bluuebunny/crossref_metadata_2025 huggingface dataset:
Study on the synergistic effect of NOx and CO2 emission reduction in the industrial sector of Guangzhou
Authors: Qin Xingcun , Xie Pengcheng , Liao Cuiping
Published: January 2025

Introduction

As a major source of pollutant and CO2 emissions, the industrial sector faces the dual challenge of pollution control and carbon reduction. Accurately identifying the synergy between pollutant and carbon emissions in different regions’ industrial sectors is crucial for developing regional policies for coordinated pollution reduction and carbon abatement.

Methods

This study takes Guangzhou as a case study to quantitatively assess the synergistic effect of NOx and CO2 emissions reduction in its industrial sector. First, the LMDI decomposition method was applied to analyze the factors influencing the change in NOx emissions in Guangzhou’s industrial sector. Next, the CFGLS model was used to quantify the synergistic effect between NOx and CO2 emissions. Finally, a robustness check was conducted on the results.

Results and discussion

The findings indicate that the synergistic effect in carbon reduction is the most significant driver of NOx reduction in Guangzhou’s industrial sector, with a 10,000-ton reduction in CO2 emissions leading to a 0.4-ton decrease in NOx emissions. The interaction effect analysis shows that increasing the use of natural gas and reducing energy intensity do not amplify this synergy. The results could provide valuable insights for coordinated pollution reduction and carbon abatement policies designing in Guangzhou’s industrial sector.
An in-depth analysis of two common methodologies used to derive hourly solar radiation values from daily ones: pros and cons
Authors: Kambezidis Harry D.
Published: January 2025

Solar radiation comprises the primary renewable source of energy on Earth and has so been exploited in the last 20 years. Despite this, solar radiation measurements are scarce worldwide, thus giving space to modelling. Nevertheless, modelling solar radiation at an hourly level is nowadays required for a short-term output forecast from solar installations. The daily global solar radiation decomposition models are one category of solar models that convert daily solar radiation values to hourly ones. The Collares-Pereira and Rabl (CPR) and Collares-Repeira, Rabl and Gueymard (CPRG) models have shown to provide a better performance than others at individual sites without exhibiting any sign of universality on the other hand. The current study looks at this gap. In this regard, twelve sites are selected around the world. To estimate hourly values, the CPR and CPRG models are applied to daily solar radiation estimates for each site in particular years. Hourly data sets that are openly accessible provide the daily values. Additionally, daily and monthly values are derived from the estimated and observed hourly values. The hourly, daily, and monthly scales are used to compare the two models’ performances. The CPR model outperforms the CPRG model across all sites and time scales. A universal coefficient of correction is used to further enhance the CPR performance, bringing the CPR-estimated solar radiation very close to the observed one.
Molecular assessment of splicing variants in a cohort of patients with inborn errors of immunity: methodological approach and interpretation remarks
Authors: Miguel Berenguel Laura , Gianelli Carla , Matas Pérez Elisabet , del Rosal Teresa , Méndez Echevarría Ana , Robles Marhuenda Ángel , Feito Rodríguez Marta , Caballero Molina Maria Teresa , Magallares García Lorena , Sánchez Garrido Brenda , Hita Díaz Samantha , Allende Martínez Luis , Nozal Aranda Pilar , Cámara Hijón Carmen , López Granados Eduardo , Rodríguez Pena Rebeca , Bravo García-Morato María
Published: January 2025

Background

Splicing is the molecular mechanism to produce mature messenger RNA (mRNA) before its translation into protein. It is estimated that 50% of disease-causing mutations disrupt splicing, mostly of them affecting canonical positions. However, variants occurring in coding regions or deep-intronic variants can also affect splicing. In these cases, interpretation of the results may be challenging and molecular validation is required.

Methods

The study includes 23 patients with splicing variants out of a cohort of 187 patients diagnosed with inborn errors of immunity (IEI). Clinical features and immunophenotypes are shown. Reverse transcription-polymerase chain reaction (RT-PCR) is the molecular assay employed for pathogenicity validation.

Results

We detected 23 patients of 20 pedigrees with splicing variants in IEI genes, which constitutes the 12.3% of our cohort. In total, 21 splicing variants were analyzed, 10 of which had previously been reported in the literature and 11 novel ones. Among the 23 patients, 16 showed variants at canonical splice sites. Molecular validation was required only in the cases of genes of uncertain significance (GUS), high homology pseudogenes or incompatible clinical phenotype. Seven patients showed variants outside canonical positions. All of them needed molecular validation, with the exception of two patients, whose variants had previously been well characterized in the medical literature.

Conclusion

This study shows the proportion of splicing variants in a cohort of IEI patients, providing their clinical phenotypic characteristics and the methodology used to validate the splicing defects. Based on the results, an algorithm is proposed to clarify when a splicing variant should be validated by complementary methodology and when, by contrast, it can be directly considered disease causing.
Radiomics-based biomarker for PD-1 status and prognosis analysis in patients with HCC
Authors: Hapaer Gulizaina , Che Feng , Xu Qing , Li Qian , Liang Ailin , Wang Zhou , Ziluo Jituome , Zhang Xin , Wei Yi , Yuan Yuan , Song Bin
Published: January 2025

Purpose

To investigate the impact of preoperative contrast-enhanced CT-based radiomics model on PD-1 prediction in hepatocellular carcinoma (HCC) patients.

