DFT study of water on graphene: Synergistic effect of multilayer p-doping.

Recent experiments related to a study concerning the adsorption of water on graphene have demonstrated the p-doping of graphene, although most of the ab initio calculations predict nearly zero doping. To shed more light on this problem, we have carried out van der Waals density functional theory calculations of water on graphene for both individual water molecules and continuous water layers with coverage ranging from one to eight monolayers. Furthermore, we have paid attention to the influence of the water molecule orientation toward graphene on its doping properties. In this article, we present the results of the band structure and the Bader charge analysis, showing the p-doping of graphene can be synergistically enhanced by putting 4-8 layers of an ice-like water structure on graphene having the water molecules oriented with oxygen atoms toward graphene.

Density functional study of gallium clusters on graphene: electronic doping and diffusion.

Motivated by experimental results on transport properties of graphene covered by gallium atoms, the density functional theory study of clustering of gallium atoms on graphene (up to a size of 8 atoms) is presented. The paper explains a rapid initial increase of graphene electron doping by individual Ga atoms with Ga coverage, which is continually reduced to zero, when bigger multiple-atom clusters have been formed. According to density functional theory calculations with and without the van der Waals correction, gallium atoms start to form a three-dimensional cluster from five and three atoms, respectively. The results also explain an easy diffusion of Ga atoms while forming clusters caused by a small diffusion barrier of 0.11 eV. Moreover, the calculations show this barrier can be additionally reduced by the application of an external electric field, which was simulated by the ionization of graphene. This effect offers a unique possibility to control the cluster size in experiments only by applying a gate-voltage to the graphene in a field-effect transistor geometry and thereby without growth temperature assistance.

Granular Cell Tumour in a California Kingsnake (Lampropeltis californiae).

A 21-year-old female California kingsnake (Lampropeltis californiae) was presented to the University of Veterinary Medicine, Vienna, Austria, with a space-occupying mass in the caudal abdomen. Following clinical, radiological and sonographical evaluation the mass was removed surgically. Histopathology and transmission electron microscopy confirmed the diagnosis of a granular cell tumour, but immunohistochemical labelling for a range of markers was negative. This lesion is rare in mammals and birds, but has not been reported previously in a reptile.

Rapid screening test of most frequent BRCA1/BRCA2 pathogenic variants in the NGS era.

The average risk of breast cancer in general Slovak population of women is 4-5% and the risk of ovarian cancer is 2%. Probability of breast/ovarian cancer development is higher in individuals carrying a causative germline DNA variant in BRCA1 or BRCA2 gene responsible for hereditary breast/ovarian cancer (HBOC). Although a major proportion of inherited breast/ovarian cancers are due to the mentioned causal mutations, a number of new genes have emerged. Here we describe a rapid, multiplex and comprehensive approach for the detection of pathogenic variants in BRCA1 and BRCA2 genes which most frequently occur in Slovak HBOC population. Analysis comprises the combination of mutation specific methods. Fluorescent PCR amplification followed by fragment analysis for detection of insertions/deletions in exon 11 of BRCA1 gene. Second method is SNaPshot analysis for detection of the most frequent missense and ins/del variants in exons 2, 5, 13, 20 of BRCA1 and exons 11, 23 and 25 of BRCA2 gene. Altogether, we have analyzed 687 samples, 86 (12.5%) in group 1, which fulfilled indication criteria based on the positive family/personal history. Group 2 involved 601 (87.5%) cases, who did not meet the indication criteria and only the screening test was recommended. Using the combined approach, we have identified 47 mutated samples (6.8%), 40 in group 1 (46.5%) and 7 in group 2 (1.1%). However, the presented screening test would not provide complex results of BRCA1/2 gene analysis, it offers testing accessible to a broader spectrum of individuals under the threshold of indication for whole gene analysis. This approach may provide valuable information even in the NGS analysis era.

Electronic transport properties of graphene doped by gallium.

In this work we present the effect of low dose gallium (Ga) deposition (<4 ML) performed in UHV (10-7 Pa) on the electronic doping and charge carrier scattering in graphene grown by chemical vapor deposition. In situ graphene transport measurements performed with a graphene field-effect transistor structure show that at low Ga coverages a graphene layer tends to be strongly n-doped with an efficiency of 0.64 electrons per one Ga atom, while the further deposition and Ga cluster formation results in removing electrons from graphene (less n-doping). The experimental results are supported by the density functional theory calculations and explained as a consequence of distinct interaction between graphene and Ga atoms in case of individual atoms, layers, or clusters.

