Molecular spectroscopic markers of DNA damage

Every cell in a living organism is constantly exposed to physical and chemical factors which damage the molecular structure of proteins, lipids, and nucleic acids. Cellular DNA lesions are the most dangerous because the genetic information, critical for the identity and function of each eukaryotic cell, is stored in the DNA. In this review, we describe spectroscopic markers of DNA damage, which can be detected by infrared, Raman, surface-enhanced Raman, and tip-enhanced Raman spectroscopies, using data acquired from DNA solutions and mammalian cells. Various physical and chemical DNA damaging factors are taken into consideration, including ionizing and non-ionizing radiation, chemicals, and chemotherapeutic compounds. All major spectral markers of DNA damage are presented in several tables, to give the reader a possibility of fast identification of the spectral signature related to a particular type of DNA damage

Molecular spectroscopic markers of abnormal protein aggregation

Abnormal protein aggregation has been intensively studied for over 40 years and broadly discussed in the literature due to its significant role in neurodegenerative diseases etiology. Structural reorganization and conformational changes of the secondary structure upon the aggregation determine aggregation pathways and cytotoxicity of the aggregates, and therefore, numerous analytical techniques are employed for a deep investigation into the secondary structure of abnormal protein aggregates. Molecular spectroscopies, including Raman and infrared ones, are routinely applied in such studies. Recently, the nanoscale spatial resolution of tip-enhanced Raman and infrared nanospectroscopies, as well as the high sensitivity of the surface-enhanced Raman spectroscopy, have brought new insights into our knowledge of abnormal protein aggregation. In this review, we order and summarize all nano- and micro-spectroscopic marker bands related to abnormal aggregation. Each part presents the physical principles of each particular spectroscopic technique listed above and a concise description of all spectral markers detected with these techniques in the spectra of neurodegenerative proteins and their model systems. Finally, a section concerning the application of multivariate data analysis for extraction of the spectral marker bands is included

Fusion of morphological data obtained by coronary computed tomography angiography with quantitative echocardiographic data on regional myocardial function

Background: Three-dimensional (3D) fusion of morphological data obtained by coronary computed tomography angiography (CCTA) with functional data from resting and stress echocardiography could potentially provide additional information compared to examination results analyzed separately and increase the diagnostic and prognostic value of non-invasive imaging in patients with suspected coronary artery disease (CAD). Using vendor-independent software developed in our institution, we aimed to assess the feasibility and reproducibility of 3D fusion of morphological CCTA data with echocardiographic data regarding regional myocardial function. Methods: Thirty patients with suspected CAD underwent CCTA and resting transthoracic echocardiography. From CCTA we obtained 3D reconstructions of coronary arteries and left ventricle (LV). Offline speckle-tracking analysis of the echocardiographic images provided parametric maps depicting myocardial longitudinal strain in 17 segments of the LV. Using our software, 3 independent investigators fused echocardiographic maps with CCTA reconstruc­tions in all patients. Based on the obtained fused models, each segment of the LV was assigned to one of the major coronary artery branches. Results: Mean time necessary for data fusion was 65 ± 7 s. Complete agreement between independent investigators in assignment of LV segments to coronary branches was obtained in 94% of the segments. The average coefficient of agreement (kappa) between the investigators was 0.950 and the intra-class correlation coefficient was 0.9329 (95% CI 0.9227–0.9420). Conclusions: Three-dimensional fusion of morphological CCTA data with quantitative echocardiographic data on regional myocardial function is feasible and allows highly repro­ducible assignment of myocardial segments to coronary artery branches

Variabilities in global DNA methylation and β\beta-sheet richness establish spectroscopic landscapes among subtypes of pancreatic cancer

