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1.
Radon anomalies in soil gas caused by seismic activity
Boris Zmazek, Mladen Živčić, Ljupčo Todorovski, Sašo Džeroski, Janja Vaupotič, Ivan Kobal, 2004, original scientific article

Abstract: At the Orlica fault in the Krško basin, combined barasol detectors were buried in six boreholes, two along the fault itself and four on either side of it, to measure and record radon activity, temperature and pressure in soil gas every 60 minutes for four years. Data collected have been analysed in a manner aimed at distinguishing radon anomalies resulting from environmental parameters (air and soil temperature, barometric pressure, rainfall) from those caused solely by seismic events. The following approaches have been used to identify anomalies: (i) ± 2σ deviation of radon concentration from the seasonal average, (ii) correlation between time gradients of radon concentration and barometric pressure, and (iii) prediction with regression trees within a machine learning program. In this paper results obtained with regression trees are presented. A model has been built in which the program was taught to predict radon concentration from the data collected during the seismically inactive periods when radon is presumably influenced only by environmental parameters. A correlation coefficient of 0.83 between measured and predicted values was obtained. Then, the whole data time series was included and a significantly lowered correlation was observed during the seismically active periods. This reduced correlation is thus an indicator of seismic effect.
Keywords: radon in soil gas, environmental parameters, earthquakes, correlation, regression trees, forecasting
Published in DKUM: 15.05.2018; Views: 1071; Downloads: 67
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2.
Evaluating the effect of Clostridium difficile conditioned medium on fecal microbiota community structure
Sabina Horvat, Aleksander Mahnič, Martin Breskvar, Sašo Džeroski, Maja Rupnik, 2017, original scientific article

Abstract: Clostridium difficile infection (CDI) is typically associated with disturbed gut microbiota and changes related to decreased colonization resistance against C. difficile are well described. However, nothing is known about possible effects of C. difficile on gut microbiota restoration during or after CDI. In this study, we have mimicked such a situation by using C. difficile conditioned medium of six different C. difficile strains belonging to PCR ribotypes 027 and 014/020 for cultivation of fecal microbiota. A marked decrease of microbial diversity was observed in conditioned medium of both tested ribotypes. The majority of differences occurred within the phylum Firmicutes, with a general decrease of gut commensals with putative protective functions (i.e. Lactobacillus, Clostridium_XIVa) and an increase in opportunistic pathogens (i.e. Enterococcus). Bacterial populations in conditioned medium differed between the two C. difficile ribotypes, 027 and 014/020 and are likely associated with nutrient availability. Fecal microbiota cultivated in medium conditioned by E. coli, Salmonella Enteritidis or Staphylococcus epidermidis grouped together and was clearly different from microbiota cultivated in C. difficile conditioned medium suggesting that C. difficile effects are specific. Our results show that the changes observed in microbiota of CDI patients are partially directly influenced by C. difficile.
Keywords: Clostridium difficile, infection, gut microbiota
Published in DKUM: 12.12.2017; Views: 1032; Downloads: 341
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3.
TMPRSS2:ERG gene aberrations may provide insight into pT stage in prostate cancer
Zoran Krstanoski, Nadja Kokalj-Vokač, Andreja Zagorac, Boris Pospihalj, Miha Munda, Sašo Džeroski, Rastko Golouh, 2016, original scientific article

Abstract: Background: TMPRSS2:ERG gene aberration may be a novel marker that improves risk stratification of prostate cancer before definitive cancer therapy, but studies have been inconclusive. Methods: The study cohort consisted of 202 operable prostate cancer Slovenian patients who underwent laparoscopic radical prostatectomy. We retrospectively constructed tissue microarrays of their prostatic specimens for fluorescence in situ hybridization, with appropriate signals obtained in 148 patients for subsequent statistical analyses. Results: The following genetic aberrations were found: TMPRSS2:ERG fusion, TMPRSS2 split (a non-ERG translocation) and ERG split (an ERG translocation without involvement of TMPRSS2). TMPRSS2:ERG gene fusion happened in 63 patients (42 %), TMPRSS2 split in 12 patients and ERG split in 8 patients. Association was tested between TMPRSS2:ERG gene fusion and several clinicopathological variables, i.e., pT stage, extended lymph node dissection status, and Gleason score, correcting for multiple comparisons. Only the association with pT stage was significant at p = 0.05: Of 62 patients with pT3 stage, 34 (55 %) had TMPRSS2:ERG gene fusion. In pT3 stage patients, stronger (but not significant) association between eLND status and TMPRSS2:ERG gene fusion was detected. We detected TMPRSS2:ERG gene fusion in 64 % of the pT3 stage patients where we did not perform an extended lymph node dissection. Conclusions: Our results indicate that it is possible to predict pT3 stage at final histology from TMPRSS2:ERG gene fusion at initial core needle biopsy. FISH determination of TMPRSS2:ERG gene fusion may be particularly useful for patients scheduled to undergo a radical prostatectomy in order to improve oncological and functional results.
Keywords: FISH, predicting pT stage, radical prostatectomy, prostate cancer, TMPRSS2:ERG fusion
Published in DKUM: 29.06.2017; Views: 1255; Downloads: 365
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4.
Gut microbiota patterns associated with colonization of different clostridium difficile ribotypes
Jure Škraban, Sašo Džeroski, Bernard Ženko, Domen Mongus, Simon Gangl, Maja Rupnik, 2013, original scientific article

Abstract: Abstract Introduction Materials and Methods Results Discussion Supporting Information Acknowledgments Author Contributions References Reader Comments (0) Figures Abstract C. difficile infection is associated with disturbed gut microbiota and changes in relative frequencies and abundance of individual bacterial taxons have been described. In this study we have analysed bacterial, fungal and archaeal microbiota by denaturing high pressure liquid chromatography (DHPLC) and with machine learning methods in 208 faecal samplesfrom healthy volunteers and in routine samples with requested C. difficile testing. The latter were further divided according to stool consistency, C. difficile presence or absence and C. difficile ribotype (027 or non-027). Lower microbiota diversity was a common trait of all routine samples and not necessarily connected only to C. difficile colonisation. Differences between the healthy donors and C. difficile positive routine samples were detected in bacterial, fungal and archaeal components. Bifidobacterium longum was the single most important species associated with C. difficile negative samples. However, by machine learning approaches we haveidentified patterns of microbiota composition predictive for C. difficile colonization. Those patterns also differed between samples with C. difficile ribotype 027 and other C. difficile ribotypes. The results indicate that not only the presence of a single species/group is important but that certain combinations of gut microbes are associated with C. difficile carriage and that some ribotypes (027) might be associated with more disturbed microbiota than the others.
Keywords: microbiota, clostridium difficile, chromatography
Published in DKUM: 19.06.2017; Views: 916; Downloads: 334
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