The 2023 MDPI Annual Report has
been released!
 
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)
13 pages, 432 KiB  
Article
ALDRESS: A Retrospective Pilot Study to Develop a Pharmacological Causality Algorithm for Drug Reaction with Eosinophilia and Systemic Symptoms (DRESS)
by Stefan Stewart, Arturo Gómez López de las Huertas, María Jiménez-González, Antonio J. Carcas, Alberto M. Borobia and Elena Ramírez
J. Clin. Med. 2024, 13(9), 2622; https://doi.org/10.3390/jcm13092622 (registering DOI) - 29 Apr 2024
Abstract
Background: The drug reaction with eosinophilia and systemic symptoms (DRESS) syndrome represents a severe form of drug hypersensitivity reaction characterized by significant morbidity, mortality, and long-term sequelae, coupled with limited therapeutic avenues. Accurate identification of the causative drug(s) is paramount for acute management, [...] Read more.
Background: The drug reaction with eosinophilia and systemic symptoms (DRESS) syndrome represents a severe form of drug hypersensitivity reaction characterized by significant morbidity, mortality, and long-term sequelae, coupled with limited therapeutic avenues. Accurate identification of the causative drug(s) is paramount for acute management, exploration of safe therapeutic alternatives, and prevention of future occurrences. However, the absence of a standardized diagnostic test and a specific causality algorithm tailored to DRESS poses a significant challenge in its clinical management. Methods: We conducted a retrospective case–control study involving 37 DRESS patients to validate a novel causality algorithm, the ALDRESS, designed explicitly for this syndrome, comparing it against the current standard algorithm, SEFV. Results: The ALDRESS algorithm showcased superior performance, exhibiting an 85.7% sensitivity and 93% specificity with comparable negative predictive values (80.6% vs. 97%). Notably, the ALDRESS algorithm yielded a substantially higher positive predictive value (75%) compared to SEFV (51.40%), achieving an overall accuracy rate of 92%. Conclusions: Our findings underscore the efficacy of the ALDRESS algorithm in accurately attributing causality to drugs implicated in DRESS syndrome. However, further validation studies involving larger, diverse cohorts are warranted to consolidate its clinical utility and broaden its applicability. This study lays the groundwork for a refined causality assessment tool, promising advancements in the diagnosis and management of DRESS syndrome. Full article
(This article belongs to the Section Pharmacology)
21 pages, 1869 KiB  
Article
Neuroreceptor Inhibition by Clozapine Triggers Mitohormesis and Metabolic Reprogramming in Human Blood Cells
by Karin Fehsel, Marie-Luise Bouvier, Loredana Capobianco, Paola Lunetti, Bianca Klein, Marko Oldiges, Marc Majora and Stefan Löffler
Cells 2024, 13(9), 762; https://doi.org/10.3390/cells13090762 (registering DOI) - 29 Apr 2024
Abstract
The antipsychotic drug clozapine demonstrates superior efficacy in treatment-resistant schizophrenia, but its intracellular mode of action is not completely understood. Here, we analysed the effects of clozapine (2.5–20 µM) on metabolic fluxes, cell respiration, and intracellular ATP in human HL60 cells. Some results [...] Read more.
