced by gamma rays, neutrons, EI or EMS, amylose content ranged from 0 to 20%, i.e. there are intermediate phenotypes as well. Some of them had the same amount of the enzyme as a 'non-waxy' cultivar, even fully 'waxy' mutants showed a certain amount of the enzyme. This suggests that in mutants there may be no structural change in the enzyme gene but the enzyme produced might be less active. By molecular analysis of the mutants' genes it was found that only two mutants induced by thermal neutrons show structural alterations, the changes in other mutants are either too small to be detected by Southern analysis or are outside the structural gene in question. (author)

  15. Polymer Molecular Weight Analysis by [Superscript 1]H NMR Spectroscopy

    Science.gov (United States)

    Izunobi, Josephat U.; Higginbotham, Clement L.

    2011-01-01

    The measurement and analysis of molecular weight and molecular weight distribution remain matters of fundamental importance for the characterization and physical properties of polymers. Gel permeation chromatography (GPC) is the most routinely used method for the molecular weight determination of polymers whereas matrix-assisted laser…

  16. Morphometric and molecular identification of individual barnacle cyprids from wild plankton: an approach to detecting fouling and invasive barnacle species.

    Science.gov (United States)

    Chen, Hsi-Nien; Høeg, Jens T; Chan, Benny K K

    2013-01-01

    The present study used DNA barcodes to identify individual cyprids to species. This enables accurate quantification of larvae of potential fouling species in the plankton. In addition, it explains the settlement patterns of barnacles and serves as an early warning system of unwanted immigrant species. Sequences from a total of 540 individual cypris larvae from Taiwanese waters formed 36 monophyletic clades (species) in a phylogenetic tree. Of these clades, 26 were identified to species, but 10 unknown monophyletic clades represented non-native species. Cyprids of the invasive barnacle, Megabalanus cocopoma, were identified. Multivariate analysis of antennular morphometric characters revealed three significant clusters in a nMDS plot, viz. a bell-shaped attachment organ (most species), a shoe-shaped attachment organ (some species), and a spear-shaped attachment organ (coral barnacles only). These differences in attachment organ structure indicate that antennular structures interact directly with the diverse substrata involved in cirripede settlement.

  17. Analysis of a native whitefly transcriptome and its sequence divergence with two invasive whitefly species

    Directory of Open Access Journals (Sweden)

    Wang Xiao-Wei

    2012-10-01

    Full Text Available Abstract Background Genomic divergence between invasive and native species may provide insight into the molecular basis underlying specific characteristics that drive the invasion and displacement of closely related species. In this study, we sequenced the transcriptome of an indigenous species, Asia II 3, of the Bemisia tabaci complex and compared its genetic divergence with the transcriptomes of two invasive whiteflies species, Middle East Asia Minor 1 (MEAM1 and Mediterranean (MED, respectively. Results More than 16 million reads of 74 base pairs in length were obtained for the Asia II 3 species using the Illumina sequencing platform. These reads were assembled into 52,535 distinct sequences (mean size: 466 bp and 16,596 sequences were annotated with an E-value above 10-5. Protein family comparisons revealed obvious diversification among the transcriptomes of these species suggesting species-specific adaptations during whitefly evolution. On the contrary, substantial conservation of the whitefly transcriptomes was also evident, despite their differences. The overall divergence of coding sequences between the orthologous gene pairs of Asia II 3 and MEAM1 is 1.73%, which is comparable to the average divergence of Asia II 3 and MED transcriptomes (1.84% and much higher than that of MEAM1 and MED (0.83%. This is consistent with the previous phylogenetic analyses and crossing experiments suggesting these are distinct species. We also identified hundreds of highly diverged genes and compiled sequence identify data into gene functional groups and found the most divergent gene classes are Cytochrome P450, Glutathione metabolism and Oxidative phosphorylation. These results strongly suggest that the divergence of genes related to metabolism might be the driving force of the MEAM1 and Asia II 3 differentiation. We also analyzed single nucleotide polymorphisms within the orthologous gene pairs of indigenous and invasive whiteflies which are helpful for

  18. Molecular evidence for the predation of Critically Endangered endemic Aphanius transgrediens from the stomach contents of world wide invasive Gambusia affinis.

    Science.gov (United States)

    Keskin, Emre

    2016-01-01

    Predation and competition among native and invasive species are difficult to study in aquatic environments. Identification of preys from semi-digested body parts sampled from stomach contents of the predator is very challenging. Recent studies were mainly based on use of DNA extracted from stomach content to identify the prey species. This study presents the molecular evidence that reveals the predation of critically endangered Aphanius transgrediens by world-wide invasive Gambusia affinis for a better understanding of the link between the invasion and the extinction of native species in freshwater ecosystems. DNA samples were extracted from semi-digested stomach contents of the invader and short fragments of mitochondrial NADH1 gene were amplified using species-specific primers designed in this study to make identification at species level. Existence of both the prey and the predator species were also confirmed using environmental DNA extracted from water samples.

  19. Non invasive methods for genetic analysis applied to ecological and behavioral studies in Latino-America

    Directory of Open Access Journals (Sweden)

    Susana González

    2007-07-01

    Full Text Available Documenting the presence and abundance of the neotropical mammals is the first step for understanding their population ecology, behavior and genetic dynamics in designing conservation plans. The combination of field research with molecular genetics techniques are new tools that provide valuable biological information avoiding the disturbance in the ecosystems, trying to minimize the human impact in the process to gather biological information. The objective of this paper is to review the available non invasive sampling techniques that have been used in Neotropical mammal studies to apply to determine the presence and abundance, population structure, sex ratio, taxonomic diagnostic using mitochondrial markers, and assessing genetic variability using nuclear markers. There are a wide range of non invasive sampling techniques used to determine the species identification that inhabit an area such as searching for tracks, feces, and carcasses. Other useful equipment is the camera traps that can generate an image bank that can be valuable to assess species presence and abundance by morphology. With recent advances in molecular biology, it is now possible to use the trace amounts of DNA in feces and amplify it to analyze the species diversity in an area, and the genetic variability at intraspecific level. This is particularly helpful in cases of sympatric and cryptic species in which morphology failed to diagnose the taxonomic status of several species of brocket deer of the genus Mazama.

  20. Floristic analysis of perennial species on flowerbeds in Belgrade with special attention on invasiveness of the recorded species

    Directory of Open Access Journals (Sweden)

    Popović Marija

    2012-01-01

    Full Text Available Urban areas are among the most important centres of invasive plant species distribution due to their richness in alien species. Because of that, a detailed floristic analysis of perennial flowerbeds was conducted in the central parks of Belgrade. A total of 53 perennial species were found, of which 55% were the alien species planted on 75% of the research area. Among them, two species (Aster novi belgii and Solidago canadensis are invasive and six species are potentially invasive in Serbia. These are planted on 5% and 20% of the flowerbeds, respectively. We can conclude that both the experts and institutions should be informed about the invasive species and potential damages. In the meantime, planting of native decorative species should be encouraged, since they will not pose a threat to natural habitats. Also, detailed research should be conducted in order to eradicate invasive and potentially invasive species from the surfaces around the research area.

  1. Molecular Analysis Research at Community College of Philadelphia

    Science.gov (United States)

    2015-09-21

    YOUR FORM TO THE ABOVE ADDRESS. Community College of Philadelphia Community College of Philadelphia 1700 Spring Garden Street Philadelphia, PA 19130...Approved for Public Release; Distribution Unlimited Final Report: Molecular Analysis Research at Community College of Philadelphia The views, opinions...Molecular Analysis Research at Community College of Philadelphia Report Title AXIMA Assurance mass spectrometer, Leica DMI-8 fluorescent microscope

  2. An assessment of invasive plant species monitored by the Northern Research Station Forest Inventory and Analysis Program, 2005 through 2010

    Science.gov (United States)

    Cassandra M. Kurtz

    2013-01-01

    Invasive plant species are a worldwide concern due to the high ecological and economic costs associated with their presence. This document describes the plant characteristics and regional distribution of the 50 invasive plant species monitored from 2005 through 2010 on forested Phase 2 (P2) Forest Inventory and Analysis (FIA) plots in the 24 states of the Northern...

  3. Comparative Molecular Analysis of Gastrointestinal Adenocarcinomas

    NARCIS (Netherlands)

    Liu, Yang; Sethi, Nilay S; Hinoue, Toshinori; Schneider, Barbara G; Cherniack, Andrew D; Sanchez-Vega, Francisco; Seoane, Jose A; Farshidfar, Farshad; Bowlby, Reanne; Islam, Mirazul; Kim, Jaegil; Chatila, Walid; Akbani, Rehan; Kanchi, Rupa S; Rabkin, Charles S; Willis, Joseph E; Wang, Kenneth K; McCall, Shannon J; Mishra, Lopa; Ojesina, Akinyemi I; Bullman, Susan; Pedamallu, Chandra Sekhar; Lazar, Alexander J; Sakai, Ryo; Thorsson, Vésteinn; Bass, Adam J; Laird, Peter W; de Krijger, RR

    2018-01-01

    We analyzed 921 adenocarcinomas of the esophagus, stomach, colon, and rectum to examine shared and distinguishing molecular characteristics of gastrointestinal tract adenocarcinomas (GIACs). Hypermutated tumors were distinct regardless of cancer type and comprised those enriched for

  4. Molecular Composition Analysis of Distant Targets

    Data.gov (United States)

    National Aeronautics and Space Administration — We propose a system capable of probing the molecular composition of cold solar system targets such as asteroids, comets, planets and moons from a distant vantage....

  5. Comparative Outer Membrane Protein Analysis of High and Low-Invasive Strains of Cronobacter malonaticus

    Directory of Open Access Journals (Sweden)

    Maha A. Aldubyan

    2017-11-01

    Full Text Available Cronobacter are an important group of foodborne pathogens that has been linked to life-threatening infections in both infants and adults. The major infections associated with Cronobacter species are neonatal meningitis, necrotizing enterocolitis, and septicaemia. There are seven species in the Cronobacter genus, of which only three are of clinical importance; Cronobacter sakazakii, Cronobacter malonaticus, and Cronobacter turicensis. To date most studies have focussed on C. sakazakii as it is the major species associated with neonatal infections. However, recently C. malonaticus, in particular sequence type 7 (ST7, has been noted as being prevalent in adult infections and therefore warranting further investigation. In this study, eight strains of C. malonaticus ST7, that had been isolated from a wide range of sources and varied in their in vitro virulence, were chosen for proteomic analysis of their outer membrane proteins (OMPs. One-dimensional gel analysis revealed a ~29 kDa size band that was only present in the highly invasive strains. Subsequent mass spectrometric analysis identified several peptides that matched the flagellin protein. The presence of flagellin protein was confirmed in 2D gel spot. Mass spectrometry analysis of total OMPs revealed that the four highly invasive C. malonaticus strains expressed the main flagellum proteins that were absent from the four low invasive strains. These were the flagellar hook protein FlgE, flagellar hook-associated protein 1, flagellar hook-associated protein, flagellin, and flagellar hook-filament junction protein FlgL. This data indicates that C. malonaticus flagellar proteins may have an important role in the organism's invasion properties.

  6. Positive Analysis of Invasive Species Control as a Dynamic Spatial Process

    OpenAIRE

    Buyuktahtakin, Esra; Feng, Zhuo; Olsson, Aaryn; Frisvold, George B.; Szidarovszky, Ferenc

    2010-01-01

    This paper models control of invasive buffelgrass (Pennisetum ciliare), a fire-prone African bunchgrass spreading rapidly across the southern Arizona desert as a spatial dynamic process. Buffelgrass spreads over a gridded landscape. Weed carrying capacity, treatment costs, and damages vary over grid cells. Damage from buffelgrass depends on its spatial distribution in relation to valued resources. We conduct positive analysis of recommended heuristic strategies for buffelgrass control, evalua...

  7. Evaluation of Open and Minimally Invasive Adrenalectomy: A Systematic Review and Network Meta-analysis.

    Science.gov (United States)

    Heger, Patrick; Probst, Pascal; Hüttner, Felix J; Gooßen, Käthe; Proctor, Tanja; Müller-Stich, Beat P; Strobel, Oliver; Büchler, Markus W; Diener, Markus K

    2017-11-01

    Adrenalectomy can be performed via open and various minimally invasive approaches. The aim of this systematic review was to summarize the current evidence on surgical techniques of adrenalectomy. Systematic literature searches (MEDLINE, EMBASE, Web of Science, Cochrane Library) were conducted to identify randomized controlled trials (RCTs) and controlled clinical trials (CCTs) comparing at least two surgical procedures for adrenalectomy. Statistical analyses were performed, and meta-analyses were conducted. Furthermore, an indirect comparison of RCTs and a network meta-analysis of CCTs were carried out for each outcome. Twenty-six trials (1710 patients) were included. Postoperative complication rates did not show differences for open and minimally invasive techniques. Operation time was significantly shorter for open adrenalectomy than for the robotic approach (p meta-analysis showed open adrenalectomy to be the fastest technique. Blood loss was significantly reduced in the robotic arm compared with open and laparoscopic adrenalectomy (p = 0.01). Length of hospital stay (LOS) was significantly lower after conventional laparoscopy than open adrenalectomy in CCTs (p meta-analysis revealed the lowest LOS after retroperitoneoscopic adrenalectomy. Minimally invasive adrenalectomy is safe and should be preferred over open adrenalectomy due to shorter LOS, lower blood loss, and equivalent complication rates. The retroperitoneoscopic access features the shortest LOS and operating time. Further high-quality RCTs are warranted, especially to compare the posterior retroperitoneoscopic and the transperitoneal robotic approach.

  8. Molecular analysis of pancreatic cyst fluid changes clinical management.

    Science.gov (United States)

    Arner, David M; Corning, Brooke E; Ahmed, Ali M; Ho, Henry C; Weinbaum, Bradley J; Siddiqui, Uzma; Aslanian, Harry; Adams, Reid B; Bauer, Todd W; Wang, Andrew Y; Shami, Vanessa M; Sauer, Bryan G

    2018-01-01

    DNA molecular analysis has been suggested as a tool to evaluate pancreatic cysts. This study assesses whether the addition of DNA molecular analysis alters clinical management. This is a retrospective review of 46 consecutive patients who underwent EUS-FNA of pancreatic cysts with DNA molecular analysis at two major academic institutions. Cases were presented to two pancreaticobiliary surgeons first without and then with DNA molecular analysis data. The primary outcome was the frequency with which clinical management was altered with the addition of DNA molecular analysis. Forty-six patients with a mean age of 62.0 (±13.4) years and mean cyst size of 3.2 (±2.3) cm were included in the study. Cyst carcinoembryonic antigen (CEA) was available in 30 patients and ranged from 0.4 to 15,927 ng/mL. DNA molecular analysis was described as benign in 23 (50%), statistically indolent in 13 (28%), statistically higher risk in 9 (20%), and indeterminate in 1 (2%). Surgeon #1 changed the management in 13/46 cases (28%) and surgeon #2 changed the management in 12/46 cases (26%) with the addition of DNA molecular analysis. When organized by CEA concentration, those with an intermediate CEA (45-800 ng/mL) or without a CEA concentration had a management changed more frequently (40%) compared to all others (P molecular analysis alters the clinical management of pancreatic cystic lesions most often when CEA levels are intermediate (45-800 ng/mL) or when no CEA concentration is available. Use of DNA molecular analysis can be considered in this cohort. Further study of molecular markers in pancreatic cystic lesions is recommended.

  9. Role of Molecular Genetics in Identifying ‘Fine Tuned’ Natural Enemies of the Invasive Brazilian Peppertree, Schinus terebinthifolius

    Science.gov (United States)

    Brazilian peppertree is a highly successful invasive species in the continental United States, Hawaiian archipelago, several Caribbean Islands, Australia, Bermuda, and a number of other countries worldwide. It also is one of only a few invasive intraspecific hybrids that has been well characterized ...

  10. Synchrotron-Based Microspectroscopic Analysis of Molecular and Biopolymer Structures Using Multivariate Techniques and Advanced Multi-Components Modeling

    International Nuclear Information System (INIS)

    Yu, P.

    2008-01-01

    More recently, advanced synchrotron radiation-based bioanalytical technique (SRFTIRM) has been applied as a novel non-invasive analysis tool to study molecular, functional group and biopolymer chemistry, nutrient make-up and structural conformation in biomaterials. This novel synchrotron technique, taking advantage of bright synchrotron light (which is million times brighter than sunlight), is capable of exploring the biomaterials at molecular and cellular levels. However, with the synchrotron RFTIRM technique, a large number of molecular spectral data are usually collected. The objective of this article was to illustrate how to use two multivariate statistical techniques: (1) agglomerative hierarchical cluster analysis (AHCA) and (2) principal component analysis (PCA) and two advanced multicomponent modeling methods: (1) Gaussian and (2) Lorentzian multi-component peak modeling for molecular spectrum analysis of bio-tissues. The studies indicated that the two multivariate analyses (AHCA, PCA) are able to create molecular spectral corrections by including not just one intensity or frequency point of a molecular spectrum, but by utilizing the entire spectral information. Gaussian and Lorentzian modeling techniques are able to quantify spectral omponent peaks of molecular structure, functional group and biopolymer. By application of these four statistical methods of the multivariate techniques and Gaussian and Lorentzian modeling, inherent molecular structures, functional group and biopolymer onformation between and among biological samples can be quantified, discriminated and classified with great efficiency.

  11. Biostatistical analysis of treatment results of bacterial liver abscesses using minimally invasive techniques and open surgery

    Directory of Open Access Journals (Sweden)

    Кipshidze A.A.

    2013-12-01

    Full Text Available Today bacterial abscesses remain one of the most difficult complications in surgical hepatology, both traditional and minimally invasive methods of their treatment are used. Bio-statistical analysis is used due to the fact that strong evidences are required for the effectiveness of one or another method of surgical intervention. The estimation of statistical significance of differences between the control and the main group of patients with liver abscesses is given in this paper. Depending on the treatment method patients were divided into two groups: 1 - minimally invasive surgery (89 cases; 2 – laporatomy surgery (74 patients. Data compa¬ri¬son was performed by means of Stjudent's criterion. The effectiveness of method of abscesses drainage using inter¬ventional sonography, outer nazobiliar drainage with reorganization of ductal liver system and abscess cavity with the help of modern antiseptics was considered. The percentage of cured patients was also estimated.

  12. Hypofractionated radiation therapy for invasive thyroid carcinoma in dogs: a retrospective analysis of survival

    International Nuclear Information System (INIS)

    Brearley, M.J.; Hayes, A.M.; Murphy, S.

    1999-01-01

    Thirteen dogs with invasive thyroid carcinoma (WHO classification T2b or T3b) seen between January 1991 and October 1997 were treated by external beam Irradiation. Four once-weekly fractions of 9 gray of 4 MeV X-rays were administered. Four of the dogs died of progression of the primary disease and four from metastatic spread. Of the remaining dogs, three died of unrelated problems, although two were still alive at the time of the censor. Kaplan-Meier analysis of the survival time from first dose to death from either primary or metastatic disease gave a median survival time of 96 weeks (mean 85 weeks, range six to 247 weeks). Radiographic evidence of pulmonary metastatic disease at presentation had no prognostic value whereas crude growth rate was a highly significant factor. The present series Indicates that radiation therapy should be considered an important modality for the control of invasive thyroid carcinoma in the dog

  13. Molecular marker analysis of 'Shatangju' and 'Wuzishatangju ...

    African Journals Online (AJOL)

    'Wuzishatangju'(Citrus reticulata Blanco) is an excellent cultivar derived from a bud sport of a seedy 'Shatangju' cultivar found in Guangdong Province in the 1980s. In this study, six molecular markers including random amplified polymorphic DNA (RAPD), inter-simple sequence repeat (ISSR), simple sequence repeat (SSR) ...

  14. Non- invasive in vivo analysis of a murine aortic graft using high resolution ultrasound microimaging

    International Nuclear Information System (INIS)

    Rowinska, Zuzanna; Zander, Simone; Zernecke, Alma; Jacobs, Michael; Langer, Stephan; Weber, Christian; Merx, Marc W.; Koeppel, Thomas A.

    2012-01-01

    Introduction: As yet, murine aortic grafts have merely been monitored histopathologically. The aim of our study was to examine how these grafts can be monitored in vivo and non-invasively by using high-resolution ultrasound microimaging to evaluate function and morphology. A further aim was to prove if this in vivo monitoring can be correlated to immunohistological data that indicates graft integrity. Methods: Murine infrarenal aortic isografts were orthotopically transplanted into 14 female mice (C57BL/6-Background) whereas a group of sham-operated animals (n = 10) served as controls. To assess the graft morphology and hemodynamics, we examined the mice over a post-operative period of 8 weeks with a sophisticated ultrasound system (Vevo 770, Visual Sonics). Results: The non-invasive graft monitoring was feasible in all transplanted mice. We could demonstrate a regular post-transplant graft function and morphology, such as anterior/posterior wall displacement and wall thickness. Mild alterations of anterior wall motion dynamics could only be observed at the site of distal graft anastomosis (8 weeks after grafting (transplant vs. sham mice: 0.02 mm ± 0.01 vs. 0.03 mm ± 0.01, p < 0.05). However, the integrity of the entire graft wall could be confirmed by histopathological evaluation of the grafts. Conclusions: With regard to graft patency, function and morphology, high resolution ultrasound microimaging has proven to be a valuable tool for longitudinal, non-invasive, in vivo graft monitoring in this murine aortic transplantation model. Consequently, this experimental animal model provides an excellent basis for molecular and pharmacological studies using genetically engineered mice.

  15. Breath Analysis as a Potential and Non-Invasive Frontier in Disease Diagnosis: An Overview

    Directory of Open Access Journals (Sweden)

    Jorge Pereira

    2015-01-01

    Full Text Available Currently, a small number of diseases, particularly cardiovascular (CVDs, oncologic (ODs, neurodegenerative (NDDs, chronic respiratory diseases, as well as diabetes, form a severe burden to most of the countries worldwide. Hence, there is an urgent need for development of efficient diagnostic tools, particularly those enabling reliable detection of diseases, at their early stages, preferably using non-invasive approaches. Breath analysis is a non-invasive approach relying only on the characterisation of volatile composition of the exhaled breath (EB that in turn reflects the volatile composition of the bloodstream and airways and therefore the status and condition of the whole organism metabolism. Advanced sampling procedures (solid-phase and needle traps microextraction coupled with modern analytical technologies (proton transfer reaction mass spectrometry, selected ion flow tube mass spectrometry, ion mobility spectrometry, e-noses, etc. allow the characterisation of EB composition to an unprecedented level. However, a key challenge in EB analysis is the proper statistical analysis and interpretation of the large and heterogeneous datasets obtained from EB research. There is no standard statistical framework/protocol yet available in literature that can be used for EB data analysis towards discovery of biomarkers for use in a typical clinical setup. Nevertheless, EB analysis has immense potential towards development of biomarkers for the early disease diagnosis of diseases.

  16. Breath analysis as a potential and non-invasive frontier in disease diagnosis: an overview.

    Science.gov (United States)

    Pereira, Jorge; Porto-Figueira, Priscilla; Cavaco, Carina; Taunk, Khushman; Rapole, Srikanth; Dhakne, Rahul; Nagarajaram, Hampapathalu; Câmara, José S

    2015-01-09

    Currently, a small number of diseases, particularly cardiovascular (CVDs), oncologic (ODs), neurodegenerative (NDDs), chronic respiratory diseases, as well as diabetes, form a severe burden to most of the countries worldwide. Hence, there is an urgent need for development of efficient diagnostic tools, particularly those enabling reliable detection of diseases, at their early stages, preferably using non-invasive approaches. Breath analysis is a non-invasive approach relying only on the characterisation of volatile composition of the exhaled breath (EB) that in turn reflects the volatile composition of the bloodstream and airways and therefore the status and condition of the whole organism metabolism. Advanced sampling procedures (solid-phase and needle traps microextraction) coupled with modern analytical technologies (proton transfer reaction mass spectrometry, selected ion flow tube mass spectrometry, ion mobility spectrometry, e-noses, etc.) allow the characterisation of EB composition to an unprecedented level. However, a key challenge in EB analysis is the proper statistical analysis and interpretation of the large and heterogeneous datasets obtained from EB research. There is no standard statistical framework/protocol yet available in literature that can be used for EB data analysis towards discovery of biomarkers for use in a typical clinical setup. Nevertheless, EB analysis has immense potential towards development of biomarkers for the early disease diagnosis of diseases.

  17. Transcriptome analysis and comparison reveal divergence between two invasive whitefly cryptic species

    Directory of Open Access Journals (Sweden)

    Xia Jun

    2011-09-01

    Full Text Available Abstract Background Invasive species are valuable model systems for examining the evolutionary processes and molecular mechanisms associated with their specific characteristics by comparison with closely related species. Over the past 20 years, two species of the whitefly Bemisia tabaci species complex, Middle East-Asia Minor 1 (MEAM1 and Mediterranean (MED, have both spread from their origin Middle East/Mediterranean to many countries despite their apparent differences in many life history parameters. Previously, we have sequenced the transcriptome of MED. In this study, we sequenced the transcriptome of MEAM1 and took a comparative genomic approach to investigate the transcriptome evolution and the genetic factors underlying the differences between MEAM1 and MED. Results Using Illumina sequencing technology, we generated 17 million sequencing reads for MEAM1. These reads were assembled into 57,741 unique sequences and 15,922 sequences were annotated with an E-value above 10-5. Compared with the MED transcriptome, we identified 3,585 pairs of high quality orthologous genes and inferred their sequence divergences. The average differences in coding, 5' untranslated and 3' untranslated region were 0.83%, 1.66% and 1.43%, respectively. The level of sequence divergence provides additional support to the proposition that MEAM1 and MED are two species. Based on the ratio of nonsynonymous and synonymous substitutions, we identified 24 sequences that have evolved in response to positive selection. Many of those genes are predicted to be involved in metabolism and insecticide resistance which might contribute to the divergence of the two whitefly species. Conclusions Our data present a comprehensive sequence comparison between the two invasive whitefly species. This study will provide a road map for future investigations on the molecular mechanisms underlying their biological differences.

  18. A genetic analysis of segregation distortion revealed by molecular ...

    Indian Academy of Sciences (India)

    Journal of Genetics, Vol. 90, No. ... Segregation analysis was based on 64 molecular markers, including 26 .... FHB of RIL populations was controlled by quantitative trait ... The authors acknowledge financial support by the National Basic.

  19. Phenotypic and molecular genetic analysis of Pyruvate Kinase ...

    African Journals Online (AJOL)

    Phenotypic and molecular genetic analysis of Pyruvate Kinase deficiency in a Tunisian family. Jaouani Mouna, Hamdi Nadia, Chaouch Leila, Kalai Miniar, Mellouli Fethi, Darragi Imen, Boudriga Imen, Chaouachi Dorra, Bejaoui Mohamed, Abbes Salem ...

  20. MOLECULAR ANALYSIS OF HUMAN SPERMATOZOA: POTENTIAL FOR INFERTILITY RESEARCH

    Science.gov (United States)

    Gordon Research Conference: Mammalian Gametogenesis and Embryogenesis New London, CT, July 1-6, 2000Molecular Analysis of Human Spermatozoa: Potential for Infertility ResearchDavid Miller 1, David Dix2, Robert Reid 3, Stephen A Krawetz 3 1Reproductive ...

  1. Placental invasion, preeclampsia risk and adaptive molecular evolution at the origin of the great apes: evidence from genome-wide analyses.

    Science.gov (United States)

    Crosley, E J; Elliot, M G; Christians, J K; Crespi, B J

    2013-02-01

    Recent evidence from chimpanzees and gorillas has raised doubts that preeclampsia is a uniquely human disease. The deep extravillous trophoblast (EVT) invasion and spiral artery remodeling that characterizes our placenta (and is abnormal in preeclampsia) is shared within great apes, setting Homininae apart from Hylobatidae and Old World Monkeys, which show much shallower trophoblast invasion and limited spiral artery remodeling. We hypothesize that the evolution of a more invasive placenta in the lineage ancestral to the great apes involved positive selection on genes crucial to EVT invasion and spiral artery remodeling. Furthermore, identification of placentally-expressed genes under selection in this lineage may identify novel genes involved in placental development. We tested for positive selection in approximately 18,000 genes using the ratio of non-synonymous to synonymous amino acid substitution for protein-coding DNA. DAVID Bioinformatics Resources identified biological processes enriched in positively selected genes, including processes related to EVT invasion and spiral artery remodeling. Analyses revealed 295 and 264 genes under significant positive selection on the branches ancestral to Hominidae (Human, Chimp, Gorilla, Orangutan) and Homininae (Human, Chimp, Gorilla), respectively. Gene ontology analysis of these gene sets demonstrated significant enrichments for several functional gene clusters relevant to preeclampsia risk, and sets of placentally-expressed genes that have been linked with preeclampsia and/or trophoblast invasion in other studies. Our study represents a novel approach to the identification of candidate genes and amino acid residues involved in placental pathologies by implicating them in the evolution of highly-invasive placenta. Copyright © 2012 Elsevier Ltd. All rights reserved.

  2. Non-invasive Drosophila ECG recording by using eutectic gallium-indium alloy electrode: a feasible tool for future research on the molecular mechanisms involved in cardiac arrhythmia.

    Directory of Open Access Journals (Sweden)

    Po-Hung Kuo

    Full Text Available BACKGROUND: Drosophila heart tube is a feasible model for cardiac physiological research. However, obtaining Drosophila electrocardiograms (ECGs is difficult, due to the weak signals and limited contact area to apply electrodes. This paper presents a non-invasive Gallium-Indium (GaIn based recording system for Drosophila ECG measurement, providing the heart rate and heartbeat features to be observed. This novel, high-signal-quality system prolongs the recording time of insect ECGs, and provides a feasible platform for research on the molecular mechanisms involved in cardiovascular diseases. METHODS: In this study, two types of electrode, tungsten needle probes and GaIn electrodes, were used respectively to noiselessly conduct invasive and noninvasive ECG recordings of Drosophila. To further analyze electrode properties, circuit models were established and simulated. By using electromagnetic shielded heart signal acquiring system, consisted of analog amplification and digital filtering, the ECG signals of three phenotypes that have different heart functions were recorded without dissection. RESULTS AND DISCUSSION: The ECG waveforms of different phenotypes of Drosophila recorded invasively and repeatedly with n value (n>5 performed obvious difference in heart rate. In long period ECG recordings, non-invasive method implemented by GaIn electrodes acts relatively stable in both amplitude and period. To analyze GaIn electrode, the correctness of GaIn electrode model established by this paper was validated, presenting accuracy, stability, and reliability. CONCLUSIONS: Noninvasive ECG recording by GaIn electrodes was presented for recording Drosophila pupae ECG signals within a limited contact area and signal strength. Thus, the observation of ECG changes in normal and SERCA-depleted Drosophila over an extended period is feasible. This method prolongs insect survival time while conserving major ECG features, and provides a platform for

  3. Formalizing the definition of meta-analysis in Molecular Ecology.

    Science.gov (United States)

    ArchMiller, Althea A; Bauer, Eric F; Koch, Rebecca E; Wijayawardena, Bhagya K; Anil, Ammu; Kottwitz, Jack J; Munsterman, Amelia S; Wilson, Alan E

    2015-08-01

    Meta-analysis, the statistical synthesis of pertinent literature to develop evidence-based conclusions, is relatively new to the field of molecular ecology, with the first meta-analysis published in the journal Molecular Ecology in 2003 (Slate & Phua 2003). The goal of this article is to formalize the definition of meta-analysis for the authors, editors, reviewers and readers of Molecular Ecology by completing a review of the meta-analyses previously published in this journal. We also provide a brief overview of the many components required for meta-analysis with a more specific discussion of the issues related to the field of molecular ecology, including the use and statistical considerations of Wright's FST and its related analogues as effect sizes in meta-analysis. We performed a literature review to identify articles published as 'meta-analyses' in Molecular Ecology, which were then evaluated by at least two reviewers. We specifically targeted Molecular Ecology publications because as a flagship journal in this field, meta-analyses published in Molecular Ecology have the potential to set the standard for meta-analyses in other journals. We found that while many of these reviewed articles were strong meta-analyses, others failed to follow standard meta-analytical techniques. One of these unsatisfactory meta-analyses was in fact a secondary analysis. Other studies attempted meta-analyses but lacked the fundamental statistics that are considered necessary for an effective and powerful meta-analysis. By drawing attention to the inconsistency of studies labelled as meta-analyses, we emphasize the importance of understanding the components of traditional meta-analyses to fully embrace the strengths of quantitative data synthesis in the field of molecular ecology. © 2015 John Wiley & Sons Ltd.

  4. Experimental bifurcation analysis of an impact oscillator - Tuning a non-invasive control scheme

    DEFF Research Database (Denmark)

    Bureau, Emil; Schilder, Frank; Santos, Ilmar

    2013-01-01

    We investigate a non-invasive, locally stabilizing control scheme necessary for an experimental bifurcation analysis. Our test-rig comprises a harmonically forced impact oscillator with hardening spring nonlinearity controlled by electromagnetic actuators, and serves as a prototype...... for electromagnetic bearings and other machinery with build-in actuators. We propose a sequence of experiments that allows one to choose optimal control-gains, filter parameters and settings for a continuation method without a priori study of a model. Depending on the algorithm for estimating the Jacobian required...

  5. Prevalence of molecular subtypes and prognosis of invasive breast cancer in north-east of Morocco: retrospective study

    Directory of Open Access Journals (Sweden)

    Bennis Sanae

    2012-08-01

    Full Text Available Abstract Background Breast carcinoma is known as a heterogeneous disease because gene expression analyses identify several subtypes and the molecular profiles are prognostic and predictive for patients. Our aim, in this study, is to estimate the prevalence of breast cancer subtypes and to determine the relationship between clinico-pathological characteristics, overall survival (OS and disease free survival (DFS for patients coming from north-east of Morocco. Methods We reviewed 366 cases of breast cancer diagnosed between January 2007 to June 2010 at the Department of pathology. Age, size tumor, metastatic profile, node involvement profile, OS and DFS were analyzed on 181 patients. These last parameters were estimated by Kaplan-Meier analysis and log-rank test to estimate outcome differences among subgroups. Results The average age was 45 years, our patients were diagnosed late (57% stage III, 17.5% stage IV with a high average tumor size. Luminal A subtype was more prevalent (53.6% associated with favorable clinic-pathological characteristics, followed by luminal B (16.4%, Her2-overexpressing (12.6%, basal-like (12.6% and unclassified subtype (4.9%. Survival analysis showed a significant difference between subtypes. The triple negative tumors were associated with poor prognosis (49% OS, 39% DFS, whereas the luminal A were associated with a better prognosis (88% OS, 59% DFS. The luminal B and the Her2-overexpressing subtypes were associated with an intermediate prognosis (77% and 75% OS, and 41% and 38% DFS respectively. Conclusion This study showed that molecular classification by immunohistochemistry was necessary for therapeutic decision and prognosis of breast carcinoma. The luminal A subtype was associated with favorable biological characteristics and a better prognosis than triple negative tumors that were associated with a poor prognosis and unfavorable clinic-pathological characteristics.

  6. Molecular characterization of Trypanosoma cruzi SAP proteins with host-cell lysosome exocytosis-inducing activity required for parasite invasion.

    Science.gov (United States)

    Zanforlin, Tamiris; Bayer-Santos, Ethel; Cortez, Cristian; Almeida, Igor C; Yoshida, Nobuko; da Silveira, José Franco

    2013-01-01

    To invade target cells, Trypanosoma cruzi metacyclic forms engage distinct sets of surface and secreted molecules that interact with host components. Serine-, alanine-, and proline-rich proteins (SAP) comprise a multigene family constituted of molecules with a high serine, alanine and proline residue content. SAP proteins have a central domain (SAP-CD) responsible for interaction with and invasion of mammalian cells by metacyclic forms. Using a 513 bp sequence from SAP-CD in blastn analysis, we identified 39 full-length SAP genes in the genome of T. cruzi. Although most of these genes were mapped in the T. cruzi in silico chromosome TcChr41, several SAP sequences were spread out across the genome. The level of SAP transcripts was twice as high in metacyclic forms as in epimastigotes. Monoclonal (MAb-SAP) and polyclonal (anti-SAP) antibodies produced against the recombinant protein SAP-CD were used to investigate the expression and localization of SAP proteins. MAb-SAP reacted with a 55 kDa SAP protein released by epimastigotes and metacyclic forms and with distinct sets of SAP variants expressed in amastigotes and tissue culture-derived trypomastigotes (TCTs). Anti-SAP antibodies reacted with components located in the anterior region of epimastigotes and between the nucleus and the kinetoplast in metacyclic trypomastigotes. In contrast, anti-SAP recognized surface components of amastigotes and TCTs, suggesting that SAP proteins are directed to different cellular compartments. Ten SAP peptides were identified by mass spectrometry in vesicle and soluble-protein fractions obtained from parasite conditioned medium. Using overlapping sequences from SAP-CD, we identified a 54-aa peptide (SAP-CE) that was able to induce host-cell lysosome exocytosis and inhibit parasite internalization by 52%. This study provides novel information about the genomic organization, expression and cellular localization of SAP proteins and proposes a triggering role for extracellular SAP

  7. Non-Invasive Ventilation in Patients with Heart Failure: A Systematic Review and Meta-Analysis

    Directory of Open Access Journals (Sweden)

    Hugo Souza Bittencourt

    Full Text Available Abstract Non-invasive ventilation (NIV may perfect respiratory and cardiac performance in patients with heart failure (HF. The objective of the study to establish, through systematic review and meta-analysis, NIV influence on functional capacity of HF patients. A systematic review with meta-analysis of randomized studies was carried out through research of databases of Cochrane Library, SciELO, Pubmed and PEDro, using the key-words: heart failure, non-invasive ventilation, exercise tolerance; and the free terms: bi-level positive airway pressure (BIPAP, continuous positive airway pressure (CPAP, and functional capacity (terms were searched for in English and Portuguese using the Boolean operators AND and OR. Methodological quality was ensured through PEDro scale. Weighted averages and a 95% confidence interval (CI were calculated. The meta-analysis was done thorugh the software Review Manager, version 5.3 (Cochrane Collaboration. Four randomized clinical trials were included. Individual studies suggest NIV improved functional capacity. NIV resulted in improvement in the distance of the six-minute walk test (6MWT (68.7m 95%CI: 52.6 to 84.9 in comparison to the control group. We conclude that the NIV is an intervention that promotes important effects in the improvement of functional capacity of HF patients. However, there is a gap in literature on which are the most adequate parameters for the application of this technique.

  8. A coherent and non-invasive open analysis architecture and framework with applications in CMS

    International Nuclear Information System (INIS)

    Alverson, G.; Osborne, I.; Taylor, L.; Tuura, L.A.

    2001-01-01

    The CMS IGUANA project has implemented an open analysis architecture that enables the creation of an integrated analysis environment. In this 'analysis desktop' environment a physicist is able to perform most analysis-related tasks, not just the presentation and visualisation steps usually associated with analysis tools. The motivation behind IGUANA's approach is that physics analysis includes much more than just the visualisation and data presentation. Many factors contribute to the increasing importance of making analysis and visualisation software an integral part of the experiment's software: object oriented and ever more advanced data models, GRID, and automated hierarchical storage management systems to name just a few. At the the same time the analysis toolkits should be modular and non-invasive to be usable in different contexts within one experiment and generally across experiments. Ideally the analysis environment would appear to be perfectly customised to the experiment and the context, but would mostly consist of generic components. The authors describe how the IGUANA project is addressing these issues and present both the architecture and examples of how different aspects of analysis appear to the users and the developers

  9. Dynamical analysis of highly excited molecular spectra

    Energy Technology Data Exchange (ETDEWEB)

    Kellman, M.E. [Univ. of Oregon, Eugene (United States)

    1993-12-01

    The goal of this program is new methods for analysis of spectra and dynamics of highly excited vibrational states of molecules. In these systems, strong mode coupling and anharmonicity give rise to complicated classical dynamics, and make the simple normal modes analysis unsatisfactory. New methods of spectral analysis, pattern recognition, and assignment are sought using techniques of nonlinear dynamics including bifurcation theory, phase space classification, and quantization of phase space structures. The emphasis is chaotic systems and systems with many degrees of freedom.

  10. Cytological preparations for molecular analysis: A review of technical procedures, advantages and limitations for referring samples for testing.

    Science.gov (United States)

    da Cunha Santos, G; Saieg, M A; Troncone, G; Zeppa, P

    2018-04-01

    Minimally invasive procedures such as endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) must yield not only good quality and quantity of material for morphological assessment, but also an adequate sample for analysis of molecular markers to guide patients to appropriate targeted therapies. In this context, cytopathologists worldwide should be familiar with minimum requirements for refereeing cytological samples for testing. The present manuscript is a review with comprehensive description of the content of the workshop entitled Cytological preparations for molecular analysis: pre-analytical issues for EBUS TBNA, presented at the 40th European Congress of Cytopathology in Liverpool, UK. The present review emphasises the advantages and limitations of different types of cytology substrates used for molecular analysis such as archival smears, liquid-based preparations, archival cytospin preparations and FTA (Flinders Technology Associates) cards, as well as their technical requirements/features. These various types of cytological specimens can be successfully used for an extensive array of molecular studies, but the quality and quantity of extracted nucleic acids rely directly on adequate pre-analytical assessment of those samples. In this setting, cytopathologists must not only be familiar with the different types of specimens and associated technical procedures, but also correctly handle the material provided by minimally invasive procedures, ensuring that there is sufficient amount of material for a precise diagnosis and correct management of the patient through personalised care. © 2018 John Wiley & Sons Ltd.

  11. Molecular markers for tracking the origin and worldwide distribution of invasive strains of Puccinia striiformis

    DEFF Research Database (Denmark)

    Walter, Stephanie; Ali, Sajid; Kemen, Eric

    2016-01-01

    .g., the spreading of two aggressive and high temperature adapted strains to three continents since 2000. The combination of sequence-characterized amplified region (SCAR) markers, which were developed from two specific AFLP fragments, differentiated the two invasive strains, PstS1 and PstS2 from all other P....... striiformis strains investigated at a worldwide level. The application of the SCAR markers on 566 isolates showed that PstS1 was present in East Africa in the early 1980s and then detected in the Americas in 2000 and in Australia in 2002. PstS2 which evolved from PstS1 became widespread in the Middle East...... as the most plausible origin of the two invasive strains. The SCAR markers developed in the present study provide a rapid, inexpensive, and efficient tool to track the distribution of P. striiformis invasive strains, PstS1 and PstS2....

  12. A human breast cell model of pre-invasive to invasive transition

    Energy Technology Data Exchange (ETDEWEB)

    Bissell, Mina J; Rizki, Aylin; Weaver, Valerie M.; Lee, Sun-Young; Rozenberg, Gabriela I.; Chin, Koei; Myers, Connie A.; Bascom, Jamie L.; Mott, Joni D.; Semeiks, Jeremy R.; Grate, Leslie R.; Mian, I. Saira; Borowsky, Alexander D.; Jensen, Roy A.; Idowu, Michael O.; Chen, Fanqing; Chen, David J.; Petersen, Ole W.; Gray, Joe W.; Bissell, Mina J.

    2008-03-10

    A crucial step in human breast cancer progression is the acquisition of invasiveness. There is a distinct lack of human cell culture models to study the transition from pre-invasive to invasive phenotype as it may occur 'spontaneously' in vivo. To delineate molecular alterations important for this transition, we isolated human breast epithelial cell lines that showed partial loss of tissue polarity in three-dimensional reconstituted-basement membrane cultures. These cells remained non-invasive; however, unlike their non-malignant counterparts, they exhibited a high propensity to acquire invasiveness through basement membrane in culture. The genomic aberrations and gene expression profiles of the cells in this model showed a high degree of similarity to primary breast tumor profiles. The xenograft tumors formed by the cell lines in three different microenvironments in nude mice displayed metaplastic phenotypes, including squamous and basal characteristics, with invasive cells exhibiting features of higher grade tumors. To find functionally significant changes in transition from pre-invasive to invasive phenotype, we performed attribute profile clustering analysis on the list of genes differentially expressed between pre-invasive and invasive cells. We found integral membrane proteins, transcription factors, kinases, transport molecules, and chemokines to be highly represented. In addition, expression of matrix metalloproteinases MMP-9,-13,-15,-17 was up regulated in the invasive cells. Using siRNA based approaches, we found these MMPs to be required for the invasive phenotype. This model provides a new tool for dissection of mechanisms by which pre-invasive breast cells could acquire invasiveness in a metaplastic context.

  13. Meta-analysis reveals evolution in invasive plant species but little support for Evolution of Increased Competitive Ability (EICA).

    Science.gov (United States)

    Felker-Quinn, Emmi; Schweitzer, Jennifer A; Bailey, Joseph K

    2013-03-01

    Ecological explanations for the success and persistence of invasive species vastly outnumber evolutionary hypotheses, yet evolution is a fundamental process in the success of any species. The Evolution of Increased Competitive Ability (EICA) hypothesis (Blossey and Nötzold 1995) proposes that evolutionary change in response to release from coevolved herbivores is responsible for the success of many invasive plant species. Studies that evaluate this hypothesis have used different approaches to test whether invasive populations allocate fewer resources to defense and more to growth and competitive ability than do source populations, with mixed results. We conducted a meta-analysis of experimental tests of evolutionary change in the context of EICA. In contrast to previous reviews, there was no support across invasive species for EICA's predictions regarding defense or competitive ability, although invasive populations were more productive than conspecific native populations under noncompetitive conditions. We found broad support for genetically based changes in defense and competitive plant traits after introduction into new ranges, but not in the manner suggested by EICA. This review suggests that evolution occurs as a result of plant introduction and population expansion in invasive plant species, and may contribute to the invasiveness and persistence of some introduced species.

  14. Invasive species' leaf traits and dissimilarity from natives shape their impact on nitrogen cycling: a meta-analysis.

    Science.gov (United States)

    Lee, Marissa R; Bernhardt, Emily S; van Bodegom, Peter M; Cornelissen, J Hans C; Kattge, Jens; Laughlin, Daniel C; Niinemets, Ülo; Peñuelas, Josep; Reich, Peter B; Yguel, Benjamin; Wright, Justin P

    2017-01-01

    Many exotic species have little apparent impact on ecosystem processes, whereas others have dramatic consequences for human and ecosystem health. There is growing evidence that invasions foster eutrophication. We need to identify species that are harmful and systems that are vulnerable to anticipate these consequences. Species' traits may provide the necessary insights. We conducted a global meta-analysis to determine whether plant leaf and litter functional traits, and particularly leaf and litter nitrogen (N) content and carbon: nitrogen (C : N) ratio, explain variation in invasive species' impacts on soil N cycling. Dissimilarity in leaf and litter traits among invaded and noninvaded plant communities control the magnitude and direction of invasion impacts on N cycling. Invasions that caused the greatest increases in soil inorganic N and mineralization rates had a much greater litter N content and lower litter C : N in the invaded than the reference community. Trait dissimilarities were better predictors than the trait values of invasive species alone. Quantifying baseline community tissue traits, in addition to those of the invasive species, is critical to understanding the impacts of invasion on soil N cycling. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

  15. Correlation analysis of the Taurus molecular cloud complex

    International Nuclear Information System (INIS)

    Kleiner, S.C.

    1985-01-01

    Autocorrelation and power spectrum methods were applied to the analysis of the density and velocity structure of the Taurus Complex and Heiles Cloud 2 as traced out by 13 CO J = 1 → 0 molecular line observations obtained with the 14m antenna of the Five College Radio Astronomy Observatory. Statistically significant correlations in the spacing of density fluctuations within the Taurus Complex and Heiles 2 were uncovered. The length scales of the observed correlations correspond in magnitude to the Jeans wavelengths characterizing gravitational instabilities with (i) interstellar atomic hydrogen gas for the case of the Taurus complex, and (ii) molecular hydrogen for Heiles 2. The observed correlations may be the signatures of past and current gravitational instabilities frozen into the structure of the molecular gas. The appendices provide a comprehensive description of the analytical and numerical methods developed for the correlation analysis of molecular clouds

  16. Molecular insights into the interaction between Plasmodium falciparum apical membrane antigen 1 and an invasion-inhibitory peptide.

    Directory of Open Access Journals (Sweden)

    Geqing Wang

    Full Text Available Apical membrane antigen 1 (AMA1 of the human malaria parasite Plasmodium falciparum has been implicated in invasion of the host erythrocyte. It interacts with malarial rhoptry neck (RON proteins in the moving junction that forms between the host cell and the invading parasite. Agents that block this interaction inhibit invasion and may serve as promising leads for anti-malarial drug development. The invasion-inhibitory peptide R1 binds to a hydrophobic cleft on AMA1, which is an attractive target site for small molecules that block parasite invasion. In this work, truncation and mutational analyses show that Phe5-Phe9, Phe12 and Arg15 in R1 are the most important residues for high affinity binding to AMA1. These residues interact with two well-defined binding hot spots on AMA1. Computational solvent mapping reveals that one of these hot spots is suitable for small molecule targeting. We also confirm that R1 in solution binds to AMA1 with 1:1 stoichiometry and adopts a secondary structure consistent with the major form of R1 observed in the crystal structure of the complex. Our results provide a basis for designing high affinity inhibitors of the AMA1-RON2 interaction.

  17. Fragrance analysis using molecular and biochemical methods in ...

    African Journals Online (AJOL)

    admin

    Biochemical analysis of aroma was performed with the 1.7% KOH solution and molecular analysis of aroma was carried out with microsatellite markers present on chromosome 8 (BAD2, BADEX7-5, SCUSSR1) to determine the extent of association between trait, marker and chromosome 8. Among these markers, BAD2 ...

  18. Molecular responses and expression analysis of genes in a ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-06-17

    Jun 17, 2009 ... Molecular responses and expression analysis of genes in a xerophytic desert shrub Haloxylon ammodendron .... physiological determination and cDNA-AFLP analysis, three groups of seeds were sowed in pots with sand and .... HaDR27. U. 234. PDR-like ABC transporter. AT1G59870. HaDR28. U. 135.

  19. Results of salvage radiotherapy after inadequate surgery in invasive cervical carcinoma patients: A retrospective analysis

    International Nuclear Information System (INIS)

    Saibishkumar, Elantholi P.; Patel, Firuza D.; Ghoshal, Sushmita; Kumar, Vinay; Karunanidhi, Gunaseelan; Sharma, Suresh C.

    2005-01-01

    Purpose: To evaluate the results of salvage radiotherapy (RT) after inadequate surgery in patients with invasive carcinoma of the cervix. Methods and Materials: Between 1996 and 2001, 105 invasive cervical carcinoma patients were treated at our center with external beam RT with or without intracavitary RT after having undergone total/subtotal hysterectomy at outside institutions. Results: The median follow-up was 34 months. The gap between surgery and RT was 23-198 days (median, 80). Clinically visible residual disease was present in 81 patients (77.1%). Total hysterectomy had been done in 82 patients (78%) and subtotal hysterectomy in 23 patients (22%). The 5-year overall survival, disease-free survival, and pelvic control rates of all patients were 55.2%, 53.3%, and 72.4%, respectively. On univariate analysis, older age, total hysterectomy, hemoglobin level >10 g% before RT, nonsquamous histologic type, use of intracavitary RT, a shorter gap between surgery and RT, and the absence of, or a small volume of, residual disease favorably affected the outcome. The 5-year actuarial rate of late toxicity (Radiation Therapy Oncology Group Criteria) was 19% in the rectum, 4.8% in the bladder, 24.8% in the skin, and 14.3% in the small intestine. Conclusions: Inadequate and inappropriate surgery in invasive cervical cancer with resulting gross residual disease is common in India. Factors such as the use of intracavitary RT, the correction of anemia, and a shorter gap between surgery and RT will enable postoperative RT to achieve acceptable results with minimal morbidity

  20. Three-Dimensional Echocardiography-Derived Non-Invasive Right Ventricular Pressure-Volume Analysis.

    Science.gov (United States)

    Huang, Kuan-Chih; Lin, Lian-Yu; Hwang, Juey-Jen; Lin, Lung-Chun

    2017-09-01

    In patients with pulmonary hypertension, repeated evaluations of right ventricular (RV) function are still required for clinical decision making, but the invasive nature of current pressure-volume analysis makes conducting regular follow-ups in a clinical setting infeasible. We enrolled 12 patients with pulmonary arterial hypertension (PAH) and 10 with pulmonary venous hypertension (PVH) May 2016-October 2016. All patients underwent a clinically indicated right heart catheterization (RHC), from which the yielded right ventricular pressure recordings were conjugated with RV volume by 3-D echocardiography to generate a pressure-volume loop. A continuous-wave Doppler envelope of tricuspid regurgitation was transformed into a pressure gradient recording by the simplified Bernoulli equation, and then a systolic pressure gradient-volume (PG-V) diagram was generated from similar methods. The area enclosed by the pressure-volume loop was calculated to represent semi-invasive right ventricular stroke work (RVSW RHC ). The area between the PG-V diagram and x-axis was calculated to estimate non-invasive RVSW (RVSW echo ). Patients with PAH have higher RV pressure, lower pulmonary arterial wedge pressure and larger RV volume that was contributed by the dilation of RV mid-cavity minor dimension. We found no significant difference of traditional parameters between these two groups, but RVSW values were significantly higher in PAH patients. The RVSW values of these two methods were significantly correlated by the equation RVSW echo  = 0.8447 RVSW RHC  + 129.38 (R 2  = 0.9151, p rights reserved.

  1. Prevalence and invasiveness of community-acquired methicillin-resistant Staphylococcus aureus: A meta-analysis

    Directory of Open Access Journals (Sweden)

    Shipeng Li

    2014-01-01

    Full Text Available Background: Reports suggest that the prevalence of community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA has increased, and that CA-MRSA is more virulent than healthcare-associated (HA-MRSA. Aims: The aim of this study is to gain a better understanding of the invasiveness and prevalence of CA-MRSA in patients; we systematically reviewed the literature by conducting a meta-analysis. Materials and Methods: We searched the MEDLINE and PUBMED databases from the year these databases were established to January 2013. Results: The pooled CA-MRSA prevalence among 50,737 patients from 33 studies was 39.0% (range, 30.8-47.8%. The pooled CA-MRSA prevalence rates among pediatric and adult patients with MRSA infection were 50.2% (range, 37.5-62.8% and 42.3% (range, 16.4-73.3%, respectively. The pooled CA-MRSA prevalence rates of MRSA-infected patients in Asia, Europe, and North America were 23.1% (range, 12.0-39.8%, 37.4% (range, 21.1-56.4%, and 47.4% (range, 35.8-59.4%, respectively. Using the random effects model, we determined that the pooled odds ratio of invasive infections in CA- and HA-MRSA was 0.30 (95% confidence interval: 0.08-1.10; P = 0.07, test for heterogeneity P < 0.00001. Conclusions: The prevalence of CA-MRSA in MRSA infection varied with area and population. No difference in the ability to cause invasive infections was found between CA- and HA-MRSA. This finding challenges the view that CA-MRSA is more virulent than HA-MRSA.

  2. Interactive analysis of systems biology molecular expression data

    Directory of Open Access Journals (Sweden)

    Prabhakar Sunil

    2008-02-01

    Full Text Available Abstract Background Systems biology aims to understand biological systems on a comprehensive scale, such that the components that make up the whole are connected to one another and work through dependent interactions. Molecular correlations and comparative studies of molecular expression are crucial to establishing interdependent connections in systems biology. The existing software packages provide limited data mining capability. The user must first generate visualization data with a preferred data mining algorithm and then upload the resulting data into the visualization package for graphic visualization of molecular relations. Results Presented is a novel interactive visual data mining application, SysNet that provides an interactive environment for the analysis of high data volume molecular expression information of most any type from biological systems. It integrates interactive graphic visualization and statistical data mining into a single package. SysNet interactively presents intermolecular correlation information with circular and heatmap layouts. It is also applicable to comparative analysis of molecular expression data, such as time course data. Conclusion The SysNet program has been utilized to analyze elemental profile changes in response to an increasing concentration of iron (Fe in growth media (an ionomics dataset. This study case demonstrates that the SysNet software is an effective platform for interactive analysis of molecular expression information in systems biology.

  3. Long-term use of metformin and the molecular subtype in invasive breast carcinoma patients – a retrospective study of clinical and tumor characteristics

    International Nuclear Information System (INIS)

    Besic, Nikola; Satej, Nika; Ratosa, Ivica; Horvat, Andreja Gojkovic; Marinko, Tanja; Gazic, Barbara; Petric, Rok

    2014-01-01

    Metformin may exhibit inhibitory effects on cancer cells by inhibiting mTOR signaling pathway. The aim of our retrospective study was to examine if patients with breast carcinoma (BC) and diabetes mellitus (DM) receiving metformin have a lower stage of carcinoma in comparison to patients not receiving metformin, and if the use of metformin correlates with the molecular subtype of BC. A chart review of 253 patients with invasive BC and DM (128 on metformin and 125 not on metformin) was performed. Control group consisted of 320 consecutive patients with invasive BC without DM. BC subtypes were classified by immunohistochemical surrogates as luminal A (estrogen receptor [ER] + and/or progesterone receptor [PR]+, HER-2-), luminal B (ER + and/or PR+, HER-2+), HER-2 (ER-, PR-, HER-2+), triple-negative/basal (ER-, PR-, HER-2-). Patients on metformin had a lower proportion of T3 or T4 tumors than patients who were not receiving metformin (16% vs. 26%; p = 0.035). No statistical difference was found between the two study groups in N stage. Patients with DM on metformin, with DM not on metformin and the control group had different molecular subtypes of BC (p = 0.01): the luminal A subtype was found in 78%, 83% and 71%, the luminal B in 12.6%, 9% and 11%, HER-2 in 0.8%, 1.6% and 8%, and the triple-negative/basal-like subtype in 8.6%, 6.4% and 10%, respectively. Our data indicate that long-term use of metformin use correlates with molecular subtype of BC in diabetics on metformin in comparison to diabetics not on metformin and patients without DM. However, most likely, different distribution of the molecular subtypes of BC in these three groups of patients was caused by other risk factors for breast carcinoma, such as age of patients or obesity

  4. Fluid Vessel Quantity using Non-Invasive PZT Technology Flight Volume Measurements Under Zero G Analysis

    Science.gov (United States)

    Garofalo, Anthony A.

    2013-01-01

    The purpose of the project is to perform analysis of data using the Systems Engineering Educational Discovery (SEED) program data from 2011 and 2012 Fluid Vessel Quantity using Non-Invasive PZT Technology flight volume measurements under Zero G conditions (parabolic Plane flight data). Also experimental planning and lab work for future sub-orbital experiments to use the NASA PZT technology for fluid volume measurement. Along with conducting data analysis of flight data, I also did a variety of other tasks. I provided the lab with detailed technical drawings, experimented with 3d printers, made changes to the liquid nitrogen skid schematics, and learned how to weld. I also programmed microcontrollers to interact with various sensors and helped with other things going on around the lab.

