Article
Spectroscopy
Joanna Depciuch, Magdalena Parlinska-Wojtan, Kursat Rahmi Serin, Huri Bulut, Engin Ulukaya, Nevzat Tarhan, Zozan Guleken
Summary: This study investigated the use of Raman spectroscopy as a promising analytical tool in medical diagnostics and a method to distinguish between healthy individuals and those with cholangiocarcinoma. The results showed that there were differences in the Raman spectra of amino acids, proteins, and lipid vibrations between healthy individuals and cancer patients. Specific ranges in the Raman spectra were identified as effective in distinguishing between the two groups.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2022)
Article
Plant Sciences
Manju Kumari, Siddhant Ranjan Padhi, Sushil Kumar Chourey, Vishal Kondal, Swapnil S. Thakare, Ankita Negi, Veena Gupta, Mamta Arya, Jeshima Khan Yasin, Rakesh Singh, Chellapilla Bharadwaj, Atul Kumar, Kailash Chandra Bhatt, Rakesh Bhardwaj, Jai Chand Rana, Tanay Joshi, Amritbir Riar
Summary: Horsegram is an underutilized pulse crop with significant nutritional variability. This study assessed the nutritional profile of 139 horsegram germplasm lines from various Indian states and identified promising accessions with desirable traits. The findings highlight the potential of horsegram for future food and nutritional security.
Article
Plant Sciences
Reetu Verma, Nageswer Singh, Maharishi Tomar, Rakesh Bhardwaj, Dibyendu Deb, Anita Rana
Summary: This study characterized the phytochemical properties of 15 wild Murraya koenigii (L.) Spreng. (MK) leaves obtained from different locations in Himachal Pradesh. The results showed significant variations in total phenolics, flavonoids, essential oils, quinones, tannins, and antioxidant activity at different growth stages. The study also found that these phytochemical parameters reached their highest levels during the flowering stage.
FRONTIERS IN PLANT SCIENCE
(2022)
Review
Instruments & Instrumentation
J. Renwick Beattie, Francis W. L. Esmonde-White
Summary: Spectroscopy rapidly captures a large amount of data, which is processed using principal component analysis to simplify complex spectral datasets into comprehensible information. Despite its wide use, the linear algebra behind principal component analysis is often not well understood by applied scientists and spectroscopists. The process traces the journey of spectra and relies solely on the information within the spectra to provide meaningful interpretation and analysis.
APPLIED SPECTROSCOPY
(2021)
Article
Multidisciplinary Sciences
Racheal John, Haritha Bollinedi, Christine Jeyaseelan, Siddhant Ranjan Padhi, Neha Sajwan, Dhrubjyoti Nath, Rakesh Singh, Sudhir Pal Ahlawat, Rakesh Bhardwaj, Jai Chand Rana
Summary: The study conducted nutritional profiling of 395 Assam rice landraces for various traits. The results revealed high diversity and nutritional potential in these landraces, including low glycemic index varieties. Correlations between different traits were found, and multivariate analyses identified clusters of accessions with distinct nutritional attributes. These findings have implications for cultivar development and breeding programs.
Article
Chemistry, Applied
Maharishi Tomar, Rakesh Bhardwaj, Manoj Kumar, Sumer Pal Singh, Veda Krishnan, Rekha Kansal, Reetu Verma, Vijay Kumar Yadav, Anil Dahuja, Sudhir Pal Ahlawat, Jai Chand Rana, Haritha Bollinedi, Ranjeet Ranjan Kumar, Suneha Goswami, T. Vinutha, C. Tara Satyavathi, Shelly Praveen, Archana Sachdev
Summary: The study analyzed the nutritional composition of 87 different Pearl millet germplasm, showing significant variations in carbohydrate, protein, lipid, antinutritional factors, phenols, and minerals. Multivariate data analysis was used to identify the diversity of these attributes across germplasm, revealing distinct variations in different nutritional contents.
