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Article ; Online: PharmacoGx: an R package for analysis of large pharmacogenomic datasets.

Smirnov, Petr / Safikhani, Zhaleh / El-Hachem, Nehme / Wang, Dong / She, Adrian / Olsen, Catharina / Freeman, Mark / Selby, Heather / Gendoo, Deena M A / Grossmann, Patrick / Beck, Andrew H / Aerts, Hugo J W L / Lupien, Mathieu / Goldenberg, Anna / Haibe-Kains, Benjamin

Bioinformatics (Oxford, England)

2016 Volume 32, Issue 8, Page(s) 1244–1246

Abstract: ... implementation: PharmacoGx is implemented in R and can be easily installed on any system. The package is ...

Abstract	Unlabelled: Pharmacogenomics holds great promise for the development of biomarkers of drug response and the design of new therapeutic options, which are key challenges in precision medicine. However, such data are scattered and lack standards for efficient access and analysis, consequently preventing the realization of the full potential of pharmacogenomics. To address these issues, we implemented PharmacoGx, an easy-to-use, open source package for integrative analysis of multiple pharmacogenomic datasets. We demonstrate the utility of our package in comparing large drug sensitivity datasets, such as the Genomics of Drug Sensitivity in Cancer and the Cancer Cell Line Encyclopedia. Moreover, we show how to use our package to easily perform Connectivity Map analysis. With increasing availability of drug-related data, our package will open new avenues of research for meta-analysis of pharmacogenomic data. Availability and implementation: PharmacoGx is implemented in R and can be easily installed on any system. The package is available from CRAN and its source code is available from GitHub. Contact: bhaibeka@uhnresearch.ca or benjamin.haibe.kains@utoronto.ca Supplementary information: Supplementary data are available at Bioinformatics online.
MeSH term(s)	Genomics ; Humans ; Neoplasms ; Pharmacogenetics ; Programming Languages ; Software
Language	English
Publishing date	2016-04-15
Publishing country	England
Document type	Journal Article
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btv723
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Article: PharmacoGx: an R package for analysis of large pharmacogenomic datasets

Smirnov, Petr / Safikhani, Zhaleh / El-Hachem, Nehme / Wang, Dong / She, Adrian / Olsen, Catharina / Freeman, Mark / Selby, Heather / Gendoo, Deena M.A / Grossmann, Patrick / Beck, Andrew H / Aerts, Hugo J.W.L / Lupien, Mathieu / Goldenberg, Anna / Haibe-Kains, Benjamin

Bioinformatics. 2016 Apr. 15, v. 32, no. 8

2016

Abstract: ... implementation: PharmacoGx is implemented in R and can be easily installed on any system. The package is ...

Abstract	Summary: Pharmacogenomics holds great promise for the development of biomarkers of drug response and the design of new therapeutic options, which are key challenges in precision medicine. However, such data are scattered and lack standards for efficient access and analysis, consequently preventing the realization of the full potential of pharmacogenomics. To address these issues, we implemented PharmacoGx, an easy-to-use, open source package for integrative analysis of multiple pharmacogenomic datasets. We demonstrate the utility of our package in comparing large drug sensitivity datasets, such as the Genomics of Drug Sensitivity in Cancer and the Cancer Cell Line Encyclopedia. Moreover, we show how to use our package to easily perform Connectivity Map analysis. With increasing availability of drug-related data, our package will open new avenues of research for meta-analysis of pharmacogenomic data. Availability and implementation: PharmacoGx is implemented in R and can be easily installed on any system. The package is available from CRAN and its source code is available from GitHub. Contact: bhaibeka@uhnresearch.ca or benjamin.haibe.kains@utoronto.ca Supplementary information: Supplementary data are available at Bioinformatics online.
Keywords	bioinformatics ; biomarkers ; cell lines ; computer software ; data collection ; drugs ; meta-analysis ; neoplasm cells ; pharmacogenomics ; precision medicine
Language	English
Dates of publication	2016-0415
Size	p. 1244-1246.
Publishing place	Oxford University Press
Document type	Article
ZDB-ID	1468345-3
ISSN	1460-2059 ; 1367-4803
ISSN (online)	1460-2059
ISSN	1367-4803
DOI	10.1093/bioinformatics/btv723
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: mRMRe: an R package for parallelized mRMR ensemble feature selection.

