| 1. |
- Grüning, Björn, et al.
(författare)
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Bioconda: A sustainable and comprehensive software distribution for the life sciences
- 2017
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- We present Bioconda (https://bioconda.github.io), a distribution of bioinformatics software for the lightweight, multi-platform and language-agnostic package manager Conda. Currently, Bioconda offers a collection of over 3000 software packages, which is continuously maintained, updated, and extended by a growing global community of more than 200 contributors. Bioconda improves analysis reproducibility by allowing users to define isolated environments with defined software versions, all of which are easily installed and managed without administrative privileges.
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| 2. |
- Herold, Sebastian, et al.
(författare)
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Towards Improving Software Architecture Degradation Mitigation by Machine Learning
- 2020
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Konferensbidrag (refereegranskat)abstract
- Mitigating software architecture degradation is a task in evolving large and complex software-intensive systems that is as important as it is challenging. One aspect adding to the complexity of the task is the amount of information in the implementations of most real-world systems to be digested in order to detect, analyse, and remedy degradation. In domains with similar challenges, machine learning techniques have been applied in recent years and partially delivered exciting results. Hence the question arises whether, and to which degree, machine learning can be successfully applied to tackle software architecture degradation. In this paper, we propose a novel combination of existing techniques for different phases of the task of mitigating software architecture degradation from detecting it to repairing it. We outline how these techniques could be complemented by machine learning to increase their accuracy and efficiency over time
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| 3. |
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| 4. |
- Metzendorf, Christoph, et al.
(författare)
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Transcriptomic and Proteomic Analysis of Clear Cell Foci (CCF) in the Human Non-Cirrhotic Liver Identifies Several Differentially Expressed Genes and Proteins with Functions in Cancer Cell Biology and Glycogen Metabolism
- 2020
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Ingår i: Molecules. - : MDPI AG. - 1431-5157 .- 1420-3049. ; 25:18, s. 4141-
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Tidskriftsartikel (refereegranskat)abstract
- Clear cell foci (CCF) of the liver are considered to be pre-neoplastic lesions of hepatocellular adenomas and carcinomas. They are hallmarked by glycogen overload and activation of AKT (v-akt murine thymoma viral oncogene homolog)/mTOR (mammalian target of rapamycin)-signaling. Here, we report the transcriptome and proteome of CCF extracted from human liver biopsies by laser capture microdissection. We found 14 genes and 22 proteins differentially expressed in CCF and the majority of these were expressed at lower levels in CCF. Using immunohistochemistry, the reduced expressions of STBD1 (starch-binding domain-containing protein 1), USP28 (ubiquitin-specific peptidase 28), monad/WDR92 (WD repeat domain 92), CYB5B (Cytochrome b5 type B), and HSPE1 (10 kDa heat shock protein, mitochondrial) were validated in CCF in independent specimens. Knockout of Stbd1, the gene coding for Starch-binding domain-containing protein 1, in mice did not have a significant effect on liver glycogen levels, indicating that additional factors are required for glycogen overload in CCF. Usp28 knockout mice did not show changes in glycogen storage in diethylnitrosamine-induced liver carcinoma, demonstrating that CCF are distinct from this type of cancer model, despite the decreased USP28 expression. Moreover, our data indicates that decreased USP28 expression is a novel factor contributing to the pre-neoplastic character of CCF. In summary, our work identifies several novel and unexpected candidates that are differentially expressed in CCF and that have functions in glycogen metabolism and tumorigenesis.
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| 5. |
- Wehner, Christian, et al.
(författare)
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Characteristics and frequency distribution of bone defect configurations in peri-implantitis lesions : A series of 193 cases
- 2021
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Ingår i: Clinical Implant Dentistry and Related Research. - : John Wiley & Sons. - 1523-0899 .- 1708-8208. ; 23:2, s. 178-188
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Tidskriftsartikel (refereegranskat)abstract
- Background:Knowledge on peri‐implantitis bone defect characteristics and predictors is still limited.Purpose:To describe peri‐implantitis bone defect characteristics and identify possible predictors.Methods:Various parameters at patient‐ (age, gender, smoking, and supra‐structure), implant‐ (surface, type, connection, platform, and misfit), and site level (region, alveolar ridge position, defect characteristics, neighboring structure) were recorded retrospectively.Results:Among 193 implants, the most prevalent defects were class Ic (25.4%), and Id (23.8%); a previously non‐described category “class Id with only one bone wall” was frequently observed (11.9%). Mean intrabony defect depth and width ranged from 4.5 to 6.2 mm and from 2.7 to 2.9 mm, respectively; mean dehiscence extent ranged from 2.8 to 7.0 mm. A total of 37.8% of the defects presented horizontal bone loss and an intrabony component; in 52.7% of the implants, total defect extent was >6 mm. Jaw region, implant position within the alveolar ridge, and implant/abutment misfit showed significant associations either to defect configuration and/or defect extent.Conclusion:(a) Most common peri‐implantitis defects exhibited a combination of intrabony component and a buccal/oral dehiscence, while purely circumferential defects were relatively seldom; (b) implants with defects with bone dehiscence were placed more frequently closer to the lateral aspect of the ridge harboring the dehiscence; (c) implants placed in the lower anterior region had the highest risk for more severe peri‐implant bone loss; and (d) peri‐implant bone defects with only a single bone wall appropriate for regenerative procedure were relatively frequent.
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