  5. Invasive plants found in Louisiana’s forests, 2009 forest inventory and analysis factsheet

    Science.gov (United States)

    Sonja N. Oswalt; Christopher M. Oswalt

    2012-01-01

    Foresters and ecologists have noted the spread of nonnative invasive species onto U.S. forest land for decades. Despite soaring costs related to the management of and removal of invasive plants, and inestimable environmental impacts (e.g., altered soil chemistry, competition with native species, altered light environment; Pimentel and others 2005), nonnative invasive...

  6. A non-invasive acoustic and vibration analysis technique for evaluation of hip joint conditions.

    Science.gov (United States)

    Glaser, Diana; Komistek, Richard D; Cates, Harold E; Mahfouz, Mohamed R

    2010-02-10

    The performance evaluation of THA outcome is difficult and surgeons often use invasive methods to investigate effectiveness. A non-invasive acoustic and vibration analysis technique has recently been developed for more-in-depth evaluation of in vivo hip conditions. Gait kinematics, corresponding vibration and sound measurement of five THA subjects were analyzed post-operatively using video-fluoroscopy, sound and accelerometer measurements while walking on a treadmill. The sound sensor and a pair of tri-axial accelerometers, externally attached to the pelvic and femoral bone prominences, detected frequencies that are propagated through the femoral head and acetabular cup interactions. A data acquisition system was used to amplify the signal and filter out noise generated by undesired frequencies. In vivo kinematics and femoral head sliding quantified using video fluoroscopy were correlated to the sound and acceleration measurements. Distinct variations between the different subjects were identified. A correlation of sound and acceleration impulses with separation has been achieved. Although, in vivo sounds are quite variable in nature and all correlated well with the visual images. This is the first study to document and correlate visual and audible effects of THA under in-vivo conditions. This study has shown that the development of the acoustic and vibration technique provides a practical method and generates new possibilities for a better understanding of THA performance. Copyright 2009 Elsevier Ltd. All rights reserved.

  7. An Analysis of Oncotype DX Recurrence Scores and Clinicopathologic Characteristics in Invasive Lobular Breast Cancer.

    Science.gov (United States)

    Felts, Jesse L; Zhu, Junjia; Han, Bing; Smith, Stanley J; Truica, Cristina I

    2017-11-01

    The Oncotype DX breast cancer assay (Genomic Health, Redwood City, CA) is increasingly being used to guide treatment decisions for patients with early stage, hormone-positive, Her-2-negative breast cancer. The utility of the Oncotype DX in decision making for treatment of invasive lobular carcinoma (ILC) has not been investigated as the results reported by Genomic Health are largely in a population with invasive ductal carcinoma (IDC). The authors hypothesized that the Oncotype DX recurrence score (RS) distribution for ILC is different than that for IDC. We performed a retrospective analysis of early stage breast cancer patients treated at Penn State Cancer Institute from 2001 to 2011 and identified 102 patients with ILC. We also pulled RS data from our institution's prospective registry of consecutive patients with early stage IDC treated during the same time period. Median follow-up was 55 months. We found that the RS distribution for ILC differed significantly from that of IDC (p = 0.024). We also found a statistically significant difference in the RS distribution between the pure ILC and pleomorphic ILC subtypes (p = 0.027). The Oncotype DX RS distribution in ILC is unique, differing significantly from that in ductal carcinoma. Consequently, the clinical usefulness and cost-effectiveness of the Oncotype DX in guiding treatment for ILC should be further investigated. © 2017 Wiley Periodicals, Inc.

  8. Pancreatic invasion of gastric carcinoma in emaciated patients: The value of combined analysis with CT and upper gastrointestinal series

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Jae Mun; Kim, Hyun; Kim, Choon Yul; Bahk, Yong Whee [Catholic University Medical College, Seoul (Korea, Republic of)

    1992-03-15

    The obliteration of a fat plane between the gastric carcinoma and the pancreas is a major criterion on CT scan for pancreatic invasion of gastric carcinoma. However, this sign is not always a reliable indicator of invasion, as the patients with gastric carcinoma are often emaciated, producing a false positive CT findings. The purpose of our study is to improve the diagnostic accuracy of pancreatic invasion of gastric carcinoma in cases which the fat plane between the gastric carcinoma and the pancreas is obliterated in conventional CT scan. The authors performed lateral decubitus as well as supine CT scans and upper gastrointestinal series(UGIS) in 49 pathologically proven cases in which the fat plane was obliterated between the gastric carcinoma and the pancreas on conventional supine CT scan. Pancreatic invasion was suggested when the fat plane was obliterated persistently in the lateral decubitus view as well as the spine CT images and the involved gastric wall and adjacent pancreas maintained constant approximation despite postural change(CT+), and when the gastric tumor moved downward on the erect view of the UGIS no more than 1.5 times the height of the first lumbar vertebral body(UGIS+). Among 49 cases in which the fat plane between the gastric carcinoma and the pancreas was obliterated on supine CT scan, pancreatic invasion was confirmed pathologically in 11 cases(22.4%). Eight of 11 cases proven as pancreatic invasion were correctly diagnosed as pancreatic invasion by this combined analysis(CT+/UGIS+, 72.7%). Twenty seven of 38 cases proven as no pancreatic invasion were correctly diagnosed as no pancreatic invasion(CT-/UGIS-, 71.1%). Twelve cases showed CT+/UGIS- or CT-/UGIS+, so it was inconclusive whether there was invasion or not. The overall diagnostic accuracy was 71.4%. In conclusion, combined analysis with supine and lateral decubitus CT and UGIS is useful for improving diagnostic accuracy for pancreatic invasion by gastric carcinoma in patients of

  9. Pancreatic invasion of gastric carcinoma in emaciated patients: The value of combined analysis with CT and upper gastrointestinal series

    International Nuclear Information System (INIS)

    Lee, Jae Mun; Kim, Hyun; Kim, Choon Yul; Bahk, Yong Whee

    1992-01-01

    The obliteration of a fat plane between the gastric carcinoma and the pancreas is a major criterion on CT scan for pancreatic invasion of gastric carcinoma. However, this sign is not always a reliable indicator of invasion, as the patients with gastric carcinoma are often emaciated, producing a false positive CT findings. The purpose of our study is to improve the diagnostic accuracy of pancreatic invasion of gastric carcinoma in cases which the fat plane between the gastric carcinoma and the pancreas is obliterated in conventional CT scan. The authors performed lateral decubitus as well as supine CT scans and upper gastrointestinal series(UGIS) in 49 pathologically proven cases in which the fat plane was obliterated between the gastric carcinoma and the pancreas on conventional supine CT scan. Pancreatic invasion was suggested when the fat plane was obliterated persistently in the lateral decubitus view as well as the spine CT images and the involved gastric wall and adjacent pancreas maintained constant approximation despite postural change(CT+), and when the gastric tumor moved downward on the erect view of the UGIS no more than 1.5 times the height of the first lumbar vertebral body(UGIS+). Among 49 cases in which the fat plane between the gastric carcinoma and the pancreas was obliterated on supine CT scan, pancreatic invasion was confirmed pathologically in 11 cases(22.4%). Eight of 11 cases proven as pancreatic invasion were correctly diagnosed as pancreatic invasion by this combined analysis(CT+/UGIS+, 72.7%). Twenty seven of 38 cases proven as no pancreatic invasion were correctly diagnosed as no pancreatic invasion(CT-/UGIS-, 71.1%). Twelve cases showed CT+/UGIS- or CT-/UGIS+, so it was inconclusive whether there was invasion or not. The overall diagnostic accuracy was 71.4%. In conclusion, combined analysis with supine and lateral decubitus CT and UGIS is useful for improving diagnostic accuracy for pancreatic invasion by gastric carcinoma in patients of

  10. Molecular Eigensolution Symmetry Analysis and Fine Structure

    Directory of Open Access Journals (Sweden)

    William G. Harter

    2013-01-01

    Full Text Available Spectra of high-symmetry molecules contain fine and superfine level cluster structure related to J-tunneling between hills and valleys on rovibronic energy surfaces (RES. Such graphic visualizations help disentangle multi-level dynamics, selection rules, and state mixing effects including widespread violation of nuclear spin symmetry species. A review of RES analysis compares it to that of potential energy surfaces (PES used in Born-Oppenheimer approximations. Both take advantage of adiabatic coupling in order to visualize Hamiltonian eigensolutions. RES of symmetric and D2 asymmetric top rank-2-tensor Hamiltonians are compared with Oh spherical top rank-4-tensor fine-structure clusters of 6-fold and 8-fold tunneling multiplets. Then extreme 12-fold and 24-fold multiplets are analyzed by RES plots of higher rank tensor Hamiltonians. Such extreme clustering is rare in fundamental bands but prevalent in hot bands, and analysis of its superfine structure requires more efficient labeling and a more powerful group theory. This is introduced using elementary examples involving two groups of order-6 (C6 and D3~C3v, then applied to families of Oh clusters in SF6 spectra and to extreme clusters.

  11. Rapid molecular detection of invasive species in ballast and harbor water by integrating environmental DNA and light transmission spectroscopy.

    Science.gov (United States)

    Egan, Scott P; Grey, Erin; Olds, Brett; Feder, Jeffery L; Ruggiero, Steven T; Tanner, Carol E; Lodge, David M

    2015-04-07

    Invasive species introduced via the ballast water of commercial ships cause enormous environmental and economic damage worldwide. Accurate monitoring for these often microscopic and morphologically indistinguishable species is challenging but critical for mitigating damages. We apply eDNA sampling, which involves the filtering and subsequent DNA extraction of microscopic bits of tissue suspended in water, to ballast and harbor water sampled during a commercial ship's 1400 km voyage through the North American Great Lakes. Using a lab-based gel electrophoresis assay and a rapid, field-ready light transmission spectroscopy (LTS) assay, we test for the presence of two invasive species: quagga (Dreissena bugensis) and zebra (D. polymorpha) mussels. Furthermore, we spiked a set of uninfested ballast and harbor samples with zebra mussel tissue to further test each assay's detection capabilities. In unmanipulated samples, zebra mussel was not detected, while quagga mussel was detected in all samples at a rate of 85% for the gel assay and 100% for the LTS assay. In the spiked experimental samples, both assays detected zebra mussel in 94% of spiked samples and 0% of negative controls. Overall, these results demonstrate that eDNA sampling is effective for monitoring ballast-mediated invasions and that LTS has the potential for rapid, field-based detection.

  12. Molecular thermal transistor: Dimension analysis and mechanism

    Science.gov (United States)

    Behnia, S.; Panahinia, R.

    2018-04-01

    Recently, large challenge has been spent to realize high efficient thermal transistors. Outstanding properties of DNA make it as an excellent nano material in future technologies. In this paper, we introduced a high efficient DNA based thermal transistor. The thermal transistor operates when the system shows an increase in the thermal flux despite of decreasing temperature gradient. This is what called as negative differential thermal resistance (NDTR). Based on multifractal analysis, we could distinguish regions with NDTR state from non-NDTR state. Moreover, Based on dimension spectrum of the system, it is detected that NDTR state is accompanied by ballistic transport regime. The generalized correlation sum (analogous to specific heat) shows that an irregular decrease in the specific heat induces an increase in the mean free path (mfp) of phonons. This leads to the occurrence of NDTR.

  13. Molecular taxonomy of Plagioscion Heckel (Perciformes, Sciaenidae and evidence from mtDNA RFLP markers for an invasive species in the Paraná river, Southern Brazil Taxonomia molecular de Plagioscion Heckel (Perciformes, Sciaenidae e evidências de marcadores moleculares RFLPs de mtDNA para uma espécie invasora no rio Paraná, Sul do Brasil

    Directory of Open Access Journals (Sweden)

    Rodrigo A. Torres

    2006-12-01

    Full Text Available Mitochondrial RFLP markers were developed to examine whether Plagioscion squamosissimus (Heckel, 1840 is invasive in natural environments of the congener P. ternetzi in the Paraná river, in southern Brazil. Specimens of P. squamosissimus and of the putative P. ternetzi (Boulenger, 1895 were obtained from the Negro river (Manaus, Amazonas, Brazil and from Paraná river, respectively. Fragments of the cytochrome b gene (900bp were amplified by PCR and four restriction enzymes (Eco RI, Mbo I, Bam HI and Alu I yielded the mitochondrial markers. An additional RFLP analysis with a cytochrome b gene sequence of Plagioncion sp. from GeneBank was carried out to validate the prior analysis. No genetic differentiation was found among either sample. While molecular variation in the cytochrome b analysis was no substantial among individuals, the combined analysis was important for demonstrating that there is no evidence for differentiation of the putative sample P. ternetzi from that of P. squamosissimus. The ecological implications of the introduced occurrence of P. squamosissimus, as well as the role of molecular taxonomic approaches for biodiversity studies are discussed.Marcadores RFLPs mitocondriais foram desenvolvidos para verificar se Plagioscion squamosissimus (Heckel, 1840 é invasora nos ambientes naturais da espécie congênere P. ternetzi no rio Paraná, no sul do Brasil. Exemplares de Plagioscion squamosissimus e supostamente de P. ternetzi (Boulenger, 1895 foram obtidos, respectivamente, do rio Negro (Manaus, AM, Brasil e rio Paraná (Foz do Iguaçu, PR, Brasil. Foram amplificados, via PCR, fragmentos de cerca de 900pb do Citocromo b e foram utilizadas quatro enzimas de restrição (Eco RI, Mbo I, Bam HI e Alu I para os fins de geração dos marcadores moleculares. Foi desenvolvida, a partir de uma seqüência de Citocromo b de Plagioscion sp. (genebank, uma análise de RFLP adicional, objetivando validar a primeira análise acima mencionada

  14. Genetic origin and dispersal of the invasive soybean aphid inferred from population genetic analysis and approximate Bayesian computation.

    Science.gov (United States)

    Fang, Fang; Chen, Jing; Jiang, Li-Yun; Qu, Yan-Hua; Qiao, Ge-Xia

    2018-01-09

    Biological invasion is considered one of the most important global environmental problems. Knowledge of the source and dispersal routes of invasion could facilitate the eradication and control of invasive species. Soybean aphid, Aphis glycines Matsumura, is one of the most destructive soybean pests. For effective management of this pest, we conducted genetic analyses and approximate Bayesian computation (ABC) analysis to determine the origins and dispersal of the aphid species, as well as the source of its invasion in the USA, using eight microsatellite loci and the mitochondrial cytochrome c oxidase subunit I (COI) gene. We were able to identify a significant isolation by distance (IBD) pattern and three genetic lineages in the microsatellite data but not in the mtDNA dataset. The genetic structure showed that the USA population has the closest relationship with those from Korea and Japan, indicating that the two latter populations might be the sources of the invasion to the USA. Both population genetic analyses and ABC showed that the northeastern populations in China were the possible sources of the further spread of A. glycines to Indonesia. The dispersal history of this aphid can provide useful information for pest management strategies and can further help predict areas at risk of invasion. This article is protected by copyright. All rights reserved.

  15. In situ non-invasive EDXRF analysis to reconstruct stratigraphy and thickness of Renaissance pictorial multilayers

    International Nuclear Information System (INIS)

    Bonizzoni, L.; Poldi, G.; Milazzo, M.; Galli, A.

    2007-01-01

    In this paper, we report a few examples showing how energy dispersive XRF analysis (EDXRF) coupled with visible reflectance spectroscopy (vis-RS) can be successfully applied for the investigation of wood or canvas paintings by performing stratigraphic analyses with non-invasive techniques. The specific aim is to reconstruct layers and their thicknesses. The method has been tested in the laboratory on paint layers similar to traditional Renaissance ones. In situ analyses of a famous wood painting by Andrea Mantegna - 'Madonna col bambino e un coro di cherubini', Pinacoteca di Brera, Milan - were also carried out. While illustrating the results concerning the identification of pigments and the discrimination of layer stratigraphy, advantages and limitation of this method are pointed out. (authors)

  16. Non-invasive method for screening and early detection of breast tumors using thermal field analysis

    Directory of Open Access Journals (Sweden)

    O. Drosu

    2009-10-01

    Full Text Available The paper refers to general presentation of international and European evaluation regarding breast cancer incidence and mortality as well as recommendations for prevention, screening, detection and treatment.The past years international research development in biomedical engineering has put a particular emphasis on the thermography use in breast pathology diagnosis and its main advantages, such as: an early diagnose of the breast cancer, in that stage when the mammography or ultrasounds can not easily detect the changes of the tissue; a totally non-invasive interaction with human body; very low costs and possibilities for the women to do a self thermographic test.We also present some important results of our research within the field of breast tumor detection using the numerical analysis of the thermal inverse problem.

  17. Non-invasive differentiation of pancreatic lesions: is analysis of FDG kinetics superior to semiquantitative uptake value analysis?

    International Nuclear Information System (INIS)

    Nitzsche, E.U.; Hoegerle, S.; Mix, M.; Brink, I.; Otte, A.; Moser, E.

    2002-01-01

    The diagnostic utility of fluorine-18 2-deoxy-D-glucose positron emission tomography (FDG PET) for the non-invasive differentiation of focal pancreatic lesions originating from cancer or chronic pancreatitis by combined visual image interpretation and semiquantitative uptake value analysis has been documented. However, in clinical routine some misdiagnosis is still observed. This is because there is potential overlap between the semiquantitative uptake values obtained for active inflammatory lesions and cancer. Therefore, this prospective study was undertaken to test the hypothesis that analysis of dynamic kinetics of focal pancreatic lesions based on FDG PET may more accurately determine the benign or malignant nature of such lesions. Thirty patients (56±17 years) were studied dynamically with FDG PET for a period of 60-90 min. Patients were assigned to one of four groups: control, acute pancreatitis, chronic pancreatitis or pancreatic cancer. Two observers, blinded to the clinical data, analysed the time-activity curves of FDG kinetics based on region of interest analysis. The diagnosis predicted by FDG PET was compared with the result of histological examination of the surgical specimen. Analysis of FDG kinetics revealed significant differences in the shape of the time-activity curve for controls, pancreatic cancer and inflammatory disease. Surprisingly, there was no significant difference in the time-activity curve shape for chronic pancreatitis and acute pancreatitis; this is, however, not a clinical issue. Furthermore, acquisition time (60 min vs 90 min) did not affect interpretation of the time-activity curve, so that scanning time may be regularly shortened to 60 min. Interobserver agreement was 1. Based on these findings, non-invasive differentiation between pancreatic cancer and chronic pancreatitis was correctly predicted in all cases, as confirmed by histology. In addition, the specificity was increased compared with that obtained from standardised

  18. Molecular analysis of deep subsurface bacteria

    International Nuclear Information System (INIS)

    Jimenez Baez, L.E.

    1989-09-01

    Deep sediments samples from site C10a, in Appleton, and sites, P24, P28, and P29, at the Savannah River Site (SRS), near Aiken, South Carolina were studied to determine their microbial community composition, DNA homology and mol %G+C. Different geological formations with great variability in hydrogeological parameters were found across the depth profile. Phenotypic identification of deep subsurface bacteria underestimated the bacterial diversity at the three SRS sites, since bacteria with the same phenotype have different DNA composition and less than 70% DNA homology. Total DNA hybridization and mol %G+C analysis of deep sediment bacterial isolates suggested that each formation is comprised of different microbial communities. Depositional environment was more important than site and geological formation on the DNA relatedness between deep subsurface bacteria, since more 70% of bacteria with 20% or more of DNA homology came from the same depositional environments. Based on phenotypic and genotypic tests Pseudomonas spp. and Acinetobacter spp.-like bacteria were identified in 85 million years old sediments. This suggests that these microbial communities might have been adapted during a long period of time to the environmental conditions of the deep subsurface

  19. Quantitative proteomic analysis reveals effects of epidermal growth factor receptor (EGFR) on invasion-promoting proteins secreted by glioblastoma cells.

    Science.gov (United States)

    Sangar, Vineet; Funk, Cory C; Kusebauch, Ulrike; Campbell, David S; Moritz, Robert L; Price, Nathan D

    2014-10-01

    Glioblastoma multiforme is a highly invasive and aggressive brain tumor with an invariably poor prognosis. The overexpression of epidermal growth factor receptor (EGFR) is a primary influencer of invasion and proliferation in tumor cells and the constitutively active EGFRvIII mutant, found in 30-65% of Glioblastoma multiforme, confers more aggressive invasion. To better understand how EGFR contributes to tumor aggressiveness, we investigated the effect of EGFR on the secreted levels of 65 rationally selected proteins involved in invasion. We employed selected reaction monitoring targeted mass spectrometry using stable isotope labeled internal peptide standards to quantity proteins in the secretome from five GBM (U87) isogenic cell lines in which EGFR, EGFRvIII, and/or PTEN were expressed. Our results show that cell lines with EGFR overexpression and constitutive EGFRvIII expression differ remarkably in the expression profiles for both secreted and intracellular signaling proteins, and alterations in EGFR signaling result in reproducible changes in concentrations of secreted proteins. Furthermore, the EGFRvIII-expressing mutant cell line secretes the majority of the selected invasion-promoting proteins at higher levels than other cell lines tested. Additionally, the intracellular and extracellular protein measurements indicate elevated oxidative stress in the EGFRvIII-expressing cell line. In conclusion, the results of our study demonstrate that EGFR signaling has a significant effect on the levels of secreted invasion-promoting proteins, likely contributing to the aggressiveness of Glioblastoma multiforme. Further characterization of these proteins may provide candidates for new therapeutic strategies and targets as well as biomarkers for this aggressive disease. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

  20. [An analysis of 68 invasive lobular breast cancer cases in clinicopathological characteristics and the prognostic determinants].

    Science.gov (United States)

    Liu, Q; Xiang, H Y; Ye, J M; Xu, L; Zhang, H; Zhang, S; Duan, X N; Liu, Y H

    2018-02-01

    Objective: To study the clinicopathological characteristics and the prognostic determinants of the invasive lobular carcinoma breast cancer. Methods: This was a retrospective single-center study of invasive lobular breast cancer cases diagnosed from January 2008 to December 2014 at Peking University First Hospital Breast Disease Center. The study enrolled 68 invasive lobular breast cancer patients, which represented 3.64% (68/1 870) of total invasive breast cancer. The median age of all selected patients was 46 years ranging from 36 to 83 years. All patients were restaged based on the 8(th) edition of AJCC cancer staging system and follow-up data including disease-free survival (DFS) and overall survival (OS) were analyzed to explore the prognostic determinants. The 5-year OS and DFS were calculated using Kaplan-Meier method; the significance of correlations between clinicopathological features and prognostic factors was estimated using log-rank test. Results: There were significant differences in OS between patients with different anatomic stage, prognostic stage, lymph node metastasis, progesterone receptor (PR) expression, lymphvascular invasion and perineural invasion (χ(2:) 4.318 to 32.394, all P invasion (χ(2:) 4.347 to 27.369, all P invasion are the prognostic factors of invasive lobular breast cancer. Regard to invasive lobular breast cancer patients, clinicians should pay close attention to the differences between prognostic stage and anatomic stage.

  1. Total abdominal hysterectomy versus minimal-invasive hysterectomy: a systemic review and meta-analysis

    International Nuclear Information System (INIS)

    Aragon Palmero, Felipe Jorge; Exposito Exposito, Moises

    2011-01-01

    INTRODUCTION. At the present time three types of hysterectomies are used: the vaginal hysterectomy and the minimal-invasive hysterectomy (MIH). The objective of present research was to compare the MIH and the total abdominal hysterectomy (TAH) in women presenting with benign uterine diseases. METHODS. A systemic review was made and a meta-analysis from the following databases: MEDLINE, EBSCO HOST AND The Cochrane Central Register of Controlled Trials. Only the controlled and randomized studies were selected. The data of all studies were combined and also the relative risk (RR) with a 95% CI was used with the Mantel-Haenszel method as an effect measure for dichotomy variables. For the analysis of continuing variables the mean difference was used. In all the comparisons performed the results were obtained with the fix effect and randomized forms. RESULTS. A total of 53 transoperative complications were registered in the MIH hysterectomy versus 17 in the TAH group (RR: 1,78; 95% CI: 1,04-3.05). Postoperative complications evolved in a similar way in both groups without significant differences from the statistical point of view. The blood losses, the hospital stay and the patient's reincorporation to usual and work activities were lesser in the laparoscopy group; however, the operative time is higher when it is compared with TAH (mean difference: 37,36; 95% CI: 34,36-39,93). CONCLUSIONS. Both techniques have advantages and disadvantages. The indication of MIH must to be individualized according to the clinical situation of each patient and these not to be performed in those centers without a properly trained surgical staff and with experience in advanced minimal invasive surgery. (author)

  2. Molecular analysis and genetic diversity of Aedes albopictus (Diptera, Culicidae) from China.

    Science.gov (United States)

    Ruiling, Zhang; Peien, Leng; Xuejun, Wang; Zhong, Zhang

    2018-05-01

    Aedes albopictus is one of the most invasive species, which can carry Dengue virus, Yellow fever virus and more than twenty arboviruses. Based on mitochondrial gene cytochrome c oxidase I (COI) and samples collected from 17 populations, we investigated the molecular character and genetic diversity of Ae. albopictus from China. Altogether, 25 haplotypes were detected, including 10 shared haplotypes and 15 private haplotypes. H1 was the dominant haplotype, which is widely distributed in 13 populations. Tajima'D value of most populations was significantly negative, demonstrating that populations experienced rapid range expansion recently. Most haplotypes clustered together both in phylogenetic and median-joining network analysis without clear phylogeographic patterns. However, neutrality tests revealed shallow divergences among Hainan and Guangxi with other populations (0.15599 ≤ F ST ≤ 0.75858), which probably due to interrupted gene flow, caused by geographical isolations. In conclusion, Ae. albopictus populations showed low genetic diversity in China.

  3. Molecular analysis of Ku redox regulation

    Directory of Open Access Journals (Sweden)

    Shatilla Andrea

    2009-08-01

    Full Text Available Abstract Background DNA double-strand breaks (DSBs can occur in response to ionizing radiation (IR, radiomimetic agents and from endogenous DNA-damaging reactive oxygen metabolites. Unrepaired or improperly repaired DSBs are potentially the most lethal form of DNA damage and can result in chromosomal translocations and contribute to the development of cancer. The principal mechanism for the repair of DSBs in humans is non-homologous end-joining (NHEJ. Ku is a key member of the NHEJ pathway and plays an important role in the recognition step when it binds to free DNA termini. Ku then stimulates the assembly and activation of other NHEJ components. DNA binding of Ku is regulated by redox conditions and evidence from our laboratory has demonstrated that Ku undergoes structural changes when oxidized that results in a reduction in DNA binding activity. The C-terminal domain and cysteine 493 of Ku80 were investigated for their contribution to redox regulation of Ku. Results We effectively removed the C-terminal domain of Ku80 generating a truncation mutant and co-expressed this variant with wild type Ku70 in an insect cell system to create a Ku70/80ΔC heterodimer. We also generated two single amino acid variants of Cys493, replacing this amino acid with either an alanine (C493A or a serine (C493S, and over-expressed the variant proteins in SF9 insect cells in complex with wild type Ku70. Neither the truncation nor the amino acid substitutions alters protein expression or stability as determined by SDS-PAGE and Western blot analysis. We show that the C493 mutations do not alter the ability of Ku to bind duplex DNA in vitro under reduced conditions while truncation of the Ku80 C-terminus slightly reduced DNA binding affinity. Diamide oxidation of cysteines was shown to inhibit DNA binding similarly for both the wild-type and all variant proteins. Interestingly, differential DNA binding activity following re-reduction was observed for the Ku70/80

  4. Image-assisted non-invasive and dynamic biomechanical analysis of human joints

    International Nuclear Information System (INIS)

    Muhit, Abdullah A; Pickering, Mark R; Scarvell, Jennifer M; Ward, Tom; Smith, Paul N

    2013-01-01

    Kinematic analysis provides a strong link between musculoskeletal injuries, chronic joint conditions, treatment planning/monitoring and prosthesis design/outcome. However, fast and accurate 3D kinematic analysis still remains a challenge in order to translate this procedure into clinical scenarios. 3D computed tomography (CT) to 2D single-plane fluoroscopy registration is a promising non-invasive technology for biomechanical examination of human joints. Although this technique has proven to be very precise in terms of in-plane translation and rotation measurements, out-of-plane motion estimations have been a difficulty so far. Therefore, to enable this technology into clinical translation, precise and fast estimation of both in-plane and out-of-plane movements is crucial, which is the aim of this paper. Here, a fast and accurate 3D/2D registration technique is proposed to evaluate biomechanical/kinematic analysis. The proposed algorithm utilizes a new multi-modal similarity measure called ‘sum of conditional variances’, a coarse-to-fine Laplacian of Gaussian filtering approach for robust gradient-descent optimization and a novel technique for the analytic calculation of the required gradients for out-of-plane rotations. Computer simulations and in vitro experiments showed that the new approach was robust in terms of the capture range, required significantly less iterations to converge and achieved good registration and kinematic accuracy when compared to existing techniques and to the ‘gold-standard’ Roentgen stereo analysis. (paper)

  5. Phylogenetic analysis of emergent Streptococcus pneumoniae serotype 22F causing invasive pneumococcal disease using whole genome sequencing.

    Directory of Open Access Journals (Sweden)

    Walter H B Demczuk

    Full Text Available Since implementation of the 13-valent polyvalent conjugate vaccine (PCV13 in Canada during 2010, the proportion of PCV13 serotypes causing invasive pneumococcal disease (IPD has declined from 55% (n = 1492 in 2010 to 31% (n = 764 in 2014. A concurrent increase of non-PCV13 serotypes has occurred and 22F has become the most prevalent serotype in Canada increasing from 7% (n = 183 to 11% (n = 283. Core single nucleotide variant phylogenetic analysis was performed on 137 Streptococcus pneumoniae serotype 22F isolates collected across Canada from 2005-2015. Six phylogenetic lineages (n = 117 were identified among a serotype 22F/ST433 clonal complex (CC, including a recently expanding erythromycin-resistant clone. Erythromycin-resistance was observed in 25 isolates possessing ermB, mef or a 23S rRNA A2061G point mutation; 2 penicillin-resistant isolates had recombinant pbp1a, pbp2a and/or pbp2x; 3 tetracycline-resistant isolates contained tetM; and 1 isolate was multidrug-resistant. Virulence factor analysis indicated a high level of homogeneity among the 22F/ST433 clonal complex strains. A group of 6 phylogenetic outlier strains had differing MLST, antimicrobial resistance and molecular profiles suggestive of capsule switching events. While capsule switch events among S. pneumoniae serotype 22F has been observed, increasing prevalence of S. pneumoniae serotype 22F can be attributed to an evolving homogenous clone expanding nationally through local transmission events.

  6. RNA-seq analysis of early enteromyxosis in turbot (Scophthalmus maximus): new insights into parasite invasion and immune evasion strategies.

    Science.gov (United States)

    Ronza, Paolo; Robledo, Diego; Bermúdez, Roberto; Losada, Ana Paula; Pardo, Belén G; Sitjà-Bobadilla, Ariadna; Quiroga, María Isabel; Martínez, Paulino

    2016-07-01

    Enteromyxum scophthalmi, an intestinal myxozoan parasite, is the causative agent of a threatening disease for turbot (Scophthalmus maximus, L.) aquaculture. The colonisation of the digestive tract by this parasite leads to a cachectic syndrome associated with high morbidity and mortality rates. This myxosporidiosis has a long pre-patent period and the first detectable clinical and histopathological changes are subtle. The pathogenic mechanisms acting in the early stages of infection are still far from being fully understood. Further information on the host-parasite interaction is needed to assist in finding efficient preventive and therapeutic measures. Here, a RNA-seq-based transcriptome analysis of head kidney, spleen and pyloric caeca from experimentally-infected and control turbot was performed. Only infected fish with early signs of infection, determined by histopathology and immunohistochemical detection of E. scophthalmi, were selected. The RNA-seq analysis revealed, as expected, less intense transcriptomic changes than those previously found during later stages of the disease. Several genes involved in IFN-related pathways were up-regulated in the three organs, suggesting that the IFN-mediated immune response plays a main role in this phase of the disease. Interestingly, an opposite expression pattern had been found in a previous study on severely infected turbot. In addition, possible strategies for immune system evasion were suggested by the down-regulation of different genes encoding complement components and acute phase proteins. At the site of infection (pyloric caeca), modulation of genes related to different structural proteins was detected and the expression profile indicated the inhibition of cell proliferation and differentiation. These transcriptomic changes provide indications regarding the mechanisms of parasite attachment to and invasion of the host. The current results contribute to a better knowledge of the events that characterise the early

  7. Analysis of the normal optical, Michel and molecular potentials on ...

    Indian Academy of Sciences (India)

    6. — journal of. June 2016 physics pp. 1275–1286. Analysis of the normal ... the levels are obtained for the three optical potentials to estimate the quality ... The experimental angular distribution data for the 40Ca(6Li, d)44Ti reaction .... analysed using the normal optical, Michel and molecular potentials within the framework.

  8. Molecular characterization and expression analysis of fat mass and ...

    Indian Academy of Sciences (India)

    Keywords. fat mass and obesity-associated gene (FTO); rabbit; mRNA expression patterns; sequence analysis; Oryctolagus cuniculus. ... In this work, the molecular characterization and expression features of rabbit (Oryctolagus cuniculus) FTO cDNA were analysed. The rabbit FTO cDNA with a size of 2158 bp was cloned, ...

  9. Fragrance analysis using molecular and biochemical methods in ...

    African Journals Online (AJOL)

    For molecular and biochemical analysis of aroma, a mapping population comprising 208 recombinant inbred lines (RILs) derived from a diverse cross between CSR10 and Taraori Basmati through Single seed descent (SSD) method was used. RILs are among the best mapping populations, which provide a novel material ...

  10. A Molecular Iodine Spectral Data Set for Rovibronic Analysis

    Science.gov (United States)

    Williamson, J. Charles; Kuntzleman, Thomas S.; Kafader, Rachael A.

    2013-01-01

    A data set of 7,381 molecular iodine vapor rovibronic transitions between the X and B electronic states has been prepared for an advanced undergraduate spectroscopic analysis project. Students apply standard theoretical techniques to these data and determine the values of three X-state constants (image omitted) and four B-state constants (image…

  11. Crime and Punishment Analysis: Land Invasion "Para-institutions" in Cali

    Directory of Open Access Journals (Sweden)

    Enrique Javier Burbano Valencia

    2014-06-01

    Full Text Available Based on the crime economics of Becker (1968 and Ehrlich (1973, including the impact of the migratory flow, this paper studies the reasons why some individuals choose to strategically, rationally, and contingently become involved in illegal land invasion "para-institutions" in Cali since the 1950s. This will be done by modeling the efficiency of justice in order to discourage invaders through simulations of sentences and arrest likelihood and deterrent punishment under three "para-institutions": invasive dynasty, organized invasion and contingent invasion (endogenous migratory flow. These simulations will be anchored to calibrated actual parameters of the relevant population. This will allow the calibration of the line of indifference (division among individuals with invasive (and incentives to illegality and non-invasive behaviors. Finally, a policy proposal will be devised to help correct the inefficiencies found in the sanctioning mechanisms, if applicable.

  12. Importance and pitfalls of molecular analysis to parasite epidemiology.

    Science.gov (United States)

    Constantine, Clare C

    2003-08-01

    Molecular tools are increasingly being used to address questions about parasite epidemiology. Parasites represent a diverse group and they might not fit traditional population genetic models. Testing hypotheses depends equally on correct sampling, appropriate tool and/or marker choice, appropriate analysis and careful interpretation. All methods of analysis make assumptions which, if violated, make the results invalid. Some guidelines to avoid common pitfalls are offered here.

  13. The lipid-reactive oxygen species phenotype of breast cancer. Raman spectroscopy and mapping, PCA and PLSDA for invasive ductal carcinoma and invasive lobular carcinoma. Molecular tumorigenic mechanisms beyond Warburg effect.

    Science.gov (United States)

    Surmacki, Jakub; Brozek-Pluska, Beata; Kordek, Radzislaw; Abramczyk, Halina

    2015-04-07

    Vibrational signatures of human breast tissue (invasive ductal carcinoma and invasive lobular carcinoma) were used to identify, characterize and discriminate structures in normal (noncancerous) and cancerous tissues by confocal Raman imaging, Raman spectroscopy and IR spectroscopy. The most important differences between normal and cancerous tissues were found in regions characteristic for vibrations of carotenoids, fatty acids, proteins, and interfacial water. Particular attention was paid to the role played by unsaturated fatty acids and their derivatives. K-means clustering and basis analysis followed by PCA and PLSDA is employed to analyze Raman spectroscopic maps of human breast tissue and for a statistical analysis of the samples (82 patients, 164 samples). Raman maps successfully identify regions of carotenoids, fatty acids, and proteins. The intensities, frequencies and profiles of the average Raman spectra differentiate the biochemical composition of normal and cancerous tissues. The paper demonstrates that Raman imaging has reached a clinically relevant level in regard to breast cancer diagnosis applications. The sensitivity and specificity obtained directly from PLSLD and cross validation are equal to 90.5% and 84.8% for calibration and 84.7% and 71.9% for cross-validation respectively.

  14. Conformational analysis of oligosaccharides and polysaccharides using molecular dynamics simulations.

    Science.gov (United States)

    Frank, Martin

    2015-01-01

    Complex carbohydrates usually have a large number of rotatable bonds and consequently a large number of theoretically possible conformations can be generated (combinatorial explosion). The application of systematic search methods for conformational analysis of carbohydrates is therefore limited to disaccharides and trisaccharides in a routine analysis. An alternative approach is to use Monte-Carlo methods or (high-temperature) molecular dynamics (MD) simulations to explore the conformational space of complex carbohydrates. This chapter describes how to use MD simulation data to perform a conformational analysis (conformational maps, hydrogen bonds) of oligosaccharides and how to build realistic 3D structures of large polysaccharides using Conformational Analysis Tools (CAT).

  15. Non-invasive quality evaluation of confluent cells by image-based orientation heterogeneity analysis.

    Science.gov (United States)

    Sasaki, Kei; Sasaki, Hiroto; Takahashi, Atsuki; Kang, Siu; Yuasa, Tetsuya; Kato, Ryuji

    2016-02-01

    In recent years, cell and tissue therapy in regenerative medicine have advanced rapidly towards commercialization. However, conventional invasive cell quality assessment is incompatible with direct evaluation of the cells produced for such therapies, especially in the case of regenerative medicine products. Our group has demonstrated the potential of quantitative assessment of cell quality, using information obtained from cell images, for non-invasive real-time evaluation of regenerative medicine products. However, image of cells in the confluent state are often difficult to evaluate, because accurate recognition of cells is technically difficult and the morphological features of confluent cells are non-characteristic. To overcome these challenges, we developed a new image-processing algorithm, heterogeneity of orientation (H-Orient) processing, to describe the heterogeneous density of cells in the confluent state. In this algorithm, we introduced a Hessian calculation that converts pixel intensity data to orientation data and a statistical profiling calculation that evaluates the heterogeneity of orientations within an image, generating novel parameters that yield a quantitative profile of an image. Using such parameters, we tested the algorithm's performance in discriminating different qualities of cellular images with three types of clinically important cell quality check (QC) models: remaining lifespan check (QC1), manipulation error check (QC2), and differentiation potential check (QC3). Our results show that our orientation analysis algorithm could predict with high accuracy the outcomes of all types of cellular quality checks (>84% average accuracy with cross-validation). Copyright © 2015 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  16. Dispersal of invasive forest insects via recreational firewood: a quantitative analysis.

    Science.gov (United States)

    Koch, Frank H; Yemshanov, Denys; Magarey, Roger D; Smith, William D

    2012-04-01

    Recreational travel is a recognized vector for the spread of invasive species in North America. However, there has been little quantitative analysis of the risks posed by such travel and the associated transport of firewood. In this study, we analyzed the risk of forest insect spread with firewood and estimated related dispersal parameters for application in geographically explicit invasion models. Our primary data source was the U.S. National Recreation Reservation Service database, which records camper reservations at > 2,500 locations nationwide. For > 7 million individual reservations made between 2004 and 2009 (including visits from Canada), we calculated the distance between visitor home address and campground location. We constructed an empirical dispersal kernel (i.e., the probability distribution of the travel distances) from these "origin-destination" data, and then fitted the data with various theoretical distributions. We found the data to be strongly leptokurtic (fat-tailed) and fairly well fit by the unbounded Johnson and lognormal distributions. Most campers ( approximately 53%) traveled 500 km (and as far as 5,500 km). Additionally, we examined the impact of geographic region, specific destinations (major national parks), and specific origin locations (major cities) on the shape of the dispersal kernel, and found that mixture distributions (i.e., theoretical distribution functions composed of multiple univariate distributions) may fit better in some circumstances. Although only a limited amount of all transported firewood is likely to be infested by forest insects, this still represents a considerable increase in dispersal potential beyond the insects' natural spread capabilities.

  17. MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.

    Science.gov (United States)

    Kumar, Sudhir; Stecher, Glen; Li, Michael; Knyaz, Christina; Tamura, Koichiro

    2018-06-01

    The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. Mega X is available in two interfaces (graphical and command line) and can be downloaded from www.megasoftware.net free of charge.

  18. Non-invasive baroreflex sensitivity assessment using wavelet transfer function-based time–frequency analysis

    International Nuclear Information System (INIS)

    Keissar, K; Gilad, O; Maestri, R; Pinna, G D; La Rovere, M T

    2010-01-01

    A novel approach for the estimation of baroreflex sensitivity (BRS) is introduced based on time–frequency analysis of the transfer function (TF). The TF method (TF-BRS) is a well-established non-invasive technique which assumes stationarity. This condition is difficult to meet, especially in cardiac patients. In this study, the classical TF was replaced with a wavelet transfer function (WTF) and the classical coherence was replaced with wavelet transform coherence (WTC), adding the time domain as an additional degree of freedom with dynamic error estimation. Error analysis and comparison between WTF-BRS and TF-BRS were performed using simulated signals with known transfer function and added noise. Similar comparisons were performed for ECG and blood pressure signals, in the supine position, of 19 normal subjects, 44 patients with a history of previous myocardial infarction (MI) and 45 patients with chronic heart failure. This yielded an excellent linear association (R > 0.94, p < 0.001) for time-averaged WTF-BRS, validating the new method as consistent with a known method. The additional advantage of dynamic analysis of coherence and TF estimates was illustrated in two physiological examples of supine rest and change of posture showing the evolution of BRS synchronized with its error estimations and sympathovagal balance

  19. Rapid assessment of populations trends of invasive species: Singular Spectrum Analysis (SSA

    Directory of Open Access Journals (Sweden)

    DANA, ED

    2010-01-01

    Full Text Available Singular Spectrum Analysis (SSA is a powerful analytical approach for biodi-versity management. Its main advan-tages are due to its intuitive processing and visualization, since mathematical workflow is conceptually similar to the widely accepted Principal Components Analysis. Detailed analyses of popula-tion trends with mathematical tools are often difficult to achieve for managers by a number of reasons (large numbers or areas monitored, large number of species, insufficient statistics skills, strong knowledge level in demographic analyses, etc.. SSA has been used since the 1970’s in signal processing to clarify signal vs. noisy information, but it has also been used in climate change analy-sis and other developmental areas. Be-sides, SSA is a rapid-learning method for technicians and managers with medium level of mathematical knowledge. Free software in Unix environment is avail-able. Unfortunately, no free and friendly software is available for Win-dows SO. Although R package may offer solutions for really advanced users, it does not fit real work situations for managers of biological invasions. Cater-pillar (Gistat Group, Ltd is by now, the best option found by the author in terms of price, facility for results inter-pretation and time consumed in learn-ing. The main disadvantage is the poor content of tutorial files

  20. Antifungal treatment for invasive Candida infections: a mixed treatment comparison meta-analysis

    Directory of Open Access Journals (Sweden)

    Nachega Jean B

    2009-06-01

    Full Text Available Objectives Invasive fungal infections are a major cause of mortality among patients at risk. Treatment guidelines vary on optimal treatment strategies. We aimed to determine the effects of different antifungal therapies on global response rates, mortality and safety. Methods We searched independently and in duplicate 10 electronic databases from inception to May 2009. We selected any randomized trial assessing established antifungal therapies for confirmed cases of invasive candidiasis among predominantly adult populations. We performed a meta-analysis and then conducted a Bayesian mixed treatment comparison to differentiate treatment effectiveness. Sensitivity analyses included dosage forms of amphotericin B and fluconazole compared to other azoles. Results Our analysis included 11 studies enrolling a total of 965 patients. For our primary analysis of global response rates, we pooled 7 trials comparing azoles to amphotericin B, Relative Risk [RR] 0.87 (95% Confidence Interval [CI], 0.78–0.96, P = 0.007, I2 = 43%, P = 0.09. We also pooled 2 trials of echinocandins versus amphotericin B and found a pooled RR of 1.10 (95% CI, 0.99–1.23, P = 0.08. One study compared anidulafungin to fluconazole and yielded a RR of 1.26 (95% CI, 1.06–1.51 in favor of anidulafungin. We pooled 7 trials assessing azoles versus amphotericin B for all-cause mortality, resulting in a pooled RR of 0.88 (95% CI, 0.74–1.05, P = 0.17, I2 = 0%, P = 0.96. Echinocandins versus amphotericin B (2 trials for all-cause mortality resulted in a pooled RR of 1.01 (95% CI, 0.84–1.20, P = 0.93. Anidulafungin versus fluconazole resulted in a RR of 0.73 (95% CI, 0.48–1.10, P = 0.34. Our mixed treatment comparison analysis found similar within-class effects across all interventions. Adverse event profiles differed, with amphotericin B exhibiting larger adverse event effects. Conclusion Treatment options appear to offer preferential effects on response rates and mortality. When

  1. Transcriptomic and Proteomic Data Integration and Two-Dimensional Molecular Maps with Regulatory and Functional Linkages: Application to Cell Proliferation and Invasion Networks in Glioblastoma.

    Science.gov (United States)

    Gupta, Manoj Kumar; Jayaram, Savita; Reddy, Divijendra Natha; Polisetty, Ravindra Varma; Sirdeshmukh, Ravi

    2015-12-04

    Glioblastoma multiforme (GBM), the most aggressive primary brain tumor, is characterized by high rates of cell proliferation, migration, and invasion. New therapeutic strategies and targets are being continuously explored with the hope for better outcome. By overlaying transcriptomic and proteomic data from GBM clinical tissues, we identified 317 differentially expressed proteins to be concordant with the messenger RNAs (mRNAs). We used these entities to generate integrated regulatory information at the level of microRNAs (miRNAs) and their mRNA and protein targets using prediction programs or experimentally verified miRNA target mode in the miRWalk database. We observed 60% or even more of the miRNA-target pairs to be consistent with experimentally observed inverse expression of these molecules in GBM. The integrated view of these regulatory cascades in the contexts of cell proliferation and invasion networks revealed two-dimensional molecular interactions with regulatory and functional linkages (miRNAs and their mRNA-protein targets in one dimension; multiple miRNAs associated in a functional network in the second dimension). A total of 28 of the 35 differentially expressed concordant mRNA-protein entities represented in the proliferation network, and 51 of the 59 such entities represented in the invasion network, mapped to altered miRNAs from GBM and conformed to an inverse relationship in their expression. We believe the two-dimensional maps of gene expression changes enhance the strength of the discovery datasets derived from omics-based studies for their applications in GBM as well as tumors in general.

  2. Comparison of intraoperative frozen section analysis for sentinel lymph node biopsy during breast cancer surgery for invasive lobular carcinoma and invasive ductal carcinoma

    Directory of Open Access Journals (Sweden)

    Povoski Stephen P

    2009-03-01

    Full Text Available Abstract Background Sentinel lymph node (SLN biopsy is the standard of care for the surgical assessment of the axilla during breast cancer surgery. However, the diagnostic accuracy of intraoperative frozen section analysis for confirming metastatic involvement of SLNs in cases of invasive lobular carcinoma (ILC versus that of invasive ductal carcinoma (IDC has generated controversy secondary to a frequently low-grade cytologic appearance and an often discohesive pattern displayed by metastatic lymph nodes in ILC. In the current report, we present a comparison of intraoperative frozen section analysis for confirming the presence of metastatic disease within SLNs during breast cancer surgery for ILC and IDC. Methods We evaluated the results of 131 consecutive cases of ILC from 1997 to 2008 and 133 cases of IDC (selected by a random sequence generator program from amongst 1163 consecutive cases of IDC from the same time period. All cases had at least one SLN that had both intraoperative frozen section analysis and confirmatory permanent section analysis performed. Results No statistically significant difference was found in the sensitivity (67% vs. 75%, P = 0.385, specificity (100% vs. 100%, accuracy (86% vs. 92%, P = 0.172, false negative rate (33% vs. 25%, P = 0.385, negative predictive value (81% vs. 89%, P = 0.158, and positive predictive value (100% vs. 100% for frozen section analysis for confirming the presence of metastatic disease within SLNs during breast cancer surgery for ILC and IDC. Conclusion Since there was no statistically significant difference in sensitivity, specificity, accuracy, false negative rate, negative predictive value, and positive predictive value between frozen section analysis of SLNs for patients with ILC and IDC, the clinical accuracy of confirming metastatic involvement of SLNs on frozen section analysis for ILC should not be considered inferior to the clinical accuracy for IDC. Therefore, frozen section analysis

  3. Parietal pleural invasion/adhesion of subpleural lung cancer: Quantitative 4-dimensional CT analysis using dynamic-ventilatory scanning

    Energy Technology Data Exchange (ETDEWEB)

    Sakuma, Kotaro, E-mail: ksakuma@ohara-hp.or.jp [Department of Radiology, Ohara General Hospital, 6-11 Omachi, Fukushima City, Fukushima 960-8611 (Japan); Department of Radiology and Nuclear Medicine, Fukushima Medical University, 1 Hikariga-oka, Fukushima City, Fukushima 960-1295 (Japan); Yamashiro, Tsuneo, E-mail: clatsune@yahoo.co.jp [Department of Radiology, University of the Ryukyus, 207 Uehara, Nishihara, Okinawa 903-0215 (Japan); Moriya, Hiroshi, E-mail: hrshmoriya@gmail.com [Department of Radiology, Ohara General Hospital, 6-11 Omachi, Fukushima City, Fukushima 960-8611 (Japan); Murayama, Sadayuki, E-mail: sadayuki@med.u-ryukyu.ac.jp [Department of Radiology, University of the Ryukyus, 207 Uehara, Nishihara, Okinawa 903-0215 (Japan); Ito, Hiroshi, E-mail: h-ito@fmu.ac.jp [Department of Radiology and Nuclear Medicine, Fukushima Medical University, 1 Hikariga-oka, Fukushima City, Fukushima 960-1295 (Japan)

    2017-02-15

    Highlights: • 4DCT can be used for assessment of pleural invasion/adhesion by lung cancer. • Quantitative 4DCT indices of lung cancer and adjacent structures are described. • An automatic analysis of pleural invasion/adhesion would be developed in the future. - Abstract: Purpose: Using 4-dimensional dynamic-ventilatory scanning by a 320-row computed tomography (CT) scanner, we performed a quantitative assessment of parietal pleural invasion and adhesion by peripheral (subpleural) lung cancers. Methods: Sixteen patients with subpleural lung cancer underwent dynamic-ventilation CT during free breathing. Neither parietal pleural invasion nor adhesion was subsequently confirmed by surgery in 10 patients, whereas the other 6 patients were judged to have parietal pleural invasion or adhesion. Using research software, we tracked the movements of the cancer and of an adjacent structure such as the rib or aorta, and converted the data to 3-dimensional loci. The following quantitative indices were compared by the Mann-Whitney test: cross-correlation coefficient between time curves for the distances moved from the inspiratory frame by the cancer and the adjacent structure, the ratio of the total movement distances (cancer/adjacent structure), and the cosine similarities between the inspiratory and expiratory vectors (from the cancer to the adjacent structure) and between vectors of the cancer and of the adjacent structure (from inspiratory to expiratory frames). Results: Generally, the movements of the loci of the lung cancer and the adjacent structure were similar in patients with parietal pleural invasion/adhesion, while they were independent in patients without. There were significant differences in all the parameters between the two patient groups (cross-correlation coefficient and the movement distance ratio, P < 0.01; cosine similarities, P < 0.05). Conclusion: These observations suggest that quantitative indices by dynamic-ventilation CT can be utilized as a

  4. A bioeconomic analysis of an emerald ash borer invasion of an urban forest with multiple jurisdictions

    Science.gov (United States)

    Kent F. Kovacs; Robert G. Haight; Rodrigo J. Mercader; Deborah G. McCullough

    2014-01-01

    Bio-invasions occur in management mosaics where local control affects spread and damage across political boundaries. We address two obstacles to local implementation of optimal regional control of a bio-invasion that damages public and private resources across jurisdictions: lack of local funds to protect the public resource and lack of access to protect the private...

  5. Proteomic analysis of human skin treated with larval schistosome peptidases reveals distinct invasion strategies among species of blood flukes.

    Directory of Open Access Journals (Sweden)

    Jessica Ingram

    2011-09-01

    Full Text Available Skin invasion is the initial step in infection of the human host by schistosome blood flukes. Schistosome larvae have the remarkable ability to overcome the physical and biochemical barriers present in skin in the absence of any mechanical trauma. While a serine peptidase with activity against insoluble elastin appears to be essential for this process in one species of schistosomes, Schistosoma mansoni, it is unknown whether other schistosome species use the same peptidase to facilitate entry into their hosts.Recent genome sequencing projects, together with a number of biochemical studies, identified alternative peptidases that Schistosoma japonicum or Trichobilharzia regenti could use to facilitate migration through skin. In this study, we used comparative proteomic analysis of human skin treated with purified cercarial elastase, the known invasive peptidase of S. mansoni, or S. mansoni cathespin B2, a close homolog of the putative invasive peptidase of S. japonicum, to identify substrates of either peptidase. Select skin proteins were then confirmed as substrates by in vitro digestion assays.This study demonstrates that an S. mansoni ortholog of the candidate invasive peptidase of S. japonicum and T. regenti, cathepsin B2, is capable of efficiently cleaving many of the same host skin substrates as the invasive serine peptidase of S. mansoni, cercarial elastase. At the same time, identification of unique substrates and the broader species specificity of cathepsin B2 suggest that the cercarial elastase gene family amplified as an adaptation of schistosomes to human hosts.

  6. Automated image analysis of cyclin D1 protein expression in invasive lobular breast carcinoma provides independent prognostic information.

    Science.gov (United States)

    Tobin, Nicholas P; Lundgren, Katja L; Conway, Catherine; Anagnostaki, Lola; Costello, Sean; Landberg, Göran

    2012-11-01

    The emergence of automated image analysis algorithms has aided the enumeration, quantification, and immunohistochemical analyses of tumor cells in both whole section and tissue microarray samples. To date, the focus of such algorithms in the breast cancer setting has been on traditional markers in the common invasive ductal carcinoma subtype. Here, we aimed to optimize and validate an automated analysis of the cell cycle regulator cyclin D1 in a large collection of invasive lobular carcinoma and relate its expression to clinicopathologic data. The image analysis algorithm was trained to optimally match manual scoring of cyclin D1 protein expression in a subset of invasive lobular carcinoma tissue microarray cores. The algorithm was capable of distinguishing cyclin D1-positive cells and illustrated high correlation with traditional manual scoring (κ=0.63). It was then applied to our entire cohort of 483 patients, with subsequent statistical comparisons to clinical data. We found no correlation between cyclin D1 expression and tumor size, grade, and lymph node status. However, overexpression of the protein was associated with reduced recurrence-free survival (P=.029), as was positive nodal status (Pinvasive lobular carcinoma. Finally, high cyclin D1 expression was associated with increased hazard ratio in multivariate analysis (hazard ratio, 1.75; 95% confidence interval, 1.05-2.89). In conclusion, we describe an image analysis algorithm capable of reliably analyzing cyclin D1 staining in invasive lobular carcinoma and have linked overexpression of the protein to increased recurrence risk. Our findings support the use of cyclin D1 as a clinically informative biomarker for invasive lobular breast cancer. Copyright © 2012 Elsevier Inc. All rights reserved.

  7. Molecular Identification of Zoonotic Tissue-Invasive Tapeworm Larvae Other than Taenia solium in Suspected Human Cysticercosis Cases.

    Science.gov (United States)

    Tappe, Dennis; Berkholz, Jörg; Mahlke, Uwe; Lobeck, Hartmut; Nagel, Thomas; Haeupler, Alexandra; Muntau, Birgit; Racz, Paul; Poppert, Sven

    2016-01-01

    Rarely, zoonotic Taenia species other than Taenia solium cause human cysticercosis. The larval stages are morphologically often indistinguishable. We therefore investigated 12 samples of suspected human cysticercosis cases at the molecular level and surprisingly identified one Taenia crassiceps and one Taenia serialis (coenurosis) infection, which were caused by tapeworm larvae normally infecting rodents and sheep via eggs released from foxes and dogs. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  8. [Histopathological Diagnosis of Invasive Fungal Infections in Formalin-Fixed and Paraffin-Embedded Tissues in Conjunction with Molecular Methods].

    Science.gov (United States)

    Shinozaki, Minoru; Tochigi, Naobumi; Sadamoto, Sota; Yamagata Murayama, Somay; Wakayama, Megumi; Nemoto, Tetsuo

    2018-01-01

    The main objective of this study was to evaluate the relationship between histopathology, polymerase chain reaction (PCR), and in situ hybridization (ISH) for the identification of causative fungi in formalin-fixed and paraffin-embedded (FFPE) tissue specimens. Since pathogenic fungi in tissue specimens can be difficult to identify morphologically, PCR and ISH have been usually employed as auxiliary procedures. However, little comparison has been made on the sensitivity and specificity of PCR and ISH using FFPE specimens. Therefore, to compare and clarify the reproducibility and usefulness of PCR and ISH as auxiliary procedures for histological identification, we performed histopathological review, PCR assays, and ISH to identify pathogenic fungi in 59 FFPE tissue specimens obtained from 49 autopsies. The following are the main findings for this retrospective review: i) even for cases classified as "mold not otherwise specified" (MNOS), two cases could be identified as Aspergillus species by molecular methods; ii) all cases classified as non-zygomycetes mold (NZM) were Aspergillus species and were not identified by molecular methods as other fungi; iii) all 3 cases classified as zygomycetes mold (ZM) could be identified by molecular methods as Mucorales; iv) except for 1 case identified by molecular methods as Trichosporon spp., 5 cases were originally identified as dimorphic yeast (DY). As a measure of nucleic acid integrity, PCR and ISH successfully detected human and fungal nucleic acids in approximately 60% of the specimens. Detection of Aspergillus DNA by nested PCR assay and by ISH against the A. fumigatus ALP gene were similarly sensitive and significant (pmolecular methods such as ISH and PCR on FFPE specimens with pathological diagnosis should improve diagnostic accuracy of fungal infection.

