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Article: Signaling in endothelial cells: 10 years Department of Vascular Biology and Thrombosis Research at the Medical University Vienna.

Binder, Bernd R

2007 Volume 97, Issue 3, Page(s) 334–335

MeSH term(s)	Animals ; Austria ; Biomedical Research/economics ; Biomedical Research/organization & administration ; Endothelial Cells/metabolism ; Humans ; Research Support as Topic ; Schools, Medical/economics ; Schools, Medical/organization & administration ; Signal Transduction ; Thrombosis/metabolism
Language	English
Publishing date	2007-03
Publishing country	Germany
Document type	Editorial
ZDB-ID	518294-3
ISSN	0340-6245
ISSN	0340-6245
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Article ; Online: A novel application for murine double minute 2 antagonists: the p53 tumor suppressor network also controls angiogenesis.

Binder, Bernd R

Circulation research

2007 Volume 100, Issue 1, Page(s) 13–14

MeSH term(s)	Angiogenesis Inhibitors/pharmacology ; Animals ; Feedback, Physiological ; Homeostasis ; Imidazoles/metabolism ; Imidazoles/pharmacology ; Neoplasms/blood supply ; Neovascularization, Pathologic/physiopathology ; Piperazines/metabolism ; Piperazines/pharmacology ; Proto-Oncogene Proteins c-mdm2/antagonists & inhibitors ; Proto-Oncogene Proteins c-mdm2/metabolism ; Tumor Suppressor Protein p53/antagonists & inhibitors ; Tumor Suppressor Protein p53/metabolism
Chemical Substances	Angiogenesis Inhibitors ; Imidazoles ; Piperazines ; Tumor Suppressor Protein p53 ; nutlin 3 (53IA0V845C) ; Mdm2 protein, mouse (EC 2.3.2.27) ; Proto-Oncogene Proteins c-mdm2 (EC 2.3.2.27)
Language	English
Publishing date	2007-01-05
Publishing country	United States
Document type	Editorial ; Research Support, Non-U.S. Gov't ; Review ; Comment
ZDB-ID	80100-8
ISSN	1524-4571 ; 0009-7330 ; 0931-6876
ISSN (online)	1524-4571
ISSN	0009-7330 ; 0931-6876
DOI	10.1161/01.RES.0000255897.84337.38
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Article ; Online: Withdrawal: Signal integration and coincidence detection in the mitogen-activated protein kinase/extracellular signal-regulated kinase (ERK) cascade: Concomitant activation of receptor tyrosine kinases and of LRP-1 leads to sustained ERK phosphorylation via down-regulation of dual specificity phosphatases (DUSP1 and -6).

Geetha, Nishamol / Mihaly, Judit / Stockenhuber, Alexander / Blasi, Francesco / Uhrin, Pavel / Binder, Bernd R / Freissmuth, Michael / Breuss, Johannes M

The Journal of biological chemistry

2019 Volume 294, Issue 35, Page(s) 13201

Language	English
Publishing date	2019-08-27
Publishing country	United States
Document type	Journal Article ; Retraction of Publication
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1074/jbc.W119.010444
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Article ; Online: A self-supervised deep learning method for data-efficient training in genomics.

Gündüz, Hüseyin Anil / Binder, Martin / To, Xiao-Yin / Mreches, René / Bischl, Bernd / McHardy, Alice C / Münch, Philipp C / Rezaei, Mina

Communications biology

2023 Volume 6, Issue 1, Page(s) 928

Abstract: Deep learning in bioinformatics is often limited to problems where extensive amounts of labeled data are available for supervised classification. By exploiting unlabeled data, self-supervised learning techniques can improve the performance of machine ... ...

