In the last two decades, Computer Aided Detection (CAD) systems were developed to help radiologists analyse screening mammograms, however benefits of current CAD technologies appear to be ...contradictory, therefore they should be improved to be ultimately considered useful. Since 2012, deep convolutional neural networks (CNN) have been a tremendous success in image recognition, reaching human performance. These methods have greatly surpassed the traditional approaches, which are similar to currently used CAD solutions. Deep CNN-s have the potential to revolutionize medical image analysis. We propose a CAD system based on one of the most successful object detection frameworks, Faster R-CNN. The system detects and classifies malignant or benign lesions on a mammogram without any human intervention. The proposed method sets the state of the art classification performance on the public INbreast database, AUC = 0.95. The approach described here has achieved 2nd place in the Digital Mammography DREAM Challenge with AUC = 0.85. When used as a detector, the system reaches high sensitivity with very few false positive marks per image on the INbreast dataset. Source code, the trained model and an OsiriX plugin are published online at https://github.com/riblidezso/frcnn_cad .
The aim of this review is to evaluate the present status of the use of cell-free DNA and its fraction of circulating tumor DNA (ctDNA) because this year July 2022, an ESMO guideline was published ...regarding the application of ctDNA in patient care. This review is for clinical oncologists to explain the concept, the terms used, the pros and cons of ctDNA; thus, the technical aspects of the different platforms are not reviewed in detail, but we try to help in navigating the current knowledge in liquid biopsy. Since the validated and adequately sensitive ctDNA assays have utility in identifying actionable mutations to direct targeted therapy, ctDNA may be used for this soon in routine clinical practice and in other different areas as well. The cfDNA fragments can be obtained by liquid biopsy and can be used for diagnosis, prognosis, and selecting among treatment options in cancer patients. A great proportion of cfDNA comes from normal cells of the body or from food uptake. Only a small part (<1%) of it is related to tumors, originating from primary tumors, metastatic sites, or circulating tumor cells (CTCs). Soon the data obtained from ctDNA may routinely be used for finding minimal residual disease, detecting relapse, and determining the sites of metastases. It might also be used for deciding appropriate therapy, and/or emerging resistance to the therapy and the data analysis of ctDNA may be combined with imaging or other markers. However, to achieve this goal, further clinical validations are inevitable. As a result, clinicians should be aware of the limitations of the assays. Of course, several open questions are still under research and because of it cfDNA and ctDNA testing are not part of routine care yet.
During the mitotic cycle, the rod‐shaped fission yeast cells grow only at their tips. The newly born cells grow first unipolarly at their old end, but later in the cycle, the ‘new end take‐off’ event ...occurs, resulting in bipolar growth. Photographs were taken of several steady‐state and induction synchronous cultures of different cell cycle mutants of fission yeast, generally larger than wild type. Length measurements of many individual cells were performed from birth to division. For all the measured growth patterns, three different functions (linear, bilinear and exponential) were fitted, and the most adequate one was chosen by using specific statistical criteria, considering the altering parameter numbers. Although the growth patterns were heterogeneous in all the cultures studied, we could find some tendencies. In cultures with sufficiently wide size distribution, cells large enough at birth tend to grow linearly, whereas the other cells generally tend to grow bilinearly. We have found that among bilinearly growing cells, the larger they are at birth, the rate change point during their bilinear pattern occurs earlier in the cycle. This shifting near to the beginning of the cycle might finally cause a linear pattern, if the cells are even larger. In all of the steady‐state cultures studied, a size control mechanism operates to maintain homeostasis. By contrast, strongly oversized cells of induction synchronous cultures lack any sizer, and their cycle rather behaves like an adder. We could determine the critical cell size for both the G1 and G2 size controls, where these mechanisms become cryptic.
TAKE AWAY
Most individual fission yeast cells in steady‐state cultures grow bilinearly.
In strongly oversized fission yeast cells, linear growth dominates over bilinear.
Above birth length thresholds, both the G1 and G2 size controls become cryptic.
Systematic monitoring of SARS-CoV-2 co-infections between different lineages and assessing the risk of intra-host recombinant emergence are crucial for forecasting viral evolution. Here we present a ...comprehensive analysis of more than 2 million SARS-CoV-2 raw read datasets submitted to the European COVID-19 Data Portal to identify co-infections and intra-host recombination. Co-infection was observed in 0.35% of the investigated cases. Two independent procedures were implemented to detect intra-host recombination. We show that sensitivity is predominantly determined by the density of lineage-defining mutations along the genome, thus we used an expanded list of mutually exclusive defining mutations of specific variant combinations to increase statistical power. We call attention to multiple challenges rendering recombinant detection difficult and provide guidelines for the reduction of false positives arising from chimeric sequences produced during PCR amplification. Additionally, we identify three recombination hotspots of Delta - Omicron BA.1 intra-host recombinants.
The aim of this study was to develop a standardised, small-scale laboratory baking method for testing the baking quality of 100% oat flours. During the method development using wholemeal flours of 5 ...Hungarian oat varieties, the mixing measurements and baking tests were performed at 300, 200 and 150 FU maximum dough consistencies applying different mixing times (6 and 10 min). Our results showed that an optimal, instrumentally registered, and numerically expressed dough consistency and corresponding water addition level for oat flours could be defined on the model of wheat flour testing methodology. Based on this, the lowest dough consistency and the shortest mixing time were found the most appropriate regarding the specific volume and crumb structure of oat breads. Then, the newly developed baking method was applied for testing 9 oat varieties, which were tested also for chemical composition and rheological (mixing, pasting) properties. Protein, fat, and β-glucan content significantly influenced both rheological and baking properties, and relationships between techno-functional parameters were also found. Our results suggested that high quality 100% oat bread can be produced by a standardised and optimised baking test as well as oat varieties being more preferable for bread making can be identified.
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•Evaluation of oat dough mixing properties at lower dough consistencies were done.•Water absorption at 150FU consistency seems to be optimal for 100% oat bread making.•Standardised small-scale baking method was developed for wholemeal oat flours.•Protein, fat and β-glucan content significantly influenced baking performance.•Relationships were found between rheological properties and baking quality.
10.1119/5.0111635.3
A mirage or fata morgana is typically an upside-down “mirror” image of a scenery in deserts, over sun-heated roads, or above bodies of water. When the temperature gradient of air ...is large, as can happen near a surface, it results in a large gradient of the density and the refractive index as a function of height. Mirages appear when light travels through a medium with a gradient in its refractive index and, therefore, get bent towards the higher values, generating reflected images. A computer program that simulates mirages above water using the method of ray tracing has been developed and is presented here in detail for educational purposes. Results on the effect are shown by simulated images for various water-air temperature-difference cases with values ranging from 5 to 0 °C. Comparison of the simulations to a real-life scenario at Lake Balaton, Hungary has also been provided.
Due to the constantly increasing number of mutations in the SARS-CoV-2 genome, concerns have emerged over the possibility of decreased diagnostic accuracy of reverse transcription-polymerase chain ...reaction (RT-PCR), the gold standard diagnostic test for SARS-CoV-2. We propose an analysis pipeline to discover genomic variations overlapping the target regions of commonly used PCR primer sets. We provide the list of these mutations in a publicly available format based on a dataset of more than 1.2 million SARS-CoV-2 samples. Our approach distinguishes among mutations possibly having a damaging impact on PCR efficiency and ones anticipated to be neutral in this sense. Samples are categorized as "prone to misclassification" vs. "likely to be correctly detected" by a given PCR primer set based on the estimated effect of mutations present. Samples susceptible to misclassification are generally present at a daily rate of 2% or lower, although particular primer sets seem to have compromised performance when detecting Omicron samples. As different variant strains may temporarily gain dominance in the worldwide SARS-CoV-2 viral population, the efficiency of a particular PCR primer set may change over time, therefore constant monitoring of variations in primer target regions is highly recommended.
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
and
. 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
(31%),
(34%),
(18%), and
(34%). Copy number alterations were most common in the
,
,
, and
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.
Breast cancer-related lymphedema may impact life quality and cause co-morbidity of several types. Though breast cancer-related lymphedema does not directly follow the initial intervention, it may ...develop even years after it; timely diagnosis and treatment are essential. The combined therapies such as radiation, chemo- and endocrine therapy, and other events (e.g., injury, infection, inflammation, or systemic disease) may further impair the lymphatic function. A prospective surveillance program for the early detection of subclinical edema in high-risk patient groups may improve quality of life. Currently, complex decongestive physiotherapy is the first-line treatment of breast cancer-related lymphedema. It should start soon after the diagnosis. After the early-stage treatment, the lifelong care and followup of the patients are necessary. The article presents pathophysiology, treatment, and future trends of therapies in breast cancer-related lymphedema.
Breast cancer is a global health problem - it is the most common malignancy among women. Triple negative breast cancers (TNBC) account for 10-20% of female breast cancer. Most TNBC cases confer poor ...prognosis. Brain metastasis appears in more than 15% in the triple negative breast cancer population, which causes serious decrease in survival. Changes of immunophenotype are not uncommon in breast cancer, offering new therapeutic options in cases where targetable proteins or pathways are being identified.
After five lines of chemotherapy and 82 months following the first diagnosis, our patient with brain metastatic triple negative breast cancer had human epidermal growth factor receptor 2 (HER2) genetic heterogeneity in the metastatic tissue sample interpreted as HER2 status conversion. After the removal of the metastasis, we started first line therapy for metastatic HER2 positive cancer with trastuzumab and paclitaxel. After the first cycle of trastuzumab, on day 8, she had a seizure, and neurosurgical examination showed an abscess-like lesion. The punctate proved to be sterile by microbiological and pathological examination, so we continued cytostatic therapy without the anti-HER2 antibody. 3 months later, we could not identify the previous abscess-like lesion in the control computer tomography (CT) scan, and our patient had no neurological deficits.
We emphasize the importance of regular tissue confirmation of predictive markers in progressive tumorous disease even if our presented case is not unequivocally a "conversion case". Tumor subtype is determined according to algorithms and definitions published in guidelines, nevertheless, use of different guidelines may lead to controversial interpretation in cases where HER2 genetic heterogeneity is present. Furthermore, we suggest that seronegative, aseptic intracranial fluid effusion after the removal of a brain metastasis may possibly be a side effect of trastuzumab.
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