De Jay, Nicolas / Papillon-Cavanagh, Simon / Olsen, Catharina / El-Hachem, Nehme / Bontempi, Gianluca / Haibe-Kains, Benjamin

Bioinformatics (Oxford, England)

2013 Volume 29, Issue 18, Page(s) 2365–2368

Abstract: ... for finding a set of both relevant and complementary features. Here we describe the mRMRe R package ... in terms of run-time speed when compared with previously released packages.: Availability: The R package ... mRMRe is available on Comprehensive R Archive Network and is provided open source under the Artistic-2.0 ...

Abstract	Motivation: Feature selection is one of the main challenges in analyzing high-throughput genomic data. Minimum redundancy maximum relevance (mRMR) is a particularly fast feature selection method for finding a set of both relevant and complementary features. Here we describe the mRMRe R package, in which the mRMR technique is extended by using an ensemble approach to better explore the feature space and build more robust predictors. To deal with the computational complexity of the ensemble approach, the main functions of the package are implemented and parallelized in C using the openMP Application Programming Interface. Results: Our ensemble mRMR implementations outperform the classical mRMR approach in terms of prediction accuracy. They identify genes more relevant to the biological context and may lead to richer biological interpretations. The parallelized functions included in the package show significant gains in terms of run-time speed when compared with previously released packages. Availability: The R package mRMRe is available on Comprehensive R Archive Network and is provided open source under the Artistic-2.0 License. The code used to generate all the results reported in this application note is available from Supplementary File 1. Contact: bhaibeka@ircm.qc.ca Supplementary information: Supplementary data are available at Bioinformatics online.
MeSH term(s)	Algorithms ; Antineoplastic Agents, Phytogenic/pharmacology ; Camptothecin/analogs & derivatives ; Camptothecin/pharmacology ; Drug Resistance, Neoplasm ; Genomics/methods ; Software
Chemical Substances	Antineoplastic Agents, Phytogenic ; irinotecan (7673326042) ; Camptothecin (XT3Z54Z28A)
Language	English
Publishing date	2013-09-15
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btt383
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Article ; Online: What is a clinically significant donor-specific antibody before lung transplantation?

Hachem, Ramsey R / Zeevi, Adriana

American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons

2023 Volume 23, Issue 11, Page(s) 1657–1658

MeSH term(s)	Humans ; Antibodies ; Tissue Donors ; Lung Transplantation ; HLA Antigens ; Histocompatibility Testing ; Graft Rejection/etiology ; Graft Rejection/prevention & control ; Isoantibodies
Chemical Substances	Antibodies ; HLA Antigens ; Isoantibodies
Language	English
Publishing date	2023-06-09
Publishing country	United States
Document type	Editorial ; Comment
ZDB-ID	2060594-8
ISSN	1600-6143 ; 1600-6135
ISSN (online)	1600-6143
ISSN	1600-6135
DOI	10.1016/j.ajt.2023.06.005
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Article ; Online: Antibody-Mediated Rejection: Diagnosis and Treatment.

Halverson, Laura P / Hachem, Ramsey R

Clinics in chest medicine

2023 Volume 44, Issue 1, Page(s) 95–103

Abstract: Antibody-mediated rejection (AMR) is a form of lung allograft rejection that is emerging as an important risk factor for chronic lung allograft dysfunction and decreased long-term survival. In this review, we provide a brief overview of our current ... ...

