The 2023 MDPI Annual Report has
been released!
 
29 pages, 13210 KiB  
Article
Design of Digital Twin Cutting Experiment System for Shearer
by Bing Miao, Yunwang Li and Yinan Guo
Sensors 2024, 24(10), 3194; https://doi.org/10.3390/s24103194 - 17 May 2024
Abstract
This study presents an advanced simulated shearer machine cutting experiment system enhanced with digital twin technology. Central to this system is a simulated shearer drum, designed based on similarity theory to accurately mirror the operational dynamics of actual mining cutters. The setup incorporates [...] Read more.
This study presents an advanced simulated shearer machine cutting experiment system enhanced with digital twin technology. Central to this system is a simulated shearer drum, designed based on similarity theory to accurately mirror the operational dynamics of actual mining cutters. The setup incorporates a modified machining center equipped with sophisticated sensors that monitor various parameters such as cutting states, forces, torque, vibration, temperature, and sound. These sensors are crucial for precisely simulating the shearer cutting actions. The integration of digital twin technology is pivotal, featuring a real-time data management layer, a dynamic simulation mechanism model layer, and an application service layer that facilitates virtual experiments and algorithm refinement. This multifaceted approach allows for in-depth analysis of simulated coal cutting, utilizing sensor data to comprehensively evaluate the shearer’s performance. The study also includes tests on simulated coal samples. The system effectively conducts experiments and captures cutting condition signals via the sensors. Through time domain analysis of these signals, gathered while cutting materials of varying strengths, it is determined that the cutting force signal characteristics are particularly distinct. By isolating the cutting force signal as a key feature, the system can effectively distinguish between different cutting modes. This capability provides a robust experimental basis for coal rock identification research, offering significant insights into the nuances of shearer operation. Full article
(This article belongs to the Section Physical Sensors)
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17 pages, 2021 KiB  
Article
Design and Characterisation of a Read-Out System for Wireless Monitoring of a Novel Implantable Sensor for Abdominal Aortic Aneurysm Monitoring
by Nuno P. Silva, Adnan Elahi, Eoghan Dunne, Martin O’Halloran and Bilal Amin
Sensors 2024, 24(10), 3195; https://doi.org/10.3390/s24103195 - 17 May 2024
Abstract
Abdominal aortic aneurysm (AAA) is a dilation of the aorta artery larger than its normal diameter (>3 cm). Endovascular aneurysm repair (EVAR) is a minimally invasive treatment option that involves the placement of a graft in the aneurysmal portion of the aorta artery. [...] Read more.
Abdominal aortic aneurysm (AAA) is a dilation of the aorta artery larger than its normal diameter (>3 cm). Endovascular aneurysm repair (EVAR) is a minimally invasive treatment option that involves the placement of a graft in the aneurysmal portion of the aorta artery. This treatment requires multiple follow-ups with medical imaging, which is expensive, time-consuming, and resource-demanding for healthcare systems. An alternative solution is the use of wireless implantable sensors (WIMSs) to monitor the growth of the aneurysm. A WIMS capable of monitoring aneurysm size longitudinally could serve as an alternative monitoring approach for post-EVAR patients. This study has developed and characterised a three-coil inductive read-out system to detect variations in the resonance frequency of the novel Z-shaped WIMS implanted within the AAA sac. Specifically, the spacing between the transmitter and the repeater inductors was optimised to maximise the detection of the sensor by the transmitter inductor. Moreover, an experimental evaluation was also performed for different orientations of the transmitter coil with reference to the WIMS. Finally, the FDA-approved material nitinol was used to develop the WIMS, the transmitter, and repeater inductors as a proof of concept for further studies. The findings of the characterisation from the air medium suggest that the read-out system can detect the WIMS up to 5 cm, regardless of the orientation of the Z-shape WIMS, with the detection range increasing as the orientation approaches 0°. This study provides sufficient evidence that the proposed WIMS and the read-out system can be used for AAA expansion over time. Full article
(This article belongs to the Special Issue Advances in Magnetic Sensors and Their Applications)
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23 pages, 2172 KiB  
Article
Post-Takeover Proficiency in Conditionally Automated Driving: Understanding Stabilization Time with Driving and Physiological Signals
by Timotej Gruden, Sašo Tomažič and Grega Jakus
Sensors 2024, 24(10), 3193; https://doi.org/10.3390/s24103193 - 17 May 2024
Abstract
In the realm of conditionally automated driving, understanding the crucial transition phase after a takeover is paramount. This study delves into the concept of post-takeover stabilization by analyzing data recorded in two driving simulator experiments. By analyzing both driving and physiological signals, we [...] Read more.
In the realm of conditionally automated driving, understanding the crucial transition phase after a takeover is paramount. This study delves into the concept of post-takeover stabilization by analyzing data recorded in two driving simulator experiments. By analyzing both driving and physiological signals, we investigate the time required for the driver to regain full control and adapt to the dynamic driving task following automation. Our findings show that the stabilization time varies between measured parameters. While the drivers achieved driving-related stabilization (winding, speed) in eight to ten seconds, physiological parameters (heart rate, phasic skin conductance) exhibited a prolonged response. By elucidating the temporal and cognitive dynamics underlying the stabilization process, our results pave the way for the development of more effective and user-friendly automated driving systems, ultimately enhancing safety and driving experience on the roads. Full article
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24 pages, 899 KiB  
Review
Overnutrition, Hyperinsulinemia and Ectopic Fat: It Is Time for A Paradigm Shift in the Management of Type 2 Diabetes
by Joseph A. M. J. L. Janssen
Int. J. Mol. Sci. 2024, 25(10), 5488; https://doi.org/10.3390/ijms25105488 - 17 May 2024
Abstract
The worldwide incidence of prediabetes/type 2 has continued to rise the last 40 years. In the same period, the mean daily energy intake has increased, and the quality of food has significantly changed. The chronic exposure of pancreatic β-cells to calorie excess (excessive [...] Read more.
