• Klíčová slova
• single sample predictors, molekulární profil,
• MeSH
• analýza přežití MeSH
• diagnostické techniky molekulární * metody   MeSH
• lidé MeSH
• nádory prsu * genetika   klasifikace   MeSH
• regresní analýza MeSH
• retrospektivní studie MeSH
• statistika jako téma MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• práce podpořená grantem MeSH

MOTIVATION: Accurate genotyping of DNA from a single cell is required for applications such as de novo mutation detection, linkage analysis and lineage tracing. However, achieving high precision genotyping in the single-cell environment is challenging due to the errors caused by whole-genome amplification. Two factors make genotyping from single cells using single nucleotide polymorphism (SNP) arrays challenging. The lack of a comprehensive single-cell dataset with a reference genotype and the absence of genotyping tools specifically designed to detect noise from the whole-genome amplification step. Algorithms designed for bulk DNA genotyping cause significant data loss when used for single-cell applications. RESULTS: In this study, we have created a resource of 28.7 million SNPs, typed at high confidence from whole-genome amplified DNA from single cells using the Illumina SNP bead array technology. The resource is generated from 104 single cells from two cell lines that are available from the Coriell repository. We used mother-father-proband (trio) information from multiple technical replicates of bulk DNA to establish a high quality reference genotype for the two cell lines on the SNP array. This enabled us to develop SureTypeSC-a two-stage machine learning algorithm that filters a substantial part of the noise, thereby retaining the majority of the high quality SNPs. SureTypeSC also provides a simple statistical output to show the confidence of a particular single-cell genotype using Bayesian statistics. AVAILABILITY AND IMPLEMENTATION: The implementation of SureTypeSC in Python and sample data are available in the GitHub repository: https://github.com/puko818/SureTypeSC. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

• MeSH
• Bayesova věta MeSH
• genotyp MeSH
• jednonukleotidový polymorfismus * MeSH
• normální rozdělení MeSH
• sekvenování celého genomu MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Cytogenetic information on cells from cytotrophoblast, villus mesenchyme, and one or more fetal tissues was available for 192 gestations with mosaicism or non-mosaic fetoplacental discrepancy involving a single autosomal trisomy in the chorionic villus sample (CVS), registered in a collaborative study (EUCROMIC) during the period 1986-1994. In order to identify predictors of confined placental mosaicism (CPM), generalized mosaicism and/or uniparental disomy (UPD), distribution of the mosaic and nonmosaic aneuploid cell lines in the different fetal and extrafetal cell lineages were analyzed. Data were related to existing hypotheses on mechanisms leading to fetoplacental discrepancies and early extraembryonic cell differentiation. Trisomy 21 mosaicism was the one most frequently confirmed in the fetus. Non-mosaic trisomy 13, 18, and 21 in the villus mesenchyme indicated the presence of a trisomic cell line in the fetus proper. Non-mosaic trisomy 2, 7, and 16 in villus mesenchyme was always found with concomitant mosaic or non-mosaic trisomy in the cytotrophoblast, but was never recovered in the fetus. Mosaic trisomy 3, 7, and 20 was predominantly restricted to the cytotrophoblast, mosaic trisomy 2 to the villus mesenchyme. Trisomies 15 and 16 were most often found in both cytotrophoblast and villus mesenchyme and not in fetal cells. This supports the hypothesis that mosaicism/discrepancy for trisomies 15 and 16 results more often than for the other trisomies from trisomic zygote rescue, enhancing their risk for UPD. We recommend, due to the risk of fetal trisomy, amniocentesis in all gestations involving mosaic autosomal trisomy in villus mesenchyme. In gestations with mosaic or non-mosaic autosomal trisomy in both cytotrophoblast and villus mesenchyme we recommend, in order to exclude fetal trisomy and/or UPD, depending on the chromosome involved, further examination by amniocentesis, ultrasound and/or test for UPD. We also recommend, due to a small but not negligible risk of false negative and false positive diagnoses, not to solely use direct preparation.