  9. TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics

    Directory of Open Access Journals (Sweden)

    von Haeseler Arndt

    2004-06-01

    Full Text Available Abstract Background Most analysis programs for inferring molecular phylogenies are difficult to use, in particular for researchers with little programming experience. Results TREEFINDER is an easy-to-use integrative platform-independent analysis environment for molecular phylogenetics. In this paper the main features of TREEFINDER (version of April 2004 are described. TREEFINDER is written in ANSI C and Java and implements powerful statistical approaches for inferring gene tree and related analyzes. In addition, it provides a user-friendly graphical interface and a phylogenetic programming language. Conclusions TREEFINDER is a versatile framework for analyzing phylogenetic data across different platforms that is suited both for exploratory as well as advanced studies.

  10. Accommodating error analysis in comparison and clustering of molecular fingerprints.

    OpenAIRE

    Salamon, H.; Segal, M. R.; Ponce de Leon, A.; Small, P. M.

    1998-01-01

    Molecular epidemiologic studies of infectious diseases rely on pathogen genotype comparisons, which usually yield patterns comprising sets of DNA fragments (DNA fingerprints). We use a highly developed genotyping system, IS6110-based restriction fragment length polymorphism analysis of Mycobacterium tuberculosis, to develop a computational method that automates comparison of large numbers of fingerprints. Because error in fragment length measurements is proportional to fragment length and is ...

  11. Association of secondhand smoke exposure with pediatric invasive bacterial disease and bacterial carriage: a systematic review and meta-analysis.

    Directory of Open Access Journals (Sweden)

    Chien-Chang Lee

    2010-12-01

    Full Text Available A number of epidemiologic studies have observed an association between secondhand smoke (SHS exposure and pediatric invasive bacterial disease (IBD but the evidence has not been systematically reviewed. We carried out a systematic review and meta-analysis of SHS exposure and two outcomes, IBD and pharyngeal carriage of bacteria, for Neisseria meningitidis (N. meningitidis, Haemophilus influenzae type B (Hib, and Streptococcus pneumoniae (S. pneumoniae.Two independent reviewers searched Medline, EMBASE, and selected other databases, and screened articles for inclusion and exclusion criteria. We identified 30 case-control studies on SHS and IBD, and 12 cross-sectional studies on SHS and bacterial carriage. Weighted summary odd ratios (ORs were calculated for each outcome and for studies with specific design and quality characteristics. Tests for heterogeneity and publication bias were performed. Compared with those unexposed to SHS, summary OR for SHS exposure was 2.02 (95% confidence interval [CI] 1.52-2.69 for invasive meningococcal disease, 1.21 (95% CI 0.69-2.14 for invasive pneumococcal disease, and 1.22 (95% CI 0.93-1.62 for invasive Hib disease. For pharyngeal carriage, summary OR was 1.68 (95% CI, 1.19-2.36 for N. meningitidis, 1.66 (95% CI 1.33-2.07 for S. pneumoniae, and 0.96 (95% CI 0.48-1.95 for Hib. The association between SHS exposure and invasive meningococcal and Hib diseases was consistent regardless of outcome definitions, age groups, study designs, and publication year. The effect estimates were larger in studies among children younger than 6 years of age for all three IBDs, and in studies with the more rigorous laboratory-confirmed diagnosis for invasive meningococcal disease (summary OR 3.24; 95% CI 1.72-6.13.When considered together with evidence from direct smoking and biological mechanisms, our systematic review and meta-analysis indicates that SHS exposure may be associated with invasive meningococcal disease. The

  12. New concepts in molecular imaging: non-invasive MRI spotting of proteolysis using an Overhauser effect switch.

    Directory of Open Access Journals (Sweden)

    Philippe Mellet

    Full Text Available Proteolysis, involved in many processes in living organisms, is tightly regulated in space and time under physiological conditions. However deregulation can occur with local persistent proteolytic activities, e.g. in inflammation, cystic fibrosis, tumors, or pancreatitis. Furthermore, little is known about the role of many proteases, hence there is a need of new imaging methods to visualize specifically normal or disease-related proteolysis in intact bodies.In this paper, a new concept for non invasive proteolysis imaging is proposed. Overhauser-enhanced Magnetic Resonance Imaging (OMRI at 0.2 Tesla was used to monitor the enzymatic hydrolysis of a nitroxide-labeled protein. In vitro, image intensity switched from 1 to 25 upon proteolysis due to the associated decrease in the motional correlation time of the substrate. The OMRI experimental device used in this study is consistent with protease imaging in mice at 0.2 T without significant heating. Simulations show that this enzymatic-driven OMRI signal switch can be obtained at lower frequencies suitable for larger animals or humans.The method is highly sensitive and makes possible proteolysis imaging in three dimensions with a good spatial resolution. Any protease could be targeted specifically through the use of taylor-made cleavable macromolecules. At short term OMRI of proteolysis may be applied to basic research as well as to evaluate therapeutic treatments in small animal models of experimental diseases.

  13. Fouling development in direct contact membrane distillation: Non-invasive monitoring and destructive analysis

    KAUST Repository

    Fortunato, Luca

    2017-12-26

    Fouling development in direct contact membrane distillation (DCMD) for seawater desalination was evaluated combining in-situ monitoring performed using optical coherence tomography (OCT) together with destructive techniques. The non-invasive monitoring with OCT provided a better understanding of the fouling mechanism by giving an appropriate sampling timing for the membrane autopsy. The on-line monitoring system allowed linking the flux trend with the structure of fouling deposited on the membrane surface. The water vapor flux trend was divided in three phases based on the deposition and formation of different foulants over time. The initial flux decline was due to the deposition of a 50–70 nm porous fouling layer consisting of a mixture of organic compounds and salts. Liquid chromatography with organic carbon detection (LC-OCD) analysis revealed the abundance of biopolymer in the fouling layer formed at the initial phase. In the second phase, formation of carbonate crystals on the membrane surface was observed but did not affect the flux significantly. In the last phase, the water vapor flux dropped to almost zero due to the deposition of a dense thick layer of sulfate crystals on the membrane surface.

  14. A Cost Analysis of Preoperative Breast MRI Use for Patients with Invasive Lobular Cancer.

    Science.gov (United States)

    Bedrosian, Isabelle; Xing, Yan; Abdel Rahman, Shereen; Allen, Lisa; Le-Petross, Huong; Whitman, Gary J; Meric-Bernstam, Funda; Hunt, Kelly K; Babiera, Gildy V; Cormier, Janice N

    2016-01-01

    Whereas the impact of magnetic resonance imaging (MRI) of the breast on the surgical management of breast cancer patients is well documented, less is known about its effect on health care costs. This study aimed to evaluate whether MRI use for women with invasive lobular carcinoma (ILC) significantly changes the cost of care. Patients with ILC were recruited to a prospective registry study of breast MRI. Women who met the same inclusion criteria but had not undergone breast MRI were retrospectively identified for comparison. A micro-costing analysis using institutional billing records was conducted. Nonparametric bootstrapping was used to compare the unadjusted cost differences between the patients receiving MRI and those receiving no MRI. Of the patients in this study, 51 had preoperative MRI, and 60 did not. Method of diagnostic biopsy, disease stage, oncologic procedure, and rates of contralateral prophylactic mastectomy were similar between the two groups. The patients in the MRI group were younger (median age 55 vs. 64 years; p = 0.01) and more likely to undergo reconstruction (45.1 vs. 25 %; p = 0.03). The median costs of care were significantly higher in the MRI group ($24,781 vs. $18,921; p 1; p < 0.01), and use of reconstruction (p < 0.01). Preoperative breast MRI increases the median total cost of care per patient. However, the contribution to the overall cost of care is modest compared with the cost of other interventions.

  15. Psychomotor skills assessment by motion analysis in minimally invasive surgery on an animal organ.

    Science.gov (United States)

    Hofstad, Erlend Fagertun; Våpenstad, Cecilie; Bø, Lars Eirik; Langø, Thomas; Kuhry, Esther; Mårvik, Ronald

    2017-08-01

    A high level of psychomotor skills is required to perform minimally invasive surgery (MIS) safely. To be able to measure these skills is important in the assessment of surgeons, as it enables constructive feedback during training. The aim of this study was to test the validity of an objective and automatic assessment method using motion analysis during a laparoscopic procedure on an animal organ. Experienced surgeons in laparoscopy (experts) and medical students (novices) performed a cholecystectomy on a porcine liver box model. The motions of the surgical tools were acquired and analyzed by 11 different motion-related metrics, i.e., a total of 19 metrics as eight of them were measured separately for each hand. We identified for which of the metrics the experts outperformed the novices. In total, two experts and 28 novices were included. The experts achieved significantly better results for 13 of the 19 instrument motion metrics. Expert performance is characterized by a low time to complete the cholecystectomy, high bimanual dexterity (instrument coordination), a limited amount of movement and low measurement of motion smoothness of the dissection instrument, and relatively high usage of the grasper to optimize tissue positioning for dissection.

  16. Non-Invasive Detection of Anastomotic Leakage Following Esophageal and Pancreatic Surgery by Urinary Analysis.

    Science.gov (United States)

    Plat, Victor D; van Gaal, Nora; Covington, James A; Neal, Matthew; de Meij, Tim G J; van der Peet, Donald L; Zonderhuis, Babs; Kazemier, Geert; de Boer, Nanne K H; Daams, Freek

    2018-06-15

    Esophagectomy or pancreaticoduodenectomy is the standard surgical approach for patients with tumors of the esophagus or pancreatic head. Postoperative mortality is strongly correlated with the occurrence of anastomotic leakage (AL). Delay in diagnosis leads to delay in treatment, which ratifies the need for development of novel and accurate non-invasive diagnostic tests for detection of AL. Urinary volatile organic compounds (VOCs) reflect the metabolic status of an individual, which is associated with a systemic immunological response. The aim of this study was to determine the diagnostic accuracy of urinary VOCs to detect AL after esophagectomy or pancreaticoduodenectomy. In the present study, urinary VOCs of 63 patients after esophagectomy (n = 31) or pancreaticoduodenectomy (n = 32) were analyzed by means of field asymmetric ion mobility spectrometry. AL was defined according to international study groups. AL was observed in 15 patients (24%). Urinary VOCs of patients with AL after pancreaticoduodenectomy could be distinguished from uncomplicated controls, area under the curve 0.85 (95% CI 0.76-0.93), sensitivity 76%, and specificity 77%. However, this was not observed following esophagectomy, area under the curve 0.51 (95% CI 0.37-0.65). In our study population AL following pancreaticoduodenectomy could be discriminated from uncomplicated controls by means of urinary VOC analysis, NTC03203434. © 2018 The Author(s) Published by S. Karger AG, Basel.

  17. New aids for the non-invasive prenatal diagnosis of achondroplasia: dysmorphic features, charts of fetal size and molecular confirmation using cell-free fetal DNA in maternal plasma

    NARCIS (Netherlands)

    Chitty, L. S.; Griffin, D. R.; Meaney, C.; Barrett, A.; Khalil, A.; Pajkrt, E.; Cole, T. J.

    2011-01-01

    To improve the prenatal diagnosis of achondroplasia by constructing charts of fetal size, defining frequency of sonographic features and exploring the role of non-invasive molecular diagnosis based on cell-free fetal deoxyribonucleic acid (DNA) in maternal plasma. Data on fetuses with a confirmed

  18. Functional proteomic analysis reveals the involvement of KIAA1199 in breast cancer growth, motility and invasiveness

    International Nuclear Information System (INIS)

    Jami, Mohammad-Saeid; Huang, Xin; Peng, Hong; Fu, Kai; Li, Yan; Singh, Rakesh K; Ding, Shi-Jian; Hou, Jinxuan; Liu, Miao; Varney, Michelle L; Hassan, Hesham; Dong, Jixin; Geng, Liying; Wang, Jing; Yu, Fang

    2014-01-01

    KIAA1199 is a recently identified novel gene that is up-regulated in human cancer with poor survival. Our proteomic study on signaling polarity in chemotactic cells revealed KIAA1199 as a novel protein target that may be involved in cellular chemotaxis and motility. In the present study, we examined the functional significance of KIAA1199 expression in breast cancer growth, motility and invasiveness. We validated the previous microarray observation by tissue microarray immunohistochemistry using a TMA slide containing 12 breast tumor tissue cores and 12 corresponding normal tissues. We performed the shRNA-mediated knockdown of KIAA1199 in MDA-MB-231 and HS578T cells to study the role of this protein in cell proliferation, migration and apoptosis in vitro. We studied the effects of KIAA1199 knockdown in vivo in two groups of mice (n = 5). We carried out the SILAC LC-MS/MS based proteomic studies on the involvement of KIAA1199 in breast cancer. KIAA1199 mRNA and protein was significantly overexpressed in breast tumor specimens and cell lines as compared with non-neoplastic breast tissues from large-scale microarray and studies of breast cancer cell lines and tumors. To gain deeper insights into the novel role of KIAA1199 in breast cancer, we modulated KIAA1199 expression using shRNA-mediated knockdown in two breast cancer cell lines (MDA-MB-231 and HS578T), expressing higher levels of KIAA1199. The KIAA1199 knockdown cells showed reduced motility and cell proliferation in vitro. Moreover, when the knockdown cells were injected into the mammary fat pads of female athymic nude mice, there was a significant decrease in tumor incidence and growth. In addition, quantitative proteomic analysis revealed that knockdown of KIAA1199 in breast cancer (MDA-MB-231) cells affected a broad range of cellular functions including apoptosis, metabolism and cell motility. Our findings indicate that KIAA1199 may play an important role in breast tumor growth and invasiveness, and that it

  19. Comparative Analysis of Dynamic Cell Viability, Migration and Invasion Assessments by Novel Real-Time Technology and Classic Endpoint Assays

    Science.gov (United States)

    Limame, Ridha; Wouters, An; Pauwels, Bea; Fransen, Erik; Peeters, Marc; Lardon, Filip; De Wever, Olivier; Pauwels, Patrick

    2012-01-01

    Background Cell viability and motility comprise ubiquitous mechanisms involved in a variety of (patho)biological processes including cancer. We report a technical comparative analysis of the novel impedance-based xCELLigence Real-Time Cell Analysis detection platform, with conventional label-based endpoint methods, hereby indicating performance characteristics and correlating dynamic observations of cell proliferation, cytotoxicity, migration and invasion on cancer cells in highly standardized experimental conditions. Methodology/Principal Findings Dynamic high-resolution assessments of proliferation, cytotoxicity and migration were performed using xCELLigence technology on the MDA-MB-231 (breast cancer) and A549 (lung cancer) cell lines. Proliferation kinetics were compared with the Sulforhodamine B (SRB) assay in a series of four cell concentrations, yielding fair to good correlations (Spearman's Rho 0.688 to 0.964). Cytotoxic action by paclitaxel (0–100 nM) correlated well with SRB (Rho>0.95) with similar IC50 values. Reference cell migration experiments were performed using Transwell plates and correlated by pixel area calculation of crystal violet-stained membranes (Rho 0.90) and optical density (OD) measurement of extracted dye (Rho>0.95). Invasion was observed on MDA-MB-231 cells alone using Matrigel-coated Transwells as standard reference method and correlated by OD reading for two Matrigel densities (Rho>0.95). Variance component analysis revealed increased variances associated with impedance-based detection of migration and invasion, potentially caused by the sensitive nature of this method. Conclusions/Significance The xCELLigence RTCA technology provides an accurate platform for non-invasive detection of cell viability and motility. The strong correlations with conventional methods imply a similar observation of cell behavior and interchangeability with other systems, illustrated by the highly correlating kinetic invasion profiles on different

  20. Comparative analysis of dynamic cell viability, migration and invasion assessments by novel real-time technology and classic endpoint assays.

    Directory of Open Access Journals (Sweden)

    Ridha Limame

    Full Text Available BACKGROUND: Cell viability and motility comprise ubiquitous mechanisms involved in a variety of (pathobiological processes including cancer. We report a technical comparative analysis of the novel impedance-based xCELLigence Real-Time Cell Analysis detection platform, with conventional label-based endpoint methods, hereby indicating performance characteristics and correlating dynamic observations of cell proliferation, cytotoxicity, migration and invasion on cancer cells in highly standardized experimental conditions. METHODOLOGY/PRINCIPAL FINDINGS: Dynamic high-resolution assessments of proliferation, cytotoxicity and migration were performed using xCELLigence technology on the MDA-MB-231 (breast cancer and A549 (lung cancer cell lines. Proliferation kinetics were compared with the Sulforhodamine B (SRB assay in a series of four cell concentrations, yielding fair to good correlations (Spearman's Rho 0.688 to 0.964. Cytotoxic action by paclitaxel (0-100 nM correlated well with SRB (Rho>0.95 with similar IC(50 values. Reference cell migration experiments were performed using Transwell plates and correlated by pixel area calculation of crystal violet-stained membranes (Rho 0.90 and optical density (OD measurement of extracted dye (Rho>0.95. Invasion was observed on MDA-MB-231 cells alone using Matrigel-coated Transwells as standard reference method and correlated by OD reading for two Matrigel densities (Rho>0.95. Variance component analysis revealed increased variances associated with impedance-based detection of migration and invasion, potentially caused by the sensitive nature of this method. CONCLUSIONS/SIGNIFICANCE: The xCELLigence RTCA technology provides an accurate platform for non-invasive detection of cell viability and motility. The strong correlations with conventional methods imply a similar observation of cell behavior and interchangeability with other systems, illustrated by the highly correlating kinetic invasion profiles on

  1. Application of atomic absorption in molecular analysis (spectrophotometry)

    International Nuclear Information System (INIS)

    Baliza, S.V.; Soledade, L.E.B.

    1981-01-01

    The apparatus of atomic absorption has been considered by all the experts in chemical analysis as one of the most important equipments in actual utilization in such field. Among its several applications one should emphasize direct and indirect metals analyses using flame, graphite furnace, cold vapor generator,... Besides such known applications, the authors have developed at the R and D Center of CSN a patent pendent method for the utilization of such equipment for molecular analysis, in substitution of a sophisticated and specific apparatus. (Author) [pt

  2. The high resolution melting analysis (HRM) as a molecular tool for monitoring parasites of the wildlife.

    Science.gov (United States)

    Héritier, Laurent; Verneau, Olivier; Breuil, Gregory; Meistertzheim, Anne-Leila

    2017-04-01

    In an interconnected world, the international pet trade on wild animals is becoming increasingly important. As a consequence, non-native parasite species are introduced, which affect the health of wildlife and contribute to the loss of biodiversity. Because the investigation of parasite diversity within vulnerable host species implies the molecular identification of large samples of parasite eggs, the sequencing of DNA barcodes is time-consuming and costly. Thereby, the objectives of our study were to apply the high resolution melting (HRM) approach for species determination from pools of parasite eggs. Molecular assays were validated on flatworm parasites (polystomes) infecting the Mediterranean pond turtle Mauremys leprosa and the invasive red-eared slider Trachemys scripta elegans in French natural environments. HRM analysis results indicated that double or multiple parasitic infections could be detected from wild animal populations. They also showed that the cycle of parasite eggs production was not regular over time and may depend on several factors, among which the ecological niche and the target species. Thereby, monitoring parasites from wild endangered animals implies periodic parasitological surveys to avoid false negative diagnostics, based solely on eggs production.

  3. Molecular detection of native and invasive marine invertebrate larvae present in ballast and open water environmental samples collected in Puget Sound

    Science.gov (United States)

    Harvey, J.B.J.; Hoy, M.S.; Rodriguez, R.J.

    2009-01-01

    Non-native marine species have been and continue to be introduced into Puget Sound via several vectors including ship's ballast water. Some non-native species become invasive and negatively impact native species or near shore habitats. We present a new methodology for the development and testing of taxon specific PCR primers designed to assess environmental samples of ocean water for the presence of native and non-native bivalves, crustaceans and algae. The intergenic spacer regions (IGS; ITS1, ITS2 and 5.8S) of the ribosomal DNA were sequenced for adult samples of each taxon studied. We used these data along with those available in Genbank to design taxon and group specific primers and tested their stringency against artificial populations of plasmid constructs containing the entire IGS region for each of the 25 taxa in our study, respectively. Taxon and group specific primer sets were then used to detect the presence or absence of native and non-native planktonic life-history stages (propagules) from environmental samples of ballast water and plankton tow net samples collected in Puget Sound. This methodology provides an inexpensive and efficient way to test the discriminatory ability of taxon specific oligonucleotides (PCR primers) before creating molecular probes or beacons for use in molecular ecological applications such as probe hybridizations or microarray analyses. This work addresses the current need to develop molecular tools capable of diagnosing the presence of planktonic life-history stages from non-native marine species (potential invaders) in ballast water and other environmental samples. ?? 2008 Elsevier B.V.

  4. Clinical and economic analysis of voriconazole using for treatment of invasive aspergillosis in Russian Federation

    Directory of Open Access Journals (Sweden)

    V. I. Ignatieva

    2015-01-01

    Full Text Available Introduction. Based on clinical studies data voriconazole is recommended as the drug of choice for treatment of invasive aspergillosis (IA – a widespread infectious complications occurring in immunocompromised patients and is characterized by severe clinical course and high mortality.The aim of this study was to assess the cost-effectiveness of voriconazole compared to other preparations recommended in the Russian practice for the treatment of IA in adult patients.Materials and methods. The authors constructed a «decision tree» type of model, which compared the three treatment alternatives for the IA in adult patients, depending on the drug in first-line therapy: 1 voriconazole, 2, caspofungin, or 3 amphotericin B lipid complex (LC. Efficacy was assessed as the probability of patient survival within 14 weeks of starting treatment. We took into account the drugs cost and an increase in the hospitalization duration due to the development of serious adverse events. The model parameters were determined on the basis of the published results of clinical studies, the costs were calculated on the basis of medicines prices in the public procurement and the average bed-day cost in system of obligatory health insurance. Probabilistic sensitivity analysis was performed.Results. It has been shown that the use of voriconazole for treatment of IA is the dominant strategy compared to the use of caspofungin and amphotericin B LC, providing cost reduction while achieving maximum effect. Probabilistic sensitivity analysis (1000 simulations showed stability of the revealed pattern.Conclusion. The use of voriconazole in the treatment of IA allows to save the greatest number of lives at minimal cost compared to other preparations recommended in the Russian practice.

  5. Prognostic Value of Perineural Invasion in Esophageal and Esophagogastric Junction Carcinoma: A Meta-Analysis

    Directory of Open Access Journals (Sweden)

    Aiqin Gao

    2016-01-01

    Full Text Available Objective. Here we aimed to clarify the prognostic significance of perineural invasion (PNI in esophageal and esophagogastric junction (EGJ carcinoma. Methods. A comprehensive literature search for relevant reports published up to July 2015 was performed using Pubmed and Embase databases. The pooled HR and 95% CI for overall survival (OS and disease-free survival (DFS were used to assess the prognostic value. The association of PNI with pathological characteristics was evaluated by OR and 95% CI. Results. A total of 13 cohorts were retrieved, covering 2770 patients treated by surgery. The cumulative analysis revealed a statistical correlation between PNI and poor OS (HR = 1.76, 95% CI: 1.54–2.20, and P<0.00001, as well as poor DFS (HR = 1.96, 95% CI: 1.42–2.71, and P<0.001. Moreover, analysis of 1475 patients showed improved PNI in T3 + T4 (OR = 0.39, 95% CI: 0.21–0.70, and P=0.002, N+ (OR = 0.52, 95% CI: 0.40–0.69, and P<0.00001, and G3 + G4 (OR = 0.66, 95% CI: 0.48–0.90, and P=0.008 patients compared with T1 + T2, N−, and G1 + G2 ones, respectively. No significant heterogeneity was found between the studies. Conclusions. PNI is an adverse prognostic biomarker in esophageal and EGJ carcinoma. Moreover, PNI implies advanced T, N stage and poor cell differentiation.

  6. Fish gut microbiota analysis differentiates physiology and behavior of invasive Asian carp and indigenous American fish

    Science.gov (United States)

    Ye, Lin; Amberg, Jon J.; Chapman, Duane C.; Gaikowski, Mark P.; Liu, Wen-Tso

    2014-01-01

    Gut microbiota of invasive Asian silver carp (SVCP) and indigenous planktivorous gizzard shad (GZSD) in Mississippi river basin were compared using 16S rRNA gene pyrosequencing. Analysis of more than 440 000 quality-filtered sequences obtained from the foregut and hindgut of GZSD and SVCP revealed high microbial diversity in these samples. GZSD hindgut (GZSD_H) samples (n=23) with >7000 operational taxonomy units (OTUs) exhibited the highest alpha-diversity indices followed by SVCP foregut (n=15), GZSD foregut (n=9) and SVCP hindgut (SVCP_H) (n=24). UniFrac distance-based non-metric multidimensional scaling (NMDS) analysis showed that the microbiota of GZSD_H and SVCP_H were clearly separated into two clusters: samples in the GZSD cluster were observed to vary by sampling location and samples in the SVCP cluster by sampling date. NMDS further revealed distinct microbial community between foregut to hindgut for individual GZSD and SVCP. Cyanobacteria, Proteobacteria, Actinobacteria and Bacteroidetes were detected as the predominant phyla regardless of fish or gut type. The high abundance of Cyanobacteria observed was possibly supported by their role as the fish’s major food source. Furthermore, unique and shared OTUs and OTUs in each gut type were identified, three OTUs from the order Bacteroidales, the genus Bacillariophyta and the genus Clostridium were found significantly more abundant in GZSD_H (14.9–22.8%) than in SVCP_H (0.13–4.1%) samples. These differences were presumably caused by the differences in the type of food sources including bacteria ingested, the gut morphology and digestion, and the physiological behavior between GZSD and SVCP.

  7. Cost-Effectiveness Analysis of Isavuconazole vs. Voriconazole as First-Line Treatment for Invasive Aspergillosis.

    Science.gov (United States)

    Harrington, Rachel; Lee, Edward; Yang, Hongbo; Wei, Jin; Messali, Andrew; Azie, Nkechi; Wu, Eric Q; Spalding, James

    2017-01-01

    Invasive aspergillosis (IA) is associated with a significant clinical and economic burden. The phase III SECURE trial demonstrated non-inferiority in clinical efficacy between isavuconazole and voriconazole. No studies have evaluated the cost-effectiveness of isavuconazole compared to voriconazole. The objective of this study was to evaluate the costs and cost-effectiveness of isavuconazole vs. voriconazole for the first-line treatment of IA from the US hospital perspective. An economic model was developed to assess the costs and cost-effectiveness of isavuconazole vs. voriconazole in hospitalized patients with IA. The time horizon was the duration of hospitalization. Length of stay for the initial admission, incidence of readmission, clinical response, overall survival rates, and experience of adverse events (AEs) came from the SECURE trial. Unit costs were from the literature. Total costs per patient were estimated, composed of drug costs, costs of AEs, and costs of hospitalizations. Incremental costs per death avoided and per additional clinical responders were reported. Deterministic and probabilistic sensitivity analyses (DSA and PSA) were conducted. Base case analysis showed that isavuconazole was associated with a $7418 lower total cost per patient than voriconazole. In both incremental costs per death avoided and incremental costs per additional clinical responder, isavuconazole dominated voriconazole. Results were robust in sensitivity analysis. Isavuconazole was cost saving and dominant vs. voriconazole in most DSA. In PSA, isavuconazole was cost saving in 80.2% of the simulations and cost-effective in 82.0% of the simulations at the $50,000 willingness to pay threshold per additional outcome. Isavuconazole is a cost-effective option for the treatment of IA among hospitalized patients. Astellas Pharma Global Development, Inc.

  8. Incidental serous tubal intraepithelial carcinoma and early invasive serous carcinoma in the nonprophylactic setting: analysis of a case series.

    Science.gov (United States)

    Morrison, Jane C; Blanco, Luis Z; Vang, Russell; Ronnett, Brigitte M

    2015-04-01

    A precursor for invasive ovarian/pelvic high-grade serous carcinoma, termed serous tubal intraepithelial carcinoma (STIC), has been identified and characterized through careful analysis of the fallopian tubes in both prophylactic salpingo-oophorectomy specimens obtained from women with either a family history of breast and/or ovarian cancer or germline mutations of BRCA1 and BRCA2 and in cases of pelvic high-grade serous carcinoma. Data on incidental STICs and clinically occult microscopic invasive high-grade serous carcinomas are limited. We analyzed the clinicopathologic features of 22 cases, including 15 pure STICs and 7 STICs associated with microscopic invasive high-grade serous carcinomas, identified incidentally in fallopian tubes removed for nonprophylactic indications. Patient age ranged from 39 to 79 years (mean: 62.7; median: 61), with only 1 patient under the age of 50. No patients were known to carry BRCA1 or BRCA2 mutations. Of the 12 pure STICs for which the location in the fallopian tube could be established, 9 were in the fimbriated portion, 1 was at the junction of the fimbria and infundibulum, and 2 were in the nonfimbriated tube. Of the 7 STICs with associated invasive high-grade serous carcinoma, 3 were located in the fimbriated portion, 2 were at the junction of the fimbria and infundibulum, and 2 were in the nonfimbriated tube. The invasive components were in the fallopian tube in 6 cases, 4 in subepithelial stroma of tubal mucosa, and 2 as an intramucosal (exophytic) luminal lesion without invasion of underlying subepithelial stroma (size range: 1 to 4 mm). The remaining case had a microscopic focus of high-grade serous carcinoma within the ipsilateral ovary (1.3 mm cortical focus) identified only on deeper sections, without an associated invasive component in the fallopian tube. The preferential finding of atypical epithelium with the cytologic features of high-grade serous carcinoma, namely STIC, in the fallopian tubes rather than the

  9. Accommodating error analysis in comparison and clustering of molecular fingerprints.

    Science.gov (United States)

    Salamon, H; Segal, M R; Ponce de Leon, A; Small, P M

    1998-01-01

    Molecular epidemiologic studies of infectious diseases rely on pathogen genotype comparisons, which usually yield patterns comprising sets of DNA fragments (DNA fingerprints). We use a highly developed genotyping system, IS6110-based restriction fragment length polymorphism analysis of Mycobacterium tuberculosis, to develop a computational method that automates comparison of large numbers of fingerprints. Because error in fragment length measurements is proportional to fragment length and is positively correlated for fragments within a lane, an align-and-count method that compensates for relative scaling of lanes reliably counts matching fragments between lanes. Results of a two-step method we developed to cluster identical fingerprints agree closely with 5 years of computer-assisted visual matching among 1,335 M. tuberculosis fingerprints. Fully documented and validated methods of automated comparison and clustering will greatly expand the scope of molecular epidemiology.

  10. Non-Invasive Ventilation in Patients with Heart Failure: A Systematic Review and Meta-Analysis.

    Science.gov (United States)

    Bittencourt, Hugo Souza; Reis, Helena França Correia Dos; Lima, Melissa Santos; Gomes, Mansueto

    2017-02-01

    Non-invasive ventilation (NIV) may perfect respiratory and cardiac performance in patients with heart failure (HF). The objective of the study to establish, through systematic review and meta-analysis, NIV influence on functional capacity of HF patients. A systematic review with meta-analysis of randomized studies was carried out through research of databases of Cochrane Library, SciELO, Pubmed and PEDro, using the key-words: heart failure, non-invasive ventilation, exercise tolerance; and the free terms: bi-level positive airway pressure (BIPAP), continuous positive airway pressure (CPAP), and functional capacity (terms were searched for in English and Portuguese) using the Boolean operators AND and OR. Methodological quality was ensured through PEDro scale. Weighted averages and a 95% confidence interval (CI) were calculated. The meta-analysis was done thorugh the software Review Manager, version 5.3 (Cochrane Collaboration). Four randomized clinical trials were included. Individual studies suggest NIV improved functional capacity. NIV resulted in improvement in the distance of the six-minute walk test (6MWT) (68.7m 95%CI: 52.6 to 84.9) in comparison to the control group. We conclude that the NIV is an intervention that promotes important effects in the improvement of functional capacity of HF patients. However, there is a gap in literature on which are the most adequate parameters for the application of this technique. Resumo A ventilação não invasiva (VNI) pode aperfeiçoar o desempenho cardíaco e respiratório dos pacientes com insuficiência cardíaca (IC). O objetivo do estudo é estabelecer, por meio de revisão sistemática e meta-análise, a influência da VNI na capacidade funcional (CF) de indivíduos com IC. Foi realizada uma revisão sistemática com meta-análise de estudos randomizados através da pesquisa nas bases de dados Biblioteca Cochrane, SciELO, Pubmed e PEDro, utilizando-se as palavras-chave: insuficiência cardíaca, ventilação n

  11. New aids for the non-invasive prenatal diagnosis of achondroplasia: dysmorphic features, charts of fetal size and molecular confirmation using cell-free fetal DNA in maternal plasma.

    Science.gov (United States)

    Chitty, L S; Griffin, D R; Meaney, C; Barrett, A; Khalil, A; Pajkrt, E; Cole, T J

    2011-03-01

    To improve the prenatal diagnosis of achondroplasia by constructing charts of fetal size, defining frequency of sonographic features and exploring the role of non-invasive molecular diagnosis based on cell-free fetal deoxyribonucleic acid (DNA) in maternal plasma. Data on fetuses with a confirmed diagnosis of achondroplasia were obtained from our databases, records reviewed, sonographic features and measurements determined and charts of fetal size constructed using the LMS (lambda-mu-sigma) method and compared with charts used in normal pregnancies. Cases referred to our regional genetics laboratory for molecular diagnosis using cell-free fetal DNA were identified and results reviewed. Twenty-six cases were scanned in our unit. Fetal size charts showed that femur length was usually on or below the 3(rd) centile by 25 weeks' gestation, and always below the 3(rd) by 30 weeks. Head circumference was above the 50(th) centile, increasing to above the 95(th) when compared with normal for the majority of fetuses. The abdominal circumference was also increased but to a lesser extent. Commonly reported sonographic features were bowing of the femora, frontal bossing, short fingers, a small chest and polyhydramnios. Analysis of cell-free fetal DNA in six pregnancies confirmed the presence of the c.1138G > A mutation in the FGRF3 gene in four cases with achondroplasia, but not the two subsequently found to be growth restricted. These data should improve the accuracy of diagnosis of achondroplasia based on sonographic findings, and have implications for targeted molecular confirmation that can reliably and safely be carried out using cell-free fetal DNA. Copyright © 2011 ISUOG. Published by John Wiley & Sons, Ltd.

  12. Integrating archaeology and ancient DNA analysis to address invasive species colonization in the Gulf of Alaska.

    Science.gov (United States)

    West, Catherine; Hofman, Courtney A; Ebbert, Steve; Martin, John; Shirazi, Sabrina; Dunning, Samantha; Maldonado, Jesus E

    2017-10-01

    The intentional and unintentional movement of plants and animals by humans has transformed ecosystems and landscapes globally. Assessing when and how a species was introduced are central to managing these transformed landscapes, particularly in island environments. In the Gulf of Alaska, there is considerable interest in the history of mammal introductions and rehabilitating Gulf of Alaska island environments by eradicating mammals classified as invasive species. The Arctic ground squirrel (Urocitellus parryii) is of concern because it affects vegetation and seabirds on Gulf of Alaska islands. This animal is assumed to have been introduced by historic settlers; however, ground squirrel remains in the prehistoric archaeological record of Chirikof Island, Alaska, challenge this timeline and suggest they colonized the islands long ago. We used 3 lines of evidence to address this problem: direct radiocarbon dating of archaeological squirrel remains; evidence of prehistoric human use of squirrels; and ancient DNA analysis of dated squirrel remains. Chirikof squirrels dated to at least 2000 years ago, and cut marks on squirrel bones suggested prehistoric use by people. Ancient squirrels also shared a mitochondrial haplotype with modern Chirikof squirrels. These results suggest that squirrels have been on Chirikof longer than previously assumed and that the current population of squirrels is closely related to the ancient population. Thus, it appears ground squirrels are not a recent, human-mediated introduction and may have colonized the island via a natural dispersal event or an ancient human translocation. © 2016 The Authors. Conservation Biology published by Wiley Periodicals, Inc. on behalf of Society for Conservation Biology.

  13. Long-term Non-Invasive Ventilation in Infants: A Systematic Review and Meta-Analysis.

    Science.gov (United States)

    Bedi, Prabhjot K; Castro-Codesal, Maria Luisa; Featherstone, Robin; AlBalawi, Mohammed M; Alkhaledi, Bashar; Kozyrskyj, Anita L; Flores-Mir, Carlos; MacLean, Joanna E

    2018-01-01

    The use of long-term non-invasive ventilation (NIV) to treat sleep and breathing disorders in children has increased substantially in the last decade; however, less data exist about its use in infants. Given that infants have distinct sleep and breathing patterns when compared to older children, the outcomes of infants on long-term NIV may differ as well. The aim of this study is to systematically review the use and outcomes of long-term NIV in infants. Ovid Medline, Ovid Embase, CINAHL (via EbscoHOST), PubMed, and Wiley Cochrane Library were systematically searched from January 1990 to July 2017. Studies on infants using long-term NIV outside of an acute care setting were included. Data were extracted on study design, population characteristics, and NIV outcomes. A total of 327 studies were full-text reviewed, with final inclusion of 60. Studies were distributed across airway (40%), neuromuscular (28%), central nervous system (10%), cardio-respiratory (2%), and multiple (20%) disease categories. Of the 18 airway studies reporting on NIV outcomes, 13 (72%) reported improvements in respiratory parameters. Of the 12 neuromuscular studies exclusively on spinal muscular atrophy type 1 (SMA1), six (50%) reported decreased hospitalizations and nine (75%) reported on mortality outcomes. Risk of bias was moderate to serious, and quality of the evidence was low to very low for all studies. Most studies had an observational design with no control group, limiting the potential for a meta-analysis. The outcomes reported in studies differed by the disease category being studied. Studies on airway conditions showed improvements in respiratory parameters for infants using NIV. Studies on neuromuscular disorder, which were almost exclusively on SMA1, reported decreased hospitalizations and prolonged survival. Overall, it appears that NIV is an effective long-term therapy for infants. However, the high risk of bias and low quality of the available evidence limited strong

  14. Non-invasive brain stimulation for fine motor improvement after stroke: a meta-analysis.

    Science.gov (United States)

    O'Brien, A T; Bertolucci, F; Torrealba-Acosta, G; Huerta, R; Fregni, F; Thibaut, A

    2018-05-09

    The aim of this study was to determine whether non-invasive brain stimulation (NIBS) techniques improve fine motor performance in stroke. We searched PubMed, EMBASE, Web of Science, SciELO and OpenGrey for randomized clinical trials on NIBS for fine motor performance in stroke patients and healthy participants. We computed Hedges' g for active and sham groups, pooled data as random-effects models and performed sensitivity analysis on chronicity, montage, frequency of stimulation and risk of bias. Twenty-nine studies (351 patients and 152 healthy subjects) were reviewed. Effect sizes in stroke populations for transcranial direct current stimulation and repeated transcranial magnetic stimulation were 0.31 [95% confidence interval (CI), 0.08-0.55; P = 0.010; Tau 2 , 0.09; I 2 , 34%; Q, 18.23; P = 0.110] and 0.46 (95% CI, 0.00-0.92; P = 0.05; Tau 2 , 0.38; I 2 , 67%; Q, 30.45; P = 0.007). The effect size of non-dominant healthy hemisphere transcranial direct current stimulation on non-dominant hand function was 1.25 (95% CI, 0.09-2.41; P = 0.04; Tau 2 , 1.26; I 2 , 93%; Q, 40.27; P < 0.001). Our results show that NIBS is associated with gains in fine motor performance in chronic stroke patients and healthy subjects. This supports the effects of NIBS on motor learning and encourages investigation to optimize their effects in clinical and research settings. © 2018 EAN.

  15. Molecular Isotopic Distribution Analysis (MIDAs) with adjustable mass accuracy.

    Science.gov (United States)

    Alves, Gelio; Ogurtsov, Aleksey Y; Yu, Yi-Kuo

    2014-01-01

    In this paper, we present Molecular Isotopic Distribution Analysis (MIDAs), a new software tool designed to compute molecular isotopic distributions with adjustable accuracies. MIDAs offers two algorithms, one polynomial-based and one Fourier-transform-based, both of which compute molecular isotopic distributions accurately and efficiently. The polynomial-based algorithm contains few novel aspects, whereas the Fourier-transform-based algorithm consists mainly of improvements to other existing Fourier-transform-based algorithms. We have benchmarked the performance of the two algorithms implemented in MIDAs with that of eight software packages (BRAIN, Emass, Mercury, Mercury5, NeutronCluster, Qmass, JFC, IC) using a consensus set of benchmark molecules. Under the proposed evaluation criteria, MIDAs's algorithms, JFC, and Emass compute with comparable accuracy the coarse-grained (low-resolution) isotopic distributions and are more accurate than the other software packages. For fine-grained isotopic distributions, we compared IC, MIDAs's polynomial algorithm, and MIDAs's Fourier transform algorithm. Among the three, IC and MIDAs's polynomial algorithm compute isotopic distributions that better resemble their corresponding exact fine-grained (high-resolution) isotopic distributions. MIDAs can be accessed freely through a user-friendly web-interface at http://www.ncbi.nlm.nih.gov/CBBresearch/Yu/midas/index.html.

  16. Breaking biogeographic barriers: Molecular and morphological evidences for the Lessepsian invasion of soritid foraminifers to the Mediterranean Sea

    Science.gov (United States)

    Merkado, G.; Abramovich, S.; Abdu, U.; Almogi-Labin, A.; Pawlowski, J.; Holzmann, M.

    2012-04-01

    In recent years we have been witnessing a large-scale invasion (tropicalization) into the Eastern Mediterranean of many alien tropical species. The main factors that promote this process includes: 1. The ongoing warming of sea surface temperatures in the last decades. 2. The opening of the Suez Canal in 1869 that created an artificial connection between the Mediterranean and the Indo-Pacific realm of the Red Sea. This connection resulted in an ongoing unidirectional migration (termed the Lessepsian migration) of hundreds of species from Red Sea to the Mediterranean Sea. 3. The closure of the Nile River by the High Aswan Dam that blocked its nutrient discharge and created hyper-oligotrophic conditions in the Eastern Mediterranean. Larger symbiont-bearing benthic foraminifera were chosen in this study as an ideal target group for documenting this process. Their main advantage is that some of these species are clearly Indo-Pacific migrants while others represent re-encountering of allopatric populations that were isolated for at least 5.5 m.y. The first stage of this study involved the genetic characterization of soritids. Living specimens of Sorites and Amphisorus morphospecies were collected from the Red Sea and the Mediterranean and their ribosomal DNA (rDNA) sequences were determined in order to see the genetic relation between these two "recently connected" locations. The morphological characteristics of each specimen were documented by Scanning Electron Microscope micrographs and digital imaging. In the Red Sea, the specimens were collected from two shallow stations (5-6 m water depth) in the Gulf of Elat, representing different habitats: 1. Tur-Yam, characterizes by abundant Halophila sea grass. 2. The Inter University Institution in Elat, characterizes by pebbles with no sea grass. In the Mediterranean, specimens were collected along the shore of Northern Israel at Shikmona, Haifa, one of the few locations along the Israeli Mediterranean coast where living

  17. Spatial analysis of the invasion of lionfish in the western Atlantic and Caribbean.

    Science.gov (United States)

    Johnston, Matthew W; Purkis, Samuel J

    2011-06-01

    Pterois volitans and Pterois miles, two sub-species of lionfish, have become the first non-native, invasive marine fish established along the United States Atlantic coast and Caribbean. The route and timing of the invasion is poorly understood, however historical sightings and captures have been robustly documented since their introduction. Herein we analyze these records based on spatial location, dates of arrival, and prevailing physical factors at the capture sights. Using a cellular automata model, we examine the relationship between depth, salinity, temperature, and current, finding the latter as the most influential parameter for transport of lionfish to new areas. The model output is a synthetic validated reproduction of the lionfish invasion, upon which predictive simulations in other locations can be based. This predictive model is simple, highly adaptable, relies entirely on publicly available data, and is applicable to other species. Copyright © 2011 Elsevier Ltd. All rights reserved.

  18. Usefulness of molecular biology performed with formaldehyde-fixed paraffin embedded tissue for the diagnosis of combined pulmonary invasive mucormycosis and aspergillosis in an immunocompromised patient

    Directory of Open Access Journals (Sweden)

    Vénissac Nicolas

    2010-01-01

    Full Text Available Abstract Immunocompromised patients who develop invasive filamentous mycotic infections can be efficiently treated if rapid identification of the causative fungus is obtained. We report a case of fatal necrotic pneumonia caused by combined pulmonary invasive mucormycosis and aspergillosis in a 66 year-old renal transplant recipient. Aspergillus was first identified during the course of the disease by cytological examination and culture (A. fumigatus of bronchoalveolar fluid. Hyphae of Mucorales (Rhizopus microsporus were subsequently identified by culture of a tissue specimen taken from the left inferior pulmonary lobe, which was surgically resected two days before the patient died. Histological analysis of the lung parenchyma showed the association of two different filamentous mycoses for which the morphological features were evocative of aspergillosis and mucormycosis. However, the definitive identification of the associative infection was made by polymerase chain reaction (PCR performed on deparaffinized tissue sections using specific primers for aspergillosis and mucormycosis. This case demonstrates that discrepancies between histological, cytological and mycological analyses can occur in cases of combined mycotic infection. In this regard, it shows that PCR on selected paraffin blocks is a very powerful method for making or confirming the association of different filamentous mycoses and that this method should be made available to pathology laboratories.

  19. Molecular evolution of the rice blast resistance gene Pi-ta in invasive weedy rice in the USA.

    Directory of Open Access Journals (Sweden)

    Seonghee Lee

    Full Text Available The Pi-ta gene in rice has been effectively used to control rice blast disease caused by Magnaporthe oryzae worldwide. Despite a number of studies that reported the Pi-ta gene in domesticated rice and wild species, little is known about how the Pi-ta gene has evolved in US weedy rice, a major weed of rice. To investigate the genome organization of the Pi-ta gene in weedy rice and its relationship to gene flow between cultivated and weedy rice in the US, we analyzed nucleotide sequence variation at the Pi-ta gene and its surrounding 2 Mb region in 156 weedy, domesticated and wild rice relatives. We found that the region at and around the Pi-ta gene shows very low genetic diversity in US weedy rice. The patterns of molecular diversity in weeds are more similar to cultivated rice (indica and aus, which have never been cultivated in the US, rather than the wild rice species, Oryza rufipogon. In addition, the resistant Pi-ta allele (Pi-ta found in the majority of US weedy rice belongs to the weedy group strawhull awnless (SH, suggesting a single source of origin for Pi-ta. Weeds with Pi-ta were resistant to two M. oryzae races, IC17 and IB49, except for three accessions, suggesting that component(s required for the Pi-ta mediated resistance may be missing in these accessions. Signatures of flanking sequences of the Pi-ta gene and SSR markers on chromosome 12 suggest that the susceptible pi-ta allele (pi-ta, not Pi-ta, has been introgressed from cultivated to weedy rice by out-crossing.

  20. Molecular Evolution of the Rice Blast Resistance Gene Pi-ta in Invasive Weedy Rice in the USA

    Science.gov (United States)

    Lee, Seonghee; Jia, Yulin; Jia, Melissa; Gealy, David R.; Olsen, Kenneth M.; Caicedo, Ana L.

    2011-01-01

    The Pi-ta gene in rice has been effectively used to control rice blast disease caused by Magnaporthe oryzae worldwide. Despite a number of studies that reported the Pi-ta gene in domesticated rice and wild species, little is known about how the Pi-ta gene has evolved in US weedy rice, a major weed of rice. To investigate the genome organization of the Pi-ta gene in weedy rice and its relationship to gene flow between cultivated and weedy rice in the US, we analyzed nucleotide sequence variation at the Pi-ta gene and its surrounding 2 Mb region in 156 weedy, domesticated and wild rice relatives. We found that the region at and around the Pi-ta gene shows very low genetic diversity in US weedy rice. The patterns of molecular diversity in weeds are more similar to cultivated rice (indica and aus), which have never been cultivated in the US, rather than the wild rice species, Oryza rufipogon. In addition, the resistant Pi-ta allele (Pi-ta) found in the majority of US weedy rice belongs to the weedy group strawhull awnless (SH), suggesting a single source of origin for Pi-ta. Weeds with Pi-ta were resistant to two M. oryzae races, IC17 and IB49, except for three accessions, suggesting that component(s) required for the Pi-ta mediated resistance may be missing in these accessions. Signatures of flanking sequences of the Pi-ta gene and SSR markers on chromosome 12 suggest that the susceptible pi-ta allele (pi-ta), not Pi-ta, has been introgressed from cultivated to weedy rice by out-crossing. PMID:22043312

  1. An Economic Analysis of Cell-Free DNA Non-Invasive Prenatal Testing in the US General Pregnancy Population.

    Directory of Open Access Journals (Sweden)

    Peter Benn

    Full Text Available Analyze the economic value of replacing conventional fetal aneuploidy screening approaches with non-invasive prenatal testing (NIPT in the general pregnancy population.Using decision-analysis modeling, we compared conventional screening to NIPT with cell-free DNA (cfDNA analysis in the annual US pregnancy population. Sensitivity and specificity for fetal aneuploidies, trisomy 21, trisomy 18, trisomy 13, and monosomy X, were estimated using published data and modeling of both first- and second trimester screening. Costs were assigned for each prenatal test component and for an affected birth. The overall cost to the healthcare system considered screening costs, the number of aneuploid cases detected, invasive procedures performed, procedure-related euploid losses, and affected pregnancies averted. Sensitivity analyses evaluated the effect of variation in parameters. Costs were reported in 2014 US Dollars.Replacing conventional screening with NIPT would reduce healthcare costs if it can be provided for $744 or less in the general pregnancy population. The most influential variables were timing of screening entry, screening costs, and pregnancy termination rates. Of the 13,176 affected pregnancies undergoing screening, NIPT detected 96.5% (12,717/13,176 of cases, compared with 85.9% (11,314/13,176 by conventional approaches. NIPT reduced invasive procedures by 60.0%, with NIPT and conventional methods resulting in 24,596 and 61,430 invasive procedures, respectively. The number of procedure-related euploid fetal losses was reduced by 73.5% (194/264 in the general screening population.Based on our analysis, universal application of NIPT would increase fetal aneuploidy detection rates and can be economically justified. Offering this testing to all pregnant women is associated with substantial prenatal healthcare benefits.

  2. Correlation of molecular subtypes of invasive ductal carcinoma of breast with glucose metabolism in FDG PET/CT: Based on the recommendations of the St. Gallen Consenesus Meeting 2013

    Energy Technology Data Exchange (ETDEWEB)

    Bae, Sang Kyun [Dept. of Nuclear Medicine, Haeundae Paik Hospital, University of Inje College of Medicine, Busan (Korea, Republic of); Lee, Sun Seong; Park, Yun Soo; Park, Ji Sun; Kim, Tae Hyun; Yoon, Hye Kyoung; Ahn, Hyo Jung; Lee, Seok Mo [Busan Paik Hospital, University of Inje College of Medicine, Busan (Korea, Republic of)

    2017-03-15

    This study aimed to investigate the relationship between the SUVmax of primary breast cancer lesions and the molecular subtypes based on the recommendations of the St. Gallen consensus meeting 2013. Clinical records of patients who underwent F-18 FDG PET/CT for initial staging of invasive ductal carcinoma (IDC) of the breast were reviewed. A total of 183 patients were included. SUV{sub max} was correlated with the molecular subtypes defined by the St. Gallen Consensus Meeting 2013, i.e., luminal A-like (LA), luminal B-like HER2 negative (LBHER2-), luminal B-like HER2 positive (LBHER2+), HER2 positive (HER2+), and triple negative (TN), and with the clinicohistopathologic characteristics. The molecular subtype was LA in 38 patients, LBHER2- in 72, LBHER2+ in 21, HER2+ in 30, and TN in 22. The mean SUV{sub max} in the LA, LBHER2-, LBHER2+, HER2+, and TN groups were 4.5 ± 2.3, 7.2 ± 4.9, 7.2 ± 4.3, 10.2 ± 5.5, and 8.8 ± 7.1, respectively. Although SUV{sub max} differed significantly among these subtypes (p < 0.001), the values showed a wide overlap. Optimal cut-off SUV{sub max} to differentiate LA from LBHER2-, LBHER2+, HER2+ and TN were 5.9, 5.8, 7.5, and 10.2 respectively, with area under curve (AUC) of 0.648, 0.709, 0.833, and 0.697 respectively. The cut-off value of 5.9 yielded the highest accuracy for differentiation between the LA and non-LA subtypes, with sensitivity, specificity, and AUC of 79.4 %, 57.9 %, and 0.704 respectively. The SUV{sub max} showed a significant correlation with the molecular subtype. Although SUV{sub max} measurements could be used along with immunohistochemical analysis for differentiating between molecular subtypes, its application to individual patients may be limited due to the wide overlaps in SUV{sub max}.

  3. Correlation of molecular subtypes of invasive ductal carcinoma of breast with glucose metabolism in FDG PET/CT: Based on the recommendations of the St. Gallen Consenesus Meeting 2013

    International Nuclear Information System (INIS)

    Bae, Sang Kyun; Lee, Sun Seong; Park, Yun Soo; Park, Ji Sun; Kim, Tae Hyun; Yoon, Hye Kyoung; Ahn, Hyo Jung; Lee, Seok Mo

    2017-01-01

    This study aimed to investigate the relationship between the SUVmax of primary breast cancer lesions and the molecular subtypes based on the recommendations of the St. Gallen consensus meeting 2013. Clinical records of patients who underwent F-18 FDG PET/CT for initial staging of invasive ductal carcinoma (IDC) of the breast were reviewed. A total of 183 patients were included. SUV_m_a_x was correlated with the molecular subtypes defined by the St. Gallen Consensus Meeting 2013, i.e., luminal A-like (LA), luminal B-like HER2 negative (LBHER2-), luminal B-like HER2 positive (LBHER2+), HER2 positive (HER2+), and triple negative (TN), and with the clinicohistopathologic characteristics. The molecular subtype was LA in 38 patients, LBHER2- in 72, LBHER2+ in 21, HER2+ in 30, and TN in 22. The mean SUV_m_a_x in the LA, LBHER2-, LBHER2+, HER2+, and TN groups were 4.5 ± 2.3, 7.2 ± 4.9, 7.2 ± 4.3, 10.2 ± 5.5, and 8.8 ± 7.1, respectively. Although SUV_m_a_x differed significantly among these subtypes (p < 0.001), the values showed a wide overlap. Optimal cut-off SUV_m_a_x to differentiate LA from LBHER2-, LBHER2+, HER2+ and TN were 5.9, 5.8, 7.5, and 10.2 respectively, with area under curve (AUC) of 0.648, 0.709, 0.833, and 0.697 respectively. The cut-off value of 5.9 yielded the highest accuracy for differentiation between the LA and non-LA subtypes, with sensitivity, specificity, and AUC of 79.4 %, 57.9 %, and 0.704 respectively. The SUV_m_a_x showed a significant correlation with the molecular subtype. Although SUV_m_a_x measurements could be used along with immunohistochemical analysis for differentiating between molecular subtypes, its application to individual patients may be limited due to the wide overlaps in SUV_m_a_x

  4. Invasive Candidiasis

    Science.gov (United States)

    ... Waterborne, and Environmental Diseases Mycotic Diseases Branch Invasive Candidiasis Recommend on Facebook Tweet Share Compartir Global Emergence ... antifungal drugs. Learn more about C. auris Invasive candidiasis is an infection caused by a yeast (a ...

  5. Towards Breath Gas Analysis Based on Millimeter-Wave Molecular Spectroscopy

    Science.gov (United States)

    Rothbart, Nick; Hübers, Heinz-Wilhelm; Schmalz, Klaus; Borngräber, Johannes; Kissinger, Dietmar

    2018-03-01

    Breath gas analysis is a promising non-invasive tool for medical diagnosis as there are thousands of Volatile Organic Compounds (VOCs) in human breath that can be used as health monitoring markers. Millimeter-wave/terahertz molecular spectroscopy is highly suitable for breath gas analysis due to unique fingerprint spectra of many VOCs in that frequency range. We present our recent work on sensor systems for gas spectroscopy based on integrated transmitters (TX) and receivers (RX) fabricated in IHP's 0.13 μm SiGe BiCMOS technology. For a single-band system, spectroscopic measurements and beam profiles are presented. The frequency is tuned by direct voltage-frequency tuning and by a fractional-n PLL, respectively. The spectroscopic system includes a folded gas absorption cell with gas pre-concentration abilities demonstrating the detection of a 50 ppm mixture of ethanol in ambient air corresponding to a minimum detectable concentration of 260 ppb. Finally, the design of a 3-band system covering frequencies from 225 to 273 GHz is introduced.

  6. ANALYSIS OF APOPTOSIS FACTORS IN PATIENTS WITH PREINVASIVE AND INVASIVE CERVICAL CANCER

    Directory of Open Access Journals (Sweden)

    P. I. Kovchur

    2015-01-01

    Full Text Available This article assesses the disturbance degree of apoptotic program in patients with preinvasive and invasive cervical cancer by investigating the expression level of genes of caspases-3, -6, -8 и -9 in mononuclear cells of periphery blood and in tumor tissue on the two regulating levels – on mRNA level (transcriptional and proteolytic activity (post transcriptional. 75 patients with stage III of cervical intraepithelial neoplasias (CIN III  (middle age of 32,9 ± 7,4,45 patients with stage IA (31,3 ± 6,0, 21 – with stage II (43,6 ± 13,2, 15 – with stage III–IV (46,9 ± 11,1 have been examined. The control group has been formed from 30 almost healthy donors without any cervical pathology and papilloma human virus (control 1 and 30 patients with a preinvasive and microinvasive cervical cancer (control 2. It has been found that in proportion of progress of cervix cancer, the membranous expression of CD95 increases in MPB – fraction (peripheral blood monocytes when the a CIN and initial stages of cervix cancer, more than two times. Herewith number CD95+-lymphocytes is positively correlated with stage of cervical cancer (r = 0,91; R2  = 0,82; p << 0,01. It has been found out that the activity gain of caspase-8 (r = 0,92; R2  = 0,86; p << 0,01, caspase-6 (r = 0,77; R2 = 0,59; p << 0,01 and reduction activity of caspase-9 (r = –0,60;  R2 = 0,36; p < 0,01 in mononuclear cells of peripheral blood pointed out on the sensitivity increase to Fas-induced apoptosis. Opposite, in tumor tissue, beginning from CIN stage III, apoptosis-resistant phenotype is formed, it were defined by the expression of caspase-3 (r = –0,72; R2 = 0,52, p < 0,01, caspase-6 (r = –0,59; R2 = 0, 38; p < 0,01 и caspase-9 (r = –0,67; R2 = 0,45; p < 0,01 by mRNA level and proteolytic activity. It has been shown, that the cervical cancer development is accompanied by multilateral disturbances of apoptotic processes, which are realized in decreased function of

  7. Implementation of force distribution analysis for molecular dynamics simulations

    Directory of Open Access Journals (Sweden)

    Seifert Christian

    2011-04-01

    Full Text Available Abstract Background The way mechanical stress is distributed inside and propagated by proteins and other biopolymers largely defines their function. Yet, determining the network of interactions propagating internal strain remains a challenge for both, experiment and theory. Based on molecular dynamics simulations, we developed force distribution analysis (FDA, a method that allows visualizing strain propagation in macromolecules. Results To be immediately applicable to a wide range of systems, FDA was implemented as an extension to Gromacs, a commonly used package for molecular simulations. The FDA code comes with an easy-to-use command line interface and can directly be applied to every system built using Gromacs. We provide an additional R-package providing functions for advanced statistical analysis and presentation of the FDA data. Conclusions Using FDA, we were able to explain the origin of mechanical robustness in immunoglobulin domains and silk fibers. By elucidating propagation of internal strain upon ligand binding, we previously also successfully revealed the functionality of a stiff allosteric protein. FDA thus has the potential to be a valuable tool in the investigation and rational design of mechanical properties in proteins and nano-materials.

