Extended time Petri nets

In many complex systems that can be modeled using Petri nets time can be a very important factor which should be taken into account during creation and analysis of the model. Time data can describe starting moments of some actions or their duration before their immediate effects start to influence some other areas of the modeled system. Places in a Petri net often describe static components of the system, but they can also describe states. Such a state can have time restrictions, for example, telling how long it can influence other elements in the model. Time values describing some system may be inconsistent or incomplete, which can cause problems during the creation of the model. In this paper, a new extension of time Petri nets is proposed, which allows the creation of models with different types of time data, which previously were possible to be properly used in separate types of well-known time Petri nets. The proposed new time Petri net solves this problem by integrating different aspects of already existing time Petri nets into one unified net

Integrating UAV-Enabled Base Stations in 3D Networks: QoS-Aware Joint Fronthaul and Backhaul Design

The emerging concept of 3D networks, integrating terrestrial, aerial, and space layers, introduces a novel and complex structure characterized by stations relaying backhaul loads through point-to-point wireless links, forming a wireless 3D backhaul mesh. A key challenge is the strategic placement of aerial platform such as drone base stations (DBSs), considering the locations and service demands of ground nodes and the connectivity to backhaul gateway nodes for core network access. This paper addresses these complexities with a two-fold approach: a novel Agglomerative Hierarchical Clustering (HC) algorithm that optimizes DBS locations to satisfy minimum backhaul adjacency and maximum fronthaul coverage radius requirements; and a Genetic Algorithm (GA) that designs backhaul connections to satisfy the cumulative load across the network and maximize the throughput margin which translates to network resilience to increasing demands. Our results showcase the effectiveness of these algorithms against benchline schemes, offering insights into the operational dynamics of these novel 3D networks

Some aspects of the anemia of chronic disorders modeled and analyzed by petri net based approach

Anemia of chronic disorders is a very important phenomenon and iron is a crucial factor of this complex process. To better understand this process and its influence on some other factors we have built a mathematical model of the human body iron homeostasis, which possibly most exactly would reflect the metabolism of iron in the case of anemia and inflammation. The model has been formulated in the language of Petri net theory, which allows for its simulation and precise analysis. The obtained results of the analysis of the model’s behavior, concerning the influence of anemia and inflammation on the transferrin receptors, and hepcidin concentration changes are the valuable complements to the knowledge following from clinical research. This analysis is one of the first attempts to investigate properties and behavior of a not fully understood biological system on a basis of its Petri net based model

Klasyfikacja problemów asemblacji i sekwencjonowania peptydów

Sekwencjonowanie peptydów polega na ustaleniu kolejności aminokwasów (sekwencji) w cząsteczce. Bezpośrednie metody chemii analitycznej pozwalają˛na określenie jedynie krótkich sekwencji. Alternatywa˛dla tych metod jest spektrometria masowa. Widmo masowe powstałe w wyniku przeprowadzenia eksperymentu za pomocą spektrometru wymaga dodatkowej analizy. Z punktu widzenia nauk obliczeniowych analiza takiego widma jest źródłem ciekawych problemów. Ta metoda sekwencjonowania posiada swoje ograniczenia co do długości sekwencji. Rodzi to naturalna˛ potrzebę projektowania metod asemblacyjnych, które pozwolą połączyć wiele krótkich łańcuchów w oryginalna˛cząsteczkę. W pracy tej przedstawiono problemy sekwencjonowania i asemblacji oraz zaproponowano ich klasyfikacje˛. Przedstawiono również wybrane metody rozwiązujące te problemy

A tiling microarray for global analysis of chloroplast genome expression in cucumber and other plants

Plastids are small organelles equipped with their own genomes (plastomes). Although these organelles are involved in numerous plant metabolic pathways, current knowledge about the transcriptional activity of plastomes is limited. To solve this problem, we constructed a plastid tiling microarray (PlasTi-microarray) consisting of 1629 oligonucleotide probes. The oligonucleotides were designed based on the cucumber chloroplast genomic sequence and targeted both strands of the plastome in a non-contiguous arrangement. Up to 4 specific probes were designed for each gene/exon, and the intergenic regions were covered regularly, with 70-nt intervals. We also developed a protocol for direct chemical labeling and hybridization of as little as 2 micrograms of chloroplast RNA. We used this protocol for profiling the expression of the cucumber chloroplast plastome on the PlasTi-microarray. Owing to the high sequence similarity of plant plastomes, the newly constructed microarray can be used to study plants other than cucumber. Comparative hybridization of chloroplast transcriptomes from cucumber, Arabidopsis, tomato and spinach showed that the PlasTi-microarray is highly versatile

AUTOMATYZACJA PROCESÓW DYSKRETNYCH

Długie peptydy nazywane są białkami i pełnia˛ wiele funkcji w ludzkim organizmie m.in są katalizatorami, transportują inne substancje, chronią przed antygenami. Peptydy zbudowane są z 20 typów aminokwasów połączonych w długie nierozgałęzione łańcuchy (sekwencje). Znajomość sekwencji to pierwszy krok do poznania funkcji białka. Znane metody pozwalają na określenie kolejności aminokwasów (sekwencjonowanie) jedynie krótkich łańuchów. Długie peptydy są częściowo trawione do wielu krótkich sekwencji, które są następnie sekwencjonowane. W dalszej kolejności wykorzystuje się metody asemblacyjne do rekonstrukcji badanego białka. W pracy przedstawiono dwa problemy asemblacji. Zaproponowany został nowy model grafowy jako reprezentacja jednego z tych problemów

O algorytmach asemblacji długich łańcuchów peptydowych

tomasz glowack

Transferrin changes in haemodialysed patients

Transferrin (Tf) is a glycoprotein responsible for iron transport in the human body. Physiologically in reaction with Concanavalin A, Tf occurs in four distinct variants Tf1, Tf2, Tf3 (apo-Tf) and Tf4. It was reported recently that Tf is changing, particularly during acute phase response, taking place among others in end-stage renal disease. In this study, we wanted to find the answer to three main questions: firstly, how Tf is changing in patients treated with maintenance haemodialysis (mHD), secondly, whether there are any Tf changes in the course of mHD treatment, and thirdly, what factors can affect Tf microheterogeneity in these patients. Studies were performed on 80 haemodialysed patients and 21 healthy volunteers. The Tf concentration was determined by the rocket immunoelectrophoresis, and its microheterogeneity was assessed by the ConA crossed immunoaffinity electrophoresis. During the annual observation of the distribution of the Tf variants, we have found both changes of the percentage contents of all Tf variants in the whole Tf concentration and a significant decrease in Tf2, Tf3 and Tf4 serum concentrations. Moreover, we found that decrease in the renal function, duration of mHD, and inflammation may contribute to these above-mentioned changes, which are probably the factors that should be taken into account when explaining the mechanisms of persistence of anaemia in haemodialysed patients