bluuebunny/crossref_metadata_2025 huggingface dataset:
Influence of Genotype and Anaerobic Fermentation on In Vitro Rumen Fermentation Characteristics and Greenhouse Gas Production of Whole-Plant Maize
Authors: Alvarado-Ramírez Edwin Rafael , Elghandour Mona Mohamed Mohamed Yasseen , Rivas-Jacobo Marco Antonio , Calabrò Serena , Vastolo Alessandro , Cutrignelli Monica Isabella , Hernández-Ruiz Pedro Enrique , Figueroa-Pacheco Edson Brodeli , Salem Abdelfattah Zeidan Mohamed
Published: January 2024

The objective of this study was to evaluate the effect of anaerobic fermentation on the in vitro ruminal production of total gas (TG), methane (CH4), carbon monoxide (CO) and hydrogen sulfide (H2S), as well as on the characteristics of ruminal fermentation and CH4 conversion efficiency of whole-plant maize (WPM) from four native maize genotypes (Amarillo, Olotillo, Tampiqueño and Tuxpeño) from Mexico, and a commercial hybrid was used as a control. In all genotypes, the fermented WPM produced the lowest amounts (p ≤ 0.0236) of TG and CH4 from degraded dry matter (DM), and Tampiqueño and Tuxpeño presented the highest production of these gases. In addition, Tuxpeño also presented the highest proportion of CH4 (mL 100 mL−1 TG), and Olotillo presented the lowest proportion of both gases. Something similar occurred in H2S, where the fermented WPM produced the lowest (p ≤ 0.0077) amount per DM degraded, and Amarillo and Tampiqueño presented the highest and lowest production, respectively. However, the fermented WPM presented the highest (p = 0.0128) CO production from degraded DM, and Tuxpeño and Olotillo presented the highest and lowest production, while the rumen pH was lower (p < 0.0001) in the fermented WPM, and Tuxpeño and Olotillo presented the highest and lowest pH, respectively. Furthermore, the fermented plant presented the greatest (p ≤ 0.0055) DM degradation, and the Amarillo and hybrid genotypes presented the highest percentages, while Olotillo presented the lowest. The short-chain fatty acid (SCFA) content and metabolizable energy (ME) did not differ (p ≥ 0.0899) between genotypes and were higher (p = 0.0009) in the fresh WPM. Despite the above, the fermented WPM was more efficient (p ≤ 0.0249), and the Amarillo and hybrid genotypes produced less CH4 per unit of SCFAs, ME and organic matter. In conclusion, the Amarillo genotype equaled the hybrid one, and although the production of CO increased, anaerobic fermentation showed the potential to reduce the rumen production of TG, CH4 and H2S, as well as to improve DM degradability and CH4 conversion efficiency.
The Relationship between Preparation and Biological Activities of Animal-Derived Polysaccharides: A Comprehensive Review
Authors: Yang Bochun , Yang Conghao , Liu Rui , Sui Wenjie , Zhu Qiaomei , Jin Yan , Wu Tao , Zhang Min
Published: January 2024

Polysaccharides are biomolecules found in microorganisms, plants, and animals that constitute living organisms. Glycosaminoglycans, unique acidic polysaccharides in animal connective tissue, are often combined with proteins in the form of covalent bonds due to their potent biological activity, low toxicity, and minimal side effects, which have the potential to be utilized as nutrition healthcare and dietary supplements. Existing studies have demonstrated that the bioactivity of polysaccharides is closely dependent on their structure and chain conformation. The characteristic functional groups and primary structure directly determine the strength of activity. However, the relationship between structure and function is still unclear, and the target and mechanism of action are not fully understood, resulting in limited clinical applications. As a result, the clinical applications of these polysaccharides are currently limited. This review provides a comprehensive summary of the extraction methods, structures, and biological activities of animal-derived polysaccharides that have been discovered so far. The aim is to promote developments in animal active polysaccharide science and provide theoretical support for exploring other unknown natural products.
A Numerical Scheme and Application to the Fractional Integro-Differential Equation Using Fixed-Point Techniques
Authors: Gnanaprakasam Arul Joseph , Ramalingam Balaji , Mani Gunaseelan , Ege Ozgur , George Reny
Published: January 2024

In this paper, we introduce the notion of orthogonal α–F–convex contraction mapping and prove some fixed-point theorems for self-mapping in orthogonal complete metric spaces. The proven results generalize and extend some of the well-known results in the literature. Following the derivation of these fixed-point results, we propose a solution for the fractional integro-differential equation, utilizing the fixed-point technique within the context of orthogonal complete metric spaces.
The Multiscale Principle in Nature (Principium luxuriæ): Linking Multiscale Thermodynamics to Living and Non-Living Complex Systems
Authors: Venegas-Aravena Patricio , Cordaro Enrique G.
Published: January 2024