  8. A comparative analysis of minimally invasive and open spine surgery patient education resources.

    Science.gov (United States)

    Agarwal, Nitin; Feghhi, Daniel P; Gupta, Raghav; Hansberry, David R; Quinn, John C; Heary, Robert F; Goldstein, Ira M

    2014-09-01

    The Internet has become a widespread source for disseminating health information to large numbers of people. Such is the case for spine surgery as well. Given the complexity of spinal surgeries, an important point to consider is whether these resources are easily read and understood by most Americans. The average national reading grade level has been estimated to be at about the 7th grade. In the present study the authors strove to assess the readability of open spine surgery resources and minimally invasive spine surgery resources to offer suggestions to help improve the readability of patient resources. Online patient education resources were downloaded in 2013 from 50 resources representing either traditional open back surgery or minimally invasive spine surgery. Each resource was assessed using 10 scales from Readability Studio Professional Edition version 2012.1. Patient education resources representing traditional open back surgery or minimally invasive spine surgery were all found to be written at a level well above the recommended 6th grade level. In general, minimally invasive spine surgery materials were written at a higher grade level. The readability of patient education resources from spine surgery websites exceeds the average reading ability of an American adult. Revisions may be warranted to increase quality and patient comprehension of these resources to effectively reach a greater patient population.

  9. Analysis of the Trojan Y-Chromosome eradication strategy for an invasive species

    KAUST Repository

    Wang, Xueying; Walton, Jay R.; Parshad, Rana; Storey, Katie; Boggess, May M.

    2013-01-01

    of the TYC eradication and control strategy of an invasive species. In particular, because the constant introduction of sex-reversed trojan females for all time is not possible in practice, there arises the question: What happens if this injection is stopped

  10. Predicting and explaining plant invasions through analysis of source area floras: some critical considerations

    Czech Academy of Sciences Publication Activity Database

    Pyšek, Petr; Richardson, D. M.; Williamson, M.

    2004-01-01

    Roč. 10, - (2004), s. 179-187 ISSN 1366-9516 R&D Projects: GA AV ČR KSK6005114; GA ČR GA206/03/1216 Institutional research plan: CEZ:AV0Z6005908 Keywords : archaeophytes * biological invasions * distribution ranges Subject RIV: EF - Botanics Impact factor: 2.109, year: 2002

  11. Does global warning increase establishment rates of invasive alien species? A centurial time series analysis

    Science.gov (United States)

    Dingcheng Huang; Robert A. Haack; Runzhi. Zhang

    2011-01-01

    The establishment rate of invasive alien insect species has been increasing worldwide during the past century. This trend has been widely attributed to increased rates of international trade and associated species introductions, but rarely linked to environmental change. To better understand and manage the bioinvasion process, it is crucial to understand the...

  12. Plastid DNA analysis reveals cryptic hybridization in invasive dalmatian toadflax populations

    Science.gov (United States)

    Andrew Boswell; Sharlene E. Sing; Sarah M. Ward

    2016-01-01

    Gene flow between Dalmatian toadflax (DT) and yellow toadflax (YT), both aggressive invaders throughout the Intermountain West, is creating hybrid populations potentially more invasive than either parent species. To determine the direction of gene flow in these hybrid populations, species-diagnostic cytoplasmic markers were developed. Markers were based on...

  13. An Ethical Analysis of Reagan's Rhetoric Justifying the Invasion of Grenada.

    Science.gov (United States)

    Dowling, Ralph E.

    A study examined the Ronald Reagan Administration's rhetoric about the invasion of Grenada to determine its ethical quality and whether the American public could make a fair judgment about the incident based on this rhetoric. Examination of President Reagan's rhetorical efforts revealed numerous violations of democratic ethical standards.…

  14. Delineation of Chondroid Lipoma: An Immunohistochemical and Molecular Biological Analysis

    Science.gov (United States)

    de Vreeze, Ronald S. A.; van Coevorden, Frits; Boerrigter, Lucie; Nederlof, Petra M.; Haas, Rick L.; Bras, Johannes; Rosenwald, Andreas; Mentzel, Thomas; de Jong, Daphne

    2011-01-01

    Aims. Chondroid lipoma (CL) is a benign tumor that mimics a variety of soft tissue tumors and is characterized by translocation t(11;16). Here, we analyze CL and its histological mimics. Methods. CL (n = 4) was compared to a variety of histological mimics (n = 83) for morphological aspects and immunohistochemical features including cyclinD1(CCND1). Using FISH analysis, CCND1 and FUS were investigated as potential translocation partners. Results. All CLs were strongly positive for CCND1. One of 4 myoepitheliomas, CCND1, was positive. In well-differentiated lipomatous tumors and in chondrosarcomas, CCND1 was frequently expressed, but all myxoid liposarcomas were negative. FISH analysis did not give support for direct involvement of CCND1 and FUS as translocation partners. Conclusions. Chondroid lipoma is extremely rare and has several and more prevalent histological mimics. The differential diagnosis of chondroid lipomas can be unraveled using immunohistochemical and molecular support. PMID:21559269

  15. Molecular activation analysis for organo-halogen contaminants in yogurt

    International Nuclear Information System (INIS)

    Zhang Hong; Chai Zhifang

    2004-01-01

    The concentrations of total halogen (TX), extractable organo-halogen (EOX), extractable persistent organo-halogen (EPOX), organo-chlorine pesticides (OCPs) and polychlorinated biphenyls (PCBs) in 18 different yogurt specimens of 14 brands from Beijing, Tianjin, Shanghai, Guangzhou and Shijiazhuang were determined by epithermal neutron activation analysis (ENAA), molecular activation analysis (MAA) and GC-Mass Spectrometry (GC-MS), respectively. The results indicated that the halogen in yogurt mainly existed as inorganic species and non-extractable organo-halogen compounds. About 1/3 to 1/4 of EOX was EPOX. Further, EOCl and EPOCl were the main organo-halogen species in yogurt. The average concentration of the unknown organo-chlorine was 96% of the EPOCl. HCHs and DDTs were still the main contaminants of OCPs in the yogurt of interest. Also, PCB202, PCB103 and PCB208 were the main contaminants of PCBs. (authors)

  16. Molecular analysis of radiation-induced mutations in vitro

    International Nuclear Information System (INIS)

    Kronenberg, A.

    1996-01-01

    This review will focus on the nature of specific locus mutations detected in mammalian cells exposed in vitro to different types of ionizing radiations. Ionizing radiation has been shown to produce a wide variety of heritable alterations in DNA. These range from single base pair substitutions to stable loss or translocation of large portions of whole chromosomes. Data will be reviewed for certain test systems that reveal different mutation spectra. Techniques for the analysis of molecular alterations include applications of the polymerase chain reaction, some of which may be coupled with DNA sequence analysis, and a variety of hybridization-based techniques. The complexity of large scale rearrangements is approached with cytogenetic techniques including high resolution banding and various applications of the fluorescence in situ hybridization (FISH) technique. Radiation-induced mutant frequencies and mutation spectra are a function of the linkage constraints on the recovery of viable mutants for a given locus and test system. 44 refs

  17. Development and application of non-invasive biomarkers for carcinogen-DNA adduct analysis in occupationally exposed populations.

    Science.gov (United States)

    Talaska, G; Cudnik, J; Jaeger, M; Rothman, N; Hayes, R; Bhatnagar, V J; Kayshup, S J

    1996-07-17

    Biological monitoring of exposures to carcinogenic compounds in the workplace can be a valuable adjunct to environmental sampling and occupational medicine. Carcinogen-DNA adduct analysis has promise as a biomarker of effective dose if target organ samples can be obtained non-invasively. We have developed non-invasive techniques using exfoliated urothelial and bronchial cells collected in urine and sputum, respectively. First morning urine samples were collected from 33 workers exposed to benzidine or benzidine-based dyes and controls matched for age, education, and smoking status. Sufficient DNA for 32P-postlabelling analysis was obtained from every sample. Mean levels of a specific DNA adduct (which co-chromatographed with standard characterized by MS) were elevated significantly in the benzidine-exposed workers relative to controls. In addition, workers exposed to benzidine had higher adduct levels than those exposed to benzidine-based dyes. This study demonstrates the usefulness of these non-invasive techniques for exposure/effect assessment. To be useful in occupational studies, biomarkers must also be sensitive to exposure interventions. We have conducted topical application studies of used gasoline engine oils in mice and found that the levels of carcinogen-DNA adducts in skin and lung can be significantly lowered if skin cleaning is conducted in a timely manner. The combination of useful, non-invasive techniques to monitor exposure and effect and industrial hygiene interventions can be used to detect and prevent exposures to a wide range of carcinogens including those found in used gasoline engine oils and jet exhausts.

  18. Genomic analysis reveals multi-drug resistance clusters in Group B Streptococcus CC17 hypervirulent isolates causing neonatal invasive disease in southern mainland China

    Directory of Open Access Journals (Sweden)

    Edmondo Campisi

    2016-08-01

    Full Text Available Neonatal invasive disease caused by group B Streptococcus (GBS represents a significant public health care concern globally. However, data related to disease burden, serotype distribution and molecular epidemiology in China and other Asian countries are very few and specifically relative to confined regions. The aim of this study was to investigate the genetic characteristics of GBS isolates recovered from neonates with invasive disease during 2013-2014 at Guangzhou and Changsha hospitals in southern mainland China. We assessed the capsular polysaccharide (CPS type, pilus islands (PIs distribution and hvgA gene presence in a panel of 26 neonatal clinical isolates, of which 8 were recovered from Early Onset Disease (EOD and 18 from Late Onset Disease (LOD. Among 26 isolates examined, five serotypes were identified. Type III was the most represented (15 cases, particularly among LOD strains (n=11, followed by types Ib (n=5, V (n=3, Ia (n=2 and II (n=1. We performed whole-genome sequencing (WGS analysis and antimicrobial susceptibility testing on the 14 serotype III isolates belonging to the hypervirulent Clonal Complex 17 (serotype III-CC17.The presence of PI-2b alone was associated with 13 out of 14 serotype III-CC17 strains. Genome analysis led us to identify two multi-drug resistance gene clusters harbored in two new versions of integrative and conjugative elements (ICEs, carrying five or eight antibiotic resistance genes, respectively. These ICEs replaced the 16 kb-locus that normally contains the PI-1 operon. All isolates harboring the identified ICEs showed multiple resistances to aminoglycoside, macrolide and tetracycline antibiotic classes. In conclusion, we report the first whole-genome sequence analysis of 14 GBS serotype III-CC17 strains isolated in China, representing the most prevalent lineage causing neonatal invasive disease. The acquisition of newly identified ICEs conferring multiple antibiotic resistances could in part explain

  19. A Comparative Proteomic Analysis of Erinacine A’s Inhibition of Gastric Cancer Cell Viability and Invasiveness

    Directory of Open Access Journals (Sweden)

    Hsing-Chun Kuo

    2017-08-01

    Full Text Available Background / Aims: Erinacine A, isolated from the ethanol extract of the Hericium erinaceus mycelium, has been demonstrated as a new alternative anticancer medicine. Drawing upon current research, this study presents an investigation of the molecular mechanism of erinacine A inhibition associated with gastric cancer cell growth. Methods: Cell viability was determined by Annexin V–FITC/propidium iodide staining and migration using a Boyden chamber assay to determine the effects of erinacine A treatment on the proliferation capacity and invasiveness of gastric cancer cells. A proteomic assay provided information that was used to identify the differentially-expressed proteins following erinacine A treatment, as well as the mechanism of its targets in the apoptotic induction of erinacine A. Results: Our results demonstrate that erinacine A treatment of TSGH 9201 cells increased cytotoxicity and the generation of reactive oxygen species (ROS, as well as decreased the invasiveness. Treatment of TSGH 9201 cells with erinacine A resulted in the activation of caspases and the expression of TRAIL. Erinacine A induction of apoptosis was accompanied by sustained phosphorylation of FAK/AKT/p70S6K and the PAK1 pathways, as well as the generation of ROS. Furthermore, the induction of apoptosis and anti-invasion properties by erinacine A could involve the differential expression of the 14-3-3 sigma protein (1433S and microtubule-associated tumor suppressor candidate 2 (MTUS2, with the activation of the FAK/AKT/p70S6K and PAK1 signaling pathways. Conclusions: These results lead us to speculate that erinacine A may generate an apoptotic cascade in TSGH 9201 cells by activating the FAK/AKT/p70S6K/PAK1 pathway and upregulating proteins 1433S and MTUS2, providing a new mechanism underlying the anti-cancer effects of erinacine A in human gastric cancer cells.

  20. Non-invasive analysis of swelling in polymer dispersions by means of time-domain(TD)-NMR

    Energy Technology Data Exchange (ETDEWEB)

    Nestle, Nikolaus, E-mail: nikolaus.nestle@basf.com [BASF SE, GKP/R - G 201, D-67056 Ludwigshafen (Germany); Haeberle, Karl [BASF SE, GKP/R - G 201, D-67056 Ludwigshafen (Germany)

    2009-11-03

    In this contribution, we discuss the potential of low-field time-domain(TD)-NMR to study the swelling of (aqueous) polymer dispersions by a volatile solvent. Due to the sensitivity of transverse relaxation times (T{sub 2}) to swelling-induced changes in the molecular dynamics of the polymer component, the effects of swelling can be measured without spectral resolution. The measurement is performed on polymer dispersions in native state with solids contents around 50% in a non-invasive way without separating the polymeric phase and the water phase from each other. Using acetone in two polyurethane (PU) dispersions with different hard phase contents, we explore the sensitivity of the method and present a data evaluation strategy based on multicomponent fitting and proton balancing. Furthermore, we report exchange continualization as a further effect that needs to be taken into account for correct interpretation of the data.

  1. Non-invasive analysis of swelling in polymer dispersions by means of time-domain(TD)-NMR.

    Science.gov (United States)

    Nestle, Nikolaus; Häberle, Karl

    2009-11-03

    In this contribution, we discuss the potential of low-field time-domain(TD)-NMR to study the swelling of (aqueous) polymer dispersions by a volatile solvent. Due to the sensitivity of transverse relaxation times (T2) to swelling-induced changes in the molecular dynamics of the polymer component, the effects of swelling can be measured without spectral resolution. The measurement is performed on polymer dispersions in native state with solids contents around 50% in a non-invasive way without separating the polymeric phase and the water phase from each other. Using acetone in two polyurethane (PU) dispersions with different hard phase contents, we explore the sensitivity of the method and present a data evaluation strategy based on multicomponent fitting and proton balancing. Furthermore, we report exchange continualization as a further effect that needs to be taken into account for correct interpretation of the data.

  2. Pokemon and MEF2D co-operationally promote invasion of hepatocellular carcinoma.

    Science.gov (United States)

    Hong, Xin; Hong, Xing-Yu; Li, Tao; He, Cheng-Yan

    2015-12-01

    Hepatocellular carcinoma (HCC) is one of the most deadly human malignancy, and frequent invasion and metastasis is closely associated with its poor prognosis. However, the molecular mechanism underlying HCC invasion is still not completely elucidated. Pokemon is a well-established oncogene for HCC growth, but its contribution to HCC invasion has not been studied yet. In this paper, Pokemon was found to be overexpressed in MHCC-97H HCC cell line, which possesses higher invasiveness. Downregulation of Pokemon abolished the invasion of MHCC-97H HCC cell lines. Pokemon overexpression was able to enhance the invasion of MHCC-97L cells with lower invasiveness. MEF2D, an oncogene promoting the invasion of HCC cells, was further detected to be upregulated and downregulated when Pokemon was overexpressed and silenced, respectively. Online database analysis indicated that one Pokemon recognition site was located within the promoter of MEF2D. Chromatin co-precipitation, luciferase, and qPCR assays all proved that Pokemon can promote the expression of MEF2D in HCC cells. Restoration of MEF2D expression can prevent the impaired invasion of HCC cells with Pokemon silencing, while suppression of MEF2D abolished the effect of Pokemon overexpression on HCC invasion. More interestingly, MEF2D was also found to increase the transcription of Pokemon by binding myocyte enhancer factor 2 (MEF2) sites within its promoter region, implying an auto-regulatory circuit consisting of these two oncogenes that can promote HCC invasion. Our findings can contribute to the understanding of molecular mechanism underlying HCC invasion, and provided evidence that targeting this molecular loop may be a promising strategy for anti-invasion therapy.

  3. From data to decision - learning by probabilistic risk analysis of biological invasions

    OpenAIRE

    Sahlin, Ullrika

    2010-01-01

    Predicting an uncertain future with uncertain knowledge is a challenge. The success of efforts to preserve biodiversity, to maintain biosecurity and to reduce a negative impact from climate change, depend on scientifically based predictions of future events. The ongoing introduction of non-indigenous species threatens ecological systems for which empirical data is sparse and scientific knowledge is uncertain. Since biological invasions constitute a type of risk characterized by small probabil...

  4. In vitro analysis of the invasive phenotype of SUM 149, an inflammatory breast cancer cell line

    Directory of Open Access Journals (Sweden)

    Dharmawardhane Suranganie F

    2005-04-01

    Full Text Available Abstract Background Inflammatory breast cancer (IBC is the most lethal form of locally invasive breast cancer known. However, very little information is available on the cellular mechanisms responsible for manifestation of the IBC phenotype. To understand the unique phenotype of IBC, we compared the motile and adhesive interactions of an IBC cell line, SUM 149, to the non-IBC cell line SUM 102. Results Our results demonstrate that both IBC and non-IBC cell lines exhibit similar adhesive properties to basal lamina, but SUM 149 showed a marked increase in adhesion to collagen I. In vitro haptotaxis assays demonstrate that SUM 149 was less invasive, while wound healing assays show a less in vitro migratory phenotype for SUM 149 cells relative to SUM 102 cells. We also demonstrate a role for Rho and E-cadherin in the unique invasive phenotype of IBC. Immunoblotting reveals higher E-cadherin and RhoA expression in the IBC cell line but similar RhoC expression. Rhodamine phalloidin staining demonstrates increased formation of actin stress fibers and larger focal adhesions in SUM 149 relative to the SUM 102 cell line. Conclusion The observed unique actin and cellular architecture as well as the invasive and adhesive responses to the extracellular matrix of SUM 149 IBC cells suggest that the preference of IBC cells for connective tissue, possibly a mediator important for the vasculogenic mimicry via tubulogenesis seen in IBC pathological specimens. Overexpression of E-cadherin and RhoA may contribute to passive dissemination of IBC by promoting cell-cell adhesion and actin cytoskeletal structures that maintain tissue integrity. Therefore, we believe that these findings indicate a passive metastatic mechanism by which IBC cells invade the circulatory system as tumor emboli rather than by active migratory mechanisms.

  5. Cell invasion in the spheroid sprouting assay: a spatial organisation analysis adaptable to cell behaviour.

    Directory of Open Access Journals (Sweden)

    Silvia Blacher

    Full Text Available The endothelial cell spheroid assay provides a suitable in vitro model to study (lymph angiogenesis and test pro- and anti-(lymph angiogenic factors or drugs. Usually, the extent of cell invasion, observed through optical microscopy, is measured. The present study proposes the spatial distribution of migrated cells as a new descriptor of the (lymph angiogenic response. The utility of this novel method rests with its capacity to locally characterise spheroid structure, allowing not only the investigation of single and collective cell invasion but also the evolution of the spheroid core itself. Moreover, the proposed method can be applied to 2D-projected spheroid images obtained by optical microscopy, as well as to 3D images acquired by confocal microscopy. To validate the proposed methodology, endothelial cell invasion was evaluated under different experimental conditions. The results were compared with widely used global parameters. The comparison shows that our method prevents local spheroid modifications from being overlooked and leading to the possible misinterpretation of results.

  6. Non-invasive detection of urothelial cancer through the analysis of driver gene mutations and aneuploidy

    Science.gov (United States)

    Li, Lu; Douville, Christopher; Wang, Yuxuan; Cohen, Joshua David; Taheri, Diana; Silliman, Natalie; Schaefer, Joy; Ptak, Janine; Dobbyn, Lisa; Papoli, Maria; Kinde, Isaac; Afsari, Bahman; Tregnago, Aline C; Bezerra, Stephania M; VandenBussche, Christopher; Fujita, Kazutoshi; Ertoy, Dilek; Cunha, Isabela W; Yu, Lijia; Bivalacqua, Trinity J; Grollman, Arthur P; Diaz, Luis A; Karchin, Rachel; Danilova, Ludmila; Huang, Chao-Yuan; Shun, Chia-Tung; Turesky, Robert J; Yun, Byeong Hwa; Rosenquist, Thomas A; Pu, Yeong-Shiau; Hruban, Ralph H; Tomasetti, Cristian; Papadopoulos, Nickolas; Kinzler, Ken W

    2018-01-01

    Current non-invasive approaches for detection of urothelial cancers are suboptimal. We developed a test to detect urothelial neoplasms using DNA recovered from cells shed into urine. UroSEEK incorporates massive parallel sequencing assays for mutations in 11 genes and copy number changes on 39 chromosome arms. In 570 patients at risk for bladder cancer (BC), UroSEEK was positive in 83% of those who developed BC. Combined with cytology, UroSEEK detected 95% of patients who developed BC. Of 56 patients with upper tract urothelial cancer, 75% tested positive by UroSEEK, including 79% of those with non-invasive tumors. UroSEEK detected genetic abnormalities in 68% of urines obtained from BC patients under surveillance who demonstrated clinical evidence of recurrence. The advantages of UroSEEK over cytology were evident in low-grade BCs; UroSEEK detected 67% of cases whereas cytology detected none. These results establish the foundation for a new non-invasive approach for detection of urothelial cancer. PMID:29557778

  7. Curative effect analysis of invasive bladder cancer by joint surgical operation with interventional therapy

    International Nuclear Information System (INIS)

    Xu Biao; Wen Bin; Liu Tisheng; Wei Liqian

    2007-01-01

    Objective: To explore the effective therapy for invasive bladder cancer. Methods: Forty patients with invasive bladder cancer were divided into group A and group B. Intra-internal lilac-arterial chemotherapy and infusion pump chemotherapy combined with surgical operation were performed in group A and only surgical operation for group B. The differences of recurrence rates and survival rates between the two groups together with the effectiveness of intra-arterial chemotherapy combined surgical operation were evaluated at the same time. Results: Reduction in volumes of cancer and hematuria were obvious and nearly disappeared in group A patients with pathomorphological features demonstrating large pachyareas of necrosis together with degeneration and inflammatory changes of carcinoma tissue; outcoming with five recurrent cases (20%) and 2 deaths (10%). In group B, 9 cases relapsed(45%) and 4 eases died(20%). Conclusion: The combination of intra-internal lilac-arterial chemoembolization with infusion pump chemotherapy together with surgical operation is safe, effective for invasive bladder cancer, resulting in high raise of survival and life quality. (authors)

  8. Genetic diversity analysis of common beans based on molecular markers

    Directory of Open Access Journals (Sweden)

    Homar R. Gill-Langarica

    Full Text Available A core collection of the common bean (Phaseolus vulgaris L., representing genetic diversity in the entire Mexican holding, is kept at the INIFAP (Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias, Mexico Germplasm Bank. After evaluation, the genetic structure of this collection (200 accessions was compared with that of landraces from the states of Oaxaca, Chiapas and Veracruz (10 genotypes from each, as well as a further 10 cultivars, by means of four amplified fragment length polymorphisms (AFLP +3/+3 primer combinations and seven simple sequence repeats (SSR loci, in order to define genetic diversity, variability and mutual relationships. Data underwent cluster (UPGMA and molecular variance (AMOVA analyses. AFLP analysis produced 530 bands (88.5% polymorphic while SSR primers amplified 174 alleles, all polymorphic (8.2 alleles per locus. AFLP indicated that the highest genetic diversity was to be found in ten commercial-seed classes from two major groups of accessions from Central Mexico and Chiapas, which seems to be an important center of diversity in the south. A third group included genotypes from Nueva Granada, Mesoamerica, Jalisco and Durango races. Here, SSR analysis indicated a reduced number of shared haplotypes among accessions, whereas the highest genetic components of AMOVA variation were found within accessions. Genetic diversity observed in the common-bean core collection represents an important sample of the total Phaseolus genetic variability at the main Germplasm Bank of INIFAP. Molecular marker strategies could contribute to a better understanding of the genetic structure of the core collection as well as to its improvement and validation.

  9. Genetic diversity analysis of common beans based on molecular markers

    Directory of Open Access Journals (Sweden)

    Homar R. Gill-Langarica

    2011-01-01

    Full Text Available A core collection of the common bean (Phaseolus vulgaris L., representing genetic diversity in the entire Mexican holding, is kept at the INIFAP (Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias, Mexico Germplasm Bank. After evaluation, the genetic structure of this collection (200 accessions was compared with that of landraces from the states of Oaxaca, Chiapas and Veracruz (10 genotypes from each, as well as a further 10 cultivars, by means of four amplified fragment length polymorphisms (AFLP +3/+3 primer combinations and seven simple sequence repeats (SSR loci, in order to define genetic diversity, variability and mutual relationships. Data underwent cluster (UPGMA and molecular variance (AMOVA analyses. AFLP analysis produced 530 bands (88.5% polymorphic while SSR primers amplified 174 alleles, all polymorphic (8.2 alleles per locus. AFLP indicated that the highest genetic diversity was to be found in ten commercial-seed classes from two major groups of accessions from Central Mexico and Chiapas, which seems to be an important center of diversity in the south. A third group included genotypes from Nueva Granada, Mesoamerica, Jalisco and Durango races. Here, SSR analysis indicated a reduced number of shared haplotypes among accessions, whereas the highest genetic components of AMOVA variation were found within accessions. Genetic diversity observed in the common-bean core collection represents an important sample of the total Phaseolus genetic variability at the main Germplasm Bank of INIFAP. Molecular marker strategies could contribute to a better understanding of the genetic structure of the core collection as well as to its improvement and validation.

  10. Genetic diversity of popcorn genotypes using molecular analysis.

    Science.gov (United States)

    Resh, F S; Scapim, C A; Mangolin, C A; Machado, M F P S; do Amaral, A T; Ramos, H C C; Vivas, M

    2015-08-19

    In this study, we analyzed dominant molecular markers to estimate the genetic divergence of 26 popcorn genotypes and evaluate whether using various dissimilarity coefficients with these dominant markers influences the results of cluster analysis. Fifteen random amplification of polymorphic DNA primers produced 157 amplified fragments, of which 65 were monomorphic and 92 were polymorphic. To calculate the genetic distances among the 26 genotypes, the complements of the Jaccard, Dice, and Rogers and Tanimoto similarity coefficients were used. A matrix of Dij values (dissimilarity matrix) was constructed, from which the genetic distances among genotypes were represented in a more simplified manner as a dendrogram generated using the unweighted pair-group method with arithmetic average. Clusters determined by molecular analysis generally did not group material from the same parental origin together. The largest genetic distance was between varieties 17 (UNB-2) and 18 (PA-091). In the identification of genotypes with the smallest genetic distance, the 3 coefficients showed no agreement. The 3 dissimilarity coefficients showed no major differences among their grouping patterns because agreement in determining the genotypes with large, medium, and small genetic distances was high. The largest genetic distances were observed for the Rogers and Tanimoto dissimilarity coefficient (0.74), followed by the Jaccard coefficient (0.65) and the Dice coefficient (0.48). The 3 coefficients showed similar estimations for the cophenetic correlation coefficient. Correlations among the matrices generated using the 3 coefficients were positive and had high magnitudes, reflecting strong agreement among the results obtained using the 3 evaluated dissimilarity coefficients.

  11. Genetic diversity analysis of common beans based on molecular markers.

    Science.gov (United States)

    Gill-Langarica, Homar R; Muruaga-Martínez, José S; Vargas-Vázquez, M L Patricia; Rosales-Serna, Rigoberto; Mayek-Pérez, Netzahualcoyotl

    2011-10-01

    A core collection of the common bean (Phaseolus vulgaris L.), representing genetic diversity in the entire Mexican holding, is kept at the INIFAP (Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias, Mexico) Germplasm Bank. After evaluation, the genetic structure of this collection (200 accessions) was compared with that of landraces from the states of Oaxaca, Chiapas and Veracruz (10 genotypes from each), as well as a further 10 cultivars, by means of four amplified fragment length polymorphisms (AFLP) +3/+3 primer combinations and seven simple sequence repeats (SSR) loci, in order to define genetic diversity, variability and mutual relationships. Data underwent cluster (UPGMA) and molecular variance (AMOVA) analyses. AFLP analysis produced 530 bands (88.5% polymorphic) while SSR primers amplified 174 alleles, all polymorphic (8.2 alleles per locus). AFLP indicated that the highest genetic diversity was to be found in ten commercial-seed classes from two major groups of accessions from Central Mexico and Chiapas, which seems to be an important center of diversity in the south. A third group included genotypes from Nueva Granada, Mesoamerica, Jalisco and Durango races. Here, SSR analysis indicated a reduced number of shared haplotypes among accessions, whereas the highest genetic components of AMOVA variation were found within accessions. Genetic diversity observed in the common-bean core collection represents an important sample of the total Phaseolus genetic variability at the main Germplasm Bank of INIFAP. Molecular marker strategies could contribute to a better understanding of the genetic structure of the core collection as well as to its improvement and validation.

  12. Reactivity of etoricoxib based on computational study of molecular orbitals, molecular electrostatic potential surface and Mulliken charge analysis

    Science.gov (United States)

    Sachdeva, Ritika; Soni, Abhinav; Singh, V. P.; Saini, G. S. S.

    2018-05-01

    Etoricoxib is one of the selective cyclooxygenase inhibitor drug which plays a significant role in the pharmacological management of arthritis and pain. The theoretical investigation of its reactivity is done using Density Functional Theory calculations. Molecular Electrostatic Potential Surface of etoricoxib and its Mulliken atomic charge distribution are used for the prediction of its electrophilic and nucleophilic sites. The detailed analysis of its frontier molecular orbitals is also done.

  13. Outcome analysis of retrograde nailing and less invasive stabilization system in distal femoral fractures: A retrospective analysis

    Directory of Open Access Journals (Sweden)

    Christian Hierholzer

    2011-01-01

    Full Text Available Background: Two major therapeutic principles can be employed for the treatment of distal femoral fractures: retrograde intramedullary (IM nailing (RN or less invasive stabilization on system (LISS. Both operative stabilizing systems follow the principle of biological osteosynthesis. IM nailing protects the soft-tissue envelope due to its minimally invasive approach and closed reduction techniques better than distal femoral locked plating. The purpose of this study was to evaluate and compare outcome of distal femur fracture stabilization using RN or LISS techniques. Materials and Methods: In a retrospective study from 2003 to 2008, we analyzed 115 patients with distal femur fracture who had been treated by retrograde IM nailing (59 patients or LISS plating (56 patients. In the two cohort groups, mean age was 54 years (17-89 years. Mechanism of injury was high energy impact in 57% (53% RN, 67% LISS and low-energy injury in 43% (47% RN, 33% LISS, respectively. Fractures were classified according to AO classification: there were 52 type A fractures (RN 31, LISS 21 and 63 type C fractures (RN 28, LISS 35; 32% (RN and 56% (LISS were open and 68% (RN and 44% (LISS were closed fractures, respectively. Functional and radiological outcome was assessed. Results: Clinical and radiographic evaluation demonstrated osseous healing within 6 months following RN and following LISS plating in over 90% of patients. However, no statistically significant differences were found for the parameters time to osseous healing, rate of nonunion, and postoperative complications. The following complications were treated: hematoma formation (one patient RN and three patients LISS, superficial infection (one patient RN and three patients LISS, deep infection (2 patients LISS. Additional secondary bone grafting for successful healing 3 months after the primary operation was required in four patients in the RN (7% of patients and six in the LISS group (10% of patients

  14. Indirect effects of childhood pneumococcal conjugate vaccination on invasive pneumococcal disease: a systematic review and meta-analysis

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    Tinevimbo Shiri, DrPhD

    2017-01-01

    Full Text Available Summary: Background: The full extent to which childhood pneumococcal conjugate vaccines (PCV can indirectly reduce illness in unvaccinated populations is not known. We aimed to estimate the magnitude and timing of indirect effects of PCVs on invasive pneumococcal disease. Methods: In this systematic review and meta-analysis, we searched bibliographic databases for non-randomised quasi-experimental or observational studies reporting invasive pneumococcal disease changes following PCV introduction in unvaccinated populations (studies published Sept 1, 2010, to Jan 6, 2016, updating the previous systematic review of the same topic (studies published Jan 1, 1994, to Sept 30, 2010. Two reviewers extracted summary data by consensus. We used a Bayesian mixed-effects model to account for between-study heterogeneity to estimate temporal indirect effects by pooling of invasive pneumococcal disease changes by serotype and serogroup. Findings: Data were extracted from 70 studies included in the previous review and 172 additional studies, covering 27 high-income and seven middle-income countries. The predicted mean times to attaining a 90% reduction in invasive pneumococcal disease were 8·9 years (95% credible interval [CrI] 7·8–10·3 for grouped serotypes contained in the seven-valent PCV (PCV7, and 9·5 years (6·1–16·6 for the grouped six additional serotypes contained in the 13-valent PCV (PCV13 but not in PCV7. Disease due to grouped serotypes contained in the 23-valent pneumococcal polysaccharide vaccine (PPV23 decreased at similar rates per year in adults aged 19–64 years (relative risk [RR] 0·85, 95% CrI 0·75–0·95 and 65 years and older (0·87, 0·84–0·90. However, we noted no changes in either group in invasive pneumococcal disease caused by the additional 11 serotypes covered by PPV23 but not PCV13. Interpretation: Population childhood PCV programmes will lead, on average, to substantial protection across the whole population

  15. Analysis of invasive pneumonia-causing strains of Streptococcus pneumoniae: serotypes and antimicrobial susceptibility.

    Science.gov (United States)

    Yoshioka, Cristina R M; Martinez, Marina B; Brandileone, Maria C C; Ragazzi, Selma B; Guerra, Maria L L S; Santos, Silvia R; Shieh, Huei H; Gilio, Alfredo E

    2011-01-01

    To identify the most common pneumococcal serotypes in children hospitalized with invasive pneumonia, correlate isolated serotypes with those included in conjugate vaccines, and ascertain the sensitivity of the isolated pneumococcal strains to penicillin and other antibiotics. From January 2003 to October 2008, a retrospective study of hospitalized children with a diagnosis of Streptococcus pneumoniae pneumonia was conducted at the university hospital of Universidade de São Paulo. Criteria for inclusion were: age greater than 29 days and less than 15 years, radiological and clinical diagnosis of pneumonia, and isolation of Streptococcus pneumoniae in blood cultures and/or pleural effusion. The study included 107 children. The most common serotypes were 14 (36.5%), 1 (16%), 5 (14.6%), 6B (6.3%) and 3 (4.2%). The proportion of identified serotypes contained in the heptavalent, 10-valent and 13-valent conjugate vaccines was 53.1, 86.5, and 96.9%, respectively. Pneumococcal strains were sensitive to penicillin (minimum inhibitory concentration, MIC ≤ 2 µg/mL) in 100 cases (93.5%) and displayed intermediate resistance (MIC = 4 µg/mL) in 7 cases (6.5%). No strains were penicillin-resistant (MIC ≥ 8 µg/mL) according to the Clinical and Laboratory Standards Institute 2008 standards. Tested isolates were highly sensitive to vancomycin, rifampicin, ceftriaxone, clindamycin, erythromycin, and chloramphenicol. Our results confirm a significant potential impact of conjugate vaccines, mainly 10-valent and 13-valent, on invasive pneumonia. Furthermore, susceptibility testing results show that penicillin is still the treatment of choice for invasive pneumonia in our setting.

  16. Mammographic findings predicting an extensive intraductal component in early stage invasive breast cancer : analysis on microcalcification

    International Nuclear Information System (INIS)

    Kim, Jeong Ah; Kim, Mi Hye; Lee, Mi Kyung; Oh, Ki Keun; Kim, Eun Kyung

    2000-01-01

    To analyze the mammographic findings of extensive intraductal component (EIC)-positive early invasive breast carcinoma and to determine the mammographic features which predict an EIC positivity in an invasive carcinoma. The mammographic and pathologic findings in 71 patients aged 34-79 (mean 50) years in whom stage I or II invasive breast carcinoma had been diagnosed were retrospectively analysed. The mammographic findings were assigned to one of three groups: mass, mass with microcalcification, or microcalcification only. The shape and distribution of a calcification were classified according to the BI-RADS lexicon, and its extent was classified as either more or less than 3 cm. To detect the presence or absence of EIC and the type of ductal carcinoma in situ (DCIS), the findings were re-examined by means of slide mappings. Twenty-eight of 71 patients (39%) showed ECI positivity. The mammographic findings of EIC-positive invasive cancer (n=3D28) were mass with microcalcification (n=3D14), microcalcification only (n=3D7) and mass only (n=3D7). The mammographic finding which predicted EIC positivity was mass with microcalcification (PPV:0.67, NPV:0.33, p=3D0.02). A mammographic of mass only (n=3D39) showed a significantly high negative predictive value for EIC positivity. (PPV 0.18, NPV 0.82, P less than 0.01). A comparison of cases with or without calcification showed that those with microcalcifications (n=3D32) showed a significantly high PPV of 0.66 (NPV:0.34, p less than 0.01) while those without calcification (n=3D39) showed a significantly high NPV of 0.82 (PPV:0.18, p less than 0.01). There were no significant differences in positive predictive values for EIC between the shape, distribution and extent of calcifications. Whenever microcalcification with or without mass is seen on mammographs obtained during early breast cancer, we can predict EIC-positivity, regardless of shape or distribution according to the BI-RADS lexicon. (author)

  17. Analysis of virus susceptibility in the invasive insect pest Drosophila suzukii.

    Science.gov (United States)

    Lee, Kwang-Zin; Vilcinskas, Andreas

    2017-09-01

    The invasive insect pest Drosophila suzukii infests ripening fruits and causes massive agricultural damage in North America and Europe (Cini et al., 2012). Environmentally sustainable strategies are urgently needed to control the spread of this species, and entomopathogenic viruses offer one potential solution for global crop protection. Here we report the status of intrinsic and extrinsic factors that influence the susceptibility of D. suzukii to three model insect viruses: Drosophila C virus, Cricket paralysis virus and Flock house virus. Our work provides the basis for further studies using D. suzukii as a host system to develop viruses as biological control agents. Copyright © 2017 Elsevier Inc. All rights reserved.

  18. Mathematical analysis of compressive/tensile molecular and nuclear structures

    Science.gov (United States)

    Wang, Dayu

    Mathematical analysis in chemistry is a fascinating and critical tool to explain experimental observations. In this dissertation, mathematical methods to present chemical bonding and other structures for many-particle systems are discussed at different levels (molecular, atomic, and nuclear). First, the tetrahedral geometry of single, double, or triple carbon-carbon bonds gives an unsatisfying demonstration of bond lengths, compared to experimental trends. To correct this, Platonic solids and Archimedean solids were evaluated as atoms in covalent carbon or nitrogen bond systems in order to find the best solids for geometric fitting. Pentagonal solids, e.g. the dodecahedron and icosidodecahedron, give the best fit with experimental bond lengths; an ideal pyramidal solid which models covalent bonds was also generated. Second, the macroscopic compression/tension architectural approach was applied to forces at the molecular level, considering atomic interactions as compressive (repulsive) and tensile (attractive) forces. Two particle interactions were considered, followed by a model of the dihydrogen molecule (H2; two protons and two electrons). Dihydrogen was evaluated as two different types of compression/tension structures: a coaxial spring model and a ring model. Using similar methods, covalent diatomic molecules (made up of C, N, O, or F) were evaluated. Finally, the compression/tension model was extended to the nuclear level, based on the observation that nuclei with certain numbers of protons/neutrons (magic numbers) have extra stability compared to other nucleon ratios. A hollow spherical model was developed that combines elements of the classic nuclear shell model and liquid drop model. Nuclear structure and the trend of the "island of stability" for the current and extended periodic table were studied.

  19. Molecular analysis of radiation-induced experimental tumors in mice

    International Nuclear Information System (INIS)

    Niwa, O.; Muto, M.; Suzuki, F.

    1992-01-01

    Molecular analysis was made on mouse tumors induced by radiation and chemicals. Expression of oncogenes was studied in 12 types of 178 mouse tumors. Southern blotting was done on tumors in which overexpression of oncogenes was noted. Amplification of the myc oncogene was found in chemically induced sarcomas, but not those induced by radiations. Radiogenic thymomas were studied in detail. These thymomas were induced in two different ways. The first was thymomas induced by direct irradiation of F1 mice between C57BL/6NxC3H/He. Southern analysis of DNA revealed deletion of specific minisatellite bands in these tumors. DNA from directly induced thymomas induced focus formation when transfected into normal Golden hamster cells. The mouse K-ras oncogene was detected in these transformants. The second type of thymomas was induced by X-irradiation of thymectomized B10.thy1.2 mice in which normal thymus from congenic B10,thy1.1. mice was grafted. Thymomas of the donor origin was analysed by transfection and the transformants by DNA from those indirectly induced thymomas did not contain activated ras oncogenes. (author)

  20. MDAnalysis: a toolkit for the analysis of molecular dynamics simulations.

    Science.gov (United States)

    Michaud-Agrawal, Naveen; Denning, Elizabeth J; Woolf, Thomas B; Beckstein, Oliver

    2011-07-30

    MDAnalysis is an object-oriented library for structural and temporal analysis of molecular dynamics (MD) simulation trajectories and individual protein structures. It is written in the Python language with some performance-critical code in C. It uses the powerful NumPy package to expose trajectory data as fast and efficient NumPy arrays. It has been tested on systems of millions of particles. Many common file formats of simulation packages including CHARMM, Gromacs, Amber, and NAMD and the Protein Data Bank format can be read and written. Atoms can be selected with a syntax similar to CHARMM's powerful selection commands. MDAnalysis enables both novice and experienced programmers to rapidly write their own analytical tools and access data stored in trajectories in an easily accessible manner that facilitates interactive explorative analysis. MDAnalysis has been tested on and works for most Unix-based platforms such as Linux and Mac OS X. It is freely available under the GNU General Public License from http://mdanalysis.googlecode.com. Copyright © 2011 Wiley Periodicals, Inc.

  1. Molecular Characterization and Expression Analysis of Equine ( Gene in Horse (

    Directory of Open Access Journals (Sweden)

    Ki-Duk Song

    2014-05-01

    Full Text Available The objective of this study was to determine the molecular characteristics of the horse vascular endothelial growth factor alpha gene (VEGFα by constructing a phylogenetic tree, and to investigate gene expression profiles in tissues and blood leukocytes after exercise for development of suitable biomarkers. Using published amino acid sequences of other vertebrate species (human, chimpanzee, mouse, rat, cow, pig, chicken and dog, we constructed a phylogenetic tree which showed that equine VEGFα belonged to the same clade of the pig VEGFα. Analysis for synonymous (Ks and non-synonymous substitution ratios (Ka revealed that the horse VEGFα underwent positive selection. RNA was extracted from blood samples before and after exercise and different tissue samples of three horses. Expression analyses using reverse transcription-polymerase chain reaction (RT-PCR and quantitative-polymerase chain reaction (qPCR showed ubiquitous expression of VEGFα mRNA in skeletal muscle, kidney, thyroid, lung, appendix, colon, spinal cord, and heart tissues. Analysis of differential expression of VEGFα gene in blood leukocytes after exercise indicated a unimodal pattern. These results will be useful in developing biomarkers that can predict the recovery capacity of racing horses.

  2. Optimal timing of an invasive strategy in patients with non-ST-elevation acute coronary syndrome: a meta-analysis of randomised trials.

    Science.gov (United States)

    Jobs, Alexander; Mehta, Shamir R; Montalescot, Gilles; Vicaut, Eric; Van't Hof, Arnoud W J; Badings, Erik A; Neumann, Franz-Josef; Kastrati, Adnan; Sciahbasi, Alessandro; Reuter, Paul-Georges; Lapostolle, Frédéric; Milosevic, Aleksandra; Stankovic, Goran; Milasinovic, Dejan; Vonthein, Reinhard; Desch, Steffen; Thiele, Holger

    2017-08-19

    A routine invasive strategy is recommended for patients with non-ST-elevation acute coronary syndromes (NSTE-ACS). However, optimal timing of invasive strategy is less clearly defined. Individual clinical trials were underpowered to detect a mortality benefit; we therefore did a meta-analysis to assess the effect of timing on mortality. We identified randomised controlled trials comparing an early versus a delayed invasive strategy in patients presenting with NSTE-ACS by searching MEDLINE, Cochrane Central Register of Controlled Trials, and Embase. We included trials that reported all-cause mortality at least 30 days after in-hospital randomisation and for which the trial investigators agreed to collaborate (ie, providing individual patient data or standardised tabulated data). We pooled hazard ratios (HRs) using random-effects models. This meta-analysis is registered at PROSPERO (CRD42015018988). We included eight trials (n=5324 patients) with a median follow-up of 180 days (IQR 180-360). Overall, there was no significant mortality reduction in the early invasive group compared with the delayed invasive group HR 0·81, 95% CI 0·64-1·03; p=0·0879). In pre-specified analyses of high-risk patients, we found lower mortality with an early invasive strategy in patients with elevated cardiac biomarkers at baseline (HR 0·761, 95% CI 0·581-0·996), diabetes (0·67, 0·45-0·99), a GRACE risk score more than 140 (0·70, 0·52-0·95), and aged 75 years older (0·65, 0·46-0·93), although tests for interaction were inconclusive. An early invasive strategy does not reduce mortality compared with a delayed invasive strategy in all patients with NSTE-ACS. However, an early invasive strategy might reduce mortality in high-risk patients. None. Copyright © 2017 Elsevier Ltd. All rights reserved.

  3. Analysis of failure following definitive radiotherapy for invasive transitional cell carcinoma of the bladder

    Energy Technology Data Exchange (ETDEWEB)

    Mameghan, Hedy; Fisher, Richard; Mameghan, Jill; Brook, Susan

    1995-01-15

    Purpose: To assess prognostic factors for bladder relapse and distant failure following definitive radiotherapy for invasive transitional cell carcinoma (TCC) of the bladder. Methods and Materials: Retrospective review of patients treated in the period 1977 to 1990 by definitive radiotherapy. The factors studied included age, sex, T stage, histological grade, tumor multiplicity, ureteric obstruction, total radiation dose, and use of neoadjuvant chemotherapy. The endpoints studied were bladder relapse and distant failure. Results: There were 342 patients with a mean follow-up time of 7.9 years. Bladder relapse was observed in 159 patients. The overall actuarial bladder relapse rate at 5 years was 55% (SE = 3%). Prognostic factors for a higher bladder relapse rate were: tumor multiplicity (p < 0.001), presence of ureteric obstruction (p = 0.001), and higher T stage (p 0.044). Distant failure occurred in 39 patients. The overall actuarial distant failure rate at 5 years was 28% (SE = 3%). Prognostic factors for a higher distant failure rate were: ureteric obstruction (p = 0.003) and higher T stage (p = 0.030). Conclusion: In our study, patients with invasive bladder TCC fell into distinct prognostic groups determined by the three independent factors, ureteric obstruction, tumor multiplicity, and T stage. These factors provided estimated risks of bladder relapse by 5 years which ranged from 34% to 91%. Knowledge of these prognostic factors can help in the selection of patients more suited for bladder preservation by definitive radiotherapy.

  4. Analysis of failure following definitive radiotherapy for invasive transitional cell carcinoma of the bladder

    International Nuclear Information System (INIS)

    Mameghan, Hedy; Fisher, Richard; Mameghan, Jill; Brook, Susan

    1995-01-01

    Purpose: To assess prognostic factors for bladder relapse and distant failure following definitive radiotherapy for invasive transitional cell carcinoma (TCC) of the bladder. Methods and Materials: Retrospective review of patients treated in the period 1977 to 1990 by definitive radiotherapy. The factors studied included age, sex, T stage, histological grade, tumor multiplicity, ureteric obstruction, total radiation dose, and use of neoadjuvant chemotherapy. The endpoints studied were bladder relapse and distant failure. Results: There were 342 patients with a mean follow-up time of 7.9 years. Bladder relapse was observed in 159 patients. The overall actuarial bladder relapse rate at 5 years was 55% (SE = 3%). Prognostic factors for a higher bladder relapse rate were: tumor multiplicity (p < 0.001), presence of ureteric obstruction (p = 0.001), and higher T stage (p 0.044). Distant failure occurred in 39 patients. The overall actuarial distant failure rate at 5 years was 28% (SE = 3%). Prognostic factors for a higher distant failure rate were: ureteric obstruction (p = 0.003) and higher T stage (p = 0.030). Conclusion: In our study, patients with invasive bladder TCC fell into distinct prognostic groups determined by the three independent factors, ureteric obstruction, tumor multiplicity, and T stage. These factors provided estimated risks of bladder relapse by 5 years which ranged from 34% to 91%. Knowledge of these prognostic factors can help in the selection of patients more suited for bladder preservation by definitive radiotherapy

  5. Cost-benefit of minimally invasive staging of non-small cell lung cancer: a decision tree sensitivity analysis.

    Science.gov (United States)

    Steinfort, Daniel P; Liew, Danny; Conron, Matthew; Hutchinson, Anastasia F; Irving, Louis B

    2010-10-01

    Accurate staging of non-small cell lung cancer (NSCLC) is critical for optimal management. Minimally invasive pathologic assessment of mediastinal lymphadenopathy is increasingly being performed. The cost-benefit (minimization of health care costs) of such approaches, in comparison with traditional surgical methods, is yet to be established. Decision-tree analysis was applied to compare downstream costs of endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA), conventional TBNA, and surgical mediastinoscopy. Calculations were based on real costs derived from actual patient data at a major teaching hospital in Melbourne, Australia. One- and two-way sensitivity analyses were undertaken to account for potential variation in input parameter values. For the base-case analysis, initial evaluation with EBUS-TBNA (with negative results being surgically confirmed) was the most cost-beneficial approach (AU$2961) in comparison with EBUS-TBNA (negative results not surgically confirmed) ($3344), conventional TBNA ($3754), and mediastinoscopy ($8859). The sensitivity of EBUS-TBNA for detecting disease had the largest impact on cost, whereas the prevalence of mediastinal lymph node metastases determined whether surgical confirmation of negative EBUS-TBNA results remained cost-beneficial. Our study confirms that minimally invasive staging of NSCLC is cost-beneficial in comparison with traditional surgical techniques. EBUS-TBNA was the most cost-beneficial approach for mediastinal staging of patients with NSCLC across all studied parameters.

  6. Raman microspectroscopy as a diagnostic tool for the non-invasive analysis of fibrillin-1 deficiency in the skin and in the in vitro skin models.

    Science.gov (United States)

    Brauchle, Eva; Bauer, Hannah; Fernes, Patrick; Zuk, Alexandra; Schenke-Layland, Katja; Sengle, Gerhard

    2017-04-01

    Fibrillin microfibrils and elastic fibers are critical determinants of elastic tissues where they define as tissue-specific architectures vital mechanical properties such as pliability and elastic recoil. Fibrillin microfibrils also facilitate elastic fiber formation and support the association of epithelial cells with the interstitial matrix. Mutations in fibrillin-1 (FBN1) are causative for the Marfan syndrome, a congenital multisystem disorder characterized by progressive deterioration of the fibrillin microfibril/ elastic fiber architecture in the cardiovascular, musculoskeletal, ocular, and dermal system. In this study, we utilized Raman microspectroscopy in combination with principal component analysis (PCA) to analyze the molecular consequences of fibrillin-1 deficiency in skin of a mouse model (GT8) of Marfan syndrome. In addition, full-thickness skin models incorporating murine wild-type and Fbn1 GT8/GT8 fibroblasts as well as human HaCaT keratinocytes were generated and analyzed. Skin models containing GT8 fibroblasts showed an altered epidermal morphology when compared to wild-type models indicating a new role for fibrillin-1 in dermal-epidermal crosstalk. Obtained Raman spectra together with PCA allowed to discriminate between healthy and deficient microfibrillar networks in murine dermis and skin models. Interestingly, results obtained from GT8 dermis and skin models showed similar alterations in molecular signatures triggered by fibrillin-1 deficiency such as amide III vibrations and decreased levels of glycan vibrations. Overall, this study indicates that Raman microspectroscopy has the potential to analyze subtle changes in fibrillin-1 microfibrils and elastic fiber networks. Therefore Raman microspectroscopy may be utilized as a non-invasive and sensitive diagnostic tool to identify connective tissue disorders and monitor their disease progression. Mutations in building blocks of the fibrillin microfibril/ elastic fiber network manifest in disease

  7. Multicenter evaluation of molecular and culture-dependent diagnostics for Shigella species and Entero-invasive Escherichia coli in the Netherlands

    NARCIS (Netherlands)

    van den Beld, Maaike J. C.; Friedrich, Alexander W.; van Zanten, Evert; Reubsaet, Frans A. G.; Kooistra-Smid, Mirjam A. M. D.; Rossen, John W. A.

    2016-01-01

    An inter-laboratory collaborative trial for the evaluation of diagnostics for detection and identification of Shigella species and Entero-invasive Escherichia coil (EIEC) was performed. Sixteen Medical Microbiological Laboratories (MMLs) participated. MMLs were interviewed about their diagnostic

  8. Diverse effects of invasive ecosystem engineers on marine biodiversity and ecosystem functions: A global review and meta-analysis.

    Science.gov (United States)

    Guy-Haim, Tamar; Lyons, Devin A; Kotta, Jonne; Ojaveer, Henn; Queirós, Ana M; Chatzinikolaou, Eva; Arvanitidis, Christos; Como, Serena; Magni, Paolo; Blight, Andrew J; Orav-Kotta, Helen; Somerfield, Paul J; Crowe, Tasman P; Rilov, Gil

    2018-03-01

    Invasive ecosystem engineers (IEE) are potentially one of the most influential types of biological invaders. They are expected to have extensive ecological impacts by altering the physical-chemical structure of ecosystems, thereby changing the rules of existence for a broad range of resident biota. To test the generality of this expectation, we used a global systematic review and meta-analysis to examine IEE effects on the abundance of individual species and communities, biodiversity (using several indices) and ecosystem functions, focusing on marine and estuarine environments. We found that IEE had a significant effect (positive and negative) in most studies testing impacts on individual species, but the overall (cumulative) effect size was small and negative. Many individual studies showed strong IEE effects on community abundance and diversity, but the direction of effects was variable, leading to statistically non-significant overall effects in most categories. In contrast, there was a strong overall effect on most ecosystem functions we examined. IEE negatively affected metabolic functions and primary production, but positively affected nutrient flux, sedimentation and decomposition. We use the results to develop a conceptual model by highlighting pathways whereby IEE impact communities and ecosystem functions, and identify several sources of research bias in the IEE-related invasion literature. Only a few of the studies simultaneously quantified IEE effects on community/diversity and ecosystem functions. Therefore, understanding how IEE may alter biodiversity-ecosystem function relationships should be a primary focus of future studies of invasion biology. Moreover, the clear effects of IEE on ecosystem functions detected in our study suggest that scientists and environmental managers ought to examine how the effects of IEE might be manifested in the services that marine ecosystems provide to humans. © 2017 John Wiley & Sons Ltd.

  9. Sex Change in Clownfish: Molecular Insights from Transcriptome Analysis

    KAUST Repository

    Casas, Laura

    2016-10-17

    Sequential hermaphroditism is a unique reproductive strategy among teleosts that is displayed mainly in fish species living in the coral reef environment. The reproductive biology of hermaphrodites has long been intriguing; however, very little is known about the molecular pathways underlying their sex change. Here, we provide the first de novo transcriptome analyses of a hermaphrodite teleost´s undergoing sex change in its natural environment. Our study has examined relative gene expression across multiple groups—rather than just two contrasting conditions— and has allowed us to explore the differential expression patterns throughout the whole process. Our analysis has highlighted the rapid and complex genomic response of the brain associated with sex change, which is subsequently transmitted to the gonads, identifying a large number of candidate genes, some well-known and some novel, involved in the process. The present study provides strong evidence of the importance of the sex steroidogenic machinery during sex change in clownfish, with the aromatase gene playing a central role, both in the brain and the gonad. This work constitutes the first genome-wide study in a social sex-changing species and provides insights into the genetic mechanism governing social sex change and gonadal restructuring in protandrous hermaphrodites.

  10. Molecular genetic analysis of phosphomannomutase genes in Triticum monococcum

    Institute of Scientific and Technical Information of China (English)

    Chunmei; Yu; Xinyan; Liu; Qian; Zhang; Xinyu; He; Wan; Huai; Baohua; Wang; Yunying; Cao; Rong; Zhou

    2015-01-01

    In higher plants, phosphomannomutase(PMM) is essential for synthesizing the antioxidant ascorbic acid through the Smirnoff–Wheeler pathway. Previously, we characterized six PMM genes(Ta PMM-A1, A2, B1, B2, D1 and D2) in common wheat(Triticum aestivum, AABBDD).Here, we report a molecular genetic analysis of PMM genes in Triticum monococcum(AmAm), a diploid wheat species whose Amgenome is closely related to the A genome of common wheat. Two distinct PMM genes, Tm PMM-1 and Tm PMM-2, were found in T. monococcum. The coding region of Tm PMM-1 was intact and highly conserved. In contrast, two main Tm PMM-2 alleles were identified, with Tm PMM-2a possessing an intact coding sequence and Tm PMM-2b being a pseudogene. The transcript level of Tm PMM-2a was much higher than that of Tm PMM-2b, and a bacterially expressed Tm PMM-2a recombinant protein displayed relatively high PMM activity. In general, the total transcript level of PMM was substantially higher in accessions carrying Tm PMM-1 and Tm PMM-2a than those harboring Tm PMM-1 and Tm PMM-2b. However, total PMM protein and activity levels did not differ drastically between the two genotypes. This work provides new information on PMM genes in T. monococcum and expands our understanding on Triticeae PMM genes, which may aid further functional and applied studies of PMM in crop plants.