The antipsychotic drug clozapine demonstrates superior efficacy in treatment-resistant schizophrenia, but its intracellular mode of action is not completely understood. Here, we analysed the effects of clozapine (2.5–20 µM) on metabolic fluxes, cell respiration, and intracellular ATP in human HL60 cells. Some results were confirmed in leukocytes of clozapine-treated patients. Neuroreceptor inhibition under clozapine reduced Akt activation with decreased glucose uptake, thereby inducing ER stress and the unfolded protein response (UPR). Metabolic profiling by liquid-chromatography/mass-spectrometry revealed downregulation of glycolysis and the pentose phosphate pathway, thereby saving glucose to keep the electron transport chain working. Mitochondrial respiration was dampened by upregulation of the F0F1-ATPase inhibitory factor 1 (IF1) leading to 30–40% lower oxygen consumption in HL60 cells. Blocking IF1 expression by cotreatment with epigallocatechin-3-gallate (EGCG) increased apoptosis of HL60 cells. Upregulation of the mitochondrial citrate carrier shifted excess citrate to the cytosol for use in lipogenesis and for storage as triacylglycerol in lipid droplets (LDs). Accordingly, clozapine-treated HL60 cells and leukocytes from clozapine-treated patients contain more LDs than untreated cells. Since mitochondrial disturbances are described in the pathophysiology of schizophrenia, clozapine-induced mitohormesis is an excellent way to escape energy deficits and improve cell survival. Full article
(This article belongs to the Section Cellular Metabolism)
25 pages, 780 KiB  
Review
CNS Resident Innate Immune Cells: Guardians of CNS Homeostasis
by Luca Muzio and Jessica Perego
Int. J. Mol. Sci. 2024, 25(9), 4865; https://doi.org/10.3390/ijms25094865 (registering DOI) - 29 Apr 2024
Abstract
 Although the CNS has been considered for a long time an immune-privileged organ, it is now well known that both the parenchyma and non-parenchymal tissue (meninges, perivascular space, and choroid plexus) are richly populated in resident immune cells. The advent of more [...] Read more.
 Although the CNS has been considered for a long time an immune-privileged organ, it is now well known that both the parenchyma and non-parenchymal tissue (meninges, perivascular space, and choroid plexus) are richly populated in resident immune cells. The advent of more powerful tools for multiplex immunophenotyping, such as single-cell RNA sequencing technique and upscale multiparametric flow and mass spectrometry, helped in discriminating between resident and infiltrating cells and, above all, the different spectrum of phenotypes distinguishing border-associated macrophages. Here, we focus our attention on resident innate immune players and their primary role in both CNS homeostasis and pathological neuroinflammation and neurodegeneration, two key interconnected aspects of the immunopathology of multiple sclerosis.  Full article
(This article belongs to the Special Issue Molecular Mechanism in Multiple Sclerosis and Related Disorders 2.0)
18 pages, 3090 KiB  
Article
Statistical Reliability Assessment with Generalized Intuitionistic Fuzzy Burr XII Distribution
by Abdul Kalam, Weihu Cheng, Dionisis Stefanatos and Sayed Kifayat Shah
Processes 2024, 12(5), 915; https://doi.org/10.3390/pr12050915 (registering DOI) - 29 Apr 2024
Abstract
Intuitionistic fuzzy sets provide a viable framework for modelling lifetime distribution characteristics, particularly in scenarios with measurement imprecision. This is accomplished by utilizing membership and non-membership degrees to accurately express the complexities of data uncertainty. Nonetheless, the complexities of some cases necessitate a [...] Read more.
Intuitionistic fuzzy sets provide a viable framework for modelling lifetime distribution characteristics, particularly in scenarios with measurement imprecision. This is accomplished by utilizing membership and non-membership degrees to accurately express the complexities of data uncertainty. Nonetheless, the complexities of some cases necessitate a more advanced approach of imprecise data, motivating the use of generalized intuitionistic fuzzy sets (GenIFSs). The use of GenIFSs represents a flexible modeling strategy that is characterized by the careful incorporation of an extra level of hesitancy, which effectively clarifies the underlying ambiguity and uncertainty present in reliability evaluations. The study employs a methodology based on generalized intuitionistic fuzzy distributions to thoroughly examine the uncertainty related to the parameters and reliability characteristics present in the Burr XII distribution. The goal is to provide a more accurate evaluation of reliability measurements by addressing the inherent ambiguity in the distribution’s shape parameter. Various reliability measurements, such as reliability, hazard rate, and conditional reliability functions, are derived for the Burr XII distribution. This extensive analysis is carried out within the context of the generalized intuitionistic fuzzy sets paradigm, improving the understanding of the Burr XII distribution’s reliability measurements and providing important insights into its performance for the study of various types of systems. To facilitate understanding and point to practical application, the findings are shown graphically and contrasted across various cut-set values using a valuable numerical example. Full article
(This article belongs to the Section Process Control and Monitoring)
Show Figures

Figure 1

20 pages, 524 KiB  
Article
Extending Undirected Graph Techniques to Directed Graphs via Category Theory
by Sebastian Pardo-Guerra, Vivek Kurien George, Vikash Morar, Joshua Roldan and Gabriel Alex Silva
Mathematics 2024, 12(9), 1357; https://doi.org/10.3390/math12091357 (registering DOI) - 29 Apr 2024
Abstract
We use Category Theory to construct a `bridge’ relating directed graphs with undirected graphs, such that the notion of direction is preserved. Specifically, we provide an isomorphism between the category of simple directed graphs and a category we call `prime graphs category’; this [...] Read more.
We use Category Theory to construct a `bridge’ relating directed graphs with undirected graphs, such that the notion of direction is preserved. Specifically, we provide an isomorphism between the category of simple directed graphs and a category we call `prime graphs category’; this has as objects labeled undirected bipartite graphs (which we call prime graphs), and as morphisms undirected graph morphisms that preserve the labeling (which we call prime graph morphisms). This theoretical bridge allows us to extend undirected graph techniques to directed graphs by converting the directed graphs into prime graphs. To give a proof of concept, we show that our construction preserves topological features when applied to the problems of network alignment and spectral graph clustering. Full article
14 pages, 2007 KiB  
Article
Construction of Cultivated Land Ecological Network Based on Supply and Demand of Ecosystem Services and MCR Model: A Case Study of Shandong Province, China
by Yifan Xu, Yuepeng Liu, Qian Sun and Wei Qi
Sustainability 2024, 16(9), 3745; https://doi.org/10.3390/su16093745 (registering DOI) - 29 Apr 2024
Abstract
The research on the ecological protection of cultivated land has gradually become a focus and frontier of cultivated land protection. Constructing an ecological network of a cultivated land system is important to improve the effect of cultivated land ecological protection. In this study, [...] Read more.
The research on the ecological protection of cultivated land has gradually become a focus and frontier of cultivated land protection. Constructing an ecological network of a cultivated land system is important to improve the effect of cultivated land ecological protection. In this study, the supply-demand ratio of five ecosystem services was calculated from 2000 to 2020 in Shandong Province, a major grain-producing area in China. The morphological spatial pattern analysis (MSPA) model was used to construct the minimum cumulative resistance (MCR) model. The conclusions of the study are as follows: (1) the areas with a higher supply and demand ratio of various ecosystem services of cultivated land in Shandong Province are distributed in southern and southwestern areas. (2) The ecological source of cultivated land in Shandong Province has decreased by about 7000 km2 from 2000 to 2020, and the fragmentation trend is obvious. (3) The total length of the ecological corridors is 798.5 km2. The majority of these corridors are located in central and southern Shandong. The ideas and conclusions of this study are important for the formulation of ecological protection policies for regional cultivated land systems. Full article
13 pages, 538 KiB  
Review
Prevalence of and Contributors to Food Insecurity among College Athletes: A Scoping Review
by Jamie Pacenta, Brooke E. Starkoff, Elizabeth K. Lenz and Amanda Shearer
Nutrients 2024, 16(9), 1346; https://doi.org/10.3390/nu16091346 (registering DOI) - 29 Apr 2024
Abstract
Given the financial demands of attending college, the transition to new living situations, abrupt changes in social support, and overall lifestyle adjustments, college students are at an increased risk of food insecurity (FI) compared to the general population. Collegiate athletes experience an even [...] Read more.
