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Book ; Online: Automatic Authorship Attribution in the Work of Tirso de Molina

Cavadas, Miguel / Gamallo, Pablo

2023

Abstract: Automatic Authorship Attribution (AAA) is the result of applying tools and techniques from Digital Humanities to authorship attribution studies. Through a quantitative and statistical approach this discipline can draw further conclusions about renowned ... ...

Abstract	Automatic Authorship Attribution (AAA) is the result of applying tools and techniques from Digital Humanities to authorship attribution studies. Through a quantitative and statistical approach this discipline can draw further conclusions about renowned authorship issues which traditional critics have been dealing with for centuries, opening a new door to style comparison. The aim of this paper is to prove the potential of these tools and techniques by testing the authorship of five comedies traditionally attributed to Spanish playwright Tirso de Molina (1579-1648): La ninfa del cielo, El burlador de Sevilla, Tan largo me lo fiais, La mujer por fuerza and El condenado por desconfiado. To accomplish this purpose some experiments concerning clustering analysis by Stylo package from R and four distance measures are carried out on a corpus built with plays by Tirso, Andres de Claramonte (c. 1560-1626), Antonio Mira de Amescua (1577-1644) and Luis Velez de Guevara (1579-1644). The results obtained point to the denial of all the attributions to Tirso except for the case of La mujer por fuerza. Comment: 20 pages, 2 figures
Keywords	Computer Science - Computation and Language
Subject code	001
Publishing date	2023-04-01
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The complex life of rhomboid pseudoproteases.

Adrain, Colin / Cavadas, Miguel

The FEBS journal

2020 Volume 287, Issue 19, Page(s) 4261–4283

Abstract: Rhomboid pseudoproteases are catalytically inactive members of the rhomboid superfamily. The founding members, rhomboids, were first identified in Drosophila as serine intramembrane proteases that cleave transmembrane proteins, enabling signaling. This ... ...

Abstract	Rhomboid pseudoproteases are catalytically inactive members of the rhomboid superfamily. The founding members, rhomboids, were first identified in Drosophila as serine intramembrane proteases that cleave transmembrane proteins, enabling signaling. This led to the discovery of the wider rhomboid superfamily, a clan that in metazoans is dominated by pseudoproteases. These so-called rhomboid pseudoproteases inherited from their catalytically active ancestors a conserved rhomboid-like domain and a propensity to regulate signaling. Lacking catalytic activity, they developed new 'pseudoenzyme' functions that include regulating the trafficking, turnover, and activity of their client proteins. Rhomboid pseudoproteases have preeminent roles in orchestrating immune cell activation, antiviral responses, and cytokine release in response to microbial infection, or in chronic diseases, and have also been implicated in growth factor signaling, cancer, and, more recently, metabolism. Here, we discuss the mechanism(s) of action of rhomboid pseudoproteases, contrasted with rhomboid proteases. We also highlight the roles of rhomboid pseudoproteases in mammalian physiology, which, quite paradoxically among pseudoenzymes, is understood much better than active rhomboids.
MeSH term(s)	Animals ; Humans ; Membrane Proteins/metabolism ; Peptide Hydrolases
Chemical Substances	Membrane Proteins ; Peptide Hydrolases (EC 3.4.-)
Keywords	covid19
Language	English
Publishing date	2020-10-02
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2173655-8
ISSN	1742-4658 ; 1742-464X
ISSN (online)	1742-4658
ISSN	1742-464X
DOI	10.1111/febs.15548
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Article: The complex life of rhomboid pseudoproteases