• MeSH
• buněčný rodokmen MeSH
• karyotypizace metody   MeSH
• lidé MeSH
• mozaicismus * MeSH
• odběr choriových klků * statistika a číselné údaje   MeSH
• trizomie * genetika   MeSH
• výzkum MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• multicentrická studie MeSH
• práce podpořená grantem MeSH
• Geografické názvy
• Evropa MeSH

Úvod: Náhrada aortální chlopně chirurgickou metodou (transcatheter aortic valve replacement, TAVR) je stále prevalentnější metodou náhrady aortální chlopně, zejména u pacientů s vyšším operačním rizikem. I přes velké pokroky ve vývoji chlopní se však incidence poruch rytmu vyžadujících trvalou kardiostimulaci po TAVR výrazně nesnižuje. Existuje množství rizikových faktorů, pomocí nichž lze predikovat riziko nutnosti kardiostimulace po náhradě chlopně. Cíl: Přinést data o prevalenci komplikace v podobě nutnosti kardiostimulace u pacientů po TAVR z jednoho českého centra, kde probíhají implantace TAVR již déle než dekádu. Metodika: Byla analyzována skupina pacientů, kteří podstoupili TAVR v našem centru v období mezi srpnem 2009 a únorem 2021. Ze vzorku byli vyjmuti pacienti, kteří již mají naimplantovaný kardiostimulátor či defibrilátor. V souboru 717 pacientů průměrný věk dosahoval 78,8 roku, 52 % tvořily ženy, průměrný index tělesné hmotnosti (BMI) je 29,6. V tomto období byly implantovány chlopně od různých výrobců od chlopní první generace až po protézy novějších generací. Výsledky: Trvalá kardiostimulace byla nutná u 162 pacientů (22,6 %), kterým bylo implantováno srdeční implantabilní elektronické zařízení (cardiac implantable electronic device, CIED) v průměru 3,9 dnu od TAVR. Z naimplantovaných pacientů bylo signifikantně více mužů (56,2 %) v porovnání s pacienty bez CIED (45,4 %); p = 0,016. Rovněž byl zaznamenán významný rozdíl mezi výškou, hmotností a BSA mezi těmito skupinami. Pacienti s preexistující blokádou pravého Tawarova raménka (right bundle branch block, RBBB) byli četnější mezi pacienty vyžadujícími kardiostimulaci v porovnání s nestimulovaným souborem (p < 0,0001), tento parametr rovněž vyšel jako jediný nezávislý prediktor implantace CIED po TAVR (poměr šancí [OR] 3,8, 95% interval spolehlivosti [CI] 2,0-7,0; p < 0,0001). Jednotlivé typy protéz se výrazně lišily v procentuálním zastoupení pacientů s nutností kardiostimulace. Nebyl nalezen signifikantní rozdíl mezi jednotlivými velikostmi protéz, stejně jako u pacientů s predilatací či postdilatací, v zastoupení pacientů s CIED a bez nich. Závěr: Naše data jsou ve shodě s jinými studiemi zabývajícími se tímto tématem a podporují přítomnost RBBB jako jeden z rizikových faktorů pro nutnost kardiostimulace po TAVR. Mezi stimulovanými pacienty bylo rovněž četnější mužské pohlaví a pacienti s větším tělesným povrchem (BSA). Náš vzorek je však nehomogenní a další subanalýzy v rámci jednotlivých designů chlopní ve větším zastoupení by byly potřebné k vyhodnocení dalších rizikových faktorů.