Evaluation of expression profiles of microRNAs and two target genes, FOXO3a and RUNX2, effectively supports diagnostics and therapy predictions in breast cancer.

Breast cancer (BC) including its progression into bone metastasis is a complex process involving changes in gene expression and function of both, microRNAs (miRNAs) and their target genes. Deregulation of miRNAs has been described as a crucial factor responsible for the initiation and progression of BC, and specific miRNA expression profiles have been found to be associated with particular disease states, histological tumor types, and BRCA1/2 or HER status. BRCA1 tumor suppressor is involved in DNA damage response and repair and epigenetically controls miR-155 expression and its pre-cancerous potential. MiR-155 targets 3´UTR region of multiple components of the pro-oncogenic signaling cascades, including FOXO3a tumor suppressor and RUNX2 transcription factor regulating metastatic potential in BC. We employed qRT-PCR to determine expression level and examine possible regulatory role of selected miRNAs (miR-17, miR-18a, miR-19a, miR-20a, miR-21, miR-27a and miR-155) and their impact on expression modulation of FOXO3a and RUNX2 in peripheral blood mononuclear cells (PBMCs) in healthy individuals, in women carrying BRCA1 mutations with no disease manifestation, in women carrying BRCA1 mutations after tumor resection and therapy and in women with BC of unknown BRCA1 status in acute stage before tumor resection. Our results showed significant increase of miR-17, miR-19a, miR-21, miR-27, miR-155 and RUNX2 expression in PBMCs in BRCA1 patients and patients in acute stage, while FOXO3a expression was significantly decreased in these patients. MiR-18a and miR-20a expression was not affected. We propose that expressional changes reported in this study could provide significant additive information for early BC diagnosis, disease development prediction and therapy outcome monitoring.

The value of SHOX2 methylation test in peripheral blood samples used for the differential diagnosis of lung cancer and other lung disorders.

Methylation of the cytosine residues within the CpG dinucleotides plays an important role in the fundamental cellular processes, human diseases and even cancer. The DNA methylation represents a very stable sign and therefore may be used as a valuable marker for cancer screening. Epigenetic cancer biomarkers are independent of classical morphology and thus show extensive potential to overcome the limitations of cytology. Several epigenetic cancer markers have been reported to be detectable in body fluids such as bronchial aspirate, sputum, plasma and serum.Short stature homeobox gene 2 (SHOX2) encodes a homeo-domain transcription factor, which has been identified as a close homologue of the SHOX gene and both genes are involved in skeletogenesis and heart development. Methylation of SHOX2 gene has been shown to be present at high prevalence in carcinomas of lung, however may also be used to identify other tumour entities.In the presented study, we have compared suitability of two types of material associated with lung cancer for the detection of SHOX2 methylation. We have confirmed that methylation of SHOX2 gene represents reliable marker of lung malignancies. The parallel tests in the blood plasma revealed that it may represent a good alternative material for testing of the SHOX2 methylation, making the test available to patients who are unable to undergo bronchoscopy.

PTEN sequence analysis in endometrial hyperplasia and endometrial carcinoma in Slovak women.

Phosphatase and tensin homolog (PTEN) is a protein that acts as a tumor suppressor by dephosphorylating the lipid second messenger phosphatidylinositol 3,4,5-trisphosphate. Loss of PTEN function has been implicated in the pathogenesis of a number of different tumors, particularly endometrial carcinoma (ECa). ECa is the most common neoplasia of the female genital tract. Our study evaluates an association between the morphological appearance of endometrial hyperplasia and endometrial carcinoma and the degree of PTEN alterations. A total of 45 endometrial biopsies from Slovak women were included in present study. Formalin-fixed and paraffin-embedded tissue samples with simple hyperplasia (3), complex hyperplasia (5), atypical complex hyperplasia (7), endometrioid carcinomas G1 (20) and G3 (5), and serous carcinoma (5) were evaluated for the presence of mutations in coding regions of PTEN gene, the most frequently mutated tumor suppressor gene in endometrial carcinoma. 75% of the detected mutations were clustered in exons 5 and 8. Out of the 39 mutations detected in 24 cases, 20 were frameshifts and 19 were nonsense, missense, or silent mutations. Some specimens harboured more than one mutation. The results of current study on Slovak women were compared to a previous study performed on Polish population. The two sets of results were similar.

Molecular analysis of EGFR gene in different types of tumor material from NSCLC patients.