The worldwide incidence of prediabetes/type 2 has continued to rise the last 40 years. In the same period, the mean daily energy intake has increased, and the quality of food has significantly changed. The chronic exposure of pancreatic β-cells to calorie excess (excessive energy intake) and food additives may increase pancreatic insulin secretion, decrease insulin pulses and/or reduce hepatic insulin clearance, thereby causing chronic hyperinsulinemia and peripheral insulin resistance. Chronic calorie excess and hyperinsulinemia may promote lipogenesis, inhibit lipolysis and increase lipid storage in adipocytes. In addition, calorie excess and hyperinsulinemia can induce insulin resistance and contribute to progressive and excessive ectopic fat accumulation in the liver and pancreas by the conversion of excess calories into fat. The personal fat threshold hypothesis proposes that in susceptible individuals, excessive ectopic fat accumulation may eventually lead to hepatic insulin receptor resistance, the loss of pancreatic insulin secretion, hyperglycemia and the development of frank type 2 diabetes. Thus, type 2 diabetes seems (partly) to be caused by hyperinsulinemia-induced excess ectopic fat accumulation in the liver and pancreas. Increasing evidence further shows that interventions (hypocaloric diet and/or bariatric surgery), which remove ectopic fat in the liver and pancreas by introducing a negative energy balance, can normalize insulin secretion and glucose tolerance and induce the sustained biochemical remission of type 2 diabetes. This pathophysiological insight may have major implications and may cause a paradigm shift in the management of type 2 diabetes: avoiding/reducing ectopic fat accumulation in the liver and pancreas may both be essential to prevent and cure type 2 diabetes. Full article
(This article belongs to the Special Issue Latest Review Papers in Molecular Endocrinology and Metabolism 2023)
17 pages, 5054 KiB  
Article
Enhanced Sampling Molecular Dynamics Simulations Reveal Transport Mechanism of Glycoconjugate Drugs through GLUT1
by Zhuo Liu, Xueting Cao, Zhenyu Ma, Limei Xu, Lushan Wang, Jian Li, Min Xiao and Xukai Jiang
Int. J. Mol. Sci. 2024, 25(10), 5486; https://doi.org/10.3390/ijms25105486 - 17 May 2024
Abstract
Glucose transporters GLUT1 belong to the major facilitator superfamily and are essential to human glucose uptake. The overexpression of GLUT1 in tumor cells designates it as a pivotal target for glycoconjugate anticancer drugs. However, the interaction mechanism of glycoconjugate drugs with GLUT1 remains [...] Read more.
Glucose transporters GLUT1 belong to the major facilitator superfamily and are essential to human glucose uptake. The overexpression of GLUT1 in tumor cells designates it as a pivotal target for glycoconjugate anticancer drugs. However, the interaction mechanism of glycoconjugate drugs with GLUT1 remains largely unknown. Here, we employed all-atom molecular dynamics simulations, coupled to steered and umbrella sampling techniques, to examine the thermodynamics governing the transport of glucose and two glycoconjugate drugs (i.e., 6-D-glucose-conjugated methane sulfonate and 6-D-glucose chlorambucil) by GLUT1. We characterized the specific interactions between GLUT1 and substrates at different transport stages, including substrate recognition, transport, and releasing, and identified the key residues involved in these procedures. Importantly, our results described, for the first time, the free energy profiles of GLUT1-transporting glycoconjugate drugs, and demonstrated that H160 and W388 served as important gates to regulate their transport via GLUT1. These findings provide novel atomic-scale insights for understanding the transport mechanism of GLUT1, facilitating the discovery and rational design of GLUT1-targeted anticancer drugs. Full article
22 pages, 3127 KiB  
Article
Identification and Analysis of lncRNA and circRNA Related to Wheat Grain Development
by Meng Wang, Lu Wang, Shuanghong Wang, Junli Zhang, Zhe Fu, Panpan Wu, Anqi Yang, Dexiang Wu, Genlou Sun and Chengyu Wang
Int. J. Mol. Sci. 2024, 25(10), 5484; https://doi.org/10.3390/ijms25105484 - 17 May 2024
Abstract
The role of lncRNA and circRNA in wheat grain development is still unclear. The objectives of this study were to characterize the lncRNA and circRNA in the wheat grain development and to construct the interaction network among lncRNA, circRNA, and their target miRNA [...] Read more.
The role of lncRNA and circRNA in wheat grain development is still unclear. The objectives of this study were to characterize the lncRNA and circRNA in the wheat grain development and to construct the interaction network among lncRNA, circRNA, and their target miRNA to propose a lncRNA–circRNA–miRNA module related to wheat grain development. Full transcriptome sequencing on two wheat varieties (Annong 0942 and Anke 2005) with significant differences in 1000-grain weight at 10 d (days after pollination), 20 d, and 30 d of grain development were conducted. We detected 650, 736, and 609 differentially expressed lncRNA genes, and 769, 1054, and 1062 differentially expressed circRNA genes in the grains of 10 days, 20 days and 30 days after pollination between Annong 0942 and Anke 2005, respectively. An analysis of the lncRNA–miRNA and circRNA–miRNA targeting networks reveals that circRNAs exhibit a more complex and extensive interaction network in the development of cereal grains and the formation of grain shape. Central to these interactions are tae-miR1177, tae-miR1128, and tae-miR1130b-3p. In contrast, lncRNA genes only form a singular network centered around tae-miR1133 and tae-miR5175-5p when comparing between varieties. Further analysis is conducted on the underlying genes of all target miRNAs, we identified TaNF-YB1 targeted by tae-miR1122a and TaTGW-7B targeted by miR1130a as two pivotal regulatory genes in the development of wheat grains. The quantitative real-time PCR (qRT-PCR) and dual-luciferase reporter assays confirmed the target regulatory relationships between miR1130a-TaTGW-7B and miR1122a-TaNF-YB1. We propose a network of circRNA and miRNA-mediated gene regulation in the development of wheat grains. Full article
(This article belongs to the Special Issue Advances in Breeding and Genetics of Wheat Crops 2.0)
22 pages, 2243 KiB  
Review
Metabolic Contrasts: Fatty Acid Oxidation and Ketone Bodies in Healthy Brains vs. Glioblastoma Multiforme
by Corina Tamas, Flaviu Tamas, Attila Kovecsi, Alina Cehan and Adrian Balasa
Int. J. Mol. Sci. 2024, 25(10), 5482; https://doi.org/10.3390/ijms25105482 - 17 May 2024
Abstract
The metabolism of glucose and lipids plays a crucial role in the normal homeostasis of the body. Although glucose is the main energy substrate, in its absence, lipid metabolism becomes the primary source of energy. The main means of fatty acid oxidation (FAO) [...] Read more.
The metabolism of glucose and lipids plays a crucial role in the normal homeostasis of the body. Although glucose is the main energy substrate, in its absence, lipid metabolism becomes the primary source of energy. The main means of fatty acid oxidation (FAO) takes place in the mitochondrial matrix through β-oxidation. Glioblastoma (GBM) is the most common form of primary malignant brain tumor (45.6%), with an incidence of 3.1 per 100,000. The metabolic changes found in GBM cells and in the surrounding microenvironment are associated with proliferation, migration, and resistance to treatment. Tumor cells show a remodeling of metabolism with the use of glycolysis at the expense of oxidative phosphorylation (OXPHOS), known as the Warburg effect. Specialized fatty acids (FAs) transporters such as FAT, FABP, or FATP from the tumor microenvironment are overexpressed in GBM and contribute to the absorption and storage of an increased amount of lipids that will provide sufficient energy used for tumor growth and invasion. This review provides an overview of the key enzymes, transporters, and main regulatory pathways of FAs and ketone bodies (KBs) in normal versus GBM cells, highlighting the need to develop new therapeutic strategies to improve treatment efficacy in patients with GBM. Full article
(This article belongs to the Special Issue The Occurrence, Evolution and Treatment of Glioblastoma 2.0)
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25 pages, 817 KiB  
Review
Molecular Chaperonin HSP60: Current Understanding and Future Prospects
by Manish Kumar Singh, Yoonhwa Shin, Sunhee Han, Joohun Ha, Pramod K. Tiwari, Sung Soo Kim and Insug Kang
Int. J. Mol. Sci. 2024, 25(10), 5483; https://doi.org/10.3390/ijms25105483 - 17 May 2024
Abstract
Molecular chaperones are highly conserved across evolution and play a crucial role in preserving protein homeostasis. The 60 kDa heat shock protein (HSP60), also referred to as chaperonin 60 (Cpn60), resides within mitochondria and is involved in maintaining the organelle’s proteome integrity and [...] Read more.
Molecular chaperones are highly conserved across evolution and play a crucial role in preserving protein homeostasis. The 60 kDa heat shock protein (HSP60), also referred to as chaperonin 60 (Cpn60), resides within mitochondria and is involved in maintaining the organelle’s proteome integrity and homeostasis. The HSP60 family, encompassing Cpn60, plays diverse roles in cellular processes, including protein folding, cell signaling, and managing high-temperature stress. In prokaryotes, HSP60 is well understood as a GroEL/GroES complex, which forms a double-ring cavity and aids in protein folding. In eukaryotes, HSP60 is implicated in numerous biological functions, like facilitating the folding of native proteins and influencing disease and development processes. Notably, research highlights its critical involvement in sustaining oxidative stress and preserving mitochondrial integrity. HSP60 perturbation results in the loss of the mitochondria integrity and activates apoptosis. Currently, numerous clinical investigations are in progress to explore targeting HSP60 both in vivo and in vitro across various disease models. These studies aim to enhance our comprehension of disease mechanisms and potentially harness HSP60 as a therapeutic target for various conditions, including cancer, inflammatory disorders, and neurodegenerative diseases. This review delves into the diverse functions of HSP60 in regulating proteo-homeostasis, oxidative stress, ROS, apoptosis, and its implications in diseases like cancer and neurodegeneration. Full article
(This article belongs to the Special Issue Advances in Heat-Shock Response and Heat-Shock Proteins)
23 pages, 3998 KiB  
Article
Genotyping Hepatitis B virus by Next-Generation Sequencing: Detection of Mixed Infections and Analysis of Sequence Conservation
by Eva Dopico, Marta Vila, David Tabernero, Josep Gregori, Ariadna Rando-Segura, Beatriz Pacín-Ruíz, Laura Guerrero, Itziar Ubillos, Miguel J. Martínez, Josep Costa, Josep Quer, Javier Pérez-Garreta, Alejandra González-Sánchez, Andrés Antón, Tomás Pumarola, Mar Riveiro-Barciela, Roser Ferrer-Costa, Maria Buti, Francisco Rodríguez-Frías and Maria Francesca Cortese
Int. J. Mol. Sci. 2024, 25(10), 5481; https://doi.org/10.3390/ijms25105481 - 17 May 2024
Abstract
Our aim was to develop an accurate, highly sensitive method for HBV genotype determination and detection of genotype mixtures. We examined the preS and 5′ end of the HBV X gene (5X) regions of the HBV genome using next-generation sequencing (NGS). The 1852 [...] Read more.
Our aim was to develop an accurate, highly sensitive method for HBV genotype determination and detection of genotype mixtures. We examined the preS and 5′ end of the HBV X gene (5X) regions of the HBV genome using next-generation sequencing (NGS). The 1852 haplotypes obtained were subjected to genotyping via the Distance-Based discrimination method (DB Rule) using two sets of 95 reference sequences of genotypes A–H. In clinical samples from 125 patients, the main genotypes were A, D, F and H in Caucasian, B and C in Asian and A and E in Sub-Saharan patients. Genotype mixtures were identified in 28 (22.40%) cases, and potential intergenotypic recombination was observed in 29 (23.20%) cases. Furthermore, we evaluated sequence conservation among haplotypes classified into genotypes A, C, D, and E by computing the information content. The preS haplotypes exhibited limited shared conserved regions, whereas the 5X haplotypes revealed two groups of conserved regions across the genotypes assessed. In conclusion, we developed an NGS-based HBV genotyping method utilizing the DB Rule for genotype classification. We identified two regions conserved across different genotypes at 5X, offering promising targets for RNA interference-based antiviral therapies. Full article
(This article belongs to the Special Issue Molecular Pathogenesis and Therapeutics in Viral Hepatitis)
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18 pages, 1058 KiB  
Article
Luminescent Alendronic Acid-Conjugated Micellar Nanostructures for Potential Application in the Bone-Targeted Delivery of Cholecalciferol
by Federica Rizzi, Annamaria Panniello, Roberto Comparelli, Ilaria Arduino, Elisabetta Fanizza, Rosa Maria Iacobazzi, Maria Grazia Perrone, Marinella Striccoli, Maria Lucia Curri, Antonio Scilimati, Nunzio Denora and Nicoletta Depalo
Molecules 2024, 29(10), 2367; https://doi.org/10.3390/molecules29102367 - 17 May 2024
Abstract
Vitamin D, an essential micronutrient crucial for skeletal integrity and various non-skeletal physiological functions, exhibits limited bioavailability and stability in vivo. This study is focused on the development of polyethylene glycol (PEG)-grafted phospholipid micellar nanostructures co-encapsulating vitamin D3 and conjugated with alendronic acid, [...] Read more.
Vitamin D, an essential micronutrient crucial for skeletal integrity and various non-skeletal physiological functions, exhibits limited bioavailability and stability in vivo. This study is focused on the development of polyethylene glycol (PEG)-grafted phospholipid micellar nanostructures co-encapsulating vitamin D3 and conjugated with alendronic acid, aimed at active bone targeting. Furthermore, these nanostructures are rendered optically traceable in the UV–visible region of the electromagnetic spectrum via the simultaneous encapsulation of vitamin D3 with carbon dots, a newly emerging class of fluorescents, biocompatible nanoparticles characterized by their resistance to photobleaching and environmental friendliness, which hold promise for future in vitro bioimaging studies. A systematic investigation is conducted to optimize experimental parameters for the preparation of micellar nanostructures with an average hydrodynamic diameter below 200 nm, ensuring colloidal stability in physiological media while preserving the optical luminescent properties of the encapsulated carbon dots. Comprehensive chemical-physical characterization of these micellar nanostructures is performed employing optical and morphological techniques. Furthermore, their binding affinity for the principal inorganic constituent of bone tissue is assessed through a binding assay with hydroxyapatite nanoparticles, indicating significant potential for active bone-targeting. These formulated nanostructures hold promise for novel therapeutic interventions to address skeletal-related complications in cancer affected patients in the future. Full article
13 pages, 6163 KiB  
Article
Qualitative and Quantitative Detection of Typical Reproductive Hormones in Dairy Cows Based on Terahertz Spectroscopy and Metamaterial Technology
by Shuang Liang, Jingbo Zhao, Wenwen Zhao, Nan Jia, Zhiyong Zhang and Bin Li
Molecules 2024, 29(10), 2366; https://doi.org/10.3390/molecules29102366 - 17 May 2024
Abstract
Progesterone (PROG) and estrone (E1) are typical reproductive hormones in dairy cows. Assessing the levels of these hormones in vivo can aid in estrus identification. In the present work, the feasibility of the qualitative and quantitative detection of PROG and E [...] Read more.
Progesterone (PROG) and estrone (E1) are typical reproductive hormones in dairy cows. Assessing the levels of these hormones in vivo can aid in estrus identification. In the present work, the feasibility of the qualitative and quantitative detection of PROG and E1 using terahertz time-domain spectroscopy (THz-TDS) and metamaterial technology was preliminarily investigated. First, the time domain spectra, frequency domain spectra, and absorption coefficients of PROG and E1 samples were collected and analyzed. A vibration analysis was conducted using density functional theory (DFT). Subsequently, a double-ring (DR) metamaterial structure was designed and simulated using the frequency domain solution algorithm in CST Studio Suite (CST) software. This aimed to ensure that the double resonance peaks of DR were similar to the absorption peaks of PROG and E1. Finally, the response of DR to different concentrations of PROG/E1 was analyzed and quantitatively modeled. The results show that a qualitative analysis can be conducted by comparing the corresponding DR resonance peak changes in PROG and E1 samples at various concentrations. The best R2 for the PROG quantitative model was 0.9872, while for E1, it was 0.9828. This indicates that terahertz spectral–metamaterial technology for the qualitative and quantitative detection of the typical reproductive hormones PROG and E1 in dairy cows is feasible and worthy of in-depth exploration. This study provides a reference for the identification of dairy cow estrus. Full article
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20 pages, 8257 KiB  
Article
Chemical Basis for Determining the Allelopathic Potential of Invasive Plant Wall Barley (Hordeum murinum L. subsp. murinum)
by Beata Barabasz-Krasny, Agnieszka Tatoj, Marek Chyc, Wojciech Gruszka, Peiman Zandi and Alina Stachurska-Swakoń
Molecules 2024, 29(10), 2365; https://doi.org/10.3390/molecules29102365 - 17 May 2024
Abstract
The study investigated compounds present in the invasive grass Hordeum murinum L. subsp. murinum and tested the allelopathic potential of this plant against common meadow species Festuca rubra L. and Trifolium repens L. Gas chromatography–mass spectrometry (GC–MS) performed separately on the ears and [...] Read more.
The study investigated compounds present in the invasive grass Hordeum murinum L. subsp. murinum and tested the allelopathic potential of this plant against common meadow species Festuca rubra L. and Trifolium repens L. Gas chromatography–mass spectrometry (GC–MS) performed separately on the ears and stalks with leaves of wall barley revealed 32 compounds, including secondary metabolites, that may play an important role in allelopathy. Two compounds, N-butylbenzenesulfonamide (NBBS) and diphenylsulfone (DDS), were described for the first time for wall barley and the Poaceae family. The presence of 6,10,14-trimethylpentadecan-2-one (TMP) has also been documented. Aqueous extracts of H. murinum organs (ears and stalks with leaves) at concentrations of 2.5%, 5%, and 7.5% were used to evaluate its allelopathic potential. Compared to the control, all extracts inhibited germination and early growth stages of meadow species. The inhibitory effect was strongest at the highest concentration for both the underground and aboveground parts of the seedlings of the meadow species tested. Comparing the allelopathic effect, Trifolium repens proved to be more sensitive. In light of the results of the study, the removal of wall barley biomass appears to be important for the restoration of habitats where this species occurs due to its allelopathic potential. Full article
(This article belongs to the Section Chemical Biology)
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18 pages, 1447 KiB  
Article
Modelling the In Vivo and Ex Vivo DNA Damage Response after Internal Irradiation of Blood from Patients with Thyroid Cancer
by Sarah Schumann, Harry Scherthan, Philipp E. Hartrampf, Lukas Göring, Andreas K. Buck, Matthias Port, Michael Lassmann and Uta Eberlein
Int. J. Mol. Sci. 2024, 25(10), 5493; https://doi.org/10.3390/ijms25105493 (registering DOI) - 17 May 2024
Abstract
This work reports on a model that describes patient-specific absorbed dose-dependent DNA damage response in peripheral blood mononuclear cells of thyroid cancer patients during radioiodine therapy and compares the results with the ex vivo DNA damage response in these patients. Blood samples of [...] Read more.
This work reports on a model that describes patient-specific absorbed dose-dependent DNA damage response in peripheral blood mononuclear cells of thyroid cancer patients during radioiodine therapy and compares the results with the ex vivo DNA damage response in these patients. Blood samples of 18 patients (nine time points up to 168 h post-administration) were analyzed for radiation-induced γ-H2AX + 53BP1 DNA double-strand break foci (RIF). A linear one-compartment model described the absorbed dose-dependent time course of RIF (Parameters: c characterizes DSB damage induction; k1 and k2 are rate constants describing fast and slow repair). The rate constants were compared to ex vivo repair rates. A total of 14 patient datasets could be analyzed; c ranged from 0.012 to 0.109 mGy−1, k2 from 0 to 0.04 h−1. On average, 96% of the damage is repaired quickly with k1 (range: 0.19–3.03 h−1). Two patient subgroups were distinguished by k1-values (n = 6, k1 > 1.1 h−1; n = 8, k1 < 0.6 h−1). A weak correlation with patient age was observed. While induction of RIF was similar among ex vivo and in vivo, the respective repair rates failed to correlate. The lack of correlation between in vivo and ex vivo repair rates and the applicability of the model to other therapies will be addressed in further studies. Full article
(This article belongs to the Special Issue Recent Research of DNA Repair and Damage in Human Health)
17 pages, 642 KiB  
Article
Measurement and Characterization of the Electrical Properties of Actin Filaments
by Serena Paladini, Barbara Truglia, Karthik Shankar and Jack Adam Tuszynski
Int. J. Mol. Sci. 2024, 25(10), 5485; https://doi.org/10.3390/ijms25105485 (registering DOI) - 17 May 2024
Abstract
Actin filaments, as key components of the cytoskeleton, have aroused great interest due to their numerous functional roles in eukaryotic cells, including intracellular electrical signaling. The aim of this research is to characterize the alternating current (AC) conduction characteristics of both globular and [...] Read more.
Actin filaments, as key components of the cytoskeleton, have aroused great interest due to their numerous functional roles in eukaryotic cells, including intracellular electrical signaling. The aim of this research is to characterize the alternating current (AC) conduction characteristics of both globular and polymerized actin and quantitatively compare their values to those theoretically predicted earlier. Actin filaments have been demonstrated to act as conducting bionanowires, forming a signaling network capable of transmitting ionic waves in cells. We performed conductivity measurements for different concentrations of actin, considering both unpolymerized and polymerized actin to identify potential differences in their electrical properties. These measurements revealed two relevant characteristics: first, the polymerized actin, arranged in filaments, has a lower impedance than its globular counterpart; second, an increase in the actin concentration leads to higher conductivities. Furthermore, from the data collected, we developed a quantitative model to represent the electrical properties of actin in a buffer solution. We hypothesize that actin filaments can be modeled as electrical resistor–inductor–capacitor (RLC) circuits, where the resistive contribution is due to the viscous ion flows along the filaments; the inductive contribution is due to the solenoidal flows along and around the helix-shaped filament and the capacitive contribution is due to the counterion layer formed around each negatively charged filament. Full article
(This article belongs to the Collection Feature Papers in Molecular Biophysics)
16 pages, 566 KiB  
Article
Usefulness of Capillary Gel Electrophoresis-Based PCR for Detection of Clostridioides difficile Strains with Hypervirulent Ribotypes
by Tomasz Bogiel, Alicja Dura, Marcin Woźniak, Agnieszka Mikucka and Piotr Kanarek
Gels 2024, 10(5), 343; https://doi.org/10.3390/gels10050343 (registering DOI) - 17 May 2024
Abstract
Clostridioides difficile is a complex of anaerobic bacteria responsible for the epidemics of post-antibiotic diarrhea as one of the examples of CDI (Clostridioides difficile infection). As many as 70% of cases concern hospitalized patients, particularly those in intensive care units. Ribotyping is [...] Read more.
Clostridioides difficile is a complex of anaerobic bacteria responsible for the epidemics of post-antibiotic diarrhea as one of the examples of CDI (Clostridioides difficile infection). As many as 70% of cases concern hospitalized patients, particularly those in intensive care units. Ribotyping is one of the most common methods for differentiating bacterial strains. The purpose of this work was to show the effectiveness of the gel electrophoresis-based PCR ribotyping method and the Webribo database for typing C. difficile isolates, including the hypervirulent 027 ribotype. DNA samples extracted from 69 C. difficile strains with previously marked genotypes were included in this study. PCR was performed using 16S–23S primers, and capillary gel electrophoresis was performed on the Applied Biosystem 3130xl Genetic Analyzer. The Webribo database was applied for ribotype assignment. Out of 69 samples, 48 belonged to already known ribotypes, 13 represented new ribotypes and 8 was indicated as similar to the existing ones, having some differences. Capillary gel electrophoresis-based PCR is an effective method for the differentiation of C. difficile ribotypes and can be recognized as a very useful tool in epidemiological studies, while the Webribo database is a useful and an accessible database for a quick analysis of C. difficile ribotypes. Full article
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25 pages, 2513 KiB  
Systematic Review
Comprehensive Analysis of the Use of Web-GIS for Natural Hazard Management: A Systematic Review
by Muhammad Daud, Francesca Maria Ugliotti and Anna Osello
Sustainability 2024, 16(10), 4238; https://doi.org/10.3390/su16104238 (registering DOI) - 17 May 2024
Abstract
This systematic review aims to synthesise Web-GIS evidence for managing natural hazards to share state-of-the-art practices and policies. A comprehensive search in SCOPUS, among other databases, identified 1775 articles published between 2014 and 2023. Following a selection process based on the PRISMA model, [...] Read more.
This systematic review aims to synthesise Web-GIS evidence for managing natural hazards to share state-of-the-art practices and policies. A comprehensive search in SCOPUS, among other databases, identified 1775 articles published between 2014 and 2023. Following a selection process based on the PRISMA model, 65 articles met the inclusion criteria. The analysis revealed a growing trend over the past decade, with most research concentrated in the last three years. Eight crucial subtopics within the Web-GIS domain have emerged: Integrated Spatial Analysis and Modelling, Technologies and Infrastructure, Visualisation and User Interface Design, Decision Support Systems, Real-time Monitoring and Early Warning, Disaster Recovery and Resilience, Citizen and Social Media Integration, and Multi-Stakeholder Collaboration. A substantial contribution of the literature has been identified in Decision Support Systems and Integrated Spatial Analysis, reflecting their vital role in strategising and predicting hazard impacts. Furthermore, a geographical distribution analysis revealed significant Web-GIS applications in countries like Italy and China, alongside a deficit in low- and middle-income countries. It also highlights potential gaps in hazard studies, including the need to prioritise heatwave management in the face of climate change. This research calls for policymakers and practitioners to leverage evidence-informed decision making and foster community collaboration for enhanced natural disaster resilience. Full article
(This article belongs to the Section Hazards and Sustainability)
11 pages, 5012 KiB  
Article
Research on a Neutron Detector with a Boron-Lined Multilayer Converter
by Chao Deng, Qin Hu, Pengcheng Li, Qibiao Wang, Bo Xie, Jianbo Yang and Xianguo Tuo
Appl. Sci. 2024, 14(10), 4269; https://doi.org/10.3390/app14104269 (registering DOI) - 17 May 2024
Abstract
3He is a splendid neutron detection material due to its high neutron reaction cross section, gaseous state, and nonelectronegative and nonpoisonous nature. With the worldwide problem of the “3He supply crisis” arising, boron-lined gaseous neutron detectors are being widely used [...] Read more.
3He is a splendid neutron detection material due to its high neutron reaction cross section, gaseous state, and nonelectronegative and nonpoisonous nature. With the worldwide problem of the “3He supply crisis” arising, boron-lined gaseous neutron detectors are being widely used in neutron detection to replace 3He neutron detectors. In this work, to reduce the scattering neutron background coming from the substrate of a boron-lined neutron detector in the application of neutron scattering, a new design of the boron-lined gaseous neutron detector composed of a boron-lined multichip converter and a multiwire proportional chamber was proposed. The electron drift efficiency matrix simulated by Garfield++ (Version 2023.4) and the values and positions of electron energy deposition simulated by Geant4 were obtained. The α, 7Li, and total charged particle energy deposition spectra were acquired via coupling calculations of the electron drift efficiency matrix and the values and positions of electron energy deposition, and the width of the slit was selected as 3 mm. The boron-lined multilayer converter neutron detector (BMCND) was tested using a 241Am–239Pu mixture α source, and the total count rate of α charged particles was measured as 599.5 s−1, which is 89% of the theoretical α particle emission rate of 672.9 s−1. The drift voltage experiments showed that 1200 V is enough to acquire a relatively ideal count, and a 2500 V drift voltage was confirmed, considering the higher count and instrument safety. We also performed the neutron detection experiments using a photo-neutron source, and a characteristic spectrum shape of “two stairs” was measured. When borated polyethylene was used to shield the BMCND, the detected total count decreased while keeping the characteristic spectrum shape, demonstrating that the BMCND was equipped with the ability to detect neurons, indicating that BMCNDs have the potential to be an outstanding 3He alternative neutron detector. Full article
(This article belongs to the Section Applied Physics General)
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29 pages, 65805 KiB  
Article
First Account of Epibiotic Diatom Taxa from the Carapaces of Green Swimming Crab Callinectes bellicosus (Stimpson 1859) (Decapoda, Portunidae)
by Francisco Omar López-Fuerte, David Alfaro Siqueiros Beltrones, Luis Hernández and Sergio Flores-Ramírez
Diversity 2024, 16(5), 302; https://doi.org/10.3390/d16050302 (registering DOI) - 17 May 2024
Abstract
Diatoms are among the most common epibionts and have been recorded on the surfaces of various living substrates, either plants or animals. However, studies on them are still scarce in view of the many substrata available. In this study, epibiotic diatoms living on [...] Read more.