Purpose: Knowledge about pancreatic cancer (PC) biology has been growing rapidly in recent decades. Nevertheless, the survival of PC patients has not greatly improved. The development of a novel methodology suitable for deep investigation of the nature of PC tumors is of great importance. Molecular imaging techniques, such as Fourier transform infrared (FTIR) spectroscopy and Raman hyperspectral mapping (RHM) combined with advanced multivariate data analysis, were useful in studying the biochemical composition of PC tissue. Methods: Here, we evaluated the potential of molecular imaging in differentiating three groups of PC tumors, which originate from different precursor lesions. Specifically, we comprehensively investigated adenocarcinomas (ACs): conventional ductal AC, intraductal papillary mucinous carcinoma, and ampulla of Vater AC. FTIR microspectroscopy and RHM maps of 24 PC tissue slides were obtained, and comprehensive advanced statistical analyses, such as hierarchical clustering and nonnegative matrix factorization, were performed on a total of 211,355 Raman spectra. Additionally, we employed deep learning technology for the same task of PC subtyping to enable automation. The so-called convolutional neural network (CNN) was trained to recognize spectra specific to each PC group and then employed to generate CNN-prediction-based tissue maps. To identify the DNA methylation spectral markers, we used differently methylated, isolated DNA and compared the observed spectral differences with the results obtained from cellular nuclei regions of PC tissues. Results: The results showed significant differences among cancer tissues of the studied PC groups. The main findings are the varying content of β-sheet-rich proteins within the PC cells and alterations in the relative DNA methylation level. Our CNN model efficiently differentiated PC groups with 94% accuracy. The usage of CNN in the classification task did not require Raman spectral data preprocessing and eliminated the need for extensive knowledge of statistical methodologies. Conclusions: Molecular spectroscopy combined with CNN technology is a powerful tool for PC detection and subtyping. The molecular fingerprint of DNA methylation and β-sheet cytoplasmic proteins established by our results is different for the main PC groups and allowed the subtyping of pancreatic tumors, which can improve patient management and increase their survival. Our observations are of key importance in understanding the variability of PC and allow translation of the methodology into clinical practice by utilizing liquid biopsy testing

The analysis of hazel pollen count in selected Polish cities in 2008

Praca przedstawia przebieg sezonu pylenia leszczyny w wybranych punktach pomiarowych w Polsce w 2008 r. Pomiary wykonywano we Wrocławiu, w Krakowie, Warszawie, Sosnowcu, Szczecinie, Lublinie, Olsztynie i Bydgoszczy. Badania prowadzono metodą objętościową z wykorzystaniem aparatów firmy Burkard i Lanzoni. Sezon pyłkowy wyznaczono jako okres, w którym w powietrzu występuje 95% rocznej sumy ziaren pyłku leszczyny. Pylenie leszczyny w 2008 roku rozpoczęło się około 10 dni później niż w 2007 roku. Najwcześniej pyłek leszczyny zarejestrowano we Wrocławiu i Szczecinie (21 i 22 stycznia), a najpóźniej w Lublinie (4 lutego). Najwyższe wartości średniodobowych stężeń pyłku leszczyny odnotowano w Sosnowcu, gdzie 23 lutego zanotowano stężenie 115 z/m3 powietrza.This paper presents the course of hazel pollination season in selected cities of Poland in 2008. The measurements were performed in Wrocław, Kraków, Lublin, Warszawa, Sosnowiec, Szczecin, Olsztyn and Bydgoszcz. Volumetric method with the use of Volumetric Spore Trap (Burkard, Lanzoni) was implemented. Pollen season was defined as the period in which 95% of the total annual catch occurred. Pollen season of hazel in 2008 started about 10 days later in comparison to 2007. The season started first in Wrocław and Szczecin (21, 22 January). The highest 24-hour average pollen count was recorded in Sosnowiec on 23 February (115 hazel pollen grains/1m3)

Oak blossoming period and the threat to pollen allergens that tree in selected Polish cities in 2009