Abstract	Deep learning in bioinformatics is often limited to problems where extensive amounts of labeled data are available for supervised classification. By exploiting unlabeled data, self-supervised learning techniques can improve the performance of machine learning models in the presence of limited labeled data. Although many self-supervised learning methods have been suggested before, they have failed to exploit the unique characteristics of genomic data. Therefore, we introduce Self-GenomeNet, a self-supervised learning technique that is custom-tailored for genomic data. Self-GenomeNet leverages reverse-complement sequences and effectively learns short- and long-term dependencies by predicting targets of different lengths. Self-GenomeNet performs better than other self-supervised methods in data-scarce genomic tasks and outperforms standard supervised training with ~10 times fewer labeled training data. Furthermore, the learned representations generalize well to new datasets and tasks. These findings suggest that Self-GenomeNet is well suited for large-scale, unlabeled genomic datasets and could substantially improve the performance of genomic models.
MeSH term(s)	Deep Learning ; Genomics ; Computational Biology ; Machine Learning
Language	English
Publishing date	2023-09-11
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2399-3642
ISSN (online)	2399-3642
DOI	10.1038/s42003-023-05310-2
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Article ; Online: Optimized model architectures for deep learning on genomic data.

Gündüz, Hüseyin Anil / Mreches, René / Moosbauer, Julia / Robertson, Gary / To, Xiao-Yin / Franzosa, Eric A / Huttenhower, Curtis / Rezaei, Mina / McHardy, Alice C / Bischl, Bernd / Münch, Philipp C / Binder, Martin

Communications biology

2024 Volume 7, Issue 1, Page(s) 516

Abstract: The success of deep learning in various applications depends on task-specific architecture design choices, including the types, hyperparameters, and number of layers. In computational biology, there is no consensus on the optimal architecture design, and ...

Abstract	The success of deep learning in various applications depends on task-specific architecture design choices, including the types, hyperparameters, and number of layers. In computational biology, there is no consensus on the optimal architecture design, and decisions are often made using insights from more well-established fields such as computer vision. These may not consider the domain-specific characteristics of genome sequences, potentially limiting performance. Here, we present GenomeNet-Architect, a neural architecture design framework that automatically optimizes deep learning models for genome sequence data. It optimizes the overall layout of the architecture, with a search space specifically designed for genomics. Additionally, it optimizes hyperparameters of individual layers and the model training procedure. On a viral classification task, GenomeNet-Architect reduced the read-level misclassification rate by 19%, with 67% faster inference and 83% fewer parameters, and achieved similar contig-level accuracy with ~100 times fewer parameters compared to the best-performing deep learning baselines.
MeSH term(s)	Deep Learning ; Genomics/methods ; Computational Biology/methods ; Humans ; Neural Networks, Computer
Language	English
Publishing date	2024-04-30
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ISSN	2399-3642
ISSN (online)	2399-3642
DOI	10.1038/s42003-024-06161-1
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Article: Signaling in endothelial cells: 10 years Department of Vascular Biology and Thrombosis Research at the Medical University Vienna

Binder, Bernd R.

Thrombosis and Haemostasis

2007 Volume 97, Issue 03, Page(s) 334–335

Language	English
Publishing date	2007-01-01
Publisher	Schattauer GmbH
Publishing place	Stuttgart ; New York
Document type	Article
ZDB-ID	518294-3
ISSN	2567-689X ; 0340-6245
ISSN (online)	2567-689X
ISSN	0340-6245
DOI	10.1160/TH07-02-0110
Database	Thieme publisher's database

In stock of ZB MED Cologne/Königswinter

Uh III Zs.192: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular ab Jg. 2022: Lesesaal (EG)
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Article: Accuracy of Digital Impression Taking with Intraoral Scanners and Fabrication of CAD/CAM Posts and Cores in a Fully Digital Workflow.

Leven, Robert / Schmidt, Alexander / Binder, Roland / Kampschulte, Marian / Vogler, Jonas / Wöstmann, Bernd / Schlenz, Maximiliane Amelie

Materials (Basel, Switzerland)

2022 Volume 15, Issue 12

Abstract: Current intraoral scanners (IOS) enable direct impression taking for computer-aided de-sign/computer-aided manufacturing (CAD/CAM) posts and cores (P+C) with subsequent milling out of monolithic materials. The aim of this in vitro study was to ... ...

