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Poetry Discussion

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Gabriel Gomez
Gabriel Gomez

Mechanisms Software [UPDATED]


Small-molecule drugs and toxicants commonly interact with more than a single protein target, each of which may have unique effects on cellular phenotype. Although untargeted metabolomics is often applied to understand the mode of action of these chemicals, simple pairwise comparisons of treated and untreated samples are insufficient to resolve the effects of disrupting two or more independent protein targets. Here, we introduce a workflow for dose-response metabolomics to evaluate chemicals that potentially affect multiple proteins with different potencies. Our approach relies on treating samples with various concentrations of compound prior to analysis with mass spectrometry-based metabolomics. Data are then processed with software we developed called TOXcms, which statistically evaluates dose-response trends for each metabolomic signal according to user-defined tolerances and subsequently groups those that follow the same pattern. Although TOXcms was built upon the XCMS framework, it is compatible with any metabolomic data-processing software. Additionally, to enable correlation of dose responses beyond those that can be measured by metabolomics, TOXcms also accepts data from respirometry, cell death assays, other omic platforms, etc. In this work, we primarily focus on applying dose-response metabolomics to find off-target effects of drugs. Using metformin and etomoxir as examples, we demonstrate that each group of dose-response patterns identified by TOXcms signifies a metabolic response to a different protein target with a unique drug binding affinity. TOXcms is freely available on our laboratory website at .




Mechanisms Software


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Software defined network (SDN) decouples the network control and data planes. Despite various advantages of SDNs, they are vulnerable to various security attacks such anomalies, intrusions, and Denial-of-Service (DoS) attacks and so on. On the other hand, any anomaly and intrusion in SDNs can affect many important domains such as banking system and national security. Therefore, the anomaly detection topic is a broad research domain, and to mitigate these security problems, a great deal of research has been conducted in the literature. In this paper, the state-of-the-art schemes applied in detecting and mitigating anomalies in SDNs are explained, categorized, and compared. This paper categorizes the SDN anomaly detection mechanisms into five categories: (1) flow counting scheme, (2) information-based scheme, (3) entropy-based scheme, (4) deep learning, and (5) hybrid scheme. The research gaps and major existing research issues regarding SDN anomaly detection are highlighted. We hope that the analyses, comparisons, and classifications might provide directions for further research.


Software failures may be due to bugs, ambiguities, oversights or misinterpretation of the specification that the software is supposed to satisfy, carelessness or incompetence in writing code, inadequate testing, incorrect or unexpected usage of the software or other unforeseen problems.


One difference is that in the last stage, the software does not have an increasing failure rate as hardware does. In this phase, the software is approaching obsolescence; there are no motivations for any upgrades or changes to the software. Therefore, the failure rate will not change.


The second difference is that in the useful-life phase, the software will experience a radical increase in failure rate each time an upgrade is made. The failure rate levels off gradually, partly because of the defects create and fixed after the updates.


The upgrades in above figure signify feature upgrades, not upgrades for reliability. For feature upgrades, the complexity of software is possible to be increased, since the functionality of the software is enhanced. Even error fixes may be a reason for more s