oalib

Publish in OALib Journal

ISSN: 2333-9721

APC: Only $99

Submit

Any time

2019 ( 34 )

2018 ( 40 )

2017 ( 39 )

2016 ( 57 )

Custom range...

Search Results: 1 - 10 of 10238 matches for " Patrick Hogan "
All listed articles are free for downloading (OA Articles)
Page 1 /10238
Display every page Item
A Different Postcolonialism: the Cultural Ethics of Yasujiro Ozu’s Late Spring
Patrick Colm Hogan
Image and Narrative : Online Magazine of the Visual Narrative , 2010,
Abstract: (E): Critics have tended to conceive of the postcolonial condition too narrowly (in historical and geographical range) and too broadly (in temporal duration). These limitations become salient when we consider Japan from 1945-1952. Of course, Japanese responses to the American occupation were not uniform. To isolate one important strain of that response, this essay explores the cultural ethics of Ozu’s Late Spring (1949). Ozu does not affirm “tradition,” “modernization,” or “hybridity” as such. Rather, he affirms the value of one or the other only insofar as it bears on our attachment relations with those who are vulnerable, whatever their identity category. (F): Les critiques ont souvent eu tendance à définir la notion de condition postcoloniale de manière à la fois trop étroite (en termes historiques et géographiques) et trop large (en termes de durée). Ces problèmes deviennent tout à fait visibles quand on considère le cas du Japon des années 1945-1952. Bien entendu, les réponses japonaises à l’occupation américaine étaient tout sauf uniformes, mais un aspect important de cette réponse peut être reconstruite à travers l’analyse de l’éthique culturelle d’un film d’Ozu, Printemps tardif (1949). Ozu n’affiche pas les notions de tradition , modernisation , ou hybridité comme telles, il n’en affiche la valeur qu’à travers la manière dont ces notions influent sur nos rapports avec ceux qui sont vulnérables, quelle que soit leur identité.
Using Mobile Health to Support the Chronic Care Model: Developing an Institutional Initiative
Shantanu Nundy,Jonathan J. Dick,Anna P. Goddu,Patrick Hogan
International Journal of Telemedicine and Applications , 2012, DOI: 10.1155/2012/871925
Abstract:
Evolutionary Conservation and Diversification of Puf RNA Binding Proteins and Their mRNA Targets
Gregory J. Hogan,Patrick O. Brown?,Daniel Herschlag
PLOS Biology , 2015, DOI: 10.1371/journal.pbio.1002307
Abstract: Reprogramming of a gene’s expression pattern by acquisition and loss of sequences recognized by specific regulatory RNA binding proteins may be a major mechanism in the evolution of biological regulatory programs. We identified that RNA targets of Puf3 orthologs have been conserved over 100–500 million years of evolution in five eukaryotic lineages. Focusing on Puf proteins and their targets across 80 fungi, we constructed a parsimonious model for their evolutionary history. This model entails extensive and coordinated changes in the Puf targets as well as changes in the number of Puf genes and alterations of RNA binding specificity including that: 1) Binding of Puf3 to more than 200 RNAs whose protein products are predominantly involved in the production and organization of mitochondrial complexes predates the origin of budding yeasts and filamentous fungi and was maintained for 500 million years, throughout the evolution of budding yeast. 2) In filamentous fungi, remarkably, more than 150 of the ancestral Puf3 targets were gained by Puf4, with one lineage maintaining both Puf3 and Puf4 as regulators and a sister lineage losing Puf3 as a regulator of these RNAs. The decrease in gene expression of these mRNAs upon deletion of Puf4 in filamentous fungi (N. crassa) in contrast to the increase upon Puf3 deletion in budding yeast (S. cerevisiae) suggests that the output of the RNA regulatory network is different with Puf4 in filamentous fungi than with Puf3 in budding yeast. 3) The coregulated Puf4 target set in filamentous fungi expanded to include mitochondrial genes involved in the tricarboxylic acid (TCA) cycle and other nuclear-encoded RNAs with mitochondrial function not bound by Puf3 in budding yeast, observations that provide additional evidence for substantial rewiring of post-transcriptional regulation. 4) Puf3 also expanded and diversified its targets in filamentous fungi, gaining interactions with the mRNAs encoding the mitochondrial electron transport chain (ETC) complex I as well as hundreds of other mRNAs with nonmitochondrial functions. The many concerted and conserved changes in the RNA targets of Puf proteins strongly support an extensive role of RNA binding proteins in coordinating gene expression, as originally proposed by Keene. Rewiring of Puf-coordinated mRNA targets and transcriptional control of the same genes occurred at different points in evolution, suggesting that there have been distinct adaptations via RNA binding proteins and transcription factors. The changes in Puf targets and in the Puf proteins indicate an integral
Day 100 Absolute Monocyte/Lymphocyte Prognostic Score and Survival Post Autologous Peripheral Blood Hematopoietic Stem Cell Transplantation in Diffuse Large B-Cell Lymphoma  [PDF]
Ana I. Velazquez, David J. Inwards, Stephen M. Ansell, Ivana N. Micallef, Patrick B. Johnston, William J. Hogan, Svetomir N. Markovic, Luis F. Porrata
Journal of Cancer Therapy (JCT) , 2013, DOI: 10.4236/jct.2013.48153
Abstract:


