Article
Physics, Fluids & Plasmas
Takuya Imaizumi, Nobuhisa Umeki, Ryo Yoshizawa, Tomoyuki Obuchi, Yasushi Sako, Yoshiyuki Kabashima
Summary: We address the problem of evaluating transfer entropy produced by biochemical reactions from experimentally measured data. By utilizing Gaussian approximation and computational statistics techniques, we overcome the challenge of nonstationarity in biochemical signals and develop a method to screen for statistically significant estimates. Applying this method to real biological data from the ERBB-RAS-MAPK system demonstrates its usefulness in uncovering important pathways of biochemical reactions.
Review
Geography, Physical
Yue Qiu, Xuesheng Zhao, Deqin Fan, Songnian Li, Yijing Zhao
Summary: Rapid population growth has significant impacts on society, economy, and environment. Accurate population distribution data are crucial for monitoring and evaluating the achievement of Sustainable Development Goals. However, current population data lack spatial details, which can be addressed by disaggregation methods.
INTERNATIONAL JOURNAL OF DIGITAL EARTH
(2022)
Review
Endocrinology & Metabolism
David M. Simpson, Stephen J. Payne, Ronney B. Panerai
Summary: Cerebral autoregulation is a crucial physiological mechanism that maintains stable blood flow to the brain during changes in blood pressure. However, assessing autoregulation in individual patients remains a challenge without a gold standard method.
JOURNAL OF CEREBRAL BLOOD FLOW AND METABOLISM
(2022)
Article
Biotechnology & Applied Microbiology
Fernanda P. Costa, Carlos G. Schrago, Beatriz Mello
Summary: Advances in genome sequencing techniques have led to a significant increase in phylogenomic datasets, posing a computational challenge for Bayesian molecular dating. Rapid molecular dating methods have been developed and compared on empirical datasets. The study found that the relative rate framework (RRF) is a computationally efficient method with statistically comparable results to Bayesian analyses.
Article
Chemistry, Medicinal
Ilenia Giangreco, Abhik Mukhopadhyay, Jason C. Cole
Summary: This study discusses the results of a validation study of a ligand-based screening method, which can use multiple flexible ligands overlaid as a query simultaneously, thus improving virtual screening performance.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Article
Biochemistry & Molecular Biology
Deyaa Abol-Fotouh, Ola E. A. AlHagar, Mohamed A. Hassan
Summary: This study aimed to produce a highly compatible thermoalkaliphilic lipase using new thermophilic bacterial strains from fish wastes. The optimized fermentation parameters significantly increased the productivity of the TA lipase, which demonstrated outstanding activity and stability in extreme conditions. The purified enzyme showed high specific activity and fold purification, with potential for detergent formulations.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Neurosciences
Michael-Paul Schallmo, Kimberly B. Weldon, Philip C. Burton, Scott R. Sponheim, Cheryl A. Olman
Summary: Echo planar imaging (EPI) is commonly used in functional and diffusion-weighted MRI, but suffers from geometric distortions. Various techniques for distortion correction exist, and this study compared methods using B-0 field maps and opposite phase encoding scans. The performance of distortion compensation was found to be equivalent between different software packages. This study provides a framework for quantitatively comparing different distortion compensation methods using human EPI data.
HUMAN BRAIN MAPPING
(2021)
Article
Multidisciplinary Sciences
Zubair Ahmad Sheikh, Imtiaz Ahmed, Kousar Jan, Naveed Nabi, Francesco Fazio
Summary: This research investigates the effects of sex on haematological, biochemical, and blood cell morphology in cultured brown trout. The study finds significant differences in Hb content, RBC count, and Hct content between male and female fish. However, there were no significant differences in most of the other parameters analyzed. These findings suggest the potential use of the data to evaluate fish health and improve overall fish population production.
Article
Environmental Sciences
Bethanie Carney Almroth, Josefin Cartine, Christina Jonander, Max Karlsson, Julie Langlois, Matilda Lindstrom, Jakob Lundin, Nina Melander, Argus Pesqueda, Ida Rahmqvist, Juliette Renaux, Josefin Roos, Francis Spilsbury, Joel Svalin, Hanne Vestlund, Liqian Zhao, Noomi Asker, Giedre Asmonaite, Lina Birgersson, Tahereh Boloori, Frida Book, Tobias Lammel, Joachim Sturve
Summary: This study focused on the potential harmful effects of chemical residues leaching from different textiles on fish, indicating that textile leachate can induce cytotoxicity, mortality, and reduced locomotion in fish. These findings suggest a potential ecotoxicological threat to aquatic environments from chemical leaching of textiles.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2021)
Review
Genetics & Heredity
Priya Moorjani, Garrett Hellenthal
Summary: Genetic data provides a record of our evolutionary history. This review explores the statistical methods used to study population relationships and history using genomic data, highlighting their strengths and limitations. The importance of DNA as a tool to infer human evolutionary history is emphasized, complementing other disciplines such as archaeology, anthropology, and linguistics. Evaluation: 8/10.
ANNUAL REVIEW OF GENOMICS AND HUMAN GENETICS
(2023)
Article
Statistics & Probability
Qian Xu, Demetra Antimisiaris, Maiying Kong
Summary: This article proposes the use of marginal structural models to assess the causal interaction of drugs. Simulation studies show that the proposed method consistently estimates the causal parameters. Case studies examine the effects of different combination treatments on patients.
JOURNAL OF APPLIED STATISTICS
(2022)
Article
Fisheries
Burak Evren Inanan, Umit Acar, Tulden Inanan
Summary: This study evaluated the effects of Ferula elaeochytris root powder on adult male goldfish, with findings showing that 1% of FRP in the diet can have beneficial effects on certain blood parameters, while also negatively impacting spermatozoa parameters and inducing oxidative stress conditions in tissues. It was concluded that the concentration and key compounds of medicinal herbs used as supplements in fish diets should be carefully considered for optimal results.
Article
Engineering, Civil
Thakolpat Khampuengson, Wenjia Wang
Summary: Hydrological data from remote water level monitoring stations are transmitted to the national water management centre via telemetry system. However, the received data may be incomplete or anomalous due to instrument issues. Existing methods often eliminate anomalies or missing data, leading to inaccurate analysis or false alarms. This paper introduces a new approach - Full Subsequence Matching (FSM), for imputing missing values in telemetry water level data. Experimental results show that FSM technique produces more precise imputations, especially for data with strong periodic patterns.
WATER RESOURCES MANAGEMENT
(2023)
Article
Environmental Sciences
Luca Palazzo, Stefania Coppa, Andrea Camedda, Mariacristina Cocca, Francesca De Falco, Alvise Vianello, Giorgio Massaro, Giuseppe Andrea de Lucia
Summary: The assessment of microlitter distribution and composition in the sea is a major challenge, where biological indicators can be an important tool. Research on multiple fish species revealed differences in microlitter ingestion between surface and bottom compartments, providing insights into microlitter levels in different parts of the water column. Analysis of microlitter fragments using Fourier Transform Infrared Spectroscopy helped to allocate species to their respective compartments based on expected buoyancies.
ENVIRONMENTAL POLLUTION
(2021)
Article
Multidisciplinary Sciences
Minjie Shen, Yi-Tan Chang, Chiung-Ting Wu, Sarah J. Parker, Georgia Saylor, Yizhi Wang, Guoqiang Yu, Jennifer E. Van Eyk, Robert Clarke, David M. Herrington, Yue Wang
Summary: Missing values are a significant challenge in quantitative proteomics analysis. Although many methods have been developed to impute missing values, the accuracy comparison remains inconclusive due to the complexity of true missing value mechanisms and imperfect evaluation methodologies. This study evaluates and compares eight representative methods on different missing mechanisms and proposes novel approaches for integration and imputation. However, the evaluation is limited by the usage of artificial missing or masked values instead of authentic missing values.
SCIENTIFIC REPORTS
(2022)
Article
Multidisciplinary Sciences
Natalija Topic Popovic, Blanka Beer Ljubic, Ivancica Strunjak-Perovic, Sanja Babic, Vanesa Lorencin, Margita Jadan, Lara Cizmek, Daniel Matulic, Krunoslav Bojanic, Rozelindra Coz-Rakovac
Article
Chemistry, Applied
Ana Palcic, Sanja Babic, Aleksandra Marsavelski, Maja Galic, Natalija Topic Popovic, Ivancica Strunjak Perovic, Rozelindra Coz-Rakovac, Josip Bronic, Valentin Valtchev
MICROPOROUS AND MESOPOROUS MATERIALS
(2020)
Article
Multidisciplinary Sciences
Sanja Babic, Lara Cizmek, Aleksandra Marsavelski, Olga Malev, Maryline Pflieger, Ivancica Strunjak-Perovic, Natalija Topic Popovic, Rozelindra Coz-Rakovac, Polonca Trebse
Summary: This study provides a comprehensive insight into the impact of lignin degradation products on zebrafish, with results showing that 4-nitrocatechol and catechol are the most toxic substances. The potential harm of methoxyphenols on embryonic development was emphasized, and the need for evaluating these substances in ecotoxicity studies focused on aquatic organisms was highlighted.
SCIENTIFIC REPORTS
(2021)
Article
Chemistry, Multidisciplinary
Natalija Topic Popovic, Martina Krbavcic, Josip Barisic, Blanka Beer Ljubic, Ivancica Strunjak-Perovic, Sanja Babic, Vanesa Lorencin, Daniel Matulic, Tea Tomljanovic, Rozelindra Coz-Rakovac
Summary: The study reveals that seasonal fluctuations of oceanographic factors affect the physiology and antioxidant defense properties of green ormer and Mediterranean scallop in the shallow Northern Adriatic. The reproductive cycles of both species are correlated with seasonal metabolic demands and antioxidant capacity, with winter temperatures impacting enzymatic antioxidant defense. The difference in antioxidant defense between winter levels of ormers and scallops is attributed to variations in reproductive cycles and stress responses induced by seasonal changes in temperature.
APPLIED SCIENCES-BASEL
(2021)
Article
Biochemistry & Molecular Biology
Dario Matulja, Petra Grbcic, Krunoslav Bojanic, Natalija Topic-Popovic, Rozelindra Coz-Rakovac, Sylvain Laclef, Tomislav Smuc, Ozren Jovic, Dean Markovic, Sandra Kraljevic Pavelic
Summary: The study focused on chemical screening of organic extracts and semi-purified fractions from the common Adriatic gorgonian, sea fan, Eunicella cavolini. The extracts displayed various biological activities such as antioxidant, anti-inflammatory, and anti-proliferative effects. Further investigation is needed for purification and characterization of potentially active compounds.
Article
Biochemistry & Molecular Biology
Maja Galic Perecinec, Sanja Babic, Lara Cizmek, Atida Selmani, Natalija Topic Popovic, Maja Dutour Sikiric, Ivancica Strunjak-Perovic, Rozelindra Coz-Rakovac
Summary: The addition of selenite in a two-stage cultivation strategy can significantly increase algal cell density, induce oxidative stress, enhance lipid accumulation, and boost neutral lipid content in marine microalga Dunaliella tertiolecta.
APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY
(2022)
Review
Spectroscopy
Natalija Topic Popovic, Snjezana P. Kazazic, Krunoslav Bojanic, Ivancica Strunjak-Perovic, Rozelindra Coz-Rakovac
Summary: MALDI-TOF MS is an excellent tool for bacterial identification with high throughput, sensitivity, and specificity. Lack of standardized protocol and impact of various factors on its performance require specific optimizations based on bacterial representatives and strain requirements.
MASS SPECTROMETRY REVIEWS
(2021)
Article
Fisheries
Natalija Topic Popovic, Jasenka Gajdos Kljusuric, Ivancica Strunjak-Perovic, Josip Barisic, Dusan Palic, Blanka Beer Ljubic, Sanja Babic, Rozelindra Coz-Rakovac
Summary: The study aimed to evaluate the value and applicability of multivariate tools for assessing hematological and plasma biochemical responses of fish living in treated wastewater. Various data analysis methods and modeling techniques were applied to identify clustering based on parameters, significant variables, and correlations between observed variables and samples collected at different places and seasons. The prediction models showed better performance in fall variables for predicting various blood parameters from fish and demonstrated high applicability for multiple purposes.
AQUACULTURE REPORTS
(2021)
Article
Chemistry, Multidisciplinary
Silvia Krizanac, Natalija Topic Popovic, Josip Barisic, Blanka Beer-Ljubic, Maro Bujak, Sanja Babic, Krunoslav Bojanic, Rozelindra Coz-Rakovac, Daniel Matulic, Ivancica Strunjak-Perovic
Summary: This study aimed to compare the organismal responses of farmed and wild-caught turbot through analyzing biochemical plasma parameters, leukocyte profile, histological tissue profile, and gene expression. The results showed significant differences in various parameters between the two populations, including higher levels of certain biochemical parameters in the farmed population and increased gene expression in the wild-caught turbot. The wild-caught turbot were also found to be infested with two parasites.
APPLIED SCIENCES-BASEL
(2022)
Article
Chemistry, Multidisciplinary
Josipa Ferri, Sanja Matic-Skoko, Rozelindra Coz-Rakovac, Ivancica Strunjak-Perovic, Blanka Beer Ljubic, Natalija Topic Popovic
Summary: This study provides reference ranges and seasonal variations for blood parameters of black scorpionfish, Scorpaena porcus, highlighting the significant differences in these parameters between seasons. The results suggest that monitoring blood parameters can serve as a useful biomarker for the health status of S. porcus, and recommend the use of season-specific reference ranges for this species.
APPLIED SCIENCES-BASEL
(2022)
Article
Environmental Sciences
Natalija Topic Popovic, Snjezana Kazazic, Branka Bilic, Sanja Babic, Krunoslav Bojanic, Maro Bujak, Ivana Tartaro Bujak, Margita Jadan, Ivancica Strunjak-Perovic, Slavko Kepec, Rozelindra Coz-Rakovac
Summary: This study characterized Shewanella isolates from waters affected by a wastewater treatment plant and related fish, finding that they have the ability to produce fatty acids, high sensitivity to antimicrobial drugs, and low biofilm production capability. Exposure of zebrafish embryos to S. baltica resulted in significant developmental effects.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2022)
Article
Multidisciplinary Sciences
Natalija Topic Popovic, Slavko Kepec, Snjezana P. Kazazic, Ivancica Strunjak-Perovic, Krunoslav Bojanic, Rozelindra Coz-Rakovac
Summary: This study evaluated the use of the API20E biochemical identification system as a supportive tool for enhancing the discrimination of environmental bacteria by the MALDI-TOF MS method. The results showed that the API20E system can effectively identify bacterial genera, but there are issues with misidentification. In environmental isolates with lower identification scores, the API20E tests can be used as a purposeful and inexpensive identification support.
Review
Chemistry, Multidisciplinary
Natalija Topic Popovic, Vanesa Lorencin, Ivancica Strunjak-Perovic, Rozelindra Coz-Rakovac
Summary: Close to 8 million tons of waste crab, shrimp and lobster shells, and 10 million tons of waste oyster, clam, scallop and mussel shells are generated every year globally. These disposed shells often harm soils, waters, and marine ecosystems by being dumped at sea or sent to landfill. However, these waste shells have great potential as a new raw material in various fields, such as agriculture, medicine, construction, and more, and there are ongoing efforts to develop sustainable strategies for their management and reutilization.
APPLIED SCIENCES-BASEL
(2023)
Editorial Material
Chemistry, Multidisciplinary
Natalija Topic Popovic
APPLIED SCIENCES-BASEL
(2023)
Review
Environmental Sciences
Natalija Topic Popovic, Lara Cizmek, Sanja Babic, Ivancica Strunjak-Perovic, Rozelindra Coz-Rakovac
Summary: This paper provides an in-depth analysis of the impact of wastewater treatment plant contaminants on fish liver structure, physiology, and metabolism. It also examines the role of fish liver enzymes and antioxidants in metabolizing xenobiotic compounds and combating oxidative damage. The vulnerability of fish to xenobiotic compounds and the importance of biomonitoring exposed fish are highlighted.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2023)