Abstract	Current intraoral scanners (IOS) enable direct impression taking for computer-aided de-sign/computer-aided manufacturing (CAD/CAM) posts and cores (P+C) with subsequent milling out of monolithic materials. The aim of this in vitro study was to systematically investigate the accuracy of CAD/CAM-P+C in a fully digital workflow, considering different IOS impression methods (Primescan (PRI), Trios4 without (TRI) and with scanpost (TRI+SP)) (Part A), and CAD/CAM milling of zirconium dioxid (ZIR) and resin composite (COM)-P+C (Part B). Five human models were developed in this study. Micro-CT imaging was used as a reference (REF). For Part A, the models were scanned 12 times for each impression method. Then, IOS datasets (n = 180) were superimposed with REF, and scan accuracy was determined using 3D software (GOMInspect). For Part B, one CAD/CAM-P+C (n = 30) was milled for each model, impression method, and material. The triple-scan method was applied using an industrial scanner (ATOS) to determine the accuracy of the fit. Statistical analysis was performed using analysis of variance (ANOVA, p < 0.05). Part A showed for PRI significantly lower accuracy than TRI and TRI+SP (p < 0.05). The data of Part B revealed significantly higher accuracy for ZIR than for COM (p < 0.05). Within the limitations of this study, CAD/CAM-P+C of the ZIR can be recommended for fabrication in a fully digital workflow regarding the accuracy of fit.
Language	English
Publishing date	2022-06-13
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2487261-1
ISSN	1996-1944
ISSN	1996-1944
DOI	10.3390/ma15124199
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Book ; Online: counterfactuals

Dandl, Susanne / Hofheinz, Andreas / Binder, Martin / Bischl, Bernd / Casalicchio, Giuseppe

An R Package for Counterfactual Explanation Methods

2023

Abstract: ... we introduce the counterfactuals R package, which provides a modular and unified R6-based interface ...

Abstract	Counterfactual explanation methods provide information on how feature values of individual observations must be changed to obtain a desired prediction. Despite the increasing amount of proposed methods in research, only a few implementations exist whose interfaces and requirements vary widely. In this work, we introduce the counterfactuals R package, which provides a modular and unified R6-based interface for counterfactual explanation methods. We implemented three existing counterfactual explanation methods and propose some optional methodological extensions to generalize these methods to different scenarios and to make them more comparable. We explain the structure and workflow of the package using real use cases and show how to integrate additional counterfactual explanation methods into the package. In addition, we compared the implemented methods for a variety of models and datasets with regard to the quality of their counterfactual explanations and their runtime behavior.
Keywords	Statistics - Machine Learning ; Computer Science - Machine Learning ; Statistics - Computation
Subject code	004
Publishing date	2023-04-13
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: The plasminogen activator inhibitor "paradox" in cancer.

Binder, Bernd R / Mihaly, Judit

Immunology letters

2008 Volume 118, Issue 2, Page(s) 116–124

Abstract: Proteolysis in general and specifically the plasminogen activating system regulated by urokinase (uPA) its specific receptor, the GPI membrane anchored urokinase receptor (uPAR) and the specific plasminogen activator inhibitor 1 (PAI-1) plays a major ... ...

Abstract	Proteolysis in general and specifically the plasminogen activating system regulated by urokinase (uPA) its specific receptor, the GPI membrane anchored urokinase receptor (uPAR) and the specific plasminogen activator inhibitor 1 (PAI-1) plays a major role in tumorigenesis, tumor progression, tumor invasion and metastasis formation. This is exemplified by a body of published work showing a positive correlation between the expression of uPA or uPAR in several tumors and their malignancy. It is generally assumed that such a "pro-malignant" effect of the uPA-uPAR system is mediated by increased local proteolysis thus favoring tumor invasion, by a pro-angiogenic effect of this system and also by uPA-uPAR signaling towards the tumor thereby shifting the tumor phenotype to a more "malignant" one. However, when tumor patients are analyzed for long term survival, those with high levels of the inhibitor of the system, PAI-1 have a much worse prognosis than those with lower PAI-1 levels. This indicates that increased overall proteolysis alone cannot be made responsible for the adverse effects of the plasminogen activating system in tumors. Moreover, it becomes increasingly evident that components of the fibrinolytic system secreted by the tumor cells themselves are not solely responsible for a correlation between the plasminogen activating system and tumor malignancy; components of the plasminogen activating system secreted by stroma cells or cells of the immune system such as macrophages contribute also to the impact of fibrinolysis on malignancy. This review summarizes the evidence for the role of plasminogen activator inhibitor-1 in mediating the malignant phenotype and possible mechanism thereby trying to explain the "PAI-1 paradox in cancer" on a molecular level.
MeSH term(s)	Animals ; Disease Models, Animal ; Humans ; Neoplasm Metastasis/physiopathology ; Neoplasms/metabolism ; Plasminogen Activator Inhibitor 1/metabolism
Chemical Substances	Plasminogen Activator Inhibitor 1
Language	English
Publishing date	2008-06-30
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	445150-8
ISSN	1879-0542 ; 0165-2478
ISSN (online)	1879-0542
ISSN	0165-2478
DOI	10.1016/j.imlet.2008.03.017
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Article ; Online: Alpha-1-antitrypsin-deficiency is associated with lower cardiovascular risk: an approach based on federated learning.

