Motivation: The automated data processing provided by the tool enables now to reach high throughput speed analysis of thermal shift assays. While the software is powerful and freely available, it still requires installation process and command line efforts that could be discouraging.
Results: To simplify the procedure, we decided to make it available and easy to use by implementing it with a graphical interface via a web server, enabling a cross-platform usage from any web browsers.
Music is a universal human phenomenon, and can be studied for itself or as a window into the understanding of the brain. Few neuroimaging studies investigate actual playing in the MRI scanner, likely because of the lack of available experimental hardware and analysis tools. Here, we offer an innovative paradigm that addresses this issue in neuromusicology using naturalistic, polyphonic musical stimuli, presents a commercially available MRI-compatible piano, and a flexible approach to quantify participant's performance.
View Article and Find Full Text PDFHomology-directed repair (HDR), a method for repair of DNA double-stranded breaks can be leveraged for the precise introduction of mutations supplied by synthetic DNA donors, but remains limited by low efficiency and off-target effects. In this study, we report HDRobust, a high-precision method that, via the combined transient inhibition of nonhomologous end joining and microhomology-mediated end joining, resulted in the induction of point mutations by HDR in up to 93% (median 60%, s.e.
View Article and Find Full Text PDFIntroduction: The accurate detection of genetic variants such as single substitutions (IDH1/2, TERT), chromosomal abnormalities (CDKN2A, 1p/19q deletions, and EGFR amplifications), or promoter methylations (MGMT) is critical for glioma patient management, as emphasized in the World Health Organization's (WHO's) most recent classification in 2021 (WHO CNS5). The purpose of this study was to evaluate novel innovative methods for determining IDH1/2 status in the context of WHO CNS5.
Methods: Multiple biomarkers were simultaneously screened using next-generation sequencing (NGS) on 34 glioma samples.
Background: Studies have demonstrated a lower incidence of complications after video-assisted thoracoscopic surgery (VATS) lobectomy compared with thoracotomy, but the data on in-hospital and 90-day mortality are inconclusive. This study analyzed whether surgical approach, VATS or thoracotomy, was related to early mortality of lobectomy in lung cancer and determined the differences between in-hospital and 90-day mortality.
Methods: Data of all patients with non-small cell lung cancer who underwent lobectomy between January 1, 2007, and July 30, 2018, were retrieved from Polish National Lung Cancer Registry.
Sepsis is a dysregulated host inflammatory response to infection potentially leading to life-threatening organ dysfunction. The objectives of this study were to determine whether early microvascular dysfunction (MVD) in skeletal muscle can be detected as dynamic changes in microvascular hemoglobin (MVHb) levels using spectroscopy and whether MVD precedes organ histopathology in septic peritonitis. Skeletal muscle of male Sprague-Dawley rats was prepared for intravital microscopy.
View Article and Find Full Text PDFKardiochir Torakochirurgia Pol
March 2022
High-throughput synthesis and screening methods were used to measure the photochemical activity of 1440 distinct heteroleptic [Ir(C^N)(N^N)] complexes for the photoreduction of Sn(II) and Zn(II) cations to their corresponding neutral metals. Kinetic data collection was carried out using home-built photoreactors and measured initial rates, obtained through an automated fitting algorithm, spanned between 0-120 μM/s for Sn(0) deposition and 0-90 μM/s for Zn(0) deposition. Photochemical reactivity was compared to photophysical properties previously measured such as deaerated excited state lifetime and emission spectral data for these same complexes; however, no clear correlations among these features were observed.
View Article and Find Full Text PDFEur J Obstet Gynecol Reprod Biol
January 2022
Objectives: To evaluate the incidence of HPV infection, and the frequency of the various genotypes, using mRNA and DNA testing; to assess their relationship with the cervical lesions and women's age in the Polish patients.
Study Design: A group of 1840 women, most of whom had abnormal cytology, from the Franciszek Łukaszczyk Oncology Centre in Bydgoszcz, Poland were screened for presence of at least one of 13 high risk HPV. Following that, 545 HPV DNA positive women were tested for HPV infection using HPV mRNA with the Nucleic Acid Sequence-Based Amplification Assay (NASBA) method.
Gliomas are the most common central nervous system tumors. New technologies, including genetic research and advanced statistical methods, revolutionize the therapeutic approach to the patient and reveal new points of treatment options. Moreover, the 2021 World Health Organization Classification of Tumors of the Central Nervous System has fundamentally changed the classification of gliomas and incorporated many molecular biomarkers.
View Article and Find Full Text PDFIn humans, several members of the CEACAM receptor family have been shown to interact with intestinal pathogens in an inflammatory context. While CEACAMs have long been thought to be only present in mammals, recent studies have identified ceacam genes in other vertebrates, including teleosts. The function of these related genes remains however largely unknown.
View Article and Find Full Text PDF(1) Background: Although, in the mutated detected in the Polish population of patients with breast cancer, there is a large percentage of recurrent pathogenic variants, an increasing need for the assessment of rare variants using NGS can be observed. (2) Methods: We studied 75 selected patients with breast cancer (negative for the presence of 5 mutations tested in the Polish population in the prophylactic National Cancer Control Program). DNA extracted from the cancer tissue of these patients was used to prepare a library and to sequence all coding regions of the genes.
View Article and Find Full Text PDFThe fundamental units of olfactory perception are discrete 3D structures of volatile chemicals that each interact with specific subsets of a very large family of hundreds of odorant receptor proteins, in turn activating complex neural circuitry and posing a challenge to understand. We have applied computational approaches to analyze olfactory perceptual space from the perspective of odorant chemical features. We identify physicochemical features associated with ~150 different perceptual descriptors and develop machine-learning models.
View Article and Find Full Text PDFMany insects can detect carbon dioxide (CO) plumes using a conserved receptor made up of members of the gustatory receptor (Gr) family Gr1, Gr2 and Gr3. Mosquitoes are attracted to host animals for blood meals using plumes of CO in the exhaled breath using the receptor expressed in the A neuron of the capitate peg sensilla type on the maxillary palps. The receptor is known to also detect several other classes of odorants, including ones emitted from human skin.
View Article and Find Full Text PDFThere is an urgent need for the identification of effective therapeutics for COVID-19 and we have developed a machine learning drug discovery pipeline to identify several drug candidates. First, we collect assay data for 65 target human proteins known to interact with the SARS-CoV-2 proteins, including the ACE2 receptor. Next, we train machine learning models to predict inhibitory activity and use them to screen FDA registered chemicals and approved drugs (~100,000) and ~14 million purchasable chemicals.
View Article and Find Full Text PDFOdor perception in humans is initiated by activation of odorant receptors (ORs) in the nose. However, the ORs linked to specific olfactory percepts are unknown, unlike in vision or taste where receptors are linked to perception of different colors and tastes. The large family of ORs (~400) and multiple receptors activated by an odorant present serious challenges.
View Article and Find Full Text PDFAn extended set of paramagnetic relaxation enhancement (PRE) data, up to the field of 32.9 Tesla, is reported for protons in an acidified aqueous solution of a Ni(II) salt in the presence and in the absence of added glycerol. For the 55% w/w glycerol sample, a distinct maximum in the PRE vs magnetic field curve is observed for the first time.
View Article and Find Full Text PDFFluorescence in situ hybridization (FISH) is a standard technique used in routine diagnostics of genetic aberrations. Thanks to simple FISH procedure is possible to recognize tumor-specific abnormality. Its applications are limited to designed probe type.
View Article and Find Full Text PDFAim Of The Study: The main purpose of this study was to assess detection of mutations in the epidermal growth factor receptor (EGFR) gene in circulating tumor DNA (ctDNA) as a tool for EGFR tyrosine kinase inhibitor (TKI) monitoring therapy.
Material And Methods: The study was conducted using 20 samples from 7 adenocarcinoma patients treated with TKIs. Blood samples for ctDNA analysis were collected in 2015-2016.
Large‑scale projects, such as The Cancer Genome Atlas (TCGA), Human Epigenome Project (HEP) and Human Epigenome Atlas (HEA), provide an insight into DNA methylation and histone modification markers. Changes in the epigenome significantly contribute to the initiation and progression of cancer. The goal of the present study was to characterize the prostate cancer malignant transformation model using the CpG island methylation pattern.
View Article and Find Full Text PDFAims: To compare transcatheter aortic valve replacement TAVR with self-expandable first-generation Medtronic CoreValve with new-generation Evolut R devices in patients with aortic stenosis.
Methods: Multiple databases were screened for all available reports directly or indirectly comparing CoreValve vs Evolut R. Primary endpoint was device success.
The long-range control of gene expression is facilitated by chromatin looping and can be detected using chromosome conformation capture-3C. Here we focus on the chromatin architecture of the (Polypyrimidine tract binding protein 3) locus to evaluate its potential role in regulating expression of the gene. expression in prostate cancer cell lines is found significantly higher compared to skin fibroblasts using real-time PCR ( < 0.
View Article and Find Full Text PDFEpigenetic patterns, such as DNA methylation, histone modifications, and non-coding RNAs, can be both driver factors and characteristic features of certain malignancies. Aberrant DNA methylation can lead to silencing of crucial tumor suppressor genes or upregulation of oncogene expression. Histone modifications and chromatin spatial organization, which affect transcription, regulation of gene expression, DNA repair, and replication, have been associated with multiple tumors.
View Article and Find Full Text PDFOdor detection involves hundreds of olfactory receptors from diverse families, making modeling of hedonic valence of an odorant difficult, even in Drosophila melanogaster where most receptors have been deorphanised. We demonstrate that a broadly tuned heteromeric receptor that detects CO (Gr21a, Gr63a) and other odorants is a key determinant of valence along with a few members of the Odorant receptor family in a T-maze, but not in a trap assay. Gr21a and Gr63a have atypically high amino acid conservation in Dipteran insects, and they use both inhibition and activation to convey positive or negative valence for numerous odorants.
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