Why do fractals appear in so many domains of science? What is the physical principle that generates them? While it is true that fractals naturally appear in many physical systems, it has so far been impossible to derive them from first physical principles. However, a proposed interpretation could shed light on the inherent principle behind the creation of fractals. This is the multiscale thermodynamic perspective, which states that an increase in external energy could initiate energy transport mechanisms that facilitate the dissipation or release of excess energy at different scales. Within this framework, it is revealed that power law patterns, and to a lesser extent, fractals, can emerge as a geometric manifestation to dissipate energy in response to external forces. In this context, the exponent of these power law patterns (thermodynamic fractal dimension D) serves as an indicator of the balance between entropy production at small and large scales. Thus, when a system is more efficient at releasing excess energy at the microscopic (macroscopic) level, D tends to increase (decrease). While this principle, known as Principium luxuriæ, may sound promising for describing both multiscale and complex systems, there is still uncertainty about its true applicability. Thus, this work explores different physical, astrophysical, sociological, and biological systems to attempt to describe and interpret them through the lens of the Principium luxuriæ. The analyzed physical systems correspond to emergent behaviors, chaos theory, and turbulence. To a lesser extent, the cosmic evolution of the universe and geomorphology are examined. Biological systems such as the geometry of human organs, aging, human brain development and cognition, moral evolution, Natural Selection, and biological death are also analyzed. It is found that these systems can be reinterpreted and described through the thermodynamic fractal dimension. Therefore, it is proposed that the physical principle that could be behind the creation of fractals is the Principium luxuriæ, which can be defined as “Systems that interact with each other can trigger responses at multiple scales as a manner to dissipate the excess energy that comes from this interaction”. That is why this framework has the potential to uncover new discoveries in various fields. For example, it is suggested that the reduction in D in the universe could generate emergent behavior and the proliferation of complexity in numerous fields or the reinterpretation of Natural Selection.
Effect of Homogenized Callus Tissue on the Rheological and Mechanical Properties of 3D-Printed Food
Authors: Dushina Elena , Popov Sergey , Zlobin Andrey , Martinson Ekaterina , Paderin Nikita , Vityazev Fedor , Belova Kseniya , Litvinets Sergey
Published: January 2024

The aim of the study was to develop ink enriched with a high content of lupine callus tissue (CT) suitable for 3D printing. Printable ink obtained using mashed potatoes (20 g/100 mL) and a 3% agar solution was used as the parent CT-free ink (CT0). Viscosity increased from 9.6 to 75.4 kPa·s during the cooling of the CT0 ink from 50 to 20 °C, while the viscosity of the ink with 80 g/100 mL of CT (CT80) increased from 0.9 to 5.6 kPa·s under the same conditions. The inclusion of CT was shown to decrease the hardness of 3D-printed food gel from 0.32 ± 0.03 to 0.21 ± 0.03 N. The storage modulus G’ value was 7.9 times lower in CT80 samples than in CT0 samples. The values of fracture stress for CT80 and CT0 inks were 1621 ± 711 and 13,241 ± 2329 Pa, respectively. The loss tangent and the limiting strain did not differ in CT0 and CT80, although the value of the fracture strain was 1.6 times higher in the latter. Thus, the present study demonstrates that CT may be added to printing ink in order to enhance food with plant cell material and enable the 3D printing of specially shaped foods.
Relationships between Soil Moisture and Visible–NIR Soil Reflectance: A Review Presenting New Analyses and Data to Fill the Gaps
Authors: McGuirk Savannah L. , Cairns Iver H.
Published: January 2024

The ability to precisely monitor soil moisture is highly valuable in industries including agriculture and civil engineering. As soil moisture is a spatially erratic and temporally dynamic variable, rapid, cost-effective, widely applicable, and practical techniques are required for monitoring soil moisture at all scales. If a consistent numerical relationship between soil moisture content and soil reflectance can be identified, then soil spectroscopic models may be used to efficiently predict soil moisture content from proximal soil reflectance and/or remotely sensed data. Previous studies have identified a general decrease in visible–NIR soil reflectance as soil moisture content increases, however, the strength, best wavelengths for modelling, and domain of the relationship remain unclear from the current literature. After reviewing the relevant literature and the molecular interactions between water and light in the visible–NIR (400–2500 nm) range, this review presents new analyses and interprets new 1 nm resolution soil reflectance data, collected at >20 moisture levels for ten soil samples. These data are compared to the results of other published studies, extending these as required for further interpretation. Analyses of this new high-resolution dataset demonstrate that linear models are sufficient to characterise the relationship between soil moisture and reflectance in many cases, but relationships are typically exponential. Equations generalising the relationship between soil MC and reflectance are presented for a number of wavelength ranges and combinations. Guidance for the adjustment of these equations to suit other soil types is also provided, to allow others to apply the solutions presented here and to predict soil moisture content in a much wider range of soils.
Influence of Potentially Inappropriate Medication Use on Older Australians’ Admission to Emergency Department Short Stay
Authors: Tran Hoa T. M. , Roman Cristina , Yip Gary , Dooley Michael , Salahudeen Mohammed S. , Mitra Biswadev
Published: January 2024

Older people in the emergency department (ED) often pose complex medical challenges, with a significant prevalence of polypharmacy and potentially inappropriate medicines (PIMs) in Australia. A retrospective analysis of 200 consecutive patients aged over 65 years admitted to the emergency short stay unit (ESSU) aimed to identify polypharmacy (five or more regular medications), assess PIM prevalence, and explore the link between pre-admission PIMs and ESSU admissions. STOPP/START version 2 criteria were used for the PIM assessment, with an expert panel categorizing associated risks. Polypharmacy was observed in 161 patients (80.5%), who were older (mean age 82 versus 76 years) and took more regular medications (median 9 versus 3). One hundred and eighty-five (92.5%) patients had at least one PIM, 81 patients (40.5%) had STOPP PIMs, and 177 patients (88.5%) had START omissions. Polypharmacy significantly correlated with STOPP PIM (OR 4.8; 95%CI: 1.90–12.1), and for each additional medication the adjusted odds of having a STOPP PIM increased by 1.20 (95%CI: 1.11–1.28). Nineteen admissions (9.5%) were attributed to one or more PIMs (total 21 PIMs). Of these PIMs, the expert panel rated eight (38%) as high risk, five (24%) as moderate risk, and eight (38%) as low risk for causing hospital admission. The most common PIMs were benzodiazepines, accounting for 14 cases (73.6%). Older ESSU-admitted patients commonly presented with polypharmacy and PIMs, potentially contributing to their admission.
Reliability and Mental Health Correlates of a Single-Item Measure of Self-Rated Mental Health (SRMH) in the Chinese Context
Authors: Fung Hong Wang , Lam Stanley Kam Ki , Chien Wai Tong , Ling Henry Wai-Hang , Wu Zi Yi , Ross Colin A. , Chau Anson Kai Chun
Published: January 2024