Abstract	Antibody-mediated rejection (AMR) is a form of lung allograft rejection that is emerging as an important risk factor for chronic lung allograft dysfunction and decreased long-term survival. In this review, we provide a brief overview of our current understanding of its pathophysiology with an emphasis on donor-specific antibodies before moving on to focus on the current diagnostic criteria and treatment strategies. Our goal is to discuss the limitations of our current knowledge and explore how novel diagnostic and therapeutic options aim to improve outcomes through earlier definitive diagnosis and preemptive targeted treatment.
MeSH term(s)	Humans ; Lung Transplantation ; Antibodies ; Lung ; Transplantation, Homologous ; Thorax ; Graft Rejection/diagnosis ; Graft Rejection/prevention & control
Chemical Substances	Antibodies
Language	English
Publishing date	2023-02-12
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	447455-7
ISSN	1557-8216 ; 0272-5231
ISSN (online)	1557-8216
ISSN	0272-5231
DOI	10.1016/j.ccm.2022.10.008
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Article ; Online: Donor-specific antibodies in lung transplantation.

Hachem, Ramsey R

Current opinion in organ transplantation

2020 Volume 25, Issue 6, Page(s) 563–567

Abstract: Purpose of review: The development of donor-specific antibodies (DSA) after lung transplantation has been recognized as an important risk factor for poor outcomes over the past 20 years. Recently, this has been a focus of intense research, and the ... ...

Abstract	Purpose of review: The development of donor-specific antibodies (DSA) after lung transplantation has been recognized as an important risk factor for poor outcomes over the past 20 years. Recently, this has been a focus of intense research, and the purpose of this review is to summarize our current understanding of humoral responses and important recent findings as well as to identify areas of future research. Recent findings: Recent studies have identified donor-derived cell-free DNA (ddcfDNA) as an important biomarker associated with antibody-mediated rejection (AMR). Importantly, ddcfDNA levels are noted to be elevated approximately 3 months before the onset of clinical allograft dysfunction, making ddcfDNA a particularly appealing biomarker to predict the onset of AMR. Additional notable recent findings include the identification of an independent association between the isolation of Pseudomonas aeruginosa from respiratory specimens and the development of DSA. This finding provides potential insights into crosstalk between innate and alloimmune responses and identifies a potential therapeutic target to prevent the development of DSA. Summary: Progress in the field of humoral responses after lung transplantation has been slow, but ongoing and future research in this area are critically necessary to improve patient outcomes in the future.
MeSH term(s)	Female ; Humans ; Isoantibodies/immunology ; Lung Transplantation/methods ; Male
Chemical Substances	Isoantibodies
Language	English
Publishing date	2020-10-26
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Review
ZDB-ID	1390429-2
ISSN	1531-7013 ; 1087-2418
ISSN (online)	1531-7013
ISSN	1087-2418
DOI	10.1097/MOT.0000000000000816
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Article ; Online: Enhancing Concrete Properties with Agave Americana Fiber Reinforcement.

Hachem, Houda / Mehrez, Insaf / Gheith, Ramla / Jemni, Abdelmajid

ACS omega

2024 Volume 9, Issue 8, Page(s) 8743–8753

Abstract: This research article explores the potential of using agave Americana fibers (AAFs) to enhance the physical and mechanical properties of concretes. The study investigates the impact of AAFs on concrete mix proportions in detail. Different concrete ... ...

Abstract	This research article explores the potential of using agave Americana fibers (AAFs) to enhance the physical and mechanical properties of concretes. The study investigates the impact of AAFs on concrete mix proportions in detail. Different concrete compositions are systematically created by integrating AAFs into them. The chemical structure, crystallinity, morphology, and tensile strength of extracted AAFs are examined, revealing a low cellulose content and a crystallinity index of around 41.34%. The microstructural analysis highlights the rough surface morphology of the extracted AAFs. The research also evaluates how AAFs affect concrete density, water uptake, and flexural and compressive strengths across various mixtures. The results show that incorporating AAFs in a horizontal position can increase the flexural resistance by up to 99% and the compressive resistance by up to 86% without chemical reactions occurring with mud-lime concrete. However, it is worth noting that using AAFs with cement can affect fiber durability due to the alkaline environment. As the alkali concentration increases, the fiber mechanical resistance decreases. Therefore, it is recommended to use AAFs with noncement concrete for improved sustainability and durability. Overall, this study advances our understanding of eco-friendly and resilient concrete materials.
Language	English
Publishing date	2024-02-13
Publishing country	United States
Document type	Journal Article
ISSN	2470-1343
ISSN (online)	2470-1343
DOI	10.1021/acsomega.3c03687
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Article ; Online: Point-Counterpoint: Desensitization to improve the likelihood of lung transplantation.

