The 2023 MDPI Annual Report has
been released!
 
10 pages, 2581 KiB  
Article
Sex Ratio at Birth after Concurrent Events of Earthquakes and the COVID-19 Pandemic in Croatia
by Dario Pavić
Int. J. Environ. Res. Public Health 2024, 21(5), 572; https://doi.org/10.3390/ijerph21050572 (registering DOI) - 29 Apr 2024
Abstract
The sex ratio at birth (ratio of males to females) has been known to be affected by exogenous shocks such as wars, pollution, natural catastrophes, economic crises, and others. Among these stressful events, both earthquakes and the COVID-19 pandemic have been reported to [...] Read more.
The sex ratio at birth (ratio of males to females) has been known to be affected by exogenous shocks such as wars, pollution, natural catastrophes, economic crises, and others. Among these stressful events, both earthquakes and the COVID-19 pandemic have been reported to lower the sex ratio at birth. In this article, a rather unusual situation of two episodes of simultaneous events of COVID-19 lockdown and earthquakes approximately nine months apart (March and December of 2020) is investigated to assess whether they were associated with a bias in sex ratio at birth 3–5 months later (in utero loss) and 9 months later (loss at conception) in Croatia. The monthly time series of sex ratio at birth, total number of births, and total number of both male and female births from January 2010 to December 2021 were analyzed. Seasonally adjusted autoregressive moving-average models were used to estimate the functional form of the time series from January 2010 to February 2020. These results were used to predict the future values of the series until December 2021 and to compare them with the actual values. For all series used, there was no indication of deviation from the values predicted by the models, neither for 3–5 months nor for 9 months after the COVID-19 lockdown and earthquake events. The possible mechanisms of the absence of bias, such as the threshold of the stressful events and its localized reach, as well as the statistical methods employed, are discussed. Full article
(This article belongs to the Special Issue Human Behavioral Ecology and Health Outcomes)
19 pages, 756 KiB  
Article
Plasma Redox Balance in Advanced-Maternal-Age Pregnant Women and Effects of Plasma on Umbilical Cord Mesenchymal Stem Cells
by Elena Grossini, Carmen Imma Aquino, Sakthipriyan Venkatesan, Libera Troìa, Eleonora Tizzoni, Federica Fumagalli, Daniela Ferrante, Rosanna Vaschetto, Valentino Remorgida and Daniela Surico
Int. J. Mol. Sci. 2024, 25(9), 4869; https://doi.org/10.3390/ijms25094869 (registering DOI) - 29 Apr 2024
Abstract
Pregnancy at advanced maternal age (AMA) is a condition of potential risk for the development of maternal–fetal complications with possible repercussions even in the long term. Here, we analyzed the changes in plasma redox balance and the effects of plasma on human umbilical [...] Read more.
Pregnancy at advanced maternal age (AMA) is a condition of potential risk for the development of maternal–fetal complications with possible repercussions even in the long term. Here, we analyzed the changes in plasma redox balance and the effects of plasma on human umbilical cord mesenchymal cells (hUMSCs) in AMA pregnant women (patients) at various timings of pregnancy. One hundred patients and twenty pregnant women younger than 40 years (controls) were recruited and evaluated at various timings during pregnancy until after delivery. Plasma samples were used to measure the thiobarbituric acid reactive substances (TBARS), glutathione and nitric oxide (NO). In addition, plasma was used to stimulate the hUMSCs, which were tested for cell viability, reactive oxygen species (ROS) and NO release. The obtained results showed that, throughout pregnancy until after delivery in patients, the levels of plasma glutathione and NO were lower than those of controls, while those of TBARS were higher. Moreover, plasma of patients reduced cell viability and NO release, and increased ROS release in hUMSCs. Our results highlighted alterations in the redox balance and the presence of potentially harmful circulating factors in plasma of patients. They could have clinical relevance for the prevention of complications related to AMA pregnancy. Full article
22 pages, 802 KiB  
Article
A Data-Driven Approach to Discovering Process Choreography
by Jaciel David Hernandez-Resendiz, Edgar Tello-Leal and Marcos Sepúlveda
Algorithms 2024, 17(5), 188; https://doi.org/10.3390/a17050188 (registering DOI) - 29 Apr 2024
Abstract
Implementing approaches based on process mining in inter-organizational collaboration environments presents challenges related to the granularity of event logs, the privacy and autonomy of business processes, and the alignment of event data generated in inter-organizational business process (IOBP) execution. Therefore, this paper proposes [...] Read more.
Implementing approaches based on process mining in inter-organizational collaboration environments presents challenges related to the granularity of event logs, the privacy and autonomy of business processes, and the alignment of event data generated in inter-organizational business process (IOBP) execution. Therefore, this paper proposes a complete and modular data-driven approach that implements natural language processing techniques, text similarity, and process mining techniques (discovery and conformance checking) through a set of methods and formal rules that enable analysis of the data contained in the event logs and the intra-organizational process models of the participants in the collaboration, to identify patterns that allow the discovery of the process choreography. The approach enables merging the event logs of the inter-organizational collaboration participants from the identified message interactions, enabling the automatic construction of an IOBP model. The proposed approach was evaluated using four real-life and two artificial event logs. In discovering the choreography process, average values of 0.86, 0.89, and 0.86 were obtained for relationship precision, relation recall, and relationship F-score metrics. In evaluating the quality of the built IOBP models, values of 0.95 and 1.00 were achieved for the precision and recall metrics, respectively. The performance obtained in the different scenarios is encouraging, demonstrating the ability of the approach to discover the process choreography and the construction of business process models in inter-organizational environments. Full article
23 pages, 5603 KiB  
Article
Assessing Satellite Data’s Role in Substituting Ground Measurements for Urban Surfaces Characterization: A Step Towards UHI Mitigation
by Davide Parmeggiani, Francesca Despini, Sofia Costanzini, Malvina Silvestri, Federico Rabuffi, Sergio Teggi and Grazia Ghermandi
Atmosphere 2024, 15(5), 551; https://doi.org/10.3390/atmos15050551 (registering DOI) - 29 Apr 2024
Abstract
Urban surfaces play a crucial role in shaping the Urban Heat Island (UHI) effect by absorbing and retaining significant solar radiation. This paper explores the potential of high-resolution satellite imagery as an alternative method for characterizing urban surfaces to support UHI mitigation strategies [...] Read more.
Urban surfaces play a crucial role in shaping the Urban Heat Island (UHI) effect by absorbing and retaining significant solar radiation. This paper explores the potential of high-resolution satellite imagery as an alternative method for characterizing urban surfaces to support UHI mitigation strategies in urban redevelopment plans. We utilized Landsat images spanning the past 40 years to analyze trends in Land Surface Temperature (LST). Additionally, WorldView-3 (WV3) imagery was acquired for surface characterization, and the results were compared with ground truth measurements using the ASD FieldSpec 4 spectroradiometer. Our findings revealed a strong correlation between satellite-derived surface reflectance and ground truth measurements across various urban surfaces, with Root Mean Square Error (RMSE) values ranging from 0.01 to 0.14. Optimal characterization was observed for surfaces such as bituminous membranes and parking with cobblestones (RMSE < 0.03), although higher RMSE values were noted for tiled roofs, likely due to aging effects. Regarding surface albedo, the differences between satellite-derived data and ground measurements consistently remained below 12% for all surfaces, with the lowest values observed in high heat-absorbing surfaces like bituminous membranes. Despite challenges on certain surfaces, our study highlights the reliability of satellite-derived data for urban surface characterization, thus providing valuable support for UHI mitigation efforts. Full article
(This article belongs to the Special Issue UHI Analysis and Evaluation with Remote Sensing Data)
24 pages, 3750 KiB  
Article
Robust Tracking Control of Wheeled Mobile Robot Based on Differential Flatness and Sliding Active Disturbance Rejection Control: Simulations and Experiments
by Amine Abadi, Amani Ayeb, Moussa Labbadi, David Fofi, Toufik Bakir and Hassen Mekki
Sensors 2024, 24(9), 2849; https://doi.org/10.3390/s24092849 (registering DOI) - 29 Apr 2024
Abstract
This paper proposes a robust tracking control method for wheeled mobile robot (WMR) against uncertainties, including wind disturbances and slipping. Through the application of the differential flatness methodology, the under-actuated WMR model is transformed into a linear canonical form, simplifying the design of [...] Read more.
This paper proposes a robust tracking control method for wheeled mobile robot (WMR) against uncertainties, including wind disturbances and slipping. Through the application of the differential flatness methodology, the under-actuated WMR model is transformed into a linear canonical form, simplifying the design of a stabilizing feedback controller. To handle uncertainties from wheel slip and wind disturbances, the proposed feedback controller uses sliding mode control (SMC). However, increased uncertainties lead to chattering in the SMC approach due to higher control inputs. To mitigate this, a boundary layer around the switching surface is introduced, implementing a continuous control law to reduce chattering. Although increasing the boundary layer thickness reduces chattering, it may compromise the robustness achieved by SMC. To address this challenge, an active disturbance rejection control (ADRC) is integrated with boundary layer sliding mode control. ADRC estimates lumped uncertainties via an extended state observer and eliminates them within the feedback loop. This combined feedback control method aims to achieve practical control and robust tracking performance. Stability properties of the closed-loop system are established using the Lyapunov theory. Finally, simulations and experimental results are conducted to compare and evaluate the efficiency of the proposed robust tracking controller against other existing control methods. Full article
(This article belongs to the Special Issue Mobile Robots: Navigation, Control and Sensing)
19 pages, 645 KiB  
Article
Exposure of Bladder Cancer Cells to Blue Light (l = 453 nm) in the Presence of Riboflavin Synergistically Enhances the Cytotoxic Efficiency of Gemcitabine
by Sofia Sturm, Günter Niegisch, Joachim Windolf and Christoph V. Suschek
Int. J. Mol. Sci. 2024, 25(9), 4868; https://doi.org/10.3390/ijms25094868 (registering DOI) - 29 Apr 2024
Abstract
Non-muscle invasive bladder cancer is a common tumour in men and women. In case of resistance to the standard therapeutic agents, gemcitabine can be used as off-label instillation therapy into the bladder. To reduce potential side effects, continuous efforts are made to optimise [...] Read more.
Non-muscle invasive bladder cancer is a common tumour in men and women. In case of resistance to the standard therapeutic agents, gemcitabine can be used as off-label instillation therapy into the bladder. To reduce potential side effects, continuous efforts are made to optimise the therapeutic potential of drugs, thereby reducing the effective dose and consequently the pharmacological burden of the medication. We recently demonstrated that it is possible to significantly increase the therapeutic efficacy of mitomycin C against a bladder carcinoma cell line by exposure to non-toxic doses of blue light (453 nm). In the present study, we investigated whether the therapeutically supportive effect of blue light can be further enhanced by the additional use of the wavelength-specific photosensitiser riboflavin. We found that the gemcitabine-induced cytotoxicity of bladder cancer cell lines (BFTC-905, SW-1710, RT-112) was significantly enhanced by non-toxic doses of blue light in the presence of riboflavin. Enhanced cytotoxicity correlated with decreased levels of mitochondrial ATP synthesis and increased lipid peroxidation was most likely the result of increased oxidative stress. Due to these properties, blue light in combination with riboflavin could represent an effective therapy option with few side effects and increase the success of local treatment of bladder cancer, whereby the dose of the chemotherapeutic agent used and thus the chemical load could be significantly reduced with similar or improved therapeutic success. Full article
(This article belongs to the Section Molecular Oncology)
17 pages, 596 KiB  
Article
The Influence of Minimal Cultivation Techniques on Growth Rate of Robinia pseudacacia L. Seedlings
by Cristina Drăghici, Ioan Vasile Abrudan, Adela Hoble, Raluca Enescu, Gheorghe Spârchez and Iacob Crăciunesc
Forests 2024, 15(5), 785; https://doi.org/10.3390/f15050785 (registering DOI) - 29 Apr 2024
Abstract
The seed provenance, the type of substrate and its properties, as well as the watering regime in the first years after sowing are among the most important characteristics affecting the production of containerized seedlings. The objective of this study was to analyse the [...] Read more.
The seed provenance, the type of substrate and its properties, as well as the watering regime in the first years after sowing are among the most important characteristics affecting the production of containerized seedlings. The objective of this study was to analyse the growth of black locust (Robinia pseudacacia L.) seedlings on different types of substrate (six mineral and two organic) with different textures and pHs under three different regimes of available water content (no-limiting, medium drought, severe drought) over a period of five months (May–October 2023), using seeds from three sources located in the southeast, south, and west of Romania. The highest seedling emergence rate (73.7%) was obtained for the medium seeds with 18.492 g weight (1000 seed weighs) (Bucharest provenance). Direct sowing in the field and containerized seedlings both showed a trend of growing in height during unlimited water and of growing in diameter during low watering. The lowest survival rate of seedlings (86.7%) occurred in the mineral substrate in the case of rendzina with additional sand (pH 8.70), and for the organic substrate, the lowest survival rate (87.0%) occurred for the peat MKS 3 substrate (pH 4.54). Full article
35 pages, 1568 KiB  
Article
A Theory of Functional Connections-Based hp-Adaptive Mesh Refinement Algorithm for Solving Hypersensitive Two-Point Boundary-Value Problems
by Kristofer Drozd, Roberto Furfaro and Andrea D’Ambrosio
Mathematics 2024, 12(9), 1360; https://doi.org/10.3390/math12091360 (registering DOI) - 29 Apr 2024
Abstract
This manuscript introduces the first hp-adaptive mesh refinement algorithm for the Theory of Functional Connections (TFC) to solve hypersensitive two-point boundary-value problems (TPBVPs). The TFC is a mathematical framework that analytically satisfies linear constraints using an approximation method called a constrained expression. [...] Read more.
This manuscript introduces the first hp-adaptive mesh refinement algorithm for the Theory of Functional Connections (TFC) to solve hypersensitive two-point boundary-value problems (TPBVPs). The TFC is a mathematical framework that analytically satisfies linear constraints using an approximation method called a constrained expression. The constrained expression utilized in this work is composed of two parts. The first part consists of Chebyshev orthogonal polynomials, which conform to the solution of differentiation variables. The second part is a summation of products between switching and projection functionals, which satisfy the boundary constraints. The mesh refinement algorithm relies on the truncation error of the constrained expressions to determine the ideal number of basis functions within a segment’s polynomials. Whether to increase the number of basis functions in a segment or divide it is determined by the decay rate of the truncation error. The results show that the proposed algorithm is capable of solving hypersensitive TPBVPs more accurately than MATLAB R2021b’s bvp4c routine and is much better than the standard TFC method that uses global constrained expressions. The proposed algorithm’s main flaw is its long runtime due to the numerical approximation of the Jacobians. Full article
(This article belongs to the Special Issue Dynamics and Control Using Functional Interpolation)
29 pages, 754 KiB  
Article
Calcium, Phosphate, and Vitamin D in Children and Adolescents with Chronic Diseases: A Cross-Sectional Study
by Marlene Fabiola Escobedo-Monge, Pilar Bahillo-Curieses, Joaquín Parodi-Román, María Antonieta Escobedo-Monge, Pedro Alonso-López and José Manuel Marugán-Miguelsanz
Nutrients 2024, 16(9), 1349; https://doi.org/10.3390/nu16091349 (registering DOI) - 29 Apr 2024
Abstract
Chronic diseases may affect the nutritional status of children and adolescents. Calcium (Ca), phosphorus (P), and vitamin D (Vit-D) are crucial nutrients for their growth and development. Proper diagnosis and treatment are critical components of personalized and precision medicine. Hence, we conducted a [...] Read more.
Chronic diseases may affect the nutritional status of children and adolescents. Calcium (Ca), phosphorus (P), and vitamin D (Vit-D) are crucial nutrients for their growth and development. Proper diagnosis and treatment are critical components of personalized and precision medicine. Hence, we conducted a cross-sectional and comparative study to evaluate Ca, P, and Vit-D levels in their non-skeletal functions and their association with health and nutritional biomarkers in children and adolescents with diverse chronic conditions. We performed anthropometric, body composition, clinical evaluation, biochemical analysis, and dietary survey methods. A total of 78 patients (1–19 years, 43 females, 42 children) took part in this study. Overall, 24, 30, and 24 participants were obese, undernourished, and eutrophic, respectively. Results found that 74% and 35% of individuals had deficient Vit-D and Ca intake, respectively. Most cases were normocalcemic. Results also found that 47% of the subjects had Vit-D deficiency (VDD), 37% were insufficient, and 37% had hypophosphatemia. Of the 46% and 31% of patients with VDD and insufficient levels, 19% and 11% were hypophosphatemic, respectively. Calcium, P, and Vit-D levels were associated with anthropometric parameters, body mass index, body composition, physical activity, diet, growth hormones, and the immune, liver, and kidney systems. These results show the coincident risk of altered Ca, P, and Vit-D metabolism in children and adolescents with chronic diseases. Full article
(This article belongs to the Special Issue Nutritional Status in Children and Adolescents with Chronic Diseases)
16 pages, 5827 KiB  
Article
Preparation and Performance Study of HTPB-g-(PNIPAM/PEG) Thermoresponsive Polymer Brush
by Pengzhi Bi, Xiuzhong Zhu, Li Tian, Jinbang Han, Wanbin Zhang and Tong Wang
Polymers 2024, 16(9), 1248; https://doi.org/10.3390/polym16091248 (registering DOI) - 29 Apr 2024
Abstract
In recent years, a great deal of work has been devoted to the development of thermoresponsive polymers that can be made into new types of smart materials. In this paper, a branched polymer, HTPB-g-(PNIPAM/PEG), with polyolefin chain segments as the backbone [...] Read more.
In recent years, a great deal of work has been devoted to the development of thermoresponsive polymers that can be made into new types of smart materials. In this paper, a branched polymer, HTPB-g-(PNIPAM/PEG), with polyolefin chain segments as the backbone and having polyethylene glycol (PEG) and poly(N-isopropylacrylamide) (PNIPAM) as side chains was synthesized by ATRP and click reactions using N3-HTPB-Br as the macroinitiator. This initiator was designed and synthesized using hydroxyl-terminated polybutadiene (HTPB) as the substrate. The temperature-responsive behavior of the branched polymer was investigated. The lower critical solution temperature (LCST) of the branched polymer was determined by ultraviolet and visible spectrophotometry (UV-vis) and was found to be 35.2 °C. The relationship between the diameter size of micelles and temperature was determined by dynamic light scattering (DLS). It was found that the diameter size changed at 36 °C, which was nearly consistent with the result obtained by UV-vis. The results of the study indicate that HTPB-g-(PNIPAM/PEG) is a temperature-responsive polymer. At room temperature, the polymer can self-assemble into composite micelles, with the main chain as the core and the branched chain as the shell. When the temperature was increased beyond LCST, the polyolefin main chain along with the PNIPAM branched chain assembled to form the nucleus, and the PEG branched chain constituted the shell. Full article
(This article belongs to the Special Issue Feature Papers in Smart and Functional Polymers)
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12 pages, 2350 KiB  
Article
Ketogenic Diet Protects from Experimental Colitis in a Mouse Model Regardless of Dietary Fat Source
by Lotta Luiskari, Jere Lindén, Markku Lehto, Hanne Salmenkari and Riitta Korpela
Nutrients 2024, 16(9), 1348; https://doi.org/10.3390/nu16091348 (registering DOI) - 29 Apr 2024
Abstract
While ketogenic diets (KDs) may have potential as adjunct treatments for gastrointestinal diseases, there is little knowledge on how the fat source of these diets influences intestinal health. The objective of this study was to investigate how the source of dietary fat of [...] Read more.
While ketogenic diets (KDs) may have potential as adjunct treatments for gastrointestinal diseases, there is little knowledge on how the fat source of these diets influences intestinal health. The objective of this study was to investigate how the source of dietary fat of KD influences experimental colitis. We fed nine-week-old male C57BL/6J mice (n = 36) with a low-fat control diet or KD high either in saturated fatty acids (SFA-KD) or polyunsaturated linoleic acid (LA-KD) for four weeks and then induced colitis with dextran sodium sulfate (DSS). To compare the diets, we analyzed macroscopic and histological changes in the colon, intestinal permeability to fluorescein isothiocyanate−dextran (FITC–dextran), and the colonic expression of tight junction proteins and inflammatory markers. While the effects were more pronounced with LA-KD, both KDs markedly alleviated DSS-induced histological lesions. LA-KD prevented inflammation-related weight loss and the shortening of the colon, as well as preserved Il1b and Tnf expression at a healthy level. Despite no significant between-group differences in permeability to FITC–dextran, LA-KD mitigated changes in tight junction protein expression. Thus, KDs may have preventive potential against intestinal inflammation, with the level of the effect being dependent on the dietary fat source. Full article
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18 pages, 1047 KiB  
Article
Expression and Localization Profiles of Tight Junction Proteins in Immune Cells Depend on Their Activation Status
by Lena Voges, Franziska Weiß, Ana-Teresa Branco, Michael Fromm and Susanne M. Krug
Int. J. Mol. Sci. 2024, 25(9), 4861; https://doi.org/10.3390/ijms25094861 (registering DOI) - 29 Apr 2024
Abstract
The ability of the immune system to combat pathogens relies on processes like antigen sampling by dendritic cells and macrophages migrating through endo- and epithelia or penetrating them with their dendrites. In addition, other immune cell subtypes also migrate through the epithelium after [...] Read more.
The ability of the immune system to combat pathogens relies on processes like antigen sampling by dendritic cells and macrophages migrating through endo- and epithelia or penetrating them with their dendrites. In addition, other immune cell subtypes also migrate through the epithelium after activation. For paracellular migration, interactions with tight junctions (TJs) are necessary, and previous studies reported TJ protein expression in several immune cells. Our investigation aimed to characterize, in more detail, the expression profiles of TJ proteins in different immune cells in both naïve and activated states. The mRNA expression analysis revealed distinct expression patterns for TJ proteins, with notable changes, mainly increases, upon activation. At the protein level, LSR appeared predominant, being constitutively present in naïve cell membranes, suggesting roles as a crucial interaction partner. Binding experiments suggested the presence of claudins in the membrane only after stimulation, and claudin-8 translocation to the membrane occurred after stimulation. Our findings suggest a dynamic TJ protein expression in immune cells, implicating diverse functions in response to stimulation, like interaction with TJ proteins or regulatory roles. While further analysis is needed to elucidate the precise roles of TJ proteins, our findings indicate important non-canonical functions of TJ proteins in immune response. Full article
(This article belongs to the Special Issue The Tight Junction and Its Proteins: From Structure to Pathologies)
14 pages, 1640 KiB  
Article
Structural and Dynamic Features of the Recognition of 8-oxoguanosine Paired with an 8-oxoG-clamp by Human 8-oxoguanine-DNA Glycosylase
by Maria V. Lukina, Polina V. Zhdanova and Vladimir V. Koval
Curr. Issues Mol. Biol. 2024, 46(5), 4119-4132; https://doi.org/10.3390/cimb46050253 (registering DOI) - 29 Apr 2024
Abstract
8-oxoguanine (oxoG) is formed in DNA by the action of reactive oxygen species. As a highly mutagenic and the most common oxidative DNA lesion, it is an important marker of oxidative stress. Human 8-oxoguanine-DNA glycosylase (OGG1) is responsible for its prompt removal in [...] Read more.
8-oxoguanine (oxoG) is formed in DNA by the action of reactive oxygen species. As a highly mutagenic and the most common oxidative DNA lesion, it is an important marker of oxidative stress. Human 8-oxoguanine-DNA glycosylase (OGG1) is responsible for its prompt removal in human cells. OGG1 is a bifunctional DNA glycosylase with N-glycosylase and AP lyase activities. Aspects of the detailed mechanism underlying the recognition of 8-oxoguanine among numerous intact bases and its subsequent interaction with the enzyme’s active site amino acid residues are still debated. The main objective of our work was to determine the effect (structural and thermodynamic) of introducing an oxoG-clamp in model DNA substrates on the process of 8-oxoG excision by OGG1. Towards that end, we used DNA duplexes modeling OGG1-specific lesions: 8-oxoguanine or an apurinic/apyrimidinic site with either cytidine or the oxoG-clamp in the complementary strand opposite to the lesion. It was revealed that there was neither hydrolysis of the N-glycosidic bond at oxoG nor cleavage of the sugar–phosphate backbone during the reaction between OGG1 and oxoG-clamp-containing duplexes. Possible structural reasons for the absence of OGG1 enzymatic activity were studied via the stopped-flow kinetic approach and molecular dynamics simulations. The base opposite the damage was found to have a critical effect on the formation of the enzyme–substrate complex and the initiation of DNA cleavage. The oxoG-clamp residue prevented the eversion of the oxoG base into the OGG1 active site pocket and impeded the correct convergence of the apurinic/apyrimidinic site of DNA and the attacking nucleophilic group of the enzyme. An obtained three-dimensional model of the OGG1 complex with DNA containing the oxoG-clamp, together with kinetic data, allowed us to clarify the role of the contact of amino acid residues with DNA in the formation of (and rearrangements in) the enzyme–substrate complex. Full article
(This article belongs to the Special Issue DNA Damage and Repair in Health and Diseases)
14 pages, 967 KiB  
Article
Temperature Effects on Expression Levels of hsp Genes in Eggs and Second-Stage Juveniles of Meloidogyne hapla Chitwood, 1949
by Łukasz Flis, Tadeusz Malewski and Renata Dobosz
Int. J. Mol. Sci. 2024, 25(9), 4867; https://doi.org/10.3390/ijms25094867 (registering DOI) - 29 Apr 2024
Abstract
Meloidogyne hapla is one of the most important nematode pathogens. It is a sedentary, biotrophic parasite of plants that overwinters in the soil or in diseased roots. The development of M. hapla is temperature dependent. Numerous studies have been performed on the effect [...] Read more.
Meloidogyne hapla is one of the most important nematode pathogens. It is a sedentary, biotrophic parasite of plants that overwinters in the soil or in diseased roots. The development of M. hapla is temperature dependent. Numerous studies have been performed on the effect of temperature on the development of M. hapla, but only a few of them analyzed the heat shock protein (hsp) genes. The aim of the study was to perform expression profiling of eight hsp genes (Mh-hsp90, Mh-hsp1, Mh-hsp4, Mh-hsp6, Mh-hsp60, Mh-dnj19, Mh-hsp43, and Mh-hsp12.2) at two development stages of M. hapla, i.e., in eggs and second-stage juveniles (J2). The eggs and J2 were incubated under cold stress (5 °C), heat stress (35 °C, 40 °C), and non-stress (10 °C, 20 °C, and 30 °C) conditions. Expression profiling was performed by qPCR. It was demonstrated that only two genes, Mh-hsp60 and Mh-dnj19, have been upregulated by heat and cold stress at both development stages. Heat stress upregulated the expression of more hsp genes than cold stress did. The level of upregulation of most hsp genes was more marked in J2 than in eggs. The obtained results suggest that the Mh-hsp90 and Mh-hsp1 genes can be used as bioindicators of environmental impacts on nematodes of the Meloidogyne genus. Full article
12 pages, 540 KiB  
Article
Clinical Features and Patient Outcomes in Infective Endocarditis with Surgical Indication: A Single-Centre Experience
by Fausto Pizzino, Umberto Paradossi, Giancarlo Trimarchi, Giovanni Benedetti, Federica Marchi, Sara Chiappino, Mattia Conti, Gianluca Di Bella, Michele Murzi, Silvia Di Sibio, Giovanni Concistrè, Giacomo Bianchi and Marco Solinas
J. Cardiovasc. Dev. Dis. 2024, 11(5), 138; https://doi.org/10.3390/jcdd11050138 (registering DOI) - 29 Apr 2024
Abstract
Background: Infective endocarditis (IE) is marked by a heightened risk of embolic events (EEs), uncontrolled infection, or heart failure (HF). Methods: Patients with IE and surgical indication were enrolled from October 2015 to December 2018. The primary endpoint consisted of a composite of [...] Read more.
Background: Infective endocarditis (IE) is marked by a heightened risk of embolic events (EEs), uncontrolled infection, or heart failure (HF). Methods: Patients with IE and surgical indication were enrolled from October 2015 to December 2018. The primary endpoint consisted of a composite of major adverse events (MAEs) including all-cause death, hospitalizations, and IE relapses. The secondary endpoint was all-cause death. Results: A total of 102 patients (66 ± 14 years) were enrolled: 50% with IE on prosthesis, 33% with IE-associated heart failure (IE-aHF), and 38.2% with EEs. IE-aHF and EEs were independently associated with MAEs (HR 1.9, 95% CI 1.1–3.4, p = 0.03 and HR 2.1, 95% CI 1.2–3.6, p = 0.01, respectively) and Kaplan–Meier survival curves confirmed a strong difference in MAE-free survival of patients with EEs and IE-aHF (p < 0.01 for both). IE-aHF (HR 4.3, 95% CI 1.4–13, p < 0.01), CRP at admission (HR 5.6, 95% CI 1.4–22.2, p = 0.01), LVEF (HR 0.9, 95% CI 0.9–1, p < 0.05), abscess (HR 3.5, 95% CI 1.2–10.6, p < 0.05), and prosthetic detachment (HR 4.6, 95% CI 1.5–14.1, p < 0.01) were independently associated with the all-cause death endpoint. Conclusions: IE-aHF and EEs were independently associated with MAEs. IE-aHF was also independently associated with the secondary endpoint. Full article
(This article belongs to the Section Acquired Cardiovascular Disease)
27 pages, 3244 KiB  
Article
Seamless Modeling of Direct and Indirect Aerosol Effects during April 2020 Wildfire Episode in Ukraine
by Mykhailo Savenets, Valeriia Rybchynska, Alexander Mahura, Roman Nuterman, Alexander Baklanov, Markku Kulmala and Tuukka Petäjä
Atmosphere 2024, 15(5), 550; https://doi.org/10.3390/atmos15050550 (registering DOI) - 29 Apr 2024
Abstract
Wildfires frequently occur in Ukraine during agricultural open-burning seasons in spring and autumn. High aerosol concentrations from fire emissions can significantly affect meteorological processes via direct and indirect aerosol effects. To study these impacts, we selected a severe wildfire episode from April 2020 [...] Read more.
Wildfires frequently occur in Ukraine during agricultural open-burning seasons in spring and autumn. High aerosol concentrations from fire emissions can significantly affect meteorological processes via direct and indirect aerosol effects. To study these impacts, we selected a severe wildfire episode from April 2020 in the Chornobyl Exclusion Zone (CEZ) and its surrounding area as a case study. We employed the Enviro-HIRLAM modeling system to simulate reference (REF) meteorological conditions, along with direct (DAE), indirect (IDAE), and combined (COMB) aerosol effects. In our simulations, black carbon (BC) and organic carbon (OC) comprised 70–80% of all aerosol mass in the region, represented in two layers of higher concentrations: one near the surface and the other 3–4 km above the surface. Our simulations showed that the inclusion of aerosol effects into the modeling framework led to colder (up to −3 °C) and drier (relative humidity drop up to −20%) conditions near the surface. We also observed localized changes in cloudiness, precipitation (mainly redistribution), and wind speed (up to ±4 m/s), particularly during the movement of atmospheric cold fronts. Larger uncertainties were observed in coarser model simulations when direct aerosol effects were considered. Quantifying the aerosol effects is crucial for predicting and promptly detecting changes that could exacerbate unfavorable weather conditions and wildfires. Such knowledge is essential for improving the effectiveness of emergency response measures. Full article
(This article belongs to the Section Aerosols)
16 pages, 1858 KiB  
Article
Evolutionary Adaptation of an RNA Bacteriophage to Repeated Freezing and Thawing Cycles
by Mara Laguna-Castro, Alicia Rodríguez-Moreno and Ester Lázaro
Int. J. Mol. Sci. 2024, 25(9), 4863; https://doi.org/10.3390/ijms25094863 (registering DOI) - 29 Apr 2024
Abstract
Bacteriophage fitness is determined by factors influencing both their replication within bacteria and their ability to maintain infectivity between infections. The latter becomes particularly crucial under adverse environmental conditions or when host density is low. In such scenarios, the damage experienced by viral [...] Read more.
Bacteriophage fitness is determined by factors influencing both their replication within bacteria and their ability to maintain infectivity between infections. The latter becomes particularly crucial under adverse environmental conditions or when host density is low. In such scenarios, the damage experienced by viral particles could lead to the loss of infectivity, which might be mitigated if the virus undergoes evolutionary optimization through replication. In this study, we conducted an evolution experiment involving bacteriophage Qβ, wherein it underwent 30 serial transfers, each involving a cycle of freezing and thawing followed by replication of the surviving viruses. Our findings show that Qβ was capable of enhancing its resistance to this selective pressure through various adaptive pathways that did not impair the virus replicative capacity. Notably, these adaptations predominantly involved mutations located within genes encoding capsid proteins. The adapted populations exhibited higher resistance levels than individual viruses isolated from them, and the latter surpassed those observed in single mutants generated via site-directed mutagenesis. This suggests potential interactions among mutants and mutations. In conclusion, our study highlights the significant role of extracellular selective pressures in driving the evolution of phages, influencing both the genetic composition of their populations and their phenotypic properties. Full article
(This article belongs to the Section Molecular Microbiology)
13 pages, 401 KiB  
Article
Exome Sequencing for the Diagnostics of Osteogenesis Imperfecta in Six Russian Patients
by Yulia S. Koshevaya, Mariia E. Turkunova, Anastasia O. Vechkasova, Elena A. Serebryakova, Maxim Yu. Donnikov, Svyatoslav I. Papanov, Alexander N. Chernov, Lev N. Kolbasin, Lyudmila V. Kovalenko, Andrey S. Glotov and Oleg S. Glotov
Curr. Issues Mol. Biol. 2024, 46(5), 4106-4118; https://doi.org/10.3390/cimb46050252 (registering DOI) - 29 Apr 2024
Abstract
Osteogenesis imperfecta (OI) is a group of inherited disorders of connective tissue that cause significant deformities and fragility in bones. Most cases of OI are associated with pathogenic variants in collagen type I genes and are characterized by pronounced polymorphisms in clinical manifestations [...] Read more.
Osteogenesis imperfecta (OI) is a group of inherited disorders of connective tissue that cause significant deformities and fragility in bones. Most cases of OI are associated with pathogenic variants in collagen type I genes and are characterized by pronounced polymorphisms in clinical manifestations and the absence of clear phenotype–genotype correlation. The objective of this study was to conduct a comprehensive molecular–genetic and clinical analysis to verify the diagnosis of OI in six Russian patients with genetic variants in the COL1A1 and COL1A2 genes. Clinical and laboratory data were obtained from six OI patients who were observed at the Medical Genetics Center in Saint Petersburg from 2016 to 2023. Next-generation sequencing on MGISEQ G400 (MGI, China) was used for DNA analysis. The GATK bioinformatic software (version 4.5.0.0) was used for variant calling and hard filtering. Genetic variants were verified by the direct automatic sequencing of PCR products using the ABI 3500X sequencer. We identified six genetic variants, as follows pathogenic c.3505G>A (p. Gly1169Ser), c.769G>A (p.Gly257Arg), VUS c.4123G>A (p.Ala1375Thr), and c.4114A>T (p.Asn1372Tyr) in COL1A1; and likely pathogenic c.2035G>A (p.Gly679Ser) and c.739-2A>T in COL1A2. In addition, clinical cases are presented due to the presence of the c.4114A>T variant in the COL1A2 gene. Molecular genetics is essential for determining different OI types due to the high similarity across various types of the disease and the failure of unambiguous diagnosis based on clinical manifestations alone. Considering the variable approaches to OI classification, an integrated strategy is required for optimal patient management. Full article
(This article belongs to the Collection Bioinformatics Approaches to Biomedicine)
16 pages, 1274 KiB  
Article
The Genetic Landscape of Antimicrobial Resistance Genes in Enterococcus cecorum Broiler Isolates
by Yue Huang, Filip Boyen, Gunther Antonissen, Nick Vereecke and Filip Van Immerseel
Antibiotics 2024, 13(5), 409; https://doi.org/10.3390/antibiotics13050409 (registering DOI) - 29 Apr 2024
Abstract
Enterococcus cecorum is associated with bacterial chondronecrosis with osteomyelitis (BCO) in broilers. Prophylactic treatment with antimicrobials is common in the poultry industry, and, in the case of outbreaks, antimicrobial treatment is needed. In this study, the minimum inhibitory concentrations (MICs) and epidemiological cutoff [...] Read more.
Enterococcus cecorum is associated with bacterial chondronecrosis with osteomyelitis (BCO) in broilers. Prophylactic treatment with antimicrobials is common in the poultry industry, and, in the case of outbreaks, antimicrobial treatment is needed. In this study, the minimum inhibitory concentrations (MICs) and epidemiological cutoff (ECOFF) values (COWT) for ten antimicrobials were determined in a collection of E. cecorum strains. Whole-genome sequencing data were analyzed for a selection of these E. cecorum strains to identify resistance determinants involved in the observed phenotypes. Wild-type and non-wild-type isolates were observed for the investigated antimicrobial agents. Several antimicrobial resistance genes (ARGs) were detected in the isolates, linking phenotypes with genotypes for the resistance to vancomycin, tetracycline, lincomycin, spectinomycin, and tylosin. These detected resistance genes were located on mobile genetic elements (MGEs). Point mutations were found in isolates with a non-wild-type phenotype for enrofloxacin and ampicillin/ceftiofur. Isolates showing non-wild-type phenotypes for enrofloxacin had point mutations within the GyrA, GyrB, and ParC proteins, while five amino acid changes in penicillin-binding proteins (PBP2x superfamily) were observed in non-wild-type phenotypes for the tested β-lactam antimicrobials. This study is one of the first that describes the genetic landscape of ARGs within MGEs in E. cecorum, in association with phenotypical resistance determination. Full article
(This article belongs to the Special Issue Antibiotics Resistance in Animals and the Environment)
29 pages, 1863 KiB  
Article
Distinctive Nucleic Acid Recognition by Lysine-Embedded Phenanthridine Peptides
by Josipa Matić, Patryciusz Piotrowski, Lucija Vrban, Renata Kobetić, Robert Vianello, Ivona Jurić, Ivana Fabijanić, Margareta Pernar Kovač, Anamaria Brozovic, Ivo Piantanida, Carsten Schmuck and Marijana Radić Stojković
Int. J. Mol. Sci. 2024, 25(9), 4866; https://doi.org/10.3390/ijms25094866 (registering DOI) - 29 Apr 2024
Abstract
Three new phenanthridine peptide derivatives (19, 22, and 23) were synthesized to explore their potential as spectrophotometric probes for DNA and RNA. UV/Vis and circular dichroism (CD) spectra, mass spectroscopy, and computational analysis confirmed the presence of intramolecular interactions [...] Read more.
Three new phenanthridine peptide derivatives (19, 22, and 23) were synthesized to explore their potential as spectrophotometric probes for DNA and RNA. UV/Vis and circular dichroism (CD) spectra, mass spectroscopy, and computational analysis confirmed the presence of intramolecular interactions in all three compounds. Computational analysis revealed that compounds alternate between bent and open conformations, highlighting the latter’s crucial influence on successful polynucleotide recognition. Substituting one glycine with lysine in two regioisomers (22, 23) resulted in stronger binding interactions with DNA and RNA than for a compound containing two glycines (19), thus emphasizing the importance of lysine. The regioisomer with lysine closer to the phenanthridine ring (23) exhibited a dual and selective fluorimetric response with non-alternating AT and ATT polynucleotides and induction of triplex formation from the AT duplex. The best binding constant (K) with a value of 2.5 × 107 M−1 was obtained for the interaction with AT and ATT polynucleotides. Furthermore, apart from distinguishing between different types of ds-DNA and ds-RNA, the same compound could recognize GC-rich DNA through distinct induced CD signals. Full article
(This article belongs to the Special Issue Computational, Structural and Spectroscopic Studies of Macromolecules)
15 pages, 711 KiB  
Article
Effect of Peanut Butter Intake on Sleep Health in Firefighters: A Randomized Controlled Trial
by Tiffany J. Oberther, Andrew R. Moore, Austin A. Kohler, David H. Shuler, Nicole Peritore and Angelia M. Holland-Winkler
Int. J. Environ. Res. Public Health 2024, 21(5), 571; https://doi.org/10.3390/ijerph21050571 (registering DOI) - 29 Apr 2024
Abstract
Sleep is often impaired in firefighters due to the psychologically and physiologically intense nature of their work and working shift schedules. Peanut butter is affordable and a substantial source of monounsaturated fatty acids, which may aid sleep health. Thus, this study sought to [...] Read more.
Sleep is often impaired in firefighters due to the psychologically and physiologically intense nature of their work and working shift schedules. Peanut butter is affordable and a substantial source of monounsaturated fatty acids, which may aid sleep health. Thus, this study sought to determine if a daily serving of peanut butter consumed before bedtime for seven weeks altered sleep quality and quantity among full-time firefighters. Forty firefighters (peanut butter group = 20; control group = 20) participated in this eight-week randomized controlled trial. All participants completed a subjective questionnaire on mood, focus, and alertness twice daily and wore an Actigraph wristwatch to measure sleep variables, including latency, efficiency, time in bed, time asleep, wake after sleep onset, number of awakenings, and time spent awake. After a baseline week, the peanut butter group consumed two tablespoons of peanut butter two hours prior to bedtime for seven weeks. Compared to the control group, the peanut butter group did not demonstrate significant changes (p > 0.05) in sleep measures or subjective feelings of mood, focus, or alertness after consuming peanut butter for seven weeks. Therefore, peanut butter as a source of peanuts did not alter sleep quality or quantity in this group of firefighters. ClinicalTrials.gov NCT06364202. Full article
11 pages, 1208 KiB  
Article
Evaluating Agility in Pre-Adolescent Basketball: A Comparative Analysis of CODAT, IAT, and RAT
by Gökhan Deliceoğlu, Okan İbiş and Erkan Tortu
Appl. Sci. 2024, 14(9), 3815; https://doi.org/10.3390/app14093815 (registering DOI) - 29 Apr 2024
Abstract
Background: In basketball, agility is essential, characterized by the ability to change direction swiftly and accelerate. Traditional tests like the Illinois Agility Test (IAT) and the Reactive Agility Test (RAT) may not fully capture the agility demands specific to basketball. Purpose: This study [...] Read more.
Background: In basketball, agility is essential, characterized by the ability to change direction swiftly and accelerate. Traditional tests like the Illinois Agility Test (IAT) and the Reactive Agility Test (RAT) may not fully capture the agility demands specific to basketball. Purpose: This study aimed to introduce the Change of Direction and Acceleration Test (CODAT), designed specifically for young basketball players. It evaluates CODAT’s effectiveness by comparing it with IAT and RAT through comprehensive analysis. Methods: We assessed 87 pre-adolescent male basketball players, aged 9 to 13 years, with an average biological age of 11.2 years and an average estimated Peak Height Velocity (PHV) of 12.5 ± 0.5 years, using CODAT, IAT, and RAT. We employed regression analysis and the Bland–Altman method to determine CODAT’s reliability and validity. Results: The findings indicate that CODAT offers superior reliability and validity in measuring basketball-specific agility. Consistent scores highlight its potential as an effective tool for agility assessment in basketball training and talent identification. Conclusions: CODAT represents a significant advancement in agility assessment for young basketball players, advocating for its integration into sports science practices to better address the specialized demands of basketball agility. Full article
(This article belongs to the Special Issue Advances in Sports, Exercise and Health)
14 pages, 425 KiB  
Review
Therapeutic Implications of Phenolic Acids for Ameliorating Inflammatory Bowel Disease
by Yanan Lu and Xue Han
Nutrients 2024, 16(9), 1347; https://doi.org/10.3390/nu16091347 (registering DOI) - 29 Apr 2024
Abstract
Inflammatory bowel disease (IBD) is a chronic inflammatory intestinal disorder, and its complex etiology makes prevention and treatment challenging. Research on new drugs and treatment strategies is currently a focal point. Phenolic acids are widely present in plant-based diets and have demonstrated the [...] Read more.
Inflammatory bowel disease (IBD) is a chronic inflammatory intestinal disorder, and its complex etiology makes prevention and treatment challenging. Research on new drugs and treatment strategies is currently a focal point. Phenolic acids are widely present in plant-based diets and have demonstrated the potential to alleviate colitis due to their powerful antioxidant and anti-inflammatory properties. In this review, we provide an overview of the structures and main dietary sources of phenolic acids, encompassing benzoic acid and cinnamic acid. Additionally, we explore the potential of phenolic acids as a nutritional therapy for preventing and treating IBD. In animal and cell experiments, phenolic acids effectively alleviate IBD induced by drug exposure or genetic defects. The mechanisms include improving intestinal mucosal barrier function, reducing oxidative stress, inhibiting excessive activation of the immune response, and regulating the balance of the intestinal microbiota. Our observation points towards the need for additional basic and clinical investigations on phenolic acids and their derivatives as potential novel therapeutic agents for IBD. Full article
(This article belongs to the Section Nutrition and Metabolism)

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