The 2023 MDPI Annual Report has
been released!
 
14 pages, 1347 KiB  
Article
Sequential Induction of Drug Resistance and Characterization of an Initial Candida albicans Drug-Sensitive Isolate
by Setrida El Hachem, Nour Fattouh, Christy Chedraoui, Marc Finianos, Ibrahim Bitar and Roy A. Khalaf
J. Fungi 2024, 10(5), 347; https://doi.org/10.3390/jof10050347 (registering DOI) - 13 May 2024
Abstract
Background: The pathogenic fungus Candida albicans is a leading agent of death in immunocompromised individuals with a growing trend of antifungal resistance. Methods: The purpose is to induce resistance to drugs in a sensitive C. albicans strain followed by whole-genome sequencing to determine [...] Read more.
Background: The pathogenic fungus Candida albicans is a leading agent of death in immunocompromised individuals with a growing trend of antifungal resistance. Methods: The purpose is to induce resistance to drugs in a sensitive C. albicans strain followed by whole-genome sequencing to determine mechanisms of resistance. Strains will be assayed for pathogenicity attributes such as ergosterol and chitin content, growth rate, virulence, and biofilm formation. Results: We observed sequential increases in ergosterol and chitin content in fluconazole-resistant isolates by 78% and 44%. Surface thickening prevents the entry of the drug, resulting in resistance. Resistance imposed a fitness trade-off that led to reduced growth rates, biofilm formation, and virulence in our isolates. Sequencing revealed mutations in genes involved in resistance and pathogenicity such as ERG11, CHS3, GSC2, CDR2, CRZ2, and MSH2. We observed an increase in the number of mutations in key genes with a sequential increase in drug-selective pressures as the organism increased its odds of adapting to inhospitable environments. In ALS4, we observed two mutations in the susceptible strain and five mutations in the resistant strain. Conclusion: This is the first study to induce resistance followed by genotypic and phenotypic analysis of isolates to determine mechanisms of drug resistance. Full article
(This article belongs to the Section Fungal Genomics, Genetics and Molecular Biology)
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19 pages, 4945 KiB  
Article
Multivariate Time Series Change-Point Detection with a Novel Pearson-like Scaled Bregman Divergence
by Tong Si, Yunge Wang, Lingling Zhang, Evan Richmond, Tae-Hyuk Ahn and Haijun Gong
Stats 2024, 7(2), 462-480; https://doi.org/10.3390/stats7020028 (registering DOI) - 13 May 2024
Abstract
Change-point detection is a challenging problem that has a number of applications across various real-world domains. The primary objective of CPD is to identify specific time points where the underlying system undergoes transitions between different states, each characterized by its distinct data distribution. [...] Read more.
Change-point detection is a challenging problem that has a number of applications across various real-world domains. The primary objective of CPD is to identify specific time points where the underlying system undergoes transitions between different states, each characterized by its distinct data distribution. Precise identification of change points in time series omics data can provide insights into the dynamic and temporal characteristics inherent to complex biological systems. Many change-point detection methods have traditionally focused on the direct estimation of data distributions. However, these approaches become unrealistic in high-dimensional data analysis. Density ratio methods have emerged as promising approaches for change-point detection since estimating density ratios is easier than directly estimating individual densities. Nevertheless, the divergence measures used in these methods may suffer from numerical instability during computation. Additionally, the most popular α-relative Pearson divergence cannot measure the dissimilarity between two distributions of data but a mixture of distributions. To overcome the limitations of existing density ratio-based methods, we propose a novel approach called the Pearson-like scaled-Bregman divergence-based (PLsBD) density ratio estimation method for change-point detection. Our theoretical studies derive an analytical expression for the Pearson-like scaled Bregman divergence using a mixture measure. We integrate the PLsBD with a kernel regression model and apply a random sampling strategy to identify change points in both synthetic data and real-world high-dimensional genomics data of Drosophila. Our PLsBD method demonstrates superior performance compared to many other change-point detection methods. Full article
(This article belongs to the Section Statistical Methods)
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15 pages, 1493 KiB  
Perspective
Dopamine Pharmacodynamics: New Insights
by Fulvio Lauretani, Francesco Giallauria, Crescenzo Testa, Claudia Zinni, Beatrice Lorenzi, Irene Zucchini, Marco Salvi, Raffaele Napoli and Marcello Giuseppe Maggio
Int. J. Mol. Sci. 2024, 25(10), 5293; https://doi.org/10.3390/ijms25105293 (registering DOI) - 13 May 2024
Abstract
Dopamine is a key neurotransmitter involved in physiological processes such as motor control, motivation, reward, cognitive function, and maternal and reproductive behaviors. Therefore, dysfunctions of the dopaminergic system are related to a plethora of human diseases. Dopamine, via different circuitries implicated in compulsive [...] Read more.
Dopamine is a key neurotransmitter involved in physiological processes such as motor control, motivation, reward, cognitive function, and maternal and reproductive behaviors. Therefore, dysfunctions of the dopaminergic system are related to a plethora of human diseases. Dopamine, via different circuitries implicated in compulsive behavior, reward, and habit formation, also represents a key player in substance use disorder and the formation and perpetuation of mechanisms leading to addiction. Here, we propose dopamine as a model not only of neurotransmission but also of neuromodulation capable of modifying neuronal architecture. Abuse of substances like methamphetamine, cocaine, and alcohol and their consumption over time can induce changes in neuronal activities. These modifications lead to synaptic plasticity and finally to morphological and functional changes, starting from maladaptive neuro-modulation and ending in neurodegeneration. Full article
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10 pages, 2902 KiB  
Article
Ubiquitin-Specific Protease 18 in Chronic Kidney Disease—Another Emerging Biomarker to Consider?
by Paulina Dziamałek-Macioszczyk, Agata Winiarska, Anna Pawłowska, Jan Macioszczyk, Paweł Wojtacha and Tomasz Stompór
Biomedicines 2024, 12(5), 1073; https://doi.org/10.3390/biomedicines12051073 (registering DOI) - 13 May 2024
Abstract
Ubiquitin-specific protease 18 (USP18) is a protein recognized for its dual enzymatic and non-enzymatic nature. It is involved in many physiological processes like the cell cycle and cell signaling. It also suppresses heart muscle remodeling upon an increase in the afterload. The role [...] Read more.