Roux, Antoine / Hachem, Ramsey R

Human immunology

2022 Volume 84, Issue 1, Page(s) 43–45

MeSH term(s)	Humans ; Lung Transplantation ; Immunoglobulins, Intravenous ; Desensitization, Immunologic ; Lung
Chemical Substances	Immunoglobulins, Intravenous
Language	English
Publishing date	2022-10-31
Publishing country	United States
Document type	Letter ; Comment
ZDB-ID	801524-7
ISSN	1879-1166 ; 0198-8859
ISSN (online)	1879-1166
ISSN	0198-8859
DOI	10.1016/j.humimm.2022.10.006
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Article ; Online: Lung Allograft Rejection.

Levine, Deborah J / Hachem, Ramsey R

Thoracic surgery clinics

2022 Volume 32, Issue 2, Page(s) 221–229

Abstract: Rejection is a major complication following lung transplantation. Acute cellular rejection (ACR), and antibody-mediated rejection (AMR) are risk factors for the subsequent development of chronic lung allograft dysfunction and worse outcomes after ... ...

Abstract	Rejection is a major complication following lung transplantation. Acute cellular rejection (ACR), and antibody-mediated rejection (AMR) are risk factors for the subsequent development of chronic lung allograft dysfunction and worse outcomes after transplantation. Although ACR has well-defined histopathologic diagnostic criteria and grading, the diagnosis of AMR requires a multidisciplinary diagnostic approach. This article reviews the identification, clinical and pathologic features of, and therapeutic options for ACR and AMR.
MeSH term(s)	Allografts ; Antibodies ; Graft Rejection/diagnosis ; Graft Rejection/etiology ; Humans ; Lung ; Lung Transplantation/adverse effects
Chemical Substances	Antibodies
Language	English
Publishing date	2022-01-31
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	2149218-9
ISSN	1558-5069 ; 1547-4127
ISSN (online)	1558-5069
ISSN	1547-4127
DOI	10.1016/j.thorsurg.2021.12.003
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Article: The role of the immune system in lung transplantation: towards improved long-term results.

Hachem, Ramsey R

Journal of thoracic disease

2019 Volume 11, Issue Suppl 14, Page(s) S1721–S1731

Abstract: Over the past 35 years, lung transplantation has evolved from an experimental treatment to the treatment of choice for patients with end-stage lung disease. Beyond the immediate period after lung transplantation, rejection and infection are the leading ... ...

Abstract	Over the past 35 years, lung transplantation has evolved from an experimental treatment to the treatment of choice for patients with end-stage lung disease. Beyond the immediate period after lung transplantation, rejection and infection are the leading causes of death. The risk of rejection after lung transplantation is generally higher than after other solid organ transplants, and this necessitates more intensive immunosuppression. However, this more intensive treatment does not reduce the risk of rejection sufficiently, and rejection is one of the most common complications after transplantation. There are multiple forms of rejection including acute cellular rejection, antibody-mediated rejection, and chronic lung allograft dysfunction. These have posed a vexing problem for clinicians, patients, and the field of lung transplantation. Confounding matters is the inherent effect of more intensive immunosuppression on the risk of infections. Indeed, infections pose a direct problem resulting in morbidity and mortality and increase the risk of chronic lung allograft dysfunction in the ensuing weeks and months. There are complex interactions between microbes and the immune response that are the subject of ongoing studies. This review focuses on the role of the immune system in lung transplantation and highlights different forms of rejection and the impact of infections on outcomes.
Language	English
Publishing date	2019-10-14
Publishing country	China
Document type	Journal Article ; Review
ZDB-ID	2573571-8
ISSN	2077-6624 ; 2072-1439
ISSN (online)	2077-6624
ISSN	2072-1439
DOI	10.21037/jtd.2019.04.25
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