The 2023 MDPI Annual Report has
been released!
 
14 pages, 293 KiB  
Article
Quantum Information: Systems, Their States, and the Use of Variances
by Alain Deville and Yannick Deville
Information 2024, 15(5), 247; https://doi.org/10.3390/info15050247 (registering DOI) - 25 Apr 2024
Abstract
Quantum information mobilizes the description of quantum systems, their states, and their behavior. Since a measurement postulate introduced by von Neumann in 1932, if a quantum system has been prepared in two different mixed states represented by the same density operator ρ, [...] Read more.
Quantum information mobilizes the description of quantum systems, their states, and their behavior. Since a measurement postulate introduced by von Neumann in 1932, if a quantum system has been prepared in two different mixed states represented by the same density operator ρ, these preparations are said to have led to the same mixture. For more than 50 years, there has been a lack of consensus about this postulate. In a 2011 article, considering variances of spin components, Fratini and Hayrapetyan tried to show that this postulate is unjustified. The aim of the present paper is to discuss major points in this 2011 article and in their reply to a 2012 paper by Bodor and Diosi claiming that their analysis was irrelevant. Facing some ambiguities or inconsistencies in the 2011 paper and in the reply, we first try to guess their aim, establish results useful in this context, and finally discuss the use or misuse of several concepts implied in this debate. Full article
17 pages, 2865 KiB  
Article
Genome-Wide Identification, Phylogenetic and Expression Analysis of Expansin Gene Family in Medicago sativa L
by Yajing Li, Yangyang Zhang, Jing Cui, Xue Wang, Mingna Li, Lili Zhang and Junmei Kang
Int. J. Mol. Sci. 2024, 25(9), 4700; https://doi.org/10.3390/ijms25094700 (registering DOI) - 25 Apr 2024
Abstract
Expansins, a class of cell-wall-loosening proteins that regulate plant growth and stress resistance, have been studied in a variety of plant species. However, little is known about the Expansins present in alfalfa (Medicago sativa L.) due to the complexity of its tetraploidy. [...] Read more.
Expansins, a class of cell-wall-loosening proteins that regulate plant growth and stress resistance, have been studied in a variety of plant species. However, little is known about the Expansins present in alfalfa (Medicago sativa L.) due to the complexity of its tetraploidy. Based on the alfalfa (cultivar “XinjiangDaye”) reference genome, we identified 168 Expansin members (MsEXPs). Phylogenetic analysis showed that MsEXPs consist of four subfamilies: MsEXPAs (123), MsEXPBs (25), MsEXLAs (2), and MsEXLBs (18). MsEXPAs, which account for 73.2% of MsEXPs, and are divided into twelve groups (EXPA-I–EXPA-XII). Of these, EXPA-XI members are specific to Medicago trunctula and alfalfa. Gene composition analysis revealed that the members of each individual subfamily shared a similar structure. Interestingly, about 56.3% of the cis-acting elements were predicted to be associated with abiotic stress, and the majority were MYB- and MYC-binding motifs, accounting for 33.9% and 36.0%, respectively. Our short-term treatment (≤24 h) with NaCl (200 mM) or PEG (polyethylene glycol, 15%) showed that the transcriptional levels of 12 MsEXPs in seedlings were significantly altered at the tested time point(s), indicating that MsEXPs are osmotic-responsive. These findings imply the potential functions of MsEXPs in alfalfa adaptation to high salinity and/or drought. Future studies on MsEXP expression profiles under long-term (>24 h) stress treatment would provide valuable information on their involvement in the response of alfalfa to abiotic stress. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
13 pages, 495 KiB  
Article
Germline Genetic Mutations in Adult Patients with Sarcoma: Insight into the Middle East Genetic Landscape
by Ramiz Abu-Hijlih, Baha Sharaf, Samer Salah, Hira Bani Hani, Mohammad Alqaisieh, Abdulla Alzibdeh, Layan Ababneh, Suleiman Mahafdah and Hikmat Abdel-Razeq
Cancers 2024, 16(9), 1668; https://doi.org/10.3390/cancers16091668 (registering DOI) - 25 Apr 2024
Abstract
Data on germline mutations in soft tissue and bone sarcomas are scarce. We sought to identify the prevalence of germline mutations in adult sarcoma patients treated at a tertiary cancer center. Newly diagnosed patients were offered germline genetic testing via an 84-gene panel. [...] Read more.
Data on germline mutations in soft tissue and bone sarcomas are scarce. We sought to identify the prevalence of germline mutations in adult sarcoma patients treated at a tertiary cancer center. Newly diagnosed patients were offered germline genetic testing via an 84-gene panel. The prevalence of pathogenic germline variants (PGVs) and their association with disease-, and patient- related factors are reported. A total of 87 patients were enrolled, the median age was 48 (19–78) years, and 47 (54%) were females. Gastrointestinal stromal tumors (n = 12, 13.8%), liposarcoma (n = 10, 11.5%), and Ewing sarcoma (n = 10, 11.5%) were the main subtypes. A total of 20 PGVs were detected in 18 (20.7%) patients. Variants of uncertain significance, in the absence of PGVs, were detected in 40 (45.9%) patients. Young age (p = 0.031), presence of a second primary cancer (p = 0.019), and female gender (p = 0.042) were correlated with the presence of PGVs. All identified PGVs have potential clinical actionability and cascade testing, and eight (44.44%) suggested eligibility for a targeted therapy. Almost one in five adult patients with soft tissue and bone sarcomas harbor pathogenic or likely pathogenic variants. Many of these variants are potentially actionable, and almost all have implications on cancer screening and family counselling. In this cohort from the Middle East, younger age, presence of a second primary tumor, and female gender were significantly associated with higher PGVs rates. Larger studies able to correlate treatment outcomes with genetic variants are highly needed. Full article
(This article belongs to the Special Issue Recent Advances in Rare Cancers: From Bench to Bedside and Back)
15 pages, 972 KiB  
Communication
Detecting Class 1 Integrons and Their Variable Regions in Escherichia coli Whole-Genome Sequences Reported from Andean Community Countries
by María Nicole Solis, Karen Loaiza, Lilibeth Torres-Elizalde, Ivan Mina, Miroslava Anna Šefcová and Marco Larrea-Álvarez
Antibiotics 2024, 13(5), 394; https://doi.org/10.3390/antibiotics13050394 (registering DOI) - 25 Apr 2024
Abstract
Various genetic elements, including integrons, are known to contribute to the development of antimicrobial resistance. Class 1 integrons have been identified in E. coli isolates and are associated with multidrug resistance in countries of the Andean Community. However, detailed information on the gene [...] Read more.
