Vertex importance extension of betweenness centrality algorithm

Variety of real-life structures can be simplified by a graph. Such simplification emphasizes the structure represented by vertices connected via edges. A common method for the analysis of the vertices importance in a network is betweenness centrality. The centrality is computed using the information about the shortest paths that exist in a graph. This approach puts the importance on the edges that connect the vertices. However, not all vertices are equal. Some of them might be more important than others or have more significant influence on the behavior of the network. Therefore, we introduce the modification of the betweenness centrality algorithm that takes into account the vertex importance. This approach allows the further refinement of the betweenness centrality score to fulfill the needs of the network better. We show this idea on an example of the real traffic network. We test the performance of the algorithm on the traffic network data from the city of Bratislava, Slovakia to prove that the inclusion of the modification does not hinder the original algorithm much. We also provide a visualization of the traffic network of the city of Ostrava, the Czech Republic to show the effect of the vertex importance adjustment. The algorithm was parallelized by MPI (http://www.mpi-forum.org/) and was tested on the supercomputer Salomon (https://docs.it4i.cz/) at IT4Innovations National Supercomputing Center, the Czech Republic.808726

An efficient Monte Carlo-based Probabilistic Time-Dependent Routing calculation targeting a server-side car navigation system

Incorporating speed probability distribution to the computation of the route planning in car navigation systems guarantees more accurate and precise responses. In this paper, we propose a novel approach for selecting dynamically the number of samples used for the Monte Carlo simulation to solve the Probabilistic Time-Dependent Routing (PTDR) problem, thus improving the computation efficiency. The proposed method is used to determine in a proactive manner the number of simulations to be done to extract the travel-time estimation for each specific request, while respecting an error threshold as output quality level. The methodology requires a reduced effort on the application development side. We adopted an aspect-oriented programming language (LARA) together with a flexible dynamic autotuning library (mARGOt) respectively to instrument the code and to make decisions on tuning the number of samples to improve the execution efficiency. Experimental results demonstrate that the proposed adaptive approach saves a large fraction of simulations (between 36 and 81 percent) with respect to a static approach, while considering different traffic situations, paths and error requirements. Given the negligible runtime overhead of the proposed approach, the execution-time speedup is between 1.5x and 5.1x. This speedup is reflected at the infrastructure-level in terms of a reduction of 36 percent of the computing resources needed to support the whole navigation pipeline.Web of Science921019100

Proteolytic Cleavage of a Spectrin-Related Protein by Calcium-Dependent Protease in Neurospora crassa

To investigate the functional significance of a cytoskeletal spectrin-like protein, we studied its localization pattern in Neurospora crassa and sought the answer to whether it is a substrate for another apically localized protein, the calcium-dependent protease (CDP II). Immunoblots of crude extracts from exponentially growing mycelia, separated by one- and two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis using antichicken α/β-spectrin antibodies, revealed a single band of approximately relative mass (Mr) 100 kDa with an isoeletric point (pI) in the range of 6.5 to 7.0. Despite rigorous efforts, we could not confirm the presence of an Mr 240- to 220-kDa spectrin-like protein in N. crassa. The immunofluorescence- and immunogold-labeling Mr 100-kDa protein showed its predominance along the plasma membrane of the conidia during the swelling phase of germination. In contrast, in the germ tubes and the growing hyphae, the localization was polarized and concentrated mainly in the apical region. The in vitro proteolysis experiments showed that indeed this protein is a preferred substrate of CDP II which is, as mentioned previously, also localized in the apical regions of the hyphae. These results indicate a putative functional relationship between these two proteins (spectrin-like protein and CDP II) in the dynamics of tip growt

Antimicrobial peptide modification of biomaterials using supramolecular additives

Biomaterials based on non-active polymers functionalized with antimicrobial agents by covalent modification or mixing are currently regarded as high potential solutions to prevent biomaterial associated infections that are major causes of biomedical device failure. Herewith a strategy is proposed in which antimicrobial materials are prepared by simply mixing-and-matching of ureido-pyrimidinone (UPy) based supramolecular polymers with antimicrobial peptides (AMPs) modified with the same UPy-moiety. The N-terminus of the AMPs was coupled in solution to an UPy-carboxylic acid synthon resulting in formation of a new amidic bond. The UPy-functionalization of the AMPs did not affect their secondary structure, as proved by circular dichroism spectroscopy. The antimicrobial activity of the UPy-AMPs in solution was also retained. In addition, the incorporation of UPy-AMPs into an UPy-polymer was stable and the final material was biocompatible. The addition of 4 mol % of UPy-AMPs in the UPy-polymer material protected against colonization by Escherichia coli, and methicillin-sensitive and -resistant strains of Staphylococcus aureus. This modular approach enables a stable but dynamic incorporation of the antimicrobial agents, allowing at the same time for the possibility to change the nature of the polymer, as well as the use of AMPs with different activity spectra.</p

Characterization of Selective Antibacterial Peptides by Polarity Index

In the recent decades, antibacterial peptides have occupied a strategic position for pharmaceutical drug applications and became subject of intense research activities since they are used to strengthen the immune system of all living organisms by protecting them from pathogenic bacteria. This work proposes a simple and easy statistical/computational method through a peptide polarity index measure by which an antibacterial peptide subgroup can be efficiently identified, that is, characterized by a high toxicity to bacterial membranes but presents a low toxicity to mammal cells. These peptides also have the feature not to adopt to an alpha-helicoidal structure in aqueous solution. The double-blind test carried out to the whole Antimicrobial Peptide Database (November 2011) showed an accuracy of 90% applying the polarity index method for the identification of such antibacterial peptide groups

Studies on the synthesis of dicaffeoylquinic acid conjugates

Dicaffeoylquinic acid (DCQA) is a natural polyphenolic compound widely distributed in plants such as coffee beans, which possesses a range of pharmacological activities. Herein, is reported studies undertaken towards the first total synthesis of 3,5-DCQA conjugates. Two synthetic routes were investigated. The first route involves a seven step sequence beginning from quinic acid. The overall yield via this synthetic approach was 30%. The key steps involved in the sequence were a regioselective benzylation of the C-3-hydroxyl group followed by silyl protection of the C-1 and C-4 hydroxyl groups. Deprotection of the benzyl group by hydrogenolysis and opening of the lactone afforded the 3,5-diol. Esterification of the 3,5-diol with 3,4-tert-butyldimethylsilyl caffeoyl chloride afforded the di-ester. Removal of the protecting groups afforded 3,5-DCQA. The second route involved selective protection of the C-3-hydroxyl group with silyl followed by benzylation of the C-1 and C-3 hydroxyl groups. Saponification of the lactone ring followed by benzylation of the carboxylic acid gave the benzyl ester. Silyl deprotection afforded the 3,5-diol. The 3,5-diol was subsequently esterified by refluxing in toluene with commercially available Meldrum’s acid. In the final step, the synthesis of 3,5-DCQA was achieved by a Knoevenagel condensation of 3,4-dihydroxybenzaldehyde and a malonate ester of quinic acid. An efficient method for the synthesis of possible metabolites of quinic acid conjugates was also described. This protocol employs N-(4-methoxyphenyl)-trifluoroacetimidate glucuronyl as the donor. The key reaction in this sequence was the coupling of N-(4-methoxyphenyl)-trifluoroacetimidate glucuronyl with 4-hydroxy-3-methoxy-benzaldehyde

Two-Stages Clustering Untuk Segmentasi Pengunjung Web Pada Web Usage Mining

Web Usage Mining (WUM) berhubungan dengan ekstraksi knowledge dari data web log, salah satu tujuannya adalah untuk segmentasi pengunjung web. Data web log sebagai data utama dari WUM memiliki banyak item data yang tidak relevan untuk dilakukan proses penambangan lebih lanjut, sehingga perlu dilakukan tahapan-tahapan untuk menghapus data tersebut agar hasil akhir segmentasi pengunjung web lebih baik. Oleh karena itu, dalam penelitian ini dilakukan tahapan pra-pemrosesan lebih detail dan mengajukan pendekatan baru untuk tujuan segmentasi pengunjung web yang disebut dengan pendekatan klasterisasi bertahap (two-stages clustering). Klasterisasi tahap pertama dilakukan pada data yang berbentuk frequently access (frekuensi kunjungan) menggunakan metoda klaster hirarki dan non hirarki, kemudian dilanjutkan dengan klasterisasi tahap kedua pada data yang berbentuk user access pattern (pola kunjungan user). Pada klasterisasi tahap kedua digunakan kombinasi metode klaster hirarki dan non hirarki. Dari penerapan metode ini berhasil mereduksi data web log sebesar 98.38% dan memperoleh klaster-klaster/segmentasi pengunjung web beserta profilnya yang dapat dijadikan acuan untuk tujuan personalisasi web, modifikasi web dan kepentingan lainnya dalam lingkup WUM ======================================================================================================= Web Usage Mining (WUM) is associated with knowledge extraction of web log data. One of the purposes is for web visitor’s segmentation. Web log data as the primary data of WUM has many irrelevant data item for further mining process, therefore some stages need be done to reduce the data in order to make a better result of web visitor segmentation. For this purpose, this research conducted a more detail pre-processing stage and proposed a new approach for web visitor’s segmentation called twostages clustering. First stage clustering is conducted on data with frequently access form by using hierarchical and non-hierarchical method which is followed by the second stage clustering for the data with user access pattern form. On the second stage clustering the combined method of hierarchical and non-hierarchical was used. Application of the method was successful in reducing web log data for 98.38% and gained clusters of segments of web visitor and its profile that can be used as reference for web personalization, web modification, and other purposes within the WUM scope

