bluuebunny/crossref_metadata_2025 huggingface dataset:
Experimental Investigation of Fracture Propagation in Clayey Silt Hydrate-Bearing Sediments
Authors: Yu Yanjiang , Shen Kaixiang , Zhao Haifeng
Published: January 2024

More than 90% of the natural gas hydrate resources are reserved as marine clayey silt sediments. It is of great significance to efficiently develop a clayey silt hydrate. At present, there are problems of low single well production and small depressurization range in its production test, which is still a long way from commercial exploitation. The combination of hydraulic fracturing technology and other methods such as depressurization method is regarded as one of the potential technical means to achieve the commercial exploitation of the hydrate. However, compared with shale gas reservoirs and coalbed methane reservoirs, clayey silt hydrate reservoirs have special mechanical properties, resulting in unique hydraulic fracturing processes. Therefore, it is necessary to study the fracture initiation and propagation laws of clayey silt hydrate reservoirs. To this end, we carried out large-scale (30 × 30 × 30 cm) true triaxial hydraulic fracturing experiments using a simulated material with similar mechanics, porosity, and permeability to clayey silt hydrate-bearing sediments. The effects of completion method, fracturing method, and fracturing fluid displacement on hydraulic fracture propagation of clayey silt hydrate-bearing sediments were studied. The results showed that a perforated completion can significantly increase the fracture reconstruction area and decrease the fracture initiation pressure compared to an open hole completion. Due to the small horizontal stress difference, it is feasible to carry out temporary plugging fracturing in clayey silt hydrate reservoirs. Temporary plugging fracturing can form steering fractures and significantly improve fracture complexity and fracture area. Increasing the fracturing fluid displacement can significantly increase the fracture area as well. When conducting fracturing in clayey silt hydrate-bearing sediments, the fracturing fluid filtration area is obviously larger than the fracture propagation area. Therefore, it is recommended to use a high-viscosity fracturing fluid to reduce the filtration of the fracturing fluid and improve the fracturing fluid efficiency. This study preliminarily explores the feasibility of temporary plugging fracturing in clayey silt hydrate reservoirs and analyzes the effect of completion methods on the propagation of fracturing fractures, which can provide a reference for the research conducted on the fracturing stimulation of clayey silt hydrate reservoirs.
Designing a High-Order Sliding Mode Controller for Photovoltaic- and Battery Energy Storage System-Based DC Microgrids with ANN-MPPT
Authors: Roy Tushar Kanti , Oo Amanullah Maung Than , Ghosh Subarto Kumar
Published: January 2024

This paper introduces a robust proportional integral derivative higher-order sliding mode controller (PID-HOSMC) based on a double power reaching law (DPRL) to enhance large-signal stability in DC microgrids. The microgrid integrates a solar photovoltaic (SPV) system, an energy storage system (ESS), and DC loads. Efficient DC-DC converters, including bidirectional and boost converters, are employed to maintain a constant voltage level despite the lower SPV output power. An artificial neural network (ANN) generates the optimal reference voltage for the SPV system. The dynamical model, which incorporates external disturbances, is initially developed and based on this model, and the PID-HOSMC is designed to control output power by generating switching gate pulses. Afterwards, Lyapunov stability theory is used to demonstrate the model’s closed-loop stability, and theoretical analysis indicates that the controller can converge tracking errors to zero within a finite time frame. Finally, a comparative numerical simulation result is presented, demonstrating that the proposed controller exhibits a 58% improvement in settling time and an 82% improvement in overshoot compared to the existing controller. Experimental validation using processor-in-the-loop (PIL) confirms the proposed controller’s performance on a real-time platform.
Thermochemical Production of Hydrogen from Biomass: Pyrolysis and Gasification
Authors: Alvarado-Flores José , Alcaraz-Vera Jorge , Ávalos-Rodríguez María , Guzmán-Mejía Erandini , Rutiaga-Quiñones José , Pintor-Ibarra Luís , Guevara-Martínez Santiago
Published: January 2024

Today, hydrogen is one of the best options for generating electrical energy, for both industrial and residential use. The greatest volume of hydrogen produced today derives from processes that utilize petroleum. Although hydrogen has numerous benefits, continuing to produce it by these means is undesirable. This document presents a review of the literature on biohydrogen production based on an analysis of over 15 types of terrestrial and marine biomasses. The fundamental components of different production systems are described, with a focus on the thermochemical processes of pyrolysis and gasification, which have been identified as two of the most effective, practical ways to produce hydrogen from biomass. It also discusses catalysts, solid residues, and residual water that are used in the thermochemical production of biohydrogen. The article ends with an analysis of hydrogen and its benefits as an energy option with great potential in the short term to participate in the transition from fossil fuels.
Relative Comparison of Benefits of Floor Slab Insulation Methods, Using Polyiso and Extruded Polystyrene Materials in South Africa, Subject to the New National Building Energy Efficiency Standards
Authors: Kabundu Emmanuel , Mbanga Sijekula , Botha Brink , Ayesu-Koranteng Emma
Published: January 2024

