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1

Microscopic Studies of Activated Sludge Supported by Automatic Image Analysis Based on Deep Learning Neural Networks

Dziadosz Marcin, Majerek Dariusz, Łagód Grzegorz

Journal of Ecological Engineering

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2024

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Vol. 25, nr 4

360--369

EN

Paper presents microscopic studies of activated sludge supported by automatic image analysis based on deep learning neural networks. The organisms classified as Arcella vulgaris were chosen for the research. They frequently occur in the waters containing organic substances as well as WWTPs employing the activated sludge method. Usually, they can be clearly seen and counted using a standard optical microscope, as a result of their distinctive appearance, numerous population and passive behavior. Thus, these organisms constitute a viable object for detection task. Paper refers to the comparison of performance of deep learning networks namely YOLOv4 and YOLOv8, which conduct automatic image analysis of the afore-mentioned organisms. YOLO (You Only Look Once) constitutes a one-stage object detection model that look at the analyzed image once and allow real-time detection without a marked accuracy loss. The training of the applied YOLO models was carried out using sample microscopic images of activated sludge. The relevant training data set was created by manually labeling the digital images of organisms, followed by calculation and comparison of various metrics, including recall, precision, and accuracy. The architecture of the networks built for the detection task was general, which means that the structure of the layers and filters was not affected by the purpose of using the models. Accounting mentioned universal construction of the models, the results of the accuracy and quality of the classification can be considered as very good. This means that the general architecture of the YOLO networks can also be used for specific tasks such as identification of shell amoebas in activated sludge.

2

Geochemical characterization and palaeoenvironmental implications of lipids in Neogene lignites and lignitic shales in NW Poland

Czechowski Franciszek, Polowczyk Marzena, Simoneit Bernt R. T., Grelowski Cezary, Hojniak Marek

Annales Societatis Geologorum Poloniae

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2023

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Vol. 93, No. 4

447--466

EN

The lipophilic biomarker distributions in lipids of Neogene lignites and lignitic shales in western Pomerania and the midlands of Poland are presented. Twenty-six lignite samples and seven lignitic shales were obtained from twenty-four boreholes. Their extracts were separated, using thin-layer chromatography, and the saturate and aromatic fractions were analyzed by gas chromatography-mass spectrometry. The molecular compositions of n-alkanes, isoprenoids, n-alkylcyclohexanes, n-alkylbenzenes, tri- and tetracyclic diterpenoids, pentacyclic triterpenoids, as well as polycyclic aromatic hydrocarbons (PAHs) with up to five rings, were determined. The samples displayed n-alkane distributions in the range of C14–C35 and high odd-over-even carbon number predominances (CPI(25–33) from 2.9 to 7.9). Diterpanes consisted primarily of phyllocladane, abietane, isopimarane, labdane, and kaurane structures, although their abundances varied among the samples. Hopanes exhibited the biological and geochemical characteristics of low-maturity organic matter. Minor oleanane triterpenoids from angiosperms were also found. A few samples displayed evidence of biodegradation on the basis of the advanced isomerization of αβ-hopanes and the presence of short-chained n-alkanes, n-alkylcyclohexanes, and n-alkylbenzenes. A more mature stage of the above biomarkers also may have resulted in part from the oxidation of organic matter. The lignite source materials were derived from conifer and angiosperm flora as well as microbial remnants. The contribution from marine phytoplankton was excluded on the basis of the lack of C27 steroids. PAHs were predominantly perylene or phenanthrene, with minor other analogues. Thus, the data support progressive lacustrine/lagoonal sedimentation in the palaeoenvironmental mires.

3

Nieinwazyjne biomarkery do wykrywania raka pęcherza moczowego

Gruba Natalia

Wiadomości Chemiczne

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2022

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[Z] 76, 9-10

719--734

EN

Bladder cancer (BC) is one of the most common cancer in the world. About 3% of all new cancer diagnoses are due to urinary bladder cancer. BC is also a leading cause of cancer-related death, as 2.1% of all cancer deaths are caused by bladder cancer. However, lack of a reliable biomarker is the biggest issue for BC diagnosis, prognosis and treatment. Development of non-invasive, quick and economical methods in bladder cancer diagnosis still remains a great challenge. Highly specific, easy-to-perform tests are really needed. Ideally if they can identify the presence of a tumor before the first symptoms appear, as time plays an important role in cancer. In this article, an overview of the current established diagnostic tests and newly identified biomarkers will be provided.