Zöller, Daniela / Haverkamp, Christian / Makoudjou, Adeline / Sofack, Ghislain / Kiefer, Saskia / Gebele, Denis / Pfaffenlehner, Michelle / Boeker, Martin / Binder, Harald / Karki, Kapil / Seidemann, Christian / Schmeck, Bernd / Greulich, Timm / Renz, Harald / Schild, Stefanie / Seuchter, Susanne A / Tibyampansha, Dativa / Buhl, Roland / Rohde, Gernot /

Trudzinski, Franziska C / Bals, Robert / Janciauskiene, Sabina / Stolz, Daiana / Fähndrich, Sebastian

Respiratory research

2024 Volume 25, Issue 1, Page(s) 38

Abstract: Background: Chronic obstructive pulmonary disease (COPD) is an inflammatory multisystemic disease caused by environmental exposures and/or genetic factors. Inherited alpha-1-antitrypsin deficiency (AATD) is one of the best recognized genetic factors ... ...

Abstract	Background: Chronic obstructive pulmonary disease (COPD) is an inflammatory multisystemic disease caused by environmental exposures and/or genetic factors. Inherited alpha-1-antitrypsin deficiency (AATD) is one of the best recognized genetic factors increasing the risk for an early onset COPD with emphysema. The aim of this study was to gain a better understanding of the associations between comorbidities and specific biomarkers in COPD patients with and without AATD to enable future investigations aimed, for example, at identifying risk factors or improving care. Methods: We focused on cardiovascular comorbidities, blood high sensitivity troponin (hs-troponin) and lipid profiles in COPD patients with and without AATD. We used clinical data from six German University Medical Centres of the MIRACUM (Medical Informatics Initiative in Research and Medicine) consortium. The codes for the international classification of diseases (ICD) were used for COPD as a main diagnosis and for comorbidities and blood laboratory data were obtained. Data analyses were based on the DataSHIELD framework. Results: Out of 112,852 visits complete information was available for 43,057 COPD patients. According to our findings, 746 patients with AATD (1.73%) showed significantly lower total blood cholesterol levels and less cardiovascular comorbidities than non-AATD COPD patients. Moreover, after adjusting for the confounder factors, such as age, gender, and nicotine abuse, we confirmed that hs-troponin is a suitable predictor of overall mortality in COPD patients. The comorbidities associated with AATD in the current study differ from other studies, which may reflect geographic and population-based differences as well as the heterogeneous characteristics of AATD. Conclusion: The concept of MIRACUM is suitable for the analysis of a large healthcare database. This study provided evidence that COPD patients with AATD have a lower cardiovascular risk and revealed that hs-troponin is a predictor for hospital mortality in individuals with COPD.
MeSH term(s)	Humans ; alpha 1-Antitrypsin Deficiency/diagnosis ; alpha 1-Antitrypsin Deficiency/epidemiology ; alpha 1-Antitrypsin Deficiency/genetics ; Cardiovascular Diseases/diagnosis ; Cardiovascular Diseases/epidemiology ; Cardiovascular Diseases/genetics ; Heart Disease Risk Factors ; Pulmonary Disease, Chronic Obstructive/diagnosis ; Pulmonary Disease, Chronic Obstructive/epidemiology ; Pulmonary Disease, Chronic Obstructive/etiology ; Risk Factors ; Troponin
Chemical Substances	Troponin ; SERPINA1 protein, human
Language	English
Publishing date	2024-01-18
Publishing country	England
Document type	Journal Article
ZDB-ID	2041675-1
ISSN	1465-993X ; 1465-993X
ISSN (online)	1465-993X
ISSN	1465-993X
DOI	10.1186/s12931-023-02607-y
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