Introduction: Transcatheter aortic valve replacement (TAVR) is becoming more prevalent option of aortic valve replacement, predominantly amongst patients with a higher surgical risk. Despite a rapid development of TAVR prostheses, incidence of conduction abnormalities requiring cardiac pacing as a result of TAVR is not significantly decreasing. There are numerous risk factors which can help to predict the risk for cardiac pacing after TAVR. Aim: To present our data of a prevalence of this complication from one Czech center where TAVR prostheses have been implanted for over a decade. Methods: A group of patients who underwent TAVR between August 2009 and February 2021 in our center were analyzed. Patients with already implanted pacemaker or defi brillator were excluded from this group, leaving 717 patients for further analysis. The mean age was 78.8 years, 52% were females, the mean BMI was 29.6. Various different prostheses of different manufacturers and generations were implanted. Results: Permanent pacing was required in 162 patients (22.6%), in whom CIED (cardiac implantable electronic device) was implanted in average 3.9 days from TAVR. There was a signifi cantly higher amount of men in the paced group (56.2%) compared to the group without CIED (45.4%); p = 0.016. Moreover, there was a signifi cant difference between height, weight, and BSA among these groups. Patients with preexisting right bundle branch block (RBBB) were more prevalent in the paced group compared to non-paced group (p <0.0001); this parameter was the only independent predictor of the implantation of CIED after TAVR (odds ratio 3.8, 95% CI 2.0–7.0; p <0.0001). There were marked differences between the amounts of implanted prostheses of various designs. No signifi cant difference was found in the size of prostheses, predilatation or postdilatation between the two groups of patients. Conclusion: Our data are in concordance with other published studies, supporting the RBBB being one of the risk factors for pacing after TAVR. Males and patients with higher BSA were more prevalent in the paced group. Our sample is, however, rather inhomogeneous and further analysis of different designs in higher numbers would be necessary to identify other risk factors of this prevalent complication

• MeSH
• aortální stenóza chirurgie   MeSH
• blokáda Tawarova raménka terapie   MeSH
• kardiostimulace umělá metody   MeSH
• lidé středního věku MeSH
• lidé MeSH
• pooperační komplikace epidemiologie   terapie   MeSH
• rizikové faktory kardiovaskulárních chorob MeSH
• senioři nad 80 let MeSH
• senioři MeSH
• transkatetrální implantace aortální chlopně * metody   MeSH
• Check Tag
• lidé středního věku MeSH
• lidé MeSH
• senioři nad 80 let MeSH
• senioři MeSH

BACKGROUND: The aim of the current study was to explore the effect of gender, age at onset, and duration on the long-term course of schizophrenia. METHODS: Twenty-nine centers from 25 countries representing all continents participated in the study that included 2358 patients aged 37.21 ± 11.87 years with a DSM-IV or DSM-5 diagnosis of schizophrenia; the Positive and Negative Syndrome Scale as well as relevant clinicodemographic data were gathered. Analysis of variance and analysis of covariance were used, and the methodology corrected for the presence of potentially confounding effects. RESULTS: There was a 3-year later age at onset for females (P < .001) and lower rates of negative symptoms (P < .01) and higher depression/anxiety measures (P < .05) at some stages. The age at onset manifested a distribution with a single peak for both genders with a tendency of patients with younger onset having slower advancement through illness stages (P = .001). No significant effects were found concerning duration of illness. DISCUSSION: Our results confirmed a later onset and a possibly more benign course and outcome in females. Age at onset manifested a single peak in both genders, and surprisingly, earlier onset was related to a slower progression of the illness. No effect of duration has been detected. These results are partially in accord with the literature, but they also differ as a consequence of the different starting point of our methodology (a novel staging model), which in our opinion precluded the impact of confounding effects. Future research should focus on the therapeutic policy and implications of these results in more representative samples.

• MeSH
• Diagnostický a statistický manuál mentálních poruch MeSH
• lidé MeSH
• schizofrenie * diagnóza   epidemiologie   MeSH
• věk při počátku nemoci MeSH
• Check Tag
• lidé MeSH
• mužské pohlaví MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• multicentrická studie MeSH

Non-small cell lung carcinoma (NSCLC) represents the majority of lung cancer cases, comprising approximately 85 % of the total. The five-year survival rate for NSCLC patients remains discouragingly low. Recently, immunotherapy has emerged as a promising approach. Nevertheless, only a minority of patients experience considerable benefits from these treatments. This highlights the critical need for effective biomarkers that can predict both patient prognosis and response to immunotherapy. CD8+ T cells play a crucial role in cancer immunotherapy. Their presence within tumours is generally indicative of a favourable prognosis and increased efficacy of immunotherapy. This study was undertaken to identify and authenticate a novel biomarker signature based on CD8+ T-cell marker genes, to prognosticate therapeutic responses in individuals afflicted with NSCLC. This in-depth study was based on a total of 1,200 samples, which included four NSCLC specimens analysed through single-cell RNA sequencing (scRNA-seq), 1,000 NSCLC samples obtained from The Cancer Genome Atlas (TCGA) and 196 NSCLC specimens collected from the GSE37745 cohort. In patients with NSCLC, those presenting a favourable risk profile demonstrated notable elevations in specific immune cells while concurrently exhibiting reductions in other types. CD8+ T cells, with their established role in inducing apoptosis in cancer cells, have emerged as crucial predictors and modulators of treatment strategies for NSCLC patients. The combination of single-cell and bulk RNA sequencing has produced a biomarker signature, emphasizing the CD8+ T cells' crucial role in NSCLC prognosis and treatment.