4

Zastosowanie badań izotopowych do określania pochodzenia wybranych biomarkerów

Bieleń Wojciech, Janiga Marek

Nafta-Gaz

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2022

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R. 78, nr 5

336--342

PL

Badania izotopowe n-alkanów, pristanu (Pr) oraz fitanu (Ph) przeprowadzono przy pomocy aparatu GC-IRMS. Porównanie wartości δ13C – pristanu do n-C17 oraz fitanu do n-C18, a także zestawienie wartości δ13C pomiędzy pristanem a fitanem w obrębie jednej próbki pomaga zidentyfikować źródło pochodzenia tych izoprenoidów, co było celem pracy. Ta ostatnia informacja uwiarygadnia lub podaje w wątpliwość wskaźnik środowiska sedymentacji – Pr/Ph. Wartości δ13C n-alkanów dla rop naftowych z tego samego złoża: Bóbrka 113, Niepodległość 2, Bandrów wskazują na pochodzenie tych rop od roślin C3 (fotosynteza typu C3) oraz z osadów rzecznych lub/i jeziornych. N-alkany występujące w tych trzech ropach naftowych mogą mieć mieszane źródła i pochodzić zarówno od roślin lądowych, jak i wodnych. Ropa naftowa Łodyna 90K może pochodzić z różnorakich wyższych roślin. Wartości δ13C n-alkanów z próbek ekstraktów bitumicznych Dukla 2A i Dukla 2D są charakterystyczne dla roślin C3. Pristan i fitan w badanych próbkach rop naftowych i w przypadku dwóch próbek ekstraktów bitumicznych Dukla 2A i Dukla 2D mają wartości δ13C niższe niż wartości δ13C dla n-C17 i n-C18, co sugeruje pochodzenie od organizmów heterotroficznych. We wszystkich badanych próbkach rop naftowych (wyjątki: Łodyna 90K, Osobnica 35) wartości δ13C dla Pr i Ph w obrębie pojedynczej próbki świadczą o tym samym materiale źródłowym dla tych izoprenoidów. Ta informacja potwierdza, że wskaźnik Pr/Ph, mówiący o typie środowiska sedymentacji materii organicznej, jest wiarygodny. W dwóch ekstraktach bitumicznych (Dukla 2D i Krosno 8) wartości δ13C dla Pr i Ph są różne, dlatego istnieje duże prawdopodobieństwo odmiennego pochodzenia dla tych dwóch izoprenoidów (należy być ostrożnym co do wiarygodności wskaźnika środowiska sedymentacji Pr/Ph).

EN

Isotope analysis of n-alkanes, pristan (Pr) and phytane (Ph), were carried out on the GC-IRMS apparatus. Comparing the δ13C values of pristan to n-C17, phytane to n-C18 and pristan to phytane within one sample helps to identify the source of these isoprenoids. The latter information legitimises or questions the sedimentation environment index – Pr/Ph. The values of δ13C of n-alkanes for crude oil from one field: Bóbrka 113, Niepodległość 2, Bandrów indicate the origin of C3 plants (photosynthesis type C3) and river and / or lake sediments. The N-alkanes found in these three crude oils could have been sourced by organic matter from terrestrial and aquatic plants. Łodyna 90K crude oil was derived from a variety of higher plants. The δ13C values of n-alkanes for samples Dukla 2A and Dukla 2D bituminous extracts are characteristic for C3 plants. Pristan and phytan in the analyzed crude oil samples and in the case of two samples Dukla 2A and Dukla 2D bituminous extracts have δ13C values lower than the values of n-C17 and n-C18, which suggests their origin from heterotrophic organisms. In all analyzed crude oil samples (exceptions: Łodyna 90K, Osobnica 35) the δ13C values of Pr and Ph within a single sample indicate the same source material for these isoprenoids. This information confirms that the Pr/Ph ratio is reliable. In two bituminous extracts (Dukla 2D and Krosno 8) the δ13C values of Pr and Ph are different, therefore there is a high probability of different origins for these two isoprenoids (the Pr/Ph ratio may be unreliable).

5

Detection of ethane, methane, formaldehyde and water vapor in the 3.33 μm range

Winkowski Mateusz, Stacewicz Tadeusz

Metrology and Measurement Systems

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2022

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Vol. 29, nr 2

271--282

EN

We describe construction and investigation results of optical trace gas sensor working in the 3.334-3.337 μm spectral range. Laser spectroscopy was performed with a multipass cell. A setup was elaborated for detection of ethane at the 3.3368035 μm absorption line. Analysis of the gas spectra and the experiment have shown that, beside C2H6, the sensor is suitable for simultaneous detection of methane, formaldehyde and water vapor. Due to nonlinearity of the laser power characteristic we decided to detect the fourth harmonic of signal. Additional laser wavelength modulation was applied for optical interference suppression. In result, the precision of ethane detection of approximately 80 ppt has been achieved for the averaging time of 20 seconds. Long-term stability as well as the measurement linearity have also been positively tested. The system is suitable for detecting potential biomarkers directly in human breath.

