Identification of palaeoenvironments using clustering methods and indicator kriging, case study from Late Miocene sandstones, the Sava depression

Metoda združivanja (engl. clustering) i indikatorski kriging standardni su istraživački alati u rješavanju geoloških problema, a u ovom je radu prikazan primjer identifikacije taložnih okoliša koristeći dva postupka združivanja i indikatorski kriging. Združivanje se temelji na principu Kohonenove neuronske mreže (engl. Kohonen\u27s neural network) i hierarhijskom aglomerativnom združivanju. Rezultatom se može vizualizirati geometrija taložnih podokoliša te interpretirati pomoću vjerojatnosti dobivene za svaki klaster indikatorskim krigingom. U tom se slučaju združivanje može definirati kao metoda za prostorno prepoznavanje uzorka. Istraživano područje prikazano u radu nalazi se u Savskoj depresiji. Sedimenti u polju neogenske su i kvartarne starosti, a analizirane stijene pripadaju gornjem panonu, kada je na sedimentaciju utjecao paleoreljef pred-neogenske podine te mehanizmi turbiditnih sustava.The clustering and Indicator Kriging methods are standard exploration tools in some kind of geological problems and here is presented a case study for the identification of depositional environments using two kinds of clustering processes and the Indicator Kriging. The clustering is based on Kohonen\u27s neural network and hierarchical agglomerative clustering. Through the resulting clusters, the geometry of depositional sub-environment can be visualised by spatial mapping processes and it can be interpreted by the probabilities of clusters through the Indicator Kriging. In this manner the clustering tools can be defined as a spatial pattern recognition method. The research area in the demonstrated study is located in the Sava Depression, Croatia. The field sediments belong to Neogene and Quaternary, and the analysed are Upper Pannonian when sedimentation was accompanied by influence of pre-Neogene basement palaeorelief and the accumulation by turbidity system

Genomic Landscape of Normal and Breast Cancer Tissues in a Hungarian Pilot Cohort

A limited number of studies have focused on the mutational landscape of breast cancer in different ethnic populations within Europe and compared the data with other ethnic groups and databases. We performed whole-genome sequencing of 63 samples from 29 Hungarian breast cancer patients. We validated a subset of the identified variants at the DNA level using the Illumina TruSight Oncology (TSO) 500 assay. Canonical breast-cancer-associated genes with pathogenic germline mutations were CHEK2 and ATM. Nearly all the observed germline mutations were as frequent in the Hungarian breast cancer cohort as in independent European populations. The majority of the detected somatic short variants were single-nucleotide polymorphisms (SNPs), and only 8% and 6% of them were deletions or insertions, respectively. The genes most frequently affected by somatic mutations were KMT2C (31%), MUC4 (34%), PIK3CA (18%), and TP53 (34%). Copy number alterations were most common in the NBN, RAD51C, BRIP1, and CDH1 genes. For many samples, the somatic mutational landscape was dominated by mutational processes associated with homologous recombination deficiency (HRD). Our study, as the first breast tumor/normal sequencing study in Hungary, revealed several aspects of the significantly mutated genes and mutational signatures, and some of the copy number variations and somatic fusion events. Multiple signs of HRD were detected, highlighting the value of the comprehensive genomic characterization of breast cancer patient populations

Emlőrák miatti szervmegtartó műtétek reszekciós széleinek vizsgálata. Multicentrikus retrospektív elemzés = Evaluation of resection margins following breast conserving surgery for breast cancer. A multicentric retrospective study

