Emerging infectious diseases (EID) are serious problems caused by fungi in humans and plant species. They are a severe threat to food security worldwide. In our current work, we have developed a support vector machine (SVM)-based model that attempts to design and predict therapeutic plant-derived antifungal peptides (PhytoAFP). The residue composition analysis shows the preference of C, G, K, R, and S amino acids. Position preference analysis shows that residues G, K, R, and A dominate the N-terminal. Similarly, residues N, S, C, and G prefer the C-terminal. Motif analysis reveals the presence of motifs like NYVF, NYVFP, YVFP, NYVFPA, and VFPA. We have developed two models using various input functions such as mono-, di-, and tripeptide composition, as well as binary, hybrid, and physiochemical properties, based on methods that are applied to the main data set. The TPC-based monopeptide composition model achieved more accuracy, 94.4%, with a Matthews correlation coefficient (MCC) of 0.89. Correspondingly, the second-best model based on dipeptides achieved an accuracy of 94.28% under the MCC 0.89 of the training dataset.
- Publikační typ
- časopisecké články MeSH
Inspired by the standard computed tomography, a new method of 3D X-ray imaging embedded in FIB-SEM microscope is proposed. The unique combination of TEM-like specimen stage enabling in lens STEM detection (referred to as CompuStage), nanomanipulator (referred to as EasyLift) facilitating in-situ sample transfer from bulk sample to TEM-like stage and pixelated in-situ Timepix X-ray detector in Helios G4 FX FIB-SEM system offers an unprecedented workflow. Motivated by common circular CT scan known from microCT world, the object under study is placed on CompuStage rod which enables two possible rotation (in TEM/SEM terminology called tilt) movements - α-tilt - rotation of the CompuStage rod around its axis, and β-tilt - rotation around axis perpendicular to CompuStage rod. β-tilt rotation enables a circular movement of the sample while α-tilt sets the correct position of sample with respect to target and detector. Thin metal lamella of suitable material welded to EasyLift manipulator needle is used as an X-ray target. The final target-sample geometry - position, distance - can be fine-tuned using position control of CompuStage and EasyLift and in-situ monitored by SEM. Both sample and target can also be easily prepared in-situ. Radiographs are recorded by Timepix detector with inherent noise-free operation and energy filtration. For the 3D reconstruction standard microCT reconstruction algorithm is used with the procedure adjusted for the format and quality of nanoCT images. The experiments were carried out on Helios G4 FX DualBeam using titanium and tungsten targets and various semiconductor samples. The ultimate resolution of the proposed method in orders of tens of nanometers was achieved both by the possibility of close target to sample positioning and of adjustment of primary beam energy down to low energies reducing the interaction volume in the target. Since the lower energy radiation is well suited for life-science, the method was also tested on several bio-samples using silver target. The silver target, thanks to its massive low energy Lα line, allowed to distinguish subtle structures in the resin embedded stained mouse brain and also to observe and reconstruct canaliculi in the mouse bone (earlier reported by Dierolf et al. 2010, Nature 467 436).
- MeSH
- algoritmy MeSH
- fantomy radiodiagnostické MeSH
- femur ultrastruktura MeSH
- mikroskopie elektronová rastrovací * přístrojové vybavení metody MeSH
- myši MeSH
- počítačové zpracování obrazu metody MeSH
- rentgenová mikrotomografie * přístrojové vybavení metody MeSH
- zvířata MeSH
- Check Tag
- myši MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
BACKGROUND: Left bundle branch area pacing (LBBAP) has recently been introduced as a novel physiological pacing strategy. Within LBBAP, distinction is made between left bundle branch pacing (LBBP) and left ventricular septal pacing (LVSP, no left bundle capture). OBJECTIVE: To investigate acute electrophysiological effects of LBBP and LVSP as compared to intrinsic ventricular conduction. METHODS: Fifty patients with normal cardiac function and pacemaker indication for bradycardia underwent LBBAP. Electrocardiography (ECG) characteristics were evaluated during pacing at various depths within the septum: starting at the right ventricular (RV) side of the septum: the last position with QS morphology, the first position with r' morphology, LVSP and-in patients where left bundle branch (LBB) capture was achieved-LBBP. From the ECG's QRS duration and QRS morphology in lead V1, the stimulus- left ventricular activation time left ventricular activation time (LVAT) interval were measured. After conversion of the ECG into vectorcardiogram (VCG) (Kors conversion matrix), QRS area and QRS vector in transverse plane (Azimuth) were determined. RESULTS: QRS area significantly decreased from 82 ± 29 µVs during RV septal pacing (RVSP) to 46 ± 12 µVs during LVSP. In the subgroup where LBB capture was achieved (n = 31), QRS area significantly decreased from 46 ± 17 µVs during LVSP to 38 ± 15 µVs during LBBP, while LVAT was not significantly different between LVSP and LBBP. In patients with normal ventricular activation and narrow QRS, QRS area during LBBP was not significantly different from that during intrinsic activation (37 ± 16 vs. 35 ± 19 µVs, respectively). The Azimuth significantly changed from RVSP (-46 ± 33°) to LVSP (19 ± 16°) and LBBP (-22 ± 14°). The Azimuth during both LVSP and LBBP were not significantly different from normal ventricular activation. QRS area and LVAT correlated moderately (Spearman's R = 0.58). CONCLUSIONS: ECG and VCG indices demonstrate that both LVSP and LBBP improve ventricular dyssynchrony considerably as compared to RVSP, to values close to normal ventricular activation. LBBP seems to result in a small, but significant, improvement in ventricular synchrony as compared to LVSP.