Methods

The study included 105 HCC patients (training cohort: 72; validation cohort: 33) who underwent preoperative contrast-enhanced CT and received systemic sorafenib treatment after surgery. Radiomics score was built for each patient and was integrated with independent clinic radiologic predictors into the radiomics model using multivariable logistic regression analysis.

Results

Seventeen radiomics features were finally selected to construct the radiomics score. In multivariate analysis, serum creatine and peritumoral enhancement were significant independent factors for PD-1 prediction. The radiomics model integrated radiomics signature with serum creatine and peritumoral enhancement showed good discriminative performance (AUC of 0.897 and 0.794 in the training and validation cohort). Overall survival (OS) was significantly different between the radiomics-predicted PD-1-positive and PD-1-negative groups (OS: 29.66 months, CI:16.03-44.40 vs. 31.04 months, CI: 17.10-44.07, P<0.001). Radiomics-predicted PD-1 was an independent predictor of OS of patients treated with sorafenib after surgery. (Hazard ratio [HR]: 1.61 [1.23-2.1], P<0.001).

Conclusion

The proposed model based on radiomic signature helps to evaluate PD-1 status of HCC patients and may be used for evaluating patients most likely to benefit from sorafenib as a potentially combination therapy regimen with immune checkpoint therapies.
Functional and structural characterization of mouse Factor H-related B protein unveils a novel dimerization domain shared by FHR-B and FH
Authors: Martín-Ambrosio Doménech Adrián , González Sanz Silvia , Márquez Tirado Bárbara , Juana-López Lucia , Goicoechea de Jorge Elena , Rodríguez de Córdoba Santiago , Martín Merinero Héctor
Published: January 2025

Factor H-related proteins (FHRs) are found in mice, but their equivalence to human FHRs remains uncertain. This study identifies three FHRs in mouse plasma (FHR-B, FHR-C, and FHR-E) and focuses on characterizing FHR-B. Using purified plasma proteins and recombinant mutants, FHR-B was found to form dimers and bind strongly to C3, C3b, iC3b, and C3dg. It also competes with mouse Factor H (mFH) for binding to C3b-coated surfaces and disrupts mFH regulation in hemolysis assays with sheep and guinea pig erythrocytes. These functions are localized to the C-terminal region and are dependent on FHR-B dimerization. Dimerization occurs through the N-terminal region (SCR1-3), which differs from mFH SCR5-7 by only four amino acids and also shares significant homology with human FHR-3 and human FH SCR5-7. In contrast to FHR-1, AUC experiments indicate that FHR-B dimerization is pH-sensitive, reversible and that the monomers in the dimer present the same head to tail orientation. Mutant analyses revealed that mFH SCR5-7 also forms dimers, but less efficiently than FHR-B. Notably, substituting FHR-B Tyr162 (a key residue homologous to the disease-associated Tyr402 in human FH) for His reduces dimerization. We also found that a recombinant FHR-B with a duplicated dimerization domain formed stable dimers but lacked functional activity. Overall, FHR-B shows structural and functional similarities with various human FHRs, suggesting convergent evolution between mouse and human FHRs. Furthermore, this study reveals a novel dimerization domain shared by FHR-B and mouse FH and illustrates the importance of dimerization and monomer orientation in FHRs activity. It also underlines notable differences between human and mice FHRs that should be further explored before modeling FHR-associated human diseases in mice.
Vaccines for cancer interception in familial adenomatous polyposis
Authors: Johnson David E. , Disis Mary L.
Published: January 2025

Familial adenomatous polyposis (FAP) is an inherited autosomal dominant disorder caused by germline mutations in the adenomatous polyposis coli (APC) gene. FAP is associated with the development of hundreds of adenomas in the small and large intestines of individuals starting in the teenage years with a near 100% risk of developing colorectal cancer by adulthood. Eventually polyps develop throughout the gastrointestinal tract. Chemoprevention approaches have been somewhat successful in reducing polyp burden, but have not reduced the risk of the development of colorectal cancer or other cancers. The lack of efficacy of more standard drug approaches may be due to limited exposure to the agent only to specific periods while the drug is being metabolized, limited drug penetrance in the colon, and patient adherence to daily dosing and drug side effects. The success of immune therapy for the treatment of invasive cancer has led to research focused on the use of immune based approaches for polyp control in FAP, specifically polyp directed vaccines. Vaccines targeting antigens expressed in FAP lesions may be a superior method to control polyp burden and prevent disease progression as compared to classic chemoprevention drugs. A limited number of vaccines can be administered over a short period of time to generate a lasting immune response. Appropriately primed antigen specific T-cells can traffic to any site in the body where antigen is expressed, recognize, and eliminate the antigen expressing cell. Immunologic memory will allow the immune response to persist and the specificity of the immune response will limit toxicity to the targeted polyp. This review will examine the current state of vaccines directed against FAP lesions and highlight the challenges and opportunities of translating vaccines for cancer interception in FAP to the clinic.
Donor-derived cell-free DNA for detection of acute rejection in lung transplant recipients
Authors: Yavuz Gökce , Walter Julia , Hirv Kaimo , Wachter Oliver , Dick Andrea , Kovacs Julia , Zimmermann Julia , Glueck Olaf M. , Vorstandlechner Maximilian , Samm Nicole , Fertmann Jan M. , Sienel Wulf , Michel Sebastian , Irlbeck Michael , Kneidinger Nikolaus , Hatz Rudolf , Behr Jürgen , Schneider Christian , Kauke Teresa
Published: January 2025

Introduction

Acute rejection is a significant risk factor for developing chronic lung allograft dysfunction. Current monitoring tools, transbronchial biopsies and HLA antibody determination, have limitations in detecting acute rejection. This study aims to explore the potential utility of donor-derived cell-free DNA (ddcfDNA) as a non-invasive biomarker for detecting acute rejection in lung transplant recipients (LTR).