Adrain, Colin / Cavadas, Miguel

FEBS journal. 2020 Oct., v. 287, no. 19

2020

Abstract	Rhomboid pseudoproteases are catalytically inactive members of the rhomboid superfamily. The founding members, rhomboids, were first identified in Drosophila as serine intramembrane proteases that cleave transmembrane proteins, enabling signaling. This led to the discovery of the wider rhomboid superfamily, a clan that in metazoans is dominated by pseudoproteases. These so‐called rhomboid pseudoproteases inherited from their catalytically active ancestors a conserved rhomboid‐like domain and a propensity to regulate signaling. Lacking catalytic activity, they developed new ‘pseudoenzyme’ functions that include regulating the trafficking, turnover, and activity of their client proteins. Rhomboid pseudoproteases have preeminent roles in orchestrating immune cell activation, antiviral responses, and cytokine release in response to microbial infection, or in chronic diseases, and have also been implicated in growth factor signaling, cancer, and, more recently, metabolism. Here, we discuss the mechanism(s) of action of rhomboid pseudoproteases, contrasted with rhomboid proteases. We also highlight the roles of rhomboid pseudoproteases in mammalian physiology, which, quite paradoxically among pseudoenzymes, is understood much better than active rhomboids.
Keywords	Drosophila ; catalytic activity ; cytokines ; mammals ; metabolism ; proteinases ; serine
Language	English
Dates of publication	2020-10
Size	p. 4261-4283.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	NAL-AP-2-clean ; REVIEW
ZDB-ID	2173655-8
ISSN	1742-4658 ; 1742-464X
ISSN (online)	1742-4658
ISSN	1742-464X
DOI	10.1111/febs.15548
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Article: The complex life of rhomboid pseudoproteases

Adrain, Colin / Cavadas, Miguel

FEBS j

Abstract	Rhomboid pseudoproteases are catalytically inactive members of the rhomboid superfamily. The founding members, rhomboids, were first identified in Drosophila as serine intramembrane proteases that cleave transmembrane proteins, enabling signaling. This led to the discovery of the wider rhomboid superfamily, a clan that in metazoans is dominated by pseudoproteases. These so-called rhomboid pseudoproteases inherited from their catalytically active ancestors a conserved rhomboid-like domain and a propensity to regulate signaling. Lacking catalytic activity, they developed new "pseudoenzyme" functions that include regulating the trafficking, turnover and activity of their client proteins. Rhomboid pseudoproteases have preeminent roles in orchestrating immune cell activation, antiviral responses and cytokine release in response to microbial infection, or in chronic diseases, and have also been implicated in growth factor signaling, cancer and more recently, metabolism. Here we discuss the mechanism(s) of action of rhomboid pseudoproteases, contrasted with rhomboid proteases. We also highlight the roles of rhomboid pseudoproteases in mammalian physiology, which quite paradoxically among pseudoenzymes, is understood much better than active rhomboids.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #32894651
Database	COVID19

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Article ; Online: Acquisition of Temporal HIF Transcriptional Activity Using a Secreted Luciferase Assay.

Cavadas, Miguel A S / Taylor, Cormac T / Cheong, Alex

Methods in molecular biology (Clifton, N.J.)

2018 Volume 1742, Page(s) 37–44

Abstract: Here we describe a simple method based on secreted luciferase driven by a hypoxia-inducible factor (HIF) response element (HRE) that allows the acquisition of dynamic and high-throughput data on HIF transcriptional activity during hypoxia and ... ...

Abstract	Here we describe a simple method based on secreted luciferase driven by a hypoxia-inducible factor (HIF) response element (HRE) that allows the acquisition of dynamic and high-throughput data on HIF transcriptional activity during hypoxia and pharmacological activation of HIF. The sensitivity of the assay allows for the secreted luciferase to be consecutively sampled (as little as 1% of the total supernatant) over an extended time period, thus allowing the acquisition of time-resolved HIF transcriptional activity.
MeSH term(s)	Amino Acids, Dicarboxylic/metabolism ; Cell Hypoxia ; HEK293 Cells ; Humans ; Hypoxia-Inducible Factor 1, alpha Subunit/genetics ; Luciferases/genetics ; Promoter Regions, Genetic ; Recombinant Proteins ; Response Elements ; Transcriptional Activation
Chemical Substances	Amino Acids, Dicarboxylic ; HIF1A protein, human ; Hypoxia-Inducible Factor 1, alpha Subunit ; Recombinant Proteins ; Luciferases (EC 1.13.12.-) ; oxalylglycine (VVW38EB8YS)
Language	English
Publishing date	2018-01-12
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-7665-2_4
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Monitoring of transcriptional dynamics of HIF and NFκB activities.