JOURNAL OF FOOD COMPOSITION AND ANALYSIS
(2021)
Article
Computer Science, Interdisciplinary Applications
Yushan Liu, Luyi Li, Zeming Chang, Pan Wang
Summary: This paper proposes a Kriging-based analytical technique for estimating multivariate sensitivity indices (MSI). Two types of MSI are studied and analyzed, one based on principal component analysis (MSI-PCA) and the other based on covariance decomposition (MSI-CD). The accuracy and efficiency of the proposed KBA and D-Kriging methods are tested and discussed using four examples.
STRUCTURAL AND MULTIDISCIPLINARY OPTIMIZATION
(2022)
Article
Chemistry, Applied
Carla de Fatima Alves Nonato, Cicera Janaine Camilo, Debora Odilia Duarte Leite, Mario Gustavo Lucio Albuquerque da Abrega, Jaime Ribeiro-Filho, Irwin Rose Alencar de Menezes, Josean Fechine Tavares, Jose Galberto Martins da Costa
Summary: This study compared the chemical composition and antioxidant potential of essential oils from the Lippia genus through chemometric analysis. The results showed that the essential oils exhibited significant antioxidant activity, with different compounds in Lippia alba being effective in various antioxidant methods. The findings highlight the importance of Lippia compounds for protecting against oxidative stress and their potential use in food preservation.
Article
Chemistry, Multidisciplinary
Elisabetta Pittari, Luigi Moio, Paola Piombino
Summary: Gas-chromatography/mass-spectrometry and sensory descriptive analyses were used to study the volatile and olfactory properties of Aglianico and Primitivo red wines. Multivariate statistical analyses showed differences in volatile compounds between the two wines, with higher amounts in Aglianico. The analysis also revealed intra-varietal similarity and inter-varietal diversity in terms of aromatic characteristics, indicating their potential as quality markers.
APPLIED SCIENCES-BASEL
(2023)
Article
Biochemistry & Molecular Biology
Soumeya Khaled-Khodja, Hassen Cheraitia, Karima Rouibah, Hana Ferkous, Gael Durand, Semia Cherif, Gamal A. El-Hiti, Krishna Kumar Yadav, Alessandro Erto, Yacine Benguerba
Summary: In this study, the contamination of persistent organic pollutants (POPs) in Annaba Bay, Algeria, was investigated using multivariate analysis. The results showed that the main sources of PCB emissions in the bay are urban/domestic and agricultural/industrial. This research provides a potential procedure and methodological analysis for future case studies.
Article
Spectroscopy
Celine Burnier, Virginie Favre, Genevieve Massonnet
Summary: This study aimed to optimize the parameters for polydimethylsiloxane (PDMS) analysis and detection by looking at resolution and number of scans. Experimental parameters were refined through a full factorial experimental design (FFD) and extended to a face centered central composite design (FCCD) for optimization. Repeatability of the results was investigated using principal component analysis (PCA) and hierarchical cluster analysis (HCA) to select the most relevant analytical parameters.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2021)
Article
Psychiatry
Julia M. Longenecker, Gretchen L. Haas, Dean F. Salisbury
Summary: This study aimed to confirm and expand the hierarchical structure of psychosis symptoms in first-episode psychosis. The 4-component model provided the best prediction of functioning, with apathy/asociality being a strong predictor of long-term functioning.
SCHIZOPHRENIA BULLETIN
(2022)
Article
Food Science & Technology
Sunil Kumar Jha, Jian Zhang, Kenshi Hayashi, Chuanjun Liu
Summary: This study aims to identify discriminating chemical constituents in banana odors from the Philippines and Ecuador using GC-MS characterization. Ester is recognized as a major chemical class in selected banana odors, and compounds like 2-hexenal, ethyl acetate, and hexanoic acid, ethyl ester have been identified. Principal component analysis and hierarchical cluster analysis successfully differentiated the banana odors, achieving 100% discrimination of selected banana odors.
