bluuebunny/crossref_metadata_2025 huggingface dataset:
Genomic epidemiology of Streptococcus dysgalactiae subsp. equisimilis strains causing invasive disease in Norway during 2018
Authors: Kaci Alba , Jonassen Christine M. , Skrede Steinar , Sivertsen Audun ,   The Norwegian Study Group on Streptococcus dysgalactiae, Steinbakk Martin , Oppegaard Oddvar
Published: July 2023

Background

Streptococcus dysgalactiae subspecies equisimilis (SDSE) is an emerging global pathogen, yet the epidemiology and population genetics of SDSE species have not been extensively characterized.

Methods

We carried out whole genome sequencing to characterize 274 SDSE isolates causing bloodstream infections obtained through national surveillance program in 2018. We conducted multilocus sequence typing (MLST), emm-typing, core genome phylogeny, as well as investigated key features associated with virulence. Moreover, comparison to SDSE from other geographic regions were performed in order to gain more insight in the evolutionary dynamics in SDSE.

Results

The phylogenetic analysis indicated a substantial diversity of emm-types and sequence types (STs). Briefly, 17 emm-types and 58 STs were identified that formed 10 clonal complexes (CCs). The predominant ST-types were ST20 (20%), ST17 (17%), and ST29 (11%). While CC17 and CC29 clades showed a substantial heterogeneity with well-separated emm-associated subclades, the CC20 clade harboring the stG62647 emm-type was more homogenous and the most prevalent in the present study. Moreover, we observed notable differences in the distribution of clades within Norway, as well as several disseminated CCs and also distinct geographic variations when compared to data from other countries. We also revealed extensive intra-species recombination events involving surface exposed virulence factors, including the emm gene important for phylogenetic profiling.

Conclusion

Recombination events involving the emm as well as other virulence genes in SDSE, are important mechanisms in shaping the genetic variability in the SDSE population, potentially offering selective advantages to certain lineages. The enhanced phylogenetic resolution offered by whole genome sequencing is necessary to identify and delimitate outbreaks, monitor and properly characterize emerging strains, as well as elucidate bacterial population dynamics.
Saccharomyces boulardii protects against murine experimental colitis by reshaping the gut microbiome and its metabolic profile
Authors: Gao Hui , Li Yinzheng , Xu Jiqu , Zuo Xuezhi , Yue Tiantian , Xu Huzi , Sun Jie , Wang Meng , Ye Ting , Yu Yan , Yao Ying
Published: July 2023

Introduction

Saccharomyces boulardii (S. boulardii) has shown clinical beneficial effect in inflammatory bowel diseases recently. However, the underlying mechanisms remain incompletely understood. The aim of present study was to tested whether S. boulardii targets gut microbiota to protect against the development of experimental colitis in mice.

Methods

Female C57BL/6 mice were gavaged with S. boulardii for 3 weeks before being challenged with dextran sulphate sodium to induce ulcerative colitis. Bodyweight, diarrhea severity, intestinal permeability, colonic histopathology, colonic inflammatory status, and epithelial cell death of mice were examined. The fecal microbiota and its metabolomic profiles were detected by 16S rDNA sequencing and UPLC-MS, respectively.

Results and Discussion

Supplementation with S. boulardii significantly prevented weight loss and colon shortening, lowered colonic inflammation, ameliorated epithelial injury, and enhanced the intestinal barrier integrity in colitis mice. By inhibiting the abundance of pathogenic bacteria and increasing the probiotics abundance, S. boulardii improved the microbial diversity and restored the microbiota dysbiosis. Moreover, it also modulated microbial metabolome and altered the relative contents of metabolites involving amino acids, lipids, energy and vitamin metabolisms. These yeast-driven shifts in gut flora and metabolites are were associated with each other and with the inflammation profile in colitis. Collectively, S. boulardii exerts protective effects on colitis in mice by reshaping gut microbiome and its metabolic profile, indicating it as a promising therapeutic avenue.
Rapid identification of bacteria using a multiplex polymerase chain reaction system for acute abdominal infections
Authors: Kakizaki Nanako , Asai Koji , Kuroda Makoto , Watanabe Ryutaro , Kujiraoka Manabu , Sekizuka Tsuyoshi , Katagiri Miwa , Moriyama Hodaka , Watanabe Manabu , Saida Yoshihisa
Published: July 2023

Purpose

Acute abdominal infections can be fatal if the causative organism (s) are misidentified. The spread of antimicrobial-resistant bacteria has become a serious problem worldwide, making antibiotic selection extremely difficult. Using quantitative metagenomic analysis, we evaluated a commercial multiplex polymerase chain reaction (PCR) system (FilmArray™, bioMérieux, Marcy-l’Étoile, France) for the rapid identification of causative bacteria.

Methods

The cases of 10 patients with acute abdominal infections were enrolled in this retrospective study. There were six cases of perforated peritonitis and four cases of intraabdominal abscess. Fluid collected from the acute surgical abdominal infections were examined.

Results

All specimens tested positive for microorganisms in culture, and six involved two or more microorganisms. Using the multiplex PCR system, nine of ten specimens were found to involve at least one microorganism. One specimen was not included in the multiplex PCR system panel. Nineteen of 21 microorganisms (90.5%) isolated by culture were detected by the multiplex PCR system. Microorganisms with very small numbers of reads (19 reads) were detectable.

Conclusion

This multiplex PCR system showed a high detection rate for causative microorganisms in ascites and intraabdominal abscesses. This system may be suitable as an affordable rapid identification system for causative bacteria in these cases.
Identifying SARS-CoV-2 infected cells with scVDN
Authors: Hu Huan , Feng Zhen , Shuai Xinghao Steven , Lyu Jie , Li Xiang , Lin Hai , Shuai Jianwei
Published: July 2023

Introduction

Single-cell RNA sequencing (scRNA-seq) is a powerful tool for understanding cellular heterogeneity and identifying cell types in virus-related research. However, direct identification of SARS-CoV-2-infected cells at the single-cell level remains challenging, hindering the understanding of viral pathogenesis and the development of effective treatments.

Methods

In this study, we propose a deep learning framework, the single-cell virus detection network (scVDN), to predict the infection status of single cells. The scVDN is trained on scRNA-seq data from multiple nasal swab samples obtained from several contributors with varying cell types. To objectively evaluate scVDN’s performance, we establish a model evaluation framework suitable for real experimental data.

Results and Discussion

Our results demonstrate that scVDN outperforms four state-of-the-art machine learning models in identifying SARS-CoV-2-infected cells, even with extremely imbalanced labels in real data. Specifically, scVDN achieves a perfect AUC score of 1 in four cell types. Our findings have important implications for advancing virus research and improving public health by enabling the identification of virus-infected cells at the single-cell level, which is critical for diagnosing and treating viral infections. The scVDN framework can be applied to other single-cell virus-related studies, and we make all source code and datasets publicly available on GitHub at https://github.com/studentiz/scvdn.
The impact of HCN4 channels on CNS brain networks as a new target in pain development
Authors: Häfele Maximilian , Kreitz Silke , Ludwig Andreas , Hess Andreas , Wank Isabel
Published: July 2023

While it is well established that the isoform 2 of the hyperpolarization-activated cyclic nucleotide-gated cation channel (HCN2) plays an important role in the development and maintenance of pain, the role of the closely related HCN4 isoform in the processing of nociceptive signals is not known. HCN4 channels are highly expressed in the thalamus, a region important for stimulus transmission and information processing. We used a brain-specific HCN4-knockout mouse line (HCN4-KO) to explore the role of HCN4 channels in acute nociceptive processing using several behavioral tests as well as a multimodal magnetic resonance imaging (MRI) approach. Functional MRI (fMRI) brain responses were measured during acute peripheral thermal stimulation complemented by resting state (RS) before and after stimulation. The data were analyzed by conventional and graph-theoretical approaches. Finally, high-resolution anatomical brain data were acquired. HCN4-KO animals showed a central thermal, but not a mechanical hypersensitivity in behavioral experiments. The open field analysis showed no significant differences in motor readouts between HCN4-KO and controls but uncovered increased anxiety in the HCN4-KO mice. Thermal stimulus-driven fMRI (s-fMRI) data revealed increased response volumes and response amplitudes for HCN4-KO, most pronounced at lower stimulation temperatures in the subcortical input, the amygdala as well as in limbic/hippocampal regions, and in the cerebellum. These findings could be cross-validated by graph-theoretical analyses. Assessment of short-term RS before and after thermal stimulation revealed that stimulation-related modulations of the functional connectivity only occurred in control animals. This was consistent with the finding that the hippocampus was found to be smaller in HCN4-KO. In summary, the deletion of HCN4 channels impacts on processing of acute nociception, which is remarkably manifested as a thermal hypersensitive phenotype. This was mediated by the key regions hypothalamus, somatosensory cortex, cerebellum and the amygdala. As consequence, HCN4-KO mice were more anxious, and their brain-wide RS functional connectivity could not be modulated by thermal nociceptive stimulation.
Diet in treatment of autism spectrum disorders
Authors: Alam Sabiha , Westmark Cara J. , McCullagh Elizabeth A.
Published: July 2023

Altering the diet to treat disease dates to c. 400 BC when starvation was used to reduce seizures in persons with epilepsy. The current diversity of symptomology and mechanisms underlying autism spectrum disorders (ASDs) and a corresponding lack of disorder-specific effective treatments prompts an evaluation of diet as a therapeutic approach to improve symptoms of ASDs. In this review article, we summarize the main findings of nutritional studies in ASDs, with an emphasis on the most common monogenic cause of autism, Fragile X Syndrome (FXS), and the most studied dietary intervention, the ketogenic diet as well as other dietary interventions. We also discuss the gut microbiota in relation to pre- and probiotic therapies and provide insight into future directions that could aid in understanding the mechanism(s) underlying dietary efficacy.
Neurite orientation dispersion and density imaging of white matter microstructure in sensory processing dysfunction with versus without comorbid ADHD
Authors: Mark Ian T. , Wren-Jarvis Jamie , Xiao Jaclyn , Cai Lanya T. , Parekh Shalin , Bourla Ioanna , Lazerwitz Maia C. , Rowe Mikaela A. , Marco Elysa J. , Mukherjee Pratik
Published: July 2023

Introduction

Sensory Processing Dysfunction (SPD) is common yet understudied, affecting up to one in six children with 40% experiencing co-occurring challenges with attention. The neural architecture of SPD with Attention Deficit and Hyperactivity Disorder (ADHD) (SPD+ADHD) versus SPD without ADHD (SPD-ADHD) has yet to be explored in diffusion tensor imaging (DTI) and Neurite Orientation Dispersion and Density Imaging (NODDI) has yet to be examined.

Methods

The present study computed DTI and NODDI biophysical model parameter maps of one hundred children with SPD. Global, regional and voxel-level white matter tract measures were analyzed and compared between SPD+ADHD and SPD-ADHD groups.

Results

SPD+ADHD children had global WM Fractional Anisotropy (FA) and Neurite Density Index (NDI) that trended lower than SPD-ADHD children, primarily in boys only. Data-driven voxelwise and WM tract-based analysis revealed statistically significant decreases of NDI in boys with SPD+ADHD compared to those with SPD-ADHD, primarily in projection tracts of the internal capsule and commissural fibers of the splenium of the corpus callosum.

Conclusion

We conclude that WM microstructure is more delayed/disrupted in boys with SPD+ADHD compared to SPD-ADHD, with NODDI showing a larger effect than DTI. This may represent the combined WM pathology of SPD and ADHD, or it may result from a greater degree of SPD WM pathology causing the development of ADHD.
Could probiotics protect against human toxicity caused by polystyrene nanoplastics and microplastics?
Authors: Bazeli Javad , Banikazemi Zarrin , Hamblin Michael R. , Sharafati Chaleshtori Reza
Published: July 2023

Nanoplastics (NPs) and microplastics (MPs) made of polystyrene (PS) can be toxic to humans, especially by ingestion of plastic particles. These substances are often introduced into the gastrointestinal tract, where they can cause several adverse effects, including disturbances in intestinal flora, mutagenicity, cytotoxicity, reproductive toxicity, neurotoxicity, and exacerbated oxidative stress. Although there are widespread reports of the protective effects of probiotics on the harm caused by chemical contaminants, limited information is available on how these organisms may protect against PS toxicity in either humans or animals. The protective effects of probiotics can be seen in organs, such as the gastrointestinal tract, reproductive tract, and even the brain. It has been shown that both MPs and NPs could induce microbial dysbiosis in the gut, nose and lungs, and probiotic bacteria could be considered for both prevention and treatment. Furthermore, the improvement in gut dysbiosis and intestinal leakage after probiotics consumption may reduce inflammatory biomarkers and avoid unnecessary activation of the immune system. Herein, we show probiotics may overcome the toxicity of polystyrene nanoplastics and microplastics in humans, although some studies are required before any clinical recommendations can be made.
Pre-clinical toxicity assessment of Artemisia absinthium extract-loaded polymeric nanoparticles associated with their oral administration
Authors: Kauser Sana , Mughees Mohd , Swami Sanskriti , Wajid Saima
Published: July 2023

Background: This study was designed to quantify the composition of the ethanolic extract of Artemisia absinthium through gas chromatography–mass spectrometry analysis and ensure in vivo safety of A. absinthium extract-loaded polymeric nanoparticles (ANPs) before considering their application as a drug carrier via the oral route.

Methods: We synthesized N-isopropylacrylamide, N-vinyl pyrrolidone, and acrylic acid crosslinked polymeric NPs by free-radical polymerization reaction and characterized them by Fourier-transform infrared spectroscopy, transmission electron microscopy, and dynamic light scattering spectroscopy. Different concentrations of extract (50 mg/kg, 300 mg/kg, and 2,000 mg/kg body weight) were encapsulated into the hydrophobic core of polymeric micelles for the assessment of acute oral toxicity and their LD50 cut-off value as per the test procedure of OECD guideline 423. Orally administered female Wistar rats were observed for general appearance, behavioral changes, and mortality for the first 30 min, 4 h, 24 h, and then, daily once for 14 days.

Result: ANPs at the dose of 300 mg/kg body weight were used as an initial dose, and rats showed few short-lived signs of toxicity, with few histological alterations in the kidney and intestine. Based on these observations, the next set of rats were treated at a lower dose of 50 mg/kg and a higher dose of 2,000 mg/kg ANPs. Rats administered with 50 mg/kg ANPs remained normal throughout the study with insignificant histological disintegration; however, rats treated at 2,000 mg/kg ANPs showed some signs of toxicity followed by mortality among all three rats within 24–36 h, affecting the intestine, liver, and kidney. There were no significant differences in hematological and biochemical parameters among rats treated at 50 mg/kg and 300 mg/kg ANPs.

Conclusion: We conclude that the LD50 cut-off value of these ANPs will be 500 mg/kg extract loaded in polymeric NPs.
Race and sex differences in dropout from the STRRIDE trials
Authors: Collins Katherine A. , Huffman Kim M. , Wolever Ruth Q. , Smith Patrick J. , Siegler Ilene C. , Ross Leanna M. , Jakicic John M. , Costa Paul T. , Kraus William E.
Published: July 2023

Purpose

To determine if race and sex differences exist in determinants and timing of dropout among individuals enrolled in an exercise and/or caloric restriction intervention.

Methods

A total of 947 adults with dyslipidemia (STRRIDE I, STRRIDE AT/RT) or prediabetes (STRRIDE-PD) were randomized to either inactive control or to 1 of 10 exercise interventions, ranging from doses of 8–23 kcal/kg/week, intensities of 50%–75% V˙O2 peak, and durations of 6–8 months. Two groups included resistance training, and one included a dietary intervention (7% weight loss goal). Dropout was defined as an individual withdrawn from the study, with the reasons for dropout aggregated into determinant categories. Timing of dropout was defined as the last session attended and aggregated into phases (i.e., “ramp” period to allow gradual adaptation to exercise prescription). Utilizing descriptive statistics, percentages were generated according to categories of determinants and timing of dropout to describe the proportion of individuals who fell within each category.

Results

Black men and women were more likely to be lost to follow-up (Black men: 31.3% and Black women: 19.6%), or dropout due to work responsibilities (15.6% and 12.5%), “change of mind” (12.5% and 8.9%), transportation issues (6.3% and 3.6%), or reported lack of motivation (6.3% and 3.6%). Women in general noted lack of time more often than men as a reason for dropout (White women: 22.4% and Black women: 22.1%). Regardless of race and sex, most participants dropped out during the ramp period of the exercise intervention; with Black women (50%) and White men (37.1%) having the highest dropout rate during this period.

Conclusion

These findings emphasize the importance of targeted retention strategies when aiming to address race and sex differences that exist in determinants and timing of dropout among individuals enrolled in an exercise and/or caloric restriction intervention.
Incremental Nonlinear Control for Aeroelastic Wing Load Alleviation and Flutter Suppression
Authors: Schildkamp Roderick , Chang Jing , Sodja Jurij , De Breuker Roeland , Wang Xuerui
Published: July 2023

This paper proposes an incremental nonlinear control method for an aeroelastic system’s gust load alleviation and active flutter suppression. These two control objectives can be achieved without modifying the control architecture or the control parameters. The proposed method has guaranteed stability in the Lyapunov sense and also has robustness against external disturbances and model mismatches. The effectiveness of this control method is validated by wind tunnel tests of an active aeroelastic parametric wing apparatus, which is a typical wing section containing heave, pitch, flap, and spoiler degrees of freedom. Wind tunnel experiment results show that the proposed nonlinear incremental control can reduce the maximum gust loads by up to 46.7% and the root mean square of gust loads by up to 72.9%, while expanding the flutter margin by up to 15.9%.
Modified Method for Surface Probabilistic Risk Assessment of Aero Engine Compressor Disks Considering Shot Peening
Authors: Li Guo , Teng Yida , Zhou Huimin
Published: July 2023

Aero engine compressor disks are typically life-limited parts and it is necessary to secure them through the implementation of an engineering plan and a manufacturing plan. Specifically, the engineering plan recommends the quantification of the safety of life-limited parts on the basis of probabilistic risk assessment (PRA). However, the direct correlation between plans is limited, and the effect of manufacturing parameters on the safety of life-limited parts remains to be investigated. Shot peening, as a typical method of surface manufacturing, can significantly improve the safety of life-limited parts. Therefore, a modified mathematical surface PRA method considering shot peening parameters is developed in this paper to further bridge the design and manufacturing processes. Additionally, a general database is established using the response surface method to overcome the simulation complexity. On the basis of this method and the general database, an innovative direct and efficient determination of key shot peening parameters through failure risk in the design stage is proposed. The results indicate that failure risk decreased by 3.26%, 11.31%, and 9.71%, respectively, with increasing number, diameter, and velocity of shots, with the effect of diameter being the greatest. In addition, the method improves the efficiency of determining the key parameters by 75.80%, thus satisfying the requirements of abundant and efficient iterations during the design stage.
A Review on CubeSat Missions for Ionospheric Science
Authors: Francisco Cristiana , Henriques Ricardo , Barbosa Susana
Published: July 2023

The ionosphere is a fundamental component of the Earth’s atmosphere, impacting human activities such as communication transmissions, navigation systems, satellite functions, power network systems, and natural gas pipelines, even endangering human life or health. As technology moves forward, understanding the impact of the ionosphere on our daily lives becomes increasingly important. CubeSats are a promising way to increase understanding of this important atmospheric layer. This paper reviews the state of the art of CubeSat missions designed for ionospheric studies. Their main instrumentation payload and orbits are also analyzed from the point of view of their importance for the missions. It also focuses on the importance of data and metadata, and makes an approach to the aspects that need to be improved.
Trajectory Synthesis and Optimization Design of an Unmanned Five-Bar Vegetable Factory Packing Machine Based on NSGA-II and Grey Relation Analysis
Authors: Zhang Lei , Liu Yang , Chen Jianneng , Zhou Heng , Jiang Yunsheng , Tong Junhua , Wu Lianlian
Published: July 2023

To address the problems of the complex structure and single packing trajectory of a packing machine, a hybrid-driven, five-bar packing machine for same-point pickup and different points of release in unmanned plant factories was designed, and a GRA-C method based on grey correlation analysis and CRITIC weighting for the quadratic optimization of Pareto solutions was proposed. According to the agronomic requirements, the original track of the packing machine was designed. The trajectory synthesis of the packing mechanism was completed based on the NSGA-Ⅱ multi-objective optimization algorithm. To reduce the overall size of the five-bar mechanism and to ensure its good motion performance, an optimization model for trajectory synthesis was established, and the optimal solution was obtained via the quadratic optimization of the Pareto front solution. To further improve the motion performance of the mechanism, the angular displacement curve at the secondary trajectory points was fitted. Through a comparative analysis with the solutions of three special points in the Pareto front solution set, it was found that the standard deviation of the angular velocity and the standard deviation of the angular acceleration after the quadratic optimization were 26.07% and 24.42% lower than the average values of the other three groups of solutions, respectively. The final optimization results were used to design the vegetable packaging machine, and the trajectory was found to be in good agreement with the expected trajectory, with a root mean square error of only 0.74.
A New Species of Pareas (Squamata, Pareidae) from Guangxi Province, China
Authors: Gong Yanan , Wu Jiaxiang , Huang Song , Xu Yuhao , Yang Diancheng , Liu Yongjin , Liang Shengming , Lee Pingshin
Published: July 2023

We described a new species of genus Pareas from Baise City, Guangxi Zhuang Autonomous Region, China, based on morphological and molecular evidence. Pareas baiseensis sp. nov. is distinguished from its congeners by the combination of (1) Yellowish-brown body colouration; (2) Frontal subhexagonal to diamond-shaped with its lateral sides converging posteriorly; (3) The anterior pair of chin shields is longer than it is broad; (4) Loreal not in contact with the eye, prefrontal in contact with the eye, two or three suboculars; (5) Rows of 15–15–15 dorsal scales, five rows of mid-dorsal scales keeled at the middle of the body, one vertebral scale row enlarged; (6) 187–191 ventrals, 89–97 subcaudals, all divided, cloacal plate single; (7) Two postocular stripes, the nuchal area forming a dark black four-pointed fork collar with the middle tines shorter than the outside tines. The genetic divergence (uncorrected p-distance) between the new species and other representatives of Pareas ranged from 13.9% to 24.4% for Cytochrome b (Cyt b) and 12.1% to 25.5% for NADH dehydrogenase subunit 4 (ND4). Phylogenetic analyses of mitochondrial DNA gene data recovered the new species from being the sister taxon to (P. boulengeri + P. chinensis) from China.
Performance, Intake, Feed Efficiency, and Carcass Characteristics of Young Nellore Heifers under Different Days on Feed in the Feedlot
Authors: Ferreira Igor Machado , Oliveira Karla Alves , Cidrini Iorrano Andrade , de Abreu Mateus José Inácio , Sousa Luciana Melo , Batista Luis Henrique Cursino , Homem Bruno Grossi Costa , Prados Laura Franco , Siqueira Gustavo Rezende , Resende Flávio Dutra de
Published: July 2023

Two studies evaluated the productive characteristics of young Nellore heifers receiving different days on feed (DOF) to determine the biological slaughter endpoint. In Experiment 1 (Exp. 1), fifty-one Nellore heifers [324 ± 19.3 kg of body weight (BW); 16 ± 1 months] were split into three DOF lengths (45, 75, or 105 days), while in Experiment 2 (Exp. 2), thirty-six Nellore heifers (362 ± 25.5 kg of BW; 18 ± 1 months of age) were split into three DOF lengths (45, 90, or 135 days). In both studies, all animals were distributed in complete randomized blocks according to initial BW and stratified via carcass ultrasound. The diet was supplied ad libitum, allowing 3% of refusals. The point at which the animals achieved 25% of ether extract of shrunk body weight (EESBW) was defined as the biological endpoint. Thus, relationships were made between some characteristics obtained in both studies. Positive linear relationships were found between backfat thickness (BFT) vs. EESBW (p < 0.001, r = 0.84) and BFT vs. body weight (p < 0.001, r = 0.77). Our results suggest that the biological slaughter endpoint for young Nellore heifers is 6.97 mm of backfat thickness or 402 kg shrunk body weight, corresponding to around 75 DOF.
Genome-Wide Identification, Evolutionary and Mutational Analysis of the Buffalo Sox Gene Family
Authors: Abdullah Muhammad , Rehman Muhammad Saif-ur , Rehman Muhammad Shah Nawaz-ul , AlKahtane Abdullah A. , Al-Hazani Tahani Mohamed , Hassan Faiz-ul , Rehman Saif ur
Published: July 2023

The Sox gene family constitutes transcription factors with a conserved high mobility group box (HMG) that regulate a variety of developmental processes, including sex differentiation, neural, cartilage, and early embryonic development. In this study, we systematically analyzed and characterized the 20 Sox genes from the whole buffalo genome, using comparative genomic and evolutionary analyses. All the buffalo Sox genes were divided into nine sub-groups, and each gene had a specific number of exons and introns, which contributed to different gene structures. Molecular phylogeny revealed more sequence similarity of buffalo Sox genes with those of cattle. Furthermore, evolutionary analysis revealed that the HMG domain remained conserved in the all members of the Sox gene family. Similarly, all the genes are under strong purifying selection pressure; seven segmental duplications occurred from 9.65 to 21.41 million years ago (MYA), and four potential recombination breakpoints were also predicted. Mutational analysis revealed twenty non-synonymous mutations with potential effects on physiological functions, including embryonic development and cell differentiation in the buffalo. The present study provides insights into the genetic architecture of the Sox gene family in buffalo, highlights the significance of mutations, and provides their potential utility for marker-assisted selection for targeted genetic improvement in buffalo.
Staphylococcus aureus in Polymicrobial Skinand Soft Tissue Infections: Impact of Inter-Species Interactionsin Disease Outcome
Authors: Mariani Florencia , Galvan Estela Maria
Published: July 2023

Polymicrobial biofilms provide a complex environment where co-infecting microorganisms can behave antagonistically, additively, or synergistically to alter the disease outcome compared to monomicrobial infections. Staphylococcus aureus skin and soft tissue infections (Sa-SSTIs) are frequently reported in healthcare and community settings, and they can also involve other bacterial and fungal microorganisms. This polymicrobial aetiology is usually found in chronic wounds, such as diabetic foot ulcers, pressure ulcers, and burn wounds, where the establishment of multi-species biofilms in chronic wounds has been extensively described. This review article explores the recent updates on the microorganisms commonly found together with S. aureus in SSTIs, such as Pseudomonas aeruginosa, Escherichia coli, Enterococcus spp., Acinetobacter baumannii, and Candida albicans, among others. The molecular mechanisms behind these polymicrobial interactions in the context of infected wounds and their impact on pathogenesis and antimicrobial susceptibility are also revised.
Resveratrol as an Inhibitor of the NorA Efflux Pump and Resistance Modulator in Staphylococcus aureus
Authors: Santos Madalena , Santos Raquel , Soeiro Pedro , Silvestre Samuel , Ferreira Susana
Published: July 2023

Staphylococcus aureus can exhibit resistance to various antibiotics. Among its resistance mechanisms, the active efflux of antibiotics can be seen as relevant. This study aimed to evaluate the ability of resveratrol to modulate norfloxacin resistance in S. aureus. The antimicrobial activity of resveratrol was assessed using the broth microdilution method to determine the minimum inhibitory concentration (MIC). Then, the modulatory effect of resveratrol was evaluated using the MIC determination for the antibiotic or ethidium bromide in the presence and absence of resveratrol at a sub-MIC level. The MIC of norfloxacin against S. aureus SA1199B (NorA-overexpressing strain) decreased 16-fold when in the presence of resveratrol, with a similar behavior being observed for ethidium bromide. An evaluation of the ethidium bromide accumulation was also performed, showing that in the presence of resveratrol, the SA1199B strain had augmented fluorescence due to the accumulation of ethidium bromide. Altogether, the results suggested that resveratrol may act by inhibiting NorA. These in vitro data were supported by docking results, with interactions between resveratrol and the NorA efflux pump predicted to be favorable. Our findings demonstrated that resveratrol may modulate norfloxacin resistance through the inhibition of NorA, increasing the effectiveness of this antibiotic against S. aureus.
Exogenous Abscisic Acid Affects the Heat Tolerance of Rice Seedlings by Influencing the Accumulation of ROS
Authors: Wang Yingfeng , Lei Bin , Deng Huabing , Liu Xiong , Dong Yating , Chen Wenjuan , Lu Xuedan , Chen Guihua , Zhang Guilian , Tang Wenbang , Xiao Yunhua
Published: July 2023

Heat stress (HS) has become one of the major abiotic stresses that severely constrain rice growth. Abscisic acid (ABA) plays an important role in plant development and stress response. However, the effect of different concentrations of exogenous ABA on HS tolerance in rice still needs to be further elucidated. Here, we found that high concentrations of exogenous ABA increased HS damage in seedlings, whereas 10−12 M ABA treatment increased fresh and dry weight under HS relative to mock seedlings. Our further data showed that, in response to HS, 10−5 M, ABA-treated seedlings exhibited a lower chlorophyll content, as well as transcript levels of chlorophyll biosynthesis and antioxidant genes, and increased the accumulation of reactive oxygen species (ROS). In addition, the transcript abundance of some heat-, defense-, and ABA-related genes was downregulated on 10−5 M ABA-treated seedlings under HS. In conclusion, high concentrations of exogenous ABA reduced the HS tolerance of rice seedlings, and this negative effect could be achieved by regulating the accumulation of ROS, chlorophyll biosynthesis, and the transcription levels of key genes in seedlings under HS.
Rising Influence of Nanotechnology in Addressing Oxidative Stress-Related Liver Disorders
Authors: Padmanaban Sathiyamoorthy , Pully Durgasruthi , Samrot Antony V. , Gosu Vijayakumar , Sadasivam Nanthini , Park In-Kyu , Radhakrishnan Kamalakannan , Kim Don-Kyu
Published: July 2023

Reactive oxygen species (ROS) play a significant role in the survival and decline of various biological systems. In liver-related metabolic disorders such as steatohepatitis, ROS can act as both a cause and a consequence. Alcoholic steatohepatitis (ASH) and non-alcoholic steatohepatitis (NASH) are two distinct types of steatohepatitis. Recently, there has been growing interest in using medications that target ROS formation and reduce ROS levels as a therapeutic approach for oxidative stress-related liver disorders. Mammalian systems have developed various antioxidant defenses to protect against excessive ROS generation. These defenses modulate ROS through a series of reactions, limiting their potential impact. However, as the condition worsens, exogenous antioxidants become necessary to control ROS levels. Nanotechnology has emerged as a promising avenue, utilizing nanocomplex systems as efficient nano-antioxidants. These systems demonstrate enhanced delivery of antioxidants to the target site, minimizing leakage and improving targeting accuracy. Therefore, it is essential to explore the evolving field of nanotechnology as an effective means to lower ROS levels and establish efficient therapeutic interventions for oxidative stress-related liver disorders.
Lenke Classification Report Generation Method for Scoliosis Based on Spatial and Context Dual Attention
Authors: Tang Yu , He Zhiqin , Wu Qinmu , Wang Xiao , Wang Yuhang
Published: July 2023

The scoliosis report is a diagnosis made by the clinician looking at X-ray images of the spine. However, with numerous images, writing the report can be time-consuming and error-prone. Therefore, this paper proposes an automatic generation model of the end-to-end scoliosis Lenke classification report. The model automatically generates a short diagnostic text to explain the results of the classifiers’ Lenke classification diagnosis of scoliosis. Instead of reproducing the original diagnostic report, the original diagnostic report is described as a short sentence with diagnostic significance. In the model, the CBAM attention module is added to the residual’s path of ResNet-50 to extract key regional features of the image, and the improved Long Term and Short Term Memory Network (M-LSTM) fusion attention mechanism with additional gated operations is used as the decoder to generate more relevant description statements. The model was verified on the scoliosis dataset from Guizhou Orthopaedic Hospital, and the generated diagnostic text obtained good scores on BLEU and CIDEr evaluation indexes, and also satisfactory scores on the evaluation criteria of five professional clinicians. Therefore, the diagnostic text generated by this method had good performance in accuracy and semantic expression.
Balanced Foot Dorsiflexion Requires a Coordinated Activity of the Tibialis Anterior and the Extensor Digitorum Longus: A Musculoskeletal Modelling Study
Authors: Frigo Carlo Albino , Merlo Andrea , Brambilla Cristina , Mazzoli Davide
Published: July 2023

Equinus and equinovarus foot deviations (EVFD) are the most frequent lower limb acquired deformities in stroke survivors. We analysed the contribution that the tibialis anterior (TA), extensor digitorum longus (EDL) and plantarflexor muscles play in EVFD via a biomechanical musculoskeletal model of the ankle–foot complex. Our model was composed of 28 bones (connected by either revolute joints or bone surface contacts), 15 ligaments (modelled as non-linear springs), and 10 muscles, modelled as force actuators. Different combinations of muscle contractions were also simulated. Our results demonstrate that, compared to the condition when the foot is suspended off the ground, the contraction of the TA alone produces dorsiflexion (from −18° to 0°) and a greater supination/inversion (from 12° to 30°). The EDL alone produces dorsiflexion (from −18° to −6°), forefoot pronation (25°) and calcaneal eversion (5.6°). Only TA and EDL synergistic action can lead the foot to dorsiflexion suitable for most daily life activities (≥20°) without any deviation in the frontal plane. When pathological contractures of the plantarflexor muscles were simulated, foot deformities reproducing EVFD were obtained. These results can be relevant for clinical applications, highlighting the importance of EDL assessment, which may help to design appropriate functional surgery and plan targeted rehabilitation treatments.
PMMTss: A Parallel Multi-Way Merging-Based Trajectory Similarity Search for a Million Metro Passengers
Authors: Huang Wanbing , Xiong Wen , Wang Xiaoxuan
Published: July 2023

Trajectory similarity search (TSS) is a common operation for spatiotemporal data analysis. However, the existing TSS methods are mainly focused on GPS trajectories produced by moving objects such as vehicles. Further, these corresponding optimization strategies cannot be directly applied in the metro scenario because the metro passenger trajectory is totally different from the GPS trajectory. To fill this gap, we systematically analyze the unique spatiotemporal characteristics of metro passenger trajectories and propose a similarity search solution named PMMTss for the metro system. The core idea of this solution has two key points: first, we design a multi-layer index based on the spatiotemporal feature of metro trajectories, and all points of a trajectory are stored in this index. Second, we design a parallel multi-way merging-based trajectory similar search method, in which the candidate trajectory segments are merged and filtered. We evaluate this solution on a large dataset (Shenzhen Metro data for 3 consecutive months, 6.976 million trajectories with 260 million records). When lengths of input trajectories are 16, 32, and 64, respectively, the corresponding search times are 0.004 s, 0.016 s, and 0.036 s, respectively. Compared to the baseline PPJion+, the query times are reduced by 99.7%, 98.8%, and 97.6%, respectively.
Aroma Composition of Wines Produced from Grapes Treated with Organic Amendments
Authors: Palenzuela María del Valle , López de Lerma Nieves , Sánchez-Suárez Fernando , Martínez-García Rafael , Peinado Rafael Andrés , Rosal Antonio
Published: July 2023

The application to agriculture of wheat-straw spent mushroom substrate amendments (compost/vermicompost) used to grow Pleurotus ostreatus has been analyzed. The study was conducted in a vineyard where the effect on (1) the physicochemical properties of the soil and the leaf and (2) the analytical characteristics and the aromatic composition of the wine were analyzed. The application of the amendments resulted in an increase in organic matter and macronutrients (NO3−, P2O5 and K2O) in the soil. With regard to the leaves, the NO3− and K2O contents of those vines fertilized with vermicompost were higher, and the metallic content was the same regardless of the treatment applied. The analysis of the colorimetric parameters showed that there was a higher content of compounds with red and violet colorations in the case of wine obtained after treatment with vermicompost. In addition, for this type of wine, a higher concentration of volatile compounds was obtained. Thus, after grouping the aroma compounds into aroma series, the greatest differences among vermicompost wines and the rest were obtained in the fruit, floral, herbaceous, and green fruit series. The principal component analysis showed that the vermicompost treatment clearly differentiated the wine from the rest of the wines, in addition to its effects on the aromatic series, the values in the total polyphenol index, and the compounds responsible for brown tones.
Chromosome Cluster Type Identification Using a Swin Transformer
Authors: Joshi Indu , Mondal Arnab Kumar , Navab Nassir
Published: July 2023

The analysis of chromosome karyotypes is crucial for diagnosing genetic disorders such as Patau syndrome, Edward syndrome, and Down syndrome. Chromosome cluster type identification is a key step in the automated analysis of chromosome karyotypes. State-of-the-art chromosome cluster-type identification techniques are based on convolutional neural networks (CNNs) and fail to exploit the global context. To address this limitation of the state of the art, this paper proposes a transformer network, chromosome cluster transformer (CCT), that exploits a swin transformer backbone and successfully captures long-range dependencies in a chromosome image. Additionally, we find that the proposed CCT has a large number of model parameters, which makes it prone to overfitting on a (small) dataset of chromosome images. To alleviate the limited availability of training data, the proposed CCT also utilizes a transfer learning approach. Experiments demonstrate that the proposed CCT outperforms the state-of-the-art chromosome cluster type identification methods as well as the traditional vision transformer. Furthermore, to provide insights on the improved performance, we demonstrate the activation maps obtained using Gradient Attention Rollout.
Study on Dynamic Uncertainty and Sensitivity of Gear System Considering the Influence of Machining Accuracy
Authors: Guo Fang , Li Chen , Su Jinzhan , Liu Chao
Published: July 2023

Due to the limitation of machining accuracy, the transmission performance uncertainty of mass gears must be evaluated quantitatively to provide the basis for its application in the whole machine. Based on the polynomial chaotic expansion (PCE) method, a dynamic uncertainty analysis method for gear systems with a specified precision was proposed in this paper. Combined with tooth surface contact analysis and load-bearing contact analysis, a dynamic model of the gear system was established to fully reflect the influence of typical manufacturing errors. Based on this, a PCE model was established to approximate the system dynamics model. The dynamic uncertainty of the gear system was quantified based on the PCE approximation model and the Monte Carlo method, respectively, and the computational accuracy and efficiency of the PCE model with different orders and numbers of sample points were compared and analyzed. Finally, Sobol′ sensitivity indices from the PCE model of the gear system to random errors were computed, and the primary and secondary relationships of influence on the dynamic performance of the gear system were determined. The results showed that the PCE method had good applicability to the quantification of dynamic uncertainty and error sensitivity analysis of gear systems, and it had both accuracy and high efficiency.
Feeling the Future—Haptic Audio: Editorial
Authors: Paterson Justin , Wanderley Marcelo M.
Published: July 2023

This Special Issue in Arts aligns with the journal’s established theme of ‘Music and the Machine’ [...]
Fog Density Evaluation by Combining Image Grayscale Entropy and Directional Entropy
Authors: Cao Rong , Wang Xiaochun , Li Hongjun
Published: July 2023

The fog density level, as one of the indicators of weather conditions, will affect the management decisions of transportation management agencies. This paper proposes an image-based method to estimate fog density levels to improve the accuracy and efficiency of analyzing fine meteorological conditions and validating fog density predictions. The method involves two types of image entropy: a two-dimensional directional entropy derived from four-direction Sobel operators, and a combined entropy that integrates the image directional entropy and grayscale entropy. For evaluating the performance of the proposed method, an image test set and an image training set are constructed; and each image is labeled as heavy fog, moderate fog, light fog, or fog-free according to the fog density level of the image based on a user study. Using our method, the average accuracy rates of image fog level estimation were 77.27% and 79.39% on the training set using the five-fold cross-validation and the test set, respectively. Our experimental results demonstrate the effectiveness of the proposed combined entropy for image-based fog density level estimation.
A Comparison of the Evaporative Emissions Performance of Light-Duty Vehicles under US Tier 3 and China 6 Test Conditions
Authors: Peng Di , Tian Miao , Yi Fei , Yang Xinping , Ji Liang , Wang Junfang , Yin Hang , Ding Yan , Zhao Haiguang
Published: July 2023

To further improve air quality in China, especially ozone and fine particulate matter (PM2.5), additional reductions of volatile organic compounds (VOCs) are needed. Evaporative emissions from internal combustion engines (ICE) and hybrid vehicles are known to be an important source of VOCs in urban cities, which can be efficiently reduced through the introduction of more stringent regulatory standards. The most stringent global standards for evaporative emissions are the U.S. Tier 3 light-duty vehicle standards. This study compares the evaporative emissions of light-duty ICE vehicles designed to China 6 and U.S. Tier 3 regulations for both China and U.S. test conditions. Data are analyzed from manufacturer testing of full vehicle evaporative emissions conducted in the laboratory following U.S. Tier 3 and China 6 certification test methods utilizing Sealed Housing for Evaporative Determination (SHED) chambers equipped with Flame Ionization Detection (FID) analyzers. Vehicles designed to U.S. Tier 3 standards are observed to have 64% lower diurnal and hot soak evaporative emissions and 98% lower canister bleed emissions relative to vehicles designed to China 6 standards. U.S. Tier 3, U.S. Tier 2, and China 6 light-duty evaporative emission certification values submitted by manufacturers are also compared. The average of all current U.S. Tier 3 certifications is, on average, 52.4% lower than the average of all China 6 certifications. The results from the testing and data analysis of five vehicles, with comparison to the certification data, suggest that the introduction of standards equivalent in stringency to U.S. Tier 3 in China can significantly reduce evaporative emissions relative to China 6.