Joint analysis of histopathology image features and gene expression in breast cancer

BACKGROUND Genomics and proteomics are nowadays the dominant techniques for novel biomarker discovery. However, histopathology images contain a wealth of information related to the tumor histology, morphology and tumor-host interactions that is not accessible through these techniques. Thus, integrating the histopathology images in the biomarker discovery workflow could potentially lead to the identification of new image-based biomarkers and the refinement or even replacement of the existing genomic and proteomic signatures. However, extracting meaningful and robust image features to be mined jointly with genomic (and clinical, etc.) data represents a real challenge due to the complexity of the images. RESULTS We developed a framework for integrating the histopathology images in the biomarker discovery workflow based on the bag-of-features approach - a method that has the advantage of being assumption-free and data-driven. The images were reduced to a set of salient patterns and additional measurements of their spatial distribution, with the resulting features being directly used in a standard biomarker discovery application. We demonstrated this framework in a search for prognostic biomarkers in breast cancer which resulted in the identification of several prognostic image features and a promising multimodal (imaging and genomic) prognostic signature. The source code for the image analysis procedures is freely available. CONCLUSIONS The framework proposed allows for a joint analysis of images and gene expression data. Its application to a set of breast cancer cases resulted in image-based and combined (image and genomic) prognostic scores for relapse-free survival

Prognostic Factors of Early Morphological Response to Treatment with Ranibizumab in Patients with Wet Age-Related Macular Degeneration

Aim. To assess the significance of age, gender, baseline best corrected visual acuity, baseline macula thickness, and type and size of choroidal neovascularization in early morphological therapeutic response to ranibizumab treatment in patients with the wet form of age related macular degeneration. Methods. From 09/2008 to 06/2013 we evaluated 1153 newly diagnosed, treatment naive patients treated with ranibizumab. Based on the morphological findings in the macula following the initial 3 injections of ranibizumab, the patients were divided into two groups based on active and inactive choroidal neovascularization. Results. After the initial 3 injections of ranibizumab, we examined the sample of 841 eyes with active CNV and 312 eyes with inactive CNV. In the inactive group, we found a statistically higher proportion of occult CNV (P less than 0.001) and lower incidence of CNV greater than 5DA (P less than 0.001) compared with the active group. We found no statistically significant difference in age, gender, baseline best corrected visual acuity, or baseline macula thickness between the inactive and active groups. Conclusion. Occult CNV and CNV smaller than 5DA are optimistic factors for a better morphological therapeutic response at the beginning of ranibizumab treatment.Cíl. Zjistit vliv věku, pohlaví, zrakové ostrosti a tloušťky makuly na počátku léčby, typu a velikosti choroidální neovaskularizace na časnou morfologickou odpověď u pacientů s vlhkou věkem podmíněnou makulární degenerací. Metodika. Od 09/2008 do 06/2013 jsme zhodnotili výsledky léčby ranibizumabem u 1153 nově diagnostikovaných, předtím neléčených pacientů. Na základě morfologické odpovědi v makule po 3 injekcích ranibizumabu byli pacienti rozděleni do dvou skupin na základě aktivity nebo inaktivity choroidální neovaskularizace. Výsledky. Po 3 úvodních injekcích ranibizumabu jsme vyšetřili skupinu 841 očí s aktivní CNV a 312 očí s inaktivní CNV. V inaktivní skupině jsme našli statisticky vyšší počet okultních CNV (P less than 0.001) a nižší incidenci okultních CNV menších než 5DA (P less than 0.001) v porovnání s aktivní skupinou. Nenašli jsme statisticky signifikantní rozdíl u věku, pohlaví, zrakové ostrosti a tloušťky makuly na počátku léčby mezi inaktivní a aktivní skupinou. Závěr. Okultní CNV a CNV menší než 5DA je jsou faktory prognosticky prognosticky příznivější morfologické a terapeutické odpovědi na počátku léčby ranibizumabem.Aim. To assess the significance of age, gender, baseline best corrected visual acuity, baseline macula thickness, and type and size of choroidal neovascularization in early morphological therapeutic response to ranibizumab treatment in patients with the wet form of age related macular degeneration. Methods. From 09/2008 to 06/2013 we evaluated 1153 newly diagnosed, treatment naive patients treated with ranibizumab. Based on the morphological findings in the macula following the initial 3 injections of ranibizumab, the patients were divided into two groups based on active and inactive choroidal neovascularization. Results. After the initial 3 injections of ranibizumab, we examined the sample of 841 eyes with active CNV and 312 eyes with inactive CNV. In the inactive group, we found a statistically higher proportion of occult CNV (P less than 0.001) and lower incidence of CNV greater than 5DA (P less than 0.001) compared with the active group. We found no statistically significant difference in age, gender, baseline best corrected visual acuity, or baseline macula thickness between the inactive and active groups. Conclusion. Occult CNV and CNV smaller than 5DA are optimistic factors for a better morphological therapeutic response at the beginning of ranibizumab treatment

Nationwide increases in anti-SARS-CoV-2 IgG antibodies between October 2020 and March 2021 in the unvaccinated Czech population