  11. Homogenization analysis of invasion dynamics in heterogeneous landscapes with differential bias and motility.

    Science.gov (United States)

    Yurk, Brian P

    2018-07-01

    Animal movement behaviors vary spatially in response to environmental heterogeneity. An important problem in spatial ecology is to determine how large-scale population growth and dispersal patterns emerge within highly variable landscapes. We apply the method of homogenization to study the large-scale behavior of a reaction-diffusion-advection model of population growth and dispersal. Our model includes small-scale variation in the directed and random components of movement and growth rates, as well as large-scale drift. Using the homogenized model we derive simple approximate formulas for persistence conditions and asymptotic invasion speeds, which are interpreted in terms of residence index. The homogenization results show good agreement with numerical solutions for environments with a high degree of fragmentation, both with and without periodicity at the fast scale. The simplicity of the formulas, and their connection to residence index make them appealing for studying the large-scale effects of a variety of small-scale movement behaviors.

  12. Gene hunting: molecular analysis of the chicken genome

    NARCIS (Netherlands)

    Crooijmans, R.P.M.A.

    2000-01-01

    This dissertation describes the development of molecular tools to identify genes that are involved in production and health traits in poultry. To unravel the chicken genome, fluorescent molecular markers (microsatellite markers) were developed and optimized to perform high throughput

  13. Alteration of cancer pain-related signals by radiation: Proteomic analysis in an animal model with cancer bone invasion

    International Nuclear Information System (INIS)

    Park, Hee Chul; Seong, Jinsil; An, Jung Hee; Kim, Jiyoung; Kim, Un Jung; Lee, Bae Whan

    2005-01-01

    Purpose: Although radiotherapy is highly effective in relieving bone pain due to cancer invasion, its mechanism remains unclear. The aim of this study was to explore this mechanism in an animal model system. Methods and Materials: A hind paw model of cancer pain was developed by transplanting a murine hepatocarcinoma, HCa-1, into the periosteal membrane of the foot dorsum of C3H/HeJ mice. Bone invasion from HCa-1 was histopathologically confirmed from sequential tumor sampling. For three experimental groups, a control (N), tumor without radiation (T), and tumor with radiation (TR), the development and level of pain were objectively examined in mice with a growing tumor by assessing pain-associated behavior. The differential expression of pain-related signals in the spinal cord was analyzed by proteomic analysis using high-resolution two-dimensional gel electrophoresis (2-DE) and mass spectrometry, and those of proteins by Western blotting. The pain-mediating neurotransmitters in the spinal cord were also examined by immunohistochemical staining for calcitonin gene-related peptide (CGRP) and substance P. Results: In the histopathologic examinations, bone invasion from HCa-1 was seen from Day 7 and was evident at Day 14 after transplantation, and measurable pain-associated behaviors were developed from Day 7. After 25 Gy of radiation to the tumors, the objective level of pain in the TR group decreased, with higher thresholds to mechanical and thermal stimulation than in the T group. From the 2-DE of spinal cord, 107 spots were identified; 12 proteins were changed more than fivefold because of tumor formation but then reversed after radiation in the tumor-bearing mice. The proteins involved included secretagogin, syntenin, P2X purinoreceptor 6 (P2X6), and Ca 2+ /Calmodulin-dependent protein kinase 1 (CaM kinase 1), the functions of which have been known to be involved in the Ca 2+ -signaling cascade, ATP-mediated fast synaptic transmission, or control of vesicular

  14. Alteration of cancer pain-related signals by radiation: Proteomic analysis in an animal model with cancer bone invasion

    Energy Technology Data Exchange (ETDEWEB)

    Park, Hee Chul [Department of Radiation Oncology, Hallym University, Chuncheon (Korea, Republic of); Seong, Jinsil [Department of Radiation Oncology, Brain Korea 21 Project for Medicine, Yonsei University, Seoul (Korea, Republic of); An, Jung Hee [Department of Radiation Oncology, Brain Korea 21 Project for Medicine, Yonsei University, Seoul (Korea, Republic of); Kim, Jiyoung [Department of Radiation Oncology, Brain Korea 21 Project for Medicine, Yonsei University, Seoul (Korea, Republic of); Kim, Un Jung [Yonsei Medical Research Center, Brain Korea 21 Project for Medicine, Yonsei University, Seoul (Korea, Republic of); Lee, Bae Whan [Yonsei Medical Research Center, Brain Korea 21 Project for Medicine, Yonsei University, Seoul (Korea, Republic of)

    2005-04-01

    Purpose: Although radiotherapy is highly effective in relieving bone pain due to cancer invasion, its mechanism remains unclear. The aim of this study was to explore this mechanism in an animal model system. Methods and Materials: A hind paw model of cancer pain was developed by transplanting a murine hepatocarcinoma, HCa-1, into the periosteal membrane of the foot dorsum of C3H/HeJ mice. Bone invasion from HCa-1 was histopathologically confirmed from sequential tumor sampling. For three experimental groups, a control (N), tumor without radiation (T), and tumor with radiation (TR), the development and level of pain were objectively examined in mice with a growing tumor by assessing pain-associated behavior. The differential expression of pain-related signals in the spinal cord was analyzed by proteomic analysis using high-resolution two-dimensional gel electrophoresis (2-DE) and mass spectrometry, and those of proteins by Western blotting. The pain-mediating neurotransmitters in the spinal cord were also examined by immunohistochemical staining for calcitonin gene-related peptide (CGRP) and substance P. Results: In the histopathologic examinations, bone invasion from HCa-1 was seen from Day 7 and was evident at Day 14 after transplantation, and measurable pain-associated behaviors were developed from Day 7. After 25 Gy of radiation to the tumors, the objective level of pain in the TR group decreased, with higher thresholds to mechanical and thermal stimulation than in the T group. From the 2-DE of spinal cord, 107 spots were identified; 12 proteins were changed more than fivefold because of tumor formation but then reversed after radiation in the tumor-bearing mice. The proteins involved included secretagogin, syntenin, P2X purinoreceptor 6 (P2X6), and Ca{sup 2+}/Calmodulin-dependent protein kinase 1 (CaM kinase 1), the functions of which have been known to be involved in the Ca{sup 2+}-signaling cascade, ATP-mediated fast synaptic transmission, or control of

  15. Efficacy of transsphenoidal surgery in achieving biochemical cure of growth hormone-secreting pituitary adenomas among patients with cavernous sinus invasion: a systematic review and meta-analysis.

    Science.gov (United States)

    Briceno, Vanessa; Zaidi, Hasan A; Doucette, Joanne A; Onomichi, Kaho B; Alreshidi, Amer; Mekary, Rania A; Smith, Timothy R

    2017-05-01

    Growth hormone-secreting pituitary adenomas in adults can result in severe craniofacial disfigurement and potentially fatal medical complications. Surgical resection leading to remission of the disease is dependent on complete surgical resection of the tumor. Lesions that invade the cavernous sinus may not be safely accessible via an endonasal transsphenoidal surgery (TSS), and the rates of biochemical remission of patients with residual disease vary widely in the literature. We conducted a meta-analysis to examine the prevalence of biochemical remission after TSS among patients with growth hormone-secreting pituitary adenomas with and without cavernous sinus invasion. Embase, PubMed, and Cochrane Library databases were searched for relevant publications. Fourteen studies with 972 patients with biochemically confirmed growth hormone-secreting pituitary adenomas were included in the meta-analysis. The overall remission prevalence under a fixed-effect model was 47.6% (95% CI = 40.8-54.4%) for patients with invasive macroadenomas (I 2  = 74.6%, p < 0.01); 76.4% (95% CI = 72.2-80.1%) for patients with non-invasive macroadenomas (I 2  = 59.6%, p = 0.03); and 74.2% (95% CI = 66.3-80.7%) for patients with non-invasive microadenomas (I 2  = 36.4, p = 0.10). The significant difference among the three groups resulted from the difference between patients with or without cavernous sinus invasion (p = 0.01) and not from the size of adenomas among those without cavernous sinus invasion (p = 0.66). The prevalence of biochemical remission in patients with cavernous sinus invasion was lower than in patients without cavernous sinus invasion after TSS for acromegaly.

  16. Chemical Analysis of Whale Breath Volatiles: A Case Study for Non-Invasive Field Health Diagnostics of Marine Mammals

    Directory of Open Access Journals (Sweden)

    Raquel Cumeras

    2014-09-01

    Full Text Available We explored the feasibility of collecting exhaled breath from a moribund gray whale (Eschrichtius robustus for potential non-invasive health monitoring of marine mammals. Biogenic volatile organic compound (VOC profiling is a relatively new field of research, in which the chemical composition of breath is used to non-invasively assess the health and physiological processes on-going within an animal or human. In this study, two telescopic sampling poles were designed and tested with the primary aim of collecting whale breath exhalations (WBEs. Once the WBEs were successfully collected, they were immediately transferred onto a stable matrix sorbent through a custom manifold system. A total of two large volume WBEs were successfully captured and pre-concentrated onto two Tenax®-TA traps (one exhalation per trap. The samples were then returned to the laboratory where they were analyzed using solid phase micro extraction (SPME and gas chromatography/mass spectrometry (GC/MS. A total of 70 chemicals were identified (58 positively identified in the whale breath samples. These chemicals were also matched against a database of VOCs found in humans, and 44% of chemicals found in the whale breath are also released by healthy humans. The exhaled gray whale breath showed a rich diversity of chemicals, indicating the analysis of whale breath exhalations is a promising new field of research.

  17. Chemical analysis of whale breath volatiles: a case study for non-invasive field health diagnostics of marine mammals.

    Science.gov (United States)

    Cumeras, Raquel; Cheung, William H K; Gulland, Frances; Goley, Dawn; Davis, Cristina E

    2014-09-12

    We explored the feasibility of collecting exhaled breath from a moribund gray whale (Eschrichtius robustus) for potential non-invasive health monitoring of marine mammals. Biogenic volatile organic compound (VOC) profiling is a relatively new field of research, in which the chemical composition of breath is used to non-invasively assess the health and physiological processes on-going within an animal or human. In this study, two telescopic sampling poles were designed and tested with the primary aim of collecting whale breath exhalations (WBEs). Once the WBEs were successfully collected, they were immediately transferred onto a stable matrix sorbent through a custom manifold system. A total of two large volume WBEs were successfully captured and pre-concentrated onto two Tenax®-TA traps (one exhalation per trap). The samples were then returned to the laboratory where they were analyzed using solid phase micro extraction (SPME) and gas chromatography/mass spectrometry (GC/MS). A total of 70 chemicals were identified (58 positively identified) in the whale breath samples. These chemicals were also matched against a database of VOCs found in humans, and 44% of chemicals found in the whale breath are also released by healthy humans. The exhaled gray whale breath showed a rich diversity of chemicals, indicating the analysis of whale breath exhalations is a promising new field of research.

  18. Analysis of the invasion rate, impacts and control measures of Prosopis juliflora: a case study of Amibara District, Eastern Ethiopia.

    Science.gov (United States)

    Haregeweyn, N; Tsunekawa, A; Tsubo, M; Meshesha, D; Melkie, A

    2013-09-01

    The tree Prosopis juliflora, introduced to Ethiopia in the 1970s to curb desertification, is imposing significant ecosystem and socioeconomic challenges. The objectives of this study are therefore to analyze the dynamics and associated impacts of the P. juliflora invasion over the period 1973-2004 and to evaluate the effectiveness of the management measures implemented to date. This required the analysis of Landsat images, field surveys, the use of structured questionnaires, and interviews. P. juliflora was found to invade new areas at an average rate of 3.48 km(2)/annum over the period 1973-2004. The high germination nature of the seed, mechanisms of seed dispersal, and its wide-range ecological adaptability are the main drivers for the high invasion rate. By the year 2020, approximately 30.89 % of the study area is projected to be covered by P. juliflora. The expansion has affected human health, suppressed indigenous plants, and decreased livestock productivity. The management measures that have been implemented are not able to yield the desirable results because of the limited spatial scale, cost, and/or improper planning and implementation. Therefore, the formulation of a strategy for management approaches that include the engagement of the community and the limiting of the number of vector animals within the framework of the current villagization program remain important. Moreover, risk assessment should be completed in the future before an exotic species is introduced into a certain area.

  19. Pathways of cryptic invasion in a fish parasite traced using coalescent analysis and epidemiological survey

    Czech Academy of Sciences Publication Activity Database

    Bouzid, W.; Štefka, Jan; Bahri-Sfar, L.; Beerli, P.; Loot, G.; Lek, S.; Haddaoui, N.; Hypša, Václav; Scholz, Tomáš; Dkhil-Abbes, T.; Meddour, R.; Hassine, O.K.B.

    2013-01-01

    Roč. 15, č. 9 (2013), s. 1907-1923 ISSN 1387-3547 R&D Projects: GA ČR GAP506/12/1632 Grant - others:GA ČR(CZ) GA206/08/1019; Marie Curie Fellowship(XE) FP7-PEOPLE-IEF-2008 Institutional support: RVO:60077344 Keywords : Aquaculture * Coevolution * Directionality of migration * Population split * Ligula intestinalis * Parasite introduction Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.716, year: 2013

  20. The molecular turn in psychiatry: a philosophical analysis.

    Science.gov (United States)

    Rudnick, Abraham

    2002-06-01

    Biological psychiatry has been dominated by a psychopharmacologically-driven neurotransmitter dysfunction paradigm. The objective of this paper is to explore a reductionist assumption underlying this paradigm, and to suggest an improvement on it. The methods used are conceptual analysis with a comparative approach, particularly using illustrations from the history of both biological psychiatry and molecular biology. The results are that complete reduction to physicochemical explanations is not fruitful, at least in the initial stages of research in the medical and life sciences, and that an appropriate (non-reducible) integrative principle--addressing a property of the whole system under study--is required for each domain of research. This is illustrated in Pauling's use of a topological integrative principle for the discovery of the functioning of proteins and in Watson and Crick's use of the notion of a genetic code as an integrative principle for the discovery of the structure of genes. The neurotransmitter dysfunction paradigm addresses single molecules and their neural pathways, yet their interactions within the CNS as a whole seem most pertinent to mental disorders such as schizophrenia. The lack within biological psychiatry of an integrative principle addressing a property of the CNS as a whole may be responsible for the empirical failure of orthomolecular psychiatry, as well as for the central role that serendipity has played in the study of mental disorders, which is dominated by the neurotransmitter paradigm. The conclusion is that research in biological psychiatry may benefit from using, at least initially, some integrative principle(s) addressing a property of the CNS as a whole, such as connectionism or a hierarchical notion.

  1. microsatellite analysis of the correlation between molecular and ...

    African Journals Online (AJOL)

    Administrator

    3Northeast Normal University, Laboratory of Plant Molecular Epigenetics, Changchun China, Zip 130024 ... grounds. Furthermore, recent evidences that the environment can influence the ..... Forty Coffee Varieties Assessed by RAPD. Markers ...

  2. Analysis of Time Reversible Born-Oppenheimer Molecular Dynamics

    Directory of Open Access Journals (Sweden)

    Lin Lin

    2013-12-01

    Full Text Available We analyze the time reversible Born-Oppenheimer molecular dynamics (TRBOMD scheme, which preserves the time reversibility of the Born-Oppenheimer molecular dynamics even with non-convergent self-consistent field iteration. In the linear response regime, we derive the stability condition, as well as the accuracy of TRBOMD for computing physical properties, such as the phonon frequency obtained from the molecular dynamics simulation. We connect and compare TRBOMD with Car-Parrinello molecular dynamics in terms of accuracy and stability. We further discuss the accuracy of TRBOMD beyond the linear response regime for non-equilibrium dynamics of nuclei. Our results are demonstrated through numerical experiments using a simplified one-dimensional model for Kohn-Sham density functional theory.

  3. Molecular analysis of the oral microbiota of dental diseases

    OpenAIRE

    Kanasi, Eleni

    2008-01-01

    Traditionally, bacterial culture has been used for bacterial detection, allowing study of living microorganisms. Molecular methods are rapid and allow simultaneous identification of numerous species and uncultivated phylotypes. The objective of this doctoral thesis was to investigate the role of the oral microbiota, including poorly characterized and uncultivated bacteria, in dental caries and periodontitis, by comprehensive molecular, clinical, and statistical methods. The microbiota of 275 ...

  4. Effects of age on long-term outcomes after a routine invasive or selective invasive strategy in patients presenting with non-ST segment elevation acute coronary syndromes: a collaborative analysis of individual data from the FRISC II - ICTUS - RITA-3 (FIR) trials

    NARCIS (Netherlands)

    Damman, Peter; Clayton, Tim; Wallentin, Lars; Lagerqvist, Bo; Fox, Keith A. A.; Hirsch, Alexander; Windhausen, Fons; Swahn, Eva; Pocock, Stuart J.; Tijssen, Jan G. P.; de Winter, Robbert J.

    2012-01-01

    Objective To perform a patient-pooled analysis of a routine invasive versus a selective invasive strategy in elderly patients with non-ST segment elevation acute coronary syndrome. Methods A meta-analysis was performed of patient-pooled data from the FRISC IIeICTUSeRITA-3 (FIR) studies. (Un)adjusted

  5. Kinematics optimization and static analysis of a modular continuum robot used for minimally invasive surgery.

    Science.gov (United States)

    Qi, Fei; Ju, Feng; Bai, Dong Ming; Chen, Bai

    2018-02-01

    For the outstanding compliance and dexterity of continuum robot, it is increasingly used in minimally invasive surgery. The wide workspace, high dexterity and strong payload capacity are essential to the continuum robot. In this article, we investigate the workspace of a cable-driven continuum robot that we proposed. The influence of section number on the workspace is discussed when robot is operated in narrow environment. Meanwhile, the structural parameters of this continuum robot are optimized to achieve better kinematic performance. Moreover, an indicator based on the dexterous solid angle for evaluating the dexterity of robot is introduced and the distal end dexterity is compared for the three-section continuum robot with different range of variables. Results imply that the wider range of variables achieve the better dexterity. Finally, the static model of robot based on the principle of virtual work is derived to analyze the relationship between the bending shape deformation and the driven force. The simulations and experiments for plane and spatial motions are conducted to validate the feasibility of model, respectively. Results of this article can contribute to the real-time control and movement and can be a design reference for cable-driven continuum robot.

  6. Studies of particle drying using non-invasive Raman spectrometry and particle size analysis.

    Science.gov (United States)

    Hamilton, Peter; Littlejohn, David; Nordon, Alison; Sefcik, Jan; Slavin, Paul; Dallin, Paul; Andrews, John

    2011-05-21

    The evaporation of methanol from needle-shaped particles of cellobiose octaacetate (COA) has been studied directly in a jacketed vacuum drier using in situ measurements by Raman spectrometry. A design of experiments (DoE) approach was used to investigate the effects of three parameters (method of agitation, % solvent loss on drying and jacket temperature), with the intention of minimising the drying time and extent of particle attrition. Drying curves based on Raman signals for methanol and COA in the spectra of the wet particles indicated the end of drying and revealed three stages in the drying process that could be used to monitor the progress of solvent removal in real time. Off-line particle size measurements based on laser diffraction were made to obtain information on the extent of attrition, to compare with the trends revealed by the Raman drying curves. The study demonstrated that non-invasive Raman spectrometry can be used to study the progress of drying during agitation of particles in a vacuum drier, allowing optimisation of operating conditions to minimise attrition and reduce drying times. Although a correlation between particle size and off-line Raman measurements of COA was demonstrated, it was not possible to derive equivalent information from the in situ Raman spectra owing to the greater effects of particle motion or bulk density variations of the particles in the drier.

  7. A molecular phylogenetic analysis of the Scarabaeinae (dung beetles).

    Science.gov (United States)

    Monaghan, Michael T; Inward, Daegan J G; Hunt, Toby; Vogler, Alfried P

    2007-11-01

    The dung beetles (Scarabaeinae) include ca. 5000 species and exhibit a diverse array of morphologies and behaviors. This variation presumably reflects the adaptation to a diversity of food types and the different strategies used to avoid competition for vertebrate dung, which is the primary breeding environment for most species. The current classification gives great weight to the major behavioral types, separating the ball rollers and the tunnelers, but existing phylogenetic studies have been based on limited taxonomic or biogeographic sampling and have been contradictory. Here, we present a molecular phylogenetic analysis of 214 species of Scarabaeinae, representing all 12 traditionally recognized tribes and six biogeographical regions, using partial gene sequences from one nuclear (28S) and two mitochondrial (cox1, rrnL) genes. Length variation in 28S (588-621 bp) and rrnL (514-523 bp) was subjected to a thorough evaluation of alternative alignments, gap-coding methods, and tree searches using model-based (Bayesian and likelihood), maximum parsimony, and direct optimization analyses. The small-bodied, non-dung-feeding Sarophorus+Coptorhina were basal in all reconstructions. These were closely related to rolling Odontoloma+Dicranocara, suggesting an early acquisition of rolling behavior. Smaller tribes and most genera were monophyletic, while Canthonini and Dichotomiini each consisted of multiple paraphyletic lineages at hierarchical levels equivalent to the smaller tribes. Plasticity of rolling and tunneling was evidenced by a lack of monophyly (S-H test, p > 0.05) and several reversals within clades. The majority of previously unrecognized clades were geographical, including the well-supported Neotropical Phanaeini+Eucraniini, and a large Australian clade of rollers as well as tunneling Coptodactyla and Demarziella. Only three lineages, Gymnopleurini, Copris+Microcopris and Onthophagus, were widespread and therefore appear to be dispersive at a global scale. A

  8. Micro-PIXE analysis in invasive ductal carcinoma tissues after treatment of astaxanthin

    International Nuclear Information System (INIS)

    Safaverdi, S.; Roshani, F.; Lamehi Rashti, M.; Golkhoo, Sh.; Hassan, Z. M.; Langroudi, L.

    2009-01-01

    Trace elements play an important role in a number of biological processes. Astaxanthin, a carotoid pigment found in certain marine plant and animals, has shown anti cancer and anti free radical properties. This work intended to understand the effect of Astaxanthin in breast cancer (invasive ductal carcinoma) by using micro-PIXE method. For this aim the concentration of trace elements were compared in healthy, cancerous and cancer treated with astaxanthin in the breast and liver tissues of breast cancer bearing mice, using proton induced X-ray emission. Materials and Methods: Proton induced X-ray emission was used In a study intending to compare the concentration of trace elements in breast and liver tissues of mice bearing tumor, three groups of mice: healthy, cancerous, and cancerous treated by astaxanthin, were considered. Astaxanthin was supplied from Research Institute of women, Alzahra University. Results: Comparing the untreated tumor tissue, treatment with Astaxanthm significantly decreased the amount Fe, P, S, and Ca elements level in tumor tissue of the breast cancer. It is also found that the concentrations of those elements in liver of the untreated mice and the liver of treated mice with astaxanthin were fairly equal. Astaxanthln significantly decrease the accumulation of elements in the site of tumor, and caused the breast cancer cell membrane to lose their desire to collect the elements from healthy tissues. Conclusion: The micro -PIXE technique could calculate elemental concentrations in tissues. Changes in metallic elements may affect microenvironment and cell functions, which might led lead to cell degeneration or death, the results shows that astaxanthin reduces vital element concentration in tumor site, thus it could be used as an anti tumor agent.

  9. Relevance of prostate cancer in patients with synchronous invasive bladder urothelial carcinoma: a monocentric retrospective analysis

    Directory of Open Access Journals (Sweden)

    Lucio Dell’Atti

    2015-03-01

    Full Text Available Objectives: We retrospectively reviewed data of patients with incidental prostate cancer (PCa who underwent radical cystoprostatectomy (RCP for invasive bladder cancer and we analyzed their features with regard to incidence, pathologic characteristics, clinical significance, and implications for management. Material and Methods: Clinical data and pathological features of 64 patients who underwent standard RCP for bladder cancer were included in this study. Besides the urothelial carcinoma of the urinary bladder, the location and tumor volume of the PCa, prostate apex involvement, Gleason score, pathological staging and surgical margins were evaluated. Clinically significant PCa was defined as a tumor with a Gleason 4 or 5 pattern, stage ≥ pT3, lymph node involvement, positive surgical margin or multifocality of three or more lesions. Postoperative follow-up was scheduled every 3 months in the first year, every 6 months in the second and third year, annually thereafter. Results: 11 out of 64 patients (17.2% who underwent RCP had incidentally diagnosed PCa. 3 cases (27.3% were diagnosed as significant PCa, while 8 cases (72.7% were clinically insignificant. The positive surgical margin of PCa was detected in 1 patient with significant disease. The prostate apex involvement was present in 1 patient of the significant PCa group. Median follow-up period was 47.8 ± 29.2 (range 4-79. During the follow-up, biochemical recurrence occurred in 1 patient (9%. Concernig the cancer specific survival there was no statistical significance (P = 0.326 between the clinically significant and clinical insignificant cancer group. Conclusions: In line with published studies, incidental PCa does not impact on the prognosis of bladder cancer of patients undergoing RCP.

  10. Density functional theory, comparative vibrational spectroscopic studies, highest occupied molecular orbital and lowest unoccupied molecular orbital analysis of Linezolid

    Science.gov (United States)

    Rajalakshmi, K.; Gunasekaran, S.; Kumaresan, S.

    2015-06-01

    The Fourier transform infrared spectra and Fourier transform Raman spectra of Linezolid have been recorded in the regions 4,000-400 and 4,000-100 cm-1, respectively. Utilizing the observed Fourier transform infrared spectra and Fourier transform Raman spectra data, a complete vibrational assignment and analysis of the fundamental modes of the compound have been carried out. The optimum molecular geometry, harmonic vibrational frequencies, infrared intensities and Raman scattering activities, have been calculated by density functional theory with 6-31G(d,p), 6-311G(d,p) and M06-2X/6-31G(d,p) levels. The difference between the observed and scaled wavenumber values of most of the fundamentals is very small. A detailed interpretation of the infrared and Raman spectra of Linezolid is reported. Mulliken's net charges have also been calculated. Ultraviolet-visible spectrum of the title molecule has also been calculated using time-dependent density functional method. Besides, molecular electrostatic potential, highest occupied molecular orbital and lowest unoccupied molecular orbital analysis and several thermodynamic properties have been performed by the density functional theoretical method.

  11. Functional grouping and establishment of distribution patterns of invasive plants in China using self-organizing maps and indicator species analysis

    Directory of Open Access Journals (Sweden)

    Wang Zi-Bo

    2009-01-01

    Full Text Available In the present study, we introduce two techniques - self-organizing maps (SOM and indicator species analysis (INDVAL - for understanding the richness patterns of invasive species. We first employed SOM to identify functional groups and then used INDVAL to identify the representative areas characterizing these functional groups. Quantitative traits and distributional information on 127 invasive plants in 28 provinces of China were collected to form the matrices for our study. The results indicate Jiangsu to be the top province with the highest number of invasive species, while Ningxia was the lowest. Six functional groups were identified by the SOM method, and five of them were found to have significantly representative provinces by the INDVAL method. Our study represents the first attempt to combine self-organizing maps and indicator species analysis to assess the macro-scale distribution of exotic species.

  12. Sequence-Based Analysis of Thermal Adaptation and Protein Energy Landscapes in an Invasive Blue Mussel (Mytilus galloprovincialis).

    Science.gov (United States)

    Saarman, Norah P; Kober, Kord M; Simison, W Brian; Pogson, Grant H

    2017-10-01

    Adaptive responses to thermal stress in poikilotherms plays an important role in determining competitive ability and species distributions. Amino acid substitutions that affect protein stability and modify the thermal optima of orthologous proteins may be particularly important in this context. Here, we examine a set of 2,770 protein-coding genes to determine if proteins in a highly invasive heat tolerant blue mussel (Mytilus galloprovincialis) contain signals of adaptive increases in protein stability relative to orthologs in a more cold tolerant M. trossulus. Such thermal adaptations might help to explain, mechanistically, the success with which the invasive marine mussel M. galloprovincialis has displaced native species in contact zones in the eastern (California) and western (Japan) Pacific. We tested for stabilizing amino acid substitutions in warm tolerant M. galloprovincialis relative to cold tolerant M. trossulus with a generalized linear model that compares in silico estimates of recent changes in protein stability among closely related congeners. Fixed substitutions in M. galloprovincialis were 3,180.0 calories per mol per substitution more stabilizing at genes with both elevated dN/dS ratios and transcriptional responses to heat stress, and 705.8 calories per mol per substitution more stabilizing across all 2,770 loci investigated. Amino acid substitutions concentrated in a small number of genes were more stabilizing in M. galloprovincialis compared with cold tolerant M. trossulus. We also tested for, but did not find, enrichment of a priori GO terms in genes with elevated dN/dS ratios in M. galloprovincialis. This might indicate that selection for thermodynamic stability is generic across all lineages, and suggests that the high change in estimated protein stability that we observed in M. galloprovincialis is driven by selection for extra stabilizing substitutions, rather than by higher incidence of selection in a greater number of genes in this lineage

  13. Irreversible thermodynamic analysis and application for molecular heat engines

    Science.gov (United States)

    Lucia, Umberto; Açıkkalp, Emin

    2017-09-01

    Is there a link between the macroscopic approach to irreversibility and microscopic behaviour of the systems? Consumption of free energy keeps the system away from a stable equilibrium. Entropy generation results from the redistribution of energy, momentum, mass and charge. This concept represents the essence of the thermodynamic approach to irreversibility. Irreversibility is the result of the interaction between systems and their environment. The aim of this paper is to determine lost works in a molecular engine and compare results with macro (classical) heat engines. Firstly, irreversible thermodynamics are reviewed for macro and molecular cycles. Secondly, irreversible thermodynamics approaches are applied for a quantum heat engine with -1/2 spin system. Finally, lost works are determined for considered system and results show that macro and molecular heat engines obey same limitations. Moreover, a quantum thermodynamic approach is suggested in order to explain the results previously obtained from an atomic viewpoint.

  14. Molecular tools for carotenogenesis analysis in the zygomycete Mucor circinelloides.

    Science.gov (United States)

    Torres-Martínez, Santiago; Ruiz-Vázquez, Rosa M; Garre, Victoriano; López-García, Sergio; Navarro, Eusebio; Vila, Ana

    2012-01-01

    The carotene producer fungus Mucor circinelloides is the zygomycete more amenable to genetic manipulations by using molecular tools. Since the initial development of an effective procedure of genetic transformation, more than two decades ago, the availability of new molecular approaches such as gene replacement techniques and gene expression inactivation by RNA silencing, in addition to the sequencing of its genome, has made Mucor a valuable organism for the study of a number of processes. Here we describe in detail the main techniques and methods currently used to manipulate M. circinelloides, including transformation, gene replacement, gene silencing, RNAi, and immunoprecipitation.

  15. Molecular analysis of Rv0679c and Rv0180c genes of Mycobacterium tuberculosis from clinical isolates of pulmonary tuberculosis

    Directory of Open Access Journals (Sweden)

    L Rupa

    2016-01-01

    Full Text Available Context: Two novel proteins/genes Rv0679c and Rv0180c of Mycobacterium tuberculosis (MTB H37Rv were classified as a hypothetical membrane and transmembrane proteins which might have a role in the invasion. Molecular analysis of these genes in human clinical isolates of pulmonary tuberculosis (PTB patients was not well characterised. Aims: To assess the molecular diversity of Rv0679c and Rv0180c genes of MTB from clinical isolates of PTB patients. Settings and Design: DNA from 97 clinical isolates was extracted and subjected to amplification using selective primers by polymerase chain reaction (PCR. The PCR product obtained was sequenced commercially. Patients and Methods: Clinical isolates obtained from tuberculosis patients were investigated for polymorphisms in the Rv0679c and Rv0180c genes by PCR and DNA sequencing. Genomic DNA isolated by cetyltrimethylammonium bromide method was used for amplification of genes. Results: Rv0679c gene was highly conserved in 61 out of 65 clinical isolates assessed for sequence homology with wild-type H37Rv gene and was identical using ClustalW. Fifty-five out of 78 (70.5% clinical isolates assessed for Rv0180c were positive for single nucleotide polymorphism (SNP at 258th position where the nucleotide G was replaced with T (G to T. In clinical isolates of untreated cases, the frequency was 54.5% for SNP at 258th position which is low compared to cases undergoing treatment where the frequency was 73.1%. Conclusions: Molecular analysis of Rv0180c in clinical isolates of PTB assessed in this study was the first report, where an SNP at 258th position G to T was identified within the gene. Rv0679c gene was highly conserved (94%, within Indian clinical isolates as compared to reports from other nations.

  16. Minimally invasive versus open fusion for Grade I degenerative lumbar spondylolisthesis: analysis of the Quality Outcomes Database.

    Science.gov (United States)

    Mummaneni, Praveen V; Bisson, Erica F; Kerezoudis, Panagiotis; Glassman, Steven; Foley, Kevin; Slotkin, Jonathan R; Potts, Eric; Shaffrey, Mark; Shaffrey, Christopher I; Coric, Domagoj; Knightly, John; Park, Paul; Fu, Kai-Ming; Devin, Clinton J; Chotai, Silky; Chan, Andrew K; Virk, Michael; Asher, Anthony L; Bydon, Mohamad

    2017-08-01

    OBJECTIVE Lumbar spondylolisthesis is a degenerative condition that can be surgically treated with either open or minimally invasive decompression and instrumented fusion. Minimally invasive surgery (MIS) approaches may shorten recovery, reduce blood loss, and minimize soft-tissue damage with resultant reduced postoperative pain and disability. METHODS The authors queried the national, multicenter Quality Outcomes Database (QOD) registry for patients undergoing posterior lumbar fusion between July 2014 and December 2015 for Grade I degenerative spondylolisthesis. The authors recorded baseline and 12-month patient-reported outcomes (PROs), including Oswestry Disability Index (ODI), EQ-5D, numeric rating scale (NRS)-back pain (NRS-BP), NRS-leg pain (NRS-LP), and satisfaction (North American Spine Society satisfaction questionnaire). Multivariable regression models were fitted for hospital length of stay (LOS), 12-month PROs, and 90-day return to work, after adjusting for an array of preoperative and surgical variables. RESULTS A total of 345 patients (open surgery, n = 254; MIS, n = 91) from 11 participating sites were identified in the QOD. The follow-up rate at 12 months was 84% (83.5% [open surgery]; 85% [MIS]). Overall, baseline patient demographics, comorbidities, and clinical characteristics were similarly distributed between the cohorts. Two hundred fifty seven patients underwent 1-level fusion (open surgery, n = 181; MIS, n = 76), and 88 patients underwent 2-level fusion (open surgery, n = 73; MIS, n = 15). Patients in both groups reported significant improvement in all primary outcomes (all p open surgical groups. However, change in functional outcome scores for patients undergoing 2-level fusion was notably larger in the MIS cohort for ODI (-27 vs -16, p = 0.1), EQ-5D (0.27 vs 0.15, p = 0.08), and NRS-BP (-3.5 vs -2.7, p = 0.41); statistical significance was shown only for changes in NRS-LP scores (-4.9 vs -2.8, p = 0.02). On risk-adjusted analysis for 1

  17. Systematic review and meta-analysis of initial management of pneumothorax in adults: Intercostal tube drainage versus other invasive methods.

    Directory of Open Access Journals (Sweden)

    Min Joung Kim

    Full Text Available The ideal invasive management as initial approach for pneumothorax (PTX is still under debate. The purpose of this systematic review and meta-analysis was to examine the evidence for the effectiveness of intercostal tube drainage and other various invasive methods as the initial approach to all subtypes of PTX in adults.Three databases were searched from inception to May 29, 2016: MEDLINE, EMBASE, and the Cochrane CENTRAL. Randomised controlled trials that evaluated intercostal tube drainage as the control and various invasive methods as the intervention for the initial approach to PTX in adults were included. The primary outcome was the early success rate of each method, and the risk ratios (RRs were used for an effect size measure. The secondary outcomes were recurrence rate, hospitalization rate, hospital stay, and complications.Seven studies met our inclusion criteria. Interventions were aspiration in six studies and catheterization connected to a one-way valve in one study. Meta-analyses were conducted for early success rate, recurrence rate, hospitalization rate, and hospital stay. Aspiration was inferior to intercostal tube drainage in terms of early success rate (RR = 0.82, confidence interval [CI] = 0.72 to 0.95, I2 = 0%. While aspiration and intercostal tube drainage showed no significant difference in the recurrence rate (RR = 0.84, CI = 0.57 to 1.23, I2 = 0%, aspiration had shorter hospital stay than intercostal tube drainage (mean difference = -1.73, CI = -2.33 to -1.13, I2 = 0%. Aspiration had lower hospitalization rate than intercostal tube drainage, but marked heterogeneity was present (RR = 0.38, CI = 0.19 to 0.76, I2 = 85%.Aspiration was inferior to intercostal tube drainage in terms of early resolution, but it had shorter hospital stay. The recurrence rate of aspiration and intercostal tube drainage did not differ significantly. The efficacy of catheterization connected to a one-way valve was inconclusive because of the small

  18. An analysis of postoperative thigh symptoms after minimally invasive transpsoas lumbar interbody fusion.

    Science.gov (United States)

    Cummock, Matthew D; Vanni, Steven; Levi, Allan D; Yu, Yong; Wang, Michael Y

    2011-07-01

    The minimally invasive transpsoas interbody fusion technique requires dissection through the psoas muscle, which contains the nerves of the lumbosacral plexus posteriorly and genitofemoral nerve anteriorly. Retraction of the psoas is becoming recognized as a cause of transient postoperative thigh pain, numbness, paresthesias, and weakness. However, few reports have described the nature of thigh symptoms after this procedure. The authors performed a review of patients who underwent the transpsoas technique for lumbar spondylotic disease, disc degeneration, and spondylolisthesis treated at a single academic medical center. A review of patient charts, including the use of detailed patient-driven pain diagrams performed at equal preoperative and follow-up intervals, investigated the survival of postoperative thigh pain, numbness, paresthesias, and weakness of the iliopsoas and quadriceps muscles in the follow-up period on the ipsilateral side of the surgical approach. Over a 3.2-year period, 59 patients underwent transpsoas interbody fusion surgery. Of these, 62.7% had thigh symptoms postoperatively. New thigh symptoms at first follow-up visit included the following: burning, aching, stabbing, or other pain (39.0%); numbness (42.4%); paresthesias (11.9%); and weakness (23.7%). At 3 months postoperatively, these percentages decreased to 15.5%, 24.1%, 5.6%, and 11.3%, respectively. Within the patient sample, 44% underwent a 1-level, 41% a 2-level, and 15% a 3-level transpsoas operation. While not statistically significant, thigh pain, numbness, and weakness were most prevalent after L4-5 transpsoas interbody fusion at the first postoperative follow-up. The number of lumbar levels that were surgically treated had no clear association with thigh symptoms but did correlate directly with surgical time, intraoperative blood loss, and length of hospital stay. Transpsoas interbody fusion is associated with high rates of immediate postoperative thigh symptoms. While larger

  19. Cost-utility analysis of minimally invasive versus open multilevel hemilaminectomy for lumbar stenosis.

    Science.gov (United States)

    Parker, Scott L; Adogwa, Owoicho; Davis, Brandon J; Fulchiero, Erin; Aaronson, Oran; Cheng, Joseph; Devin, Clinton J; McGirt, Matthew J

    2013-02-01

    Two-year cost-utility study comparing minimally invasive (MIS) versus open multilevel hemilaminectomy in patients with degenerative lumbar spinal stenosis. The objective of the study was to determine whether MIS versus open multilevel hemilaminectomy for degenerative lumbar spinal stenosis is a cost-effective advancement in lumbar decompression surgery. MIS-multilevel hemilaminectomy for degenerative lumbar spinal stenosis allows for effective treatment of back and leg pain while theoretically minimizing blood loss, tissue injury, and postoperative recovery. No studies have evaluated comprehensive healthcare costs associated with multilevel hemilaminectomy procedures, nor assessed cost-effectiveness of MIS versus open multilevel hemilaminectomy. Fifty-four consecutive patients with lumbar stenosis undergoing multilevel hemilaminectomy through an MIS paramedian tubular approach (n=27) versus midline open approach (n=27) were included. Total back-related medical resource utilization, missed work, and health state values [quality adjusted life years (QALYs), calculated from EuroQuol-5D with US valuation] were assessed after 2-year follow-up. Two-year resource use was multiplied by unit costs based on Medicare national allowable payment amounts (direct cost) and work-day losses were multiplied by the self-reported gross-of-tax wage rate (indirect cost). Difference in mean total cost per QALY gained for MIS versus open hemilaminectomy was assessed as incremental cost-effectiveness ratio (ICER: COST(MIS)-COST(OPEN)/QALY(MIS)-QALY(OPEN)). MIS versus open cohorts were similar at baseline. MIS and open hemilaminectomy were associated with an equivalent cumulative gain of 0.72 QALYs 2 years after surgery. Mean direct medical costs, indirect societal costs, and total 2-year cost ($23,109 vs. $25,420; P=0.21) were similar between MIS and open hemilaminectomy. MIS versus open approach was associated with similar total costs and utility, making it a cost equivalent technology

  20. Minimally invasive repair of pectus excavatum: Analysis of the NSQIP database and the use of thoracoscopy.

    Science.gov (United States)

    Tetteh, Oswald; Rhee, Daniel S; Boss, Emily; Alaish, Samuel M; Garcia, Alejandro V

    2018-03-07

    The minimally invasive repair of pectus excavatum (MIRPE) has been widely accepted and has become a viable alternative to the open Ravitch technique. MIRPE has evolved over time with some advocating that a safe repair can be accomplished without direct visualization utilizing thoracoscopy. The MIRPE with and without a thoracoscopic approach has not been previously analyzed from a nationwide database to determine differences in safety and short-term outcomes. The American College of Surgeons National Surgical Quality Improvement Program-Pediatric (NSQIP-P) 2012-2015 database was used in identifying patients that had MIRPE using Current Procedural Terminology (CPT) codes and ICD-9CM/ICD-10CM postoperative diagnosis codes. Outcomes of interest were readmissions, reoperations, complications, cardiothoracic injury, operative time, and duration of hospital stay after surgery for MIRPE with and without thoracoscopy. Descriptive statistics, simple and multivariable logistic regressions, Fisher's exact, and Wilcoxon rank sum test were used to determine any differences in 30-day postoperative outcomes. There were 1569 MIRPE cases included. 15.9% (N=249) of MIRPE were done without thoracoscopy. There were no significant differences with the use of thoracoscopy compared to without thoracoscopy in the rate of readmissions (2.5 vs 4.8%; p=0.06), reoperations (1.4 vs 2.0%; p=0.57), postoperative complications (2.6% vs 3.2%; p=0.52), and cardiothoracic injuries (0.2% vs 0.0%; p=1.00). Unadjusted odds ratios (ORs) for readmission and reoperation comparing MIRPE with thoracoscopy to MIRPE without thoracoscopy were 0.51 (p<0.05) and 0.71 (p=0.50), respectively. Adjusted ORs were 0.49 (p=0.04) and 0.71 (p=0.50), respectively. There were no reported deaths, but two cardiothoracic injuries were recorded in the group with thoracoscopy. MIRPE with thoracoscopy was associated with longer operative time (mean 13.0min; p=0.00) and longer hospital stay (mean 0.37days; p<0.01) compared to

  1. Molecular cloning, structural analysis and expression of a zinc ...

    African Journals Online (AJOL)

    The results of prokaryotic expression of ZnBP and overexpression of the ZnBP gene in A. thaliana improve our understanding of the function of this gene. Future studies should investigate the molecular mechanisms involved in gland morphogenesis in cotton. Key words: Gossypium hirsutum, pigment gland, zinc binding ...

  2. RAPD-PCR molecular analysis of the threatened Cabrera's vole ...

    African Journals Online (AJOL)

    Optimal management and conservation programs of the threatened Cabrera's vole require investigating potential molecular genetic markers in the genomic background, if the few remaining fragile populations are to ... The results described Cabrera's vole populations as a single genetic unit with slightly restricted gene flow.

  3. Molecular analysis of cross-bacterial contamination detected in ...

    African Journals Online (AJOL)

    ... the isolate Delftia acidovorans BP(R2) and it is also coupled to protein with molecular weight 25-26 KDa. As well as, this bacterial contamination was the reason for the false positive results observed during the detection of HCV infections. Journal of Applied Sciences and Environmental Management Vol. 9(1) 2005: 5-10.

  4. Molecular Analysis of Multi-Drug Resistance (MDR) in ...

    African Journals Online (AJOL)

    This review therefore brings to light some of the processes involved in molecular typing of Mycobacterium tuberculosis strains like the use of restriction fragment length polymorphism (RFLP) and spoligotyping, which have become valuable tools in the epidemiology of tuberculosis, identification of genotypes and ...

  5. Cryogenic Collection of Complete Subsurface Samples for Molecular Biological Analysis

    Science.gov (United States)

    2012-05-01

    276.5318.1568 Moser, D. P., J. K. Fredrickson, D. R. Geist, E. V. Arntzen, A. D. Peacock , S.-M. W. Li, T. Spadoni, et al. (2003). Biogeochemical...Influencing Amplification Efficiency and Allele Drop-out in Single Cell PCR: Implications for Preimplantation Genetic Diagnosis. Molecular Human Reproduction

  6. Molecular Analysis of AFP and HSA Interactions with PTEN Protein

    Directory of Open Access Journals (Sweden)

    Mingyue Zhu

    2015-01-01

    Full Text Available Human cytoplasmic alpha-fetoprotein (AFP has been classified as a member of the albuminoid gene family. The protein sequence of AFP has significant homology to that of human serum albumin (HSA, but its biological characteristics are vastly different from HSA. The AFP functions as a regulator in the phosphatidylinositol 3-kinase (PI3K/protein kinase B (AKT pathway, but HSA plays a key role as a transport protein. To probe their molecular mechanisms, we have applied colocalization, coimmunoprecipitation (co-IP, and molecular docking approaches to analyze the differences between AFP and HSA. The data from colocalization and co-IP displayed a strong interaction between AFP and PTEN (phosphatase and tensin homolog, demonstrating that AFP did bind to PTEN, but HSA did not. The molecular docking study further showed that the AFP domains I and III could contact with PTEN. In silicon substitutions of AFP binding site residues at position 490M/K and 105L/R corresponding to residues K490 and R105 in HSA resulted in steric clashes with PTEN residues R150 and K46, respectively. These steric clashes may explain the reason why HSA cannot bind to PTEN. Ultimately, the experimental results and the molecular modeling data from the interactions of AFP and HSA with PTEN will help us to identify targets for designing drugs and vaccines against human hepatocellular carcinoma.

  7. Thermodynamic Models from Fluctuation Solution Theory Analysis of Molecular Simulations

    DEFF Research Database (Denmark)

    Christensen, Steen; Peters, Günther H.j.; Hansen, Flemming Yssing

    2007-01-01

    Fluctuation solution theory (FST) is employed to analyze results of molecular dynamics (MD) simulations of liquid mixtures. The objective is to generate parameters for macroscopic GE-models, here the modified Margules model. We present a strategy for choosing the number of parameters included...

  8. Molecular analysis of candidate probiotic effector molecules of Lactobacillus plantarum

    NARCIS (Netherlands)

    Remus, D.M.

    2012-01-01

    Probiotics are health-promoting microorganisms that exert their beneficial effects in several ways. While it is known that probiotic bacteria interact with cells of the host gastrointestinal tractand modulate cell-signaling responses by which they might promote health, the underlying molecular

  9. Molecular analysis of mutants of the Neurospora adenylosuccinate ...

    Indian Academy of Sciences (India)

    2012-08-07

    Aug 7, 2012 ... and mutants induced with X-ray, UV or chemical mutagens. ... We have sequenced the ad-8 locus from 13 of these mutants and identified the molecular nature ..... mutants in yeast by selection for constitutive behavior in pig-.

  10. A molecular cytogenetic analysis of introgression in Alstroemeria

    NARCIS (Netherlands)

    Kamstra, S.A.

    1999-01-01

    This thesis describes the results of a molecular cytogenetic investigation of the process of introgression in Alstroemeria . The aim of this study was to transfer chromosomes or genes from one Alstroemeria species into another. For this, two

  11. Molecular dynamic analysis of the structure of dendrimers

    Energy Technology Data Exchange (ETDEWEB)

    Canetta, E.; Maino, G. E-mail: maino@bologna.enea.it

    2004-01-01

    We present main results of molecular dynamics simulations that we have carried out in order to investigate structural properties of polyamidoamine (PAMAM) dendrimers. Obtained data confirm the PAMAM dendrimer structure proposed by experiments, performed by means of X-ray scattering (SAXS) and quasi-elastic light scattering (QELS) techniques.

  12. Molecular dynamic analysis of the structure of dendrimers

    International Nuclear Information System (INIS)

    Canetta, E.; Maino, G.

    2004-01-01

    We present main results of molecular dynamics simulations that we have carried out in order to investigate structural properties of polyamidoamine (PAMAM) dendrimers. Obtained data confirm the PAMAM dendrimer structure proposed by experiments, performed by means of X-ray scattering (SAXS) and quasi-elastic light scattering (QELS) techniques

  13. Molecular responses and expression analysis of genes in a ...

    African Journals Online (AJOL)

    Haloxylon ammodendron (C.A Mey.) Bunge is a xero-halophytic desert shrub with excellent drought resistance and salt tolerance. To decipher the molecular responses involved in its drought resistance, the cDNA-AFLP (amplified fragment length polymorphism) technique was employed to identify genes expressed ...

  14. Molecular characterization and expression analysis of a hepcidin ...

    African Journals Online (AJOL)

    Jane

    2011-08-03

    Aug 3, 2011 ... the liver, intestine and brain were 2.4, 1.5 and 2-fold increase, respectively, compared with the control animals after 5 days .... (sex change) of RFE attracted more attention (Cheng et al., 2003 ...... Molecular Biology. New York: ...

  15. Physiological response, molecular analysis and water use efficiency ...

    African Journals Online (AJOL)

    With a view to study the effects of irrigation scheduling on the water use efficiency and physiological response and molecular basis of maize hybrids of different maturity groups, a field experiment was conducted at Water Management Research Center (WMRC), Belvatagi, University of Agricultural Sciences, Dharwad, India ...

  16. Comparative molecular analysis of old olive ( Olea europaea L ...

    African Journals Online (AJOL)

    We compared the genetic profiles of six old olive cultivars from an Eastern Mediterranean Region of Turkey to 15 modern Turkish olive cultivars from different geographical origins. The RAPD profiles successfully clarified the molecular relationships among the genotypes tested. Seventeen RAPD primers generated 153 ...

  17. Comparative genomic hybridization analysis of benign and invasive male breast neoplasms

    DEFF Research Database (Denmark)

    Ojopi, Elida Paula Benquique; Cavalli, Luciane Regina; Cavalieri, Luciane Mara Bogline

    2002-01-01

    Comparative genomic hybridization (CGH) analysis was performed for the identification of chromosomal imbalances in two benign gynecomastias and one malignant breast carcinoma derived from patients with male breast disease and compared with cytogenetic analysis in two of the three cases. CGH...... analysis demonstrated overrepresentation of 8q in all three cases. One case of gynecomastia presented gain of 1p34.3 through pter, 11p14 through q12, and 17p11.2 through qter, and loss of 1q41 through qter and 4q33 through qter. The other gynecomastia presented del(1)(q41) as detected by both cytogenetic...

  18. Molecular analysis of childhood primitive neuroectodermal tumors defines markers associated with poor outcome

    DEFF Research Database (Denmark)

    Scheurlen, W G; Schwabe, G C; Joos, S

    1998-01-01

    PURPOSE: The diagnostic and prognostic significance of well-defined molecular markers was investigated in childhood primitive neuroectodermal tumors (PNET). MATERIALS AND METHODS: Using microsatellite analysis, Southern blot analysis, and fluorescence in situ hybridization (FISH), 30 primary tumors......: In our study, amplification of c-myc was a poor-prognosis marker in PNET. LOH of chromosome 17p was associated with metastatic disease. Molecular analysis of primary tumors using these markers may be useful for stratification of children with PNET in future prospective studies. The other aberrations...... investigated were not of significant prognostic value, but may provide an entry point for future large-scale molecular studies....

  19. Molecular Characterization of a Novel Family of Trypanosoma cruzi Surface Membrane Proteins (TcSMP) Involved in Mammalian Host Cell Invasion.

    Science.gov (United States)

    Martins, Nadini Oliveira; Souza, Renata Torres de; Cordero, Esteban Mauricio; Maldonado, Danielle Cortez; Cortez, Cristian; Marini, Marjorie Mendes; Ferreira, Eden Ramalho; Bayer-Santos, Ethel; Almeida, Igor Correia de; Yoshida, Nobuko; Silveira, José Franco da

    2015-11-01

    The surface coat of Trypanosoma cruzi is predominantly composed of glycosylphosphatidylinositol-anchored proteins, which have been extensively characterized. However, very little is known about less abundant surface proteins and their role in host-parasite interactions. Here, we described a novel family of T. cruzi surface membrane proteins (TcSMP), which are conserved among different T. cruzi lineages and have orthologs in other Trypanosoma species. TcSMP genes are densely clustered within the genome, suggesting that they could have originated by tandem gene duplication. Several lines of evidence indicate that TcSMP is a membrane-spanning protein located at the cellular surface and is released into the extracellular milieu. TcSMP exhibited the key elements typical of surface proteins (N-terminal signal peptide or signal anchor) and a C-terminal hydrophobic sequence predicted to be a trans-membrane domain. Immunofluorescence of live parasites showed that anti-TcSMP antibodies clearly labeled the surface of all T. cruzi developmental forms. TcSMP peptides previously found in a membrane-enriched fraction were identified by proteomic analysis in membrane vesicles as well as in soluble forms in the T. cruzi secretome. TcSMP proteins were also located intracellularly likely associated with membrane-bound structures. We demonstrated that TcSMP proteins were capable of inhibiting metacyclic trypomastigote entry into host cells. TcSMP bound to mammalian cells and triggered Ca2+ signaling and lysosome exocytosis, events that are required for parasitophorous vacuole biogenesis. The effects of TcSMP were of lower magnitude compared to gp82, the major adhesion protein of metacyclic trypomastigotes, suggesting that TcSMP may play an auxiliary role in host cell invasion. We hypothesized that the productive interaction of T. cruzi with host cells that effectively results in internalization may depend on diverse adhesion molecules. In the metacyclic forms, the signaling induced by

  20. Fouling development in direct contact membrane distillation: Non-invasive monitoring and destructive analysis

    KAUST Repository

    Fortunato, Luca; Jang, Yongsun; Lee, Jung Gil; Jeong, Sanghyun; Lee, Sangho; Leiknes, TorOve; Ghaffour, NorEddine

    2017-01-01

    of organic compounds and salts. Liquid chromatography with organic carbon detection (LC-OCD) analysis revealed the abundance of biopolymer in the fouling layer formed at the initial phase. In the second phase, formation of carbonate crystals on the membrane

  1. FieldTrip: Open source software for advanced analysis of MEG, EEG, and invasive electrophysiological data.

    Science.gov (United States)

    Oostenveld, Robert; Fries, Pascal; Maris, Eric; Schoffelen, Jan-Mathijs

    2011-01-01

    This paper describes FieldTrip, an open source software package that we developed for the analysis of MEG, EEG, and other electrophysiological data. The software is implemented as a MATLAB toolbox and includes a complete set of consistent and user-friendly high-level functions that allow experimental neuroscientists to analyze experimental data. It includes algorithms for simple and advanced analysis, such as time-frequency analysis using multitapers, source reconstruction using dipoles, distributed sources and beamformers, connectivity analysis, and nonparametric statistical permutation tests at the channel and source level. The implementation as toolbox allows the user to perform elaborate and structured analyses of large data sets using the MATLAB command line and batch scripting. Furthermore, users and developers can easily extend the functionality and implement new algorithms. The modular design facilitates the reuse in other software packages.

  2. Transmission risk assessment of invasive fluke Fascioloides magna using GIS-modelling and multicriteria analysis methods

    Directory of Open Access Journals (Sweden)

    Juhásová L.

    2017-06-01

    Full Text Available The combination of multicriteria analysis (MCA, particularly analytic hierarchy process (AHP and geographic information system (GIS were applied for transmission risk assessment of Fascioloides magna (Trematoda; Fasciolidae in south-western Slovakia. Based on the details on F. magna life cycle, the following risk factors (RF of parasite transmission were determined: intermediate (RFIH and final hosts (RFFH (biological factors, annual precipitation (RFAP, land use (RFLU, flooded area (RFFA, and annual mean air temperature (RFAT (environmental factors. Two types of risk analyses were modelled: (1 potential risk analysis was focused on the determination of the potential risk of parasite transmission into novel territories (data on F. magna occurrence were excluded; (2 actual risk analysis considered also the summary data on F. magna occurrence in the model region (risk factor parasite occurrence RFPO included in the analysis. The results of the potential risk analysis provided novel distribution pattern and revealed new geographical area as the potential risk zone of F. magna occurrence. Although the actual risk analysis revealed all four risk zones of F. magna transmission (acceptable, moderate, undesirable and unacceptable, its outputs were significantly affected by the data on parasite occurrence what reduced the informative value of the actual transmission risk assessment.

  3. Molecular analysis of MECP2 gene in Egyptian patients with Rett ...

    African Journals Online (AJOL)

    Molecular analysis of MECP2 gene in Egyptian patients with Rett syndrome. ... Egyptian Journal of Medical Human Genetics ... This study represents one of the limited MECP2 molecular analyses done on Egyptian patients with RTT, in which direct sequencing of MECP2 coding region in 10 female Egyptian patients ...

  4. Combined liver and extrahepatic bile duct resection for biliary invasion of colorectal metastasis: a case-cohort analysis and systematic review

    NARCIS (Netherlands)

    Wiggers, Jimme K.; te Riele, Wouter W.; van Dongen, Tristan H.; Verheij, Joanne; Busch, Olivier R. C.; van Gulik, Thomas M.

    2016-01-01

    Background: Colorectal liver metastases (CRLMs) with biliary invasion can be treated with a combined liver and extrahepatic bile duct resection. The aim of this study was to analyze outcomes of this procedure in a case-cohort analysis and systematic review. Methods: Consecutive patients who

  5. Early invasive vs conservative treatment strategies in women and men with unstable angina and non-ST-segment elevation myocardial infarction: a meta-analysis

    NARCIS (Netherlands)

    O'Donoghue, Michelle; Boden, William E.; Braunwald, Eugene; Cannon, Christopher P.; Clayton, Tim C.; de Winter, Robbert J.; Fox, Keith A. A.; Lagerqvist, Bo; McCullough, Peter A.; Murphy, Sabina A.; Spacek, Rudolf; Swahn, Eva; Wallentin, Lars; Windhausen, Fons; Sabatine, Marc S.

    2008-01-01

    CONTEXT: Although an invasive strategy is frequently used in patients with non-ST-segment elevation acute coronary syndromes (NSTE ACS), data from some trials suggest that this strategy may not benefit women. OBJECTIVE: To conduct a meta-analysis of randomized trials to compare the effects of an

  6. Spectroscopic analysis and molecular docking of imidazole derivatives and investigation of its reactive properties by DFT and molecular dynamics simulations

    Science.gov (United States)

    Thomas, Renjith; Hossain, Mossaraf; Mary, Y. Sheena; Resmi, K. S.; Armaković, Stevan; Armaković, Sanja J.; Nanda, Ashis Kumar; Ranjan, Vivek Kumar; Vijayakumar, G.; Van Alsenoy, C.

    2018-04-01

    Solvent-free synthesis pathway for obtaining two imidazole derivatives (2-chloro-1-(4-methoxyphenyl)-4,5-dimethyl-1H-imidazole (CLMPDI) and 1-(4-bromophenyl)-2-chloro-4,5-dimethyl-1H-imidazole (BPCLDI) has been reported in this work, followed by detailed experimental and computational spectroscopic characterization and reactivity study. Spectroscopic methods encompassed IR, FT-Raman and NMR techniques, with the mutual comparison of experimentally and computationally obtained results at DFT/B3LYP level of theory. Reactivity study based on DFT calculations encompassed molecular orbitals analysis, followed by calculations of molecular electrostatic potential (MEP) and average local ionization energy (ALIE) values, Fukui functions and bond dissociation energies (BDE). Additionally, the stability of title molecules in water has been investigated via molecular dynamics (MD) simulations, while interactivity with aspulvinonedimethylallyl transferase protein has been evaluated by molecular docking procedure. CLMPDI compound showed antimicrobial activity against all four bacterial strain in both gram positive and gram negative bacteria while, BPCLDI showed only in gram positive bacteria, Staphylococcus Aureus (MTCC1144). The first order hyperpolarizability of CLMPDI and BPCLDI are 20.15 and 6.10 times that of the standard NLO material urea.

  7. Epidemiology of invasive meningococcal disease in the Netherlands, 1960-2012: an analysis of national surveillance data

    NARCIS (Netherlands)

    Bijlsma, Merijn W.; Bekker, Vincent; Brouwer, Matthijs C.; Spanjaard, Lodewijk; van de Beek, Diederik; van der Ende, Arie

    2014-01-01

    Epidemiological data for invasive meningococcal disease is essential for public health policy and vaccine development. We analysed national surveillance data from the Netherlands for PorA coverage of two PorA-based meningococcal serogroup B vaccines to describe the epidemiology of invasive

  8. Regulation of in situ to invasive breast carcinoma transition

    Energy Technology Data Exchange (ETDEWEB)

    Polyak, Kornelia; Hu, Min; Yao, Jun; Carroll, Danielle K.; Weremowicz, Stanislawa; Chen, Haiyan; Carrasco, Daniel; Richardson, Andrea; Violette, Shelia; Gelman, Rebecca S.; Bissell, Mina J.; Schnitt, Stuart; Polyak, Kornelia

    2008-05-07

    The transition of ductal carcinoma in situ (DCIS) to invasive carcinoma is a key event in breast tumor progression that is poorly understood. Comparative molecular analysis of tumor epithelial cells from in situ and invasive tumors has failed to identify consistent tumor stage-specific differences. However, the myoepithelial cell layer, present only in DCIS, is a key distinguishing and diagnostic feature. To determine the contribution of non-epithelial cells to tumor progression, we analyzed the role of myoepithelial cells and fibroblasts in the progression of in situ carcinomas using a xenograft model of human DCIS. Progression to invasion was promoted by fibroblasts, but inhibited by normal myoepithelial cells. The invasive tumor cells from these progressed lesions formed DCIS rather than invasive cancers when re-injected into naive mice. Molecular profiles of myoepithelial and epithelial cells isolated from primary normal and cancerous human breast tissue samples corroborated findings obtained in the xenograft model. These results provide the proof of principle that breast tumor progression could occur in the absence of additional genetic alterations and that tumor growth and progression could be controlled by replacement of normal myoepithelial inhibitory signals.

  9. Regulation of In Situ to Invasive Breast CarcinomaTransition

    Energy Technology Data Exchange (ETDEWEB)

    Hu, Min; Carroll, Danielle K.; Weremowicz, Stanislawa; Chen,Haiyan; Carrasco, Daniel; Richardson, Andrea; Bissell, Mina; Violette,Shelia; Gelman, Rebecca S.; Schnitt, Stuart; Polyak, Kornelia

    2007-03-13

    The transition of ductal carcinoma in situ (DCIS) to invasive carcinoma is a key event in breast tumor progression that is poorly understood. Comparative molecular analysis of tumor epithelial cells from in situ and invasive tumors has failed to identify consistent tumor stage-specific differences. However, the myoepithelial cell layer, present only in DCIS, is a key distinguishing and diagnostic feature. To determine the contribution of non-epithelial cells to tumor progression, we analyzed the role of myoepithelial cells and fibroblasts in the progression of in situ carcinomas using a xenograft model of human DCIS. Progression to invasion was promoted by fibroblasts, but inhibited by normal myoepithelial cells. The invasive tumor cells from these progressed lesions formed DCIS rather than invasive cancers when re-injected into naive mice. Molecular profiles of myoepithelial and epithelial cells isolated from primary normal and cancerous human breast tissue samples corroborated findings obtained in the xenograft model. These results provide the proof of principle that breast tumor progression could occur in the absence of additional genetic alterations and that tumor growth and progression could be controlled by replacement of normal myoepithelial inhibitory signals.

  10. FieldTrip: Open source software for advanced analysis of MEG, EEG, and invasive electrophysiological data

    NARCIS (Netherlands)

    Oostenveld, R.; Fries, P.; Maris, E.G.G.; Schoffelen, J.M.

    2011-01-01

    This paper describes FieldTrip, an open source software package that we developed for the analysis of MEG, EEG, and other electrophysiological data. The software is implemented as a MATLAB toolbox and includes a complete set of consistent and user-friendly high-level functions that allow

  11. Minimally Invasive Percutaneous Nephrolithotomy versus Retrograde Intrarenal Surgery for Upper Urinary Stones: A Systematic Review and Meta-Analysis

    Directory of Open Access Journals (Sweden)

    Hongyang Jiang

    2017-01-01

    Full Text Available Minimally invasive percutaneous nephrolithotomy (mini-PCNL and retrograde intrarenal surgery (RIRS are both alternatives for PCNL to treat renal calculi. This study is aimed at comparing the stone-free rate (SFR and other surgery parameters of two approaches for treating upper urinary calculi. We performed this meta-analysis in September 2016 by searching studies about mini-PCNL and RIRS for treating upper urinary calculi in various databases, and RevMan v.5.3 was applied. Three randomized controlled trials and ten nonrandomized trials were included, involving a total of 1317 patients. Meta-analysis showed that mini-PCNL group led to a higher SFR [odds ratio: 1.96; 95% confidence interval: 1.46–2.64; P<0.00001] but brought a larger postoperative decrease in hemoglobin levels compared with RIRS. RIRS provided a shorter hospital time. There was no significant difference in operation time. Higher postoperative complications were detected in the mini-PCNL, but the difference was not significant. Grade I and III complications did not vary between two procedures, but grade II complications were of lower incidence in RIRS group. In the light of these results, compared with RIRS, mini-PCNL provided significantly higher SFR and efficiency quotient for managing calculi; however, it resulted in higher incidence of postoperative complications, larger hemoglobin drops, and longer hospital stay.

  12. Molecular malaria diagnostics: A systematic review and meta-analysis.

    Science.gov (United States)

    Roth, Johanna M; Korevaar, Daniël A; Leeflang, Mariska M G; Mens, Pètra F

    2016-01-01

    Accurate diagnosis of malaria is essential for identification and subsequent treatment of the disease. Currently, microscopy and rapid diagnostic tests are the most commonly used diagnostics, next to treatment based on clinical signs only. These tests are easy to deploy, but have a relatively high detection limit. With declining prevalence in many areas, there is an increasing need for more sensitive diagnostics. Molecular tools may be a suitable alternative, although costs and technical requirements currently hamper their implementation in resource limited settings. A range of (near) point-of-care diagnostics is therefore under development, including simplifications in sample preparation, amplification and/or read-out of the test. Accuracy data, in combination with technical characteristics, are essential in determining which molecular test, if any, would be the most promising to be deployed. This review presents a comprehensive overview of the currently available molecular malaria diagnostics, ranging from well-known tests to platforms in early stages of evaluation, and systematically evaluates their published accuracy. No important difference in accuracy was found between the most commonly used PCR-based assays (conventional, nested and real-time PCR), with most of them having high sensitivity and specificity, implying that there are no reasons other than practical ones to choose one technique over the other. Loop-mediated isothermal amplification and other (novel) diagnostics appear to be highly accurate as well, with some offering potential to be used in resource-limited settings.

  13. Invasive species and habitat degradation in Iberian streams: an analysis of their role in freshwater fish diversity loss.

    Science.gov (United States)

    Hermoso, Virgilio; Clavero, Miguel; Blanco-Garrido, Francisco; Prenda, José

    2011-01-01

    Mediterranean endemic freshwater fish are among the most threatened biota in the world. Distinguishing the role of different extinction drivers and their potential interactions is crucial for achieving conservation goals. While some authors argue that invasive species are a main driver of native species declines, others see their proliferation as a co-occurring process to biodiversity loss driven by habitat degradation. It is difficult to discern between the two potential causes given that few invaded ecosystems are free from habitat degradation, and that both factors may interact in different ways. Here we analyze the relative importance of habitat degradation and invasive species in the decline of native fish assemblages in the Guadiana River basin (southwestern Iberian Peninsula) using an information theoretic approach to evaluate interaction pathways between invasive species and habitat degradation (structural equation modeling, SEM). We also tested the possible changes in the functional relationships between invasive and native species, measured as the per capita effect of invasive species, using ANCOVA. We found that the abundance of invasive species was the best single predictor of natives' decline and had the highest Akaike weight among the set of predictor variables examined. Habitat degradation neither played an active role nor influenced the per capita effect of invasive species on natives. Our analyses indicated that downstream reaches and areas close to reservoirs had the most invaded fish assemblages, independently of their habitat degradation status. The proliferation of invasive species poses a strong threat to the persistence of native assemblages in highly fluctuating environments. Therefore, conservation efforts to reduce native freshwater fish diversity loss in Mediterranean rivers should focus on mitigating the effect of invasive species and preventing future invasions.

  14. Molecular-beam epitaxial growth and ion-beam analysis systems for functional materials research

    International Nuclear Information System (INIS)

    Takeshita, H.; Aoki, Y.; Yamamoto, S.; Naramoto, H.

    1992-01-01

    Experimental systems for molecular beam epitaxial growth and ion beam analysis have been designed and constructed for the research of inorganic functional materials such as thin films and superlattices. (author)

  15. Molecular cloning and anti-invasive activity of cathepsin L propeptide-like protein from Calotropis procera R. Br. against cancer cells.

    Science.gov (United States)

    Kwon, Chang Woo; Yang, Hee; Yeo, SuBin; Park, Kyung-Min; Jeong, Ae Jin; Lee, Ki Won; Ye, Sang-Kyu; Chang, Pahn-Shick

    2018-12-01

    Cathepsin L of cancer cells has been shown to play an important role in degradation of extracellular matrix for metastasis. In order to reduce cell invasion, cathepsin L propeptide-like proteins which are classified as the I29 family in the MEROPS peptidase database were characterized from Calotropis procera R. Br., rich in cysteine protease. Of 19 candidates, the cloned and expressed recombinant SnuCalCp03-propeptide (rSnuCalCp03-propeptide) showed a low nanomolar K i value of 2.3 ± 0.2 nM against cathepsin L. A significant inhibition of tumor cell invasion was observed with H1975, HT29, MDA-BM-231, PANC1, and PC3 with a 76, 67, 67, 63, and 79% reduction, respectively, in invasion observed in the presence of 400 nM of the rSnuCalCp03-propeptide. In addition, thermal and pH study showed rSnuCalCp03-propeptide consisting of secondary structures was stable at a broad range of temperatures (30-70 °C) and pH (2-10, except for 5 which is close to the isoelectric point of 5.2).

  16. Application of Deep Learning in Automated Analysis of Molecular Images in Cancer: A Survey

    Science.gov (United States)

    Xue, Yong; Chen, Shihui; Liu, Yong

    2017-01-01

    Molecular imaging enables the visualization and quantitative analysis of the alterations of biological procedures at molecular and/or cellular level, which is of great significance for early detection of cancer. In recent years, deep leaning has been widely used in medical imaging analysis, as it overcomes the limitations of visual assessment and traditional machine learning techniques by extracting hierarchical features with powerful representation capability. Research on cancer molecular images using deep learning techniques is also increasing dynamically. Hence, in this paper, we review the applications of deep learning in molecular imaging in terms of tumor lesion segmentation, tumor classification, and survival prediction. We also outline some future directions in which researchers may develop more powerful deep learning models for better performance in the applications in cancer molecular imaging. PMID:29114182

  17. Minimally-invasive Laser Ablation Inductively Coupled Plasma Mass Spectrometry analysis of model ancient copper alloys

    Energy Technology Data Exchange (ETDEWEB)

    Walaszek, Damian [University of Warsaw, Faculty of Chemistry, Biological and Chemical Research Centre, Żwirki i Wigury 101, 02-089 Warszawa (Poland); Laboratory for Analytical Chemistry, Swiss Federal Laboratories for Materials Science and Technology, Überlandstrasse 129, CH-8600 Dübendorf (Switzerland); Senn, Marianne; Wichser, Adrian [Laboratory for Analytical Chemistry, Swiss Federal Laboratories for Materials Science and Technology, Überlandstrasse 129, CH-8600 Dübendorf (Switzerland); Faller, Markus [Laboratory for Jointing Technology and Corrosion, Swiss Federal Laboratories for Materials Science and Technology, Überlandstrasse 129, CH-8600 Dübendorf (Switzerland); Wagner, Barbara; Bulska, Ewa [University of Warsaw, Faculty of Chemistry, Biological and Chemical Research Centre, Żwirki i Wigury 101, 02-089 Warszawa (Poland); Ulrich, Andrea [Laboratory for Analytical Chemistry, Swiss Federal Laboratories for Materials Science and Technology, Überlandstrasse 129, CH-8600 Dübendorf (Switzerland)

    2014-09-01

    This work describes an evaluation of a strategy for multi-elemental analysis of typical ancient bronzes (copper, lead bronze and tin bronze) by means of laser ablation inductively coupled plasma mass spectrometry (LA-ICPMS).The samples originating from archeological experiments on ancient metal smelting processes using direct reduction in a ‘bloomery’ furnace as well as historical casting techniques were investigated with the use of the previously proposed analytical procedure, including metallurgical observation and preliminary visual estimation of the homogeneity of the samples. The results of LA-ICPMS analysis were compared to the results of bulk composition obtained by X-ray fluorescence spectrometry (XRF) and by inductively coupled plasma mass spectrometry (ICPMS) after acid digestion. These results were coherent for most of the elements confirming the usefulness of the proposed analytical procedure, however the reliability of the quantitative information about the content of the most heterogeneously distributed elements was also discussed in more detail. - Highlights: • The previously proposed procedure was evaluated by analysis of model copper alloys. • The LA-ICPMS results were comparable to the obtained by means of XRF and ICPMS. • LA-ICPMS results indicated the usefulness of the proposed analytical procedure.

  18. Prognostic value of Ki-67 index in adult medulloblastoma after accounting for molecular subgroup: a retrospective clinical and molecular analysis.

    Science.gov (United States)

    Zhao, Fu; Zhang, Jing; Li, Peng; Zhou, Qiangyi; Zhang, Shun; Zhao, Chi; Wang, Bo; Yang, Zhijun; Li, Chunde; Liu, Pinan

    2018-04-23

    Medulloblastoma (MB) is a rare primary brain tumor in adults. We previously evaluated that combining both clinical and molecular classification could improve current risk stratification for adult MB. In this study, we aimed to identify the prognostic value of Ki-67 index in adult MB. Ki-67 index of 51 primary adult MBs was reassessed using a computer-based image analysis (Image-Pro Plus). All patients were followed up ranging from 12 months up to 15 years. Gene expression profiling and immunochemistry were used to establish the molecular subgroups in adult MB. Combined risk stratification models were designed based on clinical characteristics, molecular classification and Ki-67 index, and identified by multivariable Cox proportional hazards analysis. In our cohort, the mean Ki-67 value was 30.0 ± 11.3% (range 6.56-63.55%). The average Ki-67 value was significantly higher in LC/AMB than in CMB and DNMB (P = .001). Among three molecular subgroups, Group 4-tumors had the highest average Ki-67 value compared with WNT- and SHH-tumors (P = .004). Patients with Ki-67 index large than 30% displayed poorer overall survival (OS) and progression free survival (PFS) than those with Ki-67 less than 30% (OS: P = .001; PFS: P = .006). Ki-67 index (i.e. > 30%, < 30%) was identified as an independent significant prognostic factor (OS: P = .017; PFS: P = .024) by using multivariate Cox proportional hazards model. In conclusion, Ki-67 index can be considered as a valuable independent prognostic biomarker for adult patients with MB.

  19. Online molecular image repository and analysis system: A multicenter collaborative open-source infrastructure for molecular imaging research and application.

    Science.gov (United States)

    Rahman, Mahabubur; Watabe, Hiroshi

    2018-05-01

    Molecular imaging serves as an important tool for researchers and clinicians to visualize and investigate complex biochemical phenomena using specialized instruments; these instruments are either used individually or in combination with targeted imaging agents to obtain images related to specific diseases with high sensitivity, specificity, and signal-to-noise ratios. However, molecular imaging, which is a multidisciplinary research field, faces several challenges, including the integration of imaging informatics with bioinformatics and medical informatics, requirement of reliable and robust image analysis algorithms, effective quality control of imaging facilities, and those related to individualized disease mapping, data sharing, software architecture, and knowledge management. As a cost-effective and open-source approach to address these challenges related to molecular imaging, we develop a flexible, transparent, and secure infrastructure, named MIRA, which stands for Molecular Imaging Repository and Analysis, primarily using the Python programming language, and a MySQL relational database system deployed on a Linux server. MIRA is designed with a centralized image archiving infrastructure and information database so that a multicenter collaborative informatics platform can be built. The capability of dealing with metadata, image file format normalization, and storing and viewing different types of documents and multimedia files make MIRA considerably flexible. With features like logging, auditing, commenting, sharing, and searching, MIRA is useful as an Electronic Laboratory Notebook for effective knowledge management. In addition, the centralized approach for MIRA facilitates on-the-fly access to all its features remotely through any web browser. Furthermore, the open-source approach provides the opportunity for sustainable continued development. MIRA offers an infrastructure that can be used as cross-boundary collaborative MI research platform for the rapid

  20. Molecular cloning, expression and computational analysis of a water ...

    African Journals Online (AJOL)

    User

    2012-11-06

    Nov 6, 2012 ... analysis of a water stress inducible copper-containing ... Although, in slico analysis of the protein have indicated its probable structure and functions, further ..... based on protein data bank (PDB) template c1ksiA which.

  1. Non-invasive metabolomic analysis using a commercial NIR instrument for embryo selection

    Directory of Open Access Journals (Sweden)

    Ioannis A Sfontouris

    2013-01-01

    Full Text Available Context: Metabolomics was introduced in human in vitro fertilization (IVF for noninvasive identification of viable embryos with the highest developmental competence. Aims: To determine whether embryo selection using a commercial version of metabolomic analysis leads to increased implantation rates (IRs with fetal cardiac activity (FCA compared with morphology evaluation alone. Setting and Design: Randomized controlled trial from April to December 2010 at a private IVF unit. The study was terminated prematurely due to the market withdrawal of the instrument. Materials and Methods: IVF patients ≥18 and ≤43 years with ≥4 × 2PN were randomly allocated to metabolomic analysis combined with embryo morphology (ViaMetrics-E; metabolomics + morphology group or embryo morphology alone (morphology group. Cycles with frozen embryos, oocyte donations, or testicular biopsy were excluded. Statistical Analysis: Categorical and continuous data were analyzed for statistical significance using 2-tailed Fisher′s exact test and t-test, respectively. Statistical significance was accepted when P < 0.05. Results: A total of 125 patients were included in the study; 39 patients were allocated to metabolomics + morphology group and 86 patients to morphology group. Patients were stratified according to the day of embryo transfer (Days 2, 3, or 5. IRs with FCA were similar for Days 2 and 3 transfers in both groups. For Day 5 transfers, IRs with FCA were significantly higher in the metabolomics + morphology group (46.8% vs. 28.9%; P = 0.041; 95% confidence intervalp [CI]: 1.09-34.18. Pregnancy and live births rates were similar for Days 2, 3, and 5 in both groups. The study was terminated early following the voluntary market withdrawal of ViaMetrics-E in December 2010. Conclusions: Metabolomic analysis using the commercial near-infrared (NIR instrument does not appear to have a beneficial effect on pregnancy and live births, with improvement in IR with FCA for Day 5

  2. Application of a Portable XRF Spectrometer for the Non-Invasive analysis of Museum Metal Artefacts

    International Nuclear Information System (INIS)

    Karydas, A.G.

    2007-01-01

    The present paper reviews examples of the application of a portable - in house developed- X RF spectrometer for the analysis of museum metal artefacts in Greece. Specific topics are addressed, in particular, to which extent the qualitative or quantitative X RF analyses reveal important information about the raw materials and manufacture techniques used for gold, silver and bronze alloys in antiquity. The analytical information that it is gained by means of the X RF measurements is further assessed in comparison with the existing archaeometallurgical knowledge

  3. Molecular Laser Spectroscopy as a Tool for Gas Analysis Applications

    Directory of Open Access Journals (Sweden)

    Javis Anyangwe Nwaboh

    2011-01-01

    Full Text Available We have used the traceable infrared laser spectrometric amount fraction measurement (TILSAM method to perform absolute concentration measurements of molecular species using three laser spectroscopic techniques. We report results performed by tunable diode laser absorption spectroscopy (TDLAS, quantum cascade laser absorption spectroscopy (QCLAS, and cavity ring down spectroscopy (CRDS, all based on the TILSAM methodology. The measured results of the different spectroscopic techniques are in agreement with respective gravimetric values, showing that the TILSAM method is feasible with all different techniques. We emphasize the data quality objectives given by traceability issues and uncertainty analyses.

  4. Expression microarray meta-analysis identifies genes associated with Ras/MAPK and related pathways in progression of muscle-invasive bladder transition cell carcinoma.

    Directory of Open Access Journals (Sweden)

    Jonathan A Ewald

    Full Text Available The effective detection and management of muscle-invasive bladder Transition Cell Carcinoma (TCC continues to be an urgent clinical challenge. While some differences of gene expression and function in papillary (Ta, superficial (T1 and muscle-invasive (≥T2 bladder cancers have been investigated, the understanding of mechanisms involved in the progression of bladder tumors remains incomplete. Statistical methods of pathway-enrichment, cluster analysis and text-mining can extract and help interpret functional information about gene expression patterns in large sets of genomic data. The public availability of patient-derived expression microarray data allows open access and analysis of large amounts of clinical data. Using these resources, we investigated gene expression differences associated with tumor progression and muscle-invasive TCC. Gene expression was calculated relative to Ta tumors to assess progression-associated differences, revealing a network of genes related to Ras/MAPK and PI3K signaling pathways with increased expression. Further, we identified genes within this network that are similarly expressed in superficial Ta and T1 stages but altered in muscle-invasive T2 tumors, finding 7 genes (COL3A1, COL5A1, COL11A1, FN1, ErbB3, MAPK10 and CDC25C whose expression patterns in muscle-invasive tumors are consistent in 5 to 7 independent outside microarray studies. Further, we found increased expression of the fibrillar collagen proteins COL3A1 and COL5A1 in muscle-invasive tumor samples and metastatic T24 cells. Our results suggest that increased expression of genes involved in mitogenic signaling may support the progression of muscle-invasive bladder tumors that generally lack activating mutations in these pathways, while expression changes of fibrillar collagens, fibronectin and specific signaling proteins are associated with muscle-invasive disease. These results identify potential biomarkers and targets for TCC treatments, and

  5. PET-based molecular imaging in neuroscience

    International Nuclear Information System (INIS)

    Jacobs, A.H.; Heiss, W.D.; Li, H.; Knoess, C.; Schaller, B.; Kracht, L.; Monfared, P.; Vollmar, S.; Bauer, B.; Wagner, R.; Graf, R.; Wienhard, K.; Winkeler, A.; Rueger, A.; Klein, M.; Hilker, R.; Galldiks, N.; Herholz, K.; Sobesky, J.

    2003-01-01

    Positron emission tomography (PET) allows non-invasive assessment of physiological, metabolic and molecular processes in humans and animals in vivo. Advances in detector technology have led to a considerable improvement in the spatial resolution of PET (1-2 mm), enabling for the first time investigations in small experimental animals such as mice. With the developments in radiochemistry and tracer technology, a variety of endogenously expressed and exogenously introduced genes can be analysed by PET. This opens up the exciting and rapidly evolving field of molecular imaging, aiming at the non-invasive localisation of a biological process of interest in normal and diseased cells in animal models and humans in vivo. The main and most intriguing advantage of molecular imaging is the kinetic analysis of a given molecular event in the same experimental subject over time. This will allow non-invasive characterisation and ''phenotyping'' of animal models of human disease at various disease stages, under certain pathophysiological stimuli and after therapeutic intervention. The potential broad applications of imaging molecular events in vivo lie in the study of cell biology, biochemistry, gene/protein function and regulation, signal transduction, transcriptional regulation and characterisation of transgenic animals. Most importantly, molecular imaging will have great implications for the identification of potential molecular therapeutic targets, in the development of new treatment strategies, and in their successful implementation into clinical application. Here, the potential impact of molecular imaging by PET in applications in neuroscience research with a special focus on neurodegeneration and neuro-oncology is reviewed. (orig.)

  6. Effects of age on long-term outcomes after a routine invasive or selective invasive strategy in patients presenting with non-ST segment elevation acute coronary syndromes: a collaborative analysis of individual data from the FRISC II - ICTUS - RITA-3 (FIR) trials.

    Science.gov (United States)

    Damman, Peter; Clayton, Tim; Wallentin, Lars; Lagerqvist, Bo; Fox, Keith A A; Hirsch, Alexander; Windhausen, Fons; Swahn, Eva; Pocock, Stuart J; Tijssen, Jan G P; de Winter, Robbert J

    2012-02-01

    To perform a patient-pooled analysis of a routine invasive versus a selective invasive strategy in elderly patients with non-ST segment elevation acute coronary syndrome. A meta-analysis was performed of patient-pooled data from the FRISC II-ICTUS-RITA-3 (FIR) studies. (Un)adjusted HRs were calculated by Cox regression, with adjustments for variables associated with age and outcomes. The main outcome was 5-year cardiovascular death or myocardial infarction (MI) following routine invasive versus selective invasive management. Regarding the 5-year composite of cardiovascular death or MI, the routine invasive strategy was associated with a lower hazard in patients aged 65-74 years (HR 0.72, 95% CI 0.58 to 0.90) and those aged ≥75 years (HR 0.71, 95% CI 0.55 to 0.91), but not in those aged RITA-3).

  7. Prognostic significance of lymphovascular invasion in radical cystectomy on patients with bladder cancer: a systematic review and meta-analysis.

    Directory of Open Access Journals (Sweden)

    Hwanik Kim

    Full Text Available PURPOSE: The objective of the present study was to conduct a systematic review and meta-analysis of published literature to appraise the prognostic value of lymphovascular invasion (LVI in radical cystectomy specimens. MATERIALS AND METHODS: Following the PRISMA statement, PubMed, Cochrane Library, and SCOPUS database were searched from the respective dates of inception until June 2013. RESULTS: A total of 21 articles met the eligibility criteria for this systematic review, which included a total of 12,527 patients ranging from 57 to 4,257 per study. LVI was detected in 34.6% in radical cystectomy specimens. LVI was associated with higher pathological T stage and tumor grade, as well as lymph node metastasis. The pooled hazard ratio (HR was statistically significant for recurrence-free survival (pooled HR, 1.61; 95% confidence interval [CI], 1.26-2.06, cancer-specific survival (pooled HR, 1.67; 95% CI, 1.38-2.01, and overall survival (pooled HR, 1.67; 95% CI, 1.38-2.01, despite the heterogeneity among included studies. On sensitivity analysis, the pooled HRs and 95% CIs were not significantly altered when any one study was omitted. The funnel plot for overall survival demonstrated a certain degree of asymmetry, which showed slight publication bias. CONCLUSIONS: This meta-analysis indicates that LVI is significantly associated with poor outcome in patients with bladder cancer who underwent radical cystectomy. Adequately designed prospective studies are required to provide the precise prognostic significance of LVI in bladder cancer.

  8. The pathology of familial breast cancer: Immunohistochemistry and molecular analysis

    International Nuclear Information System (INIS)

    Osin, Pinchas P; Lakhani, Sunil R

    1999-01-01

    Extensive studies of BRCA1- and BRCA2-associated breast tumours have been carried out in the few years since the identification of these familial breast cancer predisposing genes. The morphological studies suggest that BRCA1 tumours differ from BRCA2 tumours and from sporadic breast cancers. Recent progress in immunohistochemistry and molecular biology techniques has enabled in-depth investigation of molecular pathology of these tumours. Studies to date have investigated issues such as steroid hormone receptor expression, mutation status of tumour suppressor genes TP53 and c-erbB2, and expression profiles of cell cycle proteins p21, p27 and cyclin D 1 . Despite relative paucity of data, strong evidence of unique biological characteristics of BRCA1-associated breast cancer is accumulating. BRCA1-associated tumours appear to show an increased frequency of TP53 mutations, frequent p53 protein stabilization and absence of imunoreactivity for steroid hormone receptors. Further studies of larger number of samples of both BRCA1- and BRCA2-associated tumours are necessary to clarify and confirm these observations

  9. Tool Sequence Trends in Minimally Invasive Surgery: Statistical Analysis and Implications for Predictive Control of Multifunction Instruments

    Directory of Open Access Journals (Sweden)

    Carl A. Nelson

    2012-01-01

    Full Text Available This paper presents an analysis of 67 minimally invasive surgical procedures covering 11 different procedure types to determine patterns of tool use. A new graph-theoretic approach was taken to organize and analyze the data. Through grouping surgeries by type, trends of common tool changes were identified. Using the concept of signal/noise ratio, these trends were found to be statistically strong. The tool-use trends were used to generate tool placement patterns for modular (multi-tool, cartridge-type surgical tool systems, and the same 67 surgeries were numerically simulated to determine the optimality of these tool arrangements. The results indicate that aggregated tool-use data (by procedure type can be employed to predict tool-use sequences with good accuracy, and also indicate the potential for artificial intelligence as a means of preoperative and/or intraoperative planning. Furthermore, this suggests that the use of multifunction surgical tools can be optimized to streamline surgical workflow.

  10. Utility of cement injection to stabilize split-depression tibial plateau fracture by minimally invasive methods: A finite element analysis.

    Science.gov (United States)

    Belaid, D; Vendeuvre, T; Bouchoucha, A; Brémand, F; Brèque, C; Rigoard, P; Germaneau, A

    2018-05-08

    Treatment for fractures of the tibial plateau is in most cases carried out by stable fixation in order to allow early mobilization. Minimally invasive technologies such as tibioplasty or stabilization by locking plate, bone augmentation and cement filling (CF) have recently been used to treat this type of fracture. The aim of this paper was to determine the mechanical behavior of the tibial plateau by numerically modeling and by quantifying the mechanical effects on the tibia mechanical properties from injury healing. A personalized Finite Element (FE) model of the tibial plateau from a clinical case has been developed to analyze stress distribution in the tibial plateau stabilized by balloon osteoplasty and to determine the influence of the cement injected. Stress analysis was performed for different stages after surgery. Just after surgery, the maximum von Mises stresses obtained for the fractured tibia treated with and without CF were 134.9 MPa and 289.9 MPa respectively on the plate. Stress distribution showed an increase of values in the trabecular bone in the treated model with locking plate and CF and stress reduction in the cortical bone in the model treated with locking plate only. The computed results of stresses or displacements of the fractured models show that the cement filling of the tibial depression fracture may increase implant stability, and decrease the loss of depression reduction, while the presence of the cement in the healed model renders the load distribution uniform. Copyright © 2018 Elsevier Ltd. All rights reserved.

  11. High Levels of Sample-to-Sample Variation Confound Data Analysis for Non-Invasive Prenatal Screening of Fetal Microdeletions.

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    Tianjiao Chu

    Full Text Available Our goal was to test the hypothesis that inter-individual genomic copy number variation in control samples is a confounding factor in the non-invasive prenatal detection of fetal microdeletions via the sequence-based analysis of maternal plasma DNA. The database of genomic variants (DGV was used to determine the "Genomic Variants Frequency" (GVF for each 50kb region in the human genome. Whole genome sequencing of fifteen karyotypically normal maternal plasma and six CVS DNA controls samples was performed. The coefficient of variation of relative read counts (cv.RTC for these samples was determined for each 50kb region. Maternal plasma from two pregnancies affected with a chromosome 5p microdeletion was also sequenced, and analyzed using the GCREM algorithm. We found strong correlation between high variance in read counts and GVF amongst controls. Consequently we were unable to confirm the presence of the microdeletion via sequencing of maternal plasma samples obtained from two sequential affected pregnancies. Caution should be exercised when performing NIPT for microdeletions. It is vital to develop our understanding of the factors that impact the sensitivity and specificity of these approaches. In particular, benign copy number variation amongst controls is a major confounder, and their effects should be corrected bioinformatically.

  12. Central Arterial Function Measured by Non-invasive Pulse Wave Analysis is Abnormal in Patients with Duchenne Muscular Dystrophy.

    Science.gov (United States)

    Ryan, Thomas D; Parent, John J; Gao, Zhiqian; Khoury, Philip R; Dupont, Elizabeth; Smith, Jennifer N; Wong, Brenda; Urbina, Elaine M; Jefferies, John L

    2017-08-01

    Duchenne muscular dystrophy (DMD) is an X-linked recessive disorder caused by mutation of dystrophin. Cardiovascular involvement includes dilated cardiomyopathy. Non-invasive assessment of vascular function has not been evaluated in DMD. We hypothesize arterial wave reflection is abnormal in patients with DMD. Pulse wave analysis was performed on DMD patients with a SphygmoCor SCOR-PVx System to determine central blood pressure and augmentation index (AIx) as an assessment of arterial wave reflection. Results were compared to a control group. A total of 43 patients with DMD were enrolled, and compared to 43 normal controls. Central systolic blood pressure was lower, while both AIx-75 (7.8 ± 9.6% vs. 2.1 ± 10.4%, p 0.01, DMD vs. normal) and AIx-not corrected (16.8 ± 10.1% vs. -3.6 ± 10.9, p wave reflection when compared to normal controls, which may represent increased arterial stiffness. Overall there appears to be no effect on ventricular systolic function, however the long-term consequence in this group is unknown. Further study is required to determine the mechanism of these differences, which may be related to the effects of systemic steroids or the role of dystrophin in vascular function.

  13. Pteros: fast and easy to use open-source C++ library for molecular analysis.

    Science.gov (United States)

    Yesylevskyy, Semen O

    2012-07-15

    An open-source Pteros library for molecular modeling and analysis of molecular dynamics trajectories for C++ programming language is introduced. Pteros provides a number of routine analysis operations ranging from reading and writing trajectory files and geometry transformations to structural alignment and computation of nonbonded interaction energies. The library features asynchronous trajectory reading and parallel execution of several analysis routines, which greatly simplifies development of computationally intensive trajectory analysis algorithms. Pteros programming interface is very simple and intuitive while the source code is well documented and easily extendible. Pteros is available for free under open-source Artistic License from http://sourceforge.net/projects/pteros/. Copyright © 2012 Wiley Periodicals, Inc.

  14. Oncological and functional outcomes of elderly men treated with HIFU vs. minimally invasive radical prostatectomy: A propensity score analysis.

    Science.gov (United States)

    Capogrosso, Paolo; Barret, Eric; Sanchez-Salas, Rafael; Nunes-Silva, Igor; Rozet, François; Galiano, Marc; Ventimiglia, Eugenio; Briganti, Alberto; Salonia, Andrea; Montorsi, Francesco; Cathelineau, Xavier

    2018-01-01

    To assess outcomes of whole gland high-intensity focused ultrasound (HIFU) as compared with minimally-invasive radical prostatectomy (MIRP) in elderly patients. Patients aged ≥70 years with, cT1-cT2 disease, biopsy Gleason score (GS) 3 + 3 or 3 + 4 and preoperative PSA ≤10 ng/mL were submitted to either whole-gland HIFU or MIRP. Propensity-score matching analysis was performed to ensure the baseline equivalence of groups. Follow-up visits were routinely performed assessing PSA and urinary function according to the International Continence Score (ICS) and the International Prostatic Symptoms Score (IPSS) questionnaires. Estimated rates of salvage-treatment free survival (SFS) overall-survival (OS), cancer-specific survival (CSS) and metastasis-free survival (MTS) were assessed and compared. Overall, 84 (33.3%) and 168 (66.7%) patients were treated with HIFU and MIRP, respectively. MIRP was associated with a 5-yrs SFS of 93.4% compared to 74.8% for HIFU (p < 0.01). The two groups did not differ in terms of OS and MTS. No cancer-related deaths were registered. Patients treated with HIFU showed better short-term (6-mos) continence outcomes [mean-ICS: 1.7 vs. 4.8; p = 0.005] but higher IPSS mean scores at 12-mos assessment. A comparable rate of patients experiencing post-treatment Clavien-Dindo grade ≥III complications was observed within the two groups. Whole-gland HIFU is a feasible treatment in elderly men with low-to intermediate-risk PCa and could be considered for patients either unfit for surgery, or willing a non-invasive treatment with a low morbidity burden, although a non-negligible risk of requiring subsequent treatment for recurrence should be expected. Copyright © 2017 Elsevier Ltd, BASO ~ The Association for Cancer Surgery, and the European Society of Surgical Oncology. All rights reserved.

  15. IN SITU NON-INVASIVE SOIL CARBON ANALYSIS: SAMPLE SIZE AND GEOSTATISTICAL CONSIDERATIONS.

    Energy Technology Data Exchange (ETDEWEB)

    WIELOPOLSKI, L.

    2005-04-01

    I discuss a new approach for quantitative carbon analysis in soil based on INS. Although this INS method is not simple, it offers critical advantages not available with other newly emerging modalities. The key advantages of the INS system include the following: (1) It is a non-destructive method, i.e., no samples of any kind are taken. A neutron generator placed above the ground irradiates the soil, stimulating carbon characteristic gamma-ray emission that is counted by a detection system also placed above the ground. (2) The INS system can undertake multielemental analysis, so expanding its usefulness. (3) It can be used either in static or scanning modes. (4) The volume sampled by the INS method is large with a large footprint; when operating in a scanning mode, the sampled volume is continuous. (5) Except for a moderate initial cost of about $100,000 for the system, no additional expenses are required for its operation over two to three years after which a NG has to be replenished with a new tube at an approximate cost of $10,000, this regardless of the number of sites analyzed. In light of these characteristics, the INS system appears invaluable for monitoring changes in the carbon content in the field. For this purpose no calibration is required; by establishing a carbon index, changes in carbon yield can be followed with time in exactly the same location, thus giving a percent change. On the other hand, with calibration, it can be used to determine the carbon stock in the ground, thus estimating the soil's carbon inventory. However, this requires revising the standard practices for deciding upon the number of sites required to attain a given confidence level, in particular for the purposes of upward scaling. Then, geostatistical considerations should be incorporated in considering properly the averaging effects of the large volumes sampled by the INS system that would require revising standard practices in the field for determining the number of spots to

  16. LincRNA-p21 inhibits invasion and metastasis of hepatocellular carcinoma through miR-9/E-cadherin cascade signaling pathway molecular mechanism

    Directory of Open Access Journals (Sweden)

    Ding G

    2017-06-01

    Full Text Available Gangqiang Ding, Zhen Peng, Jia Shang, Yi Kang, Huibin Ning, Chongshan Mao Department of Infectious Diseases, People’s Hospital of Zhengzhou University, Henan Provincial People’s Hospital, Zhengzhou, China Abstract: In the previous study, it was found that long intergenic noncoding RNA-p21 (lincRNA-p21 was downregulated in hepatocellular carcinoma (HCC and lincRNA-p21 overexpression inhibited tumor invasion through inducing epithelial–mesenchymal transition. However, the underlying mechanism was not fully elaborated. In this study, lincRNA-p21 expression was measured in 12 paired HCC and nontumor adjacent normal tissues by ­quantitative real-time polymerase chain reaction. The effects of lincRNA-p21 on HCC cells were studied using lentivirus expressing lincRNA-p21 vector in vitro. The association between lincRNA-p21 level and miR-9 level was tested with the Spearman rank correlation. The effects of miR-9 on HCC cells were studied by using miR-9 inhibitor in vitro. Luciferase assay was used to validate the target of miR-9. The results showed that lincRNA-p21 was downregulated in human HCC tissues and cell lines. LincRNA-p21 overexpression significantly inhibited HCC cell migration and invasion in vitro. Besides, lincRNA-p21 negatively regulated miR-9 expression level, and miR-9 was upregulated in human HCC tissues and cells. MiR-9 knockdown inhibited HCC cell migration and invasion in vitro. Finally, the luciferase assay results showed that E-cadherin was a direct target of miR-9. The expression level of E-cadherin was found to be regulated by lincRNA-p21 and miR-9. Altogether, the results suggested that lincRNA-p21 inhibits migration and invasion of HCC cells through regulating miR-9-mediated E-cadherin cascade signaling pathway. Keywords: hepatocellular carcinoma, lincRNA-p21, miR-9, E-cadherin, epithelial–mesenchymal transition

  17. A mistletoe tale: postglacial invasion of Psittacanthus schiedeanus (Loranthaceae) to Mesoamerican cloud forests revealed by molecular data and species distribution modeling.

    Science.gov (United States)

    Ornelas, Juan Francisco; Gándara, Etelvina; Vásquez-Aguilar, Antonio Acini; Ramírez-Barahona, Santiago; Ortiz-Rodriguez, Andrés Ernesto; González, Clementina; Mejía Saules, María Teresa; Ruiz-Sanchez, Eduardo

    2016-04-12

    Ecological adaptation to host taxa is thought to result in mistletoe speciation via race formation. However, historical and ecological factors could also contribute to explain genetic structuring particularly when mistletoe host races are distributed allopatrically. Using sequence data from nuclear (ITS) and chloroplast (trnL-F) DNA, we investigate the genetic differentiation of 31 Psittacanthus schiedeanus (Loranthaceae) populations across the Mesoamerican species range. We conducted phylogenetic, population and spatial genetic analyses on 274 individuals of P. schiedeanus to gain insight of the evolutionary history of these populations. Species distribution modeling, isolation with migration and Bayesian inference methods were used to infer the evolutionary transition of mistletoe invasion, in which evolutionary scenarios were compared through posterior probabilities. Our analyses revealed shallow levels of population structure with three genetic groups present across the sample area. Nine haplotypes were identified after sequencing the trnL-F intergenic spacer. These haplotypes showed phylogeographic structure, with three groups with restricted gene flow corresponding to the distribution of individuals/populations separated by habitat (cloud forest localities from San Luis Potosí to northwestern Oaxaca and Chiapas, localities with xeric vegetation in central Oaxaca, and localities with tropical deciduous forests in Chiapas), with post-glacial population expansions and potentially corresponding to post-glacial invasion types. Similarly, 44 ITS ribotypes suggest phylogeographic structure, despite the fact that most frequent ribotypes are widespread indicating effective nuclear gene flow via pollen. Gene flow estimates, a significant genetic signal of demographic expansion, and range shifts under past climatic conditions predicted by species distribution modeling suggest post-glacial invasion of P. schiedeanus mistletoes to cloud forests. However, Approximate

  18. A comparative analysis of three non-invasive Human-Machine Interfaces for the disabled

    Directory of Open Access Journals (Sweden)

    Vikram eRavindra

    2014-10-01

    Full Text Available In the framework of rehabilitation robotics, a major role is played by theHuman-Machine Interface (HMI used to gather the patient's intent from biologicalsignals, and convert them into control signals for the robotic artifact. Surprisingly,decades of research haven't yet declared what the optimal HMI is in this context;in particular, the traditional approach based upon surface electromyography (sEMGstill yields unreliable results due to the inherent variability of the signal. Toovercome this problem, the scientific community has recently been advocating thediscovery, analysis and usage of novel HMIs to supersede or augment sEMG; a comparativeanalysis of such HMIs is therefore a very desirable investigation.In this paper we compare three such HMIs employed in the detection of finger forces,namely sEMG, ultrasound imaging and pressure sensing. The comparison is performed alongfour main lines: the accuracy in the prediction, the stability over time, the wearabilityand the cost. A psychophysical experiment involving ten intact subjects engaged ina simple finger-flexion task was set up. Our results show that, at least in thisexperiment, pressure sensing and sEMG yield comparably good prediction accuraciesas opposed to ultrasound imaging; and that pressure sensing enjoys a much better stabilitythan sEMG.Given that pressure sensors are as wearable as sEMG electrodes but way cheaper, we claimthat this HMI could represent a valid alternative /augmentation to sEMG to control amulti-fingered hand prosthesis.

  19. MRI texture analysis in differentiating luminal A and luminal B breast cancer molecular subtypes - a feasibility study.

    Science.gov (United States)

    Holli-Helenius, Kirsi; Salminen, Annukka; Rinta-Kiikka, Irina; Koskivuo, Ilkka; Brück, Nina; Boström, Pia; Parkkola, Riitta

    2017-12-29

    The aim of this study was to use texture analysis (TA) of breast magnetic resonance (MR) images to assist in differentiating estrogen receptor (ER) positive breast cancer molecular subtypes. Twenty-seven patients with histopathologically proven invasive ductal breast cancer were selected in preliminary study. Tumors were classified into molecular subtypes: luminal A (ER-positive and/or progesterone receptor (PR)-positive, human epidermal growth factor receptor type 2 (HER2) -negative, proliferation marker Ki-67 MaZda. Texture parameters and tumour volumes were correlated with tumour prognostic factors. Textural differences were observed mainly in precontrast images. The two most discriminative texture parameters to differentiate luminal A and luminal B subtypes were sum entropy and sum variance (p = 0.003). The AUCs were 0.828 for sum entropy (p = 0.004), and 0.833 for sum variance (p = 0.003), and 0.878 for the model combining texture features sum entropy, sum variance (p = 0.001). In the LOOCV, the AUC for model combining features sum entropy and sum variance was 0.876. Sum entropy and sum variance showed positive correlation with higher Ki-67 index. Luminal B types were larger in volume and moderate correlation between larger tumour volume and higher Ki-67 index was also observed (r = 0.499, p = 0.008). Texture features which measure randomness, heterogeneity or smoothness and homogeneity may either directly or indirectly reflect underlying growth patterns of breast tumours. TA and volumetric analysis may provide a way to evaluate the biologic aggressiveness of breast tumours and provide aid in decisions regarding therapeutic efficacy.

  20. Progress on molecular imaging

    International Nuclear Information System (INIS)

    Chen Quan; Zhang Yongxue

    2011-01-01

    Molecular imaging is a new era of medical imaging,which can non-invasively monitor biological processes at the cellular and molecular level in vivo, including molecular imaging of nuclear medicine, magnetic resonance molecular imaging, ultrasound molecular imaging,optical molecular imaging and molecular imaging with X-ray. Recently, with the development of multi-subjects amalgamation, multimodal molecular imaging technology has been applied in clinical imaging, such as PET-CT and PET-MRI. We believe that with development of molecular probe and multi-modal imaging, more and more molecular imaging techniques will be applied in clinical diagnosis and treatment. (authors)

  1. Non-invasive volumetric analysis of asymptomatic hands using a 3-D scanner.

    Directory of Open Access Journals (Sweden)

    Hiroki Shinkai

    Full Text Available Hand swelling is one of the symptoms often seen in practice, but none of the available morphometric methods can quickly and efficiently quantify hand volume in an objective manner, and the current gold-standard volume measurement requires immersion in water, which can be difficult to use. Therefore, we aimed to analyze the accuracy of using 3-dimensional (3-D scanning to measure hand volume. First, we compared the hand volume calculated using the 3-D scanner to that calculated from the conventional method among 109 volunteers to determine the reliability of 3-D measurements. We defined the beginning of the hand as the distal wrist crease, and 3-D forms of the hands were captured by the 3-D scanning system. Second, 238 volunteers (87 men, 151 women with no disease or history of hand surgery underwent 3-D scanning. Data collected included age, height, weight, and shoe size. The wrist circumference (WC and the distance between distal wrist crease and tip of middle finger (DDT were measured. Statistical analyses were performed using linear regression to investigate the relationship between the hand volume and these parameters. In the first study, a significantly strong positive correlation was observed [R = 0.98] between the hand volume calculated via 3-D scanning and that calculated via the conventional method. In the second study, no significant differences between the volumes, WC or DDT of right and left hands were found. The correlations of hand volume with weight, WC, and DDT were strong. We created a formula to predict the hand volume using these parameters; these variables explained approximately 80% of the predicted volume. We confirmed that the new 3-D scanning method, which is performed without touching the hand and can record the form of the hand, yields an accurate volumetric analysis of an asymptomatic hand.

  2. Efficient distinction of invasive aquatic plant species from non-invasive related species using DNA barcoding.

    Science.gov (United States)

    Ghahramanzadeh, R; Esselink, G; Kodde, L P; Duistermaat, H; van Valkenburg, J L C H; Marashi, S H; Smulders, M J M; van de Wiel, C C M

    2013-01-01

    Biological invasions are regarded as threats to global biodiversity. Among invasive aliens, a number of plant species belonging to the genera Myriophyllum, Ludwigia and Cabomba, and to the Hydrocharitaceae family pose a particular ecological threat to water bodies. Therefore, one would try to prevent them from entering a country. However, many related species are commercially traded, and distinguishing invasive from non-invasive species based on morphology alone is often difficult for plants in a vegetative stage. In this regard, DNA barcoding could become a good alternative. In this study, 242 samples belonging to 26 species from 10 genera of aquatic plants were assessed using the chloroplast loci trnH-psbA, matK and rbcL. Despite testing a large number of primer sets and several PCR protocols, the matK locus could not be amplified or sequenced reliably and therefore was left out of the analysis. Using the other two loci, eight invasive species could be distinguished from their respective related species, a ninth one failed to produce sequences of sufficient quality. Based on the criteria of universal application, high sequence divergence and level of species discrimination, the trnH-psbA noncoding spacer was the best performing barcode in the aquatic plant species studied. Thus, DNA barcoding may be helpful with enforcing a ban on trade of such invasive species, such as is already in place in the Netherlands. This will become even more so once DNA barcoding would be turned into machinery routinely operable by a nonspecialist in botany and molecular genetics. © 2012 Blackwell Publishing Ltd.

  3. Novel markers for differentiation of lobular and ductal invasive breast carcinomas by laser microdissection and microarray analysis

    Directory of Open Access Journals (Sweden)

    Srovnal Josef

    2007-03-01

    Full Text Available Abstract Background Invasive ductal and lobular carcinomas (IDC and ILC are the most common histological types of breast cancer. Clinical follow-up data and metastatic patterns suggest that the development and progression of these tumors are different. The aim of our study was to identify gene expression profiles of IDC and ILC in relation to normal breast epithelial cells. Methods We examined 30 samples (normal ductal and lobular cells from 10 patients, IDC cells from 5 patients, ILC cells from 5 patients microdissected from cryosections of ten mastectomy specimens from postmenopausal patients. Fifty nanograms of total RNA were amplified and labeled by PCR and in vitro transcription. Samples were analysed upon Affymetrix U133 Plus 2.0 Arrays. The expression of seven differentially expressed genes (CDH1, EMP1, DDR1, DVL1, KRT5, KRT6, KRT17 was verified by immunohistochemistry on tissue microarrays. Expression of ASPN mRNA was validated by in situ hybridization on frozen sections, and CTHRC1, ASPN and COL3A1 were tested by PCR. Results Using GCOS pairwise comparison algorithm and rank products we have identified 84 named genes common to ILC versus normal cell types, 74 named genes common to IDC versus normal cell types, 78 named genes differentially expressed between normal ductal and lobular cells, and 28 named genes between IDC and ILC. Genes distinguishing between IDC and ILC are involved in epithelial-mesenchymal transition, TGF-beta and Wnt signaling. These changes were present in both tumor types but appeared to be more prominent in ILC. Immunohistochemistry for several novel markers (EMP1, DVL1, DDR1 distinguished large sets of IDC from ILC. Conclusion IDC and ILC can be differentiated both at the gene and protein levels. In this study we report two candidate genes, asporin (ASPN and collagen triple helix repeat containing 1 (CTHRC1 which might be significant in breast carcinogenesis. Besides E-cadherin, the proteins validated on tissue

  4. Novel markers for differentiation of lobular and ductal invasive breast carcinomas by laser microdissection and microarray analysis

    International Nuclear Information System (INIS)

    Turashvili, Gulisa; Srovnal, Josef; Hajduch, Marian; Murray, Paul; Kolar, Zdenek; Bouchal, Jan; Baumforth, Karl; Wei, Wenbin; Dziechciarkova, Marta; Ehrmann, Jiri; Klein, Jiri; Fridman, Eduard; Skarda, Jozef

    2007-01-01

    Invasive ductal and lobular carcinomas (IDC and ILC) are the most common histological types of breast cancer. Clinical follow-up data and metastatic patterns suggest that the development and progression of these tumors are different. The aim of our study was to identify gene expression profiles of IDC and ILC in relation to normal breast epithelial cells. We examined 30 samples (normal ductal and lobular cells from 10 patients, IDC cells from 5 patients, ILC cells from 5 patients) microdissected from cryosections of ten mastectomy specimens from postmenopausal patients. Fifty nanograms of total RNA were amplified and labeled by PCR and in vitro transcription. Samples were analysed upon Affymetrix U133 Plus 2.0 Arrays. The expression of seven differentially expressed genes (CDH1, EMP1, DDR1, DVL1, KRT5, KRT6, KRT17) was verified by immunohistochemistry on tissue microarrays. Expression of ASPN mRNA was validated by in situ hybridization on frozen sections, and CTHRC1, ASPN and COL3A1 were tested by PCR. Using GCOS pairwise comparison algorithm and rank products we have identified 84 named genes common to ILC versus normal cell types, 74 named genes common to IDC versus normal cell types, 78 named genes differentially expressed between normal ductal and lobular cells, and 28 named genes between IDC and ILC. Genes distinguishing between IDC and ILC are involved in epithelial-mesenchymal transition, TGF-beta and Wnt signaling. These changes were present in both tumor types but appeared to be more prominent in ILC. Immunohistochemistry for several novel markers (EMP1, DVL1, DDR1) distinguished large sets of IDC from ILC. IDC and ILC can be differentiated both at the gene and protein levels. In this study we report two candidate genes, asporin (ASPN) and collagen triple helix repeat containing 1 (CTHRC1) which might be significant in breast carcinogenesis. Besides E-cadherin, the proteins validated on tissue microarrays (EMP1, DVL1, DDR1) may represent novel

  5. Realizations of highly heterogeneous collagen networks via stochastic reconstruction for micromechanical analysis of tumor cell invasion

    Science.gov (United States)

    Nan, Hanqing; Liang, Long; Chen, Guo; Liu, Liyu; Liu, Ruchuan; Jiao, Yang

    2018-03-01

    of cells are analyzed by considering a nonlinear fiber model incorporating strain hardening upon large stretching and buckling upon compression. Our analysis shows that oriented fibers can significantly enhance long-range force transmission in the network. Moreover, in the oriented-collagen-Matrigel system, the forces generated by a polarized cell in collagen can penetrate deeply into the Matrigel region. The stressed Matrigel fibers could provide contact guidance for the migrating cell cells, and thus enhance their penetration into Matrigel. This suggests a possible mechanism for the observed enhanced intravasation by oriented collagen.

  6. Multidisciplinary analysis of invasive meningococcal disease as a framework for continuous quality and safety improvement in regional Australia.