The use of single-item measures of self-rated mental health (SRMH) has been increasingly valued in epidemiologic research. However, little is known about the reliability and mental health correlates of SRMH in Chinese populations. This study examined the reliability and mental health correlates of SRMH in three Chinese samples. We analyzed data collected from two convenience samples of Chinese adults from Hong Kong and/or Taiwan (Sample 1: N = 205; Sample 2: N = 377), and a random sample of Taiwan psychiatric inpatients (Sample 3: N = 100). Our results showed that the single-item measure of SRMH had moderate to good test–retest reliability (intraclass correlation [ICC] = 0.75) in Sample 1 and acceptable reliability between the self-report and interviewer-administered versions (ICC = 0.58) in Sample 3. It had a high positive correlation with self-esteem and a moderately high negative correlation with depression. It also had a consistently negative correlation with borderline personality disorder symptoms and post-traumatic stress disorder symptoms. The SRMH score was also associated with psychiatric service usage. These findings contribute to the body of knowledge regarding the use of a single-item measure of SRMH to assess overall self-perceived mental health in Chinese communities.
Bayesian Structural Time Series and Geographically Weighted Logistic Regression Modelling Impacts of COVID-19 Lockdowns on the Spatiotemporal Patterns of London’s Crimes
Authors: Wang Rui , Li Yijing
Published: January 2024

Given the paramount impacts of COVID-19 on people’s lives in the capital of the UK, London, it was foreseeable that the city’s crime patterns would have undergone significant transformations, especially during lockdown periods. This study aims to testify the crime patterns’ changes in London, using data from March 2020 to March 2021 to explore the driving forces for such changes, and hence propose data-driven insights for policy makers and practitioners on London’s crime deduction and prevention potentiality in post-pandemic era. (1) Upon exploratory data analyses on the overall crime change patterns, an innovative BSTS model has been proposed by integrating restriction-level time series into the Bayesian structural time series (BSTS) model. This novel method allows the research to evaluate the varied effects of London’s three lockdown periods on local crimes among the regions of London. (2) Based on the predictive results from the BSTS modelling, three regression models were deployed to identify the driving forces for respective types of crime experiencing significant increases during lockdown periods. (3) The findings solidified research hypotheses on the distinct factors influencing London’s specific types of crime by period and by region. In light of the received evidence, insights on a modified policing allocation model and supporting the unemployed group was proposed in the aim of effectively mitigating the surges of crimes in London.
Lipid Metabolism Modulation during SARS-CoV-2 Infection: A Spotlight on Extracellular Vesicles and Therapeutic Prospects
Authors: D’Avila Heloisa , Lima Claudia Natércia Rocha , Rampinelli Pollianne Garbero , Mateus Laiza Camila Oliveira , Sousa Silva Renata Vieira de , Correa José Raimundo , Almeida Patrícia Elaine de
Published: January 2024

Extracellular vesicles (EVs) have a significant impact on the pathophysiological processes associated with various diseases such as tumors, inflammation, and infection. They exhibit molecular, biochemical, and entry control characteristics similar to viral infections. Viruses, on the other hand, depend on host metabolic machineries to fulfill their biosynthetic requirements. Due to potential advantages such as biocompatibility, biodegradation, and efficient immune activation, EVs have emerged as potential therapeutic targets against the SARS-CoV-2 infection. Studies on COVID-19 patients have shown that they frequently have dysregulated lipid profiles, which are associated with an increased risk of severe repercussions. Lipid droplets (LDs) serve as organelles with significant roles in lipid metabolism and energy homeostasis as well as having a wide range of functions in infections. The down-modulation of lipids, such as sphingolipid ceramide and eicosanoids, or of the transcriptional factors involved in lipogenesis seem to inhibit the viral multiplication, suggesting their involvement in the virus replication and pathogenesis as well as highlighting their potential as targets for drug development. Hence, this review focuses on the role of modulation of lipid metabolism and EVs in the mechanism of immune system evasion during SARS-CoV-2 infection and explores the therapeutic potential of EVs as well as application for delivering therapeutic substances to mitigate viral infections.
Effects of Low-Level Blast on Neurovascular Health and Cerebral Blood Flow: Current Findings and Future Opportunities in Neuroimaging
Authors: Kilgore Madison O. , Hubbard W. Brad
Published: January 2024