Methods

We developed a molecular method based on digital droplet PCR to determine the total amount and the proportion of ddcfDNA. Using blood samples collected sequentially post-transplant from a cohort of 81 LTR, we compared median levels of %ddcfDNA in patients with acute cellular rejection (ACR), antibody-mediated rejection (AMR), infection, or decline in pulmonary function (FEV1).

Results

Median %ddcfDNA levels were significantly higher in groups with ACR (1.92% [0.70%, 2.30%], p=0.0006), AMR (1.27% [0.34%, 2.29%], p=0.0009), isolated lymphocytic bronchiolitis (0.54% [0.23%, 2.18%], p=0.03), and infection or prolonged ventilation over 30 days (0.50% [0.22%, 2.35%], p=0.005) versus stable allograft function group (0.26% [0.09%, 0.60%]). %ddcfDNA levels were also elevated in patients with FEV1 loss compared to those with stable or improving FEV1 after 12 months (1.98% vs. 1.36%, p=0.04). An optimal cut-off of 0.73% for %ddcfDNA was calculated to detect ACR and AMR with 80% specificity and 68% sensitivity.

Discussion

%ddcfDNA is a promising biomarker for identifying allograft injury due to acute rejection in LTR and could be a valuable tool for monitoring allograft health.
Estimates of disclosure and victimization rates for fishery observers in the maritime workplace
Authors: Jeroue Lacey , Faunce Craig , Kingham Andy , Smith Jaclyn
Published: January 2025

Seafarers working in remote ports and onboard fishing vessels often face isolated, high-risk environments, making them vulnerable to sexual harassment, intimidation, and assault. In the United States and other countries, scientists, called fishery observers, are required by the government to be deployed alongside fishing crews for extended periods to collect essential fisheries data and report potential fishing regulation violations they witness. Although many fishery observers who experience harassment submit official report statements, the true prevalence of the problem is unknown due to nondisclosure. This study uses anonymous responses from annual surveys distributed to North Pacific groundfish and halibut fishery observers to understand barriers to disclosure and estimate disclosure rates. By adjusting the annual counts of observers who submitted official harassment statements with these estimated disclosure rates, we provide the first estimates of the true number of victimized observers (prevalence) each year in a federal fisheries monitoring program in the United States. Model selection suggested that disclosure was influenced by the type of harassment experienced and not by observer demographics or employment year. Estimated disclosure rates (victimized observers who reported annually via official statement) were lowest for sexual harassment (0.18; 95% CI 0.11-0.29); higher for intimidation, coercion and hostile work environments (0.37; 95% CI 0.28-0.47); and highest for assault (0.57; 95% CI 0.41-0.73). Overall, 45% (95% CI 39-51%) of observers who experienced victimization disclosed harassment in a given year. We estimate that 22-38% of observers were victimized annually during the 2016-2022 study period, with rates of 24-60% for females and 12-24% for males. Victimization rates computed from raw survey summary statistics suffer from self-selection bias while rates derived solely from submission of official statements suffer from bias in underreporting. Supplementing official statements with estimates of disclosure rates from anonymous survey data provides a means of mitigating for these two forms of biases to obtain estimates of victimization untangled from fluctuations in reporting tendencies. When disclosure and victimization are teased apart, the effectiveness of risk reduction strategies can be better assessed over time.
Advanced visual sensing and control in CMT-based WAAM processes
Authors: Yu Rui , Li Wenhang , Wu Mingfang , Wang Jianxin , Han Qinglin , Wang Jiayou , Bing Siyu
Published: January 2025

Wire Arc Additive Manufacturing (WAAM) can flexibly produce high-performance parts that meet the requirements of deep-sea environments, but it has problems with insufficient molding accuracy and surface smoothness, which require improved precision and quality. To address these challenges, this paper establishes a WAAM experimental system based on Cold Metal Transfer (CMT) technology. First, the influence of process parameters on multi-layer single-channel forming was studied. Second, a structured light visual sensing system based on a high-speed camera was developed. Finally, a method for controlling the camera’s triggering mode at low voltage was designed, effectively eliminating arc interference. The experiment extracted and preprocessed the laser stripe ROI (Region of Interest), extracted geometric size information of the weld seam, and then performed median filtering to extract the centerline and feature points. By constructing a CMT-based WAAM monitoring system, high reliability and quality control of the manufacturing process and weld formation have been achieved.
Mapping the landscape and research trend of imaging diagnosis in lymphoma: a bibliometric analysis from 1976 to 2024
Authors: Ma Yi
Published: January 2025

Background

Over the past five decades, extensive research has been conducted on lymphoma imaging diagnostics; however, no bibliometric analysis has been performed in this area. Therefore, we undertook a bibliometric analysis to clarify the progress and current state of research in this field.

Methods

We conducted a search of the Web of Science Core Collection database for articles related to imaging diagnosis and lymphoma, focusing exclusively on English-language publications up to June 20, 2024. We analyzed and visualized various aspects, including publication trends, journals, co-authorship networks, countries, institutions, and keywords. To examine research trends in this field, we utilized bibliometric analysis tools such as VOSviewer, CiteSpace, and R4.3.3.