SPLITSKI ANTROPONIMI KRAJEM XVI DO 30-IH GODINA XVII STOLJEĆA

Il numero degli abitanti di Spalato, dalla fine del XVI sec. fino al IV decenio del XVII sec. varia spesso. Verso il 1570 la città conta 5.000 anime mentre all’inizio del 1600, secondo il rapporto del conte di Spalato Paolo Trevzan, ce ne sono 2.887 entro le mura della città. Questo calo della popolazione e’dovuto alle guerre devasttrici e alla peste. Presentare la cittadinanza attraverso i registri ha un grande valore, poiche’ questi sono gli unici a darci dei dati etnici e sociali su questa, a differenza dei dati statistici che sono più in uso. Nei registri di battesimo, dei matrimoni, dei morti che sono stati analizzati in quest’ordine, e che comprendono il periodo tra il 1578 e il 1635, sono registrati 2.568 battesimi di bambini, dei quali 1346 maschi e 1.118 femmine. I nati sono più numerosi tra il periodo che va dal 1610 al 1635, a meno numerosi dal 1601al 1607. Tra il 1611 al 1635 sono stati registrati 442 matrimoni, e dal 1617 al 1635 : 771 decessi. L’ età media dei doceduti adulti varia tra i 55-60 anni e per i bambini tra i 5-10 anni. Accanto ai nomi dei bambini sono notati anche i nomi dei loro genitori e patrini. Altretanto per i matrimoni accanto ai nomi degli sposi ci sono i nomi dei rispetivi genitori e testimoni, e nel registro dei morti oltare ai dati dei defunti ci sono quelli dei sacerdoti che presero parte alle ceremonie funebri. Oltre ai numerosi nomi e cognomi sono molto validi anche i dati sulle loro origini e professioni. Secondo i dati a raccolti la cittadinanza di Spalato era composta dalla lpopolazione del luogo e da immigrati stranieri. Oltre alla popolazione del luogo a Spalato c’era una grande affluenza di abitanti dalle vicine isole e dal retroterra, mentre minore era l’affluenza degli abitanti dell’ interno. Gli isolani sono più numerosi degli abitanti del retroterra. Gli isolani più numerosi sono quelli dell’ isola di Brazza, mentre del retroterra quelli di Poglizza i quali sono con frequenza menzionati nella proffessioni militari nonche’ immigrati dei Castelli. Dall’ interno si nominano spesso gli immigrati dalla Bosnia. Degli stranieri i pi`¨numerosi provengono dalla Penisola Appenninica, per la maggior parte de Venezia. I Veneziani si nominano di frequente nelle carche dell’ amministrazione comunale, e di raro come artigiani. Delle altre nazionalità sono nominati Albanesi, Francesi, Greci, nonché uno della Transilvania, e uno da Vienna. Mentre le professioni intelettuali si nominano di raro, le più numerosi, invece, sono quelle degli artigiani, seguono i cittadini, cittadini di riguardo, di raro la nobiltà, militari, armatori, professioni nel Lazaretto, sacerdoti, commercianti, marinai ed altri

Guidelines for the use and interpretation of assays for monitoring autophagy (2nd edition)

In 2008 we published the first set of guidelines for standardiz- ing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new tech- nologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in differ- ent organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes..