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Fixpoint Theorem for Continuous Functions on Chain-Complete Posets

This text includes the definition of chain-complete poset, fix-point theorem on it, and the definition of the function space of continuous functions on chain-complete posets [10].Ishida Kazuhisa - Neyagawa-shi, Osaka, JapanShidama Yasunari - Shinshu University, Nagano, JapanGrzegorz Bancerek. The fundamental properties of natural numbers. Formalized Mathematics, 1(1):41-46, 1990.Grzegorz Bancerek. Bounds in posets and relational substructures. Formalized Mathematics, 6(1):81-91, 1997.Grzegorz Bancerek and Andrzej Trybulec. Miscellaneous facts about functions. Formalized Mathematics, 5(4):485-492, 1996.Czesław Byliński. Functions and their basic properties. Formalized Mathematics, 1(1):55-65, 1990.Czesław Byliński. Functions from a set to a set. Formalized Mathematics, 1(1):153-164, 1990.Czesław Byliński. Some basic properties of sets. Formalized Mathematics, 1(1):47-53, 1990.Adam Grabowski. On the category of posets. Formalized Mathematics, 5(4):501-505, 1996. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=000258624500003&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=b7bc2757938ac7a7a821505f8243d9f3Piotr Rudnicki and Andrzej Trybulec. Abian's fixed point theorem. Formalized Mathematics, 6(3):335-338, 1997.Wojciech A. Trybulec and Grzegorz Bancerek. Kuratowski - Zorn lemma. Formalized Mathematics, 1(2):387-393, 1990.Glynn Winskel. The Formal Semantics of Programming Languages. The MIT Press, 1993.Edmund Woronowicz. Relations and their basic properties. Formalized Mathematics, 1(1):73-83, 1990.Edmund Woronowicz. Relations defined on sets. Formalized Mathematics, 1(1):181-186, 1990.Edmund Woronowicz and Anna Zalewska. Properties of binary relations. Formalized Mathematics, 1(1):85-89, 1990.Mariusz Żynel and Czesław Byliński. Properties of relational structures, posets, lattices and maps. Formalized Mathematics, 6(1):123-130, 1997

A Primer on Data Analytics in Functional Genomics:How to Move from Data to Insight?

High-throughput technologies are now widely used in the life sciences field and are producing ever-increasing amounts and diversity of data. While many laboratories and even undergraduate students generate high-throughput data, analyzing these results requires a skill set that is traditionally reserved for bioinformaticians. Learning to program using languages such as R and Python and making sense of the vast amounts of available omics data have become easier, thanks to the multitude of available resources. This can empower bench-side researchers to perform more complex computational analyses. Tools such as KNIME or Galaxy (together with a growing number of tutorials and courses) have been crucial in providing simple user interfaces to conduct complex analyses under the hood, making the ‘big data’ revolution accessible to biologists. High-throughput methodologies and machine learning have been central in developing systems-level perspectives in molecular biology. Unfortunately, performing such integrative analyses has traditionally been reserved for bioinformaticians. This is now changing with the appearance of resources to help bench-side biologists become skilled at computational data analysis and handling large omics data sets. Here, we show an entry route into the field of omics data analytics. We provide information about easily accessible data sources and suggest some first steps for aspiring computational data analysts. Moreover, we highlight how machine learning is transforming the field and how it can help make sense of biological data. Finally, we suggest good starting points for self-learning and hope to convince readers that computational data analysis and programming are not intimidating

New Science Gateways for Advanced Computing Simulations and Visualization Using Vine Toolkit in PL-Grid

A Science Gateway is a connection between scientists and their computational tools in the form of web portal. It creates a space for communities, collaboration and data sharing and visualization in a comprehensive and efficient manner. The main purpose of such a solution is to allow users to access the computational resources, process and analyze their data and get the results in a uniform and user friendly way. In this paper we propose a complex solution based on the Rich Internet Application (RIA) approach consisting of a web portal powered by Vine Toolkit with Adobe Flex/BlazeDs technologies. There are two Science Gateways described in detail one for engineers to manage computationally intensive workflows used in advanced airplane construction simulations, and one for nanotechnology scientists to manage experiments in nano-science field calculated with Density Functional Theory (DFT). In both cases the results show how modern web solution can help scientists in their work. &nbsp

NT-proBNP increase during stress echocardiography predicts significant changes in ischemic mitral regurgitation severity in patients qualified for surgical revascularization

Background: In many patients, significant changes in ischemic mitral regurgitation (IMR) severity during exercise can be observed independent of the degree of IMR at rest. This study aimed to investigate the correlations between N-terminal fragment B-type natriuretic peptide (NT-proBNP) and echocardiography measurements at rest and at peak exercise in patients with moderate IMR who qualified for surgical revascularization. Methods: A total of 100 patients eligible for coronary artery bypass grafting, were included in this prospective study. All patients underwent exercise echocardiography. Additionally, the levels of NT-proBNP were measured at rest and after peak exercise. Results: A positive correlation of absolute NT-proBNP levels with effective regurgitant orifice area (EROA) were observed and with tricuspid regurgitant peak gradient (TRPG) at peak exercise. Absolute ∆NT-proBNP during exercise and the tenting area at rest were independent predictors of severe IMR at peak exercise. The level of absolute ∆NT-proBNP during exercise and coaptation height at rest were the most important predictors of significant increases in TRPG. The best cutoff value for ∆NT-proBNP as a predictor for increases in EROA at peak exercise was 68.9 pg/mL and to predict an increase in TRPG ≥ 50 mmHg at peak exercise was 68 pg/mL. Conclusions: The level of ∆NT-proBNP during exercise was the most important parameter in predicting significant changes in IMR severity and pulmonary pressure. Based on the present data, it can be speculated that integration of the assessment of NT-proBNP at rest and at exercise might improve patient selection for valve surgery

Wspólnota różnorodności – co łączy, a co dzieli współczesnych gdańszczan

The article depicts a vision of Gdańsk as community of plurality – residents connected to the city in various ways, at the same time different from one another in terms of sociodemographic and cultural factors. The text comprises of several main sections. First, it characterizes the discourse on urban feeling of community, emphasizing the transformations of creating urban communities. In the next part the methodology and results of research on identities of citizens of Gdańsk are brought forward. As a consequence, the authors discuss the challenges of community of plurality in Gdańsk and possible ways of its evolution.W tekście przedstawiona została wizja Gdańska jako wspólnoty różnorodności, czyli społeczności mieszkańców w różne sposoby związanych z miastem, a jednocześnie bardzo od siebie różnych pod kątem cech socjo-demograficznych czy czynników kulturowych i obyczajowych. Tekst składa się z kilku zasadniczych części. W pierwszej z nich scharakteryzowany został dyskurs miejskiej wspólnotowości, ze szczególnym naciskiem na przemiany budowania miejskich wspólnot. Kolejny fragment poświęcony jest przedstawieniu założeń metodologicznych i syntetycznych wniosków z badań na temat gdańskich tożsamości. Ostatnia część tekstu poświęcona jest wyzwaniom dla gdańskiej wspólnoty różnorodności i możliwym kierunkom jej ewolucji.&nbsp

Multiclassifier combinatorial proteomics of organelle shadows at the example of mitochondria in chromatin data

Subcellular localization is an important aspect of protein function, but the protein composition of many intracellular compartments is poorly characterized. For example, many nuclear bodies are challenging to isolate biochemically and thus remain inaccessible to proteomics. Here, we explore covariation in proteomics data as an alternative route to subcellular proteomes. Rather than targeting a structure of interest biochemically, we target it by machine learning. This becomes possible by taking data obtained for one organelle and searching it for traces of another organelle. As an extreme example and proof-of-concept we predict mitochondrial proteins based on their covariation in published interphase chromatin data. We detect about 1/3 of the known mitochondrial proteins in our chromatin data, presumably most as contaminants. However, these proteins are not present at random. We show covariation of mitochondrial proteins in chromatin proteomics data. We then exploit this covariation by multiclassifier combinatorial proteomics to define a list of mitochondrial proteins. This list agrees well with different databases on mitochondrial composition. This benchmark test raises the possibility that, in principle, covariation proteomics may also be applicable to structures for which no biochemical isolation procedures are available

DNA barcoding of Chironomidae from the Lake Skadar region: Reference library and a comparative analysis of the European fauna