Praca przedstawia przebieg sezonu pylenia dębu w wybranych punktach pomiarowych większych miast Polski w 2009 r. Pomiary wykonywano we Wrocławiu, w Sosnowcu, Krakowie, Lublinie, Bydgoszczy, Białymstoku, Drawsku Pomorskim, Olsztynie, Warszawie i Szczecinie. Badania prowadzono metodą objętościową przy wykorzystaniu aparatów firmy Burkard i Lanzoni. Sezon pyłkowy wyznaczono jako okres, w którym w powietrzu występuje 95% rocznej sumy ziaren pyłku dębu. Pylenie dębu w 2009 roku rozpoczęło się z lekkim przyspieszeniem w stosunku do 2008 roku. Najwcześniej pyłek dębu zarejestrowano w Szczecinie, bo już 14 kwietnia. Najpóźniej pyłek tego taksonu pojawił się w Lublinie, dopiero 27 kwietnia. Najwyższe wartości średniodobowych stężeń pyłku dębu odnotowano w Lublinie, gdzie 30 kwietnia wystąpiło stężenie 454 z/m3 powietrza.This paper presents the course of oak pollination season in selected cities of Poland in 2009. The measurements were performed in Wrocław, Sosnowiec, Kraków, Lublin, Bydgoszcz, Białystok, Drawsko Pomorskie, Olsztyn, Warszawa and Szczecin. Volumetric method with the use of Volumetric Spore Trap (Burkard, Lanzoni) was implemented. Pollen season was defined as the period in which 95% of the annual total catch occurred. Pollen season of oak in 2009 started ealier in comparison to 2008. The season started first in Szczecin (14 April). The highest 24-hour average pollen count was recorded in Lublin on 30 April (454 oak pollen grains/1 m3)

The analysis of Poplar pollen count in selected Polish cities in 2008

Praca przedstawia przebieg sezonu pylenia topoli w wybranych miastach Polski w 2008 roku. Pomiary wykonano w Białymstoku, Bydgoszczy, Drawsku Pomorskim, Krakowie, Lublinie, Olsztynie, Szczecinie i Warszawie. Badania prowadzono metodą objętościową przy wykorzystaniu aparatów firmy Burkard i Lanzoni 2000. Sezon pyłkowy wyznaczono jako okres, w którym w powietrzu występuje 95% rocznej sumy ziaren pyłku. Początek sezonu pyłkowego wyznaczono również metodą 30 ziaren. Indeks SPI obliczono jako sumę średnich dobowych stężeń pyłku w danym sezonie. Najwyższe wartości średniodobowych stężeń pyłku topoli odnotowano w Lublinie, gdzie 11 kwietnia stężenie pyłku wyniosło 273 z/m3 powietrza.This paper presents the course of poplar pollination season in selected cities of Poland in 2007. The measurements were performed in Bialystok, Bydgoszcz, Krakow, Lublin, Lody, Olsztyn, Sosnowiec, Szczecin, Warsaw and Wroclaw. Volumetric method with the use of Volumetric Spore Trap (Burkard, Lanzoni 2000) was implemented. Pollen season was defined as the period in which 95% of the annual total catch occurred. The start of the season was also determined by the 30 grains method. Seasonal Pollen Index (SPI) was estimated as the annual sum of daily average pollen concentrations. The highest 24-hour average pollen count was recorded in Lublin on 11 April (273 poplar pollen grains/1 m3)