Various genetic elements, including integrons, are known to contribute to the development of antimicrobial resistance. Class 1 integrons have been identified in E. coli isolates and are associated with multidrug resistance in countries of the Andean Community. However, detailed information on the gene cassettes located on the variable regions of integrons is lacking. Here, we investigated the presence and diversity of class 1 integrons, using an in silico approach, in 2533 whole-genome sequences obtained from EnteroBase. IntFinder v1.0 revealed that almost one-third of isolates contained these platforms. Integron-bearing isolates were associated with environmental, food, human, and animal origins reported from all countries under scrutiny. Moreover, they were identified in clones known for their pathogenicity or multidrug resistance. Integrons carried cassettes associated with aminoglycoside (aadA), trimethoprim (dfrA), cephalosporin (blaOXA; blaDHA), and fluoroquinolone (aac(6′)-Ib-cr; qnrB) resistance. These platforms showed higher diversity and larger numbers than previously reported. Moreover, integrons carrying more than three cassettes in their variable regions were determined. Monitoring the prevalence and diversity of genetic elements is necessary for recognizing emergent patterns of resistance in pathogenic bacteria, especially in countries where various factors are recognized to favor the selection of resistant microorganisms. Full article
(This article belongs to the Special Issue Genomic Analysis of Antimicrobial Drug-Resistant Bacteria)
24 pages, 7162 KiB  
Article
How to Personalize General Anesthesia—A Prospective Theoretical Approach to Conformational Changes of Halogenated Anesthetics in Fire Smoke Poisoning
by Flavius Nicușor Truicu, Roni Octavian Damian, Mihai Alexandru Butoi, Vlad Ionuț Belghiru, Luciana Teodora Rotaru, Monica Puticiu and Renata Maria Văruț
Int. J. Mol. Sci. 2024, 25(9), 4701; https://doi.org/10.3390/ijms25094701 (registering DOI) - 25 Apr 2024
Abstract
Smoke intoxication is a central event in mass burn incidents, and toxic smoke acts at different levels of the body, blocking breathing and oxygenation. The majority of these patients require early induction of anesthesia to preserve vital functions. We studied the influence of [...] Read more.
Smoke intoxication is a central event in mass burn incidents, and toxic smoke acts at different levels of the body, blocking breathing and oxygenation. The majority of these patients require early induction of anesthesia to preserve vital functions. We studied the influence of hemoglobin (HMG) and myoglobin (MGB) blockade by hydrochloric acid (HCl) in an interaction model with gaseous anesthetics using molecular docking techniques. In the next part of the study, molecular dynamics (MD) simulations were performed on the top-scoring ligand–receptor complexes to investigate the stability of the ligand–receptor complexes and the interactions between ligands and receptors in more detail. Through docking analysis, we observed that hemoglobin creates more stable complexes with anesthetic gases than myoglobin. Intoxication with gaseous hydrochloric acid produces conformational and binding energy changes of anesthetic gases to the substrate (both the pathway and the binding site), the most significant being recorded in the case of desflurane and sevoflurane, while for halothane and isoflurane, they remain unchanged. According to our theoretical model, the selection of anesthetic agents for patients affected by fire smoke containing hydrochloric acid is critical to ensure optimal anesthetic effects. In this regard, our model suggests that halothane and isoflurane are the most suitable choices for predicting the anesthetic effects in such patients when compared to sevoflurane and desflurane. Full article
(This article belongs to the Special Issue Molecular Toxicology of New Drugs: New Insights)
19 pages, 1548 KiB  
Article
Research on the Effect of Structural Parameters on Cavitation Performance of Shear Hydrodynamic Cavitation Generator
by Fengxia Lyu, Ming Tang, Faqi Zhou, Xintong Zhang, Saiyue Han and Sheng Zhang
Appl. Sci. 2024, 14(9), 3676; https://doi.org/10.3390/app14093676 (registering DOI) - 25 Apr 2024
Abstract
The method of cavitation is increasingly applied in water environmental protection. Based on the numerical simulation method, a study on the structural parameters of the shear-type hydrodynamic cavitation generators for wastewater treatment is proceeded. The internal flow field is described by employing the [...] Read more.