    Science.gov (United States)

    Taylor, Kathryn A; Durrheim, David N; Merritt, Tony; Massey, Peter; Ferguson, John; Ryan, Nick; Hullick, Carolyn

    2018-01-01

    System factors in a regional Australian health district contributed to avoidable care deviations from invasive meningococcal disease (IMD) management guidelines. Traditional root cause analysis (RCA) is not well-suited to IMD, focusing on individual cases rather than system improvements. As IMD requires complex care across healthcare silos, it presents an opportunity to explore and address system-based patient safety issues. Baseline assessment of IMD cases (2005-2006) identified inadequate triage, lack of senior clinician review, inconsistent vital sign recording and laboratory delays as common issues, resulting in antibiotic administration delays and inappropriate or premature discharge. Clinical governance, in partnership with clinical and public health services, established a multidisciplinary Meningococcal Reference Group (MRG) to routinely review management of all IMD cases. The MRG comprised representatives from primary care, acute care, public health, laboratory medicine and clinical governance. Baseline data were compared with two subsequent evaluation points (2011-2012 and 2013-2015). Phase I involved multidisciplinary process mapping and development of a standardised audit tool from national IMD management guidelines. Phase II involved formalisation of group processes and advocacy for operational change. Phase III focused on dissemination of findings to clinicians and managers. Greatest care improvements were observed in the final evaluation. Median antibiotic delay decreased from 72 to 42 min and proportion of cases triaged appropriately improved from 38% to 75% between 2013 and 2015. Increasing fatal outcomes were attributed to the emergence of more virulent meningococcal serotypes. The MRG was a key mechanism for identifying system gaps, advocating for change and enhancing communication and coordination across services. Employing IMD case review as a focus for district-level process reflection presents an innovative patient safety approach

  7. Cost-benefit analysis for invasive species control: the case of greater Canada goose Branta canadensis in Flanders (northern Belgium

    Directory of Open Access Journals (Sweden)

    Nikolaas Reyns

    2018-01-01

    Full Text Available Background Sound decisions on control actions for established invasive alien species (IAS require information on ecological as well as socio-economic impact of the species and of its management. Cost-benefit analysis provides part of this information, yet has received relatively little attention in the scientific literature on IAS. Methods We apply a bio-economic model in a cost-benefit analysis framework to greater Canada goose Branta canadensis, an IAS with documented social, economic and ecological impacts in Flanders (northern Belgium. We compared a business as usual (BAU scenario which involved non-coordinated hunting and egg destruction with an enhanced scenario based on a continuation of these activities but supplemented with coordinated capture of moulting birds. To assess population growth under the BAU scenario we fitted a logistic growth model to the observed pre-moult capture population. Projected damage costs included water eutrophication and damage to cultivated grasslands and were calculated for all scenarios. Management costs of the moult captures were based on a representative average of the actual cost of planning and executing moult captures. Results Comparing the scenarios with different capture rates, different costs for eutrophication and various discount rates, showed avoided damage costs were in the range of 21.15 M€ to 45.82 M€ under the moult capture scenario. The lowest value for the avoided costs applied to the scenario where we lowered the capture rate by 10%. The highest value occurred in the scenario where we lowered the real discount rate from 4% to 2.5%. Discussion The reduction in damage costs always outweighed the additional management costs of moult captures. Therefore, additional coordinated moult captures could be applied to limit the negative economic impact of greater Canada goose at a regional scale. We further discuss the strengths and weaknesses of our approach and its potential application to other

  8. Computed tomography for preoperative planning in minimal-invasive total hip arthroplasty: Radiation exposure and cost analysis

    Energy Technology Data Exchange (ETDEWEB)

    Huppertz, Alexander, E-mail: Alexander.Huppertz@charite.de [Imaging Science Institute Charite Berlin, Robert-Koch-Platz 7, D-10115 Berlin (Germany); Department of Radiology, Medical Physics, Charite-University Hospitals of Berlin, Chariteplatz 1, D-10117 Berlin (Germany); Radmer, Sebastian, E-mail: s.radmer@immanuel.de [Department of Orthopedic Surgery and Rheumatology, Immanuel-Krankenhaus, Koenigstr. 63, D-14109, Berlin (Germany); Asbach, Patrick, E-mail: Patrick.Asbach@charite.de [Department of Radiology, Medical Physics, Charite-University Hospitals of Berlin, Chariteplatz 1, D-10117 Berlin (Germany); Juran, Ralf, E-mail: ralf.juran@charite.de [Department of Radiology, Medical Physics, Charite-University Hospitals of Berlin, Chariteplatz 1, D-10117 Berlin (Germany); Schwenke, Carsten, E-mail: carsten.schwenke@scossis.de [Biostatistician, Scossis Statistical Consulting, Zeltinger Str. 58G, D-13465 Berlin (Germany); Diederichs, Gerd, E-mail: gerd.diederichs@charite.de [Department of Radiology, Medical Physics, Charite-University Hospitals of Berlin, Chariteplatz 1, D-10117 Berlin (Germany); Hamm, Bernd, E-mail: Bernd.Hamm@charite.de [Department of Radiology, Medical Physics, Charite-University Hospitals of Berlin, Chariteplatz 1, D-10117 Berlin (Germany); Sparmann, Martin, E-mail: m.sparmann@immanuel.de [Department of Orthopedic Surgery and Rheumatology, Immanuel-Krankenhaus, Koenigstr. 63, D-14109, Berlin (Germany)

    2011-06-15

    Computed tomography (CT) was used for preoperative planning of minimal-invasive total hip arthroplasty (THA). 92 patients (50 males, 42 females, mean age 59.5 years) with a mean body-mass-index (BMI) of 26.5 kg/m{sup 2} underwent 64-slice CT to depict the pelvis, the knee and the ankle in three independent acquisitions using combined x-, y-, and z-axis tube current modulation. Arthroplasty planning was performed using 3D-Hip Plan (Symbios, Switzerland) and patient radiation dose exposure was determined. The effects of BMI, gender, and contralateral THA on the effective dose were evaluated by an analysis-of-variance. A process-cost-analysis from the hospital perspective was done. All CT examinations were of sufficient image quality for 3D-THA planning. A mean effective dose of 4.0 mSv (SD 0.9 mSv) modeled by the BMI (p < 0.0001) was calculated. The presence of a contralateral THA (9/92 patients; p = 0.15) and the difference between males and females were not significant (p = 0.08). Personnel involved were the radiologist (4 min), the surgeon (16 min), the radiographer (12 min), and administrative personnel (4 min). A CT operation time of 11 min and direct per-patient costs of 52.80 Euro were recorded. Preoperative CT for THA was associated with a slight and justifiable increase of radiation exposure in comparison to conventional radiographs and low per-patient costs.

  9. Cost-benefit analysis for invasive species control: the case of greater Canada goose Branta canadensis in Flanders (northern Belgium)

    Science.gov (United States)

    Casaer, Jim; De Smet, Lieven; Devos, Koen; Huysentruyt, Frank; Robertson, Peter A.; Verbeke, Tom

    2018-01-01

    Background Sound decisions on control actions for established invasive alien species (IAS) require information on ecological as well as socio-economic impact of the species and of its management. Cost-benefit analysis provides part of this information, yet has received relatively little attention in the scientific literature on IAS. Methods We apply a bio-economic model in a cost-benefit analysis framework to greater Canada goose Branta canadensis, an IAS with documented social, economic and ecological impacts in Flanders (northern Belgium). We compared a business as usual (BAU) scenario which involved non-coordinated hunting and egg destruction with an enhanced scenario based on a continuation of these activities but supplemented with coordinated capture of moulting birds. To assess population growth under the BAU scenario we fitted a logistic growth model to the observed pre-moult capture population. Projected damage costs included water eutrophication and damage to cultivated grasslands and were calculated for all scenarios. Management costs of the moult captures were based on a representative average of the actual cost of planning and executing moult captures. Results Comparing the scenarios with different capture rates, different costs for eutrophication and various discount rates, showed avoided damage costs were in the range of 21.15 M€ to 45.82 M€ under the moult capture scenario. The lowest value for the avoided costs applied to the scenario where we lowered the capture rate by 10%. The highest value occurred in the scenario where we lowered the real discount rate from 4% to 2.5%. Discussion The reduction in damage costs always outweighed the additional management costs of moult captures. Therefore, additional coordinated moult captures could be applied to limit the negative economic impact of greater Canada goose at a regional scale. We further discuss the strengths and weaknesses of our approach and its potential application to other IAS. PMID

  10. Estrogen receptor beta rs1271572 polymorphism and invasive ovarian carcinoma risk: pooled analysis within the Ovarian Cancer Association Consortium.

    Directory of Open Access Journals (Sweden)

    Galina Lurie

    Full Text Available The association of ovarian carcinoma risk with the polymorphism rs1271572 in the estrogen receptor beta (ESR2 gene was examined in 4946 women with primary invasive ovarian carcinoma and 6582 controls in a pooled analysis of ten case-control studies within the Ovarian Cancer Association Consortium (OCAC. All participants were non-Hispanic white women. Odds ratios (ORs and 95% confidence intervals (CIs were estimated using unconditional logistic regression adjusted for site and age. Women with the TT genotype were at increased risk of ovarian carcinoma compared to carriers of the G allele (OR = 1.10; 95%; CI: 1.01-1.21; p = 0.04; the OR was 1.09 (CI: 0.99-1.20; p = 0.07 after excluding data from the center (Hawaii that nominated this SNP for OCAC genotyping A stronger association of rs1271572 TT versus GT/GG with risk was observed among women aged ≤50 years versus older women (OR = 1.35; CI: 1.12-1.62; p = 0.002; p for interaction = 0.02 that remained statistically significant after excluding Hawaii data (OR = 1.34; CI: 1.11-1.61; p = 0.009. No heterogeneity of the association was observed by study, menopausal status, gravidity, parity, use of contraceptive or menopausal hormones, tumor histological type, or stage at diagnosis. This pooled analysis suggests that rs1271572 might influence the risk of ovarian cancer, in particular among younger women.

  11. Women's perspectives on the ethical implications of non-invasive prenatal testing: a qualitative analysis to inform health policy decisions.

    Science.gov (United States)

    Vanstone, Meredith; Cernat, Alexandra; Nisker, Jeff; Schwartz, Lisa

    2018-04-16

    Non-Invasive Prenatal Testing (NIPT) is a technology which provides information about fetal genetic characteristics (including sex) very early in pregnancy by examining fetal DNA obtained from a sample of maternal blood. NIPT is a morally complex technology that has advanced quickly to market with a strong push from industry developers, leaving many areas of uncertainty still to be resolved, and creating a strong need for health policy that reflects women's social and ethical values. We approach the need for ethical policy-making by studying the use of NIPT and emerging policy in the province of Ontario, Canada. Using an adapted version of constructivist grounded theory, we conducted interviews with 38 women who have had personal experiences with NIPT. We used an iterative process of data collection and analysis and a staged coding strategy to conduct a descriptive analysis of ethics issues identified implicitly and explicitly by women who have been affected by this technology. The findings of this paper focus on current ethical issues for women seeking NIPT, including place in the prenatal pathway, health care provider counselling about the test, industry influence on the diffusion of NIPT, consequences of availability of test results. Other issues gain relevance in the context of future policy decisions regarding NIPT, including funding of NIPT and principles that may govern the expansion of the scope of NIPT. These findings are not an exhaustive list of all the potential ethical issues related to NIPT, but rather a representation of the issues which concern women who have personal experience with this test. Women who have had personal experience with NIPT have concerns and priorities which sometimes contrast dramatically with the theoretical ethics literature. These findings suggest the importance of engaging patients in ethical deliberation about morally complex technologies, and point to the need for more deliberative patient engagement work in this area.

  12. Clinical and molecular genetic analysis of best vitelliform macular dystrophy.

    NARCIS (Netherlands)

    Boon, C.J.F.; Theelen, T.; Hoefsloot, L.H.; Schooneveld, M.J. van; Keunen, J.E.E.; Cremers, F.P.M.; Klevering, B.J.; Hoyng, C.B.

    2009-01-01

    PURPOSE: To describe the phenotype of Best vitelliform macular dystrophy (BVMD) and to evaluate genotype-phenotype and histopathologic correlations. METHODS: Retrospective analysis of patients with BVMD who underwent an extensive ophthalmic examination, including best-corrected Snellen visual

  13. CLINICAL AND MOLECULAR GENETIC ANALYSIS OF BEST VITELLIFORM MACULAR DYSTROPHY

    NARCIS (Netherlands)

    Boon, Camiel J. F.; Theelen, Thomas; Hoefsloot, Elisabeth H.; van Schooneveld, Mary J.; Keunen, Jan E. E.; Cremers, Frans P. M.; Klevering, B. Jeroen; Hoyng, Carel B.

    2009-01-01

    Purpose: To describe the phenotype of Best vitelliform macular dystrophy (BVMD) and to evaluate genotype-phenotype and histopathologic correlations. Methods: Retrospective analysis of patients with BVMD who underwent an extensive ophthalmic examination, including best-corrected Snellen visual

  14. Molecular cloning, characterization and functional analysis of a 3 ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-08-04

    Aug 4, 2009 ... other plant HMGRs and contained 2 transmembrane domains and a catalytic domain. The potential significance ... used as animal feed. Therefore ... Table 1. Primers used in the cloning and analysis of JcHMGR gene. Primers.

  15. Molecular cloning and characterization of NcROP2Fam-1, a member of the ROP2 family of rhoptry proteins in Neospora caninum that is targeted by antibodies neutralizing host cell invasion in vitro.

    Science.gov (United States)

    Alaeddine, Ferial; Hemphill, Andrew; Debache, Karim; Guionaud, Christophe

    2013-07-01

    Recent publications demonstrated that a fragment of a Neospora caninum ROP2 family member antigen represents a promising vaccine candidate. We here report on the cloning of the cDNA encoding this protein, N. caninum ROP2 family member 1 (NcROP2Fam-1), its molecular characterization and localization. The protein possesses the hallmarks of ROP2 family members and is apparently devoid of catalytic activity. NcROP2Fam-1 is synthesized as a pre-pro-protein that is matured to 2 proteins of 49 and 55 kDa that localize to rhoptry bulbs. Upon invasion the protein is associated with the nascent parasitophorous vacuole membrane (PVM), evacuoles surrounding the host cell nucleus and, in some instances, the surface of intracellular parasites. Staining was also observed within the cyst wall of 'cysts' produced in vitro. Interestingly, NcROP2Fam-1 was also detected on the surface of extracellular parasites entering the host cells and antibodies directed against NcROP2Fam-1-specific peptides partially neutralized invasion in vitro. We conclude that, in spite of the general belief that ROP2 family proteins are intracellular antigens, NcROP2Fam-1 can also be considered as an extracellular antigen, a property that should be taken into account in further experiments employing ROP2 family proteins as vaccines.

  16. Open-Source Processing and Analysis of Aerial Imagery Acquired with a Low-Cost Unmanned Aerial System to Support Invasive Plant Management

    Directory of Open Access Journals (Sweden)

    Jan R. K. Lehmann

    2017-07-01

    Full Text Available Remote sensing by Unmanned Aerial Systems (UAS is a dynamic evolving technology. UAS are particularly useful in environmental monitoring and management because they have the capability to provide data at high temporal and spatial resolutions. Moreover, data acquisition costs are lower than those of conventional methods such as extensive ground sampling, manned airplanes, or satellites. Small fixed-wing UAS in particular offer further potential benefits as they extend the operational coverage of the area under study at lower operator risks and accelerate data deployment times. Taking these aspects into account, UAS might be an effective tool to support management of invasive plant based on early detection and regular monitoring. A straightforward UAS approach to map invasive plant species is presented in this study with the intention of providing ready-to-use field maps essential for action-oriented management. Our UAS utilizes low-cost sensors, free-of-charge software for mission planning and an affordable, commercial aerial platform to reduce operational costs, reducing expenses with personnel while increasing overall efficiency. We illustrate our approach using a real example of invasion by Acacia mangium in a Brazilian Savanna ecosystem. A. mangium was correctly identified with an overall accuracy of 82.7% from the analysis of imagery. This approach provides land management authorities and practitioners with new prospects for environmental restoration in areas where invasive plant species are present.

  17. Molecular analysis of manufactured gas plant soils for naphthalene mineralization

    International Nuclear Information System (INIS)

    Sanseverino, J.; Werner, C.; Fleming, J.; Applegate, B.M.; King, J.M.H.; Sayler, G.S.; Blackburn, J.

    1991-01-01

    New molecular tools are being developed and tested to ascertain the biodegradability of hazardous wastes by soil bacterial population. The potential for manufactured gas plant (MGP) soil bacterial populations to degrade naphthalene, as a component mixture of polynuclear aromatic hydrocarbons, was evaluated by the detection of a naphthalene biodegradative genotype by DNA probe hybridization with DNA extracts and colonies of cultured bacteria of the MGP soils. The activity of the naphthalene-degrading populations was evaluated by mineralization assays, 14 CO 2 production from 14 C-naphthalene. Direct messenger RNA (mRNA) extraction from MGP soil was evaluated as an instantaneous measure of naphthalene catabolic gene expression in MGP soil. The bioavailability of naphthalene for bacterial degradation within the MGP soils was assessed by measuring the bioluminescent response of a naphthalene-lux catabolic reporter strain Pseudomonas fluorescens HK44 (pUTK21). DNA extracted from 5 MGP soils and 1 creosote-contaminated soil and hybridized with a nahA gene probe indicated that the naphthalene degradative genes were present in all samples in the range of 0.06 to 0.95 ng/100 μl DNA extract which was calculated to represent 3.58 x 10 8 to 1.05 x 10 10 nahA positive cells/g soil. Phenanthrene, anthracene, and benzo(a)pyrene were mineralized also by some of the soils. NAH7 homologous messenger RNA transcripts were detectable in one MGP soil and in the creosote-contaminated soil

  18. Molecular analysis of carnitine palmitoyltransferase II deficiency with hepatocardiomuscular expression

    Energy Technology Data Exchange (ETDEWEB)

    Bonnefont, J.P.; Cepanec, C.; Leroux, J.P. [Unite INSERM, Paris (France)] [and others

    1996-05-01

    Carnitine palmitoyltransferase (CPT) II deficiency, an inherited disorder of mitochondrial long-chain fatty-acid (LCFA) oxidation, results in two distinct clinical act phenotypes, namely, an adult (muscular) form and an infantile (hepatocardiomuscular) form. The rationale of this phenotypic heterogeneity is poorly understood. The adult form of the disease is commonly ascribed to the Ser-113-Leu substitution in CPT II. Only few data are available regarding the molecular basis of the infantile form of the disease. We report herein a homozygous A-2399-C transversion predicting a Tyr-628-Ser substitution in a CPT II-deficient infant. In vitro expression of mutant cDNA in COS-1 cells demonstrated the responsibility of this mutation for the disease. Metabolic consequences of the Ser-113-Leu and Tyr-628-Ser substitutions were studied in fibroblasts. The Tyr-628-Ser substitution (infantile form) resulted in a 10% CPT II residual activity, markedly impairing LCFA oxidation, whereas the Ser-113-Leu substitution (adult form) resulted in a 20% CPT II residual activity, without consequence on LCFA oxidation. These data show that CPT II activity has to be reduced below a critical threshold in order for LCFA oxidation in fibroblasts to be impaired. The hypothesis that this critical threshold differs among tissues could provide a basis to explain phenotypic heterogeneity of CPT II deficiency. 32 refs., 5 figs.

  19. Molecular characterization and phylogenetic analysis of Fasciola gigantica from Nigeria.

    Science.gov (United States)

    Ichikawa-Seki, Madoka; Tokashiki, Minami; Opara, Maxwell Nwachukwu; Iroh, Gabriel; Hayashi, Kei; Kumar, Uday Mohanta; Itagaki, Tadashi

    2017-02-01

    Fasciola gigantica is considered the major pathogen causing fasciolosis in Africa; however, molecular characterization of this fluke has not been adequately elucidated. It is important to scientifically elucidate the dispersal history of F. gigantica by analyzing its genetic diversity. Fasciola flukes from Nigeria were analyzed using nuclear and mitochondrial DNA markers. A total of 172 Fasciola flukes collected from cattle were identified as F. gigantica because they displayed the F. gigantica fragment pattern in multiplex PCR for the nuclear marker, phosphoenolpyruvate carboxykinase (pepck). In total, 70 haplotypes were detected from Nigerian F. gigantica on the basis of the concatenated sequence of mitochondrial NADH dehydrogenase subunit 1 (nad1) and cytochrome c oxidase 1 (cox1). The index of neutrality (Fu's Fs) suggests rapid expansion of the Nigerian F. gigantica population. Although four haplogroups, Nigeria 1A, 1B, 2A, and 2B, were detected from Nigerian F. gigantica, a climate-specific genetic structure was not observed among F. gigantica populations from three agro-climatic regions (Sahel, Savannah, and Forest). This is probably because of the frequent transportation of livestock from one part of the country to the other. Nigeria 1A and 1B had close relationships with the Egyptian population of F. gigantica, whereas Nigeria 2A and 2B were comparatively related to the Zambian population. No haplotype was shared among the three countries, and it therefore is difficult to estimate the dispersal route of F. gigantica within the African continent. Copyright © 2016. Published by Elsevier Ireland Ltd.

  20. Molecular analysis of peroxisome proliferation in the hamster.

    Science.gov (United States)

    Choudhury, Agharul I; Sims, Helen M; Horley, Neill J; Roberts, Ruth A; Tomlinson, Simon R; Salter, Andrew M; Bruce, Mary; Shaw, P Nicholas; Kendall, David; Barrett, David A; Bell, David R

    2004-05-15

    Three novel P450 members of the cytochrome P450 4A family were cloned as partial cDNAs from hamster liver, characterised as novel members of the CYP4A subfamily, and designated CYP4A17, 18, and 19. Hamsters were treated with the peroxisome proliferator-activated receptor alpha (PPARalpha) agonists, methylclofenapate (MCP) or Wy-14,643, and shown to develop hepatomegaly and induction of CYP4A17 RNA, and concomitant induction of lauric acid 12- hydroxylase. This treatment also resulted in hypolipidaemia, which was most pronounced in the VLDL fraction, with up to 50% reduction in VLDL-triglycerides; by contrast, blood cholesterol concentration was unaffected by this treatment. These data show that hamster is highly responsive to induction of CYP4A by peroxisome proliferators. To characterise the molecular basis of peroxisome proliferation, the hamster PPARalpha was cloned and shown to encode a 468-amino-acid protein, which is highly similar to rat and mouse PPARalpha proteins. The level of expression of hamster PPARalpha in liver is intermediate between mouse and guinea pig. These results fail to support the hypothesis that the level of PPARalpha in liver is directly responsible for species differences in peroxisome proliferation.

  1. [Molecular, genetic and physiological analysis of photoinhibition and photosynthetic

    Energy Technology Data Exchange (ETDEWEB)

    1992-01-01

    A major goal of this project is to use a combined molecular genetic, biochemical and physiological approach to understand the relationship between photosynthetic performance and the structure of the multifunctional D1 reaction center protein of Photosystem II encoded by the chloroplast psbA gene. Relative to other chloroplast proteins, turover of D1 is rapid and highly light dependent and de novo synthesis of D1 is required for a plant's recovery from short term exposure to irradiances which induce photoinhibitory damage. These observations have led to models for a damage/repair cycle of PSII involving the targeted degradation and replacement of photodamaged D1. To investigate the effects of perturbing the D1 cycle on photosynthesis and autotrophic growth under high and low irradiance, we have examined the consequences of site-specific mutations of the psbA and 16S rRNA genes affecting synthesis, maturation and function/stability of the D1 protein introduced into the chloroplast genome of wildtype strain of the green alga Chlamydomonas reinhardtii using biolistic transformation.

  2. Projection methods for the analysis of molecular-frame photoelectron angular distributions

    International Nuclear Information System (INIS)

    Lucchese, R.R.; Montuoro, R.; Grum-Grzhimailo, A.N.; Liu, X.-J.; Pruemper, G.; Morishita, Y.; Saito, N.; Ueda, K.

    2007-01-01

    The analysis of the molecular-frame photoelectron angular distributions (MFPADs) is discussed within the dipole approximation. The general expressions are reviewed and strategies for extracting the maximum amount of information from different types of experimental measurements are considered. The analysis of the N 1s photoionization of NO is given to illustrate the method

  3. Using Molecular Modeling in Teaching Group Theory Analysis of the Infrared Spectra of Organometallic Compounds

    Science.gov (United States)

    Wang, Lihua

    2012-01-01

    A new method is introduced for teaching group theory analysis of the infrared spectra of organometallic compounds using molecular modeling. The main focus of this method is to enhance student understanding of the symmetry properties of vibrational modes and of the group theory analysis of infrared (IR) spectra by using visual aids provided by…

  4. Introduction to basic molecular biologic techniques for molecular imaging researches

    International Nuclear Information System (INIS)

    Kang, Joo Hyun

    2004-01-01

    Molecular imaging is a rapidly growing field due to the advances in molecular biology and imaging technologies. With the introduction of imaging reporter genes into the cell, diverse cellular processes can be monitored, quantified and imaged non-invasively in vivo. These processes include the gene expression, protein-protein interactions, signal transduction pathways, and monitoring of cells such as cancer cells, immune cells, and stem cells. In the near future, molecular imaging analysis will allow us to observe the incipience and progression of the disease. These will make us easier to give a diagnosis in the early stage of intractable diseases such as cancer, neuro-degenerative disease, and immunological disorders. Additionally, molecular imaging method will be a valuable tool for the real-time evaluation of cells in molecular biology and the basic biological studies. As newer and more powerful molecular imaging tools become available, it will be necessary to corporate clinicians, molecular biologists and biochemists for the planning, interpretation, and application of these techniques to their fullest potential. In order for such a multidisciplinary team to be effective, it is essential that a common understanding of basic biochemical and molecular biologic techniques is achieved. Basic molecular techniques for molecular imaging methods are presented in this paper

  5. Invasive micropapillary carcinoma of the breast has a better long-term survival than invasive ductal carcinoma of the breast in spite of its aggressive clinical presentations: a comparison based on large population database and case-control analysis.

    Science.gov (United States)

    Chen, Hongliang; Wu, Kejin; Wang, Maoli; Wang, Fuwen; Zhang, Mingdi; Zhang, Peng

    2017-12-01

    There are controversies in the comparison of overall survival between invasive micropapillary carcinoma of the breast (IMPC) and invasive ductal carcinoma (IDC). The objective of this study was to compare the long-term survival outcome between non-metastatic IMPC and IDC. The Surveillance, Epidemiology, and End Results database was searched to identify women with non-metastatic IMPC and IDC diagnosed between 2001 and 2013. Comparisons of patient and tumor characteristics were performed using Pearson's chi-square. The propensity score matching method was applied with each IMPC matched to one IDC. Breast cancer-specific survival (BCSS) and overall survival (OS) were estimated using the Kaplan-Meier product limit method and compared across groups using the log-rank statistic. Multivariate analysis was performed through Cox models. IMPC was presented with aggressive clinical presentations such as larger tumor, more positive lymph nodes, and more advanced stage compared with IDC. A higher rate of estrogen receptor (ER)/progesterone receptor (PR) positivity was also observed in IMPC. With a median follow-up of 64 months, IMPC had a better BCSS (P = 0.031) and OS (P = 0.012) compared with IDC. In a case-control analysis IMPC was still an independent favorable prognostic factor for BCSS (HR = 0.410, P analysis, IMPC always showed a better survival outcome compared with IDC except in AJCC stage I and histologic grade I disease. IMPC has a better long-term survival outcome compared with IDC in spite of its highly aggressive clinical presentation. © 2017 The Authors. Cancer Medicine published by John Wiley & Sons Ltd.

  6. Accuracy assessment of Tri-plane B-mode ultrasound for non-invasive 3D kinematic analysis of knee joints.

    Science.gov (United States)

    Masum, Md Abdullah; Pickering, Mark; Lambert, Andrew; Scarvell, Jennie; Smith, Paul

    2014-08-26

    Currently the clinical standard for measuring the motion of the bones in knee joints with sufficient precision involves implanting tantalum beads into the bones. These beads appear as high intensity features in radiographs and can be used for precise kinematic measurements. This procedure imposes a strong coupling between accuracy and invasiveness. In this paper, a tri-plane B-mode ultrasound (US) based non-invasive approach is proposed for use in kinematic analysis of knee joints in 3D space. The 3D analysis is performed using image processing procedures on the 2D US slices. The novelty of the proposed procedure and its applicability to the unconstrained 3D kinematic analysis of knee joints is outlined. An error analysis for establishing the method's feasibility is included for different artificial compositions of a knee joint phantom. Some in-vivo and in-vitro scans are presented to demonstrate that US scans reveal enough anatomical details, which further supports the experimental setup used using knee bone phantoms. The error between the displacements measured by the registration of the US image slices and the true displacements of the respective slices measured using the precision mechanical stages on the experimental apparatus is evaluated for translation and rotation in two simulated environments. The mean and standard deviation of errors are shown in tabular form. This method provides an average measurement precision of less than 0.1 mm and 0.1 degrees, respectively. In this paper, we have presented a novel non-invasive approach to measuring the motion of the bones in a knee using tri-plane B-mode ultrasound and image registration. In our study, the image registration method determines the position of bony landmarks relative to a B-mode ultrasound sensor array with sub-pixel accuracy. The advantages of our proposed system over previous techniques are that it is non-invasive, does not require the use of ionizing radiation and can be used conveniently if

  7. Radical Cystectomy Compared to Combined Modality Treatment for Muscle-Invasive Bladder Cancer: A Systematic Review and Meta-Analysis

    International Nuclear Information System (INIS)

    Vashistha, Vishal; Wang, Hanzhang; Mazzone, Andrew; Liss, Michael A.; Svatek, Robert S.; Schleicher, Mary; Kaushik, Dharam

    2017-01-01

    Purpose: To perform a comprehensive comparison of overall survival (OS), disease-specific survival (DSS), progression-free survival (PFS), and treatment-related complications between radical cystectomy (RC) and combined modality treatment (CMT—radiation therapy, concurrent chemotherapy, and maximal transurethral resection of bladder tumor) in the setting of muscle-invasive bladder cancer. Methods and Materials: We searched 7 databases (PubMed, Scopus, EMBASE, Proquest, CINAHL, and (ClinicalTrials.gov)) for randomized, controlled trials and prospective and retrospective studies directly comparing RC with CMT from database inception to March 2016. We conducted meta-analyses evaluating OS, DSS, and PFS with hazard ratios (HRs) and 95% confidence intervals (CIs). Results: Nineteen studies evaluating 12,380 subjects were selected. For the 8 studies encompassing 9554 subjects eligible for meta-analyses, we found no difference in OS at 5 years (HR 0.96, favoring CMT, 95% CI 0.72-1.29; P=.778) or 10 years (HR 1.02, favoring cystectomy, 95% CI 0.73-1.42; P=.905). No difference was observed in DSS at 5 years (HR 0.83, favoring radiation, 95% CI 0.54-1.28; P=.390) or 10 years (HR 1.17, favoring cystectomy, 95% CI 0.89-1.55; P=.264), or PFS at 10 years (HR 0.85, favoring CMT, 95% CI 0.43-1.67; P=.639). The cystectomy arms had higher rates of early major complications, whereas rates of minor complications were similar between the 2 treatments. Conclusion: Current meta-analysis reveals no differences in OS, DSS, or PFS between RC and CMT. Further randomized, controlled trials are necessary to identify the optimal treatment for specific patients.

  8. Urine leak in minimally invasive partial nephrectomy: analysis of risk factors and role of intraoperative ureteral catheterization

    Directory of Open Access Journals (Sweden)

    Homayoun Zargar

    2014-12-01

    Full Text Available Purpose To investigate risk factors for urine leak in patients undergoing minimally invasive partial nephrectomy (MIPN and to determine the role of intraoperative ureteral catheterization in preventing this postoperative complication. Materials and Methods MIPN procedures done from September 1999 to July 2012 at our Center were reviewed from our IRB-approved database. Patient and tumor characteristics, operative techniques and outcomes were analyzed. Patients with evidence of urine leak were identified. Outcomes were compared between patients with preoperative ureteral catheterization (C-group and those without (NC-group. Univariable and multivariable analyses were performed to identify factors predicting postoperative urine leak. Results A total of 1,019 cases were included (452 robotic partial nephrectomy cases and 567 laparoscopic partial nephrectomy cases. Five hundred twenty eight patients (51.8% were in the C-group, whereas 491 of them (48.2% in the NC-group. Urine leak occurred in 31(3% cases, 4.6% in the C-group and 1.4% in the NC-group (p<0.001. Tumors in NC-group had significantly higher RENAL score, shorter operative and warm ischemic times. On multivariable analysis, tumor proximity to collecting system (OR=9.2; p<0.01, surgeon’s early operative experience (OR=7.8; p<0.01 and preoperative moderate to severe CKD (OR=3.1; p<0.01 significantly increased the odds of the occurrence of a postoperative urine leak. Conclusion Clinically significant urine leak after MIPN in a high volume institution setting is uncommon. This event is more likely to occur in cases of renal masses that are close to the collecting system, in patients with preoperative CKD and when operating surgeon is still in the learning curve for the procedure. Our findings suggest that routine intraoperative ureteral catheterization during MIPN does not reduce the probability of postoperative urine leak. In addition, it adds to the overall operative time.

  9. Non-invasive clinical parameters for the prediction of urodynamic bladder outlet obstruction: analysis using causal Bayesian networks.

    Directory of Open Access Journals (Sweden)

    Myong Kim

    Full Text Available To identify non-invasive clinical parameters to predict urodynamic bladder outlet obstruction (BOO in patients with benign prostatic hyperplasia (BPH using causal Bayesian networks (CBN.From October 2004 to August 2013, 1,381 eligible BPH patients with complete data were selected for analysis. The following clinical variables were considered: age, total prostate volume (TPV, transition zone volume (TZV, prostate specific antigen (PSA, maximum flow rate (Qmax, and post-void residual volume (PVR on uroflowmetry, and International Prostate Symptom Score (IPSS. Among these variables, the independent predictors of BOO were selected using the CBN model. The predictive performance of the CBN model using the selected variables was verified through a logistic regression (LR model with the same dataset.Mean age, TPV, and IPSS were 6.2 (±7.3, SD years, 48.5 (±25.9 ml, and 17.9 (±7.9, respectively. The mean BOO index was 35.1 (±25.2 and 477 patients (34.5% had urodynamic BOO (BOO index ≥40. By using the CBN model, we identified TPV, Qmax, and PVR as independent predictors of BOO. With these three variables, the BOO prediction accuracy was 73.5%. The LR model showed a similar accuracy (77.0%. However, the area under the receiver operating characteristic curve of the CBN model was statistically smaller than that of the LR model (0.772 vs. 0.798, p = 0.020.Our study demonstrated that TPV, Qmax, and PVR are independent predictors of urodynamic BOO.

  10. Determinants of accepting non-invasive ventilation treatment in motor neurone disease: a quantitative analysis at point of need.

    Science.gov (United States)

    Cousins, Rosanna; Ando, Hikari; Thornton, Everard; Chakrabarti, Biswajit; Angus, Robert; Young, Carolyn

    2013-01-01

    Objectives : Motor neurone disease (MND) progressively damages the nervous system causing wasting to muscles, including those used for breathing. There is robust evidence that non-invasive ventilation (NIV) relieves respiratory symptoms and improves quality of life in MND. Nevertheless, about a third of those who would benefit from NIV decline the treatment. The purpose of the study was to understand this phenomenon. Design : A cross-sectional quantitative analysis. Methods : Data including age, sex, MND symptomatology, general physical and mental health and psychological measures were collected from 27 patients and their family caregivers at the point of being offered ventilatory support based on physiological markers. Results : Quantitative analyses indicated no difference in patient characteristics or symptomatology between those who tolerated ( n  = 17) and those who declined ( n  = 10) NIV treatment. A comparison of family caregivers found no differences in physical or mental health or in caregiving distress, emphasising that this was high in both groups; however, family caregivers supporting NIV treatment were significantly more resilient, less neurotic and less anxious than family caregivers who did not. Regression analyses, forcing MND symptoms to enter the equation first, found caregiver resilience:commitment the strongest predictor of uptake of NIV treatment adding 22% to the 56% explained variance. Conclusion : Patients who tolerated NIV treatment had family caregivers who cope through finding meaning and purpose in their situation. Psychological support and proactive involvement for family caregivers in the management of the illness situation is indicated if acceptance of NIV treatment is to be maximised in MND.

  11. Metagenomic Analysis of the Microbiota from the Crop of an Invasive Snail Reveals a Rich Reservoir of Novel Genes

    Science.gov (United States)

    Cardoso, Alexander M.; Cavalcante, Janaína J. V.; Cantão, Maurício E.; Thompson, Claudia E.; Flatschart, Roberto B.; Glogauer, Arnaldo; Scapin, Sandra M. N.; Sade, Youssef B.; Beltrão, Paulo J. M. S. I.; Gerber, Alexandra L.; Martins, Orlando B.; Garcia, Eloi S.; de Souza, Wanderley; Vasconcelos, Ana Tereza R.

    2012-01-01

    The shortage of petroleum reserves and the increase in CO2 emissions have raised global concerns and highlighted the importance of adopting sustainable energy sources. Second-generation ethanol made from lignocellulosic materials is considered to be one of the most promising fuels for vehicles. The giant snail Achatina fulica is an agricultural pest whose biotechnological potential has been largely untested. Here, the composition of the microbial population within the crop of this invasive land snail, as well as key genes involved in various biochemical pathways, have been explored for the first time. In a high-throughput approach, 318 Mbp of 454-Titanium shotgun metagenomic sequencing data were obtained. The predominant bacterial phylum found was Proteobacteria, followed by Bacteroidetes and Firmicutes. Viruses, Fungi, and Archaea were present to lesser extents. The functional analysis reveals a variety of microbial genes that could assist the host in the degradation of recalcitrant lignocellulose, detoxification of xenobiotics, and synthesis of essential amino acids and vitamins, contributing to the adaptability and wide-ranging diet of this snail. More than 2,700 genes encoding glycoside hydrolase (GH) domains and carbohydrate-binding modules were detected. When we compared GH profiles, we found an abundance of sequences coding for oligosaccharide-degrading enzymes (36%), very similar to those from wallabies and giant pandas, as well as many novel cellulase and hemicellulase coding sequences, which points to this model as a remarkable potential source of enzymes for the biofuel industry. Furthermore, this work is a major step toward the understanding of the unique genetic profile of the land snail holobiont. PMID:23133637

  12. Exploiting gas diffusion for non-invasive sampling in flow analysis: determination of ethanol in alcoholic beverages

    Directory of Open Access Journals (Sweden)

    Simone Vicente

    2006-03-01

    Full Text Available A tubular gas diffusion PTFE membrane is exploited for non-invasive sampling in flow analysis, aiming to develop an improved spectrophotometric determination of ethanol in alcoholic beverages. The probe is immersed into the sample, allowing ethanol to diffuse through the membrane. It is collected into the acceptor stream (acidic dichromate solution, leading to formation of Cr(III, monitored at 600 nm. The analytical curve is linear up to 50% (v/v ethanol, baseline drift is Uma membrana tubular de PTFE permeável a espécies gasosas foi empregada como sonda em sistemas de análises em fluxo visando a proposta de uma estratégia de amostragem não invasiva. Como aplicação, foi selecionada a determinação espectrofotométrica de etanol em bebidas alcoólicas. A sonda é imersa na amostra, permitindo que o analito se difunda através desta e seja coletado pelo fluxo aceptor (solução ácida de dicromato, levando à formação de Cr(III, o qual é monitorado a 600 nm. Linearidade da curva analítica é verificada até 50,0% (v/v de etanol (r > 0,998; n = 8, derivas de linha base são menores do que 0,005 absorbância durante períodos de 4 horas de operação e a velocidade analítica é de 30 h-1 o que corresponde a 0.6 mmol K2Cr2O7 por determinação. Os resultados são precisos (d.p.r. < 2% e concordantes com aqueles obtidos por um método oficial.

  13. Expression analysis of E-cadherin, Slug and GSK3β in invasive ductal carcinoma of breast

    International Nuclear Information System (INIS)

    Prasad, Chandra P; Rath, Gayatri; Mathur, Sandeep; Bhatnagar, Dinesh; Parshad, Rajinder; Ralhan, Ranju

    2009-01-01

    Cancer progression is linked to a partially dedifferentiated epithelial cell phenotype. The signaling pathways Wnt, Hedgehog, TGF-β and Notch have been implicated in experimental and developmental epithelial mesenchymal transition (EMT). Recent findings from our laboratory confirm that active Wnt/β-catenin signaling is critically involved in invasive ductal carcinomas (IDCs) of breast. In the current study, we analyzed the expression patterns and relationships between the key Wnt/β-catenin signaling components- E-cadherin, Slug and GSK3β in IDCs of breast. Of the 98 IDCs analyzed, 53 (54%) showed loss/or reduced membranous staining of E-cadherin in tumor cells. Nuclear accumulation of Slug was observed in 33 (34%) IDCs examined. Loss or reduced level of cytoplasmic GSK3β expression was observed in 52/98 (53%) cases; while 34/98 (35%) tumors showed nuclear accumulation of GSK3β. Statistical analysis revealed associations of nuclear Slug expression with loss of membranous E-cadherin (p = 0.001); nuclear β-catenin (p = 0.001), and cytoplasmic β-catenin (p = 0.005), suggesting Slug mediated E-cadherin suppression via the activation of Wnt/β-catenin signaling pathway in IDCs. Our study also demonstrated significant correlation between GSK3β nuclear localization and tumor grade (p = 0.02), suggesting its association with tumor progression. The present study for the first time provided the clinical evidence in support of Wnt/β-catenin signaling upregulation in IDCs and key components of this pathway - E-cadherin, Slug and GSK3β with β-catenin in implementing EMT in these cells

  14. Expression analysis of E-cadherin, Slug and GSK3β in invasive ductal carcinoma of breast

    Energy Technology Data Exchange (ETDEWEB)

    Prasad, Chandra P [Department of Anatomy, Vardhman Mahavir Medical College and Safdarjung Hospital, New Delhi (India); Department of Biochemistry, All India Institute of Medical Sciences, New Delhi (India); Rath, Gayatri [Department of Anatomy, Vardhman Mahavir Medical College and Safdarjung Hospital, New Delhi (India); Mathur, Sandeep [Department of Pathology, All India Institute of Medical Sciences, New Delhi (India); Bhatnagar, Dinesh [Department of Surgery, Vardhman Mahavir Medical College and Safdarjung Hospital, New Dehi (India); Parshad, Rajinder [Department of Surgery, All India Institute of Medical Sciences, New Delhi -110029 (India); Ralhan, Ranju [Department of Biochemistry, All India Institute of Medical Sciences, New Delhi (India); Sonshine Family Centre for Head & Neck Disease, Mount Sinai Hospital, 600 University Avenue, Room 6-500, Toronto, Ontario M5G 1X5 (Canada); Department of Otolaryngology-Head and Neck Surgery, Mount Sinai Hospital, 600 University Avenue, Room 6-500, Toronto, Ontario M5G 1X5 (Canada); Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, 600 University Avenue, Room 6-500, Toronto, Ontario M5G 1X5 (Canada); Department of Otolaryngology-Head and Neck Surgery, University of Toronto, Toronto, M5G 2N2 (Canada)

    2009-09-14

    Cancer progression is linked to a partially dedifferentiated epithelial cell phenotype. The signaling pathways Wnt, Hedgehog, TGF-β and Notch have been implicated in experimental and developmental epithelial mesenchymal transition (EMT). Recent findings from our laboratory confirm that active Wnt/β-catenin signaling is critically involved in invasive ductal carcinomas (IDCs) of breast. In the current study, we analyzed the expression patterns and relationships between the key Wnt/β-catenin signaling components- E-cadherin, Slug and GSK3β in IDCs of breast. Of the 98 IDCs analyzed, 53 (54%) showed loss/or reduced membranous staining of E-cadherin in tumor cells. Nuclear accumulation of Slug was observed in 33 (34%) IDCs examined. Loss or reduced level of cytoplasmic GSK3β expression was observed in 52/98 (53%) cases; while 34/98 (35%) tumors showed nuclear accumulation of GSK3β. Statistical analysis revealed associations of nuclear Slug expression with loss of membranous E-cadherin (p = 0.001); nuclear β-catenin (p = 0.001), and cytoplasmic β-catenin (p = 0.005), suggesting Slug mediated E-cadherin suppression via the activation of Wnt/β-catenin signaling pathway in IDCs. Our study also demonstrated significant correlation between GSK3β nuclear localization and tumor grade (p = 0.02), suggesting its association with tumor progression. The present study for the first time provided the clinical evidence in support of Wnt/β-catenin signaling upregulation in IDCs and key components of this pathway - E-cadherin, Slug and GSK3β with β-catenin in implementing EMT in these cells.

  15. Radical Cystectomy Compared to Combined Modality Treatment for Muscle-Invasive Bladder Cancer: A Systematic Review and Meta-Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Vashistha, Vishal [Department of Internal Medicine, Cleveland Clinic Foundation, Cleveland, Ohio (United States); Wang, Hanzhang [Department of Urology, University of Texas Health Science Center at San Antonio, San Antonio, Texas (United States); Mazzone, Andrew [Rush Medical College, Rush University Medical Center, Chicago, Illinois (United States); Liss, Michael A.; Svatek, Robert S. [Department of Urology, University of Texas Health Science Center at San Antonio, San Antonio, Texas (United States); Schleicher, Mary [Department of Internal Medicine, Cleveland Clinic Foundation, Cleveland, Ohio (United States); Kaushik, Dharam, E-mail: Kaushik@uthscsa.edu [Department of Urology, University of Texas Health Science Center at San Antonio, San Antonio, Texas (United States)

    2017-04-01

    Purpose: To perform a comprehensive comparison of overall survival (OS), disease-specific survival (DSS), progression-free survival (PFS), and treatment-related complications between radical cystectomy (RC) and combined modality treatment (CMT—radiation therapy, concurrent chemotherapy, and maximal transurethral resection of bladder tumor) in the setting of muscle-invasive bladder cancer. Methods and Materials: We searched 7 databases (PubMed, Scopus, EMBASE, Proquest, CINAHL, and (ClinicalTrials.gov)) for randomized, controlled trials and prospective and retrospective studies directly comparing RC with CMT from database inception to March 2016. We conducted meta-analyses evaluating OS, DSS, and PFS with hazard ratios (HRs) and 95% confidence intervals (CIs). Results: Nineteen studies evaluating 12,380 subjects were selected. For the 8 studies encompassing 9554 subjects eligible for meta-analyses, we found no difference in OS at 5 years (HR 0.96, favoring CMT, 95% CI 0.72-1.29; P=.778) or 10 years (HR 1.02, favoring cystectomy, 95% CI 0.73-1.42; P=.905). No difference was observed in DSS at 5 years (HR 0.83, favoring radiation, 95% CI 0.54-1.28; P=.390) or 10 years (HR 1.17, favoring cystectomy, 95% CI 0.89-1.55; P=.264), or PFS at 10 years (HR 0.85, favoring CMT, 95% CI 0.43-1.67; P=.639). The cystectomy arms had higher rates of early major complications, whereas rates of minor complications were similar between the 2 treatments. Conclusion: Current meta-analysis reveals no differences in OS, DSS, or PFS between RC and CMT. Further randomized, controlled trials are necessary to identify the optimal treatment for specific patients.

  16. Targeted capture massively parallel sequencing analysis of LCIS and invasive lobular cancer: Repertoire of somatic genetic alterations and clonal relationships.

    Science.gov (United States)

    Sakr, Rita A; Schizas, Michail; Carniello, Jose V Scarpa; Ng, Charlotte K Y; Piscuoglio, Salvatore; Giri, Dilip; Andrade, Victor P; De Brot, Marina; Lim, Raymond S; Towers, Russell; Weigelt, Britta; Reis-Filho, Jorge S; King, Tari A

    2016-02-01

    Lobular carcinoma in situ (LCIS) has been proposed as a non-obligate precursor of invasive lobular carcinoma (ILC). Here we sought to define the repertoire of somatic genetic alterations in pure LCIS and in synchronous LCIS and ILC using targeted massively parallel sequencing. DNA samples extracted from microdissected LCIS, ILC and matched normal breast tissue or peripheral blood from 30 patients were subjected to massively parallel sequencing targeting all exons of 273 genes, including the genes most frequently mutated in breast cancer and DNA repair-related genes. Single nucleotide variants and insertions and deletions were identified using state-of-the-art bioinformatics approaches. The constellation of somatic mutations found in LCIS (n = 34) and ILC (n = 21) were similar, with the most frequently mutated genes being CDH1 (56% and 66%, respectively), PIK3CA (41% and 52%, respectively) and CBFB (12% and 19%, respectively). Among 19 LCIS and ILC synchronous pairs, 14 (74%) had at least one identical mutation in common, including identical PIK3CA and CDH1 mutations. Paired analysis of independent foci of LCIS from 3 breasts revealed at least one common mutation in each of the 3 pairs (CDH1, PIK3CA, CBFB and PKHD1L1). LCIS and ILC have a similar repertoire of somatic mutations, with PIK3CA and CDH1 being the most frequently mutated genes. The presence of identical mutations between LCIS-LCIS and LCIS-ILC pairs demonstrates that LCIS is a clonal neoplastic lesion, and provides additional evidence that at least some LCIS are non-obligate precursors of ILC. Copyright © 2015 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

  17. Metagenomic analysis of the microbiota from the crop of an invasive snail reveals a rich reservoir of novel genes.

    Directory of Open Access Journals (Sweden)

    Alexander M Cardoso

    Full Text Available The shortage of petroleum reserves and the increase in CO(2 emissions have raised global concerns and highlighted the importance of adopting sustainable energy sources. Second-generation ethanol made from lignocellulosic materials is considered to be one of the most promising fuels for vehicles. The giant snail Achatina fulica is an agricultural pest whose biotechnological potential has been largely untested. Here, the composition of the microbial population within the crop of this invasive land snail, as well as key genes involved in various biochemical pathways, have been explored for the first time. In a high-throughput approach, 318 Mbp of 454-Titanium shotgun metagenomic sequencing data were obtained. The predominant bacterial phylum found was Proteobacteria, followed by Bacteroidetes and Firmicutes. Viruses, Fungi, and Archaea were present to lesser extents. The functional analysis reveals a variety of microbial genes that could assist the host in the degradation of recalcitrant lignocellulose, detoxification of xenobiotics, and synthesis of essential amino acids and vitamins, contributing to the adaptability and wide-ranging diet of this snail. More than 2,700 genes encoding glycoside hydrolase (GH domains and carbohydrate-binding modules were detected. When we compared GH profiles, we found an abundance of sequences coding for oligosaccharide-degrading enzymes (36%, very similar to those from wallabies and giant pandas, as well as many novel cellulase and hemicellulase coding sequences, which points to this model as a remarkable potential source of enzymes for the biofuel industry. Furthermore, this work is a major step toward the understanding of the unique genetic profile of the land snail holobiont.

  18. High excitation rovibrational molecular analysis in warm environments

    Science.gov (United States)

    Zhang, Ziwei; Stancil, Phillip C.; Cumbee, Renata; Ferland, Gary J.

    2017-06-01

    Inspired by advances in infrared observation (e.g., Spitzer, Herschel and ALMA), we investigate rovibrational emission CO and SiO in warm astrophysical environments. With recent innovation in collisional rate coefficients and rescaling methods, we are able to construct more comprehensive collisional data with high rovibrational states (vibration up to v=5 and rotation up to J=40) and multiple colliders (H2, H and He). These comprehensive data sets are used in spectral simulations with the radiative transfer codes RADEX and Cloudy. We obtained line ratio diagnostic plots and line spectra for both near- and far-infrared emission lines over a broad range of density and temperature for the case of a uniform medium. Considering the importance of both molecules in probing conditions and activities of UV-irradiated interstellar gas, we model rovibrational emission in photodissociation region (PDR) and AGB star envelopes (such as VY Canis Majoris, IK Tau and IRC +10216) with Cloudy. Rotational diagrams, energy distribution diagrams, and spectra are produced to examine relative state abundances, line emission intensity, and other properties. With these diverse models, we expect to have a better understanding of PDRs and expand our scope in the chemical architecture and evolution of AGB stars and other UV-irradiated regions. The soon to be launched James Webb Space Telescope (JWST) will provide high resolution observations at near- to mid-infrared wavelengths, which opens a new window to study molecular vibrational emission calling for more detailed chemical modeling and comprehensive laboratory astrophysics data on more molecules. This work was partially supported by NASA grants NNX12AF42G and NNX15AI61G. We thank Benhui Yang, Kyle Walker, Robert Forrey, and N. Balakrishnan for collaborating on the collisional data adopted in the current work.

  19. Molecular analysis of radiation injury in rat taste buds

    International Nuclear Information System (INIS)

    Nakagawa, K.; Abe, K.

    2003-01-01

    Full text: A critical adverse effect of radiation therapy for head and neck cancer is the resulting decreased sense of taste, which greatly impairs patients' quality of life. Irradiation of the head and neck area decreases the sense of taste within one or two weeks and recovery takes about one month. Although taste bud cells are intimately involved in these manifestations, few basic studies in this area have been reported. Here, we investigate the injury and recovery process of taste bud tissue after irradiation, at the molecular and cellular levels. Rat tongues were selectively irradiated once with 15 Gy of 6 MV X-rays. Immediately thereafter and at periods up to 30 days samples were collected for HE staining, BrdU labelling, p21 and p53 immunohistochemistry, and TUNEL staining. Six days after irradiation, morphologically-identified taste bud cells, as well as the surrounding epithelial tissue, were no longer visible. Immature bud cells reappeared ten days after irradiation, and looked morphologically normal at 13 to 15 days.BrdU labelling revealed DNA synthesis arrest in of epithelial cells 10 days after irradiation. Cells in the basal layer expressed p21 four hours after irradiation. Prior to that, it, p53 accumulation was observed in the nucleus. Expression of p21 was no longer detectable by on the sixth day or later, and DNA synthesis resumed around the eighth day. No apoptosis was detected at any time. The disappearance and reappearance of taste bud cells after a single 15-Gy irradiation dose can be explained by temporary cell cycle arrest in taste bud stem cells, which is regulated by p21

  20. Molecular analysis of the bacterial diversity in uranium mill tailings

    International Nuclear Information System (INIS)

    Geissler, A.

    2003-04-01

    A culture-independent molecular approach has been applied to investigate the bacterial diversity in three uranium contaminated sites. The three analysed soil samples have been collected from the uranium waste pile Haberland near Johanngeorgenstadt (Germany), from the uranium mill tailings in Gunnison, Colorado (USA) and from the uranium mill tailings in Shiprock, New Mexico (USA). The 16S rDNA fragments which has been isolated through direct lysis of the whole-DNA were amplified by the use of the universal primers 16S 43f and 16S 1404r and cloned. With restriction fragment length polymorphismus (RFLP) were the clones screened and one representative of all RFLP types that occurred more than once in the clone library was sequenced and analysed. In spite of the contamination a considerable diversity and significant differences in the composition of the natural bacterial communities in these three sites have been found. In the sample collected from the waste pile Haberland near Johanngeorgenstadt α-Proteobacteria and representatives of the Holophaga/Acidobacterium were numerically predominant. The distribution of bacteria in the sample collected from uranium mill tailings Gunnison was very similar to those found in the Haberland waste pile, but there were found besides α-Proteobacteria and representatives of Holophaga/Acidobacterium a lot of γ-Proteobacteria. The structure of the bacterial community in the sample collected from the uranium mill tailings Shiprock was significantly different. Only some representatives of the Holophaga/Acidobacterium and α-Proteobacteria were represented. Large populations of Bacilli, γ-Proteobacteria and green non sulfur bacteria were dominant in this sample. (orig.)

  1. Molecular cloning and expression analysis of a zeta-class ...

    African Journals Online (AJOL)

    Jane

    2011-07-27

    Jul 27, 2011 ... sugar-signalling pathway (Chi et al., 2010). All the earlier mentioned ... real-time qPCR analysis was the ABI PRISM7500 real-time PCR system. ... Construction of prokaryotic expression vector of Sc-GST gene. pET29a (+) ...

  2. Molecular analysis of genetic diversity in elite II synthetic hexaploid ...

    African Journals Online (AJOL)

    The present study was conducted to assess the genetic diversity of Elite-II synthetic hexaploid (SH) wheat by genome DNA fingerprinting as revealed by random amplified polymorphic DNA (RAPD) analysis. Ten decamer RAPD primers (OPG-1, OPG-2, OPG-3, OPG-4, OPG-5, OPA-3, OPA-4, OPA-5, OPA-8, and OPA-15) ...

  3. Molecular cloning and characteristic analysis of a thioredoxin from ...

    African Journals Online (AJOL)

    Sequence comparison and phylogenetic tree analysis confirmed NmTrx as a distinct member of thioredoxin. Real-time quantitative polymerase chain reaction (PCR) revealed a significantly higher expression of NmTrx transcript in the adult stage compared with the egg and oncomiracidium stages. In the egg and adult ...

  4. Molecular cloning, expression analysis and sequence prediction of ...

    African Journals Online (AJOL)

    CCAAT/enhancer-binding protein beta as an essential transcriptional factor, regulates the differentiation of adipocytes and the deposition of fat. Herein, we cloned the whole open reading frame (ORF) of bovine C/EBPβ gene and analyzed its putative protein structures via DNA cloning and sequence analysis. Then, the ...

  5. Molecular characterization and diversity analysis in chilli pepper ...

    African Journals Online (AJOL)

    India is considered to be the secondary center of diversity of chilli pepper, especially of Capsicum annuum. Simple sequence repeats (SSRs) are the most widely used marker system for plant variety characterization and diversity analysis especially in cultivated species which have low levels of polymorphism. The diversity ...

  6. Gas chromatographic column for the Viking 1975 molecular analysis experiment

    Science.gov (United States)

    Novotny, M.; Hayes, J. M.; Bruner, F.; Simmonds, P. G.

    1975-01-01

    A gas chromatographic column has been developed for use in the remote analysis of the Martian surface. The column, which utilizes a liquid-modified organic adsorbent (Tenax) as the stationary phase, provides efficient transmission and resolution of nanogram quantities of organic materials in the presence of millionfold excesses of water and carbon dioxide.

  7. Molecular marker analysis to differentiate a clonal selection of ...

    African Journals Online (AJOL)

    Lalit Kumar

    2013-04-03

    Apr 3, 2013 ... Microsatellite and amplified fragment length polymorphism (AFLP) markers were used to differentiate. Manjari Naveen, a clonal selection of Centennial Seedless variety of grape. Twenty one (21) microsatellite primers could not detect variation between parent variety and its clone. AFLP analysis.

  8. Raman spectroscopy combined with principal component analysis and k nearest neighbour analysis for non-invasive detection of colon cancer

    Science.gov (United States)

    Li, Xiaozhou; Yang, Tianyue; Li, Siqi; Wang, Deli; Song, Youtao; Zhang, Su

    2016-03-01

    This paper attempts to investigate the feasibility of using Raman spectroscopy for the diagnosis of colon cancer. Serum taken from 75 healthy volunteers, 65 colon cancer patients and 60 post-operation colon cancer patients was measured in this experiment. In the Raman spectra of all three groups, the Raman peaks at 750, 1083, 1165, 1321, 1629 and 1779 cm-1 assigned to nucleic acids, amino acids and chromophores were consistently observed. All of these six Raman peaks were observed to have statistically significant differences between groups. For quantitative analysis, the multivariate statistical techniques of principal component analysis (PCA) and k nearest neighbour analysis (KNN) were utilized to develop diagnostic algorithms for classification. In PCA, several peaks in the principal component (PC) loadings spectra were identified as the major contributors to the PC scores. Some of the peaks in the PC loadings spectra were also reported as characteristic peaks for colon tissues, which implies correlation between peaks in PC loadings spectra and those in the original Raman spectra. KNN was also performed on the obtained PCs, and a diagnostic accuracy of 91.0% and a specificity of 92.6% were achieved.

  9. Raman spectroscopy combined with principal component analysis and k nearest neighbour analysis for non-invasive detection of colon cancer

    International Nuclear Information System (INIS)

    Li, Xiaozhou; Yang, Tianyue; Wang, Deli; Li, Siqi; Song, Youtao; Zhang, Su

    2016-01-01

    This paper attempts to investigate the feasibility of using Raman spectroscopy for the diagnosis of colon cancer. Serum taken from 75 healthy volunteers, 65 colon cancer patients and 60 post-operation colon cancer patients was measured in this experiment. In the Raman spectra of all three groups, the Raman peaks at 750, 1083, 1165, 1321, 1629 and 1779 cm −1 assigned to nucleic acids, amino acids and chromophores were consistently observed. All of these six Raman peaks were observed to have statistically significant differences between groups. For quantitative analysis, the multivariate statistical techniques of principal component analysis (PCA) and k nearest neighbour analysis (KNN) were utilized to develop diagnostic algorithms for classification. In PCA, several peaks in the principal component (PC) loadings spectra were identified as the major contributors to the PC scores. Some of the peaks in the PC loadings spectra were also reported as characteristic peaks for colon tissues, which implies correlation between peaks in PC loadings spectra and those in the original Raman spectra. KNN was also performed on the obtained PCs, and a diagnostic accuracy of 91.0% and a specificity of 92.6% were achieved. (paper)

  10. Molecular cloning and functional analysis of the gene encoding ...

    African Journals Online (AJOL)

    Here we report for the first time the cloning of a full-length cDNA encoding GGPPS (Jc-GGPPS) from Jatropha curcas L. The full-length cDNA was 1414 base pair (bp), with an 1110-bp open reading frame (ORF) encoding a 370- amino-acids polypeptide. Bioinformatic analysis revealed that Jc-GGPPS is a member of the ...