6

Oddech codzienny

Ligor Tomasz, Rudnicka Joanna, Ratiu Ileana Andreea, Monedeiro Fernanda, Monedeiro-Milanowski Maciej, Buszewski Bogusław

Wiadomości Chemiczne

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2021

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[Z] 75, 7-8

911--922

EN

The odor of human body has facilitated diagnosis for a long time. Sniffing the body, breath, urine and even feces became one of the useful methods in ancient medicine. For centuries, the sweet smell of the breath was associated with diabetes, the fishy smell was associated with liver disease, measles was associated with the smell of feathers, typhoid with the smell of fresh bread, and tuberculosis with stale beer. Hippocrates also linked the smell of the human body and disease, claiming that the smell of a sick person is different from that of a healthy one. He classified the characteristic odors of the body into sweet, musty, fishy and rotten. The father of chemical analysis of breath was Antonie Lavoisier, who found that carbon dioxide is exhaled by guinea pigs. The pioneer of modem breath analysis was Linus Pauling, who in 1971 presented the results of breath studies using gas chromatography (GC), showing the presence of over 200 substances. Exhaled air containing approximately 78% N2, 17% OSub>2, 3% CO2 and up to 6% water vapor. The exact concentrations of individual inorganic gases depend on many factors, mainly physical exercise, cardiac output, and lung ventilation. A mixture of many volatile organic compounds is a much smaller group of substances at concentrations 100 ppm. The substances in the breath can come from human metabolism and enter into the body by inhaled air and food. Volatile organic compounds present in the breath that can be divided into different chemical classes e.g. saturated hydrocarbons (ethane, pentane, aldehydes), unsaturated hydrocarbons (isoprene), ketones (acetone), sulfur-containing compounds (methyl mercaptan, dimethyl sulfide, dimethyl disulphide, carbon disulphide, carbonyl sulphide) and containing nitrogen (amines). Endogenous substances in the breath can be used to track physiological and pathological processes in the body. Chemical analysis of the breath can provide information regarding biochemical processes in the organism and human health. Compared to many medical diagnostic methods, it is painless, non-invasive and safe. Nowadays, the main purpose of breath analysis is to identify volatile organic compounds that can be used as markers of various diseases. Research focused on detection of lung cancer based on specific volatile organic compounds in the exhaled air is carried out in many laboratories. Rapid and non-invasive methods for early detection of lung cancer and chronic obstructive pulmonary disease is crucial for early diagnosis. This mini review presents background of breath, briefly describes main volatiles, their biochemical origin as well as potential application of exhaled gases analysis.

7

Spektrometria masowa i analiza izotopowa biomarkerów frakcji nasyconej

Bieleń Wojciech, Janiga Marek

Nafta-Gaz

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2021

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R. 77, nr 8

512--520

PL

Analiza GC-IRMS poszerza i potwierdza (lub nie) interpretację opartą na wynikach z analiz GC-MS. Przykładowo jest bardzo przydatna w określaniu środowiska sedymentacji materii organicznej. Analiza GC-MS biomarkerów i oparte na niej wyniki są wiary- godne, ale dopiero badania GC-IRMS mogą je potwierdzić. W niniejszej pracy próbowano poprzez analizy izotopowe potwierdzić pochodzenie: BNH (28,30-bisnorhopanu) od bakterii chemoautotroficznych, a także wyższych karotenoidów i ich pochodnych od bakterii Chlorobiaceae czy Chromatiaceae. Przeprowadzono badania biomarkerów na aparacie GC-IRMS oraz EA-IRMS. Otrzymane chromatogramy z analiz IRMS porównywano z archiwalnymi analizami GC-MS dla tych samych próbek w celu identyfikacji poszczególnych związków chemicznych. Oprócz dotychczasowej metodyki przygotowania próbek do analiz zastosowano też niestandardową metodę polegającą na rozdziale n-alkanów od węglowodorów rozgałęzionych. Oznaczono na GC-IRMS powtarzalność metody oraz wartości δ13C wybranych biomarkerów z frakcji nasyconej. Stwierdzono, że próbki z małą zawartością biomarkerów nie nadają się do analiz. Z drugiej strony zbyt duże stężenie analitu podanego na chromatograf gazowy powoduje wzrost linii bazowej i gorszy rozdział pików, co również stanowi problem. Wstępnie oznaczono wartości δ13C dla biomarkerów frakcji nasyconej z grupy hopanów: bisnorhopanu (BNH), oleananu, C29 norhopanu, C30 hopanu, moretanu i serii C31–C35 homohopanów oraz dla surowych rop naftowych. Stwierdzono względnie niewielkie różnice w wartości δ13C pomiędzy BNH a hopanami i BNH a surowymi ropami, co sugeruje najprawdopodobniej to samo źródło pochodzenia wszystkich biomarkerów (w tym BNH). Próbowano również oznaczać biomarkery we frakcji aromatycznej metodą GC-IRMS, co jednak się nie udało. Chcąc w przyszłości przeprowadzać takie oznaczenia, należy najprawdopodobniej zastosować specjalną metodykę przygotowania próbek frakcji aromatycznej.

EN

GC-IRMS analysis extends and confirms (or not) the interpretation based on the results of GC-MS analyses. For example, it is very useful in determining the sedimentation environment of organic matter. GC-MS analysis of biomarkers and the results are reliable, but only GC-IRMS studies can confirm it. In this study, the origin of BNH (28,30-bisnorhopane from chemoautotrophic bacteria) and origin of higher carotenoids and their derivatives from Chlorobiaceae or Chromotiaceae bacteria were confirmed through isotopic analyzes. Biomarkers were analyzed using the GC-IRMS and EA-IRMS apparatus. The obtained chromatograms from the IRMS analyses were compared with the archival GC-MS analyses for the same samples in order to identify individual chemical compounds. In addition to the existing methodology of sample preparation for analyses, a non-standard method was also used, consisting in the separation of n-alkanes from branched hydrocarbons. The repeatability of the method was determined on the GC-IRMS and the values of δ13C for selected biomarkers from the saturated fraction were determined. It was found that samples with low biomarker content are not suitable for analysis. On the other hand, too high concentration of the analyte causes an increase of the chromatogram baseline and worse separation of the peaks, which is also a problem. For the crude oils the δ13C values were initially determined for the biomarkers of the saturated fraction from the hopanes group: bisnorhopane (BNH), oleanane, C29 norhopane, C30 hopane, moretane and the C31-C35 homohopane series. Relatively small differences in δ13C values were found between BNH/hopanes and BNH/crude oils, which suggests the same source of origin for all biomarkers (including BNH). Determining biomarkers in the aromatic fraction using the GC-IRMS method was not successful. In the future, a special methodology for preparing samples for carbon isotopic analyses of aromatic fraction will be required.

8

Fusion of feature selection methods in gene recognition

Gil Fabian, Osowski Stanislaw

Bulletin of the Polish Academy of Sciences. Technical Sciences

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2021

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Vol. 69, nr 3

art. no. e136748

EN

The paper presents the fusion approach of different feature selection methods in pattern recognition problems. The following methods are examined: nearest component analysis, Fisher discriminant criterion, refiefF method, stepwise fit, Kolmogorov-Smirnov criteria, T2-test, Kruskall-Wallis test, feature correlation with class, and SVM recursive feature elimination. The sensitivity to the noisy data as well as the repeatability of the most important features are studied. Based on this study, the best selection methods are chosen and applied in the process of selection of the most important genes and gene sequences in a dataset of gene expression microarray in prostate and ovarian cancers. The results of their fusion are presented and discussed. The small selected set of such genes can be treated as biomarkers of cancer.

9

Positronium as a biomarker of hypoxia

Moskal Paweł, Stępień Ewa Ł.

Bio-Algorithms and Med-Systems

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2021

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Vol. 17, no. 4

311--319

EN

In this review article, we present arguments demonstrating that the advent of high sensitivity total-body PET systems and the invention of the method of positronium imaging, open realistic perspectives for the application of positronium as a biomarker for in-vivo assessment of the degree of hypoxia. Hypoxia is a state or condition, in which the availability of oxygen is not sufficient to support physiological processes in tissue and organs. Positronium is a metastable atom formed from electron and positron which is copiously produced in the intramolecular spaces in the living organisms undergoing positron emission tomography (PET). Properties of positronium, such as e.g., lifetime, depend on the size of intramolecular spaces and the concentration in them of oxygen molecules. Therefore, information on the partial pressure of oxygen (pO2) in the tissue may be derived from the positronium lifetime measurement. The partial pressure of oxygen differs between healthy and cancer tissues in the range from 10 to 50 mmHg. Such differences of pO2 result in the change of ortho-positronium lifetime e.g., in water by about 2–7 ps. Thus, the application of positronium as a biomarker of hypoxia requires the determination of the mean positronium lifetime with the resolution in the order of 2 ps. We argue that such resolution is in principle achievable for organ-wise positronium imaging with the total-body PET systems.

10

Novel biomarker and drug delivery systems for theranostics - extracellular vesicles

Stępień Ewa Ł., Rząca Carina, Moskal Paweł

Bio-Algorithms and Med-Systems

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2021

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Vol. 17, no. 4

301--309

EN

Extracellular vesicles (EVs) are nano- and micro-sized double-layered membrane entities derived from most cell types and released into biological fluids. Biological properties (cell-uptake, biocompatibility), and chemical (composition, structure) or physical (size, density) characteristics make EVs a good candidate for drug delivery systems (DDS). Recent advances in the field of EVs (e.g., scaling-up production, purification) and developments of new imaging methods (total-body positron emission tomography [PET]) revealed benefits of radiolabeled EVs in diagnostic and interventional medicine as a potential DDs in theranostics.

11

Comparative petrography and organic geochemistry of different types of organic matter occurring in the Outer Carpathians rocks

Zielińska Magdalena, Fabiańska Monika, Więcław Dariusz, Misz-Kennan Magdalena

Geological Quarterly

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2020

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Vol. 64, No. 1

165--184

EN

The characterization of organic matter (OM) in sedimentary rocks is important in many types of biological, geological and environmental research. The integrated use of microscopy and geochemistry, as here, is particularly useful in any attempt to define the origin and evolution of OM in sedimentary basins. The organic petrography and geochemistry different types of allogenic and authigenic OM from the Polish Outer Carpathian (POC) rocks were studied in present study to compare their genetic type, thermal maturity, depositional environment and post-sedimentation processes. Special attention was paid to redeposited coal clasts occurrences. The used techniques show differences in organic matter type originating from various sources. The organic petrography analysis shows that redeposited coal clasts (CC) and terrigenous organic matter (TOM) are composed predominantly of woody material (the gas-prone Type-III kerogen). Similar results were obtained during the Rock-Eval pyrolysis. Moreover, the GC-MS analysis of extracts indicated the additional source of OM, namely planktonic organic matter (POM) with oil-prone kerogen Type-I or II. This OM is in some cases high thermally mature and could potentially has allochthonous origin. The n-alkane, saturated and aromatic biomarker data revealed deposition of this POM in anoxic deltaic or close-shore sedimentary environments whereas the redeposited coal clasts were probably originally deposited in coal swamps as were the Upper Silesian bituminous coals.