Results

From 1976 to 2024, a total of 10,410 publications were produced on this topic, with 2021 marking the peak in publication numbers. The most significant contributions in this research area were found in the fields of Radiology, Nuclear Medicine & Medical Imaging, Oncology, and Hematology. The United States, China, and Japan were the leading contributors. Zucca Emanuele ranked first among authors, followed closely by Meignan Michel. In terms of institutions, Assistance Publique Hôpitaux de Paris was the most prominent. The most frequently used keywords included positron emission tomography, computed tomography, and non-Hodgkin’s lymphoma.

Conclusion

This study presented a bibliometric analysis of lymphoma imaging diagnosis, highlight showcasing research trends, influential significant studies, and collaborative networks. The analysis identified key contributions to the field and provide insights for future research directions.
Dual-stream disentangled model for microvascular extraction in five datasets from multiple OCTA instruments
Authors: Hu Xiaoyang , Hao Jinkui , Yi Quanyong , Zhao Yitian , Zhang Jiong
Published: January 2025

Introduction

Optical Coherence Tomography Angiography (OCTA) is a cutting-edge imaging technique that captures retinal capillaries at micrometer resolution using optical instrument. Accurate segmentation of retinal vasculature is essential for eye related diseases measurement and diagnosis. However, noise and artifacts from different imaging instruments can interfere with segmentation, and most existing deep learning models struggle with segmenting small vessels and capturing low-dimensional structural information. These challenges typically results in less precise segmentation performance.

Methods

Therefore, we propose a novel and robust Dual-stream Disentangled Network (D2Net) for retinal OCTA microvascular segmentation. Specifically, the D2Net includes a dual-stream encoder that separately learns image artifacts and latent vascular features. By introducing vascular structure as a prior constraint and constructing auxiliary information, the network achieves disentangled representation learning, effectively minimizing the interference of noise and artifacts. The introduced vascular structure prior includes low-dimensional neighborhood energy from the Distance Correlation Energy (DCE) module, which helps to better perceive the structural information of continuous vessels.

Results and discussion

To precisely evaluate our method on small vessels, we delicately establish OCTA microvascular labels by performing comprehensive and detailed annotations on the FOCA dataset, which includes data collected from different instruments, and evaluated the proposed D2Net effectively mitigates the challenges of microvasculature region recognition caused by noise and artifacts. The method achieves more refined segmentation performance. In addition, we validated the performance of D2Net on four OCTA datasets (OCTA-500, ROSE-O, ROSE-Z, and ROSE-H) acquired using different instruments, demonstrating its robustness and generalization capabilities in retinal vessel segmentation compared to other state-of-the-art methods.
Fermented sugarcane juice-derived probiotic Levilactobacillus brevis RAMULAB54 enhances lipid metabolism and glucose homeostasis through PPAR-γ activation
Authors: Kumari V. B. Chandana , Ramu Ramith , Huligere Sujay S. , Patil Shashank M. , Nayakvadi Shivasharanappa , Bijoor Sharath , Manjappara Uma Venkateswaran , Ahmed Mohammad Z. , Wong Ling Shing
Published: January 2025

The gut microbiota plays a significant role in metabolic disorders such as diabetes and obesity, with the peroxisome proliferator-activated receptor gamma (PPAR-γ) being a key regulator in adipogenesis and glucose metabolism. This study is a novel approach that explores the antihyperglycemic and antihyperlipidemic effects of Levilactobacillus brevis RAMULAB54 (LB13243), isolated from fermented sugarcane juice. LB13243 was cultured for SEM imaging, and its supernatant (LBR54) was analyzed. Organic acid interactions with PPAR-γ were evaluated via molecular docking, while cytotoxicity and adipocyte differentiation in 3T3-L1 cells were tested using MTT assays, Oil Red O staining, triglyceride quantification, and qRT-PCR. In vivo, male Wistar rats in hyperlipidemic and streptozotocin-induced hyperglycemic models were treated with LB13243 for 4 weeks, followed by analysis of food intake, body weight, serum glucose, lipids, and histopathology. LB13243 inhibited carbohydrate-hydrolyzing enzymes and showed an organic acid profile. In silico, hydroxycitric acid had similar binding to PPARγ as rosiglitazone (binding energy:−8.4 kcal/mol vs.−8.3 kcal/mol), with greater stability (RMSD: 1.2 Å vs. 1.7 Å). Pharmacokinetics indicated moderate GI absorption (20%) and low toxicity for hydroxycitric acid. LBR54 did not affect 3T3-L1 cell viability but reduced lipid accumulation by 13% and triglycerides by ≤ 44 mg/dL. qRT-PCR revealed upregulation of PPAR-γ and C/EBP-α, and downregulation of FAS, suggesting modulation of adipogenesis. In vivo, LB13243 reduced food intake, weight gain, and normalized organ weights in hyperlipidemic rats, while improving glucose levels and lipid profiles in hyperglycemic models. Histopathology showed improved tissue structure, indicating LB13243's potential to reduce hyperglycemia and hyperlipidemia by modulating lipid metabolism and inflammation. LB13243's modulation of PPAR-γ suggests it as a promising natural option for managing diabetes and hyperlipidemia. This study also highlights LB13243's distinctive capability to modulate PPAR-γ through its organic acids, particularly hydroxycitric acid, providing novel insights into its therapeutic potential.
Fungal planktonic community related to salinity and temperature in an oligotrophic sea
Authors: Asseri Ashwag A. , Coello-Camba Alexandra , Agustí Susana
Published: January 2025

Marine fungi play a crucial role in carbon cycling and food webs by acting as saprophytes or parasites and shaping host communities. However, our knowledge of these fungi in the marine ecosystem remains limited. To address this gap, we conducted a study to investigate the diversity of planktonic fungal communities in the Red Sea, a warm and oligotrophic sea. We collected water samples from the photic layer at six sites along the Red Sea basin and analyzed the fungal community by targeting the 28S rRNA gene. Our results showed that Chytridiomycota dominated these communities, accounting for 85% of reads, followed by members of the divisions Basidiomycota (4.7%) and Cryptomycota (4.13%). Interestingly, we found that fungal communities did not exhibit significant changes with depth or chlorophyll concentration. However, they did vary with the latitudinal gradient in environmental conditions, which is characterized by high temperature (ranging from 22.3 to 27.0°C) and salinity (ranging from 38.0 to 40.4 PSU). Specifically, the proportions of Chytridomycetes and Neocallimastigomycetes (the two dominant classes of Chytridiomycota) were negatively correlated between themselves. Chytridomycetes exhibited a negative correlation with temperature (R2 = 0.60, p = 0.0028) and a positive correlation with salinity (R2 = 0.49, p = 0.010), being more abundant in the northern Red Sea. Conversely, Neocallimastigomycetes showed an increase in abundance with increasing temperature (R2 = 0.61, p = 0.0026) and a decrease with increasing salinity (R2 = 0.40, p = 0.026), making them more prevalent in the southern Red Sea. Overall, our study described a differential distribution of the most dominant fungal classes, with potential significance in their control of planktonic populations and consequent influence in the carbon cycle in the Red Sea ecosystem. These findings underscore the importance of further research to better understand the role of marine fungi in ecosystem functioning.
Selection and evaluation of reference genes for qRT-PCR in Inonotus obliquus
Authors: Li Lulu , Guo Xiaofan , Wang Shouming
Published: January 2025

Real-time quantitative reverse transcription PCR (RT-qPCR) is one of the most effective tools for studying gene expression. Inonotus obliquus is a rare and edible medicinal fungus. Selecting an appropriate reference gene is crucial for researching its gene function. In this study, we selected 11 potential reference genes of Inonotus obliquus. Subsequently, we applied GeNorm, NormFinder, and BestKeeper algorithms to evaluate the expression stability of these 11 reference genes. Under varying carbon sources, VPS exhibited good stability and was suitable as an internal reference gene. Under different nitrogen sources, RPB2 was the most stable reference gene. For varying growth factors, PP2A was the most stable reference gene. At different pH levels, UBQ showed the highest stability. Under different temperature conditions, RPL4 was the most stable. In different strains, RPL2 was the most stable reference gene, while VAS demonstrated the greatest stability across different growth stages. Overall, VPS was the most recommended reference gene for the entire sample set. This study provides a foundation for the further application of RT-qPCR in the gene expression analysis of Inonotus obliquus.
The synergistic role of gut microbiota and RNA in metabolic diseases: mechanisms and therapeutic insights
Authors: Huang Zhuo , Yao Qinyan , Ma Shuang , Zhou Jinjie , Wang Xiaoxuan , Meng Qingguo , Liu Yaxin , Yu Zihan , Chen Xin
Published: January 2025

The gut microbiota plays a pivotal role in human metabolic health by influencing immune responses, digestion, and metabolic homeostasis. Recent research highlights the intricate interactions between gut microbiota and RNA, especially non-coding RNAs, in regulating metabolic processes. Dysbiosis of the gut microbiota has been linked to metabolic disorders such as type 2 diabetes, obesity, metabolic-associated fatty liver disease (MAFLD) and metabolic heart disease. Microbial metabolites, including short-chain fatty acids (SCFAs), modulate RNA expression, influencing lipid metabolism, glucose regulation, and inflammatory responses. Additionally, microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) serve as critical regulators in these processes, with emerging evidence showing that gut-derived metabolites affect post-transcriptional gene regulation. This review synthesizes the current understanding of the gut microbiota-RNA axis and its role in metabolic diseases. By exploring the molecular mechanisms, particularly how gut microbiota-derived signals modulate RNA pathways, the review underscores the potential of targeting this axis for therapeutic interventions. Furthermore, it examines how dysbiosis leads to epigenetic changes such as m6A RNA methylation, contributing to disease pathogenesis. These insights offer a new perspective on the prevention and treatment of metabolic diseases, with potential applications in personalized medicine.
Age and diet affect self-resilience of intestinal microbiome in mice
Authors: Shao Chenyi , Chen Shenmin , Yang Huan , Li Mufan , Liu Yinhui , Wen Shu , Xiao Jing , Tang Li
Published: January 2025

Background

Gut microbiota contributes to human health. Little is known about the self-resilience of the gut microbiota after dysbiosis. This study aimed to investigate the self-resilience of the gut microbiome at different ages and the effects of diet on its recovery capacity in adulthood.

Methods

A rodent model of antibiotic-induced dysbiosis was used. Microscopy was used to observe morphological changes in the mucosa. In addition, 16S rRNA sequencing and polymerase chain reaction-denaturing gradient gel electrophoresis were performed to identify the bacterial taxa and microbiome structure, respectively.

Results

The diversity of the gut microbiota in infant mice was recovered by the sixth week, while relative abundance of Ruminococcaceae_UCG_014 was low and did not return to normal levels. Gut microbiota in young adult mice recovered in the fourth week. Prevotellaceae and Alloprevotella were significantly higher in the high-fat-diet group than those in the control group. The elderly mice had three, two, four, and seven statistically different genera between the dysbiosis and control groups at weeks 6, 8, 10, and 12, respectively. Intestinal epithelial structure and cecum index are restored with microbiota repaired.