Ubiquitin-specific protease 18 (USP18) is a protein recognized for its dual enzymatic and non-enzymatic nature. It is involved in many physiological processes like the cell cycle and cell signaling. It also suppresses heart muscle remodeling upon an increase in the afterload. The role of USP18 in kidney pathology remains unknown. The objective of the study was to assess the relationship between serum and urine USP18 levels, the factors contributing to cardiovascular risk, and the markers of kidney disease activity at different stages of chronic kidney disease (CKD). One hundred participants, aged between 24 and 85 years (mean 53.1 ± 17.1 years), were included. Five groups (n = 20 each) were recruited according to their renal status (healthy individuals, patients with proteinuric glomerulonephritis, patients with non-proteinuric CKD, patients who were treated with hemodialysis, and kidney transplant recipients). The measurements of serum and urine USP18 levels were performed using ELISA. The median serum USP18 level was the highest in healthy participants (1143.0 pg/mL) and kidney transplant recipients (856.6 pg/mL), whereas, in individuals with different forms of CKD, it fitted within the range of 402.1–471.9 pg/mL. Urinary USP18 reached the highest level in the group of CKD patients not yet on dialysis (303.3 pg/mL). Only in this group did it correlate with serum creatinine and urea concentrations. Our results suggest the inhibition of cardioprotective USP18 signaling when kidney function is impaired. Moreover, an increased level of urinary USP18 may indicate chronic tubular damage. Full article
(This article belongs to the Special Issue Research Advances in Kidney Diseases and Sepsis)
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16 pages, 5179 KiB  
Article
A Rapid and Accurate UHPLC Method for Determination of Monosaccharides in Polysaccharides of Different Sources of Radix Astragali and Its Immune Activity Analysis
by Yali Guo, Lijun Wang, Kaishuang Liu, Meifang Li, Yibao Jin, Lifei Gu, Xie-An Yu, Shuhong Wang, Ping Wang, Bing Wang and Tiejie Wang
Molecules 2024, 29(10), 2287; https://doi.org/10.3390/molecules29102287 (registering DOI) - 13 May 2024
Abstract
With the escalating demand for Astragalus polysaccharides products developed from Radix Astragali (RA), the necessity for quality control of polysaccharides in RA has become increasingly urgent. In this study, a specific method for the simultaneous determination of seven monosaccharides in polysaccharides extracted from [...] Read more.
With the escalating demand for Astragalus polysaccharides products developed from Radix Astragali (RA), the necessity for quality control of polysaccharides in RA has become increasingly urgent. In this study, a specific method for the simultaneous determination of seven monosaccharides in polysaccharides extracted from Radix Astragali (RA) has been developed and validated using ultra-performance liquid chromatography equipped with an ultraviolet detector (UHPLC-UV) for the first time. The 1-phenyl-3-methyl-5-pyrazolone (PMP) derivatizations were separated on a C18 column (Waters ACQUITYTM, Milfor, MA, USA, 1.8 µm, 2.1 × 100 mm) using gradient elution with a binary system of 5 mm ammonium formate (0.1% formic acid)-acetonitrile for 24 min. Additionally, seven monosaccharides showed good linear relationships (R2, 0.9971–0.9995), adequate precision (RSD < 4.21%), and high recoveries (RSD < 4.70%). The established method was used to analyze 109 batches of RA. Results showed that the Astragalus polysaccharides (APSs) mainly consist of mannose (Man), rhamnose (Rha), glucose (Glu), galactose (Gal), arabinose (Ara), xylose (Xyl); and fucose (Fuc); however, their composition was different among RA samples from different growth patterns, species, growth years, and origins, and the growth mode of RA and the age of wild-simulated RA can be accurately distinguished by principal component analysis (PCA). In addition, the immunological activity of APSs were also evaluated jointly by measurement of the NO release with RAW264.7, with the results showing that APSs have a promoting effect on the release of NO and exhibit a significant correlation with Man, Glu, Xyl, and Fuc contents. Accordingly, the new established monosaccharides analytical method and APS-immune activity determination in this study can provide a reference for quality evaluation and the establishment of quality standards for RA. Full article
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53 pages, 8319 KiB  
Article
Lytic Capsule-Specific Acinetobacter Bacteriophages Encoding Polysaccharide-Degrading Enzymes
by Peter V. Evseev, Anastasia S. Sukhova, Nikolay A. Tkachenko, Yuriy P. Skryabin and Anastasia V. Popova
Viruses 2024, 16(5), 771; https://doi.org/10.3390/v16050771 (registering DOI) - 13 May 2024
Abstract
The genus Acinetobacter comprises both environmental and clinically relevant species associated with hospital-acquired infections. Among them, Acinetobacter baumannii is a critical priority bacterial pathogen, for which the research and development of new strategies for antimicrobial treatment are urgently needed. Acinetobacter spp. produce a [...] Read more.