The method of cavitation is increasingly applied in water environmental protection. Based on the numerical simulation method, a study on the structural parameters of the shear-type hydrodynamic cavitation generators for wastewater treatment is proceeded. The internal flow field is described by employing the mixed multiphase flow model and the Zwart cavitation model. Experiments were conducted by applying the wastewater from a dyeing factory as the medium. The degradation rate of COD in water characterizes the cavitation performance of the hydrodynamic cavitation generator, and the rationality of the numerical simulation approach is validated. The findings indicate that different structural parameters have a great influence on the cavitation performance. The appropriate number of tooth rows creates a flow field with a greater vapor and velocity than the other parameters. The number of teeth in a single row, the outer diameter of the hydrodynamic cavitation generator and the tooth bevel angle also affect the cavitation performance to some extent, and there is an optimal value. The study provides a reference for the applicability of a numerical simulation of the flow field inside the hydrodynamic cavitation generator and the structural optimization of the rotary hydrodynamic cavitation generator. Full article
(This article belongs to the Special Issue Flow Analysis and Structural Control of Fluid Machinery)
21 pages, 1259 KiB  
Article
New Insights into the Biological Functions of Essential TsaB/YeaZ Protein in Staphylococcus aureus
by Haiyong Guo, Ting Lei, Junshu Yang, Yue Wang, Yifan Wang and Yinduo Ji
Antibiotics 2024, 13(5), 393; https://doi.org/10.3390/antibiotics13050393 (registering DOI) - 25 Apr 2024
Abstract
TsaB/YeaZ represents a promising target for novel antibacterial agents due to its indispensable role in bacterial survival, high conservation within bacterial species, and absence of eukaryotic homologs. Previous studies have elucidated the role of the essential staphylococcal protein, TsaB/YeaZ, in binding DNA to [...] Read more.
TsaB/YeaZ represents a promising target for novel antibacterial agents due to its indispensable role in bacterial survival, high conservation within bacterial species, and absence of eukaryotic homologs. Previous studies have elucidated the role of the essential staphylococcal protein, TsaB/YeaZ, in binding DNA to mediate the transcription of the ilv-leu operon, responsible for encoding key enzymes involved in the biosynthesis of branched-chain amino acids—namely isoleucine, leucine, and valine (ILV). However, the regulation of ILV biosynthesis does not account for the essentiality of TsaB/YeaZ for bacterial growth. In this study, we investigated the impact of TsaB/YeaZ depletion on bacterial morphology and gene expression profiles using electron microscopy and deep transcriptomic analysis, respectively. Our results revealed significant alterations in bacterial size and surface smoothness upon TsaB/YeaZ depletion. Furthermore, we pinpointed specific genes and enriched biological pathways significantly affected by TsaB/YeaZ during the early and middle exponential phases and early stationary phases of growth. Crucially, our research uncovered a regulatory role for TsaB/YeaZ in bacterial autolysis. These discoveries offer fresh insights into the multifaceted biological functions of TsaB/YeaZ within S. aureus. Full article
(This article belongs to the Special Issue Genomic Analysis of Antimicrobial Drug-Resistant Bacteria)
12 pages, 1385 KiB  
Article
Sustainable and Cost-Efficient Production of Micro-Patterned Reduced Graphene Oxide on Graphene Oxide Films
by Satam Alotibi, Talal F. Qahtan, Amani M. Alansi, Taoreed O. Owolabi, Salah T. Hameed, Naveed Afzal, Sadia Bilal and Dina Salah
Coatings 2024, 14(5), 534; https://doi.org/10.3390/coatings14050534 (registering DOI) - 25 Apr 2024
Abstract
This study tackles the critical demand for sustainable synthesis methods of reduced graphene oxide (rGO), highlighting the environmental drawbacks of conventional chemical processes. We introduce a novel, green synthesis technique involving the irradiation of a 500 eV argon ion beam, which not only [...] Read more.
This study tackles the critical demand for sustainable synthesis methods of reduced graphene oxide (rGO), highlighting the environmental drawbacks of conventional chemical processes. We introduce a novel, green synthesis technique involving the irradiation of a 500 eV argon ion beam, which not only facilitates the creation of micro-patterned rGO on a graphene oxide (GO) film but also enables simultaneous material characterization and patterning. By adjusting the irradiation exposure time between 0 and 80 s, we achieve meticulous control over the attributes and the reduction process of the material. The use of X-ray photoelectron spectroscopy (XPS) allows for real-time monitoring of the reduction from GO to rGO, evidenced by a notable reduction in the intensities of C-O, C=O, and O-C=O bonds, and an increase in C-C bond intensities, indicating a significant reduction level. Our research demonstrates the efficient production of eco-friendly rGO using precise, controlled argon ion beam irradiation, proving its advantages over traditional methods. These results contribute to the development of sustainable material science technologies, with potential applications in electronics, energy storage, and more. Full article
(This article belongs to the Special Issue Advances in Low-Cost Energy Materials and Thin Films)
11 pages, 284 KiB  
Article
AKT, p-AKT, ERK1/2 and p-ERK1/2 in Mural Granulosa Cells Are Not Correlated to Different Ovarian Stimulation Protocols in Patients Undergoing Assisted Reproductive Treatment
by Giovanni Ruvolo, Domenica Matranga, Maria Magdalena Barreca and Liana Bosco
Life 2024, 14(5), 554; https://doi.org/10.3390/life14050554 (registering DOI) - 25 Apr 2024
Abstract
(1) Background: In this paper we aim to study the relationship between the expression levels of molecules involved in apoptotic/survival pathways, considered as molecular markers of oocyte competence (i.e., AKT, p-AKT, ERK1/2, and p-ERK1/2) in mural granulosa cells (MGCs) and the administration of [...] Read more.