This article aims to assess the benefits of floor slab insulation measures using extruded polystyrene (XPS) and polyisocyanurate (also referred to as polyiso or PIR) insulation materials at various levels of insulation thicknesses for a detached residential building. An EnergyPlus simulation analysis was carried out within the seven energy zones (represented by eight locations) of South Africa in accordance with the South African national code for building energy efficiency (SANS10400-XA). The energy savings and payback periods related to the use of the insulation over a lifecycle period of 50 years were assessed. Cape Town (zone 4) behaved differently from other locations and hardly benefited from the application of floor slab insulation measures. Generally, polyiso (PIR) insulation performed better than XPS for vertical gap insulation, and lower insulation thicknesses required higher insulation depths to maximize energy savings. Similarly, lower insulation thicknesses (25 mm and 50 mm) required higher perimeter insulation widths to maximize energy savings for horizontal perimeter insulation, especially in Sutherland (zone 6) and Cape Town. The maximization of energy savings was also achieved at low insulation thickness for the full floor slab insulation method, except for Sutherland and Fraserburg (zone 7). The locations that benefitted most from the floor slab insulation methods were Pretoria (zone 5), Thohoyandou (zone 3), Sutherland (zone 6), Fraserburg (zone 7), Welkom (zone 1), Ixopo (zone 5H), Witbank (zone 2), and Cape Town (zone 4), in that order. Generally, higher net energy savings are achieved in areas with lower humidity levels and areas with greater annual sums of both cooling and heating degree days.
Spatiotemporal Distribution Analysis of Spatial Vitality of Specialized Garden Plant Landscapes during Spring: A Case Study of Hangzhou Botanical Garden in China
Authors: Liu Tian , Mi Bingyi , Yan Hai , Bao Zhiyi , Wu Renwu , Wang Shuhan
Published: January 2024

Specialized gardens, as integral components of botanical gardens, bear multiple functions, encompassing plant collection and conservation, scientific research, and public education, as well as serving aesthetic and recreational purposes. Their quality profoundly reflects the landscape artistry of botanical gardens, directly influencing the quality of visitors’ enjoyment and the overall experience within the botanical garden. This study aims to investigate the spatial vitality of specialized garden plant landscapes, effectively assessing the usage patterns of plant landscape spaces and promoting the optimal utilization of underutilized spaces. Taking Hangzhou Botanical Garden as a case study, considering the warming climate and suitable temperatures in spring, when most plants enter the flowering period and outdoor visitor frequency increases, the primary observational period focuses on spring to measure the spatial vitality of specialized garden plant landscapes. We obtained data through field measurements and on-site observations. Specifically, We measured and recorded information on plant species, quantity, height, crown width, and growth conditions within the plots. Additionally, we employed ground observations and fixed-point photography to document visitor numbers and activity types. We quantified spatial vitality through four indicators: visitor density, space usage intensity, diversity of age group, and richness of activity type. We explored the spatiotemporal distribution patterns of spatial vitality and investigated the relationship between plant landscape characteristics and spatial vitality using variance analysis and correlation analysis. The results indicate that, in spring, the average spatial vitality index of specialized gardens ranks from highest to lowest as follows: Lingfeng Tanmei (1.403), Rosaceae Garden (1.245), Acer and Rhododendron Garden (0.449), and Osmanthus and Crape Myrtle Garden (0.437). Additionally, the spatial vitality of specialized garden plant landscapes in spring is significantly positively correlated with the ornamental period of specialized plants, characteristics of plant viewing, accessible lawn area, spatial accessibility, and spatial enclosure. Therefore, to create vibrant specialized plant landscapes, managers and planners, when engaging in the planning and design of specialized garden plant landscapes, need to fully consider and respect the visual aesthetics and functional needs of visitors. This study will serve as a theoretical reference for subsequent research on the vitality of plant landscape spaces and other small-scale spaces. It will also provide practical guidance for the construction of plant landscapes in specialized gardens within botanical gardens and other urban green spaces.
An Innovative Information Hiding Scheme Based on Block-Wise Pixel Reordering
Authors: Liu Jui-Chuan , Chi Heng-Xiao , Chang Ching-Chun , Chang Chin-Chen
Published: January 2024

Information has been uploaded and downloaded through the Internet, day in and day out, ever since we immersed ourselves in the Internet. Data security has become an area demanding high attention, and one of the most efficient techniques for protecting data is data hiding. In recent studies, it has been shown that the indices of a codebook can be reordered to hide secret bits. The hiding capacity of the codeword index reordering scheme increases when the size of the codebook increases. Since the codewords in the codebook are not modified, the visual performance of compressed images is retained. We propose a novel scheme making use of the fundamental principle of the codeword index reordering technique to hide secret data in encrypted images. By observing our experimental results, we can see that the obtained embedding capacity of 197,888 is larger than other state-of-the-art schemes. Secret data can be extracted when a receiver owns a data hiding key, and the image can be recovered when a receiver owns an encryption key.
A Bee Colony-Based Optimized Searching Mechanism in the Internet of Things
Authors: Ramzan Muhammad Sher , Asghar Anees , Ullah Ata , Alsolami Fawaz , Ahmad Iftikhar
Published: January 2024

The Internet of Things (IoT) consists of complex and dynamically aggregated elements or smart entities that need decentralized supervision for data exchanging throughout different networks. The artificial bee colony (ABC) is utilized in optimization problems for the big data in IoT, cloud and central repositories. The main limitation during the searching mechanism is that every single food site is compared with every other food site to find the best solution in the neighboring regions. In this way, an extensive number of redundant comparisons are required, which results in a slower convergence rate, greater time consumption and increased delays. This paper presents a solution to optimize search operations with an enhanced ABC (E-ABC) approach. The proposed algorithm compares the best food sites with neighboring sites to exclude poor sources. It achieves an efficient mechanism, where the number of redundant comparisons is decreased during the searching mechanism of the employed bee phase and the onlooker bee phase. The proposed algorithm is implemented in a replication scenario to validate its performance in terms of the mean objective function values for different functions, as well as the probability of availability and the response time. The results prove the superiority of the E-ABC in contrast to its counterparts.
Gollop–Wolfgang Complex Is Associated with a Monoallelic Variation in WNT11
Authors: Odrzywolski Adrian , Tüysüz Beyhan , Debeer Philippe , Souche Erika , Voet Arnout , Dimitrov Boyan , Krzesińska Paulina , Vermeesch Joris Robert , Tylzanowski Przemko
Published: January 2024

Gollop–Wolfgang complex (GWC) is a rare congenital limb anomaly characterized by tibial aplasia with femur bifurcation, ipsilateral bifurcation of the thigh bone, and split hand and monodactyly of the feet, resulting in severe and complex limb deformities. The genetic basis of GWC, however, has remained elusive. We studied a three-generation family with four GWC-affected family members. An analysis of whole-genome sequencing results using a custom pipeline identified the WNT11 c.1015G>A missense variant associated with the phenotype. In silico modelling and an in vitro reporter assay further supported the link between the variant and GWC. This finding further contributes to mapping the genetic heterogeneity underlying split hand/foot malformations in general and in GWC specifically.
Selection and Validation of Reference Genes for Gene Expression Studies in Euonymus japonicus Based on RNA Sequencing
Authors: Guo Wei , Yang Yihui , Ma Bo , Wang Wenbo , Hu Zenghui , Leng Pingsheng
Published: January 2024

Euonymus japonicus is one of the most low-temperature-tolerant evergreen broad-leaved tree species in the world and is widely used in urban greening. However, there are very few molecular biology studies on its low-temperature tolerance mechanism. So far, no researcher has selected and reported on its reference genes. In this study, 21 candidate reference genes (12 traditional housekeeping genes and 9 other genes) were initially selected based on gene expression and coefficient of variation (CV) through RNA-Seq (unpublished data), and qRT-PCR was used to detect the expression levels of candidate reference genes in three different groups of samples (leaves under different temperature stresses, leaves of plants at different growth stages, and different organs). After further evaluating the expression stability of these genes using geNorm, NormFinder, Bestkeeper, and RefFind, the results show that the traditional housekeeping gene eIF5A and the new reference gene RTNLB1 have good stability in the three different groups of samples, so they are reference genes with universality. In addition, we used eIF5A and RTNLB1 as reference genes to calibrate the expression pattern of the target gene EjMAH1, which confirmed this view. This article is the first to select and report on the reference gene of E. japonicus, laying the foundation for its low-temperature tolerance mechanism and other molecular biology research.
Aromatic L-Amino Acid Decarboxylase Deficiency: A Genetic Screening in Sicilian Patients with Neurological Disorders
Authors: Santa Paola Sandro , Di Blasi Francesco Domenico , Borgione Eugenia , Lo Giudice Mariangela , Giuliano Marika , Pettinato Rosa , Di Stefano Vincenzo , Brighina Filippo , Lupica Antonino , Scuderi Carmela
Published: January 2024

Aromatic L-amino acid decarboxylase deficiency (AADCd) is a rare autosomal recessive neurometabolic disorder caused by AADC deficiency, an enzyme encoded by the DDC gene. Since the enzyme is involved in the biosynthesis of serotonin and dopamine, its deficiency determines the lack of these neurotransmitters, but also of norepinephrine and epinephrine. Onset is early and the key signs are hypotonia, movement disorders (oculogyric crises, dystonia and hypokinesia), developmental delay and autonomic dysfunction. Taiwan is the site of a potential founder variant (IVS6+4A>T) with a predicted incidence of 1/32,000 births, while only 261 patients with this deficit have been described worldwide. Actually, the number of affected persons could be greater, given that the spectrum of clinical manifestations is broad and still little known. In our study we selected 350 unrelated patients presenting with different neurological disorders including heterogeneous neuromuscular disorders, cognitive deficit, behavioral disorders and autism spectrum disorder, for which the underlying etiology had not yet been identified. Molecular investigation of the DDC gene was carried out with the aim of identifying affected patients and/or carriers. Our study shows a high frequency of carriers (2.57%) in Sicilian subjects with neurological deficits, with a higher concentration in northern and eastern Sicily. Assuming these data as representative of the general Sicilian population, the risk may be comparable to some rare diseases included in the newborn screening programs such as spinal muscular atrophy, cystic fibrosis and phenylketonuria.
Translational Relevance of Advanced Age and Atherosclerosis in Preclinical Trials of Biotherapies for Peripheral Artery Disease
Authors: Webster Keith
Published: January 2024

Approximately 6% of adults worldwide suffer from peripheral artery disease (PAD), primarily caused by atherosclerosis of lower limb arteries. Despite optimal medical care and revascularization, many PAD patients remain symptomatic and progress to critical limb ischemia (CLI) and risk major amputation. Delivery of pro-angiogenic factors as proteins or DNA, stem, or progenitor cells confers vascular regeneration and functional recovery in animal models of CLI, but the effects are not well replicated in patients and no pro-angiogenic biopharmacological procedures are approved in the US, EU, or China. The reasons are unclear, but animal models that do not represent clinical PAD/CLI are implicated. Consequently, it is unclear whether the obstacles to clinical success lie in the toxic biochemical milieu of human CLI, or in procedures that were optimized on inappropriate models. The question is significant because the former case requires abandonment of current strategies, while the latter encourages continued optimization. These issues are discussed in the context of relevant preclinical and clinical data, and it is concluded that preclinical mouse models that include age and atherosclerosis as the only comorbidities that are consistently present and active in clinical trial patients are necessary to predict clinical success. Of the reviewed materials, no biopharmacological procedure that failed in clinical trials had been tested in animal models that included advanced age and atherosclerosis relevant to PAD/CLI.
Genetic Changes in Mastocytes and Their Significance in Mast Cell Tumor Prognosis and Treatment
Authors: Zmorzynski Szymon , Kimicka-Szajwaj Aleksandra , Szajwaj Angelika , Czerwik-Marcinkowska Joanna , Wojcierowski Jacek
Published: January 2024

Mast cell tumors are a large group of diseases occurring in dogs, cats, mice, as well as in humans. Systemic mastocytosis (SM) is a disease involving the accumulation of mast cells in organs. KIT gene mutations are very often seen in abnormal mast cells. In SM, high KIT/CD117 expression is observed; however, there are usually no KIT gene mutations present. Mastocytoma (MCT)—a form of cutaneous neoplasm—is common in animals but quite rare in humans. KIT/CD117 receptor mutations were studied as the typical changes for human mastocytosis. In 80% of human cases, the KIT gene substitution p.D816H was present. In about 25% of MCTs, metastasis was observed. Changes in the gene expression of certain genes, such as overexpression of the DNAJ3A3 gene, promote metastasis. In contrast, the SNORD93 gene blocks the expression of metastasis genes. The panel of miR-21-5p, miR-379, and miR-885 has a good efficiency in discriminating healthy and MCT-affected dogs, as well as MCT-affected dogs with and without nodal metastasis. Further studies on the pathobiology of mast cells can lead to clinical improvements, such as better MCT diagnosis and treatment. Our paper reviews studies on the topic of mast cells, which have been carried out over the past few years.
Empowering Riverine Communities in the Amazon: Strategies for Preventing Rabies
Authors: Silva João Gustavo Nascimento , Silva Stephanie de Sousa , Gomes Tamyres Cristine Mafra , Nascimento Gilmara dos Santos , Valentim Lívia de Aguiar , Quaresma Tatiane Costa , Fernandes Franciane de Paula , Oliveira Sheyla Mara Silva de , Moraes Waldiney Pires
Published: January 2024

Rabies, caused by the Lyssavirus genus, is a highly lethal zoonotic disease transmitted by animals such as bats and domestic and wild carnivores to humans, claiming nearly 100% of lives. In Brazil, recent evidence suggests an increasing role of bats in human deaths from rabies, particularly in the Amazon region. This neglected tropical disease disproportionately affects impoverished and vulnerable populations in rural areas, where approximately 80% of human cases are concentrated. This article presents research conducted in riverine communities of the Tapajós/Arapiuns Extractive Reserve in Brazil to combat rabies in September 2022. The study adopted a participatory and collaborative approach, involving community members, healthcare professionals, and educators. Prioritizing proactive interventions, the health team administered prophylactic vaccinations to 30 individuals residing in communities exposed to the Lyssavirus. Educational activities focused on dispelling myths and raising awareness about preventive measures, with 100% of individuals reporting prior doubts about the disease, emphasizing the essential nature of the clarification, especially regarding preventive aspects. This study underscores the importance of community involvement, personalized interventions, and ongoing education to effectively combat rabies. By reinforcing public health policies and promoting health education, we can empower communities to take proactive measures in rabies prevention, leading to a reduction in incidence and an improvement in quality of life.
Iridoid Glycosides and Coumarin Glycoside Derivatives from the Roots of Nymphoides peltata and Their In Vitro Wound Healing Properties
Authors: Kim Tae-Young , Lee Bum Soo , Jo Beom-Geun , Heo Seong Pil , Jung Young Suk , Kim Su-Nam , Kim Ki Hyun , Yang Min Hye
Published: January 2024

Nymphoides peltata has been used as a medicinal herb in traditional medicines to treat strangury, polyuria, and swelling. The phytochemical investigation of the MeOH extract of N. peltata roots led to the isolation of three iridoid glycosides and three coumarin glycoside derivatives, which were characterized as menthiafolin (1), threoninosecologanin (2), callicoside C (3), and scopolin (4), as well as two undescribed peltatamarins A (5) and B (6). The chemical structures of the undescribed compounds were determined by analyzing their 1 dimensional (D) and 2D nuclear magnetic resonance (NMR) spectra and using high-resolution (HR)-electrospray ionization mass spectroscopy (ESI-MS), along with the chemical reaction of acid hydrolysis. The wound healing activities of the isolated compounds 1–6 were evaluated using a HaCaT cell scratch test. Among the isolates, scopolin (4) and peltatamarin A (5) promoted HaCaT cell migration over scratch wounds, and compound 5 was the most effective. Furthermore, compound 5 significantly promoted cell migration without adversely affecting cell proliferation, even when treated at a high dose (100 μM). Our results demonstrate that peltatamarin A (5), isolated from N. peltata roots, has the potential for wound healing effects.
Special Issue “Mesenchymal Stromal Cells’ Involvement in Human Diseases and Their Treatment”
Authors: Jerkic Mirjana , Rabani Razieh
Published: January 2024

Mesenchymal stromal cells (MSCs) are multipotent, non-hematopoietic cells that have the ability to differentiate into several mature cell types, including adipocytes, chondrocytes, osteoblasts, and myoblasts [...]
Role of the C-Terminal β Sandwich of Thermoanaerobacter tengcongensis Thermophilic Esterase in Hydrolysis of Long-Chain Acyl Substrates
Authors: Joel Enoch B. , Aberuagba Adepeju , Bello Adebayo J. , Akanbi-Gada Mariam , Igunnu Adedoyin , Malomo Sylvia O. , Olorunniji Femi J.
Published: January 2024

To search for a novel thermostable esterase for optimized industrial applications, esterase from a thermophilic eubacterium species, Thermoanaerobacter tengcongensis MB4, was purified and characterized in this work. Sequence analysis of T. tengcongensis esterase with other homologous esterases of the same family revealed an apparent tail at the C-terminal that is not conserved across the esterase family. Hence, it was hypothesized that the tail is unlikely to have an essential structural or catalytic role. However, there is no documented report of any role for this tail region. We probed the role of the C-terminal domain on the catalytic activity and substrate preference of T. tengcongensis esterase EstA3 with a view to see how it could be engineered for enhanced properties. To achieve this, we cloned, expressed, and purified the wild-type and the truncated versions of the enzyme. In addition, a naturally occurring member of the family (from Brevibacillus brevis) that lacks the C-terminal tail was also made. In vitro characterization of the purified enzymes showed that the C-terminal domain contributes significantly to the catalytic activity and distinct substrate preference of T. tengcongensis esterase EstA3. All three recombinant enzymes showed the highest preference for paranitrophenyl butyrate (pNPC4), which suggests they are true esterases, not lipases. Kinetic data revealed that truncation had a slight effect on the substrate-binding affinity. Thus, the drop in preference towards long-chain substrates might not be a result of substrate binding affinity alone. The findings from this work could form the basis for future protein engineering allowing the modification of esterase catalytic properties through domain swapping or by attaching a modular protein domain.
Morphological and Genetic Aspects for Post-Mortem Diagnosis of Hypertrophic Cardiomyopathy: A Systematic Review
Authors: Cianci Vincenzo , Forzese Elena , Sapienza Daniela , Cardia Luigi , Cianci Alessio , Germanà Antonino , Tornese Lorenzo , Ieni Antonio , Gualniera Patrizia , Asmundo Alessio , Mondello Cristina
Published: January 2024

Hypertrophic cardiomyopathy (HCM) is one of the most common genetic cardiovascular diseases, and it shows an autosomal dominant pattern of inheritance. HCM can be clinically silent, and sudden unexpected death due to malignant arrhythmias may be the first manifestation. Thus, the HCM diagnosis could be performed at a clinical and judicial autopsy and offer useful findings on morphological features; moreover, it could integrate the knowledge on the genetic aspect of the disease. This review aims to systematically analyze the literature on the main post-mortem investigations and the related findings of HCM to reach a well-characterized and stringent diagnosis; the review was performed using PubMed and Scopus databases. The articles on the post-mortem evaluation of HCM by gross and microscopic evaluation, imaging, and genetic test were selected; a total of 36 studies were included. HCM was described with a wide range of gross findings, and there were cases without morphological alterations. Myocyte hypertrophy, disarray, fibrosis, and small vessel disease were the main histological findings. The post-mortem genetic tests allowed the diagnosis to be reached in cases without morpho-structural abnormalities; clinical and forensic pathologists have a pivotal role in HCM diagnosis; they contribute to a better definition of the disease and also provide data on the genotype–phenotype correlation, which is useful for clinical research.
Membrane-Bound Redox Enzyme Cytochrome bd-I Promotes Carbon Monoxide-Resistant Escherichia coli Growth and Respiration
Authors: Nastasi Martina R. , Borisov Vitaliy B. , Forte Elena
Published: January 2024

The terminal oxidases of bacterial aerobic respiratory chains are redox-active electrogenic enzymes that catalyze the four-electron reduction of O2 to 2H2O taking out electrons from quinol or cytochrome c. Living bacteria often deal with carbon monoxide (CO) which can act as both a signaling molecule and a poison. Bacterial terminal oxidases contain hemes; therefore, they are potential targets for CO. However, our knowledge of this issue is limited and contradictory. Here, we investigated the effect of CO on the cell growth and aerobic respiration of three different Escherichia coli mutants, each expressing only one terminal quinol oxidase: cytochrome bd-I, cytochrome bd-II, or cytochrome bo3. We found that following the addition of CO to bd-I-only cells, a minimal effect on growth was observed, whereas the growth of both bd-II-only and bo3-only strains was severely impaired. Consistently, the degree of resistance of aerobic respiration of bd-I-only cells to CO is high, as opposed to high CO sensitivity displayed by bd-II-only and bo3-only cells consuming O2. Such a difference between the oxidases in sensitivity to CO was also observed with isolated membranes of the mutants. Accordingly, O2 consumption of wild-type cells showed relatively low CO sensitivity under conditions favoring the expression of a bd-type oxidase.
EphA2- and HDAC-Targeted Combination Therapy in Endometrial Cancer
Authors: Joseph Robiya , Dasari Santosh K. , Umamaheswaran Sujanitha , Mangala Lingegowda S. , Bayraktar Emine , Rodriguez-Aguayo Cristian , Wu Yutuan , Nguyen Nghi , Powell Reid T. , Sobieski Mary , Liu Yuan , Kim Mark Seungwook , Corvigno Sara , Foster Katherine , Hanjra Pahul , Vu Thanh Chung , Chowdhury Mamur A. , Amero Paola , Stephan Clifford , Lopez-Berestein Gabriel , Westin Shannon N. , Sood Anil K.
Published: January 2024

Endometrial cancer is the most frequent malignant tumor of the female reproductive tract but lacks effective therapy. EphA2, a receptor tyrosine kinase, is overexpressed by various cancers including endometrial cancer and is associated with poor clinical outcomes. In preclinical models, EphA2-targeted drugs had modest efficacy. To discover potential synergistic partners for EphA2-targeted drugs, we performed a high-throughput drug screen and identified panobinostat, a histone deacetylase inhibitor, as a candidate. We hypothesized that combination therapy with an EphA2 inhibitor and panobinostat leads to synergistic cell death. Indeed, we found that the combination enhanced DNA damage, increased apoptosis, and decreased clonogenic survival in Ishikawa and Hec1A endometrial cancer cells and significantly reduced tumor burden in mouse models of endometrial carcinoma. Upon RNA sequencing, the combination was associated with downregulation of cell survival pathways, including senescence, cyclins, and cell cycle regulators. The Axl-PI3K-Akt-mTOR pathway was also decreased by combination therapy. Together, our results highlight EphA2 and histone deacetylase as promising therapeutic targets for endometrial cancer.
Glycogen Synthase Kinase-3 Inhibition by CHIR99021 Promotes Alveolar Epithelial Cell Proliferation and Lung Regeneration in the Lipopolysaccharide-Induced Acute Lung Injury Mouse Model
Authors: Fernandes Raquel , Barbosa-Matos Catarina , Borges-Pereira Caroline , Carvalho Ana Luísa Rodrigues Toste de , Costa Sandra
Published: January 2024

Acute respiratory distress syndrome (ARDS) is a life-threatening lung injury that currently lacks effective clinical treatments. Evidence highlights the potential role of glycogen synthase kinase-3 (GSK-3) inhibition in mitigating severe inflammation. The inhibition of GSK-3α/β by CHIR99021 promoted fetal lung progenitor proliferation and maturation of alveolar epithelial cells (AECs). The precise impact of CHIR99021 in lung repair and regeneration during acute lung injury (ALI) remains unexplored. This study intends to elucidate the influence of CHIR99021 on AEC behaviour during the peak of the inflammatory phase of ALI and, after its attenuation, during the repair and regeneration stage. Furthermore, a long-term evaluation was conducted post CHIR99021 treatment at a late phase of the disease. Our results disclosed the role of GSK-3α/β inhibition in promoting AECI and AECII proliferation. Later administration of CHIR99021 during ALI progression contributed to the transdifferentiation of AECII into AECI and an AECI/AECII increase, suggesting its contribution to the renewal of the alveolar epithelial population and lung regeneration. This effect was confirmed to be maintained histologically in the long term. These findings underscore the potential of targeted therapies that modulate GSK-3α/β inhibition, offering innovative approaches for managing acute lung diseases, mostly in later stages where no treatment is available.
STAG2: Computational Analysis of Missense Variants Involved in Disease
Authors: Ros-Pardo David , Gómez-Puertas Paulino , Marcos-Alcalde Íñigo
Published: January 2024

The human STAG2 protein is an essential component of the cohesin complex involved in cellular processes of gene expression, DNA repair, and genomic integrity. Somatic mutations in the STAG2 sequence have been associated with various types of cancer, while congenital variants have been linked to developmental disorders such as Mullegama–Klein–Martinez syndrome, X-linked holoprosencephaly-13, and Cornelia de Lange syndrome. In the cohesin complex, the direct interaction of STAG2 with DNA and with NIPBL, RAD21, and CTCF proteins has been described. The function of STAG2 within the complex is still unknown, but it is related to its DNA binding capacity and is modulated by its binding to the other three proteins. Every missense variant described for STAG2 is located in regions involved in one of these interactions. In the present work, we model the structure of 12 missense variants described for STAG2, as well as two other variants of NIPBl and two of RAD21 located at STAG2 interaction zone, and then analyze their behavior through molecular dynamic simulations, comparing them with the same simulation of the wild-type protein. This will allow the effects of variants to be rationalized at the atomic level and provide clues as to how STAG2 functions in the cohesin complex.
Unravelling the Transcriptional Response of Agaricus bisporus under Lecanicillium fungicola Infection
Authors: Quiroz Luis Felipe , Ciosek Tessa , Grogan Helen , McKeown Peter C. , Spillane Charles , Brychkova Galina
Published: January 2024

Mushrooms are a nutritionally rich and sustainably-produced food with a growing global market. Agaricus bisporus accounts for 11% of the total world mushroom production and it is the dominant species cultivated in Europe. It faces threats from pathogens that cause important production losses, including the mycoparasite Lecanicillium fungicola, the causative agent of dry bubble disease. Through quantitative real-time polymerase chain reaction (qRT-PCR), we determine the impact of L. fungicola infection on the transcription patterns of A. bisporus genes involved in key cellular processes. Notably, genes related to cell division, fruiting body development, and apoptosis exhibit dynamic transcriptional changes in response to infection. Furthermore, A. bisporus infected with L. fungicola were found to accumulate increased levels of reactive oxygen species (ROS). Interestingly, the transcription levels of genes involved in the production and scavenging mechanisms of ROS were also increased, suggesting the involvement of changes to ROS homeostasis in response to L. fungicola infection. These findings identify potential links between enhanced cell proliferation, impaired fruiting body development, and ROS-mediated defence strategies during the A. bisporus (host)–L. fungicola (pathogen) interaction, and offer avenues for innovative disease control strategies and improved understanding of fungal pathogenesis.
RNAi-Mediated Suppression of OsBBTI5 Promotes Salt Stress Tolerance in Rice
Authors: Lin Zhimin , Yi Xiaoyan , Ali Muhammad Moaaz , Zhang Lijuan , Wang Shaojuan , Tian Shengnan , Chen Faxing
Published: January 2024

This study explores the impact of RNAi in terms of selectively inhibiting the expression of the OsBBTI5 gene, with the primary objective of uncovering its involvement in the molecular mechanisms associated with salt tolerance in rice. OsBBTI5, belonging to the Bowman–Birk inhibitor (BBI) family gene, is known for its involvement in plant stress responses. The gene was successfully cloned from rice, exhibiting transcriptional self-activation in yeast. A yeast two-hybrid assay confirmed its specific binding to OsAPX2 (an ascorbate peroxidase gene). Transgenic OsBBTI5-RNAi plants displayed insensitivity to varying concentrations of 24-epibrassinolide in the brassinosteroid sensitivity assay. However, they showed reduced root and plant height at high concentrations (10 and 100 µM) of GA3 immersion. Enzyme activity assays revealed increased peroxidase (POD) and superoxide dismutase (SOD) activities and decreased malondialdehyde (MDA) content under 40-60 mM NaCl. Transcriptomic analysis indicated a significant upregulation of photosynthesis-related genes in transgenic plants under salt stress compared to the wild type. Notably, this study provides novel insights, suggesting that the BBI gene is part of the BR signaling pathway, and that OsBBTI5 potentially enhances stress tolerance in transgenic plants through interaction with the salt stress-related gene OsAPX2.
Special Issue: “Inflammatory Signaling Pathways Involved in Gastrointestinal Diseases”
Authors: Lauricella Marianna , Di Liberto Diana
Published: January 2024

Inflammation is a defensive response of the innate and adaptive immune systems against injury and/or harmful microorganisms to restore homeostasis [...]
Genotype Combinations Drive Variability in the Microbiome Configuration of the Rhizosphere of Maize/Bean Intercropping System
Authors: Lanzavecchia Giovanna , Frascarelli Giulia , Rocchetti Lorenzo , Bellucci Elisa , Bitocchi Elena , Di Vittori Valerio , Sillo Fabiano , Ferraris Irene , Carta Giada , Delledonne Massimo , Nanni Laura , Papa Roberto
Published: January 2024

In an intercropping system, the interplay between cereals and legumes, which is strongly driven by the complementarity of below-ground structures and their interactions with the soil microbiome, raises a fundamental query: Can different genotypes alter the configuration of the rhizosphere microbial communities? To address this issue, we conducted a field study, probing the effects of intercropping and diverse maize (Zea mays L.) and bean (Phaseolus vulgaris L., Phaseolus coccineus L.) genotype combinations. Through amplicon sequencing of bacterial 16S rRNA genes from rhizosphere samples, our results unveil that the intercropping condition alters the rhizosphere bacterial communities, but that the degree of this impact is substantially affected by specific genotype combinations. Overall, intercropping allows the recruitment of exclusive bacterial species and enhances community complexity. Nevertheless, combinations of maize and bean genotypes determine two distinct groups characterized by higher or lower bacterial community diversity and complexity, which are influenced by the specific bean line associated. Moreover, intercropped maize lines exhibit varying propensities in recruiting bacterial members with more responsive lines showing preferential interactions with specific microorganisms. Our study conclusively shows that genotype has an impact on the rhizosphere microbiome and that a careful selection of genotype combinations for both species involved is essential to achieve compatibility optimization in intercropping.
Coronary Slow-Flow Phenomenon in Takotsubo Syndrome: The Prevalence, Clinical Determinants, and Long-Term Prognostic Impact
Authors: Stępień Konrad , Nowak Karol , Karcińska Aleksandra , Horosin Grzegorz , del Carmen Yika Alicia , Lenart Julia , Górowska Anna , Iwańczyk Sylwia , Podolec Mateusz , Siniarski Aleksander , Nessler Jadwiga , Zalewski Jarosław
Published: January 2024

Patients with takotsubo syndrome (TTS) may present coronary slow flow (CSF) in angiography performed in the acute myocardial infarction (MI). However, the detailed clinical relevance and its long-term impact remain poorly understood. Among 7771 MI patients hospitalized between 2012 and 2019, TTS was identified in 82 (1.1%) subjects. The epicardial blood flow was assessed with thrombolysis in myocardial infarction (TIMI) scale and corrected TIMI frame count (TFC), whereas myocardial perfusion with TIMI myocardial perfusion grade (TMPG). CSF was defined as TIMI-2 or corrected TFC > 27 frames in at least one epicardial vessel. CSF was identified in 33 (40.2%) TTS patients. In the CSF-TTS versus normal-flow-TTS group, lower values of left ventricular ejection fraction on admission (33.5 (25–40) vs. 40 (35–45)%, p = 0.019), more frequent midventricular TTS (27.3 vs. 8.2%, p = 0.020) and the coexistence of both physical and emotional triggers (9.1 vs. 0%, p = 0.032) were noted. Within a median observation of 55 months, higher all-cause mortality was found in CSF-TTS compared with normal-flow TTS (30.3 vs. 10.2%, p = 0.024). CSF was identified as an independent predictor of long-term mortality (hazard ratio 10.09, 95% confidence interval 2.12–48.00, p = 0.004). CSF identified in two-fifths of TTS patients was associated with unfavorable long-term outcomes.
Network Analysis Performed on Transcriptomes of Parkinson’s Disease Patients Reveals Dysfunction in Protein Translation
Authors: D’Angiolini Simone , Lui Maria , Mazzon Emanuela , Calabrò Marco
Published: January 2024

Parkinson’s disease (PD) is a prevalent neurodegenerative disorder characterized by the progressive degeneration of dopaminergic neurons in the substantia nigra region of the brain. The hallmark pathological feature of PD is the accumulation of misfolded proteins, leading to the formation of intracellular aggregates known as Lewy bodies. Recent data evidenced how disruptions in protein synthesis, folding, and degradation are events commonly observed in PD and may provide information on the molecular background behind its etiopathogenesis. In the present study, we used a publicly available transcriptomic microarray dataset of peripheral blood of PD patients and healthy controls (GSE6613) to investigate the potential dysregulation of elements involved in proteostasis-related processes at the transcriptomic level. Our bioinformatics analysis revealed 375 differentially expressed genes (DEGs), of which 281 were down-regulated and 94 were up-regulated. Network analysis performed on the observed DEGs highlighted a cluster of 36 elements mainly involved in the protein synthesis processes. Different enriched ontologies were related to translation initiation and regulation, ribosome structure, and ribosome components nuclear export. Overall, this data consistently points to a generalized impairment of the translational machinery and proteostasis. Dysregulation of these mechanics has been associated with PD pathogenesis. Understanding the precise regulation of such processes may shed light on the molecular mechanisms of PD and provide potential data for early diagnosis.
Apolar Extracts of St. John’s Wort Alleviate the Effects of β-Amyloid Toxicity in Early Alzheimer’s Disease
Authors: El Menuawy Ahmed , Brüning Thomas , Eiriz Iván , Hähnel Urs , Marthe Frank , Möhle Luisa , Górska Anna Maria , Santos-García Irene , Wangensteen Helle , Wu Jingyun , Pahnke Jens
Published: January 2024

Hypericum perforatum (St. John’s wort) has been described to be beneficial for the treatment of Alzheimer’s disease (AD). Different extractions have demonstrated efficiency in mice and humans, esp. extracts with a low hypericin and hyperforin content to reduce side effects such as phototoxicity. In order to systematically elucidate the therapeutic effects of H. perforatum extracts with different polarities, APP-transgenic mice were treated with a total ethanol extract (TE), a polar extract obtained from TE, and an apolar supercritical CO2 (scCO2) extract. The scCO2 extract was formulated with silicon dioxide (SiO2) for better oral application. APP-transgenic mice were treated with several extracts (total, polar, apolar) at different concentrations. We established an early treatment paradigm from the age of 40 days until the age of 80 days, starting before the onset of cerebral β-amyloid (Aβ) deposition at 45 days of age. Their effects on intracerebral soluble and insoluble Aβ were analyzed using biochemical analyses. Our study confirms that the scCO2H. perforatum formulation shows better biological activity against Aβ-related pathological effects than the TE or polar extracts. Clinically, the treatment resulted in a dose-dependent improvement in food intake with augmentation of the body weight, and, biochemically, it resulted in a significant reduction in both soluble and insoluble Aβ (−27% and −25%, respectively). We therefore recommend apolar H. perforatum extracts for the early oral treatment of patients with mild cognitive impairment or early AD.
Ubiquitin Carboxyl-Terminal Hydrolase L1 and Its Role in Parkinson’s Disease
Authors: Buneeva Olga , Medvedev Alexei
Published: January 2024

Ubiquitin carboxyl-terminal hydrolase L1 (UCHL1), also known as Parkinson’s disease protein 5, is a highly expressed protein in the brain. It plays an important role in the ubiquitin–proteasome system (UPS), where it acts as a deubiquitinase (DUB) enzyme. Being the smallest member of the UCH family of DUBs, it catalyzes the reaction of ubiquitin precursor processing and the cleavage of ubiquitinated protein remnants, thus maintaining the level of ubiquitin monomers in the brain cells. UCHL1 mutants, containing amino acid substitutions, influence catalytic activity and its aggregability. Some of them protect cells and transgenic mice in toxin-induced Parkinson’s disease (PD) models. Studies of putative protein partners of UCHL1 revealed about sixty individual proteins located in all major compartments of the cell: nucleus, cytoplasm, endoplasmic reticulum, plasma membrane, mitochondria, and peroxisomes. These include proteins related to the development of PD, such as alpha-synuclein, amyloid-beta precursor protein, ubiquitin-protein ligase parkin, and heat shock proteins. In the context of the catalytic paradigm, the importance of these interactions is not clear. However, there is increasing understanding that UCHL1 exhibits various effects in a catalytically independent manner through protein–protein interactions. Since this protein represents up to 5% of the soluble protein in the brain, PD-related changes in its structure will have profound effects on the proteomes/interactomes in which it is involved. Growing evidence is accumulating that the role of UCHL1 in PD is obviously determined by a balance of canonic catalytic activity and numerous activity-independent protein–protein interactions, which still need better characterization.