Given the financial demands of attending college, the transition to new living situations, abrupt changes in social support, and overall lifestyle adjustments, college students are at an increased risk of food insecurity (FI) compared to the general population. Collegiate athletes experience an even greater risk of FI as a result of greater time commitments and energy demands associated with their sports. This heightened vulnerability poses a tremendous threat to student-athletes’ academic and athletic achievements. This study aims to address the prevalence and primary determinants of FI among collegiate athletes while providing potential solutions to navigate and alleviate the effects of diminished food security among this demographic. To address these aims, a total of 18 articles were selected from both peer-reviewed and gray literature. The U.S. Household Food Security Survey Module (US-HFSSM) survey tools were predominantly utilized across universities throughout the United States to gather data on FI. Student-athletes reported experiencing FI across various regions of the United States, including universities in the northeastern states (n = 5), the southwest region (n = 3), the southeast region (n = 3), the northwest (n = 1), and the Midwest (n = 1). Overall, FI prevalence rates ranged from 9.9% to 65%, and the most significant contributors included limited financial resources, time management, meal plans, and housing location/amenities. These findings highlight a need for screening, education, and interventions to address FI among collegiate athletes. Full article
(This article belongs to the Special Issue Public Health, Nutritional Behavior and Nutritional Status)
14 pages, 785 KiB  
Article
Exploration of Genome-Wide Recombination Rate Variation Patterns at Different Scales in Pigs
by Zuoquan Chen, Meng Zhou, Yingchun Sun, Xi Tang, Zhiyan Zhang and Lusheng Huang
Animals 2024, 14(9), 1345; https://doi.org/10.3390/ani14091345 (registering DOI) - 29 Apr 2024
Abstract
Meiotic recombination is a prevalent process in eukaryotic sexual reproduction organisms that plays key roles in genetic diversity, breed selection, and species evolution. However, the recombination events differ across breeds and even within breeds. In this study, we initially computed large-scale population recombination [...] Read more.
Meiotic recombination is a prevalent process in eukaryotic sexual reproduction organisms that plays key roles in genetic diversity, breed selection, and species evolution. However, the recombination events differ across breeds and even within breeds. In this study, we initially computed large-scale population recombination rates of both sexes using approximately 52 K SNP genotypes in a total of 3279 pigs from four different Chinese and Western breeds. We then constructed a high-resolution historical recombination map using approximately 16 million SNPs from a sample of unrelated individuals. Comparative analysis of porcine recombination events from different breeds and at different resolutions revealed the following observations: Firstly, the 1Mb-scale pig recombination maps of the same sex are moderately conserved among different breeds, with the similarity of recombination events between Western pigs and Chinese indigenous pigs being lower than within their respective groups. Secondly, we identified 3861 recombination hotspots in the genome and observed medium- to high-level correlation between historical recombination rates (0.542~0.683) and estimates of meiotic recombination rates. Third, we observed that recombination hotspots are significantly far from the transcription start sites of pig genes, and the silico–predicted PRDM9 zinc finger domain DNA recognition motif is significantly enriched in the regions of recombination hotspots compared to recombination coldspots, highlighting the potential role of PRDM9 in regulating recombination hotspots in pigs. Our study analyzed the variation patterns of the pig recombination map at broad and fine scales, providing a valuable reference for genomic selection breeding and laying a crucial foundation for further understanding the molecular mechanisms of pig genome recombination. Full article
13 pages, 727 KiB  
Article
The Effect of Metronidazole versus a Synbiotic on Clinical Course and Core Intestinal Microbiota in Dogs with Acute Diarrhea
by Helene Stübing, Jan S. Suchodolski, Andrea Reisinger, Melanie Werner, Katrin Hartmann, Stefan Unterer and Kathrin Busch
Vet. Sci. 2024, 11(5), 197; https://doi.org/10.3390/vetsci11050197 (registering DOI) - 29 Apr 2024
Abstract
The usefulness of antibiotics in dogs with acute diarrhea (AD) is controversial. It is also unclear what effect metronidazole has on potential enteropathogens such as Clostridium perfringens and Escherichia coli. Thus, the aim of this study was to evaluate the effect of [...] Read more.