Background: The aim of the nationwide prospective seroconversion (PROSECO) study was to investigate the dynamics of anti-SARS-CoV-2 IgG antibodies in the Czech population. Here we report on baseline prevalence from that study. Methods: The study included the first 30,054 persons who provided a blood sample between October 2020 and March 2021. Seroprevalence was compared between calendar periods, previous RT-PCR results and other factors. Results: The data show a large increase in seropositivity over time, from 28% in October/November 2020 to 43% in December 2020/January 2021 to 51% in February/March 2021. These trends were consistent with government data on cumulative viral antigenic prevalence in the population captured by PCR testing – although the seroprevalence rates established in this study were considerably higher. There were only minor differences in seropositivity between sexes, age groups and BMI categories, and results were similar between test providing laboratories. Seropositivity was substantially higher among persons with history of symptoms (76% vs. 34%). At least one third of all seropositive participants had no history of symptoms, and 28% of participants with antibodies against SARS-CoV-2 never underwent PCR testing. Conclusions: Our data confirm the rapidly increasing prevalence in the Czech population during the rising pandemic wave prior to the beginning of vaccination. The difference between our results on seroprevalence and PCR testing suggests that antibody response provides a better marker of past infection than the routine testing program

Epidemiologie, prevence a léčba kolorektálního karcinomu dle dostupných českých a mezinárodních dat

Nádory tlustého střeva a konečníku patří mezi nejčastější onkologické diagnózy. V České republice je každoročně nově diagnostikováno téměř 8 500 pacientů s kolorektálním karcinomem a přibližně 3 900 osob tomuto onemocnění každým rokem podlehne. Celková prevalence přesáhne v roce 2012 hranici 55 000 osob. Společenské, etické i ekonomické důsledky vyplývající z takto vysoké zátěže jsou zřejmé. Publikace „Epidemiologie, prevence a léčba kolorektálního karcinomu dle dostupných českých a mezinárodních dat“ přináší ucelený přehled epidemiologické a léčebné zátěže české populace touto chorobou a věnuje se krátkodobým a dlouhodobým predikcím dalšího vývoje. Situace je rovněž hodnocena v mezinárodním srovnání, neboť v hodnotách incidence a mortality kolorektálního karcinomu obsazuje ČR přední příčky evropských i světových statistik. Z mezinárodních studií však také vyplývá pozitivní poznatek, že většině nádorů tlustého střeva a konečníku lze předejít účinnou prevencí. Kromě primární prevence je zde hlavním nástrojem organizovaný populační screening, který je založen na testech krvácení do stolice a na kolonoskopii. Otázkám prevence a výsledkům screeningu kolorektálního karcinomu jsou v publikaci věnovány zvláštní kapitoly. Ačkoli nejnovější data dokládají rostoucí výkonnost českého screeningu, celkově dosažené pokrytí populace bohužel stále není dostatečné. To platí pro včasný záchyt kolorektálního karcinomu obecně, neboť v ČR je setrvale téměř 50 % nových onemocnění diagnostikováno v pokročilých klinických stadiích, a tedy s výrazně sníženou šancí na vyléčení nebo dlouhodobé přežití pacienta. Publikace rovněž hodnotí přežití dosahované u českých pacientů jakožto zásadní ukazatel výsledků léčebné péče, u kterého v posledních 15 letech zaznamenáváme statisticky významné zlepšení. Pravděpodobnost 5letého relativního přežití je u včasně diagnostikovaného kolorektálního karcinomu v klinickém stadiu i vyšší než 88%. Tato čísla opět potvrzují nutnost účinné prevence a posílení screeningu tohoto preventabilního onemocnění. V tomto směru má publikace ambici informovat odbornou i laickou veřejnost, a proto věnuje značný prostor přehledu dostupných informačních zdrojů.The book aims to inform expert and general public about epidemiology of colorectal carcinoma in the Czech Republic and priorities resulting from high population burden for prevention, diagnostics, and treatment of this severe disease. A number of invited experts assess selected information sources that representatively describe performance and quality of preventive programmes and results of CRC treatment in the Czech Republic

Estimating the number of colorectal cancer patients treated with anti-tumour therapy in 2015: the analysis of the Czech National Cancer Registry

<p>Abstract</p> <p>Background</p> <p>Colorectal cancer (CRC) represents a serious health care problem in the Czech Republic, introducing a need for a prospective modelling of the incidence and prevalence rates. The prevalence of patients requiring anti-tumour therapy is also of great importance, as it is directly associated with planning of health care resources.</p> <p>Methods</p> <p>This work proposes a population-based model for the estimation of stage-specific prevalence of CRC patients who will require active anti-tumour therapy in a given year. Its applicability is documented on records of the Czech National Cancer Registry (CNCR), which is used to estimate the number of patients potentially treated with anti-tumour therapy in the Czech Republic in 2015.</p> <p>Results</p> <p>Several scenarios are adopted to cover the plausible development of the incidence and survival rates, and the probability of an anti-tumour therapy initiation. Based on the scenarios, the model predicts an increase in CRC prevalence from 13% to 30% in comparison with the situation in 2008. Moreover, the model predicts that 10,074 to 11,440 CRC patients will be indicated for anti-tumour therapy in the Czech Republic in 2015. Considering all patients with terminal cancer recurrence and all patients primarily diagnosed in stage IV, it is predicted that 3,485 to 4,469 CRC patients will be treated for the metastatic disease in 2015, which accounts for more than one third (34-40%) of all CRC patients treated this year.</p> <p>Conclusions</p> <p>A new model for the estimation of the number of CRC patients requiring active anti-tumour therapy is proposed in this paper. The model respects the clinical stage as the primary stratification factor and utilizes solely the population-based cancer registry data. Thus, no specific hospital data records are needed in the proposed approach. Regarding the short-term prediction of the CRC burden in the Czech Republic, the model confirms a continuous increase in the burden that must be accounted for in the future planning of health care in the Czech Republic.</p

