Ústav biomedicínského inženýrství
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- ItemEvaluation of the Spatial Structure of Windbreaks from Digital Photography(Polish Society of Ecological Engineering, 2024-09-01) Kučera, Josef; Fukalová, Petra; Středová, Hana; Blecha, Martin; Jakubíček, Roman; Chmelík, Jiří; Podhrázská, Jana; Středa, TomášThe loss of fertile soil due to wind erosion has major impacts on the landscape and the environment. Its intensity and extent depend on many factors, where vegetation cover, soil moisture and wind intensity play key roles. Climatic conditions are constantly developing towards a higher extremity. Episodes of drought associated with a higher risk of wind erosion are longer and more frequent. For farmers, this results in higher demands for management in order to increase resistance against the negative effects of wind erosion. Windbreaks effectively protect the soil by reducing wind speed. This paper describes the automation of the current procedure for the evaluation of the spatial structure of windbreaks by means of advanced image signal analysis (2D) and the subsequent use of machine learning for further classification of spatial structure parameters (optical porosity). Software called Windbreak which enables the evaluation of optical porosity, including the assessment of canopy height, has been developed. The program allows working with digital photographs at the original resolution. The output from the Windbreak software can be also used as input values for determining the effectiveness of windbreaks.
- ItemThe hare syphilis agent is related to, but distinct from, the treponeme causing rabbit syphilis(Public Library of Science, 2024-08-12) Pospíšilová, Petra; Čejková, Darina; Buršíková, Pavla; Fedrová, Pavla; Mikalova, Lenka; Najt, David; Tom, Nikola; Hisgen, Linda; Lueert, Simone; Lumeij, Johannes T.; Agren, Erik O.; Knauf, Sascha; Šmajs, DavidThe treponemes infecting lagomorphs include Treponema paraluisleporidarum ecovar Cuniculus (TPeC) and ecovar Lepus (TPeL), infecting rabbits and hares, respectively. In this study, we described the first complete genome sequence of TPeL, isolate V3603-13, from an infected mountain hare (Lepus timidus) in Sweden. In addition, we determined 99.0% of the genome sequence of isolate V246-08 (also from an infected mountain hare, Sweden) and 31.7% of the genome sequence of isolate Z27 A77/78 (from a European hare, Lepus europeaus, The Netherlands). The TPeL V3603-13 genome had considerable gene synteny with the TPeC Cuniculi A genome and with the human pathogen T. pallidum, which causes syphilis (ssp. pallidum, TPA), yaws (ssp. pertenue, TPE) and endemic syphilis (ssp. endemicum, TEN). Compared to the TPeC Cuniculi A genome, TPeL V3603-13 contained four insertions and 11 deletions longer than three nucleotides (ranging between 6 and2,932 nts). In addition, there were 25 additional indels, from one to three nucleotides long, altogether spanning 36 nts. The number of single nucleotide variants (SNVs) between TPeC Cuniculi A and TPeL V3603-13 were represented by 309 nucleotide differences. Major proteome coding differences between TPeL and TPeC were found in the tpr gene family, and (predicted) genes coding for outer membrane proteins, suggesting that these components are essential for host adaptation in lagomorph syphilis. The phylogeny revealed that the TPeL sample from the European brown hare was more distantly related to TPeC Cuniculi A than V3603-13 and V246-08.