Day 100 prognostic factors post-autologous peripheral blood hematopoietic stem cell transplantation (APBHSCT) to predict clinical outcomes in diffuse large B-cell lymphoma (DLBCL) patients have not been studied. Thus, we retrospectively examined if day 100 absolute monocyte/lymphocyte prognostic score (AMLPS-100) affects clinical outcomes by landmark analysis from day 100 post-APBHSCT in DLBCL. Only DLBCL patients in complete remission at day 100 post-APBHSCT were evaluated. From 2000 to 2007, 134 consecutive DLBCL patients are qualified for the study. Patients with a day 100 absolute monocyte count (AMC-100) ≥ 630 cells/μL and day 100 absolute lymphocyte count (ALC-100) ≤ 1000 cells/μL experienced inferior overall survival (OS) and progression free survival (PFS). On multivariate analysis, the AMC-100 and ALC-100 remained independent predictors of OS and PFS. Combining both values into the AMLPS-100, the 5-year OS rates for low, intermediate, and high AMLPS-100 risk groups were 94% (95% CI, 83.0% - 98.1%), 70% (95% CI, 58.6% - 80.1%), and 13% (95% CI, 3.4% - 40.5%), respectively; and the 5-year PFS rates were 87% (95% CI, 74.0% - 94.1%), 68% (95% CI, 56.0% - 77.8%), and 13% (95% CI, 3.4% - 40.5%), respectively. The AMLPS-100 is a simple biomarker score that can stratify clinical outcomes from day 100 post-APBHSCT in DLBCL patients.