JOURNAL OF FOOD SCIENCE AND TECHNOLOGY-MYSORE
(2022)
Article
Chemistry, Inorganic & Nuclear
Thiago G. Costa, Antonio Salvio Mangrich, Morgana H. Z. Hubner, Marcelino D. de M. Correia, Isabela da Silva Muller, Lucas Bond Reis, Sailer S. dos Santos, Juliana Salles Machado, Lucas Bueno, Felipe Rodrigues dos Santos, Fabio Lopes
Summary: Scientific analysis of archaeological ceramic samples from the Tupi-Guarani tradition provides insights into their ancient culture, production processes, and material characteristics. The study utilized scanning electron microscopy, FTIR spectroscopy, and multivariate statistical methods to identify and characterize the structures, morphologies, and elemental compositions of the ceramics, confirming correlations between samples from different geographical regions.
APPLIED RADIATION AND ISOTOPES
(2021)
Article
Water Resources
Rimon Thomas, Francisco Pinero-Garcia, Eva Forssell-Aronsson, Juan Mantero, Mats Isaksson
Summary: This study aimed to identify patterns in water quality data of pit lakes through principal component analysis and hierarchical cluster analysis, revealing differences among different types of pit lakes. While surface water parameters could separate elements into clusters based on chemical groups in most cases, the clustering of pit lake data did not clearly differentiate between types. Principal component analysis showed that three components for both water and sediment data explained a significant portion of the variance.
MINE WATER AND THE ENVIRONMENT
(2022)
Article
Chemistry, Multidisciplinary
Ewelina Lipiec, Janina Kaderli, Jan Kobierski, Roland Riek, Katarzyna Skirlinska-Nosek, Kamila Sofinska, Marek Szymonski, Renato Zenobi
Summary: Abnormal aggregation of amyloid-beta is a complex and heterogeneous process, and a new approach using TERS has provided detailed molecular structure information of single amyloid-beta aggregates, revealing a beta-sheet rearrangement. This study will contribute to a better understanding of the etiology of Alzheimer's disease.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Review
Biochemistry & Molecular Biology
Ewelina Lipiec, Kamila Sofinska, Sara Seweryn, Natalia Wilkosz, Marek Szymonski
Summary: DNA carries genetic information in all living organisms and its structure can be influenced by various factors. This paper reviews recent achievements in studying DNA structure at the nanoscale, particularly focusing on high-resolution imaging with AFM at liquid/solid interfaces. By combining structural and chemical details of samples, a comprehensive understanding of the investigated phenomenon can be achieved.
Article
Chemistry, Physical
Kamila Sofinska, Dawid Lupa, Anna Chachaj-Brekiesz, Michal Czaja, Jan Kobierski, Sara Seweryn, Katarzyna Skirlinska-Nosek, Marek Szymonski, Natalia Wilkosz, Anita Wnetrzak, Ewelina Lipiec
Summary: Lipid membranes are essential for the existence of life, playing complex functions such as separation of biological environments and participation in regulatory processes. However, the reasons behind the variability within lipid membranes and its biochemical significance are still not well understood. Simplifying the studied systems and utilizing analytical methods are important for understanding phenomena occurring in natural, complex membranes. This review discusses the structural complexity of lipid membranes and focuses on the analytical studies of artificial systems at various interfaces. It summarizes experimental and theoretical approaches providing information about the molecular structure, composition, and organization of lipid membranes, as well as the real-time visualization of the influence of various molecules on their integrity. The review also highlights the latest achievements in the field of lipid layer-based biosensors.
ADVANCES IN COLLOID AND INTERFACE SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Michal Czaja, Katarzyna Skirlinska-Nosek, Olga Adamczyk, Kamila Sofinska, Natalia Wilkosz, Zenon Rajfur, Marek Szymonski, Ewelina Lipiec
Summary: This study used Raman micro-spectroscopy to track the conformational changes of DNA in cells and discovered the cellular response to DNA damage and increased protein expression during DNA repair processes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Oncology
Krzysztof Szymonski, Katarzyna Milian-Ciesielska, Ewelina Lipiec, Dariusz Adamek
Summary: Pancreatic cancer is a highly aggressive and lethal malignancy, with ongoing uncertainty in pathological evaluation. Staying up-to-date with new research findings is crucial for clinicians and pathologists.