The genus Acinetobacter comprises both environmental and clinically relevant species associated with hospital-acquired infections. Among them, Acinetobacter baumannii is a critical priority bacterial pathogen, for which the research and development of new strategies for antimicrobial treatment are urgently needed. Acinetobacter spp. produce a variety of structurally diverse capsular polysaccharides (CPSs), which surround the bacterial cells with a thick protective layer. These surface structures are primary receptors for capsule-specific bacteriophages, that is, phages carrying tailspikes with CPS-depolymerizing/modifying activities. Phage tailspike proteins (TSPs) exhibit hydrolase, lyase, or esterase activities toward the corresponding CPSs of a certain structure. In this study, the data on all lytic capsule-specific phages infecting Acinetobacter spp. with genomes deposited in the NCBI GenBank database by January 2024 were summarized. Among the 149 identified TSPs encoded in the genomes of 143 phages, the capsular specificity (K specificity) of 46 proteins has been experimentally determined or predicted previously. The specificity of 63 TSPs toward CPSs, produced by various Acinetobacter K types, was predicted in this study using a bioinformatic analysis. A comprehensive phylogenetic analysis confirmed the prediction and revealed the possibility of the genetic exchange of gene regions corresponding to the CPS-recognizing/degrading parts of different TSPs between morphologically and taxonomically distant groups of capsule-specific Acinetobacter phages. Full article
(This article belongs to the Section Bacterial Viruses)
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15 pages, 3604 KiB  
Article
Facile Asymmetric Syntheses of Non-Natural Amino Acid (S)-Cyclopropylglycine by the Developed NADH-Driven Biocatalytic System
by Qian Tang, Shanshan Li, Liping Zhou, Lili Sun, Juan Xin and Wei Li
Catalysts 2024, 14(5), 321; https://doi.org/10.3390/catal14050321 (registering DOI) - 13 May 2024
Abstract
A self-sufficient bifunctional enzyme integrating reductive amination and coenzyme regeneration activities was developed and successfully employed to synthesize (S)-cyclopropylglycine with an improved reaction rate 2.1-fold over the native enzymes and a short bioconversion period of 6 h at a high substrate [...] Read more.
A self-sufficient bifunctional enzyme integrating reductive amination and coenzyme regeneration activities was developed and successfully employed to synthesize (S)-cyclopropylglycine with an improved reaction rate 2.1-fold over the native enzymes and a short bioconversion period of 6 h at a high substrate concentration of 120 g·L−1 and space–time yield of (S)-cyclopropylglycine up to 377.3 g·L−1·d−1, higher than that of any previously reported data. Additionally, (S)-cyclopropylglycine could be continuously synthesized for 90 h with the enzymes packed in a dialysis tube, providing 634.6 g of (S)-cyclopropylglycine with >99.5% ee and over 95% conversion yield up to 12 changes. These results confirmed that the newly developed NADH-driven biocatalytic system could be utilized as a self-sufficient biocatalyst for industrial application in the synthesis of (S)-cyclopropylglycine, which provides a chiral center and cyclopropyl fragment for the frequent synthesis of preclinical/clinical drug molecules. Full article
(This article belongs to the Section Biocatalysis)
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15 pages, 1150 KiB  
Article
Transformation and Degradation of PAH Mixture in Contaminated Sites: Clarifying Their Interactions with Native Soil Organisms
by Xiaoyu Li, Shengnan Zhang, Ruixue Guo, Xuejing Xiao, Boying Liu, Rehab Khaled Mahmoud, Mostafa R. Abukhadra, Ruijuan Qu and Zunyao Wang
Toxics 2024, 12(5), 361; https://doi.org/10.3390/toxics12050361 (registering DOI) - 13 May 2024
Abstract
Soil contamination of polycyclic aromatic hydrocarbons (PAHs), especially caused by the mixture of two or more PAHs, raised great environmental concerns. However, research on the migration and transformation processes of PAHs in soils and their interactions with native communities is limited. In this [...] Read more.
Soil contamination of polycyclic aromatic hydrocarbons (PAHs), especially caused by the mixture of two or more PAHs, raised great environmental concerns. However, research on the migration and transformation processes of PAHs in soils and their interactions with native communities is limited. In this work, soil samples from uncontaminated sites around the industrial parks in Handan, Hengshui, and Shanghai were artificially supplemented with three concentrations of anthracene (Ant), 9-chloroanthracene (9-ClAnt), benzopyrene (BaP), and chrysene (Chr). Ryegrass was planted to investigate the degradation of PAHs and its interaction with native soil organisms in the constructed ryegrass–microbe–soil microcosmic system. The bacterial and fungal communities in soil were affected by PAHs; their species diversity and relative abundance changed after exposure to different concentrations of PAHs, among which Lysobacter, Bacillus, Pseudomonas, and Massilia bacteria were correlated to the degradation of PAHs. On the 56th day, the contents of BaP, Chr, and Ant decreased with the degradation process, while the degradation of 9-ClAnt was limited. Nineteen intermediates, including hydroxylation and carboxylated compounds, were identified. The present research would help clarify the potential interactions between PAHs and native organisms in contaminated sites, providing fundamental information for evaluating the transformation risks of PAHs in the natural environment. Full article
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15 pages, 4201 KiB  
Article
Combustion Analysis of Mixed Secondary Fuel Produced from Agro-Biomass and RDF in a Fluidized Bed
by Konrad Kaczyński and Piotr Pełka
Energies 2024, 17(10), 2343; https://doi.org/10.3390/en17102343 (registering DOI) - 13 May 2024
Abstract
In recent decades, there has been growing interest in the thermal conversion of various alternative fuels, such as biomass and waste-derived fuels. One of the technological solutions for the so-called direct co-combustion of fuels is to create mixtures of various fuels, called mixed [...] Read more.