(1) Background: In this paper we aim to study the relationship between the expression levels of molecules involved in apoptotic/survival pathways, considered as molecular markers of oocyte competence (i.e., AKT, p-AKT, ERK1/2, and p-ERK1/2) in mural granulosa cells (MGCs) and the administration of r-FSH alone or combined with exogenous r-LH, in ovarian stimulation protocol. Moreover, we aim to evaluate oocyte competence by comparing normally cleaved embryos that were transferred in the uterus, with embryos that were arrested during in vitro culture. (2) Methods: The study included 34 normo-responder women undergoing ICSI procedures. All subjects were divided into two groups. Group A consisted of 18 women stimulated with r-FSH and used as a control group; Group B consisted of 14 women stimulated with r-FSH combined with r-LH. The MGCs were obtained from individual follicles. Immunoblot analyses were carried out to analyze the AKT, p-AKT, ERK1/2, and p-ERK1/2 levels in MGCs and to correlate them with the ovarian stimulation protocol. Furthermore, the oocyte competence was evaluated, for each follicle, according to the development of the embryo during in vitro culture and the pregnancy outcome. (3) Results: We found no significant difference in the levels of molecules in isolated MGCs between groups A and B. These results, in light of our previous research, suggest for the first time, to our knowledge, that cumulus cells and mural granulosa cells in the same follicle show different expression levels of molecules involved in the apoptotic mechanism. (4) Conclusions: Our results could clarify some controversial data in the literature where cumulative cell pools of cumulus and granulosa were analyzed, described as ovarian follicle cells, and used as markers of oocyte competence. In this paper, we found evidence that cumulus and granulosa cells need to be analyzed separately. Full article
(This article belongs to the Special Issue Biological and Clinical Research of Germ Cells)
20 pages, 680 KiB  
Review
Methods and Techniques Supporting Energy and Media Savings in Maintenance of Public Transport Buses—State of the Art and Recommendations
by Andrzej Wieczorek, Kinga Stecuła and Wieslaw Wes Grebski
Energies 2024, 17(9), 2051; https://doi.org/10.3390/en17092051 (registering DOI) - 25 Apr 2024
Abstract
In the article, the authors discussed the topic of energy and media savings in a public transport company. The article is of a review nature, referring to 100 sources, including scientific papers, books, conference proceedings, and websites. In the first part, a detailed [...] Read more.
In the article, the authors discussed the topic of energy and media savings in a public transport company. The article is of a review nature, referring to 100 sources, including scientific papers, books, conference proceedings, and websites. In the first part, a detailed literature review on environmental protection problems in road transport and methods of solving them was conducted. Subsequently, the authors reviewed the literature content on maintenance as a pro-environmental activity in transport companies. The great accent was paid to the problem of saving energy and media in the maintenance of public transport buses. Based on the literature and knowledge, the authors proposed the possibilities of conducting a rational method of managing the operation and maintenance of buses from the point of view of environmental protection, based on the strategy of predictive bus maintenance. Full article
(This article belongs to the Section C: Energy Economics and Policy)
21 pages, 1797 KiB  
Article
Benefits of Combined Fluorescence Lifetime Imaging Microscopy and Fluorescence Correlation Spectroscopy for Biomedical Studies Demonstrated by Using a Liposome Model System
by Kristina Bruun, Hans-Gerd Löhmannsröben and Carsten Hille
Biophysica 2024, 4(2), 207-227; https://doi.org/10.3390/biophysica4020015 (registering DOI) - 25 Apr 2024
Abstract
Drug delivery systems play a pivotal role in targeted pharmaceutical transport and controlled release at specific sites. Liposomes, commonly used as drug carriers, constitute a fundamental part of these systems. Moreover, the drug–liposome model serves as a robust platform for investigating interaction processes [...] Read more.
Drug delivery systems play a pivotal role in targeted pharmaceutical transport and controlled release at specific sites. Liposomes, commonly used as drug carriers, constitute a fundamental part of these systems. Moreover, the drug–liposome model serves as a robust platform for investigating interaction processes at both cellular and molecular levels. To advance our understanding of drug carrier uptake mechanisms, we employed fluorescence lifetime imaging microscopy (FLIM) and fluorescence correlation spectroscopy (FCS), leveraging the unique benefits of two-photon (2P) excitation. Our approach utilized giant unilamellar vesicles (GUVs) as a simplified model system for cell membranes, labelled with the amphiphilic fluorescent dye 3,3′-dioctadecyloxa-carbocyanine (DiOC18(3)). Additionally, large unilamellar vesicles (LUVs) functioned as a drug carrier system, incorporating the spectrally distinct fluorescent sulforhodamine 101 (SRh101) as a surrogate drug. The investigation emphasized the diverse interactions between GUVs and LUVs based on the charged lipids employed. We examined the exchange kinetics and structural alterations of liposome carriers during the uptake process. Our study underscores the significance of employing 2P excitation in conjunction with FLIM and FCS. This powerful combination offers a valuable methodological approach for studying liposome interactions, positioning them as an exceptionally versatile model system with a distinct technical advantage. Full article
11 pages, 535 KiB  
Communication
A Proof-of-Concept Protein Microarray-Based Approach for Serotyping of Salmonella enterica Strains
by Sascha D. Braun, Elke Müller, Katrin Frankenfeld, Dominik Gary, Stefan Monecke and Ralf Ehricht
Pathogens 2024, 13(5), 355; https://doi.org/10.3390/pathogens13050355 (registering DOI) - 25 Apr 2024
Abstract
Salmonella enterica, a bacterium causing foodborne illnesses like salmonellosis, is prevalent in Europe and globally. It is found in food, water, and soil, leading to symptoms like diarrhea and fever. Annually, it results in about 95 million cases worldwide, with increasing antibiotic [...] Read more.
