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Search Results: 1 - 10 of 319230 matches for " Julie L. V. Shaw "
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Ectopic Pregnancy as a Model to Identify Endometrial Genes and Signaling Pathways Important in Decidualization and Regulated by Local Trophoblast
W. Colin Duncan, Julie L. V. Shaw, Stewart Burgess, Sarah E. McDonald, Hilary O. D. Critchley, Andrew W. Horne
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0023595
Abstract: The endometrium in early pregnancy undergoes decidualization and functional changes induced by local trophoblast, which are not fully understood. We hypothesized that endometrium from tubal ectopic pregnancy (EP) could be interrogated to identify novel genes and pathways involved in these processes. Gestation-matched endometrium was collected from women with EP (n = 11) and intrauterine pregnancies (IUP) (n = 13). RNA was extracted from the tissue. In addition, tissues were prepared for histological analysis for degree of decidualization. We compared a) the samples from EP that were decidualized (n = 6) with non-decidualized samples (n = 5), and b) the decidualized EP (n = 6) with decidualization-matched IUP (n = 6) samples using an Affymetrix gene array platform, with Ingenuity Pathway Analysis, combined with quantitative RT-PCR. Expression of PRL and IGFBP1 was used to confirm the degree of decidualization in each group. There were no differences in PRL or IGFBP1 expression in the decidualization-matched samples but a marked reduction (P<0.001) in the non-decidualized samples. Decidualization was associated with increased expression of 428 genes including SCARA5 (181-fold), DKK1 (71-fold) and PROK1 (32-fold), and decreased expression of 230 genes including MMP-7 (35-fold) and SFRP4 (21-fold). The top canonical pathways associated with these differentially expressed genes were Natural Killer Cell and Wnt/b-Catenin signaling. Local trophoblast was associated with much less alteration of endometrial gene expression with an increase in 56 genes, including CSH1 (8-fold), and a reduction in 29 genes including CRISP3 (8-fold). The top associated canonical pathway was Antigen Presentation. The study of endometrium from tubal EP may promote novel insights into genes involved in decidualization and those influenced by factors from neighboring trophoblast. This has afforded unique information not highlighted by previous studies and adds to our understanding of the endometrium in early pregnancy.
Users' perspectives of barriers and facilitators to implementing EHR in Canada: A study protocol
Marie-Pierre Gagnon, Nicola Shaw, Claude Sicotte, Luc Mathieu, Yvan Leduc, Julie Duplantie, James Maclean, France Légaré
Implementation Science , 2009, DOI: 10.1186/1748-5908-4-20
Abstract: First, we will conduct a comprehensive review of the scientific literature and other published documentation on the barriers and facilitators to the implementation of the EHR. Standardized literature search and data extraction methods will be used. Studies' quality and relevance to inform decisions on EHR implementation will be assessed. For each group of EHR users identified, barriers and facilitators will be categorized and compiled using narrative synthesis and meta-analytical techniques. The principal factors identified for each group of EHR users will then be validated for its applicability to various Canadian contexts through a two-round Delphi study, involving representatives from each end-user groups. Continuous exchanges with decision makers and periodic knowledge transfer activities are planned to facilitate the dissemination and utilization of research results in policies regarding the implementation of EHR in the Canadian healthcare system.Given the imminence of an interoperable EHR in Canada, knowledge and evidence are urgently needed to prepare this major shift in our healthcare system and to oversee the factors that could affect its adoption and integration by all its potential users. This synthesis will be the first to systematically summarize the barriers and facilitators to EHR adoption perceived by different groups and to consider the local contexts in order to ensure the applicability of this knowledge to the particular realities of various Canadian jurisdictions. This comprehensive and rigorous strategy could be replicated in other settings.Although the electronic health record (EHR) is a clear priority for policy makers in Canada [1], this country is still lagging behind other industrialized countries in that respect [2]. Federal, provincial, and territorial governments, in partnership with Canada Health Infoway ('Infoway'), are currently developing an ambitious project consisting in the implementation of a pan-Canadian interoperable EHR, that
Interleukin-6 Contributes to Inflammation and Remodeling in a Model of Adenosine Mediated Lung Injury
Mesias Pedroza,Daniel J. Schneider,Harry Karmouty-Quintana,Julie Coote,Stevan Shaw,Rebecca Corrigan,Jose G. Molina,Joseph L. Alcorn,David Galas,Richard Gelinas,Michael R. Blackburn
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0022667
Abstract: Chronic lung diseases are the third leading cause of death in the United States due in part to an incomplete understanding of pathways that govern the progressive tissue remodeling that occurs in these disorders. Adenosine is elevated in the lungs of animal models and humans with chronic lung disease where it promotes air-space destruction and fibrosis. Adenosine signaling increases the production of the pro-fibrotic cytokine interleukin-6 (IL-6). Based on these observations, we hypothesized that IL-6 signaling contributes to tissue destruction and remodeling in a model of chronic lung disease where adenosine levels are elevated.