Cavadas, Miguel A S / Cheong, Alex

Methods in molecular biology (Clifton, N.J.)

2014 Volume 1098, Page(s) 97–105

Abstract: Genetic experiments over the last few decades have identified many regulatory proteins critical for DNA transcription. The dynamics of their transcriptional activities shape the differential expression of the genes they control. Here we describe a simple ...

Abstract	Genetic experiments over the last few decades have identified many regulatory proteins critical for DNA transcription. The dynamics of their transcriptional activities shape the differential expression of the genes they control. Here we describe a simple method, based on the secreted luciferase, to measure the activities of two transcription factors NFκB and HIF. This technique can effectively monitor dynamics of transcriptional events in a population of cells and be up-scaled for high-throughput screening and promoter analysis, making it ideal for data-demanding applications such as mathematical modelling.
MeSH term(s)	Animals ; Biosensing Techniques/methods ; Copepoda/enzymology ; Genes, Reporter/genetics ; HEK293 Cells ; Humans ; Hypoxia-Inducible Factor 1/metabolism ; Luciferases/genetics ; NF-kappa B/metabolism ; Signal Transduction ; Transcription, Genetic ; Transfection
Chemical Substances	Hypoxia-Inducible Factor 1 ; NF-kappa B ; Luciferases (EC 1.13.12.-)
Language	English
Publishing date	2014
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-62703-718-1_8
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: The regulation of transcriptional repression in hypoxia.

Cavadas, Miguel A S / Cheong, Alex / Taylor, Cormac T

Experimental cell research

2017 Volume 356, Issue 2, Page(s) 173–181

Abstract: A sufficient supply molecular oxygen is essential for the maintenance of physiologic metabolism and bioenergetic homeostasis for most metazoans. For this reason, mechanisms have evolved for eukaryotic cells to adapt to conditions where oxygen demand ... ...

Abstract	A sufficient supply molecular oxygen is essential for the maintenance of physiologic metabolism and bioenergetic homeostasis for most metazoans. For this reason, mechanisms have evolved for eukaryotic cells to adapt to conditions where oxygen demand exceeds supply (hypoxia). These mechanisms rely on the modification of pre-existing proteins, translational arrest and transcriptional changes. The hypoxia inducible factor (HIF; a master regulator of gene induction in response to hypoxia) is responsible for the majority of induced gene expression in hypoxia. However, much less is known about the mechanism(s) responsible for gene repression, an essential part of the adaptive transcriptional response. Hypoxia-induced gene repression leads to a reduction in energy demanding processes and the redirection of limited energetic resources to essential housekeeping functions. Recent developments have underscored the importance of transcriptional repressors in cellular adaptation to hypoxia. To date, at least ten distinct transcriptional repressors have been reported to demonstrate sensitivity to hypoxia. Central among these is the Repressor Element-1 Silencing Transcription factor (REST), which regulates over 200 genes. In this review, written to honor the memory and outstanding scientific legacy of Lorenz Poellinger, we provide an overview of our existing knowledge with respect to transcriptional repressors and their target genes in hypoxia.
MeSH term(s)	Animals ; Cell Hypoxia/physiology ; Gene Expression Regulation/physiology ; Humans ; Hypoxia/genetics ; Hypoxia/metabolism ; Hypoxia-Inducible Factor 1, alpha Subunit/metabolism ; Oxygen/metabolism ; Transcription, Genetic/physiology
Chemical Substances	Hypoxia-Inducible Factor 1, alpha Subunit ; Oxygen (S88TT14065)
Language	English
Publishing date	2017-07-15
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	1493-x
ISSN	1090-2422 ; 0014-4827
ISSN (online)	1090-2422
ISSN	0014-4827
DOI	10.1016/j.yexcr.2017.02.024
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Article ; Online: Registered Report: COT drives resistance to RAF inhibition through MAP kinase pathway reactivation.