Systematic Identification of mRNAs Recruited to Argonaute 2 by Specific microRNAs and Corresponding Changes in Transcript Abundance
David G. Hendrickson, Daniel J. Hogan, Daniel Herschlag, James E. Ferrell, Patrick O. Brown
PLOS ONE , 2008, DOI: 10.1371/journal.pone.0002126
Abstract: microRNAs (miRNAs) are small non-coding RNAs that regulate mRNA stability and translation through the action of the RNAi-induced silencing complex (RISC). Our current understanding of miRNA function is inferred largely from studies of the effects of miRNAs on steady-state mRNA levels and from seed match conservation and context in putative targets. Here we have taken a more direct approach to these issues by comprehensively assessing the miRNAs and mRNAs that are physically associated with Argonaute 2 (Ago2), which is a core RISC component. We transfected HEK293T cells with epitope-tagged Ago2, immunopurified Ago2 together with any associated miRNAs and mRNAs, and quantitatively determined the levels of these RNAs by microarray analyses. We found that Ago2 immunopurified samples contained a representative repertoire of the cell's miRNAs and a select subset of the cell's total mRNAs. Transfection of the miRNAs miR-1 and miR-124 caused significant changes in the association of scores of mRNAs with Ago2. The mRNAs whose association with Ago2 increased upon miRNA expression were much more likely to contain specific miRNA seed matches and to have their overall mRNA levels decrease in response to the miRNA transfection than expected by chance. Hundreds of mRNAs were recruited to Ago2 by each miRNA via seed sequences in 3′-untranslated regions and coding sequences and a few mRNAs appear to be targeted via seed sequences in 5′-untranslated regions. Microarray analysis of Ago2 immunopurified samples provides a simple, direct method for experimentally identifying the targets of miRNAs and for elucidating roles of miRNAs in cellular regulation.
Defining the Specificity of Cotranslationally Acting Chaperones by Systematic Analysis of mRNAs Associated with Ribosome-Nascent Chain Complexes
Marta del Alamo,Daniel J. Hogan,Sebastian Pechmann,Veronique Albanese,Patrick O. Brown,Judith Frydman
PLOS Biology , 2012, DOI: 10.1371/journal.pbio.1001100
Abstract: Polypeptides exiting the ribosome must fold and assemble in the crowded environment of the cell. Chaperones and other protein homeostasis factors interact with newly translated polypeptides to facilitate their folding and correct localization. Despite the extensive efforts, little is known about the specificity of the chaperones and other factors that bind nascent polypeptides. To address this question we present an approach that systematically identifies cotranslational chaperone substrates through the mRNAs associated with ribosome-nascent chain-chaperone complexes. We here focused on two Saccharomyces cerevisiae chaperones: the Signal Recognition Particle (SRP), which acts cotranslationally to target proteins to the ER, and the Nascent chain Associated Complex (NAC), whose function has been elusive. Our results provide new insights into SRP selectivity and reveal that NAC is a general cotranslational chaperone. We found surprising differential substrate specificity for the three subunits of NAC, which appear to recognize distinct features within nascent chains. Our results also revealed a partial overlap between the sets of nascent polypeptides that interact with NAC and SRP, respectively, and showed that NAC modulates SRP specificity and fidelity in vivo. These findings give us new insight into the dynamic interplay of chaperones acting on nascent chains. The strategy we used should be generally applicable to mapping the specificity, interplay, and dynamics of the cotranslational protein homeostasis network.
Diverse RNA-Binding Proteins Interact with Functionally Related Sets of RNAs, Suggesting an Extensive Regulatory System
Daniel J. Hogan,Daniel P. Riordan,André P. Gerber,Daniel Herschlag,Patrick O. Brown
PLOS Biology , 2012, DOI: 10.1371/journal.pbio.0060255
Abstract: RNA-binding proteins (RBPs) have roles in the regulation of many post-transcriptional steps in gene expression, but relatively few RBPs have been systematically studied. We searched for the RNA targets of 40 proteins in the yeast Saccharomyces cerevisiae: a selective sample of the approximately 600 annotated and predicted RBPs, as well as several proteins not annotated as RBPs. At least 33 of these 40 proteins, including three of the four proteins that were not previously known or predicted to be RBPs, were reproducibly associated with specific sets of a few to several hundred RNAs. Remarkably, many of the RBPs we studied bound mRNAs whose protein products share identifiable functional or cytotopic features. We identified specific sequences or predicted structures significantly enriched in target mRNAs of 16 RBPs. These potential RNA-recognition elements were diverse in sequence, structure, and location: some were found predominantly in 3′-untranslated regions, others in 5′-untranslated regions, some in coding sequences, and many in two or more of these features. Although this study only examined a small fraction of the universe of yeast RBPs, 70% of the mRNA transcriptome had significant associations with at least one of these RBPs, and on average, each distinct yeast mRNA interacted with three of the RBPs, suggesting the potential for a rich, multidimensional network of regulation. These results strongly suggest that combinatorial binding of RBPs to specific recognition elements in mRNAs is a pervasive mechanism for multi-dimensional regulation of their post-transcriptional fate.
Defining the Specificity of Cotranslationally Acting Chaperones by Systematic Analysis of mRNAs Associated with Ribosome-Nascent Chain Complexes
Marta del Alamo,Daniel J. Hogan,Sebastian Pechmann,Veronique Albanese,Patrick O. Brown,Judith Frydman
PLOS Biology , 2011, DOI: 10.1371/journal.pbio.1001100