The usefulness of antibiotics in dogs with acute diarrhea (AD) is controversial. It is also unclear what effect metronidazole has on potential enteropathogens such as Clostridium perfringens and Escherichia coli. Thus, the aim of this study was to evaluate the effect of metronidazole vs. a synbiotic on the clinical course and core intestinal bacteria of dogs with AD. Twenty-seven dogs with AD were enrolled in this prospective, randomized, blinded clinical trial and treated with either metronidazole (METg) or a synbiotic (SYNg; E. faecium DSM 10663; NCIMB 10415/4b170). The Canine Acute Diarrhea Severity (CADS) index was recorded daily for eleven days. Bacteria were quantified using qPCR. Data were analyzed using mixed models with repeated measures. A higher concentration of E. coli was observed in the METg group vs. the SYNg group on Day 6 (p < 0.0001) and Day 30 (p = 0.01). Metronidazole had no effect on C. perfringens. C. hiranonis was significantly lower in the METg group than in the SYNg group on Days 6 and 30 (p < 0.0001; p = 0.0015). No significant differences were observed in CADS index, fecal consistency, or defecation frequency between treatment groups (except for the CADS index on one single day). In conclusion, metronidazole negatively impacts the microbiome without affecting clinical outcomes. Thus, synbiotics might be a preferred treatment option for dogs with AD. Full article
(This article belongs to the Special Issue Digestive Diseases of Dogs and Cats)
17 pages, 12076 KiB  
Article
Magnetic Characterization of MR Fluid by Means of Neural Networks
by Paweł Kowol, Grazia Lo Sciuto, Rafał Brociek and Giacomo Capizzi
Electronics 2024, 13(9), 1723; https://doi.org/10.3390/electronics13091723 (registering DOI) - 29 Apr 2024
Abstract
Magnetorheological and electrorheological fluids manifest a change in rheological behavior when subjected to a magnetic or electric field, respectively, such that they require electrical and magnetic characterization. In this paper, a simple and accurate mathematical model based on a small number of parameters [...] Read more.
Magnetorheological and electrorheological fluids manifest a change in rheological behavior when subjected to a magnetic or electric field, respectively, such that they require electrical and magnetic characterization. In this paper, a simple and accurate mathematical model based on a small number of parameters provides the relative magnetic permeability of magnetorheological fluids as a function of the applied magnetic field. Furthermore, for the testing and magnetic characterization of magnetorheological fluids, a new metering equipment setup is implemented. Starting with the achieved experimental data, the mathematical relation μr=f(B) is represented by means of a radial basis function neural network, with neurons having a Gaussian activation function; by means of post-training pruning procedures, the trained neural network is applied using the proposed data. Therefore, the obtained mathematical relation μr=f(B) is in good agreement with the experimental data, with an approximate error of 8%. Full article
(This article belongs to the Section Computer Science & Engineering)
Show Figures

Figure 1

22 pages, 2889 KiB  
Article
Antiplatelet Effects of Flavonoid Aglycones Are Mediated by Activation of Cyclic Nucleotide-Dependent Protein Kinases
by Anna Balykina, Lidia Naida, Kürsat Kirkgöz, Viacheslav O. Nikolaev, Ekaterina Fock, Michael Belyakov, Anastasiia Whaley, Andrei Whaley, Valentina Shpakova, Natalia Rukoyatkina and Stepan Gambaryan
Int. J. Mol. Sci. 2024, 25(9), 4864; https://doi.org/10.3390/ijms25094864 (registering DOI) - 29 Apr 2024
Abstract
Flavonoid aglycones are secondary plant metabolites that exhibit a broad spectrum of pharmacological activities, including anti-inflammatory, antioxidant, anticancer, and antiplatelet effects. However, the precise molecular mechanisms underlying their inhibitory effect on platelet activation remain poorly understood. In this study, we applied flow cytometry [...] Read more.
Flavonoid aglycones are secondary plant metabolites that exhibit a broad spectrum of pharmacological activities, including anti-inflammatory, antioxidant, anticancer, and antiplatelet effects. However, the precise molecular mechanisms underlying their inhibitory effect on platelet activation remain poorly understood. In this study, we applied flow cytometry to analyze the effects of six flavonoid aglycones (luteolin, myricetin, quercetin, eriodictyol, kaempferol, and apigenin) on platelet activation, phosphatidylserine externalization, formation of reactive oxygen species, and intracellular esterase activity. We found that these compounds significantly inhibit thrombin-induced platelet activation and decrease formation of reactive oxygen species in activated platelets. The tested aglycones did not affect platelet viability, apoptosis induction, or procoagulant platelet formation. Notably, luteolin, myricetin, quercetin, and apigenin increased thrombin-induced thromboxane synthase activity, which was analyzed by a spectrofluorimetric method. Our results obtained from Western blot analysis and liquid chromatography–tandem mass spectrometry demonstrated that the antiplatelet properties of the studied phytochemicals are mediated by activation of cyclic nucleotide-dependent signaling pathways. Specifically, we established by using Förster resonance energy transfer that the molecular mechanisms are, at least partly, associated with the inhibition of phosphodiesterases 2 and/or 5. These findings underscore the therapeutic potential of flavonoid aglycones for clinical application as antiplatelet agents. Full article
(This article belongs to the Special Issue New Advances in Thrombosis 2.0)
14 pages, 1489 KiB  
Article
Water Pipeline Leakage Detection Based on Coherent φ-OTDR and Deep Learning Technology
by Shuo Zhang, Zijian Xiong, Boyuan Ji, Nan Li, Zhangwei Yu, Shengnan Wu and Sailing He
Appl. Sci. 2024, 14(9), 3814; https://doi.org/10.3390/app14093814 (registering DOI) - 29 Apr 2024
Abstract
Leakage in water supply pipelines remains a significant challenge. It leads to resource and economic waste. Researchers have developed several leak detection methods, including the use of embedded sensors and pressure prediction. The former approach involves pre-installing detectors inside pipelines to detect leaks. [...] Read more.
Leakage in water supply pipelines remains a significant challenge. It leads to resource and economic waste. Researchers have developed several leak detection methods, including the use of embedded sensors and pressure prediction. The former approach involves pre-installing detectors inside pipelines to detect leaks. This method allows for the precise localization of leak points. The stability is compromised because of the wireless signal strength. The latter approach, which relies on pressure measurements to predict leak events, does not achieve precise leak point localization. To address these challenges, in this paper, a coherent optical time-domain reflectometry (φ-OTDR) system is employed to capture vibration signal phase information. Subsequently, two pre-trained neural network models based on CNN and Resnet18 are responsible for processing this information to accurately identify vibration events. In an experimental setup simulating water pipelines, phase information from both leaking and non-leaking pipe segments is collected. Using this dataset, classical CNN and ResNet18 models are trained, achieving accuracy rates of 99.7% and 99.5%, respectively. The multi-leakage point experiment results indicate that the Resnet18 model has better generalization compared to the CNN model. The proposed solution enables long-distance water-pipeline precise leak point localization and accurate vibration event identification. Full article
(This article belongs to the Special Issue Advanced Optical-Fiber-Related Technologies)
23 pages, 3199 KiB  
Article
Dihydrotestosterone Augments the Angiogenic and Migratory Potential of Human Endothelial Progenitor Cells by an Androgen-Dependent Mechanism
by Mirel Adrian Popa, Cristina Maria Mihai, Viorel Iulian Șuică, Felicia Antohe, Raghvendra K. Dubey, Brigitte Leeners and Maya Simionescu
Int. J. Mol. Sci. 2024, 25(9), 4862; https://doi.org/10.3390/ijms25094862 (registering DOI) - 29 Apr 2024
Abstract
Endothelial progenitor cells (EPCs) play a critical role in cardiovascular regeneration. Enhancement of their native properties would be highly beneficial to ensuring the proper functioning of the cardiovascular system. As androgens have a positive effect on the cardiovascular system, we hypothesized that dihydrotestosterone [...] Read more.
Endothelial progenitor cells (EPCs) play a critical role in cardiovascular regeneration. Enhancement of their native properties would be highly beneficial to ensuring the proper functioning of the cardiovascular system. As androgens have a positive effect on the cardiovascular system, we hypothesized that dihydrotestosterone (DHT) could also influence EPC-mediated repair processes. To evaluate this hypothesis, we investigated the effects of DHT on cultured human EPCs’ proliferation, viability, morphology, migration, angiogenesis, gene and protein expression, and ability to integrate into cardiac tissue. The results showed that DHT at different concentrations had no cytotoxic effect on EPCs, significantly enhanced the cell proliferation and viability and induces fast, androgen-receptor-dependent formation of capillary-like structures. DHT treatment of EPCs regulated gene expression of androgen receptors and the genes and proteins involved in cell migration and angiogenesis. Importantly, DHT stimulation promoted EPC migration and the cells’ ability to adhere and integrate into murine cardiac slices, suggesting it has a role in promoting tissue regeneration. Mass spectrometry analysis further highlighted the impact of DHT on EPCs’ functioning. In conclusion, DHT increases the proliferation, migration, and androgen-receptor-dependent angiogenesis of EPCs; enhances the cells’ secretion of key factors involved in angiogenesis; and significantly potentiates cellular integration into heart tissue. The data offer support for potential therapeutic applications of DHT in cardiovascular regeneration and repair processes. Full article
(This article belongs to the Special Issue Exploring Stem Cell Biology for Cardiac Regeneration)
16 pages, 731 KiB  
Article
Bacterial Lipopeptides Are Effective against Pear Fire Blight
by Ihsan ud Din, Lina Hu, Yuan Jiang, Jie Wei, Muhammad Afzal and Li Sun
Microorganisms 2024, 12(5), 896; https://doi.org/10.3390/microorganisms12050896 (registering DOI) - 29 Apr 2024
Abstract
Fire blight, a devastating disease caused by Erwinia amylovora, poses a significant threat to pear and apple trees in Xinjiang province, China. In an effort to combat this pathogen, we isolated 10 bacteria from various components of apple and crabapple trees and [...] Read more.
Fire blight, a devastating disease caused by Erwinia amylovora, poses a significant threat to pear and apple trees in Xinjiang province, China. In an effort to combat this pathogen, we isolated 10 bacteria from various components of apple and crabapple trees and conducted screenings to assess their ability to inhibit E. amylovora in vitro. Through biochemical tests and partial 16S rRNA gene sequencing, we identified two promising strains, Priestia megaterium strain H1 and Bacillus subtilis strain I2. These strains were then evaluated for their efficacy in biocontrol under controlled laboratory conditions, focusing on immature fruits and leaves. Remarkably, all selected antagonists exhibited the capability to reduce the severity of the disease on both fruit and leaves. P. megaterium strain H1 and B. subtilis strain I2 exhibited significant reductions in disease incidence on both immature fruits and leaves compared to the control. Specifically, on immature fruits, they achieved reductions of 53.39% and 44.76%, respectively, while on leaves, they demonstrated reductions of 59.55% and 55.53%, respectively. Furthermore, during the study, we detected the presence of lipopeptides, including surfactin, iturins, bacillomycin D, and fengycins, in the methanol extract obtained from these two antagonistic bacteria using thin-layer chromatography (TLC). Based on the results obtained, B. subtilis strain I2 and P. megaterium strain H1 exhibit considerable potential for controlling fire blight. However, further evaluation of their efficacy under natural field conditions is essential to validate their practicality as a biocontrol method. Full article
(This article belongs to the Special Issue Plant-Microbe Interaction State-of-the-Art Research in China)
15 pages, 1028 KiB  
Article
In Vitro Human Liver Model for Toxicity Assessment with Clinical and Preclinical Instrumentation
by Eneko Madorran, Lidija Kocbek Šaherl, Mateja Rakuša and Miha Munda
Pharmaceutics 2024, 16(5), 607; https://doi.org/10.3390/pharmaceutics16050607 (registering DOI) - 29 Apr 2024
Abstract
The existing in vitro toxicological models lack translational potential, which makes difficult the application of gathered information to clinical usage. To tackle this issue, we built a model with four different types of primary liver cells: hepatic sinusoidal endothelial cells, hepatic stellate cells, [...] Read more.
The existing in vitro toxicological models lack translational potential, which makes difficult the application of gathered information to clinical usage. To tackle this issue, we built a model with four different types of primary liver cells: hepatic sinusoidal endothelial cells, hepatic stellate cells, Kupffer cells and hepatocytes. We cultured them in different combinations of composition and volumes of cell medium, hepatocyte proportions of total cells and additions of extracellular matrixes. We added rifampicin (RIF), ibuprofen (IBU) and 5-fluorouracil (5-FU) to this model and observed the microanatomy and physiology changes for a week with preclinical and clinical instruments. Among the different model configurations, we selected the feature combination of the in vitro model that had similar biomarker values to those measured in clinical diagnostics. When we exposed the selected model configuration to RIF, IBU and 5-FU, we observed similar glucose, triglyceride and albumin dynamics as in vivo (from clinical data). Therefore, we have built an in vitro liver model that resembles the liver microenvironment, and we have analysed it with clinical instrumentation to facilitate data translation. Furthermore, during these observations, we found that Kupffer and LSEC cells are suitable candidates for the search for clinical diagnostic markers of liver function. Full article
(This article belongs to the Special Issue Alternative Model-Based Translational Drug Development)
10 pages, 1597 KiB  
Communication
Shoots and Turions of Aquatic Plants as a Source of Fatty Acids
by Maciej Strzemski, Lubomir Adamec, Sławomir Dresler, Barbara Mazurek, Katarzyna Dubaj, Piotr Stolarczyk, Marcin Feldo and Bartosz J. Płachno
Molecules 2024, 29(9), 2062; https://doi.org/10.3390/molecules29092062 (registering DOI) - 29 Apr 2024
Abstract
Background: Fatty acids are essential for human health. Currently, there is a search for alternative sources of fatty acids that could supplement such sources as staple crops or fishes. Turions of aquatic plants accumulate a variety of substances such as starch, free sugars, [...] Read more.
Background: Fatty acids are essential for human health. Currently, there is a search for alternative sources of fatty acids that could supplement such sources as staple crops or fishes. Turions of aquatic plants accumulate a variety of substances such as starch, free sugars, amino acids, reserve proteins and lipids. Our aim is to see if turions can be a valuable source of fatty acids. Methods: Overwintering shoots and turions of aquatic carnivorous plants were collected. The plant material was extracted with hexane. The oils were analyzed using a gas chromatograph with mass spectrometer. Results: The dominant compound in all samples was linolenic acid. The oil content was different in turions and shoots. The oil content of the shoots was higher than that of the turions, but the proportion of fatty acids in the oils from the shoots was low in contrast to the oils from the turions. The turions of Utricularia species were shown to be composed of about 50% fatty acids. Conclusions: The turions of Utricularia species can be used to obtain oil with unsaturated fatty acids. In addition, the high fatty acid content of turions may explain their ability to survive at low temperatures. Full article
Show Figures

Graphical abstract

15 pages, 1722 KiB  
Article
Designing a Simple Electrochemical Genosensor for the Detection of Urinary PCA3, a Prostate Cancer Biomarker
by Meriem Mokni, Amal Tlili, Yassine Khalij, Ghada Attia, Chouki Zerrouki, Wissem Hmida, Ali Othmane, Ali Bouslama, Asma Omezzine and Najla Fourati
Micromachines 2024, 15(5), 602; https://doi.org/10.3390/mi15050602 (registering DOI) - 29 Apr 2024
Abstract
This study investigates the feasibility of a simple electrochemical detection of Prostate Cancer Antigen 3 (PCA3) fragments extracted from patients’ urine, using a thiolated single-strand DNA probe immobilized on a gold surface without using a redox probe. To enhance the PCA3 recognition process, [...] Read more.
This study investigates the feasibility of a simple electrochemical detection of Prostate Cancer Antigen 3 (PCA3) fragments extracted from patients’ urine, using a thiolated single-strand DNA probe immobilized on a gold surface without using a redox probe. To enhance the PCA3 recognition process, we conducted a comparative analysis of the hybridization location using two thiolated DNA probes: Probe 1 targets the first 40 bases, while Probe 2 targets the fragment from bases 47 to 86. Hybridization with PCA3 followed, using square wave voltammetry. The limit of detection of the designed genosenors were of the order of (2.2 ng/mL), and (1.6 ng/mL) for Probes 1 and 2, respectively, and the subsequent sensitivities were of the order of (0.09 ± 0.01) µA−1 · µg−1 · mL and (0.10 ± 0.01) µA−1 · µg−1 · mL. Specificity tests were then conducted with the sensor functionalized with Probe 2, as it presents better analytical performances. The electrochemical results indicate that the designed sensor can clearly discriminate a complementary target from a non-complementary one. A further modeling of the calibration curves with the Power Law/Hill model indicates that the dissociation constant increases by one order of magnitude, confirming the ability of the designed sensor to perfectly discriminate complementary targets from non-complementary ones. Full article

Open Access Journals

Browse by Indexing Browse by Subject Selected Journals
Back to TopTop