Bell-inequality violation with "thermal" radiation

The model of a quantum-optical device for a conditional preparation of entangled states from input mixed states is presented. It is demonstrated that even thermal or pseudo-thermal radiation can be entangled in such a way, that Bell-inequalities are violated

The FLUXNET2015 dataset and the ONEFlux processing pipeline for eddy covariance data

The FLUXNET2015 dataset provides ecosystem-scale data on CO2, water, and energy exchange between the biosphere and the atmosphere, and other meteorological and biological measurements, from 212 sites around the globe (over 1500 site-years, up to and including year 2014). These sites, independently managed and operated, voluntarily contributed their data to create global datasets. Data were quality controlled and processed using uniform methods, to improve consistency and intercomparability across sites. The dataset is already being used in a number of applications, including ecophysiology studies, remote sensing studies, and development of ecosystem and Earth system models. FLUXNET2015 includes derived-data products, such as gap-filled time series, ecosystem respiration and photosynthetic uptake estimates, estimation of uncertainties, and metadata about the measurements, presented for the first time in this paper. In addition, 206 of these sites are for the first time distributed under a Creative Commons (CC-BY 4.0) license. This paper details this enhanced dataset and the processing methods, now made available as open-source codes, making the dataset more accessible, transparent, and reproducible.Peer reviewe

Changing geographical patterns and trends in cancer incidence in children and adolescents in Europe, 1991–2010 (Automated Childhood Cancer Information System): a population-based study

Background: A deceleration in the increase in cancer incidence in children and adolescents has been reported in several national and regional studies in Europe. Based on a large database representing 1·3 billion person-years over the period 1991–2010, we provide a consolidated report on cancer incidence trends at ages 0–19 years. Methods: We invited all population-based cancer registries operating in European countries to participate in this population-based registry study. We requested a listing of individual records of cancer cases, including sex, age, date of birth, date of cancer diagnosis, tumour sequence number, primary site, morphology, behaviour, and the most valid basis of diagnosis. We also requested population counts in each calendar year by sex and age for the registration area, from official national sources, and specific information about the covered area and registration practices. An eligible registry could become a contributor if it provided quality data for all complete calendar years in the period 1991–2010. Incidence rates and the average annual percentage change with 95% CIs were reported for all cancers and major diagnostic groups, by region and overall, separately for children (age 0–14 years) and adolescents (age 15–19 years). We examined and quantified the stability of the trends with joinpoint analyses. Findings: For the years 1991–2010, 53 registries in 19 countries contributed a total of 180 335 unique cases. We excluded 15 162 (8·4%) of 180 335 cases due to differing practices of registration, and considered the quality indicators for the 165 173 cases included to be satisfactory. The average annual age-standardised incidence was 137·5 (95% CI 136·7–138·3) per million person-years and incidence increased significantly by 0·54% (0·44–0·65) per year in children (age 0–14 years) with no change in trend. In adolescents, the combined European incidence was 176·2 (174·4–178·0) per million person-years based on all 35 138 eligible cases and increased significantly by 0·96% (0·73–1·19) per year, although recent changes in rates among adolescents suggest a deceleration in this increasing trend. We observed temporal variations in trends by age group, geographical region, and diagnostic group. The combined age-standardised incidence of leukaemia based on 48 458 cases in children was 46·9 (46·5–47·3) per million person-years and increased significantly by 0·66% (0·48–0·84) per year. The average overall incidence of leukaemia in adolescents was 23·6 (22·9–24·3) per million person-years, based on 4702 cases, and the average annual change was 0·93% (0·49–1·37). We also observed increasing incidence of lymphoma in adolescents (average annual change 1·04% [0·65–1·44], malignant CNS tumours in children (average annual change 0·49% [0·20–0·77]), and other tumours in both children (average annual change 0·56 [0·40–0·72]) and adolescents (average annual change 1·17 [0·82–1·53]). Interpretation: Improvements in the diagnosis and registration of cancers over time could partly explain the observed increase in incidence, although some changes in underlying putative risk factors cannot be excluded. Cancer incidence trends in this young population require continued monitoring at an international level. Funding: Federal Ministry of Health of the Federal German Government, the European Union's Seventh Framework Programme, and International Agency for Research on Cancer