Lung carcinoma is the most frequently occurring cancer worldwide and the Non-small Cell Lung Cancer (NSCLC) subtype represents 80% of all diagnosed cases. Epidermal growth factor receptor (EGFR) has an important dual role in NSCLC patients. On one hand, EGFR is frequently mutated in many types of tumors, which leads to deregulation of important downstream pathways including those affecting cell proliferation, differentiation and migration. On the other hand, presence of certain activating mutation leads to increased sensitivity of EGFR to tyrosine kinase inhibitors (TKIs) treatment. Detection of these mutations is essential for identification of NSCLC patients who would profit from such therapy. However, due to the nature of available tumor material and the relatively high number of mutation hot spots, such DNA analysis may be challenging and time consuming. Here we present an approach combining direct sequencing and SNaPshot assay for identification of EGFR mutations in FFPE tissues as well as in rarely analyzed cytological smears. Using this strategy on the set of 450 tested NSCLC samples; we have identified 29 activating mutations and 14 variants, which might be interesting in predicting the efficiency of TKI therapy.

[Treatment strategies of the colorectal anastomosis stricture]. / Strategie lécby striktury kolorektální anastomózy.

INTRODUCTION: The treatment of the stenoses of colorectal anastomoses represents a difficult area of colonic surgery. This is partly connected to the introduction of staplers and an increasing amount of sphincter-preserving surgeries. At our clinic, we solve the stenoses of colorectal anastomoses using a surgical rectoscope with a good effect. MATERIAL AND METHODS: We analysed retrospectively a group of 27 patients with benign stenosis of colorectal anastomosis of the medial and upper rectum who underwent surgery at our clinic in the period between January 2004 and December 2011. From the total amount of 27 patients, in 23 patients the stenosis was caused by the dehiscence of anastomosis, and in 4 patients the stenosis had a different etiology. RESULTS: In the group of 27 patients, in 14 patients the stenosis of colorectal anatomosis was solved radiologically using a high pressure balloon. Total of 13 patients underwent surgery, in 10 of them we used the surgical rectoscope and 3 patients underwent an open abdominal procedure. CONCLUSION: The first method of choice in treatment of the stenoses of the colorectal anastomoses is a balloon dilatation. If this is not successful we can use the surgical rectoscope as a minimally invasive though effective and safe method.

Interface-induced room-temperature ferromagnetism in hydrogenated epitaxial graphene.

We show ferromagnetic properties of hydrogen-functionalized epitaxial graphene on SiC. Ferromagnetism in such a material is not directly evident as it is inherently composed of only nonmagnetic constituents. Our results nevertheless show strong ferromagnetism with a saturation of 0.9µ(B)/hexagon projected area, which cannot be explained by simple magnetic impurities. The ferromagnetism is unique to hydrogenated epitaxial graphene on SiC, where interactions with the interfacial buffer layer play a crucial role. We argue that the origin of the observed ferromagnetism is governed by electron correlation effects of the narrow Si dangling bond states in the buffer layer exchange coupled to localized states in the hydrogenated graphene layer. This forms a quasi-three-dimensional ferromagnet with a Curie temperature higher than 300 K.

[The benefits of centralization of care for patients with acute upper gastrointestinal bleeding]. / Prínos centralizace péce o pacienty s akutním krvácením do horního trávicího traktu.

INTRODUCTION: Acute upper gastrointestinal bleeding still remains one of the serious conditions that require a rapid diagnostic and therapeutic intervention. Such procedure is highly dependent on good interdisciplinary cooperation, which, when centralized, may positively influence mortality and economic costs. OBJECTIVE: To determine the benefits of centralization of care provided to patients with acute bleeding in the upper gastrointestinal tract. PATIENTS AND METHODS: A total of 632 patients with acute bleeding were enrolled in the study at two different health-care establishments of the same type, however with a different organisation of care. We have evaluated the influence of the organisation of care on the length of hospitalization stay, mortality and economic costs. RESULTS: Centralized treatment significantly shortens the interval from hospital admission to endoscopic examination and leads to a reduction in mortality, although not statistically significant. On the other hand, it does not affect the length of hospitalization, the distribution of patients between internal and surgical departments, and provides no guarantee of lower economic costs. Many other factors play an important role in that respect. It seems, that the importance of centralization plays the main role especially in the pre-hospital and early hospital period, when it accelerates and simplifies the diagnostic and therapeutic procedure.

DNA analysis of Y chromosomal AZF region in Slovak population with fertility disorders.