Abstract: Polypeptides exiting the ribosome must fold and assemble in the crowded environment of the cell. Chaperones and other protein homeostasis factors interact with newly translated polypeptides to facilitate their folding and correct localization. Despite the extensive efforts, little is known about the specificity of the chaperones and other factors that bind nascent polypeptides. To address this question we present an approach that systematically identifies cotranslational chaperone substrates through the mRNAs associated with ribosome-nascent chain-chaperone complexes. We here focused on two Saccharomyces cerevisiae chaperones: the Signal Recognition Particle (SRP), which acts cotranslationally to target proteins to the ER, and the Nascent chain Associated Complex (NAC), whose function has been elusive. Our results provide new insights into SRP selectivity and reveal that NAC is a general cotranslational chaperone. We found surprising differential substrate specificity for the three subunits of NAC, which appear to recognize distinct features within nascent chains. Our results also revealed a partial overlap between the sets of nascent polypeptides that interact with NAC and SRP, respectively, and showed that NAC modulates SRP specificity and fidelity in vivo. These findings give us new insight into the dynamic interplay of chaperones acting on nascent chains. The strategy we used should be generally applicable to mapping the specificity, interplay, and dynamics of the cotranslational protein homeostasis network.
Diverse RNA-Binding Proteins Interact with Functionally Related Sets of RNAs, Suggesting an Extensive Regulatory System
Daniel J Hogan,Daniel P Riordan,André P Gerber ,Daniel Herschlag ,Patrick O Brown
PLOS Biology , 2008, DOI: 10.1371/journal.pbio.0060255
Abstract: RNA-binding proteins (RBPs) have roles in the regulation of many post-transcriptional steps in gene expression, but relatively few RBPs have been systematically studied. We searched for the RNA targets of 40 proteins in the yeast Saccharomyces cerevisiae: a selective sample of the approximately 600 annotated and predicted RBPs, as well as several proteins not annotated as RBPs. At least 33 of these 40 proteins, including three of the four proteins that were not previously known or predicted to be RBPs, were reproducibly associated with specific sets of a few to several hundred RNAs. Remarkably, many of the RBPs we studied bound mRNAs whose protein products share identifiable functional or cytotopic features. We identified specific sequences or predicted structures significantly enriched in target mRNAs of 16 RBPs. These potential RNA-recognition elements were diverse in sequence, structure, and location: some were found predominantly in 3′-untranslated regions, others in 5′-untranslated regions, some in coding sequences, and many in two or more of these features. Although this study only examined a small fraction of the universe of yeast RBPs, 70% of the mRNA transcriptome had significant associations with at least one of these RBPs, and on average, each distinct yeast mRNA interacted with three of the RBPs, suggesting the potential for a rich, multidimensional network of regulation. These results strongly suggest that combinatorial binding of RBPs to specific recognition elements in mRNAs is a pervasive mechanism for multi-dimensional regulation of their post-transcriptional fate.
Food Insecurity, Food Based Coping Strategies and Suboptimal Dietary Practices of Adolescents in Jimma Zone Southwest Ethiopia
Tefera Belachew, David Lindstrom, Abebe Gebremariam, Dennis Hogan, Carl Lachat, Lieven Huybregts, Patrick Kolsteren
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0057643
Abstract: Despite the high prevalence of adolescent food insecurity in Ethiopia, there is no study which documented its association with suboptimal dietary practices. The objective of this study is to determine the association between adolescent food insecurity and dietary practices. We used data on 2084 adolescents in the age group of 13–17 years involved in the first round survey of the five year longitudinal family study in Southwest Ethiopia. Adolescents were selected using residence stratified random sampling methods. Food insecurity was measured using scales validated in developing countries. Dietary practices were measured using dietary diversity score, food variety score and frequency of consuming animal source food. Multivariable regression models were used to compare dietary behaviors by food security status after controlling for socio-demographic and economic covariates. Food insecure adolescents had low dietary diversity score (P<0.001), low mean food variety score (P<0.001) and low frequency of consuming animal source foods (P<0.001). After adjusting for other variables in a multivariable logistic regression model, adolescent food insecurity (P<0.001) and rural residence (P<0.001) were negatively associated with the likelihood of having a diversified diet (P<0.001) and frequency of consuming animal source foods, while a high household income tertile was positively associated. Similarly, multivariable linear regression model showed that adolescent food insecurity was negatively associated with food variety score, while residence in semi-urban areas (P<0.001), in urban areas (P<0.001) and high household income tertile (P = 0.013) were positively associated. Girls were less likely to have diversified diet (P = 0.001) compared with boys. Our findings suggest that food insecurity has negative consequence on optimal dietary intake of adolescents. Food security interventions should look into ways of targeting adolescents to mitigate these dietary consequences and provide alternative strategies to improve dietary quality of adolescents in Southwest Ethiopia.
Page 1 /10238
Display every page Item


Home
Copyright © 2008-2017 Open Access Library. All rights reserved.