The analysis of hazel pollen count in selected Polish cities in 2009

Praca przedstawia przebieg sezonu pylenia leszczyny w wybranych punktach pomiarowych w Polsce w 2009 r. Pomiary wykonywano w Białymstoku, Bydgoszczy, Drawsku Pomorskim, Krakowie, Sosnowcu, Lublinie, Olsztynie, Szczecinie, Warszawie i we Wrocławiu. Badania prowadzono metodą objętościową przy wykorzystaniu aparatów firmy Burkard i Lanzoni. Sezon pyłkowy wyznaczono jako okres, w którym w powietrzu występuje 95% rocznej sumy ziaren pyłku leszczyny. Pylenie leszczyny w 2009 roku rozpoczęło się około 40 dni później niż w 2008 roku i około 50 dni później niż w 2007 roku. Najwcześniej pyłek leszczyny zarejestrowano w Lublinie (8 lutego stężenie wynosiło 26 ziaren/m3 powietrza), a we wszystkich pozostałych punktach pomiarowych pylenie leszczyny odnotowano w początkach marca. Najwyższe wartości średniodobowych stężeń pyłku leszczyny odnotowano w Lublinie – 28 marca zanotowano tam stężenie 362 z/m3 powietrza.This paper presents the course of hazel pollination season in selected cities of Poland in 2008. The measurements were performed in Białystok, Bydgoszcz, Drawsko Pomorskie, Cracow, Sosnowiec, Lublin, Olsztyn, Szczecin, Warsaw and Wrocław. Volumetric method with the use of Volumetric Spore Trap (Burkard, Lanzoni) was implemented. Pollen season was defined as the period in which 95% of the annual total catch occurred. Pollen season of hazel in 2009 started about 40 days later in comparison to 2008, and about 50 days later in comparison to 2007. The season started first in Lublin (08 February – 26 hazel pollen grain/1 m3). The highest 24-hour average pollen count was recorded in Lublin on 28 March (362 hazel pollen grains/1 m3)

Birch pollen in the selected Polish cities in 2008

Celem pracy była analiza sezonu pyłkowego brzozy w 2008 r. w Białymstoku, Bydgoszczy, Krakowie, Lublinie, Łodzi, Olsztynie, Sosnowcu, Szczecinie, Warszawie i Wrocławiu. Pomiary stężenia pyłku prowadzono metodą objętościową z zastosowaniem aparatów Burkard i Lanzoni 2000. Sezon pyłkowy wyznaczono jako okres, w którym w powietrzu występuje 98% i 95% rocznej sumy ziaren pyłku. Oznaczono również roczną sumę ziaren pyłku brzozy oraz liczbę dni ze stężeniem progowym wyższym od 20, 75, 90 i 120 ziaren pyłku × m3 powietrza. Sezon wyznaczony metodą 98% najwcześniej rozpoczął się w Krakowie (9 kwietnia), a w większości pozostałych miast w dniu 10 kwietnia. Najwyższe, rekordowe wartości stężeń zanotowano w Sosnowcu, maksymalne stężenie 5875 ziaren × m3 zaobserwowano 15 kwietnia.The aim of the study was to analyse the pollen seasons of birch in the cities of Białystok, Bydgoszcz, Kraków, Lublin, Łódź, Olsztyn, Sosnowiec, Szczecin, Warszawa and Wrocław in 2008. Measurements were performed by the volumetric method (Burkard and Lanzoni 2000 pollen sampler). Pollen season was defined as the period in which 98% and 95% of the total annual catch occurred. The pollen season of birch started first in Kraków on the 9th of April and in the other cities on the 10th April. The highest airborne concentration of 5875 pollen grains × m3 was noted in Sosnowiec on the 15th of April

Allergic Rhinitis and its Impact on Asthma (ARIA) Phase 4 (2018) : Change management in allergic rhinitis and asthma multimorbidity using mobile technology

Allergic Rhinitis and its Impact on Asthma (ARIA) has evolved from a guideline by using the best approach to integrated care pathways using mobile technology in patients with allergic rhinitis (AR) and asthma multimorbidity. The proposed next phase of ARIA is change management, with the aim of providing an active and healthy life to patients with rhinitis and to those with asthma multimorbidity across the lifecycle irrespective of their sex or socioeconomic status to reduce health and social inequities incurred by the disease. ARIA has followed the 8-step model of Kotter to assess and implement the effect of rhinitis on asthma multimorbidity and to propose multimorbid guidelines. A second change management strategy is proposed by ARIA Phase 4 to increase self-medication and shared decision making in rhinitis and asthma multimorbidity. An innovation of ARIA has been the development and validation of information technology evidence-based tools (Mobile Airways Sentinel Network [MASK]) that can inform patient decisions on the basis of a self-care plan proposed by the health care professional.Peer reviewe