Comparison of user groups' perspectives of barriers and facilitators to implementing electronic health records: a systematic review
Carrie McGinn, Sonya Grenier, Julie Duplantie, Nicola Shaw, Claude Sicotte, Luc Mathieu, Yvan Leduc, France Légaré, Marie-Pierre Gagnon
BMC Medicine , 2011, DOI: 10.1186/1741-7015-9-46
Abstract: Covering a period from 1999 to 2009, a literature search was conducted on nine electronic databases. Studies were included if they reported on users' perceived barriers and facilitators to shared EHR implementation, in healthcare settings comparable to Canada. Studies in all languages with an empirical study design were included. Quality and relevance of the studies were assessed. Four EHR user groups were targeted: physicians, other health care professionals, managers, and patients/public. Content analysis was performed independently by two authors using a validated extraction grid with pre-established categorization of barriers and facilitators for each group of EHR users.Of a total of 5,695 potentially relevant publications identified, 117 full text publications were obtained after screening titles and abstracts. After review of the full articles, 60 publications, corresponding to 52 studies, met the inclusion criteria. The most frequent adoption factors common to all user groups were design and technical concerns, ease of use, interoperability, privacy and security, costs, productivity, familiarity and ability with EHR, motivation to use EHR, patient and health professional interaction, and lack of time and workload. Each user group also identified factors specific to their professional and individual priorities.This systematic review presents innovative research on the barriers and facilitators to EHR implementation. While important similarities between user groups are highlighted, differences between them demonstrate that each user group also has a unique perspective of the implementation process that should be taken into account.An interoperable electronic health record (EHR) is defined as a secure and private electronic lifetime record of an individual's key health history and care within the health system [1]. This record is available electronically to authorized health providers and the individual anywhere, anytime in support of high quality care. This rec
Variability of heat and salinity content in the North Atlantic in the last decade
V. O. Ivchenko,N. C. Wells,D. L. Aleynik,A. G. P. Shaw
Ocean Science (OS) & Discussions (OSD) , 2010, DOI: 10.5194/os-6-719-2010
Abstract: The analysis of the heat and salinity contents has been made for the Northern Atlantic for the decade between January 1999 and December 2008. This analysis is based on the Argo profiling data for the upper 2000 m. Basin-averaged values of heat content deviation (HCD) and salinity content deviation (SCD) are robust and stable. The HCD and SCD demonstrate positive trends in the last decade in the upper 2000 m of the North Atlantic. The linear trend of HCD and SCD are (11.14±3.17)×1020 J/yr, and (2.80±1.17)×1013 kg/yr, respectively. Both trends are significant at 95% level of significance.
Variability of heat and salinity content in the North Atlantic in the last decade
V. O. Ivchenko,N. C. Wells,D. L. Aleynik,A. G. P. Shaw
Ocean Science Discussions (OSD) , 2009,
Abstract: The analysis of the heat and salinity contents have been made for the Northern Atlantic for the decade between January 1999 and December 2008. This analysis is based on the Argo profiling data for the upper 2000 m. Basin-averaged values of anomaly of heat (AHC) and anomaly of salinity content (ASC) are robust and stable. The AHC and ASC demonstrate positive trends in the last decade in the upper 2000 m of the North Atlantic. The linear trend of AHC and ASC are (126.43±18.52)×1020 J, and (47.07±6.90)×1013 kg, respectively. Both trends are significant at 95% level of significance. The main contribution to the positive trend of AHC/ASC comes from the northern parts of the basin.
Colorimetric and Longitudinal Analysis of Leukocoria in Recreational Photographs of Children with Retinoblastoma
Alireza Abdolvahabi, Brandon W. Taylor, Rebecca L. Holden, Elizabeth V. Shaw, Alex Kentsis, Carlos Rodriguez-Galindo, Shizuo Mukai, Bryan F. Shaw
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0076677
Abstract: Retinoblastoma is the most common primary intraocular tumor in children. The first sign that is often reported by parents is the appearance of recurrent leukocoria (i.e., “white eye”) in recreational photographs. A quantitative definition or scale of leukocoria – as it appears during recreational photography – has not been established, and the amount of clinical information contained in a leukocoric image (collected by a parent) remains unknown. Moreover, the hypothesis that photographic leukocoria can be a sign of early stage retinoblastoma has not been tested for even a single patient. This study used commercially available software (Adobe Photoshop?) and standard color space conversion algorithms (operable in Microsoft Excel?) to quantify leukocoria in actual “baby pictures” of 9 children with retinoblastoma (that were collected by parents during recreational activities i.e., in nonclinical settings). One particular patient with bilateral retinoblastoma (“Patient Zero”) was photographed >7, 000 times by his parents (who are authors of this study) over three years: from birth, through diagnosis, treatment, and remission. This large set of photographs allowed us to determine the longitudinal and lateral frequency of leukocoria throughout the patient's life. This study establishes: (i) that leukocoria can emerge at a low frequency in early-stage retinoblastoma and increase in frequency during disease progression, but decrease upon disease regression, (ii) that Hue, Saturation and Value (i.e., HSV color space) are suitable metrics for quantifying the intensity of retinoblastoma-linked leukocoria; (iii) that different sets of intraocular retinoblastoma tumors can produce distinct leukocoric reflections; and (iv) the Saturation-Value plane of HSV color space represents a convenient scale for quantifying and classifying pupillary reflections as they appear during recreational photography.
