bluuebunny/crossref_metadata_2025 huggingface dataset:
A Novel Hybrid Unsupervised Learning Approach for Enhanced Cybersecurity in the IoT
Authors: Kaliyaperumal Prabu , Periyasamy Sudhakar , Thirumalaisamy Manikandan , Balusamy Balamurugan , Benedetto Francesco
Published: July 2024

The proliferation of IoT services has spurred a surge in network attacks, heightening cybersecurity concerns. Essential to network defense, intrusion detection and prevention systems (IDPSs) identify malicious activities, including denial of service (DoS), distributed denial of service (DDoS), botnet, brute force, infiltration, and Heartbleed. This study focuses on leveraging unsupervised learning for training detection models to counter these threats effectively. The proposed method utilizes basic autoencoders (bAEs) for dimensionality reduction and encompasses a three-stage detection model: one-class support vector machine (OCSVM) and deep autoencoder (dAE) attack detection, complemented by density-based spatial clustering of applications with noise (DBSCAN) for attack clustering. Accurately delineated clusters aid in mapping attack tactics. The MITRE ATT&CK framework establishes a “Cyber Threat Repository”, cataloging attacks and tactics, enabling immediate response based on priority. Leveraging preprocessed and unlabeled normal network traffic data, this approach enables the identification of novel attacks while mitigating the impact of imbalanced training data on model performance. The autoencoder method utilizes reconstruction error, OCSVM employs a kernel function to establish a hyperplane for anomaly detection, while DBSCAN employs a density-based approach to identify clusters, manage noise, accommodate diverse shapes, automatically determining cluster count, ensuring scalability, and minimizing false positives and false negatives. Evaluated on standard datasets such as CIC-IDS2017 and CSECIC-IDS2018, the proposed model outperforms existing state of art methods. Our approach achieves accuracies exceeding 98% for the two datasets, thus confirming its efficacy and effectiveness for application in efficient intrusion detection systems.
Flame Resistance Performance of Silicone Pad for Application in Railway Industry
Authors: Jang Hong-Lae , Kwon Tae-Soon , Kang Seok-Won , Choi Kyungwho
Published: July 2024

This study investigates the applicability of eco-friendly silicone materials with improved flame retardancy as interior materials for Korean urban railway vehicles, focusing on developing nonslip pads for seats made of non-combustible materials. Fire safety standards vary worldwide, necessitating country-specific testing and analysis. For application to the interior of railway vehicles in Korea, technical standards for the flame-retardant performance of railway vehicles were evaluated, and nonslip pads for seats were tested by comparing two types of flame-retardant silicone. In addition to fire property testing on a specimen basis, experimental verification was performed on a full chair assembly including silicone pads. Passenger comfort testing through pressure measurements was also conducted alongside fire safety performance testing The actual fire test showed that the maximum average heat release rate value was about 20% lower than the standard’s upper limit. Using flame-retardant silicone pads enhances fire safety and passenger comfort, satisfactorily meeting the required performance standards for Korean railway vehicles.
Investigations of the Fire Behavior of Functionally Graded Concrete Slabs with Mineral Hollow Spheres
Authors: Strahm Benedikt , Haufe Carl Niklas , Blandini Lucio
Published: July 2024

Functionally Graded Concrete (FGC) allows for a significant reduction in the mass of concrete components while maintaining their structural and functional requirements and improving recycling capacity. This is achieved by inserting spherical mineral hollow bodies into the structure where no material is required. Within the scope of this work, the behavior of FGC slabs exposed to fire is investigated both experimentally and numerically and compared to a corresponding solid cross-section. Therefore, FGC specimens are placed in a test furnace and subjected to fire exposure for 90 min. The temperature distribution, bending load-bearing capacity, and spalling behavior are investigated. The results of the numerical simulation of the solid cross-section are in good agreement with the values provided in the building code. However, for the FGC cross-section, differences in temperature at characteristic measurement points between the experimental and numerical results are observed, presumably due to convection. The experimental results suggest that the bending load-bearing capacity of the investigated FGC cross-section could be potentially greater than that of a corresponding solid cross-section. Furthermore, as expected through analytical analysis, the fire tests confirm that no spalling of the FGC specimens occurred.
Two Distinct Maternal Lineages of Threespine Stickleback (Gasterosteus aculeatus) in a Small Norwegian Subarctic Lake
Authors: Karlsen Bård Ove , Adhikari Dhurba , Jørgensen Tor Erik , Hanssen Ida Klykken , Moum Truls Borg , Nordeide Jarle Tryti , Johansen Steinar Daae
Published: July 2024

A subarctic Norwegian watercourse is known for its population of threespine sticklebacks (Gasterosteus aculeatus Linnaeus 1758) with unusual pelvic spine polymorphism; the upper lake contains a mixture of specimens that are normal-spined, asymmetric-spined, and spineless. In contrast, the downstream lakes and the nearby marine site contain only the normal spined morph. We investigated the maternal-line genetic structure in the watercourse using mitogenomics. A total of 242 sticklebacks representing two lakes and a marine site were assessed based on individual and pooled DNA sequencing. While two distinct mitogenome clades were detected in the upper lake (Lake Storvatnet), only one of these clades was present in the downstream lake. The marine site pooled DNA sample, however, contained several mitogenome haplotypes. We present mitogenome sequence features that include gene-specific single nucleotide polymorphisms, molecular phylogeny, and genetic differentiation assessments based on pairwise comparisons of pooled population samples from each site. The Lake Storvatnet mitogenomes belong to two distinct Euro-North American (ENA) clades; one of the ancestral lineages likely corresponds to the original maternal lineage in the watercourse, and the other was introduced more recently. We hypothesize that the second invader carried nuclear genomic features responsible for the observed present-day pelvic spine polymorphism in Lake Storvatnet.
Microbial Decontamination of Cuminum cyminum Seeds Using “Intensification of Vaporization by Decompression to the Vacuum”: Effect on Color Parameters and Essential Oil Profile
Authors: Tannir Hana , Debs Espérance , Mansour Georges , Neugart Susanne , El Hage Rima , Khalil Mahmoud I. , El Darra Nada , Louka Nicolas
Published: July 2024

Cumin seeds are frequently utilized in herbal infusions and as flavoring agents in home cuisine. Nevertheless, studies have demonstrated that spices are frequently contaminated with pathogenic bacteria, including bacterial spores. The aim of this study was to assess the effectiveness of a new decontamination method called “Intensification of Vaporization by Decompression to the Vacuum” (IVDV) on intentionally contaminated Cuminum cyminum seeds. The study also examined the impact of this treatment on the color and oil profile of the treated samples. The untreated samples were inoculated with Escherichia coli (ATCC 25922) and Salmonella Typhimurium (ATCC 14028) and then subjected to IVDV treatment. Response surface methodology was employed to obtain safe, high-quality cumin seeds presenting a balance between microbial load, color, and oil profile. The optimal IVDV conditions were achieved at a pressure of 3.5 bar and a time of 133.45 s, resulting in typical 4 log reductions observed with 99.99% of Escherichia coli and Salmonella Typhimurium inactivation. The treated spices presented a mild color modification compared to the untreated ones, manifested by a darker shade (decreased L* value), reduced greenness (increased a* value), and heightened yellowness (increased b* value). The GC-MS analysis detected the existence of seven compounds in the treated cumin, with cuminaldehyde being the primary compound (83.79%). Furthermore, the use of IVDV treatment resulted in an increase in the total content of essential oils in some samples, whereby six monoterpenes were identified in the untreated sample compared to seven monoterpenes in IVDV-treated samples. This innovative technology demonstrated high efficacy in decontaminating C. cyminum seeds, improving the extractability of the essential oils while only slightly affecting the color.
Bioactivity-Guided Isolation of Secondary Metabolites with Antioxidant and Antimicrobial Activities from Camellia fascicularis
Authors: Li Ruonan , Tang Jiandong , Li Jingjing , Wu Boxiao , Tang Junrong , Kan Huan , Zhao Ping , Zhang Yingjun , Wang Weihua , Liu Yun
Published: July 2024

Camellia fascicularis has important ornamental, medicinal, and food values, which also have tremendous potential for exploiting bioactivities. We performed the bioactivity-guided (antioxidant and antimicrobial) screening of eight fractions obtained from the ethyl acetate phase of C. fascicularis. The antioxidant activity was measured by DPPH, ABTS, and FRAP, and the antibacterial activity was measured by the minimum inhibitory concentration (MIC) of Pseudomonas aeruginosa, Escherichia coli, and Staphylococcus aureus. The results of bioactivity-guided isolation indicated that the major antioxidant compounds in the ethanolic extracts of C. fascicularis may be present in fractions (Fr.) (A–G, obtained after silica gel column chromatography). Fr. (D–I, obtained after silica gel column chromatography) is a fraction of C. fascicularis with antimicrobial activity. The structures of compounds were determined by spectral analysis and nuclear magnetic resonance (NMR) combined with the available literature on secondary metabolites of C. fascicularis leaves. In this study, 17 compounds were identified, including four phenolics (1, 3–4, and 14), a phenylpropane (2), five terpenoids (5–7, 12, and 15), four flavonoids and flavonoid glycosides (8–10 and 16), and two lignins (13 and 17). Compounds 4–7, 13–15, and 17 were isolated from the genus Camellia for first time. The remaining compounds were also isolated from C. fascicularis for first time. The evaluation of antioxidant and antimicrobial activities revealed that compounds 1, 3, 9, 11, and 17 exhibited higher antioxidant activity than the positive control drug (ascorbic acid), and compounds 4, 8, 10, and 13 showed similar activity to ascorbic acid. The other compounds had weaker or no significant antioxidant activities. The MIC of antibacterial activity for compounds 4, 7, and 11–13 against P. aeruginosa was comparable to that of the positive control drug tetracycline at 125 µg/mL, and other secondary metabolites inhibited E. coli and S. aureus at 250–500 µg/mL. This is also the first report of antioxidant and antimicrobial activities of compounds 5–7, 13–15, and 17. The results of the study enriched the variety of secondary metabolites of C. fascicularis and laid the foundation for further research on the pharmacological efficacy and biological activity of this plant.
Advances in Chromatographic Analysis of Phenolic Phytochemicals in Foods: Bridging Gaps and Exploring New Horizons
Authors: Custodio-Mendoza Jorge Antonio , Pokorski Patryk , Aktaş Havva , Napiórkowska Alicja , Kurek Marcin Andrzej
Published: July 2024

Chromatographic analysis of phenolic phytochemicals in foods has significantly advanced over the past decade (2014–2024), meeting increasing demands for precision and efficiency. This review covers both conventional and advanced chromatographic techniques used for detecting phenolic phytochemicals in foods. Conventional methods like High-Performance Liquid Chromatography, Ultra High-Performance Liquid Chromatography, Thin-Layer Chromatography, and Gas Chromatography are discussed, along with their benefits and limitations. Advanced techniques, including Hydrophilic Interaction Liquid Chromatography, Nano-LC, Multidimensional Liquid Chromatography, and Capillary Electrophoresis, are highlighted for their innovations and improved capabilities. The review addresses challenges in current chromatographic methods, emphasizing the need for standardized and validated procedures according to the Food and Drug Administration, European Cooperation for Accreditation of Laboratories, and The International Organization for Standardization guidelines to ensure reliable and reproducible results. It also considers novel strategies for reducing the environmental impact of chromatographic methods, advocating for sustainable practices in analytical chemistry.
Deep Learning-Based Automated Cell Detection-Facilitated Meat Quality Evaluation
Authors: Zheng Hui , Zhao Nan , Xu Saifei , He Jin , Ospina Ricardo , Qiu Zhengjun , Liu Yufei
Published: July 2024

Meat consumption is increasing globally. The safety and quality of meat are considered important issues for human health. During evaluations of meat quality and freshness, microbiological parameters are often analyzed. Counts of indicator cells can provide important references for meat quality. In order to eliminate the error of manual operation and improve detection efficiency, this paper proposed a Convolutional Neural Network (CNN) with a backbone called Detect-Cells-Rapidly-Net (DCRNet), which can identify and count stained cells automatically. The DCRNet replaces the single channel of residual blocks with the aggregated residual blocks to learn more features with fewer parameters. The DCRNet combines the deformable convolution network to fit flexible shapes of stained animal cells. The proposed CNN with DCRNet is self-adaptive to different resolutions of images. The experimental results indicate that the proposed CNN with DCRNet achieves an Average Precision of 81.2% and is better than traditional neural networks for this task. The difference between the results of the proposed method and manual counting is less than 0.5% of the total number of cells. The results indicate that DCRNet is a promising solution for cell detection and can be equipped in future meat quality monitoring systems.
Dental Age Estimation Using Periodontal Ligament Visibility and Root Pulp Volume at the 18-Year Threshold in the Chinese Population
Authors: Khan Wafa , Jayaraman Jayakumar
Published: July 2024

Background: The concept of comparing “chronological age” vs. that of “dental age” has been well documented. Considering ethnic variations in dental development, the use of population-specific standards for age estimation has been emphasized. Mandibular maturity markers have been successfully employed to estimate the age of a person at the 18-year threshold. No such data are available for the Chinese population, which represents around one-fifth of the global human population. Aim: The aim of this research project was to analyze and grade mandibular third molars using maturity markers in the Chinese population. Materials and Methods: In total, 882 panoramic radiographs (424 females and 458 males) of 16- to 24-year-old Chinese children and young adults were obtained from patient archives. All patients were graded by a trained and calibrated examiner using stages A-D for mandibular maturity markers including Periodontal Ligament Visibility (PLV) and Root Pulp Volume (RPV). Results: The average Age at Assessment (AaA) ranged from 18.79 years for females in Stage A of PLV to 21.59 years for females in Stage D of PLV. The AaA was not statistically significant between females and males across all the stages, for both PLV and RPV. For PLV, the percentage of females below 18 years was 57.14% in Stage A and 17.14% in Stage D. For males, it was 48.84% in Stage A and 14.93% in Stage D. For RPV, the percentage of females below 18 years was 54.72% in Stage A and 12.73% in Stage D. For males, it was 49.09% in Stage A and 14.81% in Stage D. On average, for PLV, 85.30% of subjects were over 18 years of age in Stages C and D, and for RPV, 82.50% subjects were over 18 years of age in Stages C and D. Conclusions: Both RPV and PLV are considered as reliable maturity markers to estimate the age of Chinese subjects in the 18-year threshold. No difference was observed in the average Age at Assessment of mandibular maturity stages between the sexes.
On the Value of the Cosmological Constant in Entropic Gravity
Authors: Schlatter Andreas
Published: July 2024

We explicitly calculate the value of the cosmological constant, Λ, based on the recently developed theory connecting entropic gravity with quantum events induced by transactions, called transactional gravity. We suggest a novel interpretation of the cosmological constant and rigorously show its inverse proportionality to the squared radius of the causal universe Λ~RU−2.
Examination of the Expression Profile of Resistance Genes in Yuanjiang Common Wild Rice (Oryza rufipogon)
Authors: Kan Wang , Chen Ling , Wang Bo , Liu Li , Yin Fuyou , Zhong Qiaofang , Li Jinlu , Zhang Dunyu , Xiao Suqin , Zhang Yun , Jiang Cong , Yu Tengqiong , Wang Yunyue , Cheng Zaiquan
Published: July 2024

The rice blight poses a significant threat to the rice industry, and the discovery of disease-resistant genes is a crucial strategy for its control. By exploring the rich genetic resources of Yuanjiang common wild rice (Oryza rufipogon) and analyzing their expression patterns, genetic resources can be provided for molecular rice breeding. The target genes’ expression patterns, subcellular localization, and interaction networks were analyzed based on the annotated disease-resistant genes on the 9th and 10th chromosomes in the rice genome database using fluorescent quantitative PCR technology and bioinformatics tools. Thirty-three disease-resistant genes were identified from the database, including 20 on the 9th and 13 on the 10th. These genes were categorized into seven subfamilies of the NLR family, such as CNL and the G subfamily of the ABC family. Four genes were not expressed under the induction of the pathogen Y8, two genes were significantly down-regulated, and the majority were up-regulated. Notably, the expression levels of nine genes belonging to the ABCG, CN, and CNL classes were significantly up-regulated, yet the expression levels varied among roots, stems, and leaves; one was significantly expressed in the roots, one in the stems, and the remaining seven were primarily highly expressed in the leaves. Two interaction network diagrams were predicted based on the seven highly expressed genes in the leaves: complex networks regulated by CNL proteins and specific networks controlled by ABCG proteins. The disease-resistant genes on the 9th chromosome are actively expressed in response to the induction of rice blight, forming a critical gene pool for the resistance of Yuanjiang common wild rice (O. rufipogon) to rice blight. Meanwhile, the disease-resistant genes on the 10th chromosome not only participate in resisting the rice blight pathogen but may also be involved in the defense against other stem diseases.
A Comparison of Structural Variant Calling from Short-Read and Nanopore-Based Whole-Genome Sequencing Using Optical Genome Mapping as a Benchmark
Authors: Pei Yang , Tanguy Melanie , Giess Adam , Dixit Abhijit , Wilson Louise C. , Gibbons Richard J. , Twigg Stephen R. F. , Elgar Greg , Wilkie Andrew O. M.
Published: July 2024

The identification of structural variants (SVs) in genomic data represents an ongoing challenge because of difficulties in reliable SV calling leading to reduced sensitivity and specificity. We prepared high-quality DNA from 9 parent–child trios, who had previously undergone short-read whole-genome sequencing (Illumina platform) as part of the Genomics England 100,000 Genomes Project. We reanalysed the genomes using both Bionano optical genome mapping (OGM; 8 probands and one trio) and Nanopore long-read sequencing (Oxford Nanopore Technologies [ONT] platform; all samples). To establish a “truth” dataset, we asked whether rare proband SV calls (n = 234) made by the Bionano Access (version 1.6.1)/Solve software (version 3.6.1_11162020) could be verified by individual visualisation using the Integrative Genomics Viewer with either or both of the Illumina and ONT raw sequence. Of these, 222 calls were verified, indicating that Bionano OGM calls have high precision (positive predictive value 95%). We then asked what proportion of the 222 true Bionano SVs had been identified by SV callers in the other two datasets. In the Illumina dataset, sensitivity varied according to variant type, being high for deletions (115/134; 86%) but poor for insertions (13/58; 22%). In the ONT dataset, sensitivity was generally poor using the original Sniffles variant caller (48% overall) but improved substantially with use of Sniffles2 (36/40; 90% and 17/23; 74% for deletions and insertions, respectively). In summary, we show that the precision of OGM is very high. In addition, when applying the Sniffles2 caller, the sensitivity of SV calling using ONT long-read sequence data outperforms Illumina sequencing for most SV types.
Genetic Analysis of 252 Index Cases with Inherited Retinal Diseases Using a Panel of 351 Retinal Genes
Authors: Abu Elasal Maria , Mousa Samira , Salameh Manar , Blumenfeld Anat , Khateb Samer , Banin Eyal , Sharon Dror
Published: July 2024

Inherited retinal diseases (IRDs) are extremely heterogeneous with at least 350 causative genes, complicating the process of genetic diagnosis. We analyzed samples of 252 index cases with IRDs using the Blueprint Genetics panel for “Retinal Dystrophy” that includes 351 genes. The cause of disease could be identified in 55% of cases. A clear difference was obtained between newly recruited cases (74% solved) and cases that were previously analyzed by panels or whole exome sequencing (26% solved). As for the mode of inheritance, 75% of solved cases were autosomal recessive (AR), 10% were X-linked, 8% were autosomal dominant, and 7% were mitochondrial. Interestingly, in 12% of solved cases, structural variants (SVs) were identified as the cause of disease. The most commonly identified genes were ABCA4, EYS and USH2A, and the most common mutations were MAK-c.1297_1298ins353 and FAM161A-c.1355_1356del. In line with our previous IRD carrier analysis, we identified heterozygous AR mutations that were not the cause of disease in 36% of cases. The studied IRD panel was found to be efficient in gene identification. Some variants were misinterpreted by the pipeline, and therefore, multiple analysis tools are recommended to obtain a more accurate annotation of potential disease-causing variants.
TP53 p.R337H Germline Variant among Women at Risk of Hereditary Breast Cancer in a Public Health System of Midwest Brazil
Authors: Corrêa Tatiana Strava , Asprino Paula Fontes , de Oliveira Eduarda Sabá Cordeiro , Leite Ana Carolina Rathsam , Weis Luiza , Achatz Maria Isabel , de Oliveira Claudiner Pereira , Sandoval Renata Lazari , Barroso-Sousa Romualdo
Published: July 2024

Despite the high prevalence of TP53 pathogenic variants (PV) carriers in the South and Southeast regions of Brazil, germline genetic testing for hereditary breast cancer (HBC) is not available in the Brazilian public health system, and the prevalence of Li-Fraumeni syndrome (LFS) is not well established in other regions of Brazil. We assessed the occurrence of TP53 p.R337H carriers among women treated for breast cancer (BC) between January 2021 and January 2022 at public hospitals of Brasilia, DF, Brazil. A total of 180 patients who met at least one of the NCCN criteria for HBC underwent germline testing; 44.4% performed out-of-pocket germline multigene panel testing, and 55.6% were tested for the p.R337H variant by allelic discrimination PCR. The median age at BC diagnosis was 43.5 years, 93% had invasive ductal carcinoma, 50% had estrogen receptor-positive/HER2 negative tumors, and 41% and 11% were diagnosed respectively at stage III and IV. Two patients (1.11%) harbored the p.R337H variant, and cascade family testing identified 20 additional carriers. The TP53 p.R337H detection rate was lower than that reported in other studies from south/southeast Brazil. Nonetheless, identifying TP53 PV carriers through genetic testing in the Brazilian public health system could guide cancer treatment and prevention.
Challenges of Preimplantation Genetic Counselling in the Context of Cystic Fibrosis and Other CFTR-Related Disorders: A Monocentric Experience in a Cohort of 92 Couples
Authors: Sorrentino Ugo , Menegazzo Massimo , Gabbiato Ilaria , Calosci Davide , Zambon Carlo Federico , Zuccarello Daniela
Published: July 2024

Cystic fibrosis is a highly prevalent genetic disorder caused by biallelic pathogenic variants in the CFTR gene, causing an altered function of the exocrine glands and a subsequent spectrum of hypofunctional and degenerative manifestations. The increasing availability of carrier screening programmes, the enhanced life expectancy of patients due to improved treatment and care strategies and the development of more precise and affordable molecular diagnostic tools have prompted a rise in demand of prenatal diagnosis procedures for at-risk couples, including Preimplantation Genetic Testing (PGT). However, challenges remain: heterogeneity among screening programmes, nuances of variant interpretation and availability of novel treatments demand a considerate and knowledgeable approach to genetic counselling. In this work, we retrospectively evaluated the molecular data of 92 unselected couples who received a diagnosis of CFTR-related status and were referred to the genetics clinic at the University Hospital of Padua for genetic counselling on eligibility for PGT. A total of 50 couples were considered eligible for the procedure based on risk of transmitting biallelic pathogenic variants. We report and discuss our experience with this case series in the context of the Italian medical care system and present an overview of the most relevant issues regarding genetic counselling for PGT in CFTR-related disorders.
GENet: A Graph-Based Model Leveraging Histone Marks and Transcription Factors for Enhanced Gene Expression Prediction
Authors: Labani Mahdieh , Beheshti Amin , O’Brien Tracey A.
Published: July 2024

Understanding the regulatory mechanisms of gene expression is a crucial objective in genomics. Although the DNA sequence near the transcription start site (TSS) offers valuable insights, recent methods suggest that analyzing only the surrounding DNA may not suffice to accurately predict gene expression levels. We developed GENet (Gene Expression Network from Histone and Transcription Factor Integration), a novel approach that integrates essential regulatory signals from transcription factors and histone modifications into a graph-based model. GENet extends beyond simple DNA sequence analysis by incorporating additional layers of genetic control, which are vital for determining gene expression. Our method markedly enhances the prediction of mRNA levels compared to previous models that depend solely on DNA sequence data. The results underscore the significance of including comprehensive regulatory information in gene expression studies. GENet emerges as a promising tool for researchers, with potential applications extending from fundamental biological research to the development of medical therapies.
Using Genetics to Investigate Relationships between Phenotypes: Application to Endometrial Cancer
Authors: Bouttle Kelsie , Ingold Nathan , O’Mara Tracy A.
Published: July 2024

Genome-wide association studies (GWAS) have accelerated the exploration of genotype–phenotype associations, facilitating the discovery of replicable genetic markers associated with specific traits or complex diseases. This narrative review explores the statistical methodologies developed using GWAS data to investigate relationships between various phenotypes, focusing on endometrial cancer, the most prevalent gynecological malignancy in developed nations. Advancements in analytical techniques such as genetic correlation, colocalization, cross-trait locus identification, and causal inference analyses have enabled deeper exploration of associations between different phenotypes, enhancing statistical power to uncover novel genetic risk regions. These analyses have unveiled shared genetic associations between endometrial cancer and many phenotypes, enabling identification of novel endometrial cancer risk loci and furthering our understanding of risk factors and biological processes underlying this disease. The current status of research in endometrial cancer is robust; however, this review demonstrates that further opportunities exist in statistical genetics that hold promise for advancing the understanding of endometrial cancer and other complex diseases.
A Review of Experimental Studies on Natural Chalcone-Based Therapeutic Targeting of Genes and Signaling Pathways in Type 2 Diabetes Complications
Authors: Alsharairi Naser
Published: July 2024

Diabetes mellitus type 2 (T2DM) is a common chronic condition that presents as unsettled hyperglycemia (HG) and results from insulin resistance (IR) and β-cell dysfunction. T2DM is marked by an increased risk of microvascular and macrovascular complications, all of which can be the cause of increasing mortality. Diabetic nephropathy (DNE), neuropathy (DNU), and retinopathy (DR) are the most common complications of diabetic microangiopathy, while diabetic cardiomyopathy (DCM) and peripheral vascular diseases are the major diabetic macroangiopathy complications. Chalcones (CHs) are in the flavonoid family and are commonly found in certain plant species as intermediate metabolites in the biosynthesis of flavonoids and their derivatives. Natural CHs with different substituents exert diverse therapeutic activities, including antidiabetic ones. However, the therapeutic mechanisms of natural CHs through influencing genes and/or signaling pathways in T2DM complications remain unknown. Therefore, this review summarizes the existing results from experimental models which highlight the mechanisms of natural CHs as therapeutic agents for T2DM complications.
MicroRNA166: Old Players and New Insights into Crop Agronomic Traits Improvement
Authors: Zhang Zhanhui , Yang Tianxiao , Li Na , Tang Guiliang , Tang Jihua
Published: July 2024

MicroRNA (miRNA), a type of non-coding RNA, is crucial for controlling gene expression. Among the various miRNA families, miR166 stands out as a highly conserved group found in both model and crop plants. It plays a key role in regulating a wide range of developmental and environmental responses. In this review, we explore the diverse sequences of MIR166s in major crops and discuss the important regulatory functions of miR166 in plant growth and stress responses. Additionally, we summarize how miR166 interacts with other miRNAs and highlight the potential for enhancing agronomic traits by manipulating the expression of miR166 and its targeted HD-ZIP III genes.
Research on the Influence of Spatial Dimensions on the Stability of Large-Scale Slopes under Heavy Rainfall
Authors: Li Xun , Jiang Yujing , Sugimoto Satoshi
Published: July 2024

In engineering practice, slope stability is commonly assessed using a two-dimensional (2D) analysis under the assumption of plane strain conditions. However, when dealing with the complex surface geometries of three-dimensional (3D) slopes, especially under short-term heavy rainfall conditions, relying solely on a 2D cross-sectional analysis may not always yield conservative results compared to 3D slope stability assessments. To investigate the applicability of using 2D cross-sections to represent 3D slopes, this study examines the influence of surface geometries on 3D slope stability. By varying the degree and frequency of surface undulations along a certain longitudinal length of the slope, as well as different variations in slope gradient, the impacts of these factors on the safety factor of 3D slopes under rainfall conditions are analyzed. The findings indicate that for 3D slopes with significant surface undulations and high-frequency variations, the safety factor is generally lower compared to that obtained from the 2D cross-sectional analysis. Furthermore, the variation in slope gradient has a more pronounced effect on the safety factor of 3D slopes compared to surface undulations, particularly when the slope gradients are larger than 50°. Therefore, the influence of spatial dimensions on the stability of slopes can be significant when dealing with complex surface geometries of 3D large-scale slopes. It is highly recommended to conduct both 3D and 2D analyses to ensure the accuracy of the slope stability analysis.
The Impact of a Gluten-Free Diet on Pregnant Women with Celiac Disease: Do We Need a Guideline to Manage Their Health?
Authors: Serin Yeliz , Manini Camilla , Amato Pasqualino , Verma Anil K.
Published: July 2024

A healthy and balanced diet is a critical requirement for pregnant women as it directly influences both the mother’s and infant’s health. Poor maternal nutrition can lead to pregnancy-related complications with undesirable effects on the fetus. This requirement is equally important for pregnant women with celiac disease (CD) who are already on a gluten-free diet (GFD). Although the GFD is the sole treatment option for CD, it still presents some challenges and confusion for celiac women who wish to conceive. Poorly managed CD has been linked to miscarriages, preterm labor, low birth weight, and stillbirths. Current CD guidelines primarily focus on screening, diagnosis, treatment, and management but lack an evidence-based approach to determine appropriate energy requirements, recommended weight gain during pregnancy, target macronutrient distribution from the diet, the recommended intake of vitamins and minerals from diet and/or supplementation, timing for starting supplementation, and advised portions of gluten-free foods during pregnancy. We recommend and call for the development of such guidelines and/or authoritative papers in the future.
The Lady on the Sofa: Revisiting Elizabeth Barrett Browning’s Illness
Authors: Quirarte-Ruvalcaba Isadora
Published: July 2024

If there is one poet who has been widely represented under a legendary light, it is Elizabeth Barrett Browning (1806–1861), mostly through the figure of a secluded invalid. Barrett Browning’s illness and death have been romanticised ever since her own time, with multiple rumours and theories mostly focusing on the fact that her illness was ‘miraculously dispelled’ by ‘love’ and only reappeared gradually to take the poet’s life. This article proposes yet another and quite different diagnosis for Barrett Browning’s illness, theorising on the possibility that Barrett Browning’s ailment was a pulmonary congenital malformation, which remained misdiagnosed due to the lack of medical technology at the time. Several of the diagnoses given to Barrett Browning by her medical practitioners, contemporary and posthumous biographers and other scholars are presented and compared, alongside my own hypothesis. In addition, Barrett Browning’s arguable morphine dependency is reassessed in order to explore its impact on her illness, with the possibility that it exacerbated or even caused some of her symptoms. This reassessment also explores the role that morphine played in Barrett Browning’s death, suggesting an accidental overdose possibly overlooked by Robert Browning.
Recommendations for Upper Limb Motor Recovery: An Overview of the UK and European Rehabilitation after Stroke Guidelines (2023)
Authors: O’Flaherty Daniel , Ali Khalid
Published: July 2024

Upper limb impairment is common after stroke, with a significant impact on the stroke survivor’s function, social participation and quality of life. Clinical guidelines are needed to inform clinical practise, tailor interventions to improve outcomes and address unresolved research questions. This review contributes to the evidence guiding clinical practise for upper limb motor recovery after stroke by summarising the recommendations from the UK rehabilitation guidelines (National Institute for Health and Care Excellence (NICE) and the Intercollegiate Stroke Working Party (ISWP)) and the European Stroke Organisation (ESO) guidelines, all published in 2023. All three guidelines target researchers, clinical practitioners, stroke survivors and their social networks. An important feature in all three guidelines was therapeutic intensity, with all guidelines recommending increased therapeutic intensity. Unlike the ESO, the NICE and ISWP additionally include specific research recommendations. While the NICE guidelines seem more holistic and target a wider audience, the three guidelines are complimentary. We recommend that a future consensus statement should be developed in partnership between all three organisations, agreeing on scope and using the same terminology, on recommendations to improve stroke rehabilitation in the UK and Europe.
Artificial Intelligence at the Interface between Cultural Heritage and Photography: A Systematic Literature Review
Authors: Silva Carmen , Oliveira Lídia
Published: July 2024

Artificial intelligence has inspired a significant number of studies on the interface between cultural heritage and photography. The aims of these studies are, among others, to streamline damage monitoring or diagnoses for heritage preservation, enhance the production of high-fidelity 3D models of cultural assets, or improve the analysis of heritage images using computer vision. This article presents the results of a systematic literature review to highlight the recent state of these studies, published in the last five years and available in the Scopus, Web of Science, and JSTOR databases. The aim is to identify the potential and challenges of artificial intelligence through the connection between cultural heritage and photography, the latter of which represents a relevant methodological aspect in these investigations. In addition to the advances exemplified, the vast majority of studies indicate that there are also many obstacles to overcome. In particular, there is a need to improve artificial intelligence methods that still have significant flaws. These include inaccuracy in the automatic classification of images and limitations in the applications of the results. This article also aims to reflect on the meaning of these innovations when considering the direction of the relationship between cultural heritage and photography.
Correction: Sharma et al. Estimation of Heterosis and the Combining Ability Effect for Yield and Its Attributes in Field Pea (Pisum sativum L.) Using PCA and GGE Biplots. Horticulturae 2023, 9, 256
Authors: Sharma Amit , Yadav Rajesh , Sheoran Ravika , Kaushik Deepak , Mohanta Tapan Kumar , Sharma Kartik , Yadav Alpa , Dhanda Parmdeep Singh , Kaushik Prashant
Published: July 2024

The Horticulturae Editorial Office wishes to make the following changes to the author’s paper [...]
Genome-Wide Identification of Litchi SPL Gene Family and Expression Analysis in Pericarp Anthocyanin Biosynthesis
Authors: Xu Ziqiang , Wu Jiayun , Jing Xiangyang , Khan Faiza Shafique , Chen Yanzhao , Chen Zhe , Zhang Hongna , Wei Yongzan
Published: July 2024

During the ripening of litchi (Litchi chinensis Sonn.) fruit, anthocyanin biosynthesis is crucial in providing vibrant coloring. Previous studies on anthocyanin-related transcription factors have made significant discoveries relating to plants. However, the role of the SQUAMOSA promoter-binding protein-like (SPL) transcription factors in anthocyanin biosynthesis has rarely been studied in litchi. SPL genes are widely involved in the developmental mechanisms of plants. In this study, a total of 17 SPL genes have been identified from the litchi genome. Phylogenetic analysis revealed that these genes were divided into eight groups (Group I-VIII). Analysis of gene structure conserved domains, conserved motifs, and miR156 target prediction showed that LcSPLs were highly conserved during evolution. RNA-seq analysis of litchi revealed that six LcSPL genes have a role in regulating anthocyanin biosynthesis. Further, weighted correlation network analysis (WGCNA) revealed LcSPL7’s role in anthocyanin synthesis and chlorophyll degradation in litchi fruit ripening. These findings collectively suggest that the LcSPL gene family plays an essential role in anthocyanin biosynthesis in litchi pericarp. In summary, comprehensive bioinformatics analysis of the SPL family expands our understanding of anthocyanin synthesis in litchi pericarp.
Proprotein Convertase Subtilisin/Kexin Type 9 Induction in COVID-19 Is Poorly Associated with Disease Severity and Cholesterol Levels
Authors: Mester Patricia , Amend Pablo , Schmid Stephan , Wenzel Jürgen J. , Höring Marcus , Liebisch Gerhard , Krautbauer Sabrina , Müller Martina , Buechler Christa , Pavel Vlad
Published: July 2024

SARS-CoV-2 infection was shown to induce proprotein convertase subtilisin/kexin type 9 (PCSK9) plasma levels in sepsis. Here, we investigate the association between serum PCSK9 levels and disease severity. PCSK9 was measured in serum of 55 controls, 40 patients with moderate and 60 patients with severe COVID-19 disease. Serum PCSK9 was elevated in moderate COVID-19 compared to controls and further increased in severe cases. PCSK9 levels were not associated with C-reactive protein, bacterial superinfections, interventions, or survival in patients with severe COVID-19. PCSK9 regulates circulating cholesterol levels, and 15 cholesteryl ester (CE) species and free cholesterol (FC) were quantified by direct flow injection analysis using a high-resolution hybrid quadrupole-Orbitrap mass spectrometer. Most CE species with shorter fatty acid chains were decreased in severe compared to moderate COVID-19, and none of the CE species were correlated with PCSK9 in patients with severe COVID-19. Levels of all CE species negatively correlated with C-reactive protein in severe COVID-19 patients. Notably, FC was induced in severe compared to moderate COVID-19. The FC/CE ratio correlated positively with inflammatory markers and was associated with non-survival. The current study suggests that the imbalance between CE and FC levels is associated with disease severity and mortality in patients with COVID-19.
Clinical Ramifications of Bacterial Aggregation in Pleural Fluid
Authors: Doub James B. , Putnam Nicole
Published: July 2024

Background: Bacterial aggregation has been well described to occur in synovial fluid, but it is unknown if bacteria form aggregates in body fluids beyond the synovial fluid. Consequently, this translational study evaluated the ability to form bacterial aggregates in different pleural fluids. Methods: Four of the most common causes of thoracic empyema—Streptococcus mitis, Streptococcus pneumoniae, Staphylococcus aureus, and Pseudomonas aeruginosa—were used here. The different pleural fluids included one transudative and two exudative pleural fluids. Twenty-four-well microwell plates were used to form the aggregates with the aid of an incubating shaker at different dynamic conditions (120 RPM, 30 RPM, and static). The aggregates were then visualized with SEM and evaluated for antibiotic resistance and the ability of tissue plasminogen activator (TPA) to dissolve the aggregates. Statistical comparisons were made between the different groups. Results: Bacterial aggregates formed at high shaking speeds in all pleural fluid types, but no aggregates were seen in TSB. When a low shaking speed (30 RPM) was used, only exudative pleural fluid with a high protein content formed aggregates. No aggregates formed under static conditions. Furthermore, there was a statistical difference in the CFU/mL of bacteria present after antibiotics were administered compared to bacteria with no antibiotics (p < 0.005) and when TPA plus antibiotics were administered compared to antibiotics alone (p < 0.005). Conclusions: This study shows that bacteria can form aggregates in pleural fluid and at dynamic conditions similar to those seen in vivo with thoracic empyema. Importantly, this study provides a pathophysiological underpinning for the reason why antibiotics alone have a limited utility in treating empyema.
HIV/AIDS-Associated Knowledge and Attitudes towards Treating Disadvantaged Communities among Pre-Community-Based Dental Education Dental Students in the U.S.
Authors: Tomar Aditi , Balcezak Hannah , Miranda Shirley Lewis , Latortue Marie C. , Chinchkhandi Richa , Wigfall Lisa
Published: July 2024

This study examines HIV/AIDS-associated knowledge and attitudes towards treating disadvantaged communities among predoctoral dental students in U.S. dental schools who have not yet commenced their Community-Based Dental Education (CBDE) training. It also compares the difference in the knowledge and attitudes between students with reported community engagement with PLWHA and those without. Our study comprised 89 predoctoral dental students within their D1–D3 years of dental school who had not yet initiated their Community-Based Dental Education (referred to as pre-CBDE dental students). Their responses were collected via an online survey. The participants were 68% females, 94% heterosexual, and with a mean age (years) of 25.9 ± 3.5 SD. The majority (62%) were in their first (D1) and second (D2) years of dental education. Of the thirty knowledge questions, only five received a minimum of 90% correct responses. Similarly, we found no statistical differences in most of the knowledge/attitude sections between those with and without prior PLWHA exposure. Encouragingly, 90% of our participants reported prior experience working with disadvantaged communities. Early community engagement fosters a sense of professional responsibility towards administering dental care to disadvantaged communities and we propose that it must be encouraged among aspiring dental school students.
Factors Influencing Participation and Engagement in a Teen Safe Driving Intervention: A Qualitative Study
Authors: Rose Dominique M. , Sieck Cynthia J. , Kaur Archana , Wheeler Krista K. , Sullivan Lindsay , Yang Jingzhen
Published: July 2024

(1) Background: Few teen driving safety programs focus on increasing parental engagement with high-risk teen drivers, specifically those with a traffic violation. This study explored parents’/guardians’ (‘parents’) experiences with a teen driving safety program, ProjectDRIVE, including facilitators and barriers to program engagement. (2) Methods: We conducted virtual, semi-structured interviews with parents who completed ProjectDRIVE, which included in-vehicle driving feedback technology and individualized virtual training with parents on effective parent–teen communication. (3) Results: Twenty interviews (with 17 females and three males) were transcribed verbatim and independently coded by three coders using systematic, open, and focused coding. Three major themes were identified: factors influencing a parent’s initial decision to participate, factors influencing continued engagement, and perceived benefits of participation. The decision to participate was influenced by these subthemes: parental motivation to help their teen, perceived program usefulness, program endorsement, program incentives, parents’ busy schedules, and lack of access to a car/internet. Subthemes impacting continued engagement included enhanced communication skills, teen willingness to engage, strong parental engagement, and teens’ other priorities. Perceived benefits included greater self-efficacy in communication, improved communication patterns and frequency, and enhanced parent–teen relationships. (4) Conclusions: These findings may set the foundation for developing and implementing future court-ordered parent-based teen safe driving programs for teens with traffic citations.