Salmonella enterica, a bacterium causing foodborne illnesses like salmonellosis, is prevalent in Europe and globally. It is found in food, water, and soil, leading to symptoms like diarrhea and fever. Annually, it results in about 95 million cases worldwide, with increasing antibiotic resistance posing a public health challenge. Therefore, it is necessary to detect and serotype Salmonella for several reasons. The identification of the serovars of Salmonella enterica isolates is crucial to detect and trace outbreaks and to implement effective control measures. Our work presents a protein-based microarray for the rapid and accurate determination of Salmonella serovars. The microarray carries a set of antibodies that can detect different Salmonella O- and H-antigens, allowing for the identification of multiple serovars, including Typhimurium and Enteritidis, in a single miniaturized assay. The system is fast, economical, accurate, and requires only small sample volumes. Also, it is not required to maintain an extensive collection of sera for the serotyping of Salmonella enterica serovars and can be easily expanded and adapted to new serovars and sera. The scientific state of the art in Salmonella serotyping involves the comparison of traditional, molecular, and in silico methods, with a focus on economy, multiplexing, accuracy, rapidity, and adaptability to new serovars and sera. The development of protein-based microarrays, such as the one presented in our work, contributes to the ongoing advancements in this field. Full article
(This article belongs to the Special Issue New Approaches to Combating Multidrug-Resistant Pathogens)
21 pages, 1247 KiB  
Article
Patterns of Human Milk Oligosaccharides in Mature Milk Are Associated with Certain Gut Microbiota in Infants
by Shuai Mao, Ai Zhao, Hua Jiang, Jingyu Yan, Wuxian Zhong, Yiping Xun and Yumei Zhang
Nutrients 2024, 16(9), 1287; https://doi.org/10.3390/nu16091287 (registering DOI) - 25 Apr 2024
Abstract
Human milk oligosaccharides (HMOs) are complexes that play a crucial role in shaping the early-life gut microbiota. This study intends to explore whether HMO patterns are associated with the gut microbiota of infants. We included 96 Chinese breastfeeding mother–infant dyads. Breast milk and [...] Read more.
Human milk oligosaccharides (HMOs) are complexes that play a crucial role in shaping the early-life gut microbiota. This study intends to explore whether HMO patterns are associated with the gut microbiota of infants. We included 96 Chinese breastfeeding mother–infant dyads. Breast milk and infant faecal samples were collected and tested. With milk 2′-fucosyllactose, difucosyllactose, and lacto-N-fucopentaose-I as biomarkers, we divided the mothers into secretor and non-secretor groups. HMO patterns were extracted using principal component analysis. The majority (70.7%) of mothers were categorised as secretor and five different HMO patterns were identified. After adjustment, the infants of secretor mothers exhibited a lower relative abundance of Bifidobacterium bifidum (β = −0.245, 95%CI: −0.465~−0.025). An HMO pattern characterised by high levels of 3-fucosyllactose, lacto-N-fucopentaose-III, and lacto-N-neodifucohexaose-II was positively associated with the relative abundance of Bifidobacterium breve (p = 0.014), while the pattern characterised by lacto-N-neotetraose, 6′-sialyllactose, and sialyllacto-N-tetraose-b was negatively associated with Bifidobacterium breve (p = 0.027). The pattern characterised by high levels of monofucosyl-lacto-N-hexaose-III and monofucosyl-lacto-N-neohexaose was positively associated with Bifidobacterium dentium (p = 0.025) and Bifidobacterium bifidum (p < 0.001), respectively. This study suggests that HMO patterns from mature breast milk were associated with certain gut microbiota of breastfed infants. Full article
(This article belongs to the Special Issue Roles of Dairy Intake in Health Development)
7 pages, 2331 KiB  
Case Report
Hepatic Epithelioid Hemangioendothelioma in a Dog
by Luisa Vera Muscatello, Federico Massari, Paola Roccabianca, Giuseppe Sarli, Cinzia Benazzi and Marco Luigi Bianchi
Animals 2024, 14(9), 1302; https://doi.org/10.3390/ani14091302 (registering DOI) - 25 Apr 2024
Abstract
A 5-year-old spayed female Breton dog was referred for a thyroid nodule. A total body CT scan evidenced multifocal hepatic nodules. Cytological liver samples were hemodiluted and non-diagnostic. Following a thyroidectomy, the histology was consistent with a follicular-compact thyroid carcinoma. On laparoscopy, most [...] Read more.
A 5-year-old spayed female Breton dog was referred for a thyroid nodule. A total body CT scan evidenced multifocal hepatic nodules. Cytological liver samples were hemodiluted and non-diagnostic. Following a thyroidectomy, the histology was consistent with a follicular-compact thyroid carcinoma. On laparoscopy, most hepatic lobes had multifocal dark-red nodules that were biopsied for histology. Microscopically, the hepatic parenchyma in the nodules was substituted by blood channels lined by bland spindle cells but adjacent to epithelioid neoplastic cells, single or in clusters, embedded in a moderate amount of edematous collagen matrix. These cells had optically empty cytoplasmic space, occasionally containing erythrocytes (microlumina). Spindle and epithelioid cells expressed membranous-to-cytoplasmic CD31 and FVIII-RA consistent with endothelial origin. Based on morphology and immunolabelling, a hemangioendothelioma with epithelioid differentiation was diagnosed. Lesions in the liver were initially stable, showing progression with time. The dog was alive with no systemic clinical signs 36 months after laparoscopy. Full article
(This article belongs to the Section Veterinary Clinical Studies)
67 pages, 1965 KiB  
Review
A Critical Review of the Modelling Tools for the Reactive Transport of Organic Contaminants
by Katarzyna Samborska-Goik and Marta Pogrzeba
Appl. Sci. 2024, 14(9), 3675; https://doi.org/10.3390/app14093675 (registering DOI) - 25 Apr 2024
Abstract
The pollution of groundwater and soil by hydrocarbons is a significant and growing global problem. Efforts to mitigate and minimise pollution risks are often based on modelling. Modelling-based solutions for prediction and control play a critical role in preserving dwindling water resources and [...] Read more.