12

Przydatność adipokin jako biomarkerów niedokrwiennej dysfunkcji mięśnia sercowego

Mocan Hognogi Larisa-Diana, Goidescu Cerasela-Mihaela, Farcaş Anca-Daniela, Tukaj Dorota

Laboratorium Medyczne

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2019

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nr 2

14--19

PL

Choroby układu sercowo-naczyniowego są główną przyczyną zgonów zarówno wśród kobiet, jak i mężczyzn, lecz wciąż jeszcze zdarza się duży odsetek niewłaściwych rozpoznań oraz brakuje jasno określonych kryteriów diagnostycznych. Postępy nauk biomolekularnych pozwoliły na udowodnienie kluczowej roli zapalenia i co ważniejsze – również modyfikującego wpływu adipokin we wszystkich stadiach choroby niedokrwiennej serca. Sugeruje się również, że zmagazynowana tkanka tłuszczowa, a dokładnie ta zlokalizowana w obrębie klatki piersiowej, ma duży wpływ na rozwój choroby niedokrwiennej serca, tworząc lokalne środowisko proaterogenne. Układ odpornościowy ściśle współdziała z metabolicznymi czynnikami ryzyka, inicjując, promując i nasilając powstawanie zmian miażdżycowych w ścianach tętnic, a wszystko to z „pomocą” adipokin. Toteż obecnie prowadzone badania intensywnie koncentrują się na odkrywaniu biomarkerów zapewniających zwiększenie szans wykrycia subklinicznej dysfunkcji mięśnia sercowego, a także mogących dodać stałą wartość do obecnych kryteriów ryzyka, ustalonych poprzez wytyczne.

EN

Cardiovascular disease is the leading cause of death among both women and men, but there is still a great percentage of misdiagnosis and lack of clearly defined criteria. Advances in biomolecular science have proven the crucial role of inflammation and, more importantly, the role of adipokines in mediating all stages of coronary artery disease. It has also been suggested that regional fat deposits, more precisely from thoracic region, have a major influence on the development of coronary artery disease by creating a local proatherogenic environment. The immune system closely interacts with metabolic risk factors to initiate, promote, and further aggravate the atherosclerotic lesions on the arterial wall all with the „help” of adipokines. So nowadays, research extensively focuses on uncovering biomarkers that would provide an increased chance of detecting subclinical cardiac distress and also add a consistent value to current guideline-imposed risk criteria.

13

Korelacja wybranych biomarkerów z etiologią i ciężkością posocznicy

Holub Michal, Džupová Olga, Růžková Michaela, Stráníková Alžběta, Bartáková Eva, Máca Jan, Beneš Jiří, Herwald Heiko, Beran Ondřej

Laboratorium Medyczne

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2019

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nr 4

14--23

PL

Zarówno rodzaj czynnika infekcyjnego wywołującego posocznicę, jak i punkt wyjścia zakażenia uogólnionego wpływają na przebieg odpowiedzi zapalnej. W prezentowanej pracy autorzy oceniali stężenia cytokin (IL-6, IL-8 i IL-10) w osoczu, chemokin (CCL2/MCP-1, MIP-1β), białka wiążącego heparynę (HBP), rozpuszczalnego CD14 (sCD14) i kortyzolu u pacjentów z posocznicą w ciągu pierwszych 96 godzin hospitalizacji na oddziale intensywnej terapii. Etiologię ustalono u 56 spośród 62 pacjentów objętych badaniem. Stężenia MCP-1, sCD14, IL-6 i IL-10 w osoczu były znamiennie wyższe u chorych z pozaszpitalnym zapaleniem płuc (community-acquired pneumonia, CAP) i infekcyjnym zapaleniem wsierdzia (infective endocarditis, IE) niż z bakteryjnym zapaleniem opon mózgowo-rdzeniowych (bacterial meningitis, BM). Stężenia kortyzolu były wyższe u chorych z IE niż z BM i CAP, a w jednym z punktów czasowych – wyższe u chorych z posocznicą wywołaną przez bakterie Gram-ujemne niż przez Gram-dodatnie. Co więcej, stężenia kortyzolu i MCP-1 wykazywały dodatnią korelację z obliczanym codziennie wynikiem w skali SOFA. Ponadto stężenia HBP były znamiennie wyższe u chorych z IE niż u chorych z BM. Powyższe odkrycia sugerują, że na wartości: MCP1, sCD14, IL-6, IL-10, kortyzolu i HBP, wpływa punkt wyjścia posocznicy oraz że podwyższone stężenia MCP-1 i kortyzolu w osoczu są związane z zaburzeniami czynności narządów wewnętrznych w przebiegu posocznicy.

14

Diagnostyka laboratoryjna sepsy

Zielińska-Borkowska Urszula, Skirecki Tomasz

Laboratorium Medyczne

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2019

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nr 1

34--39

PL

Sepsa to nieprawidłowa odpowiedź gospodarza na zakażenie wywołane przez patogeny. Dokładna i szybka diagnoza pozwala na wdrożenie szybkiej terapii. W pracy przedstawiono niektóre badania laboratoryjne wykonywane w podejrzeniu sepsy. Od 2016 roku zalecane jest oznaczanie mleczanów. Do badań włączono również poziom bilirubiny oraz kreatyniny, a raczej ich progresje w określaniu niewydolności wielonarządowej. Zaproponowano kilka nowych markerów do rozpoznawania sepsy, jak i wskaźników prognostycznych. Do chwili obecnej nie ma jednego laboratoryjnego testu pozwalającego na jego podstawie rozpoznać sepsę.

EN

Sepsis is the host response to microbial pathogens. An accurate and timely diagnosis of sepsis allows for prompt and appropriate treatment. This paper discusses selected laboratory tests that are carried out when sepsis is suspected. The 2016 sepsis consensus definitions include lactate concentrations. Also included in the 2016 definitions are the measurements of bilirubin and creatinine, or rather their progressions, in order to determine multisystem organ failure. Several new biomarkers have been proposed to diagnose sepsis or to predict mortality. So far there has been no single laboratory test that accurately diagnoses sepsis.

15

Środowisko sedymentacji i korelacja geochemiczna dolnooligoceńskich utworów z obrębu jednostek dukielskiej i grybowskiej

Dziadzio P. S., Matyasik I.

Nafta-Gaz

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2018

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R. 74, nr 6

423--434

PL

Celem pracy była interpretacja środowisk depozycji utworów dolnego oligocenu, nazywanych warstwami podgrybowskimi i grybowskimi, z obrębu tzw. jednostki grybowskiej występujących w oknach tektonicznych Grybowa i Ropy oraz porównanie i wzajemne skorelowanie ich z warstwami menilitowymi z obrębu jednostki dukielskiej (ss.) z rejonu Dukli i Tylawy. Wyniki zostały oparte na badaniach sedymentologicznych i geochemicznych (Rock-Eval, biomarkery) uzupełnionych badaniami biostratygraficznymi, w celu określenia ich pozycji stratygraficznej. Wskazują one na odmienne warunki ich powstania niż dotychczas przyjmowano w wielu publikacjach, szczególnie w kontekście głębokości oligoceńskiego basenu sedymentacyjnego Karpat, i dają kolejne argumenty do zmiany poglądów na jego ewolucję. Przeprowadzone badania wskazują na znaczne podobieństwo litologiczne i dużo mniejsze podobieństwo geochemiczne warstw występujących w oknach tektonicznych do tych z obrębu jednostki dukielskiej (ss.). Główny powód różnicy wynika z ich stopnia pogrzebania i z wyższego zaangażowania tektonicznego warstw występujących w oknach tektonicznych, które weszły w fazę generowania węglowodorów i je wygenerowały. Niewielkie ilości ropy naftowej nadal są w ich obrębie zakumulowane.

EN

The aim of the work was to interpret the depositional environments of the Lower Oligocene Subgrybow and Grybow beds from the Grybow Unit, which are present in Grybow and Ropa tectonic windows, as well as the comparison and correlation between them and Menilite Beds from the Dukla Unit (ss.) in the area of Dukla and Tylawa. The results, based on sedimentological and geochemical studies (Rock Eval, biomarkers) supplemented by the biostratigraphic studies conducted to determine their stratigraphic position, show, that their origin differs from that presented in many previous papers, especially in the context of the depth of the Carpathian Oligocene sedimentary basin. They also provide some new arguments for revision views on its evolution. The results of research, show their lithological similarity, but to a lesser extent the geochemical similarity of beds occurring in tectonic windows and those in the area of the Dukla Unit (ss.). The main reason for such a difference is due to their different degree of burial maturation and tectonic evolution. Rocks from the tectonic windows were in the hydrocarbon generation window and generated hydrocarbons. Small amounts of crude oil are still being accumulated within them.

16

Biomarkery, Tmax oraz refleksyjność witrynitu jako wskaźniki dojrzałości termicznej materii organicznej w skałach osadowych – korelacje i zakres stosowalności

Bieleń W., Matyasik I.

Nafta-Gaz

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2018

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R. 74, nr 8

575--583

PL

Niniejsza praca przedstawia zależności między różnymi wskaźnikami określającymi stopień dojrzałości termicznej materii organicznej. W badaniach wykorzystano pomiar refleksyjności witrynitu (Ro), pomiar Tmax z analizy Rock-Eval, molekularne wskaźniki dojrzałości otrzymane z analizy GC-MS frakcji nasyconej i aromatycznej ekstrahowanej substancji organicznej. Wzięto pod uwagę próbki zawierające witrynit, a także takie, które w składzie (głównie próbki dolnopaleozoiczne) zawierały macerały witrynitopo- dobne lub bituminit. Wykonano analizę korelacyjną między wskaźnikami stopnia dojrzałości dla próbek fliszu karpackiego oraz próbek reprezentujących utwory syluru i ordowiku oraz kambru górnego. Wyniki tych badań przedstawiono w postaci diagramów korelacyjnych oraz tabel korelacyjnych z obliczonymi współczynnikami korelacji.

