BLISS: biding site level identification of shared signal-modules in DNA regulatory sequences

BACKGROUND: Regulatory modules are segments of the DNA that control particular aspects of gene expression. Their identification is therefore of great importance to the field of molecular genetics. Each module is composed of a distinct set of binding sites for specific transcription factors. Since experimental identification of regulatory modules is an arduous process, accurate computational techniques that supplement this process can be very beneficial. Functional modules are under selective pressure to be evolutionarily conserved. Most current approaches therefore attempt to detect conserved regulatory modules through similarity comparisons at the DNA sequence level. However, some regulatory modules, despite the conservation of their responsible binding sites, are embedded in sequences that have little overall similarity. RESULTS: In this study, we present a novel approach that detects conserved regulatory modules via comparisons at the binding site level. The technique compares the binding site profiles of orthologs and identifies those segments that have similar (not necessarily identical) profiles. The similarity measure is based on the inner product of transformed profiles, which takes into consideration the p values of binding sites as well as the potential shift of binding site positions. We tested this approach on simulated sequence pairs as well as real world examples. In both cases our technique was able to identify regulatory modules which could not to be identified using sequence-similarity based approaches such as rVista 2.0 and Blast. CONCLUSION: The results of our experiments demonstrate that, for sequences with little overall similarity at the DNA sequence level, it is still possible to identify conserved regulatory modules based solely on binding site profiles

Analysis of tsunami effect and structural response

Tsunami predstavlja jednu od ozbiljnih prirodnih katastrofa u svijetu, koja rezultira ogromnom horizontalnom potisnom silom na obalne zgrade, dovodeći do trenutnog urušavanja velikog broja zgrada što uzrokuje velike nesreće i ekonomske gubitke. U ovom radu, uz podršku hidrodinamičkog softvera FLOW-3D, primjenom metode Volumena fluida (VOF), zahvaćena je slobodna dodirna površina i primijenjen model idealnog pojedinačnog vala u svrhu simuliranja valova tsunamija. Zasnivajući se na simuliranju i analizi trodimenzijskog numeričkog modela okvira konstrukcije od armiranog betona pod udarnom silom tsunami valova, može se ustanoviti veličina i raspodjela sila tsunamija. Osim toga, primjenom softvera ANSYS za analizu konačnih elemenata, dobiven je model konačnih elemenata za konstrukciju okvira kako bi se analizirala reakcija konstrukcije od armiranog betona na udar tsunami sila te poduzele odgovarajuće konstrukcijske protumjere, tehničke preventivne i kontrolne mjere te tako oduprlo silama tsunamija.Tsunami is one of the serious natural disasters in the world, which produce huge horizontal thrust on costal buildings, resulting in a large number of houses collapsed instantaneously, causing serious casualties and economic losses. In this paper, based on support from the hydrodynamic software FLOW-3D, the method of Volume of Fluid (VOF) is utilized to capture free interface, and the ideal solitary wave model is applied to simulate tsunami waves. Based on simulating and analysing the three-dimensional numerical model of reinforced concrete frame structure under the impact of tsunami waves, the magnitude and distribution of tsunami forces can be obtained. Moreover, the finite element analysis software ANSYS is adopted to set up finite element model for the frame structure, so as to analyse the response of the reinforced concrete frame structure under the impact of tsunami forces, and to put forward related structural countermeasures, engineering prevention and control measures to resist tsunami forces

Ontology-based approach supporting multi-objective holistic decision making for energy pile system

The traditional way of designing energy pile system is mostly single domain/objective oriented, which lacks of means to coherently consider different while relevant factors across domains. The cost for life cycle design, construction and maintenance, return of investment, CO2 emission related sustainable requirements, and so on also need to be considered, in a systematic manner, along with the main functional design objective for loading capacity and robustness. This paper presents a novel multi-objective holistic approach for energy pile system design using ontology based multi-domain knowledge orchestration, which can holistically provide the designers with across domain factors regarding financial, safety, and environmental impact, for smart and holistic consideration during the early design stage. A prototypical ontology-based decision tool has been developed, aiming at the holistic optimization for energy pile system by combining ontology and Semantic Web Rule Language rules. A case study was performed to illustrate the details on how to apply knowledge query to provide a series of design alternatives autonomously by taking different design parameters into account. The method has demonstrated its practicability and scientific feasibility, it also shows the potential to be adopted and extended for other domains when dealing with multi-objective holistic design making

A Highly Overmoded Structure for Hundred-Kilowatt-Class <italic>Ka</italic>-Band Extended Interaction Klystron

Here, we report on the development of highly overmoded structure for a millimeter-wave (MMW) extended interaction klystron (EIK). To enhance electron beam loading, a new method for designing an oversized beam tunnel in a large cavity by concentrating the axial field is demonstrated. The transmission and oscillation characteristics of the interaction circuit operating in the quasi-TM04 mode are tested by the developed mode conversion circuit. Results suggest that a five-cavity EIK based on this highly overmoded structure can achieve an output power of 289 kW at 32.92 GHz with a saturated gain of 51.6 dB by injecting a 3.3-mm-diameter electron beam with a current of 18 A. The output power exceeds 100 kW at a bandwidth of 100 MHz.</p

Investigation of PMSE echoes characteristics using the discontinuous EISCAT UHF observation and its relation with space environment

The observations of Polar Mesosphere Summer Echoes (PMSE) were carried out using the sporadic data of EISCAT UHF radar during the summer season from 2004 to 2015. There were 25 h of PMSE echoes with EISCAT UHF radar. PMSE echoes were mostly observed only during the early morning and fore-noon time. Moreover, the PMSE echoes are positively correlated with Lyman α radiation, but the correlation is non-significant. The occurrence of PMSE echoes in the early morning and fore-noon time and there positive correlation with Lyman α radiation suggests that solar radiations might be one important factor for PMSE echoes in this study. Very weak positive, but statistically non-significant correlation is found between PMSE occurrence rate and the local geomagnetic K-indices. It is found that there is a matching between the variation in the occurrence rate of PMSE and noctilucent clouds (NLC) up to some extent and they are positively correlated. This positive correlation might support the earlier proposed idea about the role of ice particle size in producing PMSE echoes at higher frequencies