Ústav soudního inženýrství

Browse

Recent Submissions

Now showing 1 - 5 of 58
  • Item
    Augusta: From RNA-Seq to Gene Regulatory Networks and Boolean Models
    (Elsevier, 2024-01-20) Musilová, Jana; Vafek, Zdeněk; Punyia, Bhanwar; Zimmer, Ralf; Helikar, Tomáš; Sedlář, Karel
    Computational models of gene regulations help to understand regulatory mechanisms and are extensively used in a wide range of areas, e.g., biotechnology or medicine, with significant benefits. Unfortunately, there are only a few computational gene regulatory models of whole genomes allowing static and dynamic analysis due to the lack of sophisticated tools for their reconstruction. Here, we describe Augusta, an open-source Python package for Gene Regulatory Network (GRN) and Boolean Network (BN) inference from the high-throughput gene expression data. Augusta can reconstruct genome-wide models suitable for static and dynamic analyses. Augusta uses a unique approach where the first estimation of a GRN inferred from expression data is further refined by predicting transcription factor binding motifs in promoters of regulated genes and by incorporating verified interactions obtained from databases. Moreover, a refined GRN is transformed into a draft BN by searching in the curated model database and setting logical rules to incoming edges of target genes, which can be further manually edited as the model is provided in the SBML file format. The approach is applicable even if information about the organism under study is not available in the databases, which is typically the case for non-model organisms including most microbes. Augusta can be operated from the command line and, thus, is easy to use for automated prediction of models for various genomes. The Augusta package is freely available at github.com/JanaMus/Augusta. Documentation and tutorials are available at augusta.readthedocs.io.
  • Item
    0.3-V Voltage-Mode Versatile First-Order Analog Filter Using Multiple-Input DDTAs
    (MDPI, 2023-07-26) Kumngern, Montree; Khateb, Fabian; Kulej, Tomasz; Šteffan, Pavel
    This paper presents a versatile first-order analog filter using differential difference transconductance amplifiers (DDTAs). The DDTA employs the bulk-driven (BD) multiple-input MOS transistors technique (MI-MOST) operating in the subthreshold region. This results in low-voltage and low-power operational capability. Therefore, the DDTA, designed using 130 nm CMOS technology from UMC in the Cadence environment, operates with 0.3 V and consumes 357.4 nW. Unlike previous works, the proposed versatile first-order analog filter provides first-order transfer functions of low-pass, high-pass, and all-pass filters within a single topology. The non-inverting, inverting, and voltage gain of the transfer functions are available for all filters. Furthermore, the proposed structure provides high-input and low-output impedance, which is required for voltage-mode circuits. The pole frequency and voltage gain of the filters can be electronically controlled. The total harmonic distortion of the low-pass filter was calculated as -39.97 dB with an applied sine wave input signal of 50 mV(pp)@ 50 Hz. The proposed filter has been used to realize a quadrature oscillator to confirm the advantages of the new structure.
  • Item
    Current-Mode First-Order Versatile Filter Using Translinear Current Conveyors with Controlled Current Gain
    (MDPI, 2023-07-31) Kumngern, Montree; Jongchanachavawat, Wirote; Phatsornsiri, Punnavich; Wongprommoon, Natapong; Khateb, Fabian; Kulej, Tomasz
    This paper offers a new current-mode first-order versatile filter employing two translinear current conveyors with controlled current gain and one grounded capacitor. The proposed filter offers the following features: realization of first-order transfer functions of low-pass, high-pass, and all-pass current responses from single topology, availability of non-inverting and inverting transfer functions for all current responses, electronic control of current gain for all current responses, no requirement of component-matching conditions for realizing all current responses, low-input impedance and high-output impedance which are required for current-mode circuits, and electronic control of the pole frequency for all current responses. The proposed first-order versatile filter is used to realize a quadrature sinusoidal oscillator to confirm the advantage of the new topology. To confirm the functionality and workability of new circuits, the proposed circuit and its application are simulated by the SPICE program using transistor model process parameters NR100N (NPN) and PR100N (PNP) of bipolar arrays ALA400-CBIC-R from AT & T.
  • Item
    Transformation of garden settlements into a residential zone
    (Mendel University in Brno, 2023-05-31) Pokorná, Sofie; Hlavinková, Vítězslava
    The content of this paper is research on gardening settlements. These are special urban areas that, as recreational spaces for city residents, contribute to the maintenance of their mental and physical condition. At the same time, from the point of view of environmental and ecological urbanism, they are a specific ecosystem of so-called green infrastructure, whose importance is seen, for example, in the prevention of overheating in urban areas in the summer months. At the same time, the economic aspect cannot be overlooked, namely the savings in the city budget for the maintenance of greenery. For the purpose of this research, the gardening settlements in Brno were monitored. The paper deals with the gradual transformation of these settlements into residential space. It analyses the economic factors and looks for parallels in the construction of emergency colonies in the 1920s in Brno. The article draws attention to the disruption of the local ecosystem and its transformation, the disappearance of the recreational zone and the benefits of urban green infrastructure.
  • Item
    0.5-V Nano-Power Voltage-Mode First-Order Universal Filter Based on Multiple-Input OTA
    (IEEE, 2023-05-17) Khateb, Fabian; Kumngern, Montree; Kulej, Tomasz
    This paper presents a new application of the multiple-input operational transconductance amplifier (MI-OTA). The MI-OTA has been used to realize a first-order universal filter which shows that the first-order transfer functions such as low-pass, high-pass, and all-pass filters can be obtained easily from a single topology by applying the input signal to the appropriate terminals. Moreover, both non-inverting and inverting transfer functions of all filtering functions can be obtained. The pole frequency of all filters can also be controlled electronically. The first-order all-pass filters have been selected to realize high-quality band-pass filter. For low-voltage supply operation and extremely low power consumption, the proposed MI-OTA is realized by the multiple-input bulk-driven MOS transistor technique with transistors operating in subthreshold voltage region. The circuit has been simulated using the $0.18 \mu \text{m}$ TSMC CMOS technology with 0.5 V of supply voltage and it consumes 29.77 nW of power for 10 nA nominal setting current. The post-layout simulation results show that the applications of MI-OTA agree well with theory.