BACKGROUND: The Y chromosome is characterized by a low number of functional genes, relatively high number of repetitive sequences and the ability of recombination purely by short arms of telomeres PAR1 and PAR2. The long arm contains an AZF region with genes participating in spermatogenesis. Microdeletions of three subregions, namely AZFa,b,c and their mutual combinations are responsible for male infertility and the resulting azoospermia and oligospermia. OBJECTIVES: The aim of this study based on evaluating 822 patients during a period of ten years was to analyse types of microdeletions in men with fertility disorders in Slovakia. METHODS: For detecting the microdeletions in Y-chromosomal AZF region and for identifying the Y-specific sequences we used PCR while using three different sets of sY sequences. REPORTS: We reported 38 cases of deletions in AZF region, namely 18 cases when using the first set of sequences, 12 cases when using the second set, and finally 8 cases when using the third set. When using the last set of sequences according to the European Academy of Andrology and European Molecular Genetics Quality Network, we detected deletions only in patients with azoospermia. In addition to deletions in each of AZF a,b,c subregions we recorded also a complete deletion of the whole AZF region. In the AZFa subregion, we recorded a deletion of sequence sY86. CONCLUSION: The study has confirmed that the detection of microdeletions of AZF region is significant from the diagnostic and prognostic views (Tab. 5, Ref. 21). Full Text in free PDF www.bmj.sk.

[The expected worldwide burden of oesophagus, stomach and colorectal cancers]. / Ocekávaná zátez nádory jícnu, zaludku a kolorekta ve svete.

According database of Globocan 2008 of total 482 thousand worldwide new esophagel cancers are reported 16.9% cases in more developed and 83.1% in less developed regions, 6.9% in EU, 2.7% in the Eastern Europe; of total 989 thousand new stomach cancers are reported 27.8% in more developed and 72.2% in less developed regions, 8.4% in EU, 7.4% in the Eastern Europe; of total 1.235 milion new colorectal cancers are reported 59% cases in more developed and 41% in less developed regions, 27% in EU, 10.5% in the Eastern Europe. Of total 59,052 all neoplasms (without skin cancers) were reported 10,439 new cases of these three diagnoses in recent Czech Cancer Registry survey, higher by 595 cases than numbers based in Globocan 2008. However, according to these data the Czech males reached the 3rd order and females the 14th order by their cumulative risk of colorectal cancer in the world. The alarming worldwide numbers of new 4.771 milion of these three diagnoses and 3,137 thousands deaths from them, expected in 2030 with a higher risk in population of less developed regions require greater international cooperation and personal responsibility for improving the life-style, which would be failed the expected statistics.

[DNA analysis on Y chromosomal AZF region deletions in Slovak population]. / DNA analýza AZF oblasti Y chromozómu u Slovákov s poruchou plodnosti.

OBJECTIVE: Study on Y chromosomal AZF region deletions in Slovak population, application of DNA technique. DESIGN: Genetic-prospective study. SETTING: Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University in Bratislava. METHODS: For detecting microdeletions in the Y-chromosomal AZF region in men with fertility disorders and for identifying Y-specific sequences we used the method of polymerase chain reaction (PCR) with using three different sets of sY sequences. For a verification of the specific type of deletion we used also fluorescently labeled kit. RESULTS: Diagnoses of referred patients were divided into 2 groups: azoospermia, oligospermia. In the followed-up group of 822 patients there were 349 patients with azoospermia, 473 patients with oligospermia. Globally we reported 38 cases of deletions in the AZF region of the Y chromosome, i.e. 4.62%. 24 patients with deletion are from the group of patients with azoospermia, i.e. 6.88%, 14 patients are from the group of patients with oligospermia (2.95%). Considering particular types of deletions we recorded deletions in each region, AZFa, AZFb and AZFc, combinated AZFbc deletion, but also a complete deletion of the whole AZF region. CONCLUSION: The study confirmed that detection of microdeletions of the AZF region is significant from diagnostic and prognostic view and it pointed out the importance of selection criteria for selecting patients.

[Risk of colorectal carcinoma in a patient with ulcerative colitis]. / Riziko kolorektálního karcinomu v terénu ulcerózní kolitidy.

Colorectal cancer, in patients with ulcerative colitis, is detected in the resected tissue of approximately 5% of patients, according to the literature. In our set of 82 patients operated on between the years 2000-2009, malignancy was confirmed in 9/82 patients (11%). In two young patients, the peroperative findings showed inoperable generalized carcinoma. The greater incidence of malignity is surely associated with inconsistent dispensarization of these patients.

The detection of circulating tumor cells expressing E6/E7 HR-HPV oncogenes in peripheral blood in cervical cancer patients after radical hysterectomy.