- Publikační typ
- časopisecké články MeSH
Species delineation based on bacterial genomes is an essential part of the research of prokaryotes. In silico genome-to-genome comparison methods are computationally demanding, but much less tedious and error prone than the wet-lab methods. In this paper, we present a novel method for the delineation of bacterial genomes based on genomic signal processing. The proposed method uses numerical representations of whole bacterial genomes, phase signal and cumulated phase signal, from which four parameters are derived for each genome. The parameters characterize a genome and their calculation is independent of the other genomes comprising a delineation dataset. The delineation itself is processed as a calculation of the parameters' average similarity. The method was statistically verified on 1826 bacterial genomes. A similarity threshold of 96% was set based on the receiver operating characteristic curve that featured sensitivity of 99.78% and specificity of 97.25%. Additionally, comparative analysis on another 33 bacterial genomes was conducted using standard delineation tools as these tools were not able to process the dataset of 1826 genomes using desktop computer. The proposed method achieved comparable or better delineation results in comparison with the standard tools. Besides the excellent delineation results, another great advantage of the method is its small computational demands, which enables the delineation of thousands of genomes on a desktop computer. The calculation of the parameters takes tens of minutes for thousands of genomes. Moreover, they can be calculated in advance by creating a database, meaning the delineation itself is then completed in a matter of seconds.
- Publikační typ
- časopisecké články MeSH
BACKGROUND: Optical coherence tomography (OCT) is a well established imaging technique with different applications in preclinical research and clinical practice. The main potential for its application lies in the possibility of noninvasively performing "optical biopsy". Nevertheless, functional OCT imaging is also developing, in which perfusion imaging is an important approach in tissue function study. In spite of its great potential in preclinical research, advanced perfusion imaging using OCT has not been studied. Perfusion analysis is based on administration of a contrast agent (nanoparticles in the case of OCT) into the bloodstream, where during time it specifically changes the image contrast. Through analysing the concentration-intensity curves we are then able to find out further information about the examined tissue. METHODS: We have designed and manufactured a tissue mimicking phantom that provides the possibility of measuring dilution curves in OCT sequence with flow rates 200, 500, 1000 and 2000 μL/min. The methodology comprised of using bolus of 50 μL of gold nanorods as a contrast agent (with flow rate 5000 μL/min) and continuous imaging by an OCT system. After data acquisition, dilution curves were extracted from OCT intensity images and were subjected to a deconvolution method using an input-output system description. The aim of this was to obtain impulse response characteristics for our model phantom within the tissue mimicking environment. Four mathematical tissue models were used and compared: exponential, gamma, lagged and LDRW. RESULTS: We have shown that every model has a linearly dependent parameter on flow ([Formula: see text] values from 0.4914 to 0.9996). We have also shown that using different models can lead to a better understanding of the examined model or tissue. The lagged model surpassed other models in terms of the minimisation criterion and [Formula: see text] value. CONCLUSIONS: We used a tissue mimicking phantom in our study and showed that OCT can be used for advanced perfusion analysis using mathematical model and deconvolution approach. The lagged model with three parameters is the most appropriate model. Nevertheless, further research have to be performed, particularly with real tissue.
- MeSH
- 3D tisk MeSH
- design vybavení MeSH
- fantomy radiodiagnostické * MeSH
- kontrastní látky chemie MeSH
- kovové nanočástice chemie MeSH
- nanotrubičky chemie MeSH
- optická koherentní tomografie metody MeSH
- počítačové zpracování obrazu MeSH
- teoretické modely * MeSH
- tkáňové podpůrné struktury chemie MeSH
- zlato chemie MeSH
- Publikační typ
- časopisecké články MeSH