EN

This study was aimed to determine the relationship between the various thermal indices determining the degree of organic matter maturity. In the correlation studies, vitrinite reflectance Ro, Tmax parameter from Rock-Eval analysis and indicators calculated obtained from the from the GCMS analysis data of aromatic and saturated fractions were used. For these studies samples containing macerals of vitrinite as well as samples containing vitrinite-like macerals in their composition were taken into account. An analysis of the relationship between indicators of the degree of maturity for samples representing: flysch Carpathian and for Silurian, Ordovician and Cambrian rocks was done. The results of these studies are presented in the form of correlation diagrams and tables with calculated correlation coefficients.

17

Detekcja biomarkerów w pióropuszach gazowych za pomocą kamery wielospektralnej w projektowanej misji Enceladus Orbiter (NASA)

Zalewska N., Kotlarz J., Kacprzak M., Korniluk T.

Pomiary Automatyka Robotyka

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2017

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R. 21, nr 3

35--44

PL

W publikacji podjęto się próby odpowiedzi na pytanie o możliwość analizy składu chemicznego pióropuszy, wykorzystując ich wielospektralne zobrazowania wykonane za pomocą projektowanych dla nowej misji układów optycznych. Stosując teoretyczną analizę transmitancji warstw gazowych złożonych z H2O i CO2 oraz na podstawie przyjętego fizycznego modelu transmitancji promieniowania przez warstwę gazu widocznego na tle o ustalonej reflektancji wybrano pasmo optyczne 0,73 μm pozwalające na najlepsze rozróżnienie tych dwóch substancji. W celu walidacji otrzymanego wyniku przeprowadzono eksperyment fotografując za pomocą kamery wielospektralnej Quercus.6 strumienie gazowe złożone z obu biomarkerów na tłach o wysokiej (> 0,95) oraz niskiej (< 0,05) reflektancji w paśmie światła widzialnego i NIR. Pozyskane dane potwierdziły wynik analizy sygnatur spektralnych transmitancji obu biomarkerów. Na podstawie otrzymanego w doświadczeniu wyniku ustalono brzegowe parametry sensora i układu optycznego dla projektowanej dla orbitera kamery wielospektralnej pozwalające na oszacowanie względnej zawartości H2O i CO2 w pióropuszach fotografowanych na tle przestrzeni kosmicznej z dokładnością 2%: kanał optyczny λ = 0,730 ±0,020 μm, prędkość względna między orbiterem a księżycem v < 200 m/s, czas ekspozycji tEXP < 12 ms, iloczyn współczynnika efektywności kwantowej całego układu optycznego i względnych różnic reflektancji rejestrowanych obiektów w wybranym kanale ≥ 2,5%, wielkość pojedynczego piksela na detektorze CCD ≥ (3,75 · 3,75) μm2, głębokość studni potencjału piksela CCD ≥ 12 400 e–, zapis danych RAW co najmniej 8-bitowy. Otrzymany optymalny kanał nie był rejestrowany za pomocą stosowanych w poprzednich misjach sensorów optycznych MVIC. Stosowanie opisanej metodyki rozróżniania biomarkerów jest możliwe pod warunkiem, że jeden z czterech kanałów optycznych projektowanej kamery MAC będzie zawierać kanał 0,73 μm.

EN

The cause of the cryovolcanic activity on the Enceladus south hemisphere and related to this activity gas plumes are one of the biggest mysteries of the outer solar system moons. The possibility of the existence of the ocean under Enceladus icy outer layer was confirmed through direct chemical plumes composition measurement during Cassini close flyby 168.2 km over moon’s surface. Three out of the four main plumes components are standard biomarkers (H2O, CO2 and CH4). Physical plumes parameters variability observed also by Cassini, possibility of drawing conclusions about cryovolcanic activity reasons and biotic causes of biomarkers presence in plumes are important reasons of new, dedicated to Enceladus observation, NASA’s mission development. In this paper we are asking about possibility of Enceladus plumes chemical components analysis using multispectral imaging by projected for this new mission sensors. We chose band 0.73 μm for H2O and CO2 distinguish using theoretical transmittance gas layers analysis and physical radiation transmittance through gas layer visible on the background material with defined constant reflectance model. In order to validate this result an experiment was conducted. Using multispectral camera Quercus.6 we photographed H2O and CO2 gas layers visible on the high (> 0.95) and low (< 0.05) visible light and NIR reflectance backgrounds. The results confirmed theoretical spectral transmittance analysis of those two biomarkers. Based on this result we established boundary parameters of the sensor and optical system projected for the orbiter allowing relative content of the biomarkers estimation with precision up to 2%: optical band λ = 0.730 (± 0.020) μm, relative velocity between orbiter and moon v < 200 m/s, exposition time tEXP < 12 ms, quantum efficiency of the whole optical system and two biomarkers in selected wavelength reflectance difference product ≥ 2,5%, single CCD pixel physical size ≥ (3,75 · 3,75) μm2, potential well depth for one CCD pixel ≥ 12 400 e–, RAW data record at least 8-bit. Optimal result waveband wasn’t recorded before using MVIC optical systems during past missions. If we want to apply proposed in this paper biomarkers distinguish methodology one out of four optical channels of the MAC camera projected for the new mission should cover also selected wavelength.