Structure of the hDmc1-ssDNA Filament Reveals the Principles of Its Architecture
Andrei L. Okorokov,Yuriy L. Chaban,Dmitry V. Bugreev,Julie Hodgkinson,Alexander V. Mazin,Elena V. Orlova
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0008586
Abstract: In eukaryotes, meiotic recombination is a major source of genetic diversity, but its defects in humans lead to abnormalities such as Down's, Klinefelter's and other syndromes. Human Dmc1 (hDmc1), a RecA/Rad51 homologue, is a recombinase that plays a crucial role in faithful chromosome segregation during meiosis. The initial step of homologous recombination occurs when hDmc1 forms a filament on single-stranded (ss) DNA. However the structure of this presynaptic complex filament for hDmc1 remains unknown. To compare hDmc1-ssDNA complexes to those known for the RecA/Rad51 family we have obtained electron microscopy (EM) structures of hDmc1-ssDNA nucleoprotein filaments using single particle approach. The EM maps were analysed by docking crystal structures of Dmc1, Rad51, RadA, RecA and DNA. To fully characterise hDmc1-DNA complexes we have analysed their organisation in the presence of Ca2+, Mg2+, ATP, AMP-PNP, ssDNA and dsDNA. The 3D EM structures of the hDmc1-ssDNA filaments allowed us to elucidate the principles of their internal architecture. Similar to the RecA/Rad51 family, hDmc1 forms helical filaments on ssDNA in two states: extended (active) and compressed (inactive). However, in contrast to the RecA/Rad51 family, and the recently reported structure of hDmc1-double stranded (ds) DNA nucleoprotein filaments, the extended (active) state of the hDmc1 filament formed on ssDNA has nine protomers per helical turn, instead of the conventional six, resulting in one protomer covering two nucleotides instead of three. The control reconstruction of the hDmc1-dsDNA filament revealed 6.4 protein subunits per helical turn indicating that the filament organisation varies depending on the DNA templates. Our structural analysis has also revealed that the N-terminal domain of hDmc1 accomplishes its important role in complex formation through domain swapping between adjacent protomers, thus providing a mechanistic basis for coordinated action of hDmc1 protomers during meiotic recombination.
Improving pan-genome annotation using whole genome multiple alignment
Samuel V Angiuoli, Julie C Dunning Hotopp, Steven L Salzberg, Hervé Tettelin
BMC Bioinformatics , 2011, DOI: 10.1186/1471-2105-12-272
Abstract: We introduce a new tool, Mugsy-Annotator, that identifies orthologs and evaluates annotation quality in prokaryotic genomes using whole genome multiple alignment. Mugsy-Annotator identifies anomalies in annotated gene structures, including inconsistently located translation initiation sites and disrupted genes due to draft genome sequencing or pseudogenes. An evaluation of species pan-genomes using the tool indicates that such anomalies are common, especially at translation initiation sites. Mugsy-Annotator reports alternate annotations that improve consistency and are candidates for further review.Whole genome multiple alignment can be used to efficiently identify orthologs and annotation problem areas in a bacterial pan-genome. Comparisons of annotated gene structures within a species may show more variation than is actually present in the genome, indicating errors in genome annotation. Our new tool Mugsy-Annotator assists re-annotation efforts by highlighting edits that improve annotation consistency.Advances in genome sequencing technologies have enabled sequencing of thousands of microbial genomes [1]. Often a single reference genome is insufficient to describe the genetic diversity of a species, leading to sequencing of many closely related isolates and subsequent comparative analysis. To aid in the analysis, an annotation process is typically performed using computational methods that include prediction of genes and their functions. Gene prediction algorithms for prokaryotes have been shown to perform well with relatively low error rates [2-4]. Limitations of gene prediction include accurate identification of the translation initiation start (TIS) sites and pseudogenes, and over-annotation in GC-rich genomes [5]. Specialized tools have addressed these issues, such as for improved TIS prediction [6]. In addition, post-processing can be used to identify annotation anomalies, as in GenePrimp [7].While there are several tools for gene prediction of single genomes
Full Field Supercritical Angle Fluorescence Microscopy for live cell imaging
Thomas Barroca,Karla Balaa,Julie Delahaye,Sandrine Lévêque-Fort,Emmanuel Fort
Physics , 2013, DOI: 10.1364/OL.36.003051
Abstract: We introduce a full field fluorescence imaging technique with axial confinement of about 100 nm at the sample/substrate interface. Contrary to standard surface imaging techniques, this confinement is obtained through emission filtering. This technique is based on supercritical emission selectivity. It can be implemented on any epifluorescence microscope with a commercial high numerical aperture objective and offers a real time surface imaging capability. This technique is of particular interest for live cell membrane and adhesion studies. Using HEK cells, we show that one can observe simultaneously the surface and in-depth cell phenomena.
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