Low-level blast (LLB) exposure can lead to alterations in neurological health, cerebral vasculature, and cerebral blood flow (CBF). The development of cognitive issues and behavioral abnormalities after LLB, or subconcussive blast exposure, is insidious due to the lack of acute symptoms. One major hallmark of LLB exposure is the initiation of neurovascular damage followed by the development of neurovascular dysfunction. Preclinical studies of LLB exposure demonstrate impairment to cerebral vasculature and the blood–brain barrier (BBB) at both early and long-term stages following LLB. Neuroimaging techniques, such as arterial spin labeling (ASL) using magnetic resonance imaging (MRI), have been utilized in clinical investigations to understand brain perfusion and CBF changes in response to cumulative LLB exposure. In this review, we summarize neuroimaging techniques that can further our understanding of the underlying mechanisms of blast-related neurotrauma, specifically after LLB. Neuroimaging related to cerebrovascular function can contribute to improved diagnostic and therapeutic strategies for LLB. As these same imaging modalities can capture the effects of LLB exposure in animal models, neuroimaging can serve as a gap-bridging diagnostic tool that permits a more extensive exploration of potential relationships between blast-induced changes in CBF and neurovascular health. Future research directions are suggested, including investigating chronic LLB effects on cerebral perfusion, exploring mechanisms of dysautoregulation after LLB, and measuring cerebrovascular reactivity (CVR) in preclinical LLB models.
The Influence of Genetic Polymorphisms on the Expression of Interleukin-1beta, Prostaglandin E2 and Tumor Necrosis Factor Alpha in Peri-Implant Crevicular Fluid: A Cross-Sectional Study
Authors: Cardoso José Maria , Ribeiro Ana Clara , Botelho João , Proença Luís , Noronha Susana , Alves Ricardo Castro
Published: January 2024

The aim of this study was to evaluate the possible relationships between polymorphisms in the interleukin-1 (IL-1) A, IL-1B, and IL-1RN genes and concentrations of the inflammatory mediators IL-1β, tumor necrosis factor-alpha (TNF-α), and prostaglandin E2 (PGE2) in peri-implant crevicular fluid (PICF). A cross-sectional analytical study was conducted on 51 patients with dental implants. Samples from the buccal mucosa were obtained, and genetic analysis was performed using the real-time polymerase chain reaction (PCR) technique for IL-1A and IL-1B and PCR and restriction fragment length polymorphism analysis for IL-1RN. For the biochemical analysis, the concentrations of IL-1β and TNF-α were analyzed using multiplexed fluorescent sphere immunoassays, and PGE2 by enzyme-linked immunosorbent assay. In patients with detected IL-1RN polymorphism, there was an increase in the concentration of the three mediators with statistically significant differences in the mean values of TNF-α and PGE2, regardless of peri-implant health status (p = 0.002 and p = 0.049, respectively). The concentrations of all three mediators were positively and significantly correlated (IL-1β vs. TNF-α Rho = 0.480, p < 0.001; IL-1β vs. PGE2 Rho = 0.382, p = 0.006; and TNF-α vs. PGE2 Rho = 0.528, p < 0.001). We can conclude that the IL-1RN polymorphism exerts an influence on the PICF immune response, which may explain the influence of this genetic polymorphism on the occurrence of peri-implantitis.
Anti-Aging Effect of Hemerocallis citrina Baroni Polysaccharide-Rich Extract on Caenorhabditis elegans
Authors: Zou Yunxia , Qin Xiyue , Wang Wenli , Meng Qingyong , Zhang Yali
Published: January 2024

Plant polysaccharides are important for anti-aging research. Polysaccharides from Hemerocallis citrina Baroni (H. citrina) have been reported to have antioxidant activity; however, their anti-aging roles and mechanisms are not clear. In this study, we extracted polysaccharides from H. citrina by an ultrasonic-assisted water extraction–alcohol precipitation method and chemically determined the physicochemical properties such as extraction yield, content, and in vitro antioxidant properties of H. citrina polysaccharide-rich extract (HCPRE). Using Caenorhabditis elegans (C. elegans) as a model animal, the anti-aging effect of HCPRE was investigated, and the mechanism of action of HCPRE was explored by the in vivo antioxidant level assay of C. elegans and the related gene expression assay. The extraction yield of HCPRE was 11.26%, the total polysaccharide content was 77.96%, and the main monosaccharide components were glucose and galactose. In addition, HCPRE exhibited good antioxidant activity both in vitro and in vivo. Under normal thermal stress and oxidative stress conditions, being fed 1200 µg/mL of HCPRE significantly prolonged the life span of C. elegans by 32.65%, 17.71%, and 32.59%, respectively. Our study showed that HCPRE exerted an anti-aging effect on C. elegans, and its mechanism involves increasing the activities of catalase (CAT) and superoxide dismutase (SOD), reducing the level of reactive oxygen species (ROS) and regulating the expression of related genes.
Differential Response of MYB Transcription Factor Gene Transcripts to Circadian Rhythm in Tea Plants (Camellia sinensis)
Authors: Hu Zhihang , Zhang Nan , Qin Zhiyuan , Li Jinwen , Yang Ni , Chen Yi , Kong Jieyu , Luo Wei , Xiong Aisheng , Zhuang Jing
Published: January 2024