The aim of this study was to establish the sensitive, specific and clinically acceptable method for detection of tumor cells (TCs) circulating in peripheral blood (PB) of cervical cancer patients without the clinically detectable risk of disease progression. The 7.5 ml of PB of healthy donor was spiked with 5 to 100 cells from SiHa or HeLa cell lines. The spiked tumor cells were collected without gradient centrifugation, by standard gradient centrifugation or by modified gradient centrifugation combined with immunomagnetic separation using EpCAM antibody with affinity for epithelial cell adhesion molecule. The number of collected TCs was determined by EpCAM-FITC-staining and their viability was detected by nested RT-PCR amplifying E6/E7 HR-HPV 16 or HR-HPV 18 oncogenes. For the technical validation of this approach the TCs separation and RT-PCRs were repeated several times. The recovery of viable TCs was reproducibly higher using modified gradient centrifugation combined with immunomagnetic separation in comparison with standard approach. The recovery of TCs in low number of spiked TCs (range from 5 - 20 TCs in 7.5 ml of PB) using modified gradient centrifugation was not reproducible. The recovery of TCs in higher number of spiked TCs (25 TCs and more in 7.5 ml of PB) was reproducible with average recovery about 50 %. The sensitivity of nested RT-PCR amplifying E6/E7 oncogenes was decisively influenced by the number of recovered TCs and the amount of cDNA introduced to RT-PCR, as well. Using this approach we were allowed to detect circulating TCs (CTCs) in cervical cancer patients without metastases, thus this procedure might become a tool to early estimation of disease progression. According to our knowledge, this is the first report describing the use of EpCAM antibody for CTCs detection in cervical cancer patients.

Genetic analysis of KRAS mutation status in metastatic colorectal cancer patients.

Colorectal carcinoma (CRC) represents a serious problem worldwide: in the Slovak republic are diagnosed about 2600 new CRC cases annually and its incidence is increasing. Colorectal cancer patients may succumb to the disease because of local recurrence or local formation of metastasis. Therefore, it is necessary to modulate therapeutic algorithm with new methods, leading to early diagnostic of CRC or changing the existing therapeutic procedures. Recent progresses have been made in understanding of EGFR pathway involved in CRC carcinogenesis, especially the role of Ras protein. Mutations in KRAS oncogene are frequently found in human cancers, particularly colorectal, pancreatic, billiary tract and lung tumors. The presence of the KRAS mutations in metastatic colorectal cancer patients correlates with lack of response to the certain epidemal growth factor receptor (EGFR) inhibitor therapies, such as Panitumumab and Cetuximab. Consequently, screening for KRAS mutations status may be used as a prognostic marker, because the CRC patients with KRAS positive tumors have a worse prognosis. The aim of our study was to establish the methods for rapid and sensitive detection of KRAS mutation status in formalin fixed paraffin embedded (FFPE) tissues DNA. We applied Real Time PCR analysis (TheraScreen KRAS Mutation Test Kit) and sequencing analysis (optimised for the analysis of FFPE tissues) to detect somatic mutations in codon 12 and 13 of KRAS gene. Both methods were used concurrently in the panel of DNA isolated from 25 colorectal FFPE tissues tumor. The positive or negative results from all 25 samples were identified by both methods independently. The KRAS mutations were presented in 8 of 25 patients (32%). Our results demonstrate that the Real Time PCR analysis can be used for detection of somatic KRAS mutations in FFPE clinical samples. However, we also recognize that the sequencing analysis of approximately 200bp amplicons may be used for mutations status screening, but with care of method sensitivity.

[Pancreaticopleural fistula]. / Pankreatikopleurální pístele.

Pancreatic diseases are often accompanied by pleuropulmonal complications. Acute pancreatitis may induce a number of various pathological findings in respiratory tract including hypoxemia, decrease of transfer-factor (DLCO), decrease of transfer-coefficient (DLCO/VO), decrease in forced expiratory flow 25%- 75% of forced vital capacity (FEF25-75%), elevated and/or immobile diaphragm, basal atelectasis, unilateral or bilateral pulmonary infiltrations, mediastinal pseudocyst and pleural effusion. Acute respiratory distress syndrome (ARDS) is the most dangerous complication of acute pancreatitis. Large, recurrent pleural effusion is sometimes present in chronic pancreatitis, typically with a very high concentration of amylase in pleural fluid. Pancreaticopleural fistula (PPF) is the most common cause of this type of pleural effusion. We describe a study group of 3 patients with PPF and pleural effusion, their clinical symptoms, diagnostics and management.