In recent decades, there has been growing interest in the thermal conversion of various alternative fuels, such as biomass and waste-derived fuels. One of the technological solutions for the so-called direct co-combustion of fuels is to create mixtures of various fuels, called mixed secondary fuel. However, mixed secondary fuel has different properties compared to primary fuels. Due to this, by properly selecting the types and proportions of mixtures, it is possible to eliminate their potentially negative impact on both combustion technology and the natural environment. In this paper, we decided to prepare mixed secondary fuel by mixing sunflower husk pellets with RDF (refuse-derived fuel) in a ratio of 1:1 and then analyze the combustion process of the produced fuel in fluidized bed conditions. The results obtained on the basis of the presented research indicate that the mixed secondary fuel eliminated the impact of alkali metal compounds on reducing the melting point of ash and, consequently, on the combustion process of the mixed secondary fuel. An additional benefit is the reduction of emissions of harmful compounds into the atmosphere occurring during the combustion of municipal waste and compliance with the concept of the circular economy. Full article
(This article belongs to the Section B: Energy and Environment)
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19 pages, 2188 KiB  
Article
IMPI: An Interface for Low-Frequency Point Mutation Identification Exemplified on Resistance Mutations in Chronic Myeloid Leukemia
by Julia Vetter, Jonathan Burghofer, Theodora Malli, Anna M. Lin, Gerald Webersinke, Markus Wiederstein, Stephan M. Winkler and Susanne Schaller
BioMedInformatics 2024, 4(2), 1289-1307; https://doi.org/10.3390/biomedinformatics4020071 (registering DOI) - 13 May 2024
Abstract
Background: In genomics, highly sensitive point mutation detection is particularly relevant for cancer diagnosis and early relapse detection. Next-generation sequencing combined with unique molecular identifiers (UMIs) is known to improve the mutation detection sensitivity. Methods: We present an open-source bioinformatics framework named Interface [...] Read more.
Background: In genomics, highly sensitive point mutation detection is particularly relevant for cancer diagnosis and early relapse detection. Next-generation sequencing combined with unique molecular identifiers (UMIs) is known to improve the mutation detection sensitivity. Methods: We present an open-source bioinformatics framework named Interface for Point Mutation Identification (IMPI) with a graphical user interface (GUI) for processing especially small-scale NGS data to identify variants. IMPI ensures detailed UMI analysis and clustering, as well as initial raw read processing, and consensus sequence building. Furthermore, the effects of custom algorithm and parameter settings for NGS data pre-processing and UMI collapsing (e.g., UMI clustered versus unclustered (raw) reads) can be investigated. Additionally, IMPI implements optimization and quality control methods; an evolution strategy is used for parameter optimization. Results: IMPI was designed, implemented, and tested using BCR::ABL1 fusion gene kinase domain sequencing data. In summary, IMPI enables a detailed analysis of the impact of UMI clustering and parameter setting changes on the measured allele frequencies. Conclusions: Regarding the BCR::ABL1 data, IMPI’s results underlined the need for caution while designing specialized single amplicon NGS approaches due to methodical limitations (e.g., high PCR-mediated recombination rate). This cannot be corrected using UMIs. Full article
(This article belongs to the Special Issue Feature Papers in Applied Biomedical Data Science)
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15 pages, 1261 KiB  
Review
Runx2 and Polycystins in Bone Mechanotransduction: Challenges for Therapeutic Opportunities
by Antonios N. Gargalionis, Christos Adamopoulos, Christos T. Vottis, Athanasios G. Papavassiliou and Efthimia K. Basdra
Int. J. Mol. Sci. 2024, 25(10), 5291; https://doi.org/10.3390/ijms25105291 (registering DOI) - 13 May 2024
Abstract
Bone mechanotransduction is a critical process during skeletal development in embryogenesis and organogenesis. At the same time, the type and level of mechanical loading regulates bone remodeling throughout the adult life. The aberrant mechanosensing of bone cells has been implicated in the development [...] Read more.
Bone mechanotransduction is a critical process during skeletal development in embryogenesis and organogenesis. At the same time, the type and level of mechanical loading regulates bone remodeling throughout the adult life. The aberrant mechanosensing of bone cells has been implicated in the development and progression of bone loss disorders, but also in the bone-specific aspect of other clinical entities, such as the tumorigenesis of solid organs. Novel treatment options have come into sight that exploit the mechanosensitivity of osteoblasts, osteocytes, and chondrocytes to achieve efficient bone regeneration. In this regard, runt-related transcription factor 2 (Runx2) has emerged as a chief skeletal-specific molecule of differentiation, which is prominent to induction by mechanical stimuli. Polycystins represent a family of mechanosensitive proteins that interact with Runx2 in mechano-induced signaling cascades and foster the regulation of alternative effectors of mechanotransuction. In the present narrative review, we employed a PubMed search to extract the literature concerning Runx2, polycystins, and their association from 2000 to March 2024. The keywords stated below were used for the article search. We discuss recent advances regarding the implication of Runx2 and polycystins in bone remodeling and regeneration and elaborate on the targeting strategies that may potentially be applied for the treatment of patients with bone loss diseases. Full article
(This article belongs to the Special Issue Cells and Molecules in Bone Remodeling and Repair)
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18 pages, 2740 KiB  
Entry
Displacement Micropump with Check Valves for Diabetes Care—The Challenge of Pumping Insulin at Negative Pressure
by Eric Chappel
Encyclopedia 2024, 4(2), 818-835; https://doi.org/10.3390/encyclopedia4020052 (registering DOI) - 13 May 2024
Definition
The displacement micropump with passive check valves is an attractive solution for precise insulin infusion in patients with type I diabetes. Unlike most insulin pumps that push insulin from a cartridge using a piston, a displacement micropump will first pull insulin from the [...] Read more.
The displacement micropump with passive check valves is an attractive solution for precise insulin infusion in patients with type I diabetes. Unlike most insulin pumps that push insulin from a cartridge using a piston, a displacement micropump will first pull insulin from the reservoir before infusing it into the patient. This dual sequence introduces new challenges in terms of insulin stability, notably if the reservoir is not pressurized. After an introduction to displacement micropumps and a brief review of the insulin degradation mechanism, micropump design rules are discussed in light of microfluidic theory. Full article
(This article belongs to the Section Medicine & Pharmacology)
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9 pages, 646 KiB  
Communication
Sleep Quality and Interoception Are Associated with Generalized Anxiety in Baccalaureate Nursing Students: A Cross-Sectional Study
by Laura A. Robinson, Pamela R. Short and Andrew D. Frugé
Nurs. Rep. 2024, 14(2), 1184-1192; https://doi.org/10.3390/nursrep14020090 (registering DOI) - 13 May 2024
Abstract
Baccalaureate nursing students are at increased risk for anxiety and related mood disorders. We conducted a cross-sectional study to explore the relationships among anxiety symptoms measured by the Generalized Anxiety Disorder (GAD-7) questionnaire and lifestyle behaviors including habitual diet, sleep quality (Pittsburg Sleep [...] Read more.
Baccalaureate nursing students are at increased risk for anxiety and related mood disorders. We conducted a cross-sectional study to explore the relationships among anxiety symptoms measured by the Generalized Anxiety Disorder (GAD-7) questionnaire and lifestyle behaviors including habitual diet, sleep quality (Pittsburg Sleep Quality Index [PSQI]), and physical activity. Descriptive statistics were obtained for sample characteristics, and Pearson correlations and backward stepwise linear regression explored relationships between the GAD-7 scores, the Multidimensional Assessment of Interoceptive Awareness, version 2 (MAIA-2) subscales, and other variables. Sixty-eight students completed the survey, with 38% having moderate-to-severe anxiety. On average, respondents had moderate diet quality (Healthy Eating Index median 60/100 [range 51–75]), had high sleep quality (PSQI median 7/21 [range 4–10]), and were highly active, with a median of 43 (range 24–78) weekly metabolic equivalent (MET) hours. Sixty-seven out of 68 respondents indicated a willingness to change lifestyle behaviors; the most prevalent time-related factors were school and social commitments, with stress and financial constraints being reported among half or more of respondents. Regression analysis determined that PSQI (β = 0.446) and the MAIA-2 Not-Worrying subscale (β = −0.366) were significant (p < 0.001 for both) predictors of anxiety severity. These results indicate that mindfulness and sleep hygiene may be the most actionable foci for interventions to reduce anxiety in baccalaureate nursing students. This study was not registered as a clinical trial. Full article
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14 pages, 1161 KiB  
Article
Variation in Root Biomass and Distribution Based on the Topography, Soil Properties, and Tree Influence Index: The Case of Mt. Duryun in Republic of Korea
by Julia Inacio Carvalho, Mark Bryan Carayugan, Lan Thi Ngoc Tran, Jonathan O. Hernandez, Woo Bin Youn, Ji Young An and Byung Bae Park
Plants 2024, 13(10), 1340; https://doi.org/10.3390/plants13101340 (registering DOI) - 13 May 2024
Abstract
Root biomass and distribution are influenced by abiotic factors, such as topography and soil physicochemical properties, determining belowground productivity. Hence, we investigated the variation in root biomass and vertical root distribution based on the topography, soil physicochemical properties, and tree influence index, and [...] Read more.
Root biomass and distribution are influenced by abiotic factors, such as topography and soil physicochemical properties, determining belowground productivity. Hence, we investigated the variation in root biomass and vertical root distribution based on the topography, soil physicochemical properties, and tree influence index, and their relationships, across soil depths (0–10 cm, 10–20 cm, and 20–30 cm) and topographical gradients in a warm-temperate forest in Mt. Duryun, Republic of Korea. Two contrasting research sites were established: a lower slope oriented at ≤3° and an upper slope with a slope of 30°. Each site comprised eleven 400 m2 sampling plots from which root samples from various diameter classes (<2 mm, 2–5 mm, 5–10 mm, and >10 mm) were collected. While the bulk density increased with soil depth in the lower slope, the organic matter, available phosphorus, Ca2+, and Mg2+ showed a reversed pattern. Linear mixed-effects models generally revealed significant negative correlations between root biomass and soil pH, total nitrogen, and cation exchange capacity, particularly in small roots (βstd = −1.03 to −1.51) and coarse roots (βstd = −6.30). Root biomass exhibited a 10–15% increase in the upper slope compared to the lower slope, particularly in fine (median = 52.0 g m2–65.64 g m2) and medium roots (median = 56.04 g m2–69.52 g m2) at a 0–20 cm soil depth. While no significant correlation between root biomass and the tree influence index was found on the lower slope, a different pattern was found on the upper slope. Our results indicate that the variation in root biomass and distribution can also be explained by the differences in the soil environment and topographical positions. Full article
(This article belongs to the Section Plant Ecology)
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10 pages, 3703 KiB  
Article
Boil-Off Gas Generation in Vacuum-Jacketed Valve Used in Liquid Hydrogen Storage Tank
by Hae-Seong Hwang, Seong-Un Woo and Seung-Ho Han
Energies 2024, 17(10), 2341; https://doi.org/10.3390/en17102341 (registering DOI) - 13 May 2024
Abstract
The boiling point of liquid hydrogen is very low, at −253 °C under atmospheric pressure, which causes boil-off gas (BOG) to occur during storage and transport due to heat penetration. Because the BOG must be removed through processes such as re-liquefaction, venting to [...] Read more.
The boiling point of liquid hydrogen is very low, at −253 °C under atmospheric pressure, which causes boil-off gas (BOG) to occur during storage and transport due to heat penetration. Because the BOG must be removed through processes such as re-liquefaction, venting to the atmosphere, or incineration, related studies are required to estimate the heat transfer of storage and transport devices and to improve insulation to reduce BOG generation. In this study, a vaporization analysis was performed on a vacuum-jacketed valve used in liquid hydrogen storage and transport devices to calculate the amount of BOG generation considering the flow characteristics at the vena contracta and the saturation temperature. At a pressure of 1 bar in the liquid hydrogen storage tank, the maximum fluid flow velocity and minimum static pressure occurred at the vena contracta, with values of 62.9 m/s and −0.4 bar, respectively, and the BOG generation rate was estimated as 0.132 m3/h, where the saturation temperature was minimized at 19.3 K. Furthermore, through case studies, when the pressure in the liquid hydrogen storage tank increased to 1.5 and 2 bar, the static pressure and saturation temperature decreased, and the BOG generation rate increased to 0.221 and 0.283 m3/h, respectively. Full article
(This article belongs to the Topic Advanced Heat and Mass Transfer Technologies)
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15 pages, 2552 KiB  
Article
Evaluation of PD-L1 Expression in Colorectal Carcinomas by Comparing Scoring Methods and Their Significance in Relation to Clinicopathologic Parameters
by Mirela Frančina, Mislav Mikuš, Marin Mamić, Tihomir Jovanović, Mario Ćorić, Božica Lovrić, Ivan Vukoja, Goran Zukanović, Kristijan Matković, Jasmina Rajc, Ferdinand Slišurić, Mateja Jurić-Marelja, Goran Augustin and Ilijan Tomaš
Diagnostics 2024, 14(10), 1007; https://doi.org/10.3390/diagnostics14101007 (registering DOI) - 13 May 2024
Abstract
Background: This study aims to evaluate PD-L1 expression in colorectal carcinomas (CRCs) by using the tumor proportion score (TPS) and the combined positive score (CPS), and to investigate whether there is a correlation with clinicopathologic features. Methods: A cross-sectional study was conducted that [...] Read more.
Background: This study aims to evaluate PD-L1 expression in colorectal carcinomas (CRCs) by using the tumor proportion score (TPS) and the combined positive score (CPS), and to investigate whether there is a correlation with clinicopathologic features. Methods: A cross-sectional study was conducted that included samples from patients with colorectal adenocarcinoma treated with colon resection and rectal resection after neoadjuvant radio- and chemotherapy at the Department of Abdominal Surgery at Požega Hospital in the period from 2017 to 2022. The study included 102 tumor tissue samples from patients after resection and the pathohistological diagnosis of adenocarcinoma. Results: In our study, the PD-L1 positivity rate after the TPS was 42 (41%) samples, and after the CPS, 97 (95%) of them (p < 0.001). The positive expression of PD-L1 in tumor cells using the TPS method showed a statistically significant association with adenocarcinoma (TPS ≥ 10–50% and ≥50%). There were significantly more that were moderately differentiated, with TPS ≥ 50%, and those poorly differentiated had values ≥ 10–50%. There were significantly more patients with a status of more than one positive lymph node with TPS values ≥ 10–50%. Patients without metastases in the lymph nodes are significantly more likely to have CPS values > 50%, compared with other lymph node statuses. Conclusions: These results suggest that the total number of PD-L1-expressing cells, including tumor and immune cells, is a more sensitive biomarker than the number of PD-L1-expressing tumor cells alone in CRC. Full article
(This article belongs to the Section Pathology and Molecular Diagnostics)
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20 pages, 16723 KiB  
Article
The Antioxidant Dendrobium officinale Polysaccharide Modulates Host Metabolism and Gut Microbiota to Alleviate High-Fat Diet-Induced Atherosclerosis in ApoE−/− Mice
by Jingyi Qi, Shuaishuai Zhou, Guisheng Wang, Rongrong Hua, Xiaoping Wang, Jian He, Zi Wang, Yinhua Zhu, Junjie Luo, Wenbiao Shi, Yongting Luo and Xiaoxia Chen
Antioxidants 2024, 13(5), 599; https://doi.org/10.3390/antiox13050599 (registering DOI) - 13 May 2024
Abstract
Background: The discovery of traditional plants’ medicinal and nutritional properties has opened up new avenues for developing pharmaceutical and dietary strategies to prevent atherosclerosis. However, the effect of the antioxidant Dendrobium officinale polysaccharide (DOP) on atherosclerosis is still not elucidated. Purpose: This study [...] Read more.
Background: The discovery of traditional plants’ medicinal and nutritional properties has opened up new avenues for developing pharmaceutical and dietary strategies to prevent atherosclerosis. However, the effect of the antioxidant Dendrobium officinale polysaccharide (DOP) on atherosclerosis is still not elucidated. Purpose: This study aims to investigate the inhibitory effect and the potential mechanism of DOP on high-fat diet-induced atherosclerosis in Apolipoprotein E knockout (ApoE−/−) mice. Study design and methods: The identification of DOP was measured by high-performance gel permeation chromatography (HPLC) and Fourier transform infrared spectroscopy (FTIR). We used high-fat diet (HFD)-induced atherosclerosis in ApoE−/− mice as an animal model. In the DOP intervention stage, the DOP group was treated by gavage with 200 μL of 200 mg/kg DOP at regular times each day and continued for eight weeks. We detected changes in serum lipid profiles, inflammatory factors, anti-inflammatory factors, and antioxidant capacity to investigate the effect of the DOP on host metabolism. We also determined microbial composition using 16S rRNA gene sequencing to investigate whether the DOP could improve the structure of the gut microbiota in atherosclerotic mice. Results: DOP effectively inhibited histopathological deterioration in atherosclerotic mice and significantly reduced serum lipid levels, inflammatory factors, and malondialdehyde (F/B) production. Additionally, the levels of anti-inflammatory factors and the activity of antioxidant enzymes, including superoxide dismutase (SOD) and glutathione peroxidase (GSH-PX), were significantly increased after DOP intervention. Furthermore, we found that DOP restructures the gut microbiota composition by decreasing the Firmicutes/Bacteroidota (F/B) ratio. The Spearman’s correlation analysis indicated that serum lipid profiles, antioxidant activity, and pro-/anti-inflammatory factors were associated with Firmicutes, Bacteroidota, Allobaculum, and Coriobacteriaceae_UCG-002. Conclusions: This study suggests that DOP has the potential to be developed as a food prebiotic for the treatment of atherosclerosis in the future. Full article
(This article belongs to the Special Issue Antioxidants in Cardiovascular Diseases)
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24 pages, 7433 KiB  
Article
Improved YOLOv8 and SAHI Model for the Collaborative Detection of Small Targets at the Micro Scale: A Case Study of Pest Detection in Tea
by Rong Ye, Quan Gao, Ye Qian, Jihong Sun and Tong Li
Agronomy 2024, 14(5), 1034; https://doi.org/10.3390/agronomy14051034 (registering DOI) - 13 May 2024
Abstract
Pest target identification in agricultural production environments is challenging due to the dense distribution, small size, and high density of pests. Additionally, changeable environmental lighting and complex backgrounds further complicate the detection process. This study focuses on enhancing the recognition performance of tea [...] Read more.
Pest target identification in agricultural production environments is challenging due to the dense distribution, small size, and high density of pests. Additionally, changeable environmental lighting and complex backgrounds further complicate the detection process. This study focuses on enhancing the recognition performance of tea pests by introducing a lightweight pest image recognition model based on the improved YOLOv8 architecture. First, slicing-aided fine-tuning and slicing-aided hyper inference (SAHI) are proposed to partition input images for enhanced model performance on low-resolution images and small-target detection. Then, based on an ELAN, a generalized efficient layer aggregation network (GELAN) is designed to replace the C2f module in the backbone network, enhance its feature extraction ability, and construct a lightweight model. Additionally, the MS structure is integrated into the neck network of YOLOv8 for feature fusion, enhancing the extraction of fine-grained and coarse-grained semantic information. Furthermore, the BiFormer attention mechanism, based on the Transformer architecture, is introduced to amplify target characteristics of tea pests. Finally, the inner-MPDIoU, based on auxiliary borders, is utilized as a replacement for the original loss function to enhance its learning capacity for complex pest samples. Our experimental results demonstrate that the enhanced YOLOv8 model achieves a precision of 96.32% and a recall of 97.95%, surpassing those of the original YOLOv8 model. Moreover, it attains an mAP@50 score of 98.17%. Compared to Faster R-CNN, SSD, YOLOv5, YOLOv7, and YOLOv8, its average accuracy is 17.04, 11.23, 5.78, 3.75, and 2.71 percentage points higher, respectively. The overall performance of YOLOv8 outperforms that of current mainstream detection models, with a detection speed of 95 FPS. This model effectively balances lightweight design with high accuracy and speed in detecting small targets such as tea pests. It can serve as a valuable reference for the identification and classification of various insect pests in tea gardens within complex production environments, effectively addressing practical application needs and offering guidance for the future monitoring and scientific control of tea insect pests. Full article
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15 pages, 1052 KiB  
Article
Can Environmental Information Disclosure Improve Energy Efficiency in Manufacturing? Evidence from Chinese Enterprises
by Linfang Tan, Da Gao and Xiaowei Liu
Energies 2024, 17(10), 2342; https://doi.org/10.3390/en17102342 (registering DOI) - 13 May 2024
Abstract
Improving the energy efficiency of enterprises is one of the key means to solve the problem of energy shortage. It is of great significance to investigate how environmental information disclosure (EDI) promotes the green total factor energy efficiency (GTFEE) of enterprises. Based on [...] Read more.
Improving the energy efficiency of enterprises is one of the key means to solve the problem of energy shortage. It is of great significance to investigate how environmental information disclosure (EDI) promotes the green total factor energy efficiency (GTFEE) of enterprises. Based on this, this study calculates the GTFEE of enterprises by combining the database of Chinese manufacturing and the pollutant emission of industrial enterprises and investigates the impact of EDI on the GTFEE of manufacturing industries by using a difference-in-difference model. The following is found: (1) EDI can significantly promote the manufacturing enterprises’ GTFEE, and the results are still valid after a series of robustness tests; (2) Mechanism analysis shows that EDI can improve the GTFEE of manufacturing enterprises by promoting technological innovation and optimizing energy structure; (3) The heterogeneity analysis shows that EID is more positive on firms’ GTFEE in the eastern than western regions. The positive impact is greater for non-state-owned, low-energy consumption, export, and polluting enterprises. The findings of this paper provide a theoretical basis and practical enlightenment for the government to promote the green development transformation of enterprises. Full article
(This article belongs to the Collection Energy Transition towards Carbon Neutrality)
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10 pages, 3219 KiB  
Article
Evaluation of Phototoxicity of Short-Wavelength Laser Light Utilizing PCNA Accumulation
by Tetsuya Matsuyama, Noboru Osaka, Mikiya Yamaguchi, Naohiro Kanamaru, Kenji Wada, Ai Kawakita, Kaori Murata, Kenji Sugimoto and Koichi Okamoto
Micromachines 2024, 15(5), 646; https://doi.org/10.3390/mi15050646 (registering DOI) - 13 May 2024
Abstract
In recent years, diseases such as age-related macular degeneration and retinal pigment degeneration caused by excessive exposure to short-wavelength visible light have become significant concerns. With the aim of quantitatively evaluating the toxicity of short-wavelength light, proliferating cell nuclear antigen (PCNA) accumulation at [...] Read more.
In recent years, diseases such as age-related macular degeneration and retinal pigment degeneration caused by excessive exposure to short-wavelength visible light have become significant concerns. With the aim of quantitatively evaluating the toxicity of short-wavelength light, proliferating cell nuclear antigen (PCNA) accumulation at the irradiation site was investigated using live cell imaging techniques to irradiate individual living cells with short-wavelength laser light. By examining the dependency of PCNA accumulation on the irradiation site within the cells and their cell cycle, it was observed that PCNA accumulation occurred only when the cell nucleus of cells in the S phase of the cell cycle was irradiated. We investigated the accumulation of PCNA at the laser irradiation site using laser light at wavelengths of 405 nm and 375 nm, with intensities ranging from 0.5 μW to 9.0 μW. The results confirmed an increase in PCNA accumulation with increasing intensity, and a higher accumulation was observed with laser light irradiation at a wavelength of 375 nm compared to 405 nm. By comparing the PCNA accumulation and 24 h cell viability, we demonstrated the feasibility of quantitatively assessing laser light toxicity through the measurement of PCNA accumulation. Full article
(This article belongs to the Special Issue Ultraviolet Devices and Ultraviolet Germicidal Irradiation)
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14 pages, 3423 KiB  
Article
Plant Density and Health Evaluation in Green Stormwater Infrastructure Using Unmanned-Aerial-Vehicle-Based Imagery
by Jingwen Xue, Xuejun Qian, Dong Hee Kang and James G. Hunter
Appl. Sci. 2024, 14(10), 4118; https://doi.org/10.3390/app14104118 (registering DOI) - 13 May 2024
Abstract
Over the past few decades, there has been a notable surge in interest in green stormwater infrastructure (GSI). This trend is a result of the need to effectively address issues related to runoff, pollution, and the adverse effects of urbanization and impervious surfaces [...] Read more.
Over the past few decades, there has been a notable surge in interest in green stormwater infrastructure (GSI). This trend is a result of the need to effectively address issues related to runoff, pollution, and the adverse effects of urbanization and impervious surfaces on waterways. Concurrently, umanned aerial vehicles (UAVs) have gained prominence across applications, including photogrammetry, military applications, precision farming, agricultural land, forestry, environmental surveillance, remote-sensing, and infrastructure maintenance. Despite the widespread use of GSI and UAV technologies, there remains a glaring gap in research focused on the evaluation and maintenance of the GSIs using UAV-based imagery. This study aimed to develop an integrated framework to evaluate plant density and health within GSIs using UAV-based imagery. This integrated framework incorporated the UAV (commonly known as a drone), WebOpenDroneMap (WebDOM), ArcMap, PyCharm, and the Canopeo application. The UAV-based images of GSI components, encompassing trees, grass, soil, and unhealthy trees, as well as entire GSIs (e.g., bioretention and green roofs) within the Morgan State University (MSU) campus were collected, processed, and analyzed using this integrated framework. Results indicated that the framework yielded highly accurate predictions of plant density with a high R2 value of 95.8% and lower estimation errors of between 3.9% and 9.7%. Plant density was observed to vary between 63.63% and 75.30% in the GSIs at the MSU campus, potentially attributable to the different types of GSI, varying facility ages, and inadequate maintenance. Normalized difference vegetation index (NDVI) maps and scales of two GSIs were also generated to evaluate plant health. The NDVI and plant density results can be used to suggest where new plants can be added and to provide proper maintenance to achieve proper functions within the GSIs. This study provides a framework for evaluating plant performance within the GSIs using the collected UAV-based imagery. Full article
(This article belongs to the Section Environmental Sciences)
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29 pages, 2322 KiB  
Review
A Consolidated Understanding of the Contribution of Redox Dysregulation in the Development of Hearing Impairment
by Xin Yi Yeo, Soohyun Kwon, Kimberley R. Rinai, Sungsu Lee, Sangyong Jung and Raekil Park
Antioxidants 2024, 13(5), 598; https://doi.org/10.3390/antiox13050598 (registering DOI) - 13 May 2024
Abstract
The etiology of hearing impairment is multifactorial, with contributions from both genetic and environmental factors. Although genetic studies have yielded valuable insights into the development and function of the auditory system, the contribution of gene products and their interaction with alternate environmental factors [...] Read more.
The etiology of hearing impairment is multifactorial, with contributions from both genetic and environmental factors. Although genetic studies have yielded valuable insights into the development and function of the auditory system, the contribution of gene products and their interaction with alternate environmental factors for the maintenance and development of auditory function requires further elaboration. In this review, we provide an overview of the current knowledge on the role of redox dysregulation as the converging factor between genetic and environmental factor-dependent development of hearing loss, with a focus on understanding the interaction of oxidative stress with the physical components of the peripheral auditory system in auditory disfunction. The potential involvement of molecular factors linked to auditory function in driving redox imbalance is an important promoter of the development of hearing loss over time. Full article
(This article belongs to the Special Issue Oxidative Stress in Ear Damage)
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8 pages, 528 KiB  
Article
Surgical Outcomes of da Vinci Xi™ and da Vinci SP™ for Early-Stage Endometrial Cancer in Patients Undergoing Hysterectomy
by Motoki Matsuura, Sachiko Nagao, Shoko Kurokawa, Masato Tamate, Taishi Akimoto and Tsuyoshi Saito
J. Clin. Med. 2024, 13(10), 2864; https://doi.org/10.3390/jcm13102864 (registering DOI) - 13 May 2024
Abstract
Objectives: This study aimed to evaluate and compare the feasibility and outcomes of two robotic hysterectomy (da Vinci Xi™ vs. da Vinci SP™) systems without lymph node dissection in patients with early-stage endometrial cancer, and assess the postoperative recurrence rate and overall [...] Read more.
Objectives: This study aimed to evaluate and compare the feasibility and outcomes of two robotic hysterectomy (da Vinci Xi™ vs. da Vinci SP™) systems without lymph node dissection in patients with early-stage endometrial cancer, and assess the postoperative recurrence rate and overall survival of patients. Methods: A retrospective review of 84 patients who underwent robotic hysterectomy for endometrial cancer (stage 1A) was conducted. Surgical procedures, patient characteristics, intraoperative measures, and postoperative outcomes were statistically analyzed. A single gynecologist performed all surgeries. Results: Patient characteristics, average age, and body mass index showed no significant differences between the two models. The total operative time was significantly shorter with da Vinci SP™. Recurrence was identified in only one patient operated on with da Vinci Xi™. All patients were alive during analysis, with a median overall survival of 38 and 9 months for da Vinci Xi™ and da Vinci SP™, respectively. Conclusions: Robotic hysterectomy without lymph node dissection appears to be a safe and effective approach for patients with early-stage endometrial cancer. The da Vinci SP offers the advantage of shorter operative times than the da Vinci Xi™. These findings support the consideration of robotic surgery as a viable option for selected patients. Full article
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