bluuebunny/crossref_metadata_2025_split huggingface dataset:
M2 macrophage-secreted exosomes promote metastasis and increase vascular permeability in hepatocellular carcinoma
Authors: Lu Yiwei , Han Guoyong , Zhang Yao , Zhang Long , Li Zhi , Wang Qingyuan , Chen Zhiqiang , Wang Xuehao , Wu Jindao 
Published: October 2023

Abstract
Background
Metastasis is a key feature of malignant tumors and significantly contributes to their high mortality, particularly in hepatocellular carcinoma (HCC). Therefore, it is imperative to explore the mechanism of tumor metastasis. Recently, tumor-associated macrophages (TAMs) have been demonstrated to promote tumor progression, while TAM-derived molecules involved in HCC metastasis warrant further investigation.

Methods
THP-1 was treated with IL-4 (Interleukin-4) and IL-13 (Interleukin-13) for M2 polarized macrophages. Exosomes derived from M2 macrophages were characterized. Then, HCC cells or human umbilical vein endothelial cells (HUVECs) were co-cultured with M2 macrophages or treated with M2 macrophage-secreted exosomes. Next, Transwell®, Scratch assay, tube formation, and endothelial permeability assays were performed. Moreover, RT-PCR, western blotting, immunofluorescence, and ELISA were used to assess mRNA and protein expression levels. Finally, the miRNA expression profiles of exosomes derived from M2 and M0 macrophages were analyzed.

Results
M2 macrophage infiltration was correlated with metastasis and a poor prognosis in HCC patients. M2-derived exosomes were absorbed by HCC and HUVEC cells and promoted the epithelial-mesenchymal transition (EMT), vascular permeability, and angiogenesis. Notably, MiR-23a-3p levels were significantly higher in M2-derived exosomes and hnRNPA1 mediated miR-23a-3p packaging into exosomes. Phosphatase and tensin homolog (PTEN) and tight junction protein 1 (TJP1) were the targets of miