bluuebunny/crossref_metadata_2025 huggingface dataset:
Force-triggered density gradient sedimentation and cocktail enzyme digestion treatment for isolation of single dermal papilla cells from follicular unit extraction harvesting human hair follicles
Authors: Huang Junfei , Chen Jian , Li Haoyuan , Fan Zhexiang , Gan Yuyang , Chen Yangpeng , Du Lijuan
Published: October 2024

Background
Hair follicles (HFs) are dynamic structures which are readily accessible within the skin that contain various pools of stem cells with broad regenerative potential, such as dermal papilla cells (DPCs), dermal sheath cells, and epithelial HF stem cells. DPCs act as signalling centres for HF regeneration. The current method for isolating human DPCs are inefficient. These methods struggle to obtain freshly isolated original DPCs and do not maintain the characteristics of DPCs effectively.
Methods
In this study, two simple but more efficient methods were explored. Force-triggered density gradient sedimentation (FDGS) and cocktail enzyme digestion treatment (CEDT) were used to isolate purified DP spheres from human HFs, obtaining purified freshly isolated original DPCs from DP spheres. The expression profiles of isolated DPCs were tested, and gene expression of DPC-specific markers were analyzed using immunofluorescence staining, RT-qPCR and western blot.
Results
The 10% Ficoll PM400 was determined as the optimal concentration for FDGS method. Primary DPCs, DSCs and HFSCs were isolated simultaneously using the FDGS and CEDT method. The expression profiles of fresh DPCs isolated using the FDGS and CEDT methods were similar to those of traditionally isolated DPCs. DP-specific markers were expressed at significantly higher levels in freshly isolated DPCs than in traditionally isolated DPCs.
Conclusions
Compared to traditional methods, the presented laboratory protocols were able to isolate fresh DPCs with high efficiency, thereby improving their research potential.
Brain structure characteristics in children with attention-deficit/hyperactivity disorder elucidated using traveling-subject harmonization
Authors: Shou Qiulu , Yamashita Masatoshi , Hirano Yoshiyuki , Yao Akiko , Li Min , Wang Yide , Kato Yoko , Yoshida Tokiko , Matsumoto Koji , Tsujikawa Tetsuya , Okazawa Hidehiko , Tomoda Akemi , Kagitani-Shimono Kuriko , Mizuno Yoshifumi
Published: October 2024

Background Brain imaging studies for attention-deficit/hyperactivity disorder (ADHD) have not always yielded consistent findings, potentially owing to measurement bias in magnetic resonance imaging (MRI) scanners. This study aimed to elucidate the structural brain characteristics in children with ADHD by addressing measurement bias in multi-site MRI data using the traveling-subject (TS) method.Methods The MRI data of 14 traveling subjects, 181 typical development (TD), and 117 ADHD children were collected from multiple sites. The TS method and ComBat were used to correct for measurement bias. Gray matter volumes were estimated using FreeSurfer, and the ADHD and TD groups were compared using mixed-effect models.Results Compared to raw data and ComBat-corrected data, the TS method significantly reduced measurement bias while maintaining sampling bias. The results from the TS-corrected data showed that the brain volume of the ADHD group was significantly smaller than that of the TD group in the bilateral middle temporal cortex, bilateral orbitofrontal cortex, right inferior frontal gyrus, right middle frontal gyrus, left inferior temporal gyrus, left precuneus cortex, and bilateral insular cortex. Brain regions that showed significant differences differed across the TS method, ComBat, and raw data. In contrast, notably significant volumetric reductions in the right middle temporal gyrus of ADHD patients were consistently observed across all methods.Conclusions The TS method effectively reduces measurement bias across MRI scanners, which may affect the findings of a multi-site study. The right middle temporal gyrus showed significant differences in all methods, suggesting it is a crucial region for ADHD.
Hyaluronic acid stimulation of induced MSCs produces extracellular vesicles with enhanced healing for skin burn wounds
Authors: Jung Minyoung , Oh Hyun Geun , Lee Seul Ki , Kim Eun A , You Haedeun , Kim Tae Min , Kim Soo
Published: October 2024

Background
Skin injuries occur for various reasons during whole life. Some chronic wounds could cause an impaired wound healing process characterized by wound hypoxia, high levels of oxygen radicals, elevated levels of matrix metalloproteases, delayed cellular infiltration and granulation tissue formation, reduced angiogenesis, decreased collagen synthesis and organization. In this study, we report the EVs from hyaluronic acid-primed iMSCs (HA-iMSC-EVs) accelerating wound healing and regenerating damaged tissues by inducing the various growth factors in the thermal injury of mice.
Methods
EVs were collected from iMSCs primed with HA (HA-iMSC-EVs) or without HA (iMSC-EVs) and were isolated using TFF systems. Both EVs analyzed the characteristics. We investigated the proteome of HA-iMSC-EVs using the protein set ontology analysis and protein-protein interaction network. To evaluate the effect of HA-iMSC-EVs on the oxidative stress-induced wound healing delayed model, we assessed the effect of EVs on cell viability, cell migration rate, and the mRNA expression of growth factors using a hydrogen peroxide-exposed HDF model. In addition, we observed elastin and collagen expressions using an ICC staining in the HDF model. In thermal burn wound mice (BALB/c), we compared the effect of EVs in wound closure rate and histological analysis, including expression of elastin, collagen, α-SMA, and CD31.
Results
HA-iMSC-EVs exhibited typical EV characteristics, including size distribution, markers, and surface protein expression. In GO term analysis, HA-iMSC-EVs increased the proteins associated with ECM, including collagen biosynthesis and elastin fiber formation. In hydrogen peroxide exposed HDF models, HA-iMSC-EVs notably increased cell viability and migration activity. Furthermore, HA-iMSC-EVs increased RNA expression of VEGF, IGF1, and HGF and decreased IL-6 mRNA expression compared to the PBS group. Elastin and collagen expression in the HA-iMSC-EVs group were also significantly increased. In burn-injured mice, HA-iMSC-EVs accelerated wound closure and enhanced histological recovery. HA-iMSC-EVs increased collagen and elastin density on the upper dermis and decreased α-SMA expression. Additionally, HA-iMSC-EVs promoted the capillary density in the dermis.
Conclusions
Our results suggest that HA-iMSC-EVs accelerated the recovery from burn wound by providing ECM composition signal and regulating growth factors. Our strategy may contribute to the development of alternative treatment option for burn wounds.
Trial registration
: Not applicable.
Reginal dissemination of transferable repB(1701) plasmid carrying blaNDM-4 in Asia: emergence of tandem repeats with blaNDM-4 mediated by IS26 in Klebsiella pneumoniae
Authors: Zhang Huanran , Xu Hao , Liu Ruishan , Liu Xiaojing , Yang Yu , Guo Kexin , Chen Mantao , Lu Yuanqiang , Zheng Beiwen
Published: October 2024

The worldwide spread of carbapenem-resistant Klebsiella pneumoniae (CRKP) has led to a major challenge to human health. The emergence and prevalence of transferable plasmid carrying carbapenemase encoding gene is undoubtedly a potential factor in increasing the burden of carbapenem resistance. In this study, we described the reginal dissemination of repB(1701) plasmid carrying blaNDM-4 in China, with the coexistence of blaNDM-4 and blaOXA-9 in two independent K. pneumoniae isolates for the first time. Whole-genome sequencing and plasmid characterization of isolates L2388 and L3835 showed both blaNDM-4 and blaOXA-9 genes are situated on the transferable plasmid, designated as pL2388-NDM-OXA [120,100 bp, IncFII(K)-repB(R1701)] and pL3835-NDM-OXA [127,486 bp, repB(R1701)]. Notably, two copies of blaNDM-4 were identified in different orientations within pL3835-NDM-OXA. The blaNDM-4 sequence is relatively conserved (blaNDM-4-ble-trpF-dsbD-cutA-groES-groL), with various mobile genetic elements (MEGs) surrounding it, particularly IS26, which may play a pivotal role in gene-level dissemination. The previously unrecognized distribution of these plasmids across select regions of Southern China and Vietnam suggests a potentially wider epidemiological range than initially presumed in the context of microbiology and epidemiology. This is the first report of transferable IncFII(K)-repB(R1701)/repB(R1701) plasmids carrying the blaNDM-4 gene, relevant detection and investigation measures should be taken to control the prevalence.
Genome-wide analysis of C-repeat binding factor (CBF) family members in Pennisetum glaucum and the function of PgCBF21 under cold stress
Authors: Li Wei , Li Tian , Dong Ying , He Junyi , Wu Bo , Wang Hui , Guan Cong
Published: October 2024

Background
Pennisetum hybrid (Pennisetum glaucum x Pennisetum purpureum), a perennial forage grass of the Poaceae family, it has a well-developed root system, strong tillering ability, high biomass yield, and rich nutritional content, making it a premium forage grass. However, Pennisetum genera grasses are sensitive to low-temperature stress and lacks the ability to adapt to cold environments, severely limiting its cultivation in temperate and high-altitude regions.
Results
We identified 23 PgCBF genes, unevenly distributed across chromosomes 1 to 7. Physicochemical property analysis revealed that the amino acid count of PgCBF family members ranged from 187 to 324, with molecular weights between 19688.36 and 34271.70 Da and theoretical isoelectric points between 4.57 and 9.82. Promoter region analysis of PgCBF genes indicated the presence of various cis-acting elements involved in hormone response, tissue-specific expression, and stress response. Additionally, qRT-PCR results showed significant upregulation of PgCBF11 expression in stems following cold treatment, with increasing over 40-fold after 32 hours of cold treatment and about 20-fold after 8 hours of cold treatment. PgCBF21 exhibited a strong response in leaves after 8 hours of cold treatment, with expression levels rising more than 37-fold. Furthermore, through the overexpression of PgCBF21, we ascertained its capacity to enhance cold tolerance in yeast.
Conclusion
This study analyzed the molecular characteristics of the PgCBF family members in Pennisetum glaucum and identified several candidate genes responsive to cold stress, providing a theoretical foundation for future research on the innovative utilization of cold-resistant resources.
Steric colloidal stabilization of cellulose nanocrystals by dextran grafting
Authors: Tanaka Takahide , Araki Jun , Kuga Shigenori , Yabuki Akihiro
Published: October 2024

In this study, enhanced dispersion stability of cellulose nanocrystal was achieved by terminal grafting of dextran (a-1,6 glucan) onto the surface of nanocrystals. The 6-position carbon of the nanocrystal was first oxidized by TEMPO method, and the introduced carboxyl group on the surface of cellulose nanocrystal was coupled with terminal amino group of terminally aminated dextran using N-hydroxysuccinimide and 1-ethyl-3-3-dimethylaminopropyl carbodiimide. Terminally aminated dextran was obtained by reductive amination using sodium cyanoborohydride and ammonium chloride. The weight gain by grafting reached 184% of the carboxylated cellulose nanocrystal, resulting in high dispersion stability. We evaluated the dispersion stability by the change in viscosity before and after adding salt. Cellulose nanocrystals are colloids, and adding salt reduces their dispersion stability and increases their viscosity. However, addition of 50 mM CaCl2 to the suspension of dextran grafted cellulose nanocrystal did not cause noticeable increase in viscosity or in turbidity. This enhanced stability indicates the effectiveness of coating cellulose nanocrystal by water-soluble polymers.
Green Cleaner: Advanced Decontamination Algorithm for Catheterized Urine 16S rRNA Sequencing Data
Authors: Yoon Sung Min , Ki Chang-Seok , Song Ju Sun
Published: October 2024

Background
Contamination of low-biomass samples, such as urine, is a significant challenge in 16S rRNA sequencing. The presence of extraneous DNA in reagents and the environment often obscures microbial DNA, making it difficult to identify and remove contaminants. In silico decontamination algorithms developed so far still have some limitations in identifying and removing contaminants accurately. In this study, we developed a novel decontamination algorithm, Green Cleaner, to enhance the accuracy of 16S rRNA sequencing data by effectively distinguishing and removing contaminants especially from catheterized urine samples.
Results
We evaluated the performance of Green Cleaner against SCRuB using a series of vaginal microbiome dilution experiments as a proxy for low-biomass urine samples. Our results demonstrate that Green Cleaner outperforms SCRuB across all contamination levels, with higher accuracy, F1-score, and lower beta-dissimilarity. Specifically, Green Cleaner showed improved specificity and positive predictive value (PPV), correctly removing more contaminant amplicon sequence variant (ASV) features than SCRuB did. This was evidenced by the more diminished alpha diversity of the decontamination results in Green Cleaner than SCRuB, indicating a more precise elimination of contaminants by Green Cleaner.
Conclusions
Green Cleaner offers a robust solution for decontaminating 16S rRNA sequencing data from low-biomass samples, particularly catheterized urine samples, thus addressing the key limitations of the existing methods. By utilizing a single blank extraction control per batch and a set of intuitive and adjustable decontamination rules, Green Cleaner provides a practical and efficient approach for real-world applications. Our findings suggest that Green Cleaner has the potential to substantially advance urine microbiome research by providing more accurate and reliable microbial profiles.
Phylogeny and taxonomy of the polyploidy species that contains St genome (Triticeae; Poaceae) based on four nuclear DNA and three chloroplast genes
Authors: Pan XiaoYang , Zheng TingTing , Zhao Yuxin , Fan Xing , Sha Lina , Li Yinghui , Zhu Wei , Xu Lili , Wang Yi , Cheng Yiran , Zhang Haiqin , Kang Houyang , Zhou Yonghong , Wu Dandan
Published: October 2024

Background
The genus Pseudoroegneria (Nevski) Á. Löve with the St genome accounts for more than 60% of perennial Triticeae speciation. However, the strong dominant character of the St genome results in challenging to distinguish each species even genus based on single or combined morphological traits, the phylogeny and taxonomy of the St-containing polyploid genera remain under controversy.
Results
In this study, we used nuclear and chloroplast DNA-based phylogenetic analyses to reveal the systematic relationships of the St-containing polyploidy species. The maximum likelihood (ML) tree based on nuclear ribosomal internal transcribed spacer region (nrITS) and three single-copy nuclear genes data (Acc1 + Pgk1 + DMC1) showed that St-containing polyploid species were separated into StStHH, StStYY, StStYYHH, StStYYPP, StStYYWW, StStPP, and StStEE genome types and polyploidy species in Caucasus, America and Australia have unique polyploidization events. The ML tree for the chloroplast DNA fragments (matK + rbcL + trnL-trnF) displayed that the P genome serves as a maternal donor of Kengyilia melanthera and K. dingqinensis from the Hengduan Mountains region, while the St or StY genome serves as the maternal donor of other St genome containing species. Herein, we reported the genome constitution of Kengyilia tibetica, K. changduensis, and K. dingqinensis with the StStYYPP genome for the first time.
Conclusions
The St-containing polyploid species should be treated as distinct genera according to different genome constitutions, St-containing polyploid species experienced independent allopolyploidization events in different distribution regions and the St-containing polyploid species had two relatively independent maternal origins from the P genome or St/StYgenome. Besides, the Xp genome may have contributed to the unknown Y genome formation.
Integrated analysis unraveling the immunologic and clinical prognostic values of Synaptotagmin Like 4 in pan-cancer
Authors: Ren Yuehan , Wu Xiangbin , Li Jinlei , Zhou Zhenhua , Ni Shichang , Cai Jianhui
Published: October 2024

SYTL4 (Synaptotagmin Like 4) encodes a protein of synaptotagmin like protein family, which participates in intracellular membrane trafficking. Currently, its role and mechanisms in cancer remain unveiled, necessitating additional comprehensive analysis across different types of cancer to assess its potential in diagnosis, prognosis, chemotherapy, and immunotherapy in cancer. In our study, the mRNA level, threshold for copy number alterations, segmentation of masked copy number alterations, and methylation of SYTL4 DNA were analyzed based on data from TCGA pan-cancer cohort. miRNA, TCPA, mutation and clinical data were analyzed to evaluate diagnostic and prognostic significances of SYTL4. Then the results were checked using cBioPortal and GEO database. The protein levels were analyzed and evaluated based on HPA database and Clinical Proteomic Tumor Analysis Consortium (CPTAC). Biological roles of SYTL4 in pan-cancer were explored by GSEA. We use multiple immune infiltration algorithms in TIMER2.0 and TISCH database to cross-verify the associations between SYTL4 expression and tumor immune microenvironment. Additionally, we depicted a pan-cancer survival map and explored the differences of gene expressions among cancers with different molecular subtypes. Through chemotherapy data from CellMiner, GDSC, CTRP database, we clarified the relationship between SYTL4 and drug resistance. Finally, we explored the chemical substances that affect SYTL4 expression through CTD database. This study systematically and comprehensively reveals the functions of SYTL4 and potential clinical diagnostic and therapeutic predictive values of SYTL4 in pan-cancer.
MSH6 as a prognostic biomarker in bladder cancer and its correlation with immunity
Authors: He Ning , Bao Lu-ri , Fu Zhen-li , Gao Wu-niri , Wang Jing-yuan , Chen Li-Gang , meng Yan
Published: October 2024

This study aims to investigate the role of MSH6 in the diagnosis and prognosis of bladder cancer and its association with immune responses.Various analyses were conducted on The Cancer Genome Atlas (TCGA) data, and the results were validated using the Gene Expression Omnibus (GEO) database. The potential mechanism of MSH6 in bladder cancer was revealed using R tools, Gene Set Enrichment Analysis (GSEA), and Gene Ontology (GO) analysis. Bladder cancer patients admitted to the Affiliated Hospital of Inner Mongolia Medical University from June 2023 to December 2023 were enrolled. Pathological specimens of bladder cancer and adjacent tissues were obtained. The expression of MSH6 protein in bladder cancer and adjacent tissues was assessed by immunohistochemistry. High expression of MSH6 was identified as an independent prognostic factor for bladder cancer. The occurrence of bladder cancer was also influenced by age, pathological T stage, and pathological stage. According to the Kaplan-Meier survival curve, the overall survival rate of the MSH6 high-expression group was lower (P=0.003). Immunohistochemical results showed the expression of MSH6 in bladder cancer tissues was higher than in adjacent tissues. GSEA revealed a close association between MSH6 and the immune system. MSH6 may play a key role in immune infiltration in bladder cancer. MSH6 is closely related to the diagnosis and prognosis of bladder cancer, suggesting its potential utility as a biomarker for the diagnosis and prognosis of bladder cancer. MSH6 is closely related to the tumor immune microenvironment, implying a significant role in immunotherapy.
Beyond the Hertzsprung-Russell Diagram: An Enhanced Three-Dimensional Model Unveiling the Multidimensional Cosmos of Stars
Authors: Kumar Rohan
Published: October 2024

Despite its utility in identifying patterns in celestial objects, the Hertzsprung-Russell diagram is not supported in dim or small stars; it struggles to provide insights into certain celestial objects such as brown dwarfs. The purpose of this experiment is to create an improved version of the diagram with a three-dimensional model that includes a third z-axis to accurately predict and chart the life cycles of all stars regardless of size. The values of the stars’ absolute magnitude and color indices were used to chart the surface gravity and metallicity, variables that were chosen due to their ease of collection and their likeliness to be within the range of values being assessed. To obtain the values for the model, data points from the database GAIA DR2 were utilized via the TAP protocol to query the SQL database. The data was transferred into a local CSV file to facilitate data manipulation. The data could be read and interpreted, as dim stars would likely have higher values of these variables, making it easier to include them in the diagram. The Pandas DataFrames tool on Python 3 was used to organize and manage the data efficiently. Matplotlib Graphs visualized the relationships between different stellar attributes by developing a linear regression line and an algorithm and creating scatter plots and sky maps (Figure 11) to explore trends, hence designing three–dimensional diagrams. It was determined that the surface gravity diagram had a higher efficacy than metallicity due to their standard deviations of 0.4641441715272741 and 0.786577627976148, respectively.
Difference in leaf and root stoichiometric characteristics of Quercus rehderiana Hand.-Mazz. in forests with rocky and non-rocky desertification in Southwest China
Authors: Bai Xiao-Long , Feng Tu , Zou Shun , He Bin , Chen Yang , Li Wang-Jun
Published: October 2024

Quercus rehderiana Hand.-Mazz. is a genus of Quercus in the Fagaceae family, which widely distributed in Guizhou Province in Southwest China. It has important ecological significance in soil and water conservation, species diversity maintenance, and climate regulation. To date, the researches on stoichiometric characteristics of Quercus mainly focus on leaves, and few studies on roots. However, the difference of leaf and root stoichiometric characteristics of Quercus between in forests with rocky and non-rocky desertification are still unclear. In this study, we compared leaf (15 individuals) and root (9 individuals) carbon (C), nitrogen (N), phosphorus (P), potassium (K), calcium (Ca), magnesium (Mg) concentrations and their stoichiometric ratios in five 20 x 20 m quadrants of forests with rocky and non-rocky desertification. The aim was to find their resource strategies of adaptation to nutrient deficient soil environments in forests with rocky desertification. Our results show that leaf P and K concentrations in forest with non-rocky desertification were significantly higher than those in forest with rocky desertification, Ca and Mg concentrations were opposite. Root N, Ca and Mg concentrations in forest with rocky desertification were significantly higher than that in forest with non-rocky desertification, P and K concentrations were opposite. The N:P of leaves were greater than the threshold value of phosphorus (16) both in forests with rock and non-rocky desertification. Leaf P concentration was positively correlated with N concentration in forest with non-rocky desertification. Root N concentration was positively correlated with P concentration in forest with non-rocky desertification. C concentration of leaves and roots in forest with rocky desertification was negatively correlated with Ca concentration. In conclusion, leaf and root showed an obvious difference in nutrients and stoichiometric characteristics between in forests with rocky and non-rocky desertification. The growth of Q. rehderiana both in forest with rocky and non-rocky desertification was mainly limited by P. The trade-offs and synergies of nutrient absorption and utilization by different plant organs are both similar and different in different forests. Therefore, proper addition of N and P nutrients in plant growth period can promote plant growth and development, and help to improve the stability of forest ecosystem. The research results have practical significance for the vegetation restoration and protection in forests with rocky desertification.
Study on Cardiac Transcriptomic Changes and Inflammatory Responses Induced by Acute Kidney Injury in a Cardiorenal Syndrome Model
Authors: DING Xiaolu , HE Yuchen , LIU Xiaodan , WANG Chen
Published: October 2024

Cardiorenal syndrome (CRS) is a multifaceted relationship between the heart and kidney, where acute kidneys injury (AKI) directly contributes to cardiac dysfunction. The present study aimed to explore the changes of early transcriptome in heart exposed AKI via a mouse unilateral ureteral obstruction (UUO) model. This study was designed to extract differentially expressed genes (DEGs) and their implicated biological processes as well as pathways from the GSE235751 dataset of high-throughput gene expression profile via bioinformatics tools. Preprocessing-introduction of Data was undergone for data integrity and quality check, Differential expression analysis that identified significant gene expressions changes in heart tissue associated with AKI. Pathway analysis and functional annotation revealed involvement of inflammation, cardiac repair, mitochondrial function and autophagy as the major pathways influencing differences in gene expression. Between unrelated groups, validation of distinctly expressed genes was performed using Principal Component Analysis (PCA) and t-Distributed Stochastic Neighbor Embedding (t-SNE). Gene Set Enrichment Analysis (GSEA) showed downregulation of mitochondrial oxidative bioenergetics and autophagy, while upregulating cell proliferation inflammation pathways. These results indicate that AKI induces robust changes in cardiac gene expression, affecting many different pathways and provide novel information about the molecular mechanisms underlying CRS. These results identify possible early intervention and therapeutic targets for the better understanding and treatment of CRS.
The effects of PstR, a PadR family transcriptional regulatory factor, in Plesiomonas shigelloides are revealed by transcriptomics
Authors: Yan Junxiang , Zhang Zixu , Shi Hongdan , Xue Xinke , Li Ang , Liu Fenxia , Ding Peng , Guo Xi , Cao Boyang
Published: October 2024

Background: Plesiomonas shigelloides is a gram-negative opportunistic pathogen associated with gastrointestinal and extraintestinal diseases in humans. There have been reports of specific functional genes in the study of P. shigelloides, but there are also many unknown genes that may play a role in P. shigelloides pathogenesis as global regulatory proteins or virulence factors.
Results: In this study, we found a transcriptional regulator of the PadR family in P. shigelloides and named it PstR (GenBank accession number: EON87311.1), which is present in various pathogenic bacteria but whose function has rarely been reported. RNA sequencing (RNA-Seq) was used to analyze the effects of PstR on P. shigelloides, and the results indicated that PstR regulates approximately 9.83% of the transcriptome, which includes impacts on motility, virulence, and physiological metabolism. RNA-seq results showed that PstR positively regulated the expression of the flagella gene cluster, which was also confirmed by quantitative Real-Time Polymerase Chain Reaction (qRT-PCR) and lux assays. Meanwhile, the ΔpstR mutant strains lacked flagella and were non-motile, as confirmed by motility assays and transmission electron microscopy (TEM). Additionally, RNA-seq, qRT-PCR, and lux assays demonstrated that PstR also positively regulates T3SS expression, which aids in P. shigelloides' capacity to infect Caco-2 cells. Meanwhile, we also revealed that PstR negatively regulates fatty acid degradation and metabolism, as well as the regulatory relationship between PsrA, a regulator of fatty acid degradation and metabolism, and its downstream genes in P. shigelloides.
Conclusions: Overall, we revealed the effects of PstR on motility, virulence, and physiological metabolism in P. shigelloides, which will serve as a foundation for future research into the intricate regulatory network of PstR in bacteria.
The effect of proprioceptive neuromuscular facilitation techniques compared to aerobic exercise on balance, fear of falling, and quality of life in older adults: a randomized controlled trial
Authors: Kajbafvala Mehrnaz , Eshlaghi Mina Ansari , ShahAli Shabnam , pourkazem Fateme , Hejazi Anahita
Published: October 2024

Background
Aging is a long-term and unalterable phenomenon with changes in various systems such as cardiovascular, respiratory, neuromusculoskeletal, and vestibular. Exercise and physical activity reduce the progression of aging complications. Therefore, we examined the effect of proprioceptive neuromuscular facilitation techniques compared to aerobic exercise on balance, fear of falling, and quality of life in older adults.
Methods
Fifty-two older adults aged over 60 years (31 males, 21 females) were included. After initial evaluation, individuals were randomly assigned into two treatment groups (PNF techniques and aerobic exercise). Both treatment groups received 12 treatment sessions over 4 weeks. Balance, fear of falling, and quality of life were assessed at baseline and after a 4-week intervention. Analysis of covariance (ANCOVA) and paired samples t-test were utilized to between and within-group changes of variables.
Results
The results showed no significant differences in balance, fear of falling, and quality of life between groups after the intervention (P > 0.05). In within-group comparison, only the berg balance scale (BBS) significantly improved after the intervention (P < 0.05).
Conclusion
The findings suggest that PNF techniques in comparison with aerobic exercise could not contribute to improvement in balance, fear of falling, and quality of life. Therefore, more clinical trial studies with a control group are needed to determine the exact effects of these techniques.
Trial Registration Number (TRN) and date of registration:
The trial was registered at the (https://www.irct.ir), (IRCT20210505051181N4) on 9/2/2023.
Forecasting and comparing between five moderate geomagnetic storms in 2022 using artificial neural networks
Authors: Hegy Mostafa , Nahool Tareq
Published: October 2024

The current work investigates the precursor that follows coronal mass ejection (CME), through studying five moderate geomagnetic storms in 2022. We have employed the Artificial Neural Network (ANN) and supervised machine learning models to predict the SYM-H for geomagnetic storms during the solar cycle. The estimation yielded satisfactory accuracy including mean absolute error (MAE), mean square error (MSE), root mean square error (RMSE), and correlation coefficient (R2). To demonstrate the method's robustness, we have compared the predicted data set with real-world data and evaluated its performance against other supervised machine learning algorithms for regression problems, namely Decision Tree Regressor, Gradient Boosting Regressor, AdaBoost Regressor, and Linear Regression. Results revealed the proficiency of the ANN as an effective predicting tool over the Supervised machine learning for the SYM-H index.
Pediatric Hypoparathyroidism: Etiological and Clinical Evaluation in a Tertiary Center
Authors: Zümrüt Kocabey Sütçü , Kaplan Emel Hatun Aytaç , Önal Hasan
Published: October 2024

Purpose
This study aims to evaluate the etiology, clinical presentation, and management of pediatric hypoparathyroidism in a tertiary center.
Methods
A retrospective review was conducted on pediatric patients diagnosed with hypoparathyroidism at the Pediatric Endocrinology Clinic from March 2021 to June 2023. Data on demographic characteristics, presenting symptoms, laboratory findings, genetic analyses, and treatment outcomes were collected.
Results
A total of 56 patients (31 females, median age 5.5 years) were included. The etiology was genetic in 39 patients (70.9%), with syndromic forms, familial isolated hypoparathyroidism, and hypomagnesemia identified. Sixteen patients (29.1%) had acquired causes, primarily post-thyroid surgery and autoimmune conditions. Common symptoms included muscle spasms (32.7%) and seizures (21.8%). Laboratory findings revealed a median serum calcium level of 6.7 mg/dL and hyperphosphatemia in all patients. Treatment primarily involved calcitriol and calcium supplementation. Complications such as nephrocalcinosis and hypercalciuria were observed in some patients.
Conclusion
This study highlights the significant genetic component in pediatric hypoparathyroidism, necessitating comprehensive genetic evaluation and a multidisciplinary approach for effective management. Regular monitoring is essential to mitigate potential complications associated with long-term treatment.
Exploring the Photophysical Properties of Iridium (III) Complexes Using TD-DFT: A Comprehensive Study
Authors: Xinqi Ren , Yin Shiwei
Published: October 2024

Organic light-emitting diodes (OLEDs) are prominent in various applications, including screen displays, medical devices, and chemical sensors, due to their low power consumption, fast response speed, and high-resolution capability. Phosphorescent emitters, especially cyclometalated Ir(III) complexes, are particularly significant in OLEDs because they enable internal quantum efficiencies of up to 100% through strong spin-orbit coupling (SOC). This study focuses on the accurate characterization of singlet and triplet metal-to-ligand charge transfer (MLCT) states in Ir(III) complexes, which is essential for optimizing their performance. Using a combination of quantum mechanical methods, particularly time-dependent density functional theory (TDDFT) with optimally tuned range-separated functionals and the full-electron scalar relativistic Douglas-Kroll-Hess (DKH2) Hamiltonian, we evaluate the electronic structures and MLCT states of eight Ir(III) complexes. Our results highlight the efficacy of the tuned ω*B97X functional in predicting MLCT energies and higher-energy absorption peaks, demonstrating its superiority over conventional functionals like PBE0 and B3LYP. The inclusion of relativistic effects and SOC in our models ensures alignment with experimental absorption spectra, providing reliable benchmarks for computational approaches. This comprehensive analysis not only advances the understanding of MLCT transitions in phosphorescent materials but also aids in the design of new Ir(III) complexes with enhanced photophysical properties.
Design of a silver-zinc nanozeolite-based antibiofilm wound dressing activity in an in vitro biofilm model
Authors: Alobaid Sarah A. , Shrestha Sweta , Tasseff Morgan , Wang Bo , Hoek Monique L. , Dutta Prabir K.
Published: October 2024

Background
Infected wounds are a major health problem as infection can delay wound healing. Wound dressings play an important part in wound care by maintaining a suitable environment that promotes healing. Silver sulfadiazine dressings have been used for preventing infection in burn wounds. Presently, there are many commercial silver dressings that have obtained FDA clearance.
Results
In this study, we report on a novel silver dressing using microporous aluminosilicate zeolites, termed ABF-XenoMEM. Silver and zinc ion are encapsulated in the zeolite supercages. We show that the silver-zinc zeolite (AM30) alone is effective at inhibiting biofilm formation. The encapsulation protects the silver from rapidly precipitating in biological fluids. We exploit the negatively charged zeolite surface to associate positively charged quaternary ammonium ions (quat) with the zeolite. The combination of the AM30 with the quat enhances the antimicrobial activity. The colloidal nature of the zeolite materials makes it possible to make uniform deposits on a commercial extracellular matrix membrane to develop the final dressing (ABF-XenoMEM). The optimum loading of silver, zinc and quat on the dressing was found to be 30, 6 and 220 µg/cm2. Using a colony biofilm model, the activity of ABF-XenoMEM is compared with four well-studied silver-based commercial dressings towards mature biofilms of Pseudomonas aeruginosa (PAO1) and methicillin-resistant Staphylococcus aureus (MRSA). Cytotoxicity of the dressings was examined in HepG2 cells using the MTT assay.
Conclusion
This study shows that the ABF-XenoMEM is competitive with extensively used commercial dressings and demonstrates using a colony biofilm model that nanozeolite-entrapped antimicrobials have potential for alleviating biofilm-infected wounds.
The usefulness of conductimetric measurements for the proper interpretation of foaming properties on biopolymer interactions
Authors: Martinez Karina , Sanchez Cecilio Carrera
Published: October 2024

The bubbling method is unique in forming foam with precise control over the liquid and gas used, ensuring the exact density of the foam—unlike whipping and other techniques. This method also allows for analyzing parameters beyond the commonly studied foam volume and drainage or collapse time. In this study, we focused on the exact foaming time, gas volume incorporated, and liquid volume used for foam formation. Foam properties were measured using conductimetric and optical methods. Acidic conditions, typical in food and beverage preparation, can influence the performance of foams, especially when anionic polysaccharides are added for viscosity. These interactions may destabilize the foam. The objective was to examine the effect of polysaccharides on the formation and stability of foams made with whey protein isolate and two hydroxypropylmethylcelluloses (E4M and E50lv) under acidic conditions using the bubbling method. Whey protein isolate + E4M systems showed good liquid incorporation, while whey protein isolate + E50lv systems were highly efficient in gas incorporation, resulting in very stable foams with less liquid drainage.
Enrichment of electrogenic consortiums for the degradation of vinasses and molasses in MFC
Authors: Mijaylova-Nacheva Petia , Godoy-Lozano Elizabeth Ernestina , Oscar Guadarrama-Pérez , Alegría-Herrera Elian Yuritzi , Estrada-Arriaga Edson Baltazar , Jesús Hernández-Romano , Guadarrama-Pérez Victor Hugo
Published: October 2024

Energy production in bioelectrochemical systems is affected by microorganisms developed during the degradation processes of organic matter from wastewater from the sugar industry and alcoholic beverages such as tequila and mezcal. However, the efficiencies of chemical to electrical energy conversion remain insufficient for large scale implementation of this technology. Microorganisms used for bioelectricity generation; model organisms such as Geobacter sulfurreduscens and Shewanella oneidensis have been studied exhaustively. However, there are few reports about the capabilities of mixed consortiums for the degradation of organic matter and bioelectricity production. In the present study, the performance of MFC was evaluated with equivalent circuit modeling. Results suggest that internal resistances affect performance. In addition, capacitive and ion transport elements are also influenced by the consortiums that have been developed. Scanning electronic microscopy analysis showed differences in anodic biofilm density and, together with an analysis of amplicon sequences of the 16S rRNA gene, it was found that the substrate has a direct effect on the development of Electrogenic Microbial Consortiums (EMC) an their organic matter degradation and bioelectricity production capacities.
Assessing Microplastic Levels in the Al Hoceima Marine Protected Area: Effects on Finding Pollution Hotspots and Devising Conservation Strategies
Authors: BOUAZZATI Hasna , Damghi Asma , M’rini Abdelmounim El , KARIM Souhail
Published: October 2024

Global marine ecosystems are seriously threatened by microplastic contamination, which has prompted extensive research to determine its distribution and effects. This study uses glider operating data to analyze microplastic concentrations in the Al Hoceima Marine Protected Area (MPA). Our goal is to pinpoint spatial patterns that indicate hotspots for pollution and provide information for focused conservation initiatives. We seek to identify areas with higher microplastic concentrations by closely examining Microplastic Level graphs; we pay particular attention to temporal fluctuations. The findings show some interesting trends, like larger densities in the vicinity of fishing harbors and metropolitan centers, which may be related to human activity. Furthermore, we note fluctuations in pollution levels during various glider operation cycles, highlighting the significance of comprehending the spatiotemporal dynamics of microplastic dispersion. The marine protected area zones that have lower microplastic concentrations demonstrate how effective marine protected areas are at mitigating the consequences of pollution, highlighting the importance of conservation initiatives in preserving biodiversity and ecosystem resilience. In the end, our study broadens our knowledge of the stresses that humans place on marine environments and emphasizes the need of preventative conservation efforts to protect marine ecosystems from the dangers of microplastic pollution.
Single-cell Transcriptomic Profiling of Brains in Newborn Rats Following Hypoxic Ischemic Encephalopathy
Authors: Chen Xianbo , Tao Xiaohong , Wang Jingyu
Published: October 2024

Background
Neonatal hypoxic-ischemic encephalopathy (HIE) is a severe neurological condition associated with high rates of mortality or long-term disability. Despite its clinical significance, the detailed cellular mechanisms underlying HIE remain unclear. Single-cell RNA sequencing (scRNA-seq) has emerged as a powerful tool for investigating cellular heterogeneity across development, aging, and disease processes. However, no scRNA-seq studies have yet addressed neonatal HIE.
Methods
We employed scRNA-seq to examine cellular heterogeneity during the hyperacute (3 hours), acute (2 days), and subacute (7 days) phases of neonatal HIE. Uniform Manifold Approximation and Projection (UMAP) was used to visualize the cell clustering. Differentially expressed genes (DEGs) were calculated and identified using the Seurat’s FindAllMarkers function, which was enriched for pathway analysis (GO, KEGG pathway, WikiPathways, and Reactome Gene Sets). CytoTRACE v2 was used to identify the maturity state of each cell type and pseudotime analysis was performed using Monocle v3.
Results
We analyzed a total of 87,580 high-quality brain cells to identify transcriptional changes associated with HIE. In the hyperacute phase, we observed activation of astrocytes in response to reactive oxygen species, involvement of microglia in phagocytosis, Stat3-mediated ischemic responses in oligodendrocyte precursor cells, and an increase in senescent lymphatic endothelial cells. In the acute phase, astrocytes were found to exacerbate inflammation and impede brain development, while microglia proliferated. Neuroblasts were affected by metal ions, and oligodendrocytes decreased. In the subacute phase, astrocytes facilitated tissue repair, while inflammatory microglia highly expressing MHC II were induced by the IL27 and type I interferon pathways and expanded. Additionally, peripheral immune cells played vital roles in HIE. Specifically, neutrophils infiltrated and expanded throughout all phases post-HIE. Spp1high macrophages, T cells, and plasmacytoid dendritic cells increased during the acute and subacute phases, and B cells expanded during the subacute phase.
Conclusion
This study offers deep insights into the molecular alterations of key cell types following HIE, elucidating the pathological processes involved. These findings have significant implications for developing effective clinical strategies for managing HIE.
Enhancing Chickpea Growth via Arbuscular Mycorrhizal Fungal Inoculation: Facilitating Nutrient Uptake and Shifting Potential Pathogenic Fungal Communities
Authors: Basiru Sulaimon , Aitsimhand Khadija , Elfermi Rachid , Khatour Imad , Errafii Khaoula , Legeay Jean , Hijri Mohamed
Published: October 2024

The plant mycobiome makes essential contributions to the host life cycle in both healthy and diseased states. Arbuscular mycorrhizal fungi (AMF) are the most widespread plant symbionts associated with plant roots, and they perform numerous functions that contribute to plants’ health and physiology. However, there exist many knowledge gaps in how the interactions between AMF and host plants’ root mycobiomes influence the performance of host plants. To this end, we inoculated a local chickpea cultivar grown in an agricultural soil under semi-controlled conditions with Rhizophagus irregularis. The plants were subjected to low or normal levels of phosphorus (P) fertilization. In addition to examining mycorrhizal colonization, plant biomass, and mineral nutrition, we sequenced the ITS region of the rDNA to assess the chickpea mycobiome and identify key fungal taxa potentially responding to AMF inoculation. Our results showed that AMF inoculation had a stronger effect on chickpea aboveground biomass, in addition to mineral nutrition; whereas P fertilization had a more profound effect on belowground traits. Specifically, AMF promoted shoot (p = 0.06), root (p = 0.001), and total aboveground biomass (p = 0.01), while P fertilization enhanced root biomass (p = 0.02), in addition to root diameter (p = 0.007), root volume (p = 0.01), and root length (p = 0.08). Furthermore, the total P (p = 0.05) and Na contents (p = 0.09) were enhanced in the aboveground biomass by AMF inoculation. ITS metabarcoding revealed Ascomycota as the dominant phylum in both roots and soil biotopes, followed by Basidiomycota, Chytridiomycota, Glomeromycota, Monoblepharomycota, Mucoromycota, and Rozellomycota. Ten ASVs were significantly impacted by AMF inoculation in chickpea roots, including important plant pathogens belonging to Didymella, Fusarium, Neocosmospora, and Stagonosporopsis. Surprisingly, a correlation was established between shoot biomass and some fungal taxa that were differentially abundant in roots. This study confirms the significance of AMF inoculation not for only improving chickpeas’ growth and mineral nutrition in semi-arid conditions but also for shaping plants’ fungal community composition, thereby promoting resilience against both biotic and abiotic stressors.
Machine Learning Modelling of Anchovy Waste Treatment Using Solar Drying
Authors: Mohammed NAJJAR , Zakaria TAGNAMAS , Younes BAHAMMOU , Hamid BOUYGHF , Mohammed NAHID
Published: October 2024

This study aims to valorize co-products from the anchovy processing chain by obtaining compounds of interest through the implementation of environmentally friendly and energy-efficient techniques. These methods, which also apply to other fresh anchovy waste co-products, seek to minimize the environmental pollution associated with conventional systems. The investigation focused on the application of the solar drying as a treatment of anchovy waste. The resulting data were employed to model the drying behavior of anchovy waste using five machine learning algorithms. A thermo-kinetic study was conducted under both natural and forced convection solar drying to establish the optimal conditions for drying and storing sardine heads, which are a significant source of high-quality proteins for human and animal nutrition. Drying kinetics were examined at three temperatures (60°C, 70°C, and 90°C) and two airflow rates (150 m³/h and 300 m³/h). The study identified air drying temperature as the most critical factor affecting the drying kinetics of sardine heads. A machine learning modelling of Anchovy waste solar drying was conducted, evaluated models were RNN, LSTM, GRU, LightGBM, and CatBoost. CatBoost demonstrated superior performance in predicting moisture content. It achieved the lowest Mean Squared Error (MSE) of 1.1491e-06, the lowest Mean Absolute Error (MAE) of 0.0006265, and the highest coefficient of determination (R²) of 99.99%. The comparative analysis highlighted distinct differences in the predictive accuracy of the models, with CatBoost emerging as the most effective.