Aims: The main aim of this study was to fill a gap in barcoding data of the European Chironomidae of the Balkan region, developing and testing the efficiency of a reference DNA barcode library for ancient Lake Skadar basin species (Montenegro/Albania), a region of Europe never before subjected to barcoding studies on Chironomidae. Another aim was to test the efficiency of DNA barcoding for the identification of European Chironomidae, including the estimation of optimal identification thresholds, using >12,000 barcodes. Location: Lake Skadar basin and adjacent area (Montenegro/Albania). Methods: Through this study, 770 individuals of Chironomidae from the Lake Skadar region were barcoded, both at adult and pre-imaginal stages. Adults were morphologically identified, while larvae were assigned to species by molecular identification, using different methods, of which the efficiency was tested, for a total of 97 different barcoded species. Results: The identification efficiency of the reference dataset developed for the Lake Skadar region was 98.6%, a value in line with that obtained when the identification efficiency for European Chironomidae was evaluated (95.8%), which confirms the accuracy of DNA barcoding for the identification of these insects. Moreover, we found that the optimal threshold for the molecular identification of the family is 1.6% nucleotide distance, though more specific thresholds are suggested for the identification of species belonging to Chironomidae subfamilies, since they are related to lower identification errors than to the use of a general threshold. The analysis of inconsistency between molecular and morphological identification shed light on taxonomic issues within European Chironomidae. Previously postulated species synonyms were confirmed, and also further cases requiring deeper investigation were detected. Main conclusions: Our de novo DNA barcode library was shown to have a high identification efficiency. Taxon-specific thresholds increase the efficacy of molecular identification. Hypothesized species synonyms could be validated through molecular techniques

Administration of oral anticoagulants in periprocedural complications based on case report series

The use of dabigatran, a non-vitamin K antagonist (VKA) oral anticoagulant, is still increasing. Dabigatran has a good efficacy and safety ratio, as well as a more predictable anticoagulation effect compared with VKA. On the other hand, there is acenocoumarol/warfarin, a VKA which was evaluated in numerous clinical trials and is a drug of choice in a valve-related atrial fibrillation (AF).Based on the real clinical cases, we attempted to summarize current recommendations on how to manage periprocedural complications on oral anticoagulant treatment.In the first case we presented a patient on dabigatran, undergoing pulmonary vein isolation (PVI) of AF, who developed a right groin hematoma after the procedure and hence required several blood transfusions. In the second case we showed a patient on acenocoumarol, with high bleeding risk, who developed a pocket hematoma after an implantable cardioverter-defibrillator (ICD) implantation. We also reported a patient on dabigatran, who developed a femoral artery pseudoaneurysm (FAP) following PVI of AF.Periprocedural oral anticoagulation depends on the anticoagulant type and requires individual assessment of thepatient’s thromboembolic and bleeding risk factors. Our case reports showed that in case of a bleeding, dabigatranmay be quickly stopped and then restarted recently after reaching hemostasis, in contrast to acenocoumarol. They also confirm a possibility of successful pseudoaneurysm closure without dabigatran suspension.The use of dabigatran, a non-vitamin K antagonist (VKA) oral anticoagulant, is still increasing. Dabigatran has a good efficacy and safety ratio, as well as a more predictable anticoagulation effect compared with VKA. On the other hand, there is acenocoumarol/warfarin, a VKA which was evaluated in numerous clinical trials and is a drug of choice in a valve-related atrial fibrillation (AF).Based on the real clinical cases, we attempted to summarize current recommendations on how to manage periprocedural complications on oral anticoagulant treatment.In the first case we presented a patient on dabigatran, undergoing pulmonary vein isolation (PVI) of AF, who developed a right groin hematoma after the procedure and hence required several blood transfusions. In the second case we showed a patient on acenocoumarol, with high bleeding risk, who developed a pocket hematoma after an implantable cardioverter-defibrillator (ICD) implantation. We also reported a patient on dabigatran, who developed a femoral artery pseudoaneurysm (FAP) following PVI of AF.Periprocedural oral anticoagulation depends on the anticoagulant type and requires individual assessment of thepatient’s thromboembolic and bleeding risk factors. Our case reports showed that in case of a bleeding, dabigatranmay be quickly stopped and then restarted recently after reaching hemostasis, in contrast to acenocoumarol. They also confirm a possibility of successful pseudoaneurysm closure without dabigatran suspension