Discussion

The gut microbiota in infant and adult mice is more capable of self- resilience, the composition of the microbiota and mucosal morphology of the intestine can be largely restored. Adding protein and fat to the diet accelerated colony recovery in young adult mice in the short term. In elderly mice, the resilience of the gut microbiota was reduced, and the occurrence of dysbiosis at this stage may accelerate organismal aging and affect the lifespan. A limitation of this study is that all data were derived from mice. Therefore, we must be cautious about translating the microbiome results from mice to humans.
The small GTPases FoRab5, FoRab7, and FoRab8 regulate vesicle transport to modulate vegetative development and pathogenicity in Fusarium oxysporum f. sp. conglutinans
Authors: Tan Xiangyu , Chen Lin , Chen Ying , Li Yuxin , Lu Lihan , Li Erfeng
Published: January 2025

Rab GTPases play a crucial role in facilitating the transportation of vesicles during the process of fungal biogenesis. Currently, there is limited understanding regarding the specific biological functions of Rab small GTPase elements within Fusarium oxysporum. In this study, we examined the three proteins FoRab5, FoRab7, and FoRab8 of Foc, which exhibit homology to the Rab protein family found in Saccharomyces cerevisiae. In addition, we also employed a PEG-mediated homologous recombination approach to create deletion mutants and complementary strains for the FoRab5, FoRab7, and FoRab8 genes, thereby facilitating a comprehensive investigation into the functional roles of these genes. FoRab5 was localized on vesicles of various sizes within the cell. Compared to the wild-type strain, the growth rate of the mutant ΔFoRab5 strain decreased, the aerial hyphae decreased, the sporulation decreased, and the spore germination rate decreased. The sensitivity to cell membrane stress, cell wall stress, and endoplasmic reticulum stress increased, the activity of laccase and glucoamylase decreased significantly, and the pathogenicity to cabbage seedlings decreased. FoRab7 was localized on the vacuolar membrane. Compared to the wild type, the growth rate of the mutant ΔFoRab7 strain decreased, the bacteria produced a large amount of pigment deposition, the aerial hyphae decreased significantly, the hyphal branches increased, and the mutant almost lost the ability to produce spores. The sensitivity to osmotic stress, cell membrane stress, cell wall stress, metal ion stress, and endoplasmic reticulum stress was enhanced, and the vacuole was fragmented. Laccase and glucoamylase activities decreased in a significant manner. Moreover, there was a decrease in the pathogenicity of cabbage seedlings. FoRab8 was localized at the tip of the mycelium. Compared to the wild type, the growth rate of the mutant ΔFoRab8 strain decreased, the sporulation decreased, and the sensitivity of the mutant to osmotic stress and endoplasmic reticulum pressure increased. There was a significant decrease in the activity of laccase, glucoamylase, and cellulase. A reduction in the pathogenicity to cabbage seedlings occurred. In summary, these results indicate that members of the Rab family proteins FoRab5, FoRab7, and FoRab8 regulate a series of processes such as growth, sporulation, pathogenicity, and ectoenzyme secretion in Foc.
A One Health approach for the genomic characterization of antibiotic-resistant Campylobacter isolates using Nanopore whole-genome sequencing
Authors: Hurtado Ana , Ocejo Medelin , Oporto Beatriz , Lavín José Luis , Rodríguez Ruth , Marcos María Ángeles , Urrutikoetxea-Gutiérrez Mikel , Alkorta Miriam , Marimón José María
Published: January 2025

In response to the growing threat posed by the spread of antimicrobial resistance in zoonotic Campylobacter, a One Health approach was used to examine the genomic diversity, phylogenomic relationships, and the distribution of genetic determinants of resistance (GDR) in C. jejuni and C. coli isolates from humans, animals (ruminants, swine, and chickens), and avian food products collected during a regionally (Basque Country, Spain) and temporally (mostly 2021–2022) restricted sampling. Eighty-three C. jejuni and seventy-one C. coli isolates, most exhibiting resistance to ciprofloxacin and/or erythromycin, were whole-genome sequenced using Oxford Nanopore Technologies long-fragment sequencing (ONT). Multilocus sequence typing (MLST) analysis identified a high genomic diversity among isolates. Phylogenomic analysis showed that clustering based on the core genome was aligned with MLST profiles, regardless of the sample source. In contrast, accessory genome content sometimes discriminated isolates within the same STs and occasionally differentiated isolates from different sources. The majority of the identified GDRs were present in isolates from different sources, and a good correlation was observed between GDR distribution and phenotypic susceptibility profiles (based on minimum inhibitory concentrations interpreted according to the EUCAST epidemiological cutoff values). Genotypic resistance profiles were independent of genotypes, indicating no apparent association between resistance and phylogenetic origin. This study demonstrates that ONT sequencing is a powerful tool for molecular surveillance of bacterial pathogens in the One Health framework.
From hypoxic pockets to daily routines: linking brain oxygenation and cognitive resilience
Authors: Jiao Dian
Published: January 2025

The discovery of hypoxic pockets within the cortical regions has transformed the understanding of cerebral oxygen dynamics, revealing their dual role as both contributors to neuronal adaptation and potential precursors to dysfunction. These transient oxygen-deprived microenvironments play a pivotal role in neurovascular coupling, synaptic plasticity, and angiogenesis, processes crucial for maintaining cognitive resilience and neuronal health. Investigating hypoxic pockets within cortical regions is particularly relevant in aging populations and individuals with neurodegenerative conditions. Concurrently, research underscores the ability of physical, social, and cognitive activities to modulate brain oxygenation, offering natural, accessible interventions to optimize oxygen delivery and utilization. This study synthesizes findings from neuroimaging, behavioral science, and longitudinal studies, illustrating how daily routines can mitigate hypoxia-induced cognitive decline and promote resilience. By integrating insights from centenarians, hypoxia-adapted species, and multimodal intervention studies, this framework highlights the transformative potential of lifestyle-based strategies in addressing cerebral oxygen deficits. The findings advocate for an interdisciplinary approach to develop targeted interventions for public health, rehabilitation, and personalized cognitive care.
The impact of SLCO1B1 polymorphisms on homocysteine concentrations: evidence for a stronger association in men
Authors: Hu Xinyuan , Jiang Yanfang
Published: January 2025

Background

Homocysteine (Hcy) is a risk factor for stroke. In this study, we investigated the relationship between gene polymorphisms, particularly SLCO1B1 and homocysteine (Hcy) concentrations in ischemic stroke patients, with a focus on identifying potential risk factors for elevated Hcy levels.

Methods

A total of 177 ischemic stroke patients, including 99 with single nucleotide polymorphisms (SNPs), underwent pharmacogenomics (PGx) sequencing tests, from September 2022 to November 2023 at the hospital. Logistic regression analysis was used to analyze the relationship between clinical characteristics, SNPs, and Hcy concentrations. In the sub-study, 207 ischemic stroke and 244 non-stroke patients underwent SLCO1B1c.521T>C polymorphism to further demonstrate the role of SLCO1B1c.521T>C polymorphism and homocysteine.

Results

Higher Hcy concentrations were observed in men compared to women. Univariate logistic analysis identified gender, GGT concentrations, B12 concentrations, folic acid concentrations, and SLCO1B1 c.521 CC+CT polymorphism as risk factors for elevated Hcy. Multivariate logistic analysis confirmed that B12 concentrations, folic acid concentrations, and SLCO1B1 CT + CC polymorphism were significant dependent risk factors. In the sub-study, SLCO1B1 CT + CC polymorphism and the male sex were identified as risk factors for Hcy, with the effect of SLCO1B1 polymorphism being more pronounced in men.

Conclusion

Folic acid and vitamin B12 reduce Hcy concentrations, while the SLCO1B1 CT and CC polymorphisms are associated with higher Hcy levels. The impact of SLCO1B1 gene polymorphism on Hcy is notably stronger in the male population, suggesting that genetic factors play a significant role in determining Hcy levels.
Selective dorsal rhizotomy long-term effects on functional motility in Jordanian children with spastic cerebral palsy
Authors: Al-kharabsheh Yazan E. , Said Anas , Ismaiel Ismail A. , Khawaja Issam , Altaher Marwan , Bani-Ahmed Ali , Cirstea Carmen M.
Published: January 2025

Introduction

Spasticity management in children with cerebral palsy (CP) is a challenge for healthcare providers worldwide. In the US and Europe, treatment options include non-surgical and surgical (i.e., selective dorsal rhizotomy, SDR) procedures, with beneficial effects on functional motility. SDR was introduced in Jordan in 2019. We performed the first assessment of the long-term effects on motor function in Jordanian children with spastic CP (SCP) who underwent SDR.

Methods

A retrospective cohort study of 43 patients (28 boys, 15 girls, mean ± SD age at surgery, 6.2 ± 2.5 years, 67.4% with diplegia, 30.2% quadriplegia, and 2.3% hemiplegia, 97.7% bilateral deficits) who received SDR (42 bilateral) was conducted between 01/01/2019 and 03/01/2023. Gross Motor Function Classification System (GMFCS) and Functional Mobility Scale (FMS) scores were compared before and 12 months after SDR. Sex, age and clinical scores at surgery, and post-SDR surgical treatment were included in the model (IBM SPSS Statistics 29.0).

Results

Clinical scores improved 12 months after SDR: GMFCS decreased by at least one level (in 58.5% of patients), and FMS significantly increased (p < 0.001); GMFCS decreased in 77.7% of those with pre-SDR severe impairment vs. 43.5% in moderately to mildly impaired patients. An age sub-analysis demonstrated higher changes in GMFCS in younger children (GMFCS decreased in 46.9% of those aged <10 years old vs. none in those older than 10 years). These findings suggest that younger children (<10 years old) and more impaired (levels IV and V on GMFCS) are likely the best candidates for this procedure. Twelve-month functional improvement was similar in boys and girls (GMFCS decreased in 44.0% of boys vs. 37.5% of girls). Compared to pre-SDR management, all patients continued physiotherapy, less received Botox (by 97.7%), and more received adjunct orthopedic surgeries (32.6% vs. none) after SDR; out of those receiving post-SDR adjuvant surgeries, 50.0% improved GMFCS (compared to 64.0% of those without).

Conclusion

Our data demonstrated SDR’s beneficial long-term effects on functional mobility in SCP children, particularly those younger than 10 years and more severely impaired. These findings provide critical information that may aid in identifying “the best” therapeutic window and “the best” candidate for SDR in Jordan.
Electroacupuncture combined with cognitive rehabilitation outperforms cognitive rehabilitation alone in treating post-stroke cognitive impairment: a randomized controlled trial
Authors: Guo Yisha , Sun Tingting , Qiu Fengxi , Li Xueyi , Cui Weiwei , Liao Zhenhua , Yao Jiajia
Published: January 2025

This study aimed to evaluate the effects of a 12-week intervention combining electroacupuncture (EA) with conventional cognitive rehabilitation (CR) on cognitive recovery and brain network topological properties in stroke patients. Thirty-four post-stroke cognitive impairment (PSCI) patients were randomly assigned to either an EA + CR group or a CR-only group, with both undergoing five weekly interventions for 12 weeks. Cognitive assessments and Diffusion Tensor Imaging tests were performed pre- and post-intervention. Primary outcomes included the Montreal Cognitive Assessment (MoCA), Digit Span Test (DST), Auditory Verbal Learning Test (AVLT-H), and Aphasia Screening Scale. Secondary outcomes measured brain network global and nodal properties. The EA + CR group showed significant improvements in MoCA (p < 0.001), AVLT-H (p = 0.004), and in areas like naming (p = 0.022), attention (p < 0.001), and delayed recall (p < 0.001). Local brain network metrics, such as clustering coefficients (Cp) and local efficiency (Eloc), were significantly higher (p < 0.05) in the EA + CR group, though global efficiency (Eglob) was unchanged. Improvements in Eloc were positively correlated with MoCA scores (r = 0.0716, p = 0.018). Specific brain regions, including the medial and paracentral cingulate gyrus, inferior temporal gyrus, and left supramarginal gyrus, exhibited significant nodal property differences, suggesting that EA may enhance cognitive recovery by targeting cognitively relevant regions. These findings indicate that EA, combined with CR, is a safe and effective treatment for cognitive impairment following stroke, potentially via structural brain network improvements.

Clinical trial registration

https://clinicaltrials.gov/, ChiCTR2200066160.
Development and external validation of a dynamic nomogram for predicting the risk of functional outcome after 90 days in patients with acute intracerebral hemorrhage
Authors: Li Shaojie , Li Hongjian , Chen Jiani , Wu Baofang , Wang Jiayin , Hong Chaocan , Yan Changhu , Qiu Weizhi , Li Yasong , Gao Hongzhi
Published: January 2025

Background and purpose

Intracerebral hemorrhage remains a significant cause of death and disability worldwide, highlighting the urgent need for accurate prognostic assessments to optimize patient management. This study aimed to develop a practical nomogram for risk prediction of poor prognosis after 90 days in patients with intracerebral hemorrhage.

Methods

A retrospective study was conducted on 638 patients with intracerebral hemorrhage in the Second Hospital of Fujian Medical University, China, who were divided into a training set (n = 446) and a test set (n = 192) by random splitting. Then the data on demographics, clinical symptoms, imaging characteristics, and laboratory findings were collected. In this study, adverse outcomes were defined as a Modified Rankin Scale (mRS) score of 3–6 at 90 days post-ICH onset, as assessed during follow-up. Later, least absolute shrinkage and selection operator (LASSO) regression and multifactorial logistic regression were used to screen the variables and construct a nomogram. Next, the evaluation was performed using the Receiver Operating Characteristic (ROC) curve, calibration curve, and decision curve analysis. Finally, the external validation was completed using the data of 496 patients with intracerebral hemorrhage from the Jinjiang Hospital of Traditional Chinese Medicine.

Results

In the training and test sets of intracerebral hemorrhage, the incidence of poor prognosis was 60.53 and 61.46%, respectively. Through variable screening, this study identified age, Glasgow Coma Scale (GCS), blood glucose, uric acid, hemoglobin, and hematoma location as independent predictors of poor prognosis in intracerebral hemorrhage. The developed dynamic nomogram was easy to use and demonstrated strong predictive performance (training set AUC: 0.87; test set AUC: 0.839; external validation set AUC: 0.774), excellent calibration, and clinical applicability.

Conclusion

The dynamic nomogram we developed using five independent risk factors serves as a practical tool for real-time risk assessment and can help facilitate early intervention and personalized patient management, thereby improving clinical outcomes in high-risk patients.
Enhanced heart sound anomaly detection via WCOS: a semi-supervised framework integrating wavelet, autoencoder and SVM
Authors: Zeng Peipei , Kang Shuimiao , Fan Fan , Liu Jiyuan
Published: January 2025

Anomaly detection is a typical binary classification problem under the condition of unbalanced samples, which has been widely used in various fields of data mining. For example, it can help detect heart murmurs when the heart is structurally abnormal, to tell if a newborn has congenital heart disease. Due to the low time and high efficiency, most work focuses on the semi- supervised anomaly detection method. However, the anomaly detection effect of this method is not high because of massive data with uneven samples and different noise. To improve the accuracy of anomaly detection under unbalanced sample conditions, we propose a new semi-supervised anomaly detection method (WCOS) based on semi-supervised clustering, which combines wavelet reconstruction, convolutional autoencoder, and one classification support vector machine. In this way, we can not only distinguish a small proportion of abnormal heart sounds in the huge data scale but also filter the noise through the noise reduction network, thus significantly improving the detection accuracy. In addition, we evaluated our method using real datasets. When the noise of sigma = 0.5, the AUC standard deviation of the WR-CAE-OCSVM is 19.2, 54.1, and 29.8% lower than that of WR-OCSVM, CAE-OCSVM and OCSVM, respectively. The results confirmed the higher accuracy of anomaly detection in WCOS compared to other state-of-the-art methods.