Molecular Network Control Through Boolean Canalization

Boolean networks are an important class of computational models for molecular interaction networks. Boolean canalization, a type of hierarchical clustering of the inputs of a Boolean function, has been extensively studied in the context of network modeling where each layer of canalization adds a degree of stability in the dynamics of the network. Recently, dynamic network control approaches have been used for the design of new therapeutic interventions and for other applications such as stem cell reprogramming. This work studies the role of canalization in the control of Boolean molecular networks. It provides a method for identifying the potential edges to control in the wiring diagram of a network for avoiding undesirable state transitions. The method is based on identifying appropriate input-output combinations on undesirable transitions that can be modified using the edges in the wiring diagram of the network. Moreover, a method for estimating the number of changed transitions in the state space of the system as a result of an edge deletion in the wiring diagram is presented. The control methods of this paper were applied to a mutated cell-cycle model and to a p53-mdm2 model to identify potential control targets

Nested canalyzing depth and network stability

We introduce the nested canalyzing depth of a function, which measures the extent to which it retains a nested canalyzing structure. We characterize the structure of functions with a given depth and compute the expected activities and sensitivities of the variables. This analysis quantifies how canalyzation leads to higher stability in Boolean networks. It generalizes the notion of nested canalyzing functions (NCFs), which are precisely the functions with maximum depth. NCFs have been proposed as gene regulatory network models, but their structure is frequently too restrictive and they are extremely sparse. We find that functions become decreasingly sensitive to input perturbations as the canalyzing depth increases, but exhibit rapidly diminishing returns in stability. Additionally, we show that as depth increases, the dynamics of networks using these functions quickly approach the critical regime, suggesting that real networks exhibit some degree of canalyzing depth, and that NCFs are not significantly better than functions of sufficient depth for many applications of the modeling and reverse engineering of biological networks.Comment: 13 pages, 2 figure

Retrieval effectiveness for OCR text using thesauri

This thesis reports on the effects of an automatic query expansion with a subject specific thesaurus on retrieval effectiveness for document collection consisting of OCR text; The investigation encompasses several experiments with a modern retrieval engine based on the probabilistic model. Each experiment is performed on two document collections. The first version of the collection consists of raw OCR output. The second collection consists of the ground truth (retyped from hard copy) version of the same collection; It is shown that the usage of the thesaurus as a source for query expansion can significantly improve recall for Boolean queries, for both OCR and manually corrected document collections. In the case of weighted queries, the expansion has no effect on the average precision and recall. Nevertheless, some individual queries benefit from query expansion

Significance and role of the State Audit Office of the Republic of North Macedonia and the State Audit Institution of the Republic of Serbia

State audit is a procedure for examining financial transactions defined as governmentexpenditures, in terms of the legal and intended use of funds, as well as evaluating the useof funds in terms of the quality of public sector program performance. The State Audit Officeof the Republic of North Macedonia, as well as the State Audit Institution of the Republic ofSerbia, are independent in their work and independent of the executive branch. The StateAudit Office of the Republic of Northern Macedonia is an independent institution operatingon a pre-established annual program and applying a methodology consistent withinternational auditing standards. The State Audit Office of the Republic of NorthernMacedonia is accountable to the Assembly of the Republic of Northern Macedonia bysubmitting an annual report on its operations and audits, but also provides other informationrelated to the execution of the measures and recommendations given to the entities by thecertified state auditor, for removing irregularities. The State Audit Office of the Republic ofNorth Macedonia, in carrying out its work and functions, cooperates with: the Assembly ofthe Republic of North Macedonia, the Government of the Republic of North Macedonia, theMinistry of Finance, the Institutions responsible for initiating audit reports, the IPA AuditAuthority and International cooperation.The State Audit Institution of the Republic of Serbia performs its tasks in accordancewith the Constitution of the Republic of Serbia and the Law on State Audit Institution andState Audit Institution and helps the state to use and manage its resources wisely. The StateAudit Institution has a mission to contribute to better governance, transparency andaccountability in the public sector through confidential information