Absztrakt: Bevezetés: Szervmegtartó műtéttel eltávolított emlőrákoknál fontos a sebészi szélek állapotának vizsgálata, dokumentálása. Ha az eltávolítás nem az épben történik, általában kiegészítő kezelés (ismételt sebészet, tumorágy-besugárzás) javasolt. Célkitűzés: Szervmegtartó műtéttel eltávolított női emlőrákok patológiai leleteinek sebészi szélekre vonatkozó információtartalmának elemzése, a nem ép szélek gyakoriságának felmérése és nem ép szélek esetén a további kezelések gyakoriságának becslése. Módszer: Nyolc magyar patológiai részlegből származó, mellrák miatt végzett szervmegtartó műtéthez tartozó patológiai leletek elemzése, nem ép szél esetén további lokális kezelésre vonatkozó adatok gyűjtésével. Eredmények: Kizárások után 386 leletet elemeztünk. Az ép szél korábbi definíciója (<5 mm) alapján 200, az újabb értelmezés (0 mm) alapján 32 lelet dokumentált nem ép széleket. Lobularis carcinoma esetén gyakoribb volt a szélek pozitivitása, mint nem lobularis rákok esetén. Az épben eltávolított tumorok műtéti anyaga nagyobb tömegű volt. Reoperáció 43/180, illetve 12/22 esetben történt a régi és az új definíció szerinti nem ép szélek esetén. A nem reoperált betegek közül csak 75/137 kapott biztosan külön tumorágy-besugárzást; sok esetben a ’boost’ kezelésről nem állt rendelkezésre információ. Reziduális tumor a reoperált betegek közül csak 15/43-nál igazolódott, 9-nél közülük úgy, hogy a festett szélben a primer műtéti anyagban nem írtak le daganatot. Következtetések: A patológiai leletek sebészi szélre vonatkozó információtartalma nem teljes körű. Az új biztonságos szél definíciója csökkentette a nem ép szél előfordulási gyakoriságát, de alkalmazásakor ép szélek mellett is maradhat reziduális daganat az emlőben, amint azt a reoperációs minták igazolják. Nem épben történő tumoreltávolításkor az esetek egy részében nem történik sem további sebészi kezelés, sem külön tumorágy-besugárzás. Orv Hetil. 2019; 160(26): 1036–1044. | Abstract: Introduction: Breast conserving surgery for breast cancer requires the analysis of surgical margins. If the tumor is not removed completely, additional treatments (reoperation, boost irradiation) are generally recommended. Aim: To analyze the information content of histopathology reports on surgical margins in consecutive cases of breast conservation for invasive female breast cancer, to evaluate the frequency of incompletely removed tumors and to estimate the rate of further treatments after incomplete removal. Method: Analysis of margin related data of consecutive histopathology reports from 8 Hungarian pathology units with locoregional treatment related data in case of unsafe margins. Results: 386 reports were analyzed after exclusions. 200 and 32 cases were identified as having unsafe margins according to the previous (<5 mm) and the new (0 mm) definition of unclear margin, respectively. Unsafe margins were more common with lobular carcinomas. Specimens with clear margins weighed more. Reoperations for unsafe margins were performed in 43/180 and 12/22 cases according to the previous and the new definitions, respectively. Only 75/137 patients without reoperation received boost irradiation of the tumor bed; information on boost radiotherapy was often missing. Residual cancer was identified in 15/43 reoperated patients, of whom 9 had >0 mm margin distance. Conclusions: Some pathology reports lack information on surgical margins. Unsafe margin rates decreased with the new definition. Residual cancer may be left behind in case of clear margins with no ink on tumor. Neither reoperation, nor boost radiotherapy is given to some patients with unclear surgical margins. Orv Hetil. 2019; 160(26): 1036–1044

Characterization of clastic sedimentary enviroments by clustering algorithm and several statistical approaches — case study, Sava Depression in Northern Croatia

Abstract This study demonstrates a method to identify and characterize some facies of turbiditic depositional environments. The study area is a hydrocarbon field in the Sava Depression (Northern Croatia). Its Upper Miocene reservoirs have been proved to represent a lacustrine turbidite system. In the workflow, first an unsupervised neural network was applied as clustering method for two sandstone reservoirs. The elements of the input vectors were the basic petrophysical parameters. In the second step autocorrelation surfaces were used to reveal the hidden anisotropy of the grid. This anisotropy is supposed to identify the main continuity directions in the geometrical analyses of sandstone bodies. Finally, in the description of clusters several parametric and nonparametric statistics were used to characterize the identified facies. Obtained results correspond to the previously published interpretation of those reservoir facies

Neural networks in petroleum geology as interpretation tools

Abstract Three examples of the use of neural networks in analyses of geologic data from hydrocarbon reservoirs are presented. All networks are trained with data originating from clastic reservoirs of Neogene age located in the Croatian part of the Pannonian Basin. Training always included similar reservoir variables, i.e. electric logs (resistivity, spontaneous potential) and lithology determined from cores or logs and described as sandstone or marl, with categorical values in intervals. Selected variables also include hydrocarbon saturation, also represented by a categorical variable, average reservoir porosity calculated from interpreted well logs, and seismic attributes. In all three neural models some of the mentioned inputs were used for analyzing data collected from three different oil fields in the Croatian part of the Pannonian Basin. It is shown that selection of geologically and physically linked variables play a key role in the process of network training, validating and processing. The aim of this study was to establish relationships between log-derived data, core data, and seismic attributes. Three case studies are described in this paper to illustrate the use of neural network prediction of sandstone-marl facies (Case Study # 1, Okoli Field), prediction of carbonate breccia porosity (Case Study # 2, Beničanci Field), and prediction of lithology and saturation (Case Study # 3, Kloštar Field). The results of these studies indicate that this method is capable of providing better understanding of some clastic Neogene reservoirs in the Croatian part of the Pannonian Basin