Sharma, Vidhu / Young, Lisa / Cavadas, Miguel / Owen, Kate

eLife

2016 Volume 5

Abstract: The Reproducibility Project: Cancer Biology seeks to address growing concerns about reproducibility in scientific research by conducting replications of selected experiments from a number of high-profile papers in the field of cancer biology. The papers, ...

Abstract	The Reproducibility Project: Cancer Biology seeks to address growing concerns about reproducibility in scientific research by conducting replications of selected experiments from a number of high-profile papers in the field of cancer biology. The papers, which were published between 2010 and 2012, were selected on the basis of citations and Altmetric scores (Errington et al., 2014). This Registered Report describes the proposed replication plan of key experiments from "COT drives resistance to RAF inhibition through MAPK pathway reactivation" by Johannessen and colleagues, published in Nature in 2010 (Johannessen et al., 2010). The key experiments to be replicated are those reported in Figures 3B, 3D-E, 3I, and 4E-F. In Figures 3B, D-E, RPMI-7951 and OUMS023 cells were reported to exhibit robust ERK/MEK activity concomitant with reduced growth sensitivity in the presence of the BRAF inhibitor PLX4720. MAP3K8 (COT/TPL2) directly regulated MEK/ERK phosphorylation, as the treatment of RPMI-7951 cells with a MAP3K8 kinase inhibitor resulted in a dose-dependent suppression of MEK/ERK activity (Figure 3I). In contrast, MAP3K8-deficient A375 cells remained sensitive to BRAF inhibition, exhibiting reduced growth and MEK/ERK activity during inhibitor treatment. To determine if RAF and MEK inhibitors together can overcome single-agent resistance, MAP3K8-expressing A375 cells treated with PLX4720 along with MEK inhibitors significantly inhibited both cell viability and ERK activation compared to treatment with PLX4720 alone, as reported in Figures 4E-F. The Reproducibility Project: Cancer Biology is collaboration between the Center for Open Science and Science Exchange and the results of the replications will be published in eLife.
MeSH term(s)	Cell Line, Tumor ; Humans ; MAP Kinase Kinase Kinases/metabolism ; MAP Kinase Signaling System ; Proto-Oncogene Proteins/metabolism ; Proto-Oncogene Proteins B-raf/metabolism
Chemical Substances	Proto-Oncogene Proteins ; BRAF protein, human (EC 2.7.11.1) ; Proto-Oncogene Proteins B-raf (EC 2.7.11.1) ; MAP Kinase Kinase Kinases (EC 2.7.11.25) ; MAP3K8 protein, human (EC 2.7.11.25)
Language	English
Publishing date	2016-03-21
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.11414
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Hypoxia-inducible factor (HIF) network: insights from mathematical models.

Cavadas, Miguel As / Nguyen, Lan K / Cheong, Alex

Cell communication and signaling : CCS

2013 Volume 11, Issue 1, Page(s) 42

Abstract: Oxygen is a crucial molecule for cellular function. When oxygen demand exceeds supply, the oxygen sensing pathway centred on the hypoxia inducible factor (HIF) is switched on and promotes adaptation to hypoxia by up-regulating genes involved in ... ...