The pollution of groundwater and soil by hydrocarbons is a significant and growing global problem. Efforts to mitigate and minimise pollution risks are often based on modelling. Modelling-based solutions for prediction and control play a critical role in preserving dwindling water resources and facilitating remediation. The objectives of this article are to: (i) to provide a concise overview of the mechanisms that influence the migration of hydrocarbons in groundwater and to improve the understanding of the processes that affect contamination levels, (ii) to compile the most commonly used models to simulate the migration and fate of hydrocarbons in the subsurface; and (iii) to evaluate these solutions in terms of their functionality, limitations, and requirements. The aim of this article is to enable potential users to make an informed decision regarding the modelling approaches (deterministic, stochastic, and hybrid) and to match their expectations with the characteristics of the models. The review of 11 1D screening models, 18 deterministic models, 7 stochastic tools, and machine learning experiments aimed at modelling hydrocarbon migration in the subsurface should provide a solid basis for understanding the capabilities of each method and their potential applications. Full article
(This article belongs to the Special Issue Environmental Bioaccumulation and Assessment of Toxic Elements)
17 pages, 2814 KiB  
Article
Potential Role of Circulating PD-L1+ Leukocytes as a Predictor of Response to Anti-PD-(L)1 Therapy in NSCLC Patients
by Georgia Anguera, Maria Mulet, Carlos Zamora, Rubén Osuna-Gómez, Andrés Barba, Ivana Sullivan, Jorgina Serra-López, Elisabet Cantó, Silvia Vidal and Margarita Majem
Biomedicines 2024, 12(5), 958; https://doi.org/10.3390/biomedicines12050958 (registering DOI) - 25 Apr 2024
Abstract
PD-(L)1 inhibitors are part of the treatment strategy for non-small cell lung cancer (NSCLC) although its efficacy is limited to certain patients. Our study aimed to identify patients who might benefit from anti-PD-(L)1 inhibitors by analyzing the PD-L1 expression on circulating leukocytes and [...] Read more.
PD-(L)1 inhibitors are part of the treatment strategy for non-small cell lung cancer (NSCLC) although its efficacy is limited to certain patients. Our study aimed to identify patients who might benefit from anti-PD-(L)1 inhibitors by analyzing the PD-L1 expression on circulating leukocytes and its evolution during treatment. One hundred thirteen NSCLC patients, according to their radiological response after 10–12 weeks of treatment, were classified into responders, stable, and progressive disease. Percentages of circulating PD-L1+ leukocytes, PD-L1+ platelets (PLTs), and leukocyte-PLT complexes were assessed using flow cytometry, and plasma concentrations of soluble immunomodulatory factors were quantified by ELISA. Responders exhibited significantly higher pre-treatment percentages of PD-L1+ neutrophils, PD-L1+ CD14+ cells, and PD-L1+ PLTs than progressors. The percentages of these populations decreased in responders post-treatment, contrasting with stables and progressors. PLTs notably contributed to PD-L1 expression in CD14+ cells and neutrophils. Plasma cytokine analysis revealed baseline differences only in IL-17 concentration among groups, whereas network analyses highlighted distinct association patterns between plasma molecules and PD-L1+ leukocytes after 10–12 weeks of treatment. Our findings suggest that pre-treatment assessment of circulating PD-L1+ neutrophils, PD-L1+ CD14+ cells, and PD-L1+ PLTs may be helpful in identifying NSCLC patients who are potential candidates for anti-PD-(L)1 therapy. Full article
(This article belongs to the Special Issue PD-1/PD-L1 and Immunotherapy)
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25 pages, 1114 KiB  
Article
Text Mining and Multi-Attribute Decision-Making-Based Course Improvement in Massive Open Online Courses
by Pei Yang, Ying Liu, Yuyan Luo, Zhong Wang and Xiaoli Cai
Appl. Sci. 2024, 14(9), 3654; https://doi.org/10.3390/app14093654 (registering DOI) - 25 Apr 2024
Abstract
As the leading platform of online education, MOOCs provide learners with rich course resources, but course designers are still faced with the challenge of how to accurately improve the quality of courses. Current research mainly focuses on learners’ emotional feedback on different course [...] Read more.
As the leading platform of online education, MOOCs provide learners with rich course resources, but course designers are still faced with the challenge of how to accurately improve the quality of courses. Current research mainly focuses on learners’ emotional feedback on different course attributes, neglecting non-emotional content as well as the costs required to improve these attributes. This limitation makes it difficult for course designers to fully grasp the real needs of learners and to accurately locate the key issues in the course. To overcome the above challenges, this study proposes an MOOC improvement method based on text mining and multi-attribute decision-making. Firstly, we utilize word vectors and clustering techniques to extract course attributes that learners focus on from their comments. Secondly, with the help of some deep learning methods based on BERT, we conduct a sentiment analysis on these comments to reveal learners’ emotional tendencies and non-emotional content towards course attributes. Finally, we adopt the multi-attribute decision-making method TOPSIS to comprehensively consider the emotional score, attention, non-emotional content, and improvement costs of the attributes, providing course designers with a priority ranking for attribute improvement. We applied this method to two typical MOOC programming courses—C language and Java language. The experimental findings demonstrate that our approach effectively identifies course attributes from reviews, assesses learners’ satisfaction, attention, and cost of improvement, and ultimately generates a prioritized list of course attributes for improvement. This study provides a new approach for improving the quality of online courses and contributes to the sustainable development of online course quality. Full article
13 pages, 768 KiB  
Review
Agricultural Disaster Prevention System: Insights from Taiwan’s Adaptation Strategies
by Ming-Hwi Yao, Yung-Heng Hsu, Ting-Yi Li, Yung-Ming Chen, Chun-Tang Lu, Chi-Ling Chen and Pei-Yu Shih
Atmosphere 2024, 15(5), 526; https://doi.org/10.3390/atmos15050526 (registering DOI) - 25 Apr 2024
Abstract
In response to the adverse effects of climate change-induced frequent extreme disasters on agricultural production and supply stability, this study develops a comprehensive agricultural disaster prevention system based on current adaptation strategies for mitigating agricultural meteorological disasters. The primary goal is to enhance [...] Read more.