• MeSH
• CD8-pozitivní T-lymfocyty * imunologie   MeSH
• imunoterapie * metody   MeSH
• lidé středního věku MeSH
• lidé MeSH
• nádorové biomarkery MeSH
• nádory plic * imunologie   terapie   MeSH
• nemalobuněčný karcinom plic * imunologie   terapie   MeSH
• prognóza MeSH
• Check Tag
• lidé středního věku MeSH
• lidé MeSH
• mužské pohlaví MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH

Correct identification of P forms together with their main Fe and Al binding partners in non-calcareous sediments is of crucial importance for evaluation of P cycling in water bodies. In this paper, we assess extraction methods frequently used for this purpose, i.e., a sequential five-step fractionation (water, bicarbonate buffered dithionite solution (BD), NaOH, HCl, nitric-perchloric acid), ascorbate extraction (pH ~7.5), and oxalate extraction (pH ~3), directly on a range of laboratory prepared Fe and Al minerals enriched with adsorbed P. Extraction selectivity and efficiency for particular P, Fe and Al forms were also verified by specific combinations of these extraction methods applied on freshwater sediment samples. In the sequential fractionation, BD was highly effective in dissolving both amorphous and crystalline Fe (hydr)oxides and the associated P, while neither FeS nor Al (hydr)oxides were dissolved. The following NaOH extraction effectively dissolved both amorphous and crystalline Al (hydr)oxides. The high solubilizing power of BD and NaOH to dissolve crystalline Fe and Al oxides that have only a small P-sorption ability prevents the use of resulting Fe/P and Al/P ratios as simple predictors of total P sorption capacity of sediments and soils. Ascorbate non-selectively extracted small proportions of FeS and amorphous Fe and Al (hydr)oxides, but significant amounts of adsorbed P, which hinders its use for the characterization of P forms in non-calcareous sediments. Similar nonselective characteristics were found for oxalate extractions. As oxalate extracts most of the adsorbed phosphate, it is not possible to use it unambiguously to determine specific Fe/P and Al/P ratios of active complexes. However, this method is convenient (and more selective than NaOH step in the sequential fractionation) for the determination of amorphous Al (hydr)oxides.

• MeSH
• adsorpce MeSH
• chemická frakcionace metody   MeSH
• fosfor analýza   chemie   izolace a purifikace   MeSH
• geologické sedimenty chemie   MeSH
• hydroxid sodný chemie   MeSH
• indikátory a reagencie chemie   MeSH
• kvalita vody MeSH
• kyselina oxalová chemie   MeSH
• minerály analýza   chemie   izolace a purifikace   MeSH
• reprodukovatelnost výsledků MeSH
• rozpustnost MeSH
• sladká voda chemie   MeSH
• sloučeniny hliníku analýza   chemie   izolace a purifikace   MeSH
• sloučeniny železa analýza   chemie   izolace a purifikace   MeSH
• vodní zdroje analýza   MeSH
• Publikační typ
• časopisecké články MeSH
• hodnotící studie MeSH
• práce podpořená grantem MeSH
• srovnávací studie MeSH
• Geografické názvy
• Česká republika MeSH

• Klíčová slova
• single sample predictors, molekulární subtypizace,
• MeSH
• diagnostické techniky molekulární metody   MeSH
• lidé MeSH
• nádory prsu * diagnóza   genetika   klasifikace   MeSH
• prognóza MeSH
• Check Tag
• lidé MeSH
• ženské pohlaví MeSH

BACKGROUND: Patients, especially inpatients, with spinal cord lesions and disorders (SCI/D) have an elevated risk of recurrent urinary tract infections with multidrug resistant (MDR) bacteria. This study evaluated antimicrobial resistance and the prevalence of multidrug resistance and determined the risk factors for multidrug resistance. METHODS: In this retrospective cohort study, urine culture results were used to calculate the antimicrobial resistance rate and the incidence of infection with MDR bacteria in the SCI/D population. MDR was defined as acquired nonsusceptibility to at least one agent from three or more antimicrobial categories. The cohort included 402 inpatients from 2013 to 2020, with 1385 urine isolates. We included only the first isolate; duplicate isolates, defined as positive cultures of the same strain within 14 days, were excluded from the evaluation. RESULTS: The most common MDR strains were Klebsiella spp. (29%) and Escherichia coli (24%). MDR isolates were detected in 50% of the samples and extended spectrum beta-lactamase (ESBL)-producing isolates were detected in 26%, while carbapenem resistance was found in 0.1%. Significantly higher rates of infection with MDR bacteria were identified in groups of patients with indwelling urethral/suprapubic catheters (p = 0.003) and severity scores of C1-C4/AIS A-C (p = 0.01). We identified age (OR: 0.99, 95% CI; 0.98-0.99, p = 0.000), sex (OR: 1.55, 95% CI; 1.16-2.06, p = 0.003), management with urethral/suprapubic catheters (OR: 2.76, 95% CI; 2.04-3.74, p = 0.000), and spontaneous voiding (OR: 1.84, 95% CI; 1.03-3.29, p = 0.038) as independent predictors of multidrug resistance in our study population. CONCLUSIONS: We identified a high antibiotic resistance rate and an increasing prevalence of infection with MDR bacteria in the SCI/D inpatient population. Particular attention should be given to bladder management, with an emphasis on minimizing the use of indwelling catheters.

• MeSH
• antibakteriální látky farmakologie   terapeutické užití   MeSH
• beta-laktamasy MeSH
• Escherichia coli MeSH
• hospitalizovaní pacienti * MeSH
• lidé MeSH
• mikrobiální testy citlivosti MeSH
• mnohočetná bakteriální léková rezistence MeSH
• poranění míchy * komplikace   farmakoterapie   epidemiologie   MeSH
• prevalence MeSH
• retrospektivní studie MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH

INTRODUCTION: This study primarily sought to evaluate the risk factors for toxic megacolon development and treatment outcomes in Clostridium difficile-positive COVID-19 patients, secondarily to determining predictors of survival. METHODS: During the second COVID-19 wave (May 2020 to May 2021), we identified 645 patients with confirmed COVID-19 infection, including 160 patients with a severe course in the intensive care unit. We selected patients with Clostridium difficile infection (CDI) (31 patients) and patients with toxic megacolon (9 patients) and analyzed possible risk factors. RESULTS: Patients who developed toxic megacolon had a higher incidence (without statistical significance, due to small sample size) of cancer and chronic obstructive pulmonary disease, a higher proportion of them required antibiotic treatment using cephalosporins or penicillins, and there was a higher rate of extracorporeal circulation usage. C-reactive protein (CRP) and interleukin-6 values showed significant differences between the groups (CRP [median 126 mg/L in the non-toxic megacolon cohort and 237 mg/L in the toxic megacolon cohort; p = 0.037] and interleukin-6 [median 252 ng/L in the group without toxic megacolon and 1127 ng/L in those with toxic megacolon; p = 0.016]). As possible predictors of survival, age, presence of chronic venous insufficiency, cardiac disease, mechanical ventilation, and infection with Candida species were significant for increasing the risk of death, while corticosteroid and cephalosporin treatment and current Klebsiella infection decreased this risk. CONCLUSIONS: More than ever, the COVID-19 pandemic required strong up-to-date treatment recommendations to decrease the rate of serious in-hospital complications. Further studies are required to evaluate the interplay between COVID-19 and CDI/toxic megacolon.

• Publikační typ
• časopisecké články MeSH