- ItemWhole genome sequencing and characterization of Pantoea agglomerans DBM 3797, endophyte, isolated from fresh hop (Humulus lupulus L.)(Frontiers, 2024-02-08) Patáková, Petra; Vasylkivska, Maryna; Sedlář, Karel; Šabatová, Kateřina; Bezdíček, Matěj; Lovecká, Petra; Branská, Barbora; Kaštánek, Petr; Krofta, KarelBackground This paper brings new information about the genome and phenotypic characteristics of Pantoea agglomerans strain DBM 3797, isolated from fresh Czech hop (Humulus lupulus) in the Saaz hop-growing region. Although P. agglomerans strains are frequently isolated from different materials, there are not usually thoroughly characterized even if they have versatile metabolism and those isolated from plants may have a considerable potential for application in agriculture as a support culture for plant growth. Methods P. agglomerans DBM 3797 was cultured under aerobic and anaerobic conditions, its metabolites were analyzed by HPLC and it was tested for plant growth promotion abilities, such as phosphate solubilization, siderophore and indol-3-acetic acid productions. In addition, genomic DNA was extracted, sequenced and de novo assembly was performed. Further, genome annotation, pan-genome analysis and selected genome analyses, such as CRISPR arrays detection, antibiotic resistance and secondary metabolite genes identification were carried out. Results and discussion The typical appearance characteristics of the strain include the formation of symplasmata in submerged liquid culture and the formation of pale yellow colonies on agar. The genetic information of the strain (in total 4.8 Mb) is divided between a chromosome and two plasmids. The strain lacks any CRISPR-Cas system but is equipped with four restriction-modification systems. The phenotypic analysis focused on growth under both aerobic and anaerobic conditions, as well as traits associated with plant growth promotion. At both levels (genomic and phenotypic), the production of siderophores, indoleacetic acid-derived growth promoters, gluconic acid, and enzyme activities related to the degradation of complex organic compounds were found. Extracellular gluconic acid production under aerobic conditions (up to 8 g/l) is probably the result of glucose oxidation by the membrane-bound pyrroloquinoline quinone-dependent enzyme glucose dehydrogenase. The strain has a number of properties potentially beneficial to the hop plant and its closest relatives include the strains also isolated from the aerial parts of plants, yet its safety profile needs to be addressed in follow-up research.
- ItemVirtual reality exposure effect in acrophobia: psychological and physiological evidence from a single experimental session(Springer Nature, 2024-07-15) Varšová, Kristína; Szitás, Dagmar; Janoušek, Oto; Jurkovičová, Lenka; Bartošová, Kateřina; Juřík, VojtěchIn recent years, virtual reality (VR) has gained attention from researchers in diverse fields, particularly in therapy of phobias. Currently, virtual reality exposure therapy therapy (VRET) is considered a promising cognitive-behavioral therapy technique. However, specific psychological and physiological responses of VR users to virtual exposure in such a context are still only vaguely explored. In this experimental study, we mapped VR exposure in a height environment in people with a moderate fear of heights–acrophobia. Thirty-six participants were divided into experimental and control groups–with and without psychological guidance during exposure. Participants' subjective level of anxiety was examined, and objective physiological response was captured via heart rate variability (HRV) measurement. Psychological assessments recorded an anticipated rise in participant anxiety following exposure to height; nevertheless, no distinctions were observed in self-reported anxiety concerning psychological guidance. Notably, objective physiological measures revealed that VR exposure prompts physiological responses akin to real-world scenarios. Moreover, based on the analysis of heart rate variability, participants who received psychological guidance were identified as better at compensating for anxiety compared to those without such support. These findings support VRET as a promising tool for psychotherapy and advocate for psychological guidance as beneficial in reducing anxiety and managing stress during exposure. The results may help improve our understanding of anxiety during exposure to phobic stimuli.
- ItemComprehensive automatic processing and analysis of adaptive optics flood illumination retinal images on healthy subjects(Optica Publishing Group, 2023-01-30) Orságová, Eva; Unterlauft, Jan D.; Francke, Mike; Toralf, Kirsten; Kolář, Radim; Rauscher, Franziska G.This work presents a novel fully automated method for retinal analysis in images acquired with a flood illuminated adaptive optics retinal camera (AO-FIO). The proposed processing pipeline consists of several steps: First, we register single AO-FIO images in a montage image capturing a larger retinal area. The registration is performed by combination of phase correlation and the scale-invariant feature transform method. A set of 200 AO-FIO images from 10 healthy subjects (10 images from left eye and 10 images from right eye) is processed into 20 montage images and mutually aligned according to the automatically detected fovea center. As a second step, the photoreceptors in the montage images are detected using a method based on regional maxima localization, where the detector parameters were determined with Bayesian optimization according to manually labeled photoreceptors by three evaluators. The detection assessment, based on Dice coefficient, ranges from 0.72 to 0.8. In the next step, the corresponding density maps are generated for each of the montage images. As a final step, representative averaged photoreceptor density maps are created for the left and right eye and thus enabling comprehensive analysis across the montage images and a straightforward comparison with available histological data and other published studies. Our proposed method and software thus enable us to generate AO-based photoreceptor density maps for all measured locations fully automatically, and thus it is suitable for large studies, as those are in pressing need for automated approaches. In addition, the application MATADOR (MATlab ADaptive Optics Retinal Image Analysis) that implements the described pipeline and the dataset with photoreceptor labels are made publicly available.