  11. Molecular cloning and expression analysis of an Mnsuperoxide ...

    African Journals Online (AJOL)

    Superoxide dismutases (SODs) play an important role in stress-tolerance in plants. In this study, for the first time, a full-length cDNA sequence of MnSOD gene, termed as Sc-MnSOD (GenBank accession number: GQ246460), was obtained in sugarcane. Sequence analysis revealed that Sc-MnSOD gene was 919 bp long, ...

  12. Molecular Analysis of Microbial Diversity in Advanced Caries

    OpenAIRE

    Chhour, Kim-Ly; Nadkarni, Mangala A.; Byun, Roy; Martin, F. Elizabeth; Jacques, Nicholas A.; Hunter, Neil

    2005-01-01

    Real-time PCR analysis of the total bacterial load in advanced carious lesions has shown that the total load exceeds the number of cultivable bacteria. This suggests that an unresolved complexity exists in bacteria associated with advanced caries. In this report, the profile of the microflora of carious dentine was explored by using DNA extracted from 10 lesions selected on the basis of comparable total microbial load and on the relative abundance of Prevotella spp. Using universal primers fo...

  13. Molecular Analysis of Endolithic Microbial Communities in Volcanic Glasses

    Science.gov (United States)

    di Meo, C. A.; Giovannoni, S.; Fisk, M.

    2002-12-01

    Terrestrial and marine volcanic glasses become mineralogically and chemically altered, and in many cases this alteration has been attributed to microbial activity. We have used molecular techniques to study the resident microbial communities from three different volcanic environments that may be responsible for this crustal alteration. Total microbial DNA was extracted from rhyolite glass of the 7 million year old Rattlesnake Tuff in eastern Oregon. The DNA was amplified using the polymerase chain reaction (PCR) with bacterial primers targeting the 16S rRNA gene. This 16S rDNA was cloned and screened with restriction fragment length polymorphism (RFLP). Out of 89 total clones screened, 46 belonged to 13 different clone families containing two or more members, while 43 clones were unique. Sequences of eight clones representing the most dominant clone families in the library were 92 to 97% similar to soil bacterial species. In a separate study, young pillow basalts (rock- and seawater-associated archaea. The six rock community profiles were quite similar to each other, and the background water communities were also similar, respectively. Both the rock and water communities shared the same dominant peak. To identify the T-RFLP peaks corresponding to the individual members of the rock and seawater communities, clone libraries of the archaeal 16S rDNA for one basalt sample (Dive 3718) and its corresponding background water sample were constructed. The most abundant archaeal genes were closely related to uncultured Group I marine Crenarchaeota that have been previously identified from similar deep-sea habitats. These archaeal genes collectively correspond to the dominant T-RFLP peak present in both the rock and water samples. In a third study, we investigated the microbial community residing in a Hawaiian Scientific Drilling Program core collected near Hilo, Hawaii. Total microbial DNA was extracted from a depth of 1351 m in the drill core (ambient temperature in the

  14. Molecular Detection of Bladder Cancer by Fluorescence Microsatellite Analysis and an Automated Genetic Analyzing System

    Directory of Open Access Journals (Sweden)

    Sarel Halachmi

    2007-01-01

    Full Text Available To investigate the ability of an automated fluorescent analyzing system to detect microsatellite alterations, in patients with bladder cancer. We investigated 11 with pathology proven bladder Transitional Cell Carcinoma (TCC for microsatellite alterations in blood, urine, and tumor biopsies. DNA was prepared by standard methods from blood, urine and resected tumor specimens, and was used for microsatellite analysis. After the primers were fluorescent labeled, amplification of the DNA was performed with PCR. The PCR products were placed into the automated genetic analyser (ABI Prism 310, Perkin Elmer, USA and were subjected to fluorescent scanning with argon ion laser beams. The fluorescent signal intensity measured by the genetic analyzer measured the product size in terms of base pairs. We found loss of heterozygocity (LOH or microsatellite alterations (a loss or gain of nucleotides, which alter the original normal locus size in all the patients by using fluorescent microsatellite analysis and an automated analyzing system. In each case the genetic changes found in urine samples were identical to those found in the resected tumor sample. The studies demonstrated the ability to detect bladder tumor non-invasively by fluorescent microsatellite analysis of urine samples. Our study supports the worldwide trend for the search of non-invasive methods to detect bladder cancer. We have overcome major obstacles that prevented the clinical use of an experimental system. With our new tested system microsatellite analysis can be done cheaper, faster, easier and with higher scientific accuracy.

  15. Second hand smoke exposure and the risk of invasive meningococcal disease in children: systematic review and meta-analysis

    Directory of Open Access Journals (Sweden)

    Murray Rachael L

    2012-12-01

    Full Text Available Abstract Background Invasive meningococcal disease remains an important cause of serious morbidity and mortality in children and young people. There is a growing body of literature to suggest that exposure to passive smoke may play a role in the development of the disease, therefore we have performed a systematic review to provide a comprehensive estimate of the magnitude of this effect for smoking by any household member, by individual family members, and of maternal smoking before and after birth. Methods Four databases (Medline, Embase, PsychINFO and CAB Abstracts database were searched to identify studies (to June 2012 and reference lists scanned for further studies. Titles, abstracts and full texts were checked for eligibility independently by two authors. Quality of included studies was assessed using the Newcastle-Ottawa Scale. Pooled odds ratios (OR with 95% confidence intervals (CI were estimated using random effect models, with heterogeneity quantified using I2. Results We identified 18 studies which assessed the effects of SHS on the risk of invasive meningococcal disease in children. SHS in the home doubled the risk of invasive meningococcal disease (OR 2.18, 95% CI 1.63 to 2.92, I2 = 72%, with some evidence of an exposure-response gradient. The strongest effect was seen in children under 5 years (OR 2.48, 95% CI 1.51 to 4.09, I2 = 47%. Maternal smoking significantly increased the risk of invasive meningococcal disease by 3 times during pregnancy (OR 2.93, 95% CI 1.52-5.66 and by 2 times after birth (OR 2.26, 95% CI 1.54-3.31. Conclusions SHS exposure, and particularly passive foetal exposure to maternal smoking during pregnancy, significantly increases the risk of childhood invasive meningococcal disease. It is likely that an extra 630 cases of invasive meningococcal disease annually in children under 16 are directly attributable to SHS exposure in UK homes.

  16. Single-cell sequencing analysis characterizes common and cell-lineage-specific mutations in a muscle-invasive bladder cancer

    DEFF Research Database (Denmark)

    Li, Yingrui; Xu, Xun; Song, Luting

    2012-01-01

    sequencing of 66 individual tumor cells from a muscle-invasive bladder transitional cell carcinoma (TCC). Analyses of the somatic mutant allele frequency spectrum and clonal structure revealed that the tumor cells were derived from a single ancestral cell, but that subsequent evolution occurred, leading...... to two distinct tumor cell subpopulations. By analyzing recurrently mutant genes in an additional cohort of 99 TCC tumors, we identified genes that might play roles in the maintenance of the ancestral clone and in the muscle-invasive capability of subclones of this bladder cancer, respectively...

  17. Contribution of molecular analysis to the typification of the non-functioning pituitary adenomas

    Science.gov (United States)

    Sanchez-Ortiga, Ruth; Aranda, Francisco Ignacio

    2017-01-01

    Aim The WHO Classification of Tumours of Endocrine Organs considers the inmunohistochemical characterization of pituitary adenomas (PA) as mandatory for patient diagnosis. Recent advances in the knowledge of the molecular patterns of these tumours could complement this classification with gene expression profiling. Methods Within the context of the Spanish Molecular Registry of Pituitary Adenomas (REMAH), a multicentre clinical-basic research project, we analysed the molecular phenotype of 142 PAs with complete IHC and clinical information. Gene expression levels of all pituitary hormones, type 1 corticotrophin-releasing hormone receptor, dopamine receptors and arginine vasopressin receptor 1b were measured by quantitative real-time polymerase chain reaction. In addition, we used three housekeeping genes for normalization and a pool of nine healthy pituitary glands from autopsies as calibration reference standard. Results Based on the clinically functioning PA (FPA: somatotroph, corticotroph, thyrotroph and lactotroph adenomas), we established the interquartile range of relative expression for all genes studied in each PA subtype. That allowed molecularly the different PA subtypes, including the clinically non-functioning PA (NFPA). Afterwards, we estimated the concordance of the molecular and immunohistochemical classification with clinical diagnosis in FPA and between them in NFPA. The kappa values were higher in molecular than in immunohistochemical classification in FPA and showed a bad concordance in all NFPA subtypes. Conclusions According to these results, the molecular characterization of the PA complements the IHC analysis, allowing a better typification of the NFPA. PMID:28692683

  18. Contribution of molecular analysis to the typification of the non-functioning pituitary adenomas.

    Directory of Open Access Journals (Sweden)

    Laura Sanchez-Tejada

    Full Text Available The WHO Classification of Tumours of Endocrine Organs considers the inmunohistochemical characterization of pituitary adenomas (PA as mandatory for patient diagnosis. Recent advances in the knowledge of the molecular patterns of these tumours could complement this classification with gene expression profiling.Within the context of the Spanish Molecular Registry of Pituitary Adenomas (REMAH, a multicentre clinical-basic research project, we analysed the molecular phenotype of 142 PAs with complete IHC and clinical information. Gene expression levels of all pituitary hormones, type 1 corticotrophin-releasing hormone receptor, dopamine receptors and arginine vasopressin receptor 1b were measured by quantitative real-time polymerase chain reaction. In addition, we used three housekeeping genes for normalization and a pool of nine healthy pituitary glands from autopsies as calibration reference standard.Based on the clinically functioning PA (FPA: somatotroph, corticotroph, thyrotroph and lactotroph adenomas, we established the interquartile range of relative expression for all genes studied in each PA subtype. That allowed molecularly the different PA subtypes, including the clinically non-functioning PA (NFPA. Afterwards, we estimated the concordance of the molecular and immunohistochemical classification with clinical diagnosis in FPA and between them in NFPA. The kappa values were higher in molecular than in immunohistochemical classification in FPA and showed a bad concordance in all NFPA subtypes.According to these results, the molecular characterization of the PA complements the IHC analysis, allowing a better typification of the NFPA.

  19. Studies on molecular structure, vibrational spectra and molecular docking analysis of 3-Methyl-1,4-dioxo-1,4-dihydronaphthalen-2-yl 4-aminobenzoate

    Science.gov (United States)

    Suresh, D. M.; Amalanathan, M.; Hubert Joe, I.; Bena Jothy, V.; Diao, Yun-Peng

    2014-09-01

    The molecular structure, vibrational analysis and molecular docking analysis of the 3-Methyl-1,4-dioxo-1,4-dihydronaphthalen-2-yl 4-aminobenzoate (MDDNAB) molecule have been carried out using FT-IR and FT-Raman spectroscopic techniques and DFT method. The equilibrium geometry, harmonic vibrational wave numbers, various bonding features have been computed using density functional method. The calculated molecular geometry has been compared with experimental data. The detailed interpretation of the vibrational spectra has been carried out by using VEDA program. The hyper-conjugative interactions and charge delocalization have been analyzed using natural bond orbital (NBO) analysis. The simulated FT-IR and FT-Raman spectra satisfactorily coincide with the experimental spectra. The PES and charge analysis have been made. The molecular docking was done to identify the binding energy and the Hydrogen bonding with the cancer protein molecule.

  20. MOLECULARLY IMPRINTED SOLID PHASE EXTRACTION FOR TRACE ANALYSIS OF DIAZINON IN DRINKING WATER

    Directory of Open Access Journals (Sweden)

    M. Rahiminejad ، S. J. Shahtaheri ، M. R. Ganjali ، A. Rahimi Forushani ، F. Golbabaei

    2009-04-01

    Full Text Available Amongst organophosphate pesticides, the one most widely used and common environmental contaminant is diazinon; thus methods for its trace analysis in environmental samples must be developed. Use of diazinon imprinted polymers such as sorbents in solid phase extraction, is a prominent and novel application area of molecular imprinted polymers. For diazinon extraction, high performance liquid chromatography analysis was demonstrated in this study. During optimization of the molecular imprinted solid phase extraction procedure for efficient solid phase extraction of diazinon, Plackett-Burman design was conducted. Eight experimental factors with critical influence on molecular imprinted solid phase extraction performance were selected, and 12 different experimental runs based on Plackett-Burman design were carried out. The applicability of diazinon imprinted polymers as the sorbent in solid phase extraction, presented obtained good recoveries of diazinon from LC-grade water. An increase in pH caused an increase in the recovery on molecular imprinted solid phase extraction. From these results, the optimal molecular imprinted solid phase extraction procedure was as follows: solid phase extraction packing with 100 mg diazinon imprinted polymers; conditioning with 5 mL of methanol and 6 mL of LC-grade water; sample loading containing diazinon (pH=10; washing with 1 mL of LC-grade water, 1 mL LC- grade water containing 30% acetonitrile and 0.5 mL of acetonitrile, respectively; eluting with 1 mL of methanol containing 2% acetic acid. The percentage recoveries obtained by the optimized molecular imprinted solid phase extraction were more than 90% with drinking water spiked at different trace levels of diazinon. Generally speaking, the molecular imprinted solid phase extraction procedure and subsequent high performance liquid chromatography analysis can be a relatively fast and proper approach for qualitative and quantitative analysis of diazinon in

  1. Geriatric information analysis of the molecular properties of mexidole

    Directory of Open Access Journals (Sweden)

    O. A. Gromova

    2017-01-01

    Full Text Available Objective: by using the pharmacoinformation profiling, to comprehensively assess all possible effects of the molecules of mexidol, choline alfoscerate, piracetam, glycine, and semax in accordance with the anatomical therapeutic and chemical (ATC classification system.Material and methods. Chemoreactomic, pharmacoinformation, and geriatric information analyses of the properties of the molecules are based on chemoreactomic methodology. The chemoreactomic analysis uses the information from the PubChem, HMDB, and String databases; the pharmacoinformation analysis applies the information from the international ATC classification and a combined sample of data from the Therapeutic Target Database (TTD, SuperTarget, Manually Annotated Targets and Drugs Online Resource (MATADOR, and Potential Drug Target Database (PDTD; geriatric information analysis employs the data on the geroprotective effect of individual substances from the PubChem database and the data available in the literature data on geroprotection from the PubMed database, which have been collected through the artificial intelligence system.Results and discussion. Mexidol is characterized by the maximum set of positive effects (the drug is used to treat CNS and cardiovascular diseases and metabolic disorders and has anti-inflammatory and anti-infective properties, etc.. Mexidol and glycine are predicted to cause the lowest frequency of adverse reactions, such as itching, constipation, paresthesia, vomiting, etc. Geriatric information assessments of changes in the life span of model organisms have shown that mexidol contributes to the higher life expectancy of C. elegans (by 22.7±10%, Drosophila (by 14.4±15%, and mice (by 14.6±3%; the control drugs do by no more than 6.1%.Conclusion. The results of the study indicate that mexidol has a high potential to be used as a geroprotector.

  2. Extracellular Molecules Involved in Cancer Cell Invasion

    International Nuclear Information System (INIS)

    Stivarou, Theodora; Patsavoudi, Evangelia

    2015-01-01

    Nowadays it is perfectly clear that understanding and eradicating cancer cell invasion and metastasis represent the crucial, definitive points in cancer therapeutics. During the last two decades there has been a great interest in the understanding of the extracellular molecular mechanisms involved in cancer cell invasion. In this review, we highlight the findings concerning these processes, focusing in particular on extracellular molecules, including extracellular matrix proteins and their receptors, growth factors and their receptors, matrix metalloproteinases and extracellular chaperones. We report the molecular mechanisms underlying the important contribution of this pool of molecules to the complex, multi-step phenomenon of cancer cell invasion

  3. Extracellular Molecules Involved in Cancer Cell Invasion

    Directory of Open Access Journals (Sweden)

    Theodora Stivarou

    2015-01-01

    Full Text Available Nowadays it is perfectly clear that understanding and eradicating cancer cell invasion and metastasis represent the crucial, definitive points in cancer therapeutics. During the last two decades there has been a great interest in the understanding of the extracellular molecular mechanisms involved in cancer cell invasion. In this review, we highlight the findings concerning these processes, focusing in particular on extracellular molecules, including extracellular matrix proteins and their receptors, growth factors and their receptors, matrix metalloproteinases and extracellular chaperones. We report the molecular mechanisms underlying the important contribution of this pool of molecules to the complex, multi-step phenomenon of cancer cell invasion.

  4. Molecular-based recursive partitioning analysis model for glioblastoma in the temozolomide era a correlative analysis based on nrg oncology RTOG 0525

    NARCIS (Netherlands)

    Bell, Erica Hlavin; Pugh, Stephanie L.; McElroy, Joseph P.; Gilbert, Mark R.; Mehta, Minesh; Klimowicz, Alexander C.; Magliocco, Anthony; Bredel, Markus; Robe, Pierre; Grosu, Anca L.; Stupp, Roger; Curran, Walter; Becker, Aline P.; Salavaggione, Andrea L.; Barnholtz-Sloan, Jill S.; Aldape, Kenneth; Blumenthal, Deborah T.; Brown, Paul D.; Glass, Jon; Souhami, Luis; Lee, R. Jeffrey; Brachman, David; Flickinger, John; Won, Minhee; Chakravarti, Arnab

    2017-01-01

    IMPORTANCE: There is a need for a more refined, molecularly based classification model for glioblastoma (GBM) in the temozolomide era. OBJECTIVE: To refine the existing clinically based recursive partitioning analysis (RPA) model by incorporating molecular variables. DESIGN, SETTING, AND

  5. Integration of non-invasive biometrics with sensory analysis techniques to assess acceptability of beer by consumers.

    Science.gov (United States)

    Gonzalez Viejo, Claudia; Fuentes, Sigfredo; Howell, Kate; Torrico, Damir D; Dunshea, Frank R

    2018-03-05

    Traditional sensory tests rely on conscious and self-reported responses from participants. The integration of non-invasive biometric techniques, such as heart rate, body temperature, brainwaves and facial expressions can gather more information from consumers while tasting a product. The main objectives of this study were i) to assess significant differences between beers for all conscious and unconscious responses, ii) to find significant correlations among the different variables from the conscious and unconscious responses and iii) to develop a model to classify beers according to liking using only the unconscious responses. For this study, an integrated camera system with video and infrared thermal imagery (IRTI), coupled with a novel computer application was used. Videos and IRTI were automatically obtained while tasting nine beers to extract biometrics (heart rate, temperature and facial expressions) using computer vision analysis. Additionally, an EEG mobile headset was used to obtain brainwave signals during beer consumption. Consumers assessed foam, color, aroma, mouthfeel, taste, flavor and overall acceptability of beers using a 9-point hedonic scale with results showing a higher acceptability for beers with higher foamability and lower bitterness. i) There were non-significant differences among beers for the emotional and physiological responses, however, significant differences were found for the cognitive and self-reported responses. ii) Results from principal component analysis explained 65% of total data variability and, along with the covariance matrix (p sensory responses of participants and the biometric data obtained. There was a negative correlation between body temperature and liking of foam height and stability, and a positive correlation between theta signals and bitterness. iii) Artificial neural networks were used to develop three models with high accuracy to classify beers according to level of liking (low and high) of three sensory

  6. Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH-Mutant Molecular Profiles

    Directory of Open Access Journals (Sweden)

    Farshad Farshidfar

    2017-03-01

    Full Text Available Cholangiocarcinoma (CCA is an aggressive malignancy of the bile ducts, with poor prognosis and limited treatment options. Here, we describe the integrated analysis of somatic mutations, RNA expression, copy number, and DNA methylation by The Cancer Genome Atlas of a set of predominantly intrahepatic CCA cases and propose a molecular classification scheme. We identified an IDH mutant-enriched subtype with distinct molecular features including low expression of chromatin modifiers, elevated expression of mitochondrial genes, and increased mitochondrial DNA copy number. Leveraging the multi-platform data, we observed that ARID1A exhibited DNA hypermethylation and decreased expression in the IDH mutant subtype. More broadly, we found that IDH mutations are associated with an expanded histological spectrum of liver tumors with molecular features that stratify with CCA. Our studies reveal insights into the molecular pathogenesis and heterogeneity of cholangiocarcinoma and provide classification information of potential therapeutic significance.

  7. Systems theoretic analysis of the central dogma of molecular biology: some recent results.

    Science.gov (United States)

    Gao, Rui; Yu, Juanyi; Zhang, Mingjun; Tarn, Tzyh-Jong; Li, Jr-Shin

    2010-03-01

    This paper extends our early study on a mathematical formulation of the central dogma of molecular biology, and focuses discussions on recent insights obtained by employing advanced systems theoretic analysis. The goal of this paper is to mathematically represent and interpret the genetic information flow at the molecular level, and explore the fundamental principle of molecular biology at the system level. Specifically, group theory was employed to interpret concepts and properties of gene mutation, and predict backbone torsion angle along the peptide chain. Finite state machine theory was extensively applied to interpret key concepts and analyze the processes related to DNA hybridization. Using the proposed model, we have transferred the character-based model in molecular biology to a sophisticated mathematical model for calculation and interpretation.

  8. Bioinformatics analysis on molecular mechanism of rheum officinale in treatment of jaundice

    Science.gov (United States)

    Shan, Si; Tu, Jun; Nie, Peng; Yan, Xiaojun

    2017-01-01

    Objective: To study the molecular mechanism of Rheum officinale in the treatment of Jaundice by building molecular networks and comparing canonical pathways. Methods: Target proteins of Rheum officinale and related genes of Jaundice were searched from Pubchem and Gene databases online respectively. Molecular networks and canonical pathways comparison analyses were performed by Ingenuity Pathway Analysis (IPA). Results: The molecular networks of Rheum officinale and Jaundice were complex and multifunctional. The 40 target proteins of Rheum officinale and 33 Homo sapiens genes of Jaundice were found in databases. There were 19 common pathways both related networks. Rheum officinale could regulate endothelial differentiation, Interleukin-1B (IL-1B) and Tumor Necrosis Factor (TNF) in these pathways. Conclusions: Rheum officinale treat Jaundice by regulating many effective nodes of Apoptotic pathway and cellular immunity related pathways.

  9. Molecularly imprinted solid-phase extraction in the analysis of agrochemicals.

    Science.gov (United States)

    Yi, Ling-Xiao; Fang, Rou; Chen, Guan-Hua

    2013-08-01

    The molecular imprinting technique is a highly predeterminative recognition technology. Molecularly imprinted polymers (MIPs) can be applied to the cleanup and preconcentration of analytes as the selective adsorbent of solid-phase extraction (SPE). In recent years, a new type of SPE has formed, molecularly imprinted polymer solid-phase extraction (MISPE), and has been widely applied to the extraction of agrochemicals. In this review, the mechanism of the molecular imprinting technique and the methodology of MIP preparations are explained. The extraction modes of MISPE, including offline and online, are discussed, and the applications of MISPE in the analysis of agrochemicals such as herbicides, fungicides and insecticides are summarized. It is concluded that MISPE is a powerful tool to selectively isolate agrochemicals from real samples with higher extraction and cleanup efficiency than commercial SPE and that it has great potential for broad applications.

  10. In situ diffraction profile analysis during tensile deformation motivated by molecular dynamics

    International Nuclear Information System (INIS)

    Van Swygenhoven, H.; Budrovic, Z.; Derlet, P.M.; Froseth, A.G.; Van Petegem, S.

    2005-01-01

    Molecular dynamics simulations can provide insight into the slip mechanism at the atomic scale and suggest that in nanocrystalline metals dislocations are nucleated and absorbed by the grain boundaries. However, this technique is limited by very short simulation times. Using suggestions from molecular dynamics, we have developed a new in situ X-ray diffraction technique wherein the profile analysis of several Bragg diffraction peaks during tensile deformation is possible. Combining experiment and careful structural analysis the results confirm the suggestions from atomistic simulations

  11. Molecular characterization and analysis of the porcine NURR1 gene

    Directory of Open Access Journals (Sweden)

    Knud Larsen

    2016-12-01

    Here we report the isolation and characterization of porcine NURR1 cDNA. The NURR1 cDNA was RT-PCR cloned using NURR1-specific oligonucleotide primers derived from in silico sequences. The porcine NURR1 cDNA encodes a polypeptide of 598 amino acids, displaying a very high similarity with bovine, human and mouse (99% NURR1 protein. Expression analysis revealed a differential NURR1 mRNA expression in various organs and tissues. NURR1 transcripts could be detected as early as at 60 days of embryo development in different brain tissues. A significant increase in NURR1 transcript in the cerebellum and a decrease in NURR1 transcript in the basal ganglia was observed during embryo development. The porcine NURR1 gene was mapped to chromosome 15. Two missense mutations were found in exon 3, the first coding exon of NURR1. Methylation analysis of the porcine NURR1 gene body revealed a high methylation degree in brain tissue, whereas methylation of the promoter was very low. A decrease in DNA methylation in a discrete region of the NURR1 promoter was observed in pig frontal cortex during pig embryo development. This observation correlated with an increase in NURR1 transcripts. Therefore, methylation might be a determinant of NURR1 expression at certain time points in embryo development.

  12. Molecular neutron activation analysis of selenium metabolites in urine

    International Nuclear Information System (INIS)

    Blotcky, A.J.; Hansen, G.T.; Ebrahim, A.; Rack, E.P.

    1988-01-01

    Because of the biological importance of selenium in living biological systems, various analytical procedures have been developed for analysis of microquantities of elemental selenium, in urine, serum, and tissue. For urine selenium, these include atomic absorption spectrometry, solution absorption spectrometry, solution fluorescence spectrometry, volumetry, and neutron activation analysis. Of equal or greater importance is the determination of selenium metabolites present in urine for the purpose of describing the biological pathways for the metabolism of selenium in living organisms. While it is known from previous studies that trimethylselenonium ion (TMSe) is a major metabolite in urine, probably the result of reduction and methylation reaction, there are no definitive results in the literature indicating the nature or quantity of other selenium metabolic products in urine. Early techniques to measure TMSe levels in urine involved the use of the radiotracer 75 Se. Because of the long biological half-life of selenium and issues of radiation exposure, its use in humans has been limited. In this paper, the authors report the experimental procedure for the determination of total selenoamino acid concentration in urine and present total selenium values, and, where applicable, TMSe, SeO 2- 3 , and total selenoamino acid concentrations in the urine of normal and diseased subjects

  13. Genomic analysis and selected molecular pathways in rare cancers

    International Nuclear Information System (INIS)

    Liu, Stephen V; Lenkiewicz, Elizabeth; Evers, Lisa; Holley, Tara; Kiefer, Jeffrey; Demeure, Michael J; Ramanathan, Ramesh K; Von Hoff, Daniel D; Barrett, Michael T; Ruiz, Christian; Glatz, Katharina; Bubendorf, Lukas; Eng, Cathy

    2012-01-01

    It is widely accepted that many cancers arise as a result of an acquired genomic instability and the subsequent evolution of tumor cells with variable patterns of selected and background aberrations. The presence and behaviors of distinct neoplastic cell populations within a patient's tumor may underlie multiple clinical phenotypes in cancers. A goal of many current cancer genome studies is the identification of recurring selected driver events that can be advanced for the development of personalized therapies. Unfortunately, in the majority of rare tumors, this type of analysis can be particularly challenging. Large series of specimens for analysis are simply not available, allowing recurring patterns to remain hidden. In this paper, we highlight the use of DNA content-based flow sorting to identify and isolate DNA-diploid and DNA-aneuploid populations from tumor biopsies as a strategy to comprehensively study the genomic composition and behaviors of individual cancers in a series of rare solid tumors: intrahepatic cholangiocarcinoma, anal carcinoma, adrenal leiomyosarcoma, and pancreatic neuroendocrine tumors. We propose that the identification of highly selected genomic events in distinct tumor populations within each tumor can identify candidate driver events that can facilitate the development of novel, personalized treatment strategies for patients with cancer. (paper)

  14. Molecular analysis of microbial diversity in advanced caries.

    Science.gov (United States)

    Chhour, Kim-Ly; Nadkarni, Mangala A; Byun, Roy; Martin, F Elizabeth; Jacques, Nicholas A; Hunter, Neil

    2005-02-01

    Real-time PCR analysis of the total bacterial load in advanced carious lesions has shown that the total load exceeds the number of cultivable bacteria. This suggests that an unresolved complexity exists in bacteria associated with advanced caries. In this report, the profile of the microflora of carious dentine was explored by using DNA extracted from 10 lesions selected on the basis of comparable total microbial load and on the relative abundance of Prevotella spp. Using universal primers for the 16S rRNA gene, PCR amplicons were cloned, and approximately 100 transformants were processed for each lesion. Phylogenetic analysis of 942 edited sequences demonstrated the presence of 75 species or phylotypes in the 10 carious lesions. Up to 31 taxa were represented in each sample. A diverse array of lactobacilli were found to comprise 50% of the species, with prevotellae also abundant, comprising 15% of the species. Other taxa present in a number of lesions or occurring with high abundance included Selenomonas spp., Dialister spp., Fusobacterium nucleatum, Eubacterium spp., members of the Lachnospiraceae family, Olsenella spp., Bifidobacterium spp., Propionibacterium sp., and Pseudoramibacter alactolyticus. The mechanisms by which such diverse patterns of bacteria extend carious lesions, including the aspect of infection of the vital dental pulp, remain unclear.

  15. The potential role of podoplanin in tumour invasion

    Science.gov (United States)

    Wicki, A; Christofori, G

    2006-01-01

    Podoplanin is a small mucin-like transmembrane protein, widely expressed in various specialised cell types throughout the body. Here, we revisit the mechanism of podoplanin-mediated tumour invasion. We compare molecular pathways leading to single and collective cell invasion and discuss novel distinct concepts of tumour cell invasion. PMID:17179989

  16. Molecular assessment of Podarcis sicula populations in Britain, Greece and Turkey reinforces a multiple-origin invasion pattern in this species

    Directory of Open Access Journals (Sweden)

    Iolanda Silva-Rocha

    2014-12-01

    Full Text Available Biological invasions are a challenge to conservation and constitute a threat to biodiversity worldwide. The Italian wall lizard Podarcis sicula has been widely introduced, and seems capable of adapting to most of the regions where it is established and to impact on native biota. Here we construct a phylogenetic framework to assess the origin of the introduced populations in the United Kingdom, Greece and Turkey comparing cytochrome-b gene sequences of lizards from five locations to published sequences from the native range and other non-native locations. The results support an origin from central Italy for the United Kingdom population, from the Adriatic region for the Greek population and from Calabria for the population from Turkey. These results emphasise the multiple-source pattern of introduction of this species identified in previous studies. The improvement in the knowledge of the origin and pathways by which invaders arrive in new areas, as well as the monitoring of their populations, are crucial for successful strategies to deal with exotic species.

  17. Complete Chloroplast Genomes of Papaver rhoeas and Papaver orientale: Molecular Structures, Comparative Analysis, and Phylogenetic Analysis

    Directory of Open Access Journals (Sweden)

    Jianguo Zhou

    2018-02-01

    Full Text Available Papaver rhoeas L. and P. orientale L., which belong to the family Papaveraceae, are used as ornamental and medicinal plants. The chloroplast genome has been used for molecular markers, evolutionary biology, and barcoding identification. In this study, the complete chloroplast genome sequences of P. rhoeas and P. orientale are reported. Results show that the complete chloroplast genomes of P. rhoeas and P. orientale have typical quadripartite structures, which are comprised of circular 152,905 and 152,799-bp-long molecules, respectively. A total of 130 genes were identified in each genome, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Sequence divergence analysis of four species from Papaveraceae indicated that the most divergent regions are found in the non-coding spacers with minimal differences among three Papaver species. These differences include the ycf1 gene and intergenic regions, such as rpoB-trnC, trnD-trnT, petA-psbJ, psbE-petL, and ccsA-ndhD. These regions are hypervariable regions, which can be used as specific DNA barcodes. This finding suggested that the chloroplast genome could be used as a powerful tool to resolve the phylogenetic positions and relationships of Papaveraceae. These results offer valuable information for future research in the identification of Papaver species and will benefit further investigations of these species.

  18. A Critical Analysis of the Actual Role of Minimally Invasive Surgery and Active Surveillance for Kidney Cancer

    NARCIS (Netherlands)

    Heuer, Roman; Gill, Inderbir S.; Guazzoni, Giorgio; Kirkali, Ziya; Marberger, Michael; Richie, Jerome P.; de La Rosette, Jean J. M. C. H.

    2010-01-01

    CONTEXT: The incidence of renal cell carcinomas (RCCs) has increased steadily-most rapidly for small renal masses (SRMs). Paralleling the changing face of RCC in the past 2 decades, new, less invasive surgical options have been developed. Laparoscopic radical nephrectomy (LRN) is an established

  19. Efficacy of anidulafungin in 539 patients with invasive candidiasis: a patient-level pooled analysis of six clinical trials

    NARCIS (Netherlands)

    Kullberg, B.J.; Vasquez, J.; Mootsikapun, P.; Nucci, M.; Paiva, J.A.; Garbino, J.; Yan, J.L.; Aram, J.; Capparella, M.R.; Conte, U.; Schlamm, H.; Swanson, R.; Herbrecht, R.

    2017-01-01

    Objectives: To evaluate the efficacy of anidulafungin for the treatment of candidaemia and invasive candidiasis in a large dataset, including patients with deep-seated tissue candidiasis, neutropenia and infection due to non- albicans Candida species. Methods: Data were pooled from six prospective,

  20. Exhaled hydrogen peroxide in chronic obstructive pulmonary disease : an analysis of its applicability as a non-invasive biomarker

    NARCIS (Netherlands)

    Beurden, Wendy Johanna Cornelia van

    2003-01-01

    Several non-invasive biomarkers have been used to investigate the pathophysiology, treatment and prognosis of COPD. However, for most markers there is no standardized procedure and few randomised studies have been performed with COPD patients. We have developed an efficient, sensitive and

  1. Massively Parallel, Molecular Analysis Platform Developed Using a CMOS Integrated Circuit With Biological Nanopores

    Science.gov (United States)

    Roever, Stefan

    2012-01-01

    A massively parallel, low cost molecular analysis platform will dramatically change the nature of protein, molecular and genomics research, DNA sequencing, and ultimately, molecular diagnostics. An integrated circuit (IC) with 264 sensors was fabricated using standard CMOS semiconductor processing technology. Each of these sensors is individually controlled with precision analog circuitry and is capable of single molecule measurements. Under electronic and software control, the IC was used to demonstrate the feasibility of creating and detecting lipid bilayers and biological nanopores using wild type α-hemolysin. The ability to dynamically create bilayers over each of the sensors will greatly accelerate pore development and pore mutation analysis. In addition, the noise performance of the IC was measured to be 30fA(rms). With this noise performance, single base detection of DNA was demonstrated using α-hemolysin. The data shows that a single molecule, electrical detection platform using biological nanopores can be operationalized and can ultimately scale to millions of sensors. Such a massively parallel platform will revolutionize molecular analysis and will completely change the field of molecular diagnostics in the future.

  2. Adrenocortical carcinoma: the dawn of a new era of genomic and molecular biology analysis.

    Science.gov (United States)

    Armignacco, R; Cantini, G; Canu, L; Poli, G; Ercolino, T; Mannelli, M; Luconi, M

    2018-05-01

    Over the last decade, the development of novel and high penetrance genomic approaches to analyze biological samples has provided very new insights in the comprehension of the molecular biology and genetics of tumors. The use of these techniques, consisting of exome sequencing, transcriptome, miRNome, chromosome alteration, genome, and epigenome analysis, has also been successfully applied to adrenocortical carcinoma (ACC). In fact, the analysis of large cohorts of patients allowed the stratification of ACC with different patterns of molecular alterations, associated with different outcomes, thus providing a novel molecular classification of the malignancy to be associated with the classical pathological analysis. Improving our knowledge about ACC molecular features will result not only in a better diagnostic and prognostic accuracy, but also in the identification of more specific therapeutic targets for the development of more effective pharmacological anti-cancer approaches. In particular, the specific molecular alteration profiles identified in ACC may represent targetable events by the use of already developed or newly designed drugs enabling a better and more efficacious management of the ACC patient in the context of new frontiers of personalized precision medicine.

  3. Pteros 2.0: Evolution of the fast parallel molecular analysis library for C++ and python.

    Science.gov (United States)

    Yesylevskyy, Semen O

    2015-07-15

    Pteros is the high-performance open-source library for molecular modeling and analysis of molecular dynamics trajectories. Starting from version 2.0 Pteros is available for C++ and Python programming languages with very similar interfaces. This makes it suitable for writing complex reusable programs in C++ and simple interactive scripts in Python alike. New version improves the facilities for asynchronous trajectory reading and parallel execution of analysis tasks by introducing analysis plugins which could be written in either C++ or Python in completely uniform way. The high level of abstraction provided by analysis plugins greatly simplifies prototyping and implementation of complex analysis algorithms. Pteros is available for free under Artistic License from http://sourceforge.net/projects/pteros/. © 2015 Wiley Periodicals, Inc.

  4. Molecular Analysis of Bacterial Microbiota on Brazilian Currency Note Surfaces

    Directory of Open Access Journals (Sweden)

    Tairacan Augusto Pereira da Fonseca

    2015-10-01

    Full Text Available Currency notes have been implicated as a vehicle for transmitting community-acquired bacterial infections. However, the overall diversity of the bacterial population residing on banknotes is still unknown in Brazil. In this study, we aimed to investigate the overall bacterial population from 150 different Brazilian Rial (R$ notes in circulation using a culture-independent Illumina massively parallel sequencing approach of the 16S rRNA genes. Samples were randomly collected from three different street markets or “feiras” in the metropolitan region of São Paulo. Taxonomical composition revealed the abundance of Proteobacteria phyla, followed by Firmicutes and Streptophyta, with a total of 1193 bacterial families and 3310 bacterial genera. Most of these bacterial genera are of human, animal, and environmental origins. Also, our analysis revealed the presence of some potential pathogenic bacterial genera including Salmonella, Staphylococcus, and Klebsiella. The results demonstrate that there is a tremendous diversity of bacterial contamination on currency notes, including organisms known to be opportunistic pathogens. One of the factors that may contribute to the richness of bacterial diversity in currency notes is personal hygiene. Thus, our results underscore the need to increase public awareness of the importance of personal hygiene of money handlers who also handle food.

  5. Molecular gas analysis by Raman scattering in intracavity laser configuration

    International Nuclear Information System (INIS)

    Benner, R.E.; Andrade, J.D.; Van Wagenen, R.A.; Westenskow, D.R.

    1987-01-01

    A system is described for the near simultaneous analysis and quantitation of selected multiple polyatomic gases in a gas sample by Raman light scattering comprising in combination: (a) laser means capable of producing a polarized laser beam of a selected wavelength containing a laser cavity the laser cavity containing a plasma tube and wherein one end of the laser cavity contains a high reflectivity output coupler mirror; (b) a gas sampling cell located within the laser cavity between the plasma tube and the output coupler mirror, the cell having opposing parallel end windows interconnected by a continuous sidewall. The end windows and sidewall define a longitudinal gas chamber oriented such that, when the laser beam is activated, the laser beam is coincident with and traverses the axis of the longitudinal gas chamber, the end windows being positioned to be substantially normal to the axis of the longitudinal gas cell chamber. The cell also has opposing, aligned side windows in the sidewall parallel to and on either side of the axis of the longitudinal gas chamber. The gas cell further contains inlet and outlet means communicating with the chamber to pass a sample gas through the cell

  6. Molecular analysis of sourdough reveals Lactobacillus mindensis sp. nov.

    Science.gov (United States)

    Ehrmann, Matthias A; Müller, Martin R A; Vogel, Rudi F

    2003-01-01

    Genotypic fingerprinting to analyse the bacterial flora of an industrial sourdough revealed a coherent group of strains which could not be associated with a valid species. Comparative 16S rDNA sequence analysis showed that these strains formed a homogeneous cluster distinct from their closest relatives, Lactobacillus farciminis, Lactobacillus alimentarius and Lactobacillus kimchii. To characterize them further, physiological (sugar fermentation, formation of DL-lactate, hydrolysis of arginine, growth temperature, CO2 production) and chemotaxonomic properties have been determined. The DNA G +C content was 37.5 0.2 mol%. The peptidoglycan was of the lysine-D-iso-asparagine (L-Lys-D-Asp) type. The strains were homofermentative, Gram-positive, catalase-negative, non-spore-forming, non-motile rods. They were found as a major stable component of a rye flour sourdough fermentation. Physiological, biochemical as well as genotypic data suggested them to be a new species of the genus Lactobacillus. This was confirmed by DNA-DNA hybridization of genomic DNA, and the name Lactobacillus mindensis is proposed. The type strain of this species is DSM 14500T (=LMG 21508T).

  7. Molecular Analysis of Bacterial Microbiota on Brazilian Currency Note Surfaces.

    Science.gov (United States)

    Pereira da Fonseca, Tairacan Augusto; Pessôa, Rodrigo; Sanabani, Sabri Saeed

    2015-10-22

    Currency notes have been implicated as a vehicle for transmitting community-acquired bacterial infections. However, the overall diversity of the bacterial population residing on banknotes is still unknown in Brazil. In this study, we aimed to investigate the overall bacterial population from 150 different Brazilian Rial (R$) notes in circulation using a culture-independent Illumina massively parallel sequencing approach of the 16S rRNA genes. Samples were randomly collected from three different street markets or "feiras" in the metropolitan region of São Paulo. Taxonomical composition revealed the abundance of Proteobacteria phyla, followed by Firmicutes and Streptophyta, with a total of 1193 bacterial families and 3310 bacterial genera. Most of these bacterial genera are of human, animal, and environmental origins. Also, our analysis revealed the presence of some potential pathogenic bacterial genera including Salmonella, Staphylococcus, and Klebsiella. The results demonstrate that there is a tremendous diversity of bacterial contamination on currency notes, including organisms known to be opportunistic pathogens. One of the factors that may contribute to the richness of bacterial diversity in currency notes is personal hygiene. Thus, our results underscore the need to increase public awareness of the importance of personal hygiene of money handlers who also handle food.

  8. A Real-Time PCR with Melting Curve Analysis for Molecular Typing of Vibrio parahaemolyticus.

    Science.gov (United States)

    He, Peiyan; Wang, Henghui; Luo, Jianyong; Yan, Yong; Chen, Zhongwen

    2018-05-23

    Foodborne disease caused by Vibrio parahaemolyticus is a serious public health problem in many countries. Molecular typing has a great scientific significance and application value for epidemiological research of V. parahaemolyticus. In this study, a real-time PCR with melting curve analysis was established for molecular typing of V. parahaemolyticus. Eighteen large variably presented gene clusters (LVPCs) of V. parahaemolyticus which have different distributions in the genome of different strains were selected as targets. Primer pairs of 18 LVPCs were distributed into three tubes. To validate this newly developed assay, we tested 53 Vibrio parahaemolyticus strains, which were classified in 13 different types. Furthermore, cluster analysis using NTSYS PC 2.02 software could divide 53 V. parahaemolyticus strains into six clusters at a relative similarity coefficient of 0.85. This method is fast, simple, and conveniently for molecular typing of V. parahaemolyticus.

  9. Molecular characterization of Giardia psittaci by multilocus sequence analysis.

    Science.gov (United States)

    Abe, Niichiro; Makino, Ikuko; Kojima, Atsushi

    2012-12-01

    Multilocus sequence analyses targeting small subunit ribosomal DNA (SSU rDNA), elongation factor 1 alpha (ef1α), glutamate dehydrogenase (gdh), and beta giardin (β-giardin) were performed on Giardia psittaci isolates from three Budgerigars (Melopsittacus undulates) and four Barred parakeets (Bolborhynchus lineola) kept in individual households or imported from overseas. Nucleotide differences and phylogenetic analyses at four loci indicate the distinction of G. psittaci from the other known Giardia species: Giardia muris, Giardia microti, Giardia ardeae, and Giardia duodenalis assemblages. Furthermore, G. psittaci was related more closely to G. duodenalis than to the other known Giardia species, except for G. microti. Conflicting signals regarded as "double peaks" were found at the same nucleotide positions of the ef1α in all isolates. However, the sequences of the other three loci, including gdh and β-giardin, which are known to be highly variable, from all isolates were also mutually identical at every locus. They showed no double peaks. These results suggest that double peaks found in the ef1α sequences are caused not by mixed infection with genetically different G. psittaci isolates but by allelic sequence heterogeneity (ASH), which is observed in diplomonad lineages including G. duodenalis. No sequence difference was found in any G. psittaci isolates at the gdh and β-giardin, suggesting that G. psittaci is indeed not more diverse genetically than other Giardia species. This report is the first to provide evidence related to the genetic characteristics of G. psittaci obtained using multilocus sequence analysis. Copyright © 2012 Elsevier B.V. All rights reserved.

  10. Serotype-specific changes in invasive pneumococcal disease after pneumococcal conjugate vaccine introduction: a pooled analysis of multiple surveillance sites.

    Directory of Open Access Journals (Sweden)

    Daniel R Feikin

    Full Text Available BACKGROUND: Vaccine-serotype (VT invasive pneumococcal disease (IPD rates declined substantially following introduction of 7-valent pneumococcal conjugate vaccine (PCV7 into national immunization programs. Increases in non-vaccine-serotype (NVT IPD rates occurred in some sites, presumably representing serotype replacement. We used a standardized approach to describe serotype-specific IPD changes among multiple sites after PCV7 introduction. METHODS AND FINDINGS: Of 32 IPD surveillance datasets received, we identified 21 eligible databases with rate data ≥ 2 years before and ≥ 1 year after PCV7 introduction. Expected annual rates of IPD absent PCV7 introduction were estimated by extrapolation using either Poisson regression modeling of pre-PCV7 rates or averaging pre-PCV7 rates. To estimate whether changes in rates had occurred following PCV7 introduction, we calculated site specific rate ratios by dividing observed by expected IPD rates for each post-PCV7 year. We calculated summary rate ratios (RRs using random effects meta-analysis. For children <5 years old, overall IPD decreased by year 1 post-PCV7 (RR 0.55, 95% CI 0.46-0.65 and remained relatively stable through year 7 (RR 0.49, 95% CI 0.35-0.68. Point estimates for VT IPD decreased annually through year 7 (RR 0.03, 95% CI 0.01-0.10, while NVT IPD increased (year 7 RR 2.81, 95% CI 2.12-3.71. Among adults, decreases in overall IPD also occurred but were smaller and more variable by site than among children. At year 7 after introduction, significant reductions were observed (18-49 year-olds [RR 0.52, 95% CI 0.29-0.91], 50-64 year-olds [RR 0.84, 95% CI 0.77-0.93], and ≥ 65 year-olds [RR 0.74, 95% CI 0.58-0.95]. CONCLUSIONS: Consistent and significant decreases in both overall and VT IPD in children occurred quickly and were sustained for 7 years after PCV7 introduction, supporting use of PCVs. Increases in NVT IPD occurred in most sites, with variable magnitude. These findings may not

  11. Morbidity analysis in minimally invasive esophagectomy for oesophageal cancer versus conventional over the last 10 years, a single institution experience

    Directory of Open Access Journals (Sweden)

    Misbah Khan

    2017-01-01

    Full Text Available Background: There has been an increasing inclination towards minimally invasive esophagectomies (MIEs at our institute recently for resectable oesophageal cancer. Objectives: The purpose of the present study is to report peri-operative and long-term procedure specific outcomes of the two groups and analyse their changing pattern at our institute. Methods: All adult patients with a diagnosis of oesophageal cancer managed at our institute from 2005 to 2015 were included in this retrospective study. Patients' demographic and clinical characteristics were recorded through our hospital information system. The cohort of esophagectomies was allocated into two groups, conventional open esophagectomy (OE or total laparoscopic MIE; hybrid esophagectomies were taken as a separate group. The short-term outcome measures are an operative time in minutes, length of hospital and Intensive Care Unit (ICU stay in days, post-operative complications and 30 days in-hospital mortality. Complications are graded according to the Clavien-Dindo classification system. Long-term outcomes are long-term procedure related complications over a minimum follow-up of 1 year. Trends were analysed by visually inspecting the graphic plots for mean number of events in each group each year. Results: Our results showed no difference in mortality, length of hospital and ICU stays and incidence of major complications between three groups on uni- and multi-variate analysis (P > 0.05. The operative time was significantly longer in MIE group (odds ratio [OR]: 1.66, confidence interval [CI]: 2.4–11.5. The incidence of long-term complication was low for MIE (OR: 1.0, CI: 133–1.017. However, all post-operative surgical outcomes trended to improve in both groups over the course of this study and stayed better for MIE group except for the operative time. Conclusion: MIE has overall comparable surgical outcomes to its conventional counterpart. Furthermore, the peri-operative outcomes tend to

  12. Automated Analysis and Classification of Histological Tissue Features by Multi-Dimensional Microscopic Molecular Profiling.

    Directory of Open Access Journals (Sweden)

    Daniel P Riordan

    Full Text Available Characterization of the molecular attributes and spatial arrangements of cells and features within complex human tissues provides a critical basis for understanding processes involved in development and disease. Moreover, the ability to automate steps in the analysis and interpretation of histological images that currently require manual inspection by pathologists could revolutionize medical diagnostics. Toward this end, we developed a new imaging approach called multidimensional microscopic molecular profiling (MMMP that can measure several independent molecular properties in situ at subcellular resolution for the same tissue specimen. MMMP involves repeated cycles of antibody or histochemical staining, imaging, and signal removal, which ultimately can generate information analogous to a multidimensional flow cytometry analysis on intact tissue sections. We performed a MMMP analysis on a tissue microarray containing a diverse set of 102 human tissues using a panel of 15 informative antibody and 5 histochemical stains plus DAPI. Large-scale unsupervised analysis of MMMP data, and visualization of the resulting classifications, identified molecular profiles that were associated with functional tissue features. We then directly annotated H&E images from this MMMP series such that canonical histological features of interest (e.g. blood vessels, epithelium, red blood cells were individually labeled. By integrating image annotation data, we identified molecular signatures that were associated with specific histological annotations and we developed statistical models for automatically classifying these features. The classification accuracy for automated histology labeling was objectively evaluated using a cross-validation strategy, and significant accuracy (with a median per-pixel rate of 77% per feature from 15 annotated samples for de novo feature prediction was obtained. These results suggest that high-dimensional profiling may advance the

  13. Molecular detection and species-specific identification of medically important Aspergillus species by real-time PCR in experimental invasive pulmonary aspergillosis.

    Science.gov (United States)

    Walsh, Thomas J; Wissel, Mark C; Grantham, Kevin J; Petraitiene, Ruta; Petraitis, Vidmantas; Kasai, Miki; Francesconi, Andrea; Cotton, Margaret P; Hughes, Johanna E; Greene, Lora; Bacher, John D; Manna, Pradip; Salomoni, Martin; Kleiboeker, Steven B; Reddy, Sushruth K

    2011-12-01

    Diagnosis of invasive pulmonary aspergillosis (IPA) remains a major challenge to clinical microbiology laboratories. We developed rapid and sensitive quantitative PCR (qPCR) assays for genus- and species-specific identification of Aspergillus infections by use of TaqMan technology. In order to validate these assays and understand their potential diagnostic utility, we then performed a blinded study of bronchoalveolar lavage (BAL) fluid specimens from well-characterized models of IPA with the four medically important species. A set of real-time qPCR primers and probes was developed by utilizing unique ITS1 regions for genus- and species-specific detection of the four most common medically important Aspergillus species (Aspergillus fumigatus, A. flavus, A. niger, and A. terreus). Pan-Aspergillus and species-specific qPCRs with BAL fluid were more sensitive than culture for detection of IPA caused by A. fumigatus in untreated (P < 0.0007) and treated (P ≤ 0.008) animals, respectively. For infections caused by A. terreus and A. niger, culture and PCR amplification from BAL fluid yielded similar sensitivities for untreated and treated animals. Pan-Aspergillus PCR was more sensitive than culture for detection of A. flavus in treated animals (P = 0.002). BAL fluid pan-Aspergillus and species-specific PCRs were comparable in sensitivity to BAL fluid galactomannan (GM) assay. The copy numbers from the qPCR assays correlated with quantitative cultures to determine the pulmonary residual fungal burdens in lung tissue. Pan-Aspergillus and species-specific qPCR assays may improve the rapid and accurate identification of IPA in immunocompromised patients.

  14. Stenotrophomonas maltophilia isolated from patients exposed to invasive devices in a university hospital in Argentina: molecular typing, susceptibility and detection of potential virulence factors.

    Science.gov (United States)

    Alcaraz, Eliana; Garcia, Carlos; Papalia, Mariana; Vay, Carlos; Friedman, Laura; Passerini de Rossi, Beatriz

    2018-05-25

    The aim of this work was to investigate the presence of selected potential virulence factors, susceptibility and clonal relatedness among 63 Stenotrophomonas maltophilia isolates recovered from patients exposed to invasive devices in a university hospital in Argentina between January 2004 and August 2012. Genetic relatedness was assessed by enterobacterial repetitive intergenic consensus PCR (ERIC-PCR) and pulsed-field gel electrophoresis (PFGE). Isolates were characterized by antimicrobial resistance, the presence and/or expression of potential virulence determinants, and virulence in the Galleria mellonella model.Results/Key findings. ERIC-PCR generated 52 fingerprints, and PFGE added another pattern. Resistance to trimethoprim-sulfamethoxazole (6.35 %), levofloxacin (9.52 %) and ciprofloxacin (23.80 %) was detected. All isolates were susceptible to minocycline. All isolates were lipase, protease and siderophore producers, while all but Sm61 formed biofilms. However, 11/63 isolates did not amplify the major extracellular protease-coding gene (stmPr1). Sm61 is an stmPr1-negative isolate, and showed (as did Sm13 and the reference strain K279a) strong proteolysis and siderophore production, and high resistance to hydrogen peroxide. The three isolates were virulent in the G. mellonella model, while Sm10, a low-resistance hydrogen peroxide stmPr1-negative isolate, and weak proteolysis and siderophore producer, was not virulent. This is the first epidemiological study of the clonal relatedness of S. maltophilia clinical isolates in Argentina. Great genomic diversity was observed, and only two small clusters of related S. maltophilia types were found. Minocycline and trimethoprim-sulfamethoxazole were the most active agents. S. maltophilia virulence in the G. mellonella model is multifactorial, and further studies are needed to elucidate the role of each potential virulence factor.

  15. Molecular and biochemical analysis of symbiotic plant receptor kinase complexes

    Energy Technology Data Exchange (ETDEWEB)

    Cook, Douglas R; Riely, Brendan K

    2010-09-01

    -localize (i.e., the flotillin FLOT4) with symbiotic receptor-like proteins. As controls for TAP tag analysis we have generated protein isoforms that carry fluorescent domains (translational fusions to GFP) and these have been used to establish the subcellular location and dynamics of two symbiotic receptors, LYK3 and DMI2. Both proteins localize to membrane microdomains, or putative lipid rafts, and display dynamic behavior following elicitation with the Nod factor ligand. Finally, mass spectrometry of interacting proteins is yielding lists of candidate proteins that we are poised to test using semi-high throughput RNAi technology and Tnt1 knockout collections in Medicago truncatula.

  16. Advances in the Molecular Analysis of Breast Cancer: Pathway Toward Personalized Medicine.

    Science.gov (United States)

    Rosa, Marilin

    2015-04-01

    Breast cancer is a heterogeneous disease that encompasses a wide range of clinical behaviors and histological and molecular variants. It is the most common type of cancer affecting women worldwide and is the second leading cause of cancer death. A comprehensive literature search was performed to explore the advances in molecular medicine related to the diagnosis and treatment of breast cancer. During the last few decades, advances in molecular medicine have changed the landscape of cancer treatment as new molecular tests complement and, in many instances, exceed traditional methods for determining patient prognosis and response to treatment options. Personalized medicine is becoming the standard of care around the world. Developments in molecular profiling, genomic analysis, and the discovery of targeted drug therapies have significantly improved patient survival rates and quality of life. This review highlights what pathologists need to know about current molecular tests for classification and prognostic/ predictive assessment of breast carcinoma as well as their role as part of the medical team.

  17. Scarlet Fever Upsurge in England and Molecular-Genetic Analysis in North-West London, 2014

    Centers for Disease Control (CDC) Podcasts

    2016-08-16

    Sarah Gregory reads an abridged version of the article, Scarlet Fever Upsurge in England and Molecular-Genetic Analysis in North-West London, 2014.  Created: 8/16/2016 by National Center for Emerging and Zoonotic Infectious Diseases (NCEZID).   Date Released: 8/16/2016.

  18. Removing external DNA contamination from arthropod predators destined for molecular gut-content analysis

    Science.gov (United States)

    Molecular gut-content analysis enables detection of arthropod predation with minimal disruption of ecosystem processes. Field and laboratory experiments have demonstrated that mass-collection methods, such as sweep-netting, vacuum sampling, and foliage beating, can lead to contamination of fed pred...

  19. Removing external DNA decontamination from arthropod predators destined for molecular gut-content analysis

    Science.gov (United States)

    Molecular gut-content analysis enables detection of arthropod predation with minimal disruption of ecosystem processes. Field and laboratory experiments have demonstrated that mass-collection methods, such as sweep-netting, vacuum sampling, and foliage beating, can lead to contamination of fed pred...

  20. Separation and analysis of low molecular weight plasticizers in poly(vinyl chloride) tubes

    DEFF Research Database (Denmark)

    Wang, Qian; Storm, Birgit Kjærside

    2005-01-01

    ) and thermogravimetric analysis (TGA), as well as by studying the extracted low molecular weight plasticizers by gas chromatography/mass spectroscopy (GC/MS) and GC. It was found that the simple room temperature extraction in chloroform showed the best separation of plasticizers from the PVC matrix. Close results...

  1. Molecular and cytogenetic analysis of the giant genomes of Fritillaria lilies

    Czech Academy of Sciences Publication Activity Database

    Ambrožová, K.; Macas, Jiří; Neumann, Pavel; Leitch, I. J.; Lysák, M.

    2009-01-01

    Roč. 17, č. 4 (2009), s. 558-559 ISSN 0967-3849. [International Chromosome Conference (ICC) /17./. 23.6.2009-26