Diatoms are among the most common epibionts and have been recorded on the surfaces of various living substrates, either plants or animals. However, studies on them are still scarce in view of the many substrata available. In this study, epibiotic diatoms living on Callinectes bellicosus were identified for the first time from a subtropical coastal lagoon in Northwest Mexico. We tested the null hypothesis that the diatom flora living on the carapaces of C. bellicosus would not be similar to that recorded for mangrove sediments, its typical habitat. The epibiotic diatoms were brushed off from the carapaces of two specimens, acid-cleaned, mounted in synthetic resin, and identified based on frustule morphology. This way, 106 taxa from 46 genera were recorded, including 25 singletons, and 6 new records for the Mexican northwest region. The best-represented genera were Nitzschia (10 taxa), Mastogloia (9), Diploneis (8), Navicula (7), Amphora (5), Cocconeis (5), Tryblionella (4), and Gyrosigma (4). Species composition included 93% of local taxa, thus refuting the proposed hypothesis and supporting the alternate one. Although the estimated species richness was lower than that in sediments, it deems the green crab carapace a favorable substrate for the growth of benthic diatoms. Full article
(This article belongs to the Section Marine Diversity)
3 pages, 211 KiB  
Editorial
Studies on Food Physical Characterization
by Lubomír Lapčík
Foods 2024, 13(10), 1572; https://doi.org/10.3390/foods13101572 (registering DOI) - 17 May 2024
Abstract
With the growing focus on sustainable food production, there has been a surge in research aimed at developing innovative and eco-friendly food alternatives. This trend  [...] Full article
(This article belongs to the Special Issue Studies on Food Physical Characterization)
14 pages, 1733 KiB  
Article
A Comparative Study of Composition and Soluble Polysaccharide Content between Brewer’s Spent Yeast and Cultured Yeast Cells
by Hyun Ji Lee, Bo-Ram Park and Legesse Shiferaw Chewaka
Foods 2024, 13(10), 1567; https://doi.org/10.3390/foods13101567 (registering DOI) - 17 May 2024
Abstract
Yeast, crucial in beer production, holds great potential owing - to its ability to transform into a valuable by-product resource, known as brewer’s spent yeast (BSY), with potentially beneficial physiological effects. This study aimed to compare the composition and soluble polysaccharide content of [...] Read more.
Yeast, crucial in beer production, holds great potential owing - to its ability to transform into a valuable by-product resource, known as brewer’s spent yeast (BSY), with potentially beneficial physiological effects. This study aimed to compare the composition and soluble polysaccharide content of Brewer’s spent yeast with those of cultured yeast strains, namely Saccharomyces cerevisiae (SC) and S. boulardii (SB), to facilitate the utilization of BSY as an alternative source of functional polysaccharides. BSY exhibited significantly higher carbohydrate content and lower crude protein content than SC and SB cells. The residues recovered through autolysis were 53.11%, 43.83%, and 44.99% for BSY, SC, and SB, respectively. Notably, the polysaccharide content of the BSY residue (641.90 μg/mg) was higher than that of SC (553.52 μg/mg) and SB (591.56 μg/mg). The yields of alkali-extracted water-soluble polysaccharides were 33.62%, 40.76%, and 42.97% for BSY, SC, and SB, respectively, with BSY comprising a comparable proportion of water-soluble saccharides made with SC and SB, including 49.31% mannan and 20.18% β-glucan. Furthermore, BSY demonstrated antioxidant activities, including superoxide dismutase (SOD), ABTS, and DPPH scavenging potential, suggesting its ability to mitigate oxidative stress. BSY also exhibited a significantly higher total phenolic compound content, indicating its potential to act as an effective functional food material. Full article
(This article belongs to the Section Food Biotechnology)
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16 pages, 574 KiB  
Article
The Role of QRS Complex and ST-Segment in Major Adverse Cardiovascular Events Prediction in Patients with ST Elevated Myocardial Infarction: A 6-Year Follow-Up Study
by Srđan Maletin, Milovan Petrović, Anastazija Stojšić-Milosavljević, Tatjana Miljković, Aleksandra Milovančev, Ivan Petrović, Isidora Milosavljević, Ana Balenović and Milenko Čanković
Diagnostics 2024, 14(10), 1042; https://doi.org/10.3390/diagnostics14101042 (registering DOI) - 17 May 2024
Abstract
Background: as a relatively high number of ST-segment elevation myocardial infarction (STEMI) patients develop major adverse cardiovascular events (MACE) following percutaneous coronary intervention (PCI), our aim was to determine the significance, and possible predictive value of QRS complex width and ST-segment elevation. Methods: [...] Read more.