The circadian clock refers to the formation of a certain rule in the long-term evolution of an organism, which is an invisible ‘clock’ in the body of an organism. As one of the largest TF families in higher plants, the MYB transcription factor is involved in plant growth and development. MYB is also inextricably correlated with the circadian rhythm. In this study, the transcriptome data of the tea plant ‘Baiyeyihao’ were measured at a photoperiod interval of 4 h (24 h). A total of 25,306 unigenes were obtained, including 14,615 unigenes that were annotated across 20 functional categories within the GO classification. Additionally, 10,443 single-gene clusters were annotated to 11 sublevels of metabolic pathways using KEGG. Based on the results of gene annotation and differential gene transcript analysis, 22 genes encoding MYB transcription factors were identified. The G10 group in the phylogenetic tree had 13 members, of which 5 were related to the circadian rhythm, accounting for 39%. The G1, G2, G8, G9, G15, G16, G18, G19, G20, G21 and G23 groups had no members associated with the circadian rhythm. Among the 22 differentially expressed MYB transcription factors, 3 members of LHY, RVE1 and RVE8 were core circadian rhythm genes belonging to the G10, G12 and G10 groups, respectively. Real-time fluorescence quantitative PCR was used to detect and validate the expression of the gene transcripts encoding MYB transcription factors associated with the circadian rhythm.
The Current Situation and Development Prospect of Whole-Genome Screening
Authors: Yang Caiting , Lei Yu , Ren Tinglin , Yao Mingze
Published: January 2024

High-throughput genetic screening is useful for discovering critical genes or gene sequences that trigger specific cell functions and/or phenotypes. Loss-of-function genetic screening is mainly achieved through RNA interference (RNAi), CRISPR knock-out (CRISPRko), and CRISPR interference (CRISPRi) technologies. Gain-of-function genetic screening mainly depends on the overexpression of a cDNA library and CRISPR activation (CRISPRa). Base editing can perform both gain- and loss-of-function genetic screening. This review discusses genetic screening techniques based on Cas9 nuclease, including Cas9-mediated genome knock-out and dCas9-based gene activation and interference. We compare these methods with previous genetic screening techniques based on RNAi and cDNA library overexpression and propose future prospects and applications for CRISPR screening.
Increased Dentate Gyrus Excitability in the Intrahippocampal Kainic Acid Mouse Model for Temporal Lobe Epilepsy
Authors: Vergaelen Marijke , Manzella Simona , Vonck Kristl , Craey Erine , Spanoghe Jeroen , Sprengers Mathieu , Carrette Evelien , Wadman Wytse Jan , Delbeke Jean , Boon Paul , Larsen Lars Emil , Raedt Robrecht
Published: January 2024

The intrahippocampal kainic acid (IHKA) mouse model is an extensively used in vivo model to investigate the pathophysiology of mesial temporal lobe epilepsy (mTLE) and to develop novel therapies for drug-resistant epilepsy. It is characterized by profound hippocampal sclerosis and spontaneously occurring seizures with a major role for the injected damaged hippocampus, but little is known about the excitability of specific subregions. The purpose of this study was to electrophysiologically characterize the excitability of hippocampal subregions in the chronic phase of the induced epilepsy in the IHKA mouse model. We recorded field postsynaptic potentials (fPSPs) after electrical stimulation in the CA1 region and in the dentate gyrus (DG) of hippocampal slices of IHKA and healthy mice using a multielectrode array (MEA). In the DG, a significantly steeper fPSP slope was found, reflecting higher synaptic strength. Population spikes were more prevalent with a larger spatial distribution in the IHKA group, reflecting a higher degree of granule cell output. Only minor differences were found in the CA1 region. These results point to increased neuronal excitability in the DG but not in the CA1 region of the hippocampus of IHKA mice. This method, in which the excitability of hippocampal slices from IHKA mice is investigated using a MEA, can now be further explored as a potential new model to screen for new interventions that can restore DG function and potentially lead to novel therapies for mTLE.
In Silico Safety Assessment of Bacillus Isolated from Polish Bee Pollen and Bee Bread as Novel Probiotic Candidates
Authors: Bin Hafeez Ahmer , Pełka Karolina , Worobo Randy , Szweda Piotr
Published: January 2024

Bacillus species isolated from Polish bee pollen (BP) and bee bread (BB) were characterized for in silico probiotic and safety attributes. A probiogenomics approach was used, and in-depth genomic analysis was performed using a wide array of bioinformatics tools to investigate the presence of virulence and antibiotic resistance properties, mobile genetic elements, and secondary metabolites. Functional annotation and Carbohydrate-Active enZYmes (CAZYme) profiling revealed the presence of genes and a repertoire of probiotics properties promoting enzymes. The isolates BB10.1, BP20.15 (isolated from bee bread), and PY2.3 (isolated from bee pollen) genome mining revealed the presence of several genes encoding acid, heat, cold, and other stress tolerance mechanisms, adhesion proteins required to survive and colonize harsh gastrointestinal environments, enzymes involved in the metabolism of dietary molecules, antioxidant activity, and genes associated with the synthesis of vitamins. In addition, genes responsible for the production of biogenic amines (BAs) and D-/L-lactate, hemolytic activity, and other toxic compounds were also analyzed. Pan-genome analyses were performed with 180 Bacillus subtilis and 204 Bacillus velezensis genomes to mine for any novel genes present in the genomes of our isolates. Moreover, all three isolates also consisted of gene clusters encoding secondary metabolites.
Binding Free Energy Calculation Based on the Fragment Molecular Orbital Method and Its Application in Designing Novel SHP-2 Allosteric Inhibitors
Authors: Yuan Zhen , Chen Xingyu , Fan Sisi , Chang Longfeng , Chu Linna , Zhang Ying , Wang Jie , Li Shuang , Xie Jinxin , Hu Jianguo , Miao Runyu , Zhu Lili , Zhao Zhenjiang , Li Honglin , Li Shiliang
Published: January 2024

The accurate prediction of binding free energy is a major challenge in structure-based drug design. Quantum mechanics (QM)-based approaches show promising potential in predicting ligand–protein binding affinity by accurately describing the behavior and structure of electrons. However, traditional QM calculations face computational limitations, hindering their practical application in drug design. Nevertheless, the fragment molecular orbital (FMO) method has gained widespread application in drug design due to its ability to reduce computational costs and achieve efficient ab initio QM calculations. Although the FMO method has demonstrated its reliability in calculating the gas phase potential energy, the binding of proteins and ligands also involves other contributing energy terms, such as solvent effects, the ‘deformation energy’ of a ligand’s bioactive conformations, and entropy. Particularly in cases involving ionized fragments, the calculation of solvation free energy becomes particularly crucial. We conducted an evaluation of some previously reported implicit solvent methods on the same data set to assess their potential for improving the performance of the FMO method. Herein, we develop a new QM-based binding free energy calculation method called FMOScore, which enhances the performance of the FMO method. The FMOScore method incorporates linear fitting of various terms, including gas-phase potential energy, deformation energy, and solvation free energy. Compared to other widely used traditional prediction methods such as FEP+, MM/PBSA, MM/GBSA, and Autodock vina, FMOScore showed good performance in prediction accuracies. By constructing a retrospective case study, it was observed that incorporating calculations for solvation free energy and deformation energy can further enhance the precision of FMO predictions for binding affinity. Furthermore, using FMOScore-guided lead optimization against Src homology-2-containing protein tyrosine phosphatase 2 (SHP-2), we discovered a novel and potent allosteric SHP-2 inhibitor (compound 8).
Programmed Cell Death Ligand 1 Immunohistochemical Expression and Cutaneous Melanoma: A Controversial Relationship
Authors: Fiorentino Vincenzo , Pizzimenti Cristina , Franchina Mariausilia , Pepe Ludovica , Russotto Fernanda , Tralongo Pietro , Micali Marina Gloria , Militi Gaetano Basilio , Lentini Maria
Published: January 2024

Cutaneous melanoma (CM) is traditionally considered one of the most “immunogenic” tumors, eliciting a high immune response. However, despite the presence of tumor-infiltrating lymphocytes (TILs), melanoma cells use strategies to suppress antitumor immunity and avoid being eliminated by immune surveillance. The PD-1 (programmed death-1)/PD-L1 (programmed death-ligand 1) axis is a well-known immune escape system adopted by neoplastic cells. Therefore, immunotherapy with PD-1 and PD-L1 inhibitors is quickly becoming the main treatment approach for metastatic melanoma patients. However, the clinical utility of PD-L1 expression assessment in CM is controversial, and the interpretation of PD-L1 scores in clinical practice is still a matter of debate. Nonetheless, the recent literature data show that by adopting specific PD-L1 assessment methods in melanoma samples, a correlation between the expression of such a biomarker and a positive response to PD-1-based immunotherapy can be seen. Our review aims to describe the state-of-the-art knowledge regarding the prognostic and predictive role of PD-L1 expression in CM while also referring to possible biological explanations for the variability in its expressions and related treatment responses.
Two-Stage Recognition Mechanism of the SARS-CoV-2 Receptor-Binding Domain to Angiotensin-Converting Enzyme-2 (ACE2)
Authors: Biskupek Iga , Gieldon Artur
Published: January 2024

The SARS-CoV-2 virus, commonly known as COVID-19, occurred in 2019. It is a highly contagious illness with effects ranging from mild symptoms to severe illness. It is also one of the best-known pathogens since more than 200,000 scientific papers occurred in the last few years. With the publication of the SARS-CoV-2 (SARS-CoV-2-CTD) spike (S) protein in a complex with human ACE2 (hACE2) (PDB (6LZG)), the molecular analysis of one of the most crucial steps on the infection pathway was possible. The aim of this manuscript is to simulate the most widely spread mutants of SARS-CoV-2, namely Alpha, Beta, Gamma, Delta, Omicron, and the first recognized variant (natural wild type). With the wide search of the hypersurface of the potential energy performed using the UNRES force field, the intermediate state of the ACE2–RBD complex was found. R403, K/N/T417, L455, F486, Y489, F495, Y501, and Y505 played a crucial role in the protein recognition mechanism. The intermediate state cannot be very stable since it will prevent the infection cascade.
Multiparametric Monitoring of Disease Progression in Contemporary Patients with Wild-Type Transthyretin Amyloid Cardiomyopathy Initiating Tafamidis Treatment
Authors: Ney Svenja , Gertz Roman Johannes , Pennig Lenhard , Nies Richard J. , Holtick Udo , Völker Linus A. , Wunderlich Gilbert , Seuthe Katharina , Hohmann Christopher , Metze Clemens , Nähle Claas Philip , von Stein Jennifer , Brüwer Monique , ten Freyhaus Henrik , Pfister Roman
Published: January 2024

Background: Recently, a disease modifying therapy has become available for transthyretin amyloid cardiomyopathy (ATTR-CM). A validated monitoring concept of treatment is lacking, but a current expert consensus recommends three clinical domains (clinical, biomarker and ECG/imaging) assessed by several measurable features to define disease progression. Methods: We retrospectively analyzed data of wild-type ATTR-CM patients initiating tafamidis therapy assessed within our local routine protocol at baseline and 6-months follow-up with respect to the frequency of values beyond the proposed thresholds defining disease progression. Additionally, associations of cardiac magnetic resonance (CMR) tomography with clinical domains were examined within a subgroup. Results: Sixty-two ATTR-CM patients were included (88.7% male, mean age 79 years). In total, 16.1% of patients had progress in the clinical and functional domain, 33.9% in the biomarker domain and 43.5% in the imaging/electrocardiography (ECG) domain, with the latter driven by deterioration of the diastolic dysfunction grade and global longitudinal strain. In total, 35.5% of patients showed progress in none, 35.5% in one, 29.0% in two and no patient in three domains, the latter indicating overall disease progression. A subgroup analysis of twenty-two patients with available baseline and follow-up CMR data revealed an increase in CMR-based extracellular volume by more than 5% in 18.2% of patients, with no significant correlation with progress in one of the clinical domains. Conclusions: We provide first frequency estimates of the markers of disease progression according to a recent expert consensus statement, which might help refine the multiparametric monitoring concept in patients with ATTR-CM.
From Clinical Suspicion to Diagnosis: A Review of Diagnostic Approaches and Challenges in Fungal Keratitis
Authors: Toumasis Panagiotis , Tsantes Andreas G. , Tsiogka Anastasia , Samonis George , Vrioni Georgia
Published: January 2024

Fungal keratitis is a relatively rare yet severe ocular infection that can lead to profound vision impairment and even permanent vision loss. Rapid and accurate diagnosis plays a crucial role in the effective management of the disease. A patient’s history establishes the initial clinical suspicion since it can provide valuable clues to potential predisposing factors and sources of fungal exposure. Regarding the evaluation of the observed symptoms, they are not exclusive to fungal keratitis, but their timeline can aid in distinguishing fungal keratitis from other conditions. Thorough clinical examination of the affected eye with a slit-lamp microscope guides diagnosis because some clinical features are valuable predictors of fungal keratitis. Definitive diagnosis is established through appropriate microbiological investigations. Direct microscopic examination of corneal scrapings or biopsy specimens can assist in the presumptive diagnosis of fungal keratitis, but culture remains the gold standard for diagnosing fungal keratitis. Advanced molecular techniques such as PCR and MALDI-ToF MS are explored for their rapid and sensitive diagnostic capabilities. Non-invasive techniques like in vivo confocal microscopy (IVCM) and optical coherence tomography (OCT) are useful for real-time imaging. Every diagnostic technique has both advantages and drawbacks. Also, the selection of a diagnostic approach can depend on various factors, including the specific clinical context, the availability of resources, and the proficiency of healthcare personnel.
How Age Affects Graves’ Orbitopathy—A Tertiary Center Study
Authors: Oeverhaus Michael , Sander Julius , Smetana Nicolai , Bechrakis Nikolaos E. , Inga Neumann , Al-Ghazzawi Karim , Chen Ying , Eckstein Anja
Published: January 2024

Purpose: Graves’ orbitopathy (GO) is an autoimmune disorder leading to inflammation, adipogenesis, and fibrosis. The severity of GO can vary widely among individuals, making it challenging to predict the natural course of the disease accurately, which is important for tailoring the treatment approach to the individual patient. The aim of this study was to compare the clinical characteristics, course, treatment, and prognosis of GO patients under 50 years with older patients. Methods: We reviewed the medical records of a random sample of 1000 patients in our GO database Essen (GODE) comprising 4260 patients at our tertiary referral center. Patients were divided into two groups: Group 1 (≤50 years) and Group 2 (>50 years). Only patients with a complete data set were included in the further statistical analysis. Results: The results showed that younger patients (n = 484) presented significantly more often with mild GO (53% vs. 33%, p < 0.0001), while older patients (n = 448) were more likely to experience moderate-to-severe disease (44% vs. 64%, p < 0.0001). Older patients showed more severe strabismus, motility, and clinical activity scores (5.9 vs. 2.3 PD/310° vs. 330° both p < 0.0001, CAS: 2.1 vs. 1.7, p = 0.001). Proptosis and occurrence of dysthyroid optic neuropathy (DON) showed no significant difference between groups (both 3%). Multiple logistic regression revealed that the need for a second step of eye muscle surgery was most strongly associated with prior decompression (OR = 0.12, 95% CI: 0.1–0.2, p < 0.0001) followed by orbital irradiation and age. The model showed good fitness regarding the area under the curve (AUC = 0.83). Discussion: In conclusion, younger GO patients present with milder clinical features such as a lower rate of restrictive motility disorders and less pronounced inflammatory signs. Therefore, older patients tend to need more steroids, irradiation, and lid and eye muscle surgery. Still, the risk of DON and the necessity of secondary eye muscle surgery are not or only slightly associated with age, respectively.
The National Early Warning Score 2 with Age and Body Mass Index (NEWS2 Plus) to Determine Patients with Severe COVID-19 Pneumonia
Authors: Trongtrakul Konlawij , Tajarernmuang Pattraporn , Limsukon Atikun , Theerakittikul Theerakorn , Niyatiwatchanchai Nutchanok , Surasit Karjbundid , Glunriangsang Pimpimok , Liwsrisakun Chalerm , Bumroongkit Chaiwat , Pothirat Chaicharn , Inchai Juthamas , Chaiwong Warawut , Chanayat Panida , Deesomchok Athavudh
Published: January 2024

(1) Background: Early identification of severe coronavirus disease 2019 (COVID-19) pneumonia at the initial phase of hospitalization is very crucial. To address this, we validated and updated the National Early Warning Score 2 (NEWS2) for this purpose. (2) Methods: We conducted a study on adult patients with COVID-19 infection in Chiang Mai, Thailand, between May 2021 and October 2021. (3) Results: From a total of 725 COVID-19 adult patients, 350 (48.3%) patients suffered severe COVID-19 pneumonia. In determining severe COVID-19 pneumonia, NEWS2 and NEWS2 + Age + BMI (NEWS2 Plus) showed the C-statistic values of 0.798 (95% CI, 0.767–0.830) and 0.821 (95% CI, 0.791–0.850), respectively. The C-statistic values of NEWS2 Plus were significantly improved compared to those of NEWS2 alone (p = 0.012). Utilizing a cut-off point of five, NEWS2 Plus exhibited better sensitivity and negative predictive value than the traditional NEWS2, with values of 99.7% vs. 83.7% and 98.9% vs. 80.7%, respectively. (4) Conclusions: The incorporation of age and BMI into the traditional NEWS2 score enhanced the efficacy of determining severe COVID-19 pneumonia. Physicians can rely on NEWS2 Plus (NEWS2 + Age + BMI) as a more effective decision-making tool for triaging COVID-19 patients during early hospitalization.
Exploring 3D Pelvis Orientation: A Cross-Sectional Study in Athletes Engaged in Activities with and without Impact Loading and Non-Athletes
Authors: Glakousakis Georgios , Kalatzis Perikles , Mandalidis Dimitris
Published: January 2024

Female athletes subjected to various types of impact loading, especially over a long period of time, may experience changes in their pelvic orientation, which may affect their sport performance and increase the likelihood of injury. The aim of the present study was to determine whether female athletes involved in high-impact loading sports (HILS), odd-impact loading sports (OILS), and repetitive non-impact loading sports (NILS) demonstrate changes in pelvis orientation compared to non-athletes (NATH). Pelvic orientation was determined using Euler/Cardan angles, calculated from the coordinates of the right, and left anterior superior iliac spines and pubic symphysis via a novel method. Two-way ANOVA tests showed significant differences between groups for pelvis position in the frontal plane (p < 0.05), with HILS and OILS demonstrating greater pelvic obliquity compared to NILS athletes and NATH. Significant main effects were also obtained for directions within the sagittal plane (p < 0.001). Significant within-group differences were observed in sagittal pelvic position among female athletes engaged in NILS (p < 0.01) and non-athletes (NATH) (p < 0.05), with a greater anterior pelvic tilt compared to posterior. Our findings suggest that pelvis orientation in female athletes across sports is influenced by sport-specific impact loads, potentially affecting performance and injury occurrence.
Food Safety Aspects of Breeding Maize to Multi-Resistance against the Major (Fusarium graminearum, F. verticillioides, Aspergillus flavus) and Minor Toxigenic Fungi (Fusarium spp.) as Well as to Toxin Accumulation, Trends, and Solutions—A Review
Authors: Mesterhazy Akos
Published: January 2024

Maize is the crop which is most commonly exposed to toxigenic fungi that produce many toxins that are harmful to humans and animals alike. Preharvest grain yield loss, preharvest toxin contamination (at harvest), and storage loss are estimated to be between 220 and 265 million metric tons. In the past ten years, the preharvest mycotoxin damage was stable or increased mainly in aflatoxin and fumonisins. The presence of multiple toxins is characteristic. The few breeding programs concentrate on one of the three main toxigenic fungi. About 90% of the experiments except AFB1 rarely test toxin contamination. As disease resistance and resistance to toxin contamination often differ in regard to F. graminearum, F. verticillioides, and A. flavus and their toxins, it is not possible to make a food safety evaluation according to symptom severity alone. The inheritance of the resistance is polygenic, often mixed with epistatic and additive effects, but only a minor part of their phenotypic variation can be explained. All tests are made by a single inoculum (pure isolate or mixture). Genotype ranking differs between isolates and according to aggressiveness level; therefore, the reliability of such resistance data is often problematic. Silk channel inoculation often causes lower ear rot severity than we find in kernel resistance tests. These explain the slow progress and raise skepticism towards resistance breeding. On the other hand, during genetic research, several effective putative resistance genes were identified, and some overlapped with known QTLs. QTLs were identified as securing specific or general resistance to different toxicogenic species. Hybrids were identified with good disease and toxin resistance to the three toxigenic species. Resistance and toxin differences were often tenfold or higher, allowing for the introduction of the resistance and resistance to toxin accumulation tests in the variety testing and the evaluation of the food safety risks of the hybrids within 2–3 years. Beyond this, resistance breeding programs and genetic investigations (QTL-analyses, GWAM tests, etc.) can be improved. All other research may use it with success, where artificial inoculation is necessary. The multi-toxin data reveal more toxins than we can treat now. Their control is not solved. As limits for nonregulated toxins can be introduced, or the existing regulations can be made to be stricter, the research should start. We should mention that a higher resistance to F. verticillioides and A. flavus can be very useful to balance the detrimental effect of hotter and dryer seasons on aflatoxin and fumonisin contamination. This is a new aspect to secure food and feed safety under otherwise damaging climatic conditions. The more resistant hybrids are to the three main agents, the more likely we are to reduce the toxin losses mentioned by about 50% or higher.