In response to the adverse effects of climate change-induced frequent extreme disasters on agricultural production and supply stability, this study develops a comprehensive agricultural disaster prevention system based on current adaptation strategies for mitigating agricultural meteorological disasters. The primary goal is to enhance disaster preparedness and recovery through three core platforms: a fine-scale weather forecast service system, a crop disaster early warning system, and an agricultural information service platform for disasters. The results show that every major agricultural production township in Taiwan now has dedicated agricultural weather stations and access to refined weather forecasts. Additionally, a disaster prevention calendar for 76 important crops is established, integrating cultivation management practices and critical disaster thresholds for different growth periods. Utilizing this calendar, the crop disaster early warning system can provide timely disaster-related information and pre-disaster prevention assistance to farmers through various information dissemination tools. As a disaster approaches, the agricultural information service platform for disasters provides updates on current crop growth conditions. This service not only pinpoints areas at higher risk of disasters and vulnerable crop types but also offers mitigation suggestions to prevent potential damage. Administrative efficiency is then improved with a response mechanism incorporating drones and image analysis for early disaster detection and rapid response. In summary, the collaborative efforts outlined in this study demonstrate a proactive approach to agricultural disaster prevention. By leveraging technological advancements and interdisciplinary cooperation, the aim is to safeguard agricultural livelihoods and ensure food security in the face of climate-induced challenges. Full article
(This article belongs to the Special Issue Agriculture-Climate Interactions in Tropical Regions)
9 pages, 235 KiB  
Article
The Blow-Up of the Local Energy Solution to the Wave Equation with a Nontrivial Boundary Condition
by Yulong Liu
Mathematics 2024, 12(9), 1317; https://doi.org/10.3390/math12091317 (registering DOI) - 25 Apr 2024
Abstract
In this study, we examine the wave equation with a nontrivial boundary condition. The main target of this study is to prove the local-in-time existence and the blow-up in finite time of the energy solution. Through the construction of an auxiliary function and [...] Read more.
In this study, we examine the wave equation with a nontrivial boundary condition. The main target of this study is to prove the local-in-time existence and the blow-up in finite time of the energy solution. Through the construction of an auxiliary function and the imposition of appropriate conditions on the initial data, we establish the both lower and upper bounds for the blow-up time of the solution. Meanwhile, based on these estimates, we obtain the result of the local-in-time existence and the blow-up of the energy solution. This approach enhances our understanding of the dynamics leading to blow-up in the considered condition. Full article
19 pages, 2965 KiB  
Article
Structural, Optical and Dielectric Properties of Some Nanocomposites Derived from Copper Oxide Nanoparticles Embedded in Poly(vinylpyrrolidone) Matrix
by Carmen Gherasim, Mihai Asandulesa, Nicusor Fifere, Florica Doroftei, Daniel Tîmpu and Anton Airinei
Nanomaterials 2024, 14(9), 759; https://doi.org/10.3390/nano14090759 (registering DOI) - 25 Apr 2024
Abstract
Polymer nanocomposite films based on poly(vinyl pyrrolidone) incorporated with different amounts of copper oxide (CuO) nanoparticles were prepared by the solution casting technique. The PVP/CuO nanocomposites were analyzed by X-ray diffractometry (XRD), scanning electron microscopy, UV–Visible absorption spectroscopy and dielectric spectroscopy. The XRD [...] Read more.
Polymer nanocomposite films based on poly(vinyl pyrrolidone) incorporated with different amounts of copper oxide (CuO) nanoparticles were prepared by the solution casting technique. The PVP/CuO nanocomposites were analyzed by X-ray diffractometry (XRD), scanning electron microscopy, UV–Visible absorption spectroscopy and dielectric spectroscopy. The XRD analysis showed that the monoclinic structure of cupric oxide was maintained in the PVP host matrix. The key optical parameters, such as optical energy gap Eg, Urbach energy EU, absorption coefficient and refractive index, were estimated based on the UV-Vis data. The optical characteristics of the nanocomposite films revealed that their transmittance and absorption were influenced by the addition of CuO nanoparticles in the PVP matrix. Incorporation of CuO nanoparticles into the PVP matrix led to a significant decrease in band gap energy and an increase in the refractive index. The dielectric and electrical behaviors of the PVP/CuO nanocomposites were analyzed over a frequency range between 10 Hz and 1 MHz. The effect of CuO loading on the dielectric parameters (dielectric constant and dielectric loss) of the metal oxide nanocomposites was also discussed. Full article
12 pages, 512 KiB  
Article
The Current Achievements of Multi-Gene Panel Tests in Clinical Settings for Patients with Non-Small-Cell Lung Cancer
by Tadashi Sakaguchi, Akemi Iketani, Seiya Esumi, Maki Esumi, Yuta Suzuki, Kentaro Ito, Kentaro Fujiwara, Yoichi Nishii, Koji Katsuta, Hiroki Yasui, Osamu Taguchi and Osamu Hataji
Cancers 2024, 16(9), 1670; https://doi.org/10.3390/cancers16091670 (registering DOI) - 25 Apr 2024
Abstract
Some multi-gene panel tests have been implemented in clinical settings to guide targeted therapy in non-small-cell lung cancer (NSCLC) in Japan. The current performance of multi-gene panel tests under the condition that the Oncomine Dx Target Test (ODxTT) and Amoy Dx® Pan [...] Read more.