Background: as a relatively high number of ST-segment elevation myocardial infarction (STEMI) patients develop major adverse cardiovascular events (MACE) following percutaneous coronary intervention (PCI), our aim was to determine the significance, and possible predictive value of QRS complex width and ST-segment elevation. Methods: our patient sample included 200 PCI-treated STEMI patients, which were divided into two groups based on the following duration of symptoms: (I) less than 6 h, and (II) 6 to 12 h. For every patient, an ECG was performed at six different time points, patients were followed for up to six years for the occurrence of MACE. Results: the mean age was 60.6 ± 11.39 years, and 142 (71%) were male. The 6–12 h group had significantly wider QRS complex, higher ST-segment elevation, lower prevalence of ST-segment resolution as well as MACE prevalence (p < 0.05). ECG parameters, QRS width, and magnitude of ST-segment elevation were proved to be independent significant predictors of MACE in all measured time points (p < 0.05). Even after controlling for biomarkers of myocardial injury, these ECG parameters remained statistically significant predictors of MACE (p < 0.05). Conclusion: our study highlights that wider QRS complex and a more pronounced ST-segment elevation are associated with longer total ischemic time and higher risk of long-term MACE. Full article
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19 pages, 3108 KiB  
Article
Tomato (Solanum lycopersicum L.) YTH Domain-Containing RNA-Binding Protein (YTP) Family Members Participate in Low-Temperature Treatment and Waterlogging Stress Responses
by Yidan Zhang, Tianli Guo, Jingyuan Li, Libo Jiang and Na Wang
Horticulturae 2024, 10(5), 522; https://doi.org/10.3390/horticulturae10050522 (registering DOI) - 17 May 2024
Abstract
YT521-B homology (YTH) domain-containing RNA-binding proteins (YTPs) are important N6-methyladenosine (m6A) readers that have crucial roles in determining the destiny of m6A-modified RNAs, which are the most widespread RNA modifications in eukaryotes. Tomatoes (Solanum lycopersicum L.) [...] Read more.
YT521-B homology (YTH) domain-containing RNA-binding proteins (YTPs) are important N6-methyladenosine (m6A) readers that have crucial roles in determining the destiny of m6A-modified RNAs, which are the most widespread RNA modifications in eukaryotes. Tomatoes (Solanum lycopersicum L.) hold significant importance in both dietary consumption patterns and scientific inquiries. While the YTP gene family has been characterized in tomatoes, their specific reactions to the low temperature and waterlogging stresses remain to be elucidated. In our study, nine tomato SlYTPs could be divided into five subclasses, YTHDFa-c and YTHDCa-b. After gene cloning and measuring their expression levels under stress conditions, it was revealed that SlYTP8 exhibited increased sensitivity to low-temperature treatment, while the expression levels of SlYTP9 were notably upregulated in leaf tissues subjected to waterlogging conditions. As members of the YTHDFc subfamily, SlYTP8 and SlYTP9 are both localized in the cytoplasm. Nevertheless, overexpression (OE) of SlYTP8 increased the sensitivity of tomato plants to low-temperature treatment, which was manifested by a higher accumulation of malondialdehyde (MDA) and hydrogen peroxide (H2O2) and a weaker reactive oxygen species scavenging ability compared to wild-type (WT) tomatoes. However, in comparison to WT plants, the leaves of SlYTP9 OE tomatoes showed higher chlorophyll content and a stronger reactive oxygen species scavenging ability after 3 days of waterlogging treatment, thereby increasing the resistance of tomatoes to waterlogging stress. Moreover, in order to investigate the possible molecular mechanisms underlying their responses to the low temperature and waterlogging stresses, the transcription factors and interacting protein networks associated with SlYTP8/9 promoters and proteins were also predicted, respectively. These results could fill the gap in the understanding of tomato YTPs in response to the low temperature and waterlogging stresses, while also providing a theoretical and experimental basis for subsequent studies on their molecular mechanisms. Full article
(This article belongs to the Section Biotic and Abiotic Stress)
20 pages, 1719 KiB  
Article
Aboveground Spatiotemporal Carbon Storage Model in the Changing Landscape of Jatigede, West Java, Indonesia
by Susanti Withaningsih, Annas Dwitri Malik and Parikesit Parikesit
Forests 2024, 15(5), 874; https://doi.org/10.3390/f15050874 (registering DOI) - 17 May 2024
Abstract
Land use and land cover (LULC) change is the variable with the maximum influence on carbon storage in terrestrial ecosystems, due to a fundamental alteration of the ecosystem, structure, function, and variability over time. Understanding the dynamics of aboveground carbon stocks in underway [...] Read more.
Land use and land cover (LULC) change is the variable with the maximum influence on carbon storage in terrestrial ecosystems, due to a fundamental alteration of the ecosystem, structure, function, and variability over time. Understanding the dynamics of aboveground carbon stocks in underway constructions and urban expansions is crucial to provide a basis for land use management and planning. The objective of this study was to analyze the spatiotemporal dynamics of aboveground carbon storage and assess how the LULC change is affected by human intervention, as well as how aboveground carbon stocks respond to these changes in the tropical highland landscape of Jatigede. In this study, changes in aboveground carbon stocks were investigated between 2014 and 2021 by using the integrated valuation of ecosystem services and tradeoffs (InVEST) model. The results revealed that the total aboveground carbon stock decreased between 2014 and 2021. Forests showed the greatest decline in the aboveground carbon stock in terms of space. The primary cause of the reduction in the aboveground carbon stock was the conversion of vegetated land to agricultural and urban land cover. The aboveground carbon stock change was also caused by the continuing construction, which resulted in the extension of construction zones. However, an increase in the aboveground carbon stock was mostly observed in mixed gardens that were close to forest areas. The preservation of mixed gardens as a tree-based agroforestry system can be suggested for enhancing the aboveground carbon stock, as mixed gardens play a significant role in carbon storage in the midst of the increasingly massive deforestation due to the expansion of urban areas. Full article

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