Article
Engineering, Multidisciplinary
Kamila Sofi, Michal Ciesla, Jakub Barbasz, Natalia Wilkosz, Ewelina Lipiec, Marek Szymonski, Piotr Bialas
Summary: DNA is susceptible to various damaging factors, which can cause single- or double-strand breaks. Atomic force microscopy is used to determine the length of DNA fragments deposited on surfaces and quantify double-strand breaks. To overcome the underestimation caused by image resolution, a new methodology based on statistics of DNA fragment length is proposed, along with software for automatic calculation of double-strand breaks. The method is applied to characterize DNA plasmid fragmentation caused by the anticancer chemotherapeutic drug bleomycin.
Article
Multidisciplinary Sciences
Sara Seweryn, Katarzyna Skirlinska-Nosek, Natalia Wilkosz, Kamila Sofinska, David Perez-Guaita, Magdalena Ocwieja, Jakub Barbasz, Marek Szymonski, Ewelina Lipiec
Summary: This study investigated the repair process of DNA double-strand breaks (DSBs) induced by the anticancer antibiotic bleomycin (BLM) using a multimodal approach. By analyzing the SERS results, spectral bands associated with DSBs were identified, indicating conformational modifications and strand ruptures. A model was established to predict the number of DSBs and detect spectroscopic markers of DNA damage and conformational changes.
SCIENTIFIC REPORTS
(2022)
Article
Spectroscopy
Sara Seweryn, Katarzyna Skirlinska-Nosek, Kamila Sofinska, Konrad Szajna, Jan Kobierski, Kamil Awsiuk, Marek Szymonski, Ewelina Lipiec
Summary: This work focuses on optimizing the TERS technique for efficient DNA measurements by preparing atomically-flat gold substrates, depositing DNA without fixatives, and optimizing TERS probe preparation. Through comprehensive comparison of different probes, reliable and reproducible TER spectra of DNA are obtained, providing a foundation for further research on DNA and its interaction with other biomolecules.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2022)
Article
Radiology, Nuclear Medicine & Medical Imaging
Krzysztof Szymonski, Ewelina Lipiec, Kamila Sofinska, Katarzyna Skirlinska-Nosek, Michal Czaja, Sara Seweryn, Natalia Wilkosz, Giovanni Birarda, Federica Piccirilli, Lisa Vaccari, Lukasz Chmura, Joanna Szpor, Dariusz Adamek, Marek Szymonski
Summary: Knowledge about the biology of pancreatic cancer has been growing, but the survival rate of patients has not greatly improved. This study used molecular imaging techniques and a convolutional neural network (CNN) to investigate the biochemical composition of pancreatic cancer tissue and successfully differentiate different groups of pancreatic tumors.
EUROPEAN JOURNAL OF NUCLEAR MEDICINE AND MOLECULAR IMAGING
(2023)
Article
Reproductive Biology
Kinga Kaminska, Kasun Godakumara, Bianka Swiderska, Agata Malinowska, Getnet Midekessa, Kamila Sofinska, Jakub Barbasz, Alireza Fazeli, Malgorzata Grzesiak
Summary: Extracellular vesicles (EVs) are membrane-bound nanoparticles released by different cell types, playing a crucial role in intercellular communication by carrying various biomolecular compounds. This study assessed the use of size-exclusion chromatography (SEC) for effectively isolating EVs from porcine ovarian follicular fluid. The characterization of EVs was performed using multiple techniques, and the results showed that SEC is an effective method for isolating and studying EVs from porcine follicular fluid, providing opportunities for further functional analyses such as proteomics.
Article
Chemistry, Multidisciplinary
Kamila Sofinska, Piotr Batys, Adrian Cernescu, Dhiman Ghosh, Katarzyna Skirlinska-Nosek, Jakub Barbasz, Sara Seweryn, Natalia Wilkosz, Roland Riek, Marek Szymonski, Ewelina Lipiec
Summary: Through experimental and theoretical studies, we have revealed the influence of the anti-aggregation drug bexarotene on the secondary structure and primary aggregation of amyloid-beta aggregates. We observed that bexarotene limits the formation of parallel beta-sheets in the aggregates and slows down the aggregation process. Molecular dynamics simulations also provided insights into the interaction mechanism between bexarotene and the protein.