Abstract	Oxygen is a crucial molecule for cellular function. When oxygen demand exceeds supply, the oxygen sensing pathway centred on the hypoxia inducible factor (HIF) is switched on and promotes adaptation to hypoxia by up-regulating genes involved in angiogenesis, erythropoiesis and glycolysis. The regulation of HIF is tightly modulated through intricate regulatory mechanisms. Notably, its protein stability is controlled by the oxygen sensing prolyl hydroxylase domain (PHD) enzymes and its transcriptional activity is controlled by the asparaginyl hydroxylase FIH (factor inhibiting HIF-1).To probe the complexity of hypoxia-induced HIF signalling, efforts in mathematical modelling of the pathway have been underway for around a decade. In this paper, we review the existing mathematical models developed to describe and explain specific behaviours of the HIF pathway and how they have contributed new insights into our understanding of the network. Topics for modelling included the switch-like response to decreased oxygen gradient, the role of micro environmental factors, the regulation by FIH and the temporal dynamics of the HIF response. We will also discuss the technical aspects, extent and limitations of these models. Recently, HIF pathway has been implicated in other disease contexts such as hypoxic inflammation and cancer through crosstalking with pathways like NFκB and mTOR. We will examine how future mathematical modelling and simulation of interlinked networks can aid in understanding HIF behaviour in complex pathophysiological situations. Ultimately this would allow the identification of new pharmacological targets in different disease settings.
Language	English
Publishing date	2013-06-10
Publishing country	England
Document type	Journal Article
ISSN	1478-811X
ISSN	1478-811X
DOI	10.1186/1478-811X-11-42
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Article ; Online: Pathogen-mimetic stealth nanocarriers for drug delivery: a future possibility.

Cavadas, Miguel / González-Fernández, Africa / Franco, Ricardo

Nanomedicine : nanotechnology, biology, and medicine

2011 Volume 7, Issue 6, Page(s) 730–743

Abstract: The Mononuclear Phagocyte System (MPS) is a major constraint to nanocarrier-based drug-delivery systems (DDS) by exerting a negative impact on blood circulation times and biodistribution. Current approaches rely on the protein- and cell-repelling ... ...

Abstract	The Mononuclear Phagocyte System (MPS) is a major constraint to nanocarrier-based drug-delivery systems (DDS) by exerting a negative impact on blood circulation times and biodistribution. Current approaches rely on the protein- and cell-repelling properties of inert hydrophilic polymers, to enable escape from the MPS. Poly(ethylene glycol) (PEG) has been particularly useful in this regard, and it also exerts positive effects in other blood compatibility parameters, being correlated with decreased hemolysis, thrombogenicity, complement activation and protein adsorption, due to its uncharged and hydrophilic nature. However, PEGylated nanocarriers are commonly found in the liver and spleen, the major MPS organs. In fact, a hydrophilic and cell-repelling delivery system is not always beneficial, as it might decrease the interaction with the target cell and hinder drug release. Here, a full scope of the immunological and biochemical barriers is presented along with some selected examples of alternatives to PEGylation. We present a novel conceptual approach that includes virulence factors for the engineering of bioactive, immune system-evasive stealth nanocarriers. From the clinical editor: The efficacy of nanocarrier-based drug-delivery systems is often dampened by the Mononuclear Phagocyte System (MPS). Current approaches to circumvent MPS rely on protein- and cell-repelling properties of inert hydrophilic polymers, including PEG. This paper discusses the full scope of the immunological and biochemical barriers along with selected examples of alternatives to PEGylation.
MeSH term(s)	Animals ; Complement System Proteins/immunology ; Drug Delivery Systems/methods ; Hemolysis ; Humans ; Nanoparticles/adverse effects ; Nanoparticles/chemistry ; Phagocytosis ; Polymers/adverse effects ; Polymers/chemistry ; Thrombosis/chemically induced ; Virulence Factors/chemistry ; Virulence Factors/immunology
Chemical Substances	Polymers ; Virulence Factors ; Complement System Proteins (9007-36-7)
Language	English
Publishing date	2011-05-19
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2183417-9
ISSN	1549-9642 ; 1549-9634
ISSN (online)	1549-9642
ISSN	1549-9634
DOI	10.1016/j.nano.2011.04.006
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