Some multi-gene panel tests have been implemented in clinical settings to guide targeted therapy in non-small-cell lung cancer (NSCLC) in Japan. The current performance of multi-gene panel tests under the condition that the Oncomine Dx Target Test (ODxTT) and Amoy Dx® Pan Lung Cancer PCR panel (AmoyDx-multi) are available remains relatively unknown. We retrospectively reviewed consecutive patients with NSCLC, whose FFPE samples were considered for genetic testing. We assessed the submission rates, the success rates, and the driver oncogene detection rates of multi-gene panel tests. A total of 225 patients were histologically newly diagnosed with NSCLC or diagnosed with a recurrence of NSCLC without a previous multi-gene panel test at our institution. Among the 225 patients, the FFPE samples of 212 patients (94.2%) were submitted for multi-gene panel testing, including 191 samples (84.9%) for the ODxTT and 21 samples (9.3%) for the AmoyDx-multi. Among the 212 samples submitted to multi-gene panel tests, the success rate was 99.5% (211/212). The detection rate of driver oncogene alterations for all histologies was 52.4% (111/212), and that for adenocarcinoma was 69.7% (106/152). A favorable submission rate and success rate of multi-gene panel tests were shown, along with a favorable detection rate in recent clinical settings. Full article
(This article belongs to the Section Cancer Biomarkers)
21 pages, 12256 KiB  
Article
GC-IMS-Based Volatile Characteristic Analysis of Hypsizygus marmoreus Dried by Different Methods
by Pufu Lai, Longxiang Li, Yingying Wei, Junzheng Sun, Baosha Tang, Yanrong Yang, Junchen Chen and Li Wu
Foods 2024, 13(9), 1322; https://doi.org/10.3390/foods13091322 (registering DOI) - 25 Apr 2024
Abstract
Gas chromatography–ion mobility spectroscopy (GC-IMS) was used to analyze the volatile components in dried Hypsizygus marmoreus of different drying methods, including hot air drying (HAD), heat pump drying (HPD), heated freeze-drying (HFD), and unheated freeze-drying (UFD). A total of 116 signal peaks corresponding [...] Read more.
Gas chromatography–ion mobility spectroscopy (GC-IMS) was used to analyze the volatile components in dried Hypsizygus marmoreus of different drying methods, including hot air drying (HAD), heat pump drying (HPD), heated freeze-drying (HFD), and unheated freeze-drying (UFD). A total of 116 signal peaks corresponding to 96 volatile compounds were identified, including 25 esters, 24 aldehydes, 23 alcohols, 13 ketones, 10 heterocyclic compounds, 8 carboxylic acids, 7 terpenes, 3 sulfur-containing compounds, 2 nitrogen-containing compounds, and 1 aromatic hydrocarbon. The total content of volatile compounds in H. marmoreus dried by the four methods, from highest to lowest, was as follows: HAD, HPD, HFD, and UFD. The main volatile compounds included carboxylic acids, alcohols, esters, and aldehydes. Comparing the peak intensities of volatile compounds in dried H. marmoreus using different drying methods, it was found that the synthesis of esters, aldehydes, and terpenes increased under hot drying methods such as HAD and HPD, while the synthesis of compounds containing sulfur and nitrogen increased under freeze-drying methods such as HFD and UFD. Nine common key characteristic flavor compounds of dried H. marmoreus were screened using relative odor activity values (ROAV > 1), including ethyl 3-methylbutanoate, acetic acid, 2-methylbutanal, propanal, methyl 2-propenyl sulfate, trimethylamine, 3-octanone, acetaldehide, and thiophene. In the odor description of volatile compounds with ROAV > 0.1, it was found that important flavor components such as trimethylamine, 3-octanone, (E)-2-octenal, and dimethyl disulfide are related to the aroma of seafood. Their ROAV order is HFD > UFD > HPD > HAD, indicating that H. marmoreus using the HFD method have the strongest seafood flavor. The research findings provide theoretical guidance for selecting drying methods and refining the processing of H. marmoreus. Full article
(This article belongs to the Section Food Analytical Methods)
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20 pages, 3897 KiB  
Article
Meshless Generalized Finite Difference Method Based on Nonlocal Differential Operators for Numerical Simulation of Elastostatics
by Yeying Zhou, Chunguang Li, Xinshan Zhuang and Zhifen Wang
Mathematics 2024, 12(9), 1316; https://doi.org/10.3390/math12091316 (registering DOI) - 25 Apr 2024
Abstract
This study proposes an innovative meshless approach that merges the peridynamic differential operator (PDDO) with the generalized finite difference method (GFDM). Based on the PDDO theory, this method introduces a new nonlocal differential operator that aims to reduce the pre-assumption required for the [...] Read more.
This study proposes an innovative meshless approach that merges the peridynamic differential operator (PDDO) with the generalized finite difference method (GFDM). Based on the PDDO theory, this method introduces a new nonlocal differential operator that aims to reduce the pre-assumption required for the PDDO method and simplify the calculation process. By discretizing through the particle approximation method, this technique proficiently preserves the PDDO’s nonlocal features, enhancing the numerical simulation’s flexibility and usability. Through the numerical simulation of classical elastic static problems, this article focuses on the evaluation of the calculation accuracy, calculation efficiency, robustness, and convergence of the method. This method is significantly stronger than the finite element method in many performance indicators. In fact, this study demonstrates the practicability and superiority of the proposed method in the field of elastic statics and provides a new approach to more complex problems. Full article

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