18

Genetic correlation of source rocks and natural gas in the Polish Outer Carpathians and Paleozoic–Mesozoic basement east of Kraków (southern Poland)

Kotarba M. J., Więcław D., Bilkiewicz E., Dziadzio P., Kowalski A.

Geological Quarterly

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2017

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Vol. 61, No. 4

795--824

EN

Natural gas-source rock correlations in the Polish Outer Carpathians and Paleozoic–Mesozoic basement in the Kraków–Brzesko–Nowy Sącz area (southern Poland) have been established. In the Dukla and Sub-Silesian units, mixed kerogen Type-II/III or III/II occurs. The organic matter is immature or low-mature. The Oligocene Menilite beds of the Silesian Unit are rich in TOC and contain gas-prone Type III kerogen of low maturity. In the Paleozoic–Mesozoic basement, the TOC content and residual hydrocarbon potential vary in the Middle and Upper Devonian strata, Mississippian carbonate and clastic facies and Middle Jurassic strata. The Paleozoic strata are capable of thermogenic hydrocarbon generation, while organic matter in the Middle Jurassic rocks is generally immature. Gaseous hydrocarbons accumulated both in the Silesian and Dukla units of the Polish Outer Carpathians and in the Mesozoic basement are genetically related to thermogenic and microbial processes. The Outer Carpathian natural gas was generated mainly from the Type-II/III kerogen of the Oligocene Menilite beds. The thermogenic gases from the Mesozoic basement were generated from Devonian and Mississippian (carbonate) Type-II and mixed II/III kerogens and probably from Silurian/Ordovician Type-II kerogen and Middle Jurassic Type-III/II kerogen occurring at more than 7 km depth. Microbial methane migrated into the Outer Carpathian flysch succession from the Miocene strata of the Carpathian Foredeep.

19

System of Optoelectronic Sensors for Breath Analysis

Mikołajczyk J., Wojtas J., Bielecki Z., Stacewicz T., Szabra D., Magryta P., Prokopiuk A., Tkacz A., Panek M.

Metrology and Measurement Systems

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2016

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Vol. 23, nr 3

481--489

EN

The paper describes an integrated laser absorption system as a potential tool for breath analysis for clinical diagnostics, online therapy monitoring and metabolic disorder control. The sensors operate basing on cavity enhanced spectroscopy and multi-pass spectroscopy supported by wavelength modulation spectroscopy. The aspects concerning selection of operational spectral range and minimization of interference are also discussed. Tests results of the constructed devices collected with reference samples of biomarkers are also presented. The obtained data provide an opportunity to analyse applicability of optoelectronic sensors in medical screening.

20

Origin and migration of oil from the Ukrainian Outer Carpathians to their Mesozoic basement: a case of Lopushna traps

Radkovets N. Y., Kotarba M., Koltun Y., Kowalski A., Kosakowski P., Więclaw D.

Geological Quarterly

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2016

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Vol. 60, No. 1

133--148

EN

Lopushna oil field has been discovered in Mesozoic-Paleogene strata of the platform basement under the Ukrainian Outer (Flysch) Carpathians. Oils from two main accumulations, occurring in the Upper Cretaceous sandstone and Upper Jurassic limestone reservoirs, have been analysed in order to identify their origin and relation to the known petroleum systems in the region of the Outer Carpathians and the basement of the Carpathian Foredeep. Results of geochemical investigations of oils, including biomarker and isotopic data, show a good correlation with oils, accumulated in the Carpathian flysch strata. Oils are low-sulphur and did not undergo significant degradation. They were generated from Type II or II/III kerogen, deposited in anoxic environments in clastic sediments. Generation occurred at the peak of “oil window”, probably in the temperature range of 122 to 126oC. The presence of oleanane indicates the Cretaceous or younger source rocks. Good correlation on biomarker and isotopic data with the organic matter dispersed in Oligocene Menilite Beds, occurring at the top of the Carpathian flysch succession, allowed authors to identify them as source rocks for oils of the Lopushna field, which thus can be regarded as an oil family of the Outer Carpathians. The migration distance for both Lopushna oils and oils accumulated in the Carpathian flysch strata was similar. A number of sub-vertical dislocations, on which the subsided flysch strata occur at the same depth level with the Jurassic and Cretaceous rocks of the platform, can be assumed as possible migration pathways from the mature source rocks of the Oligocene Menilite Beds of Boryslav-Pokuttya, Skyba or Krosno units to the Lopushna type traps, which suggests the possibility of existence of other hydrocarbon accumulations of this type. The Lopushna field so far is unique containing this type of oil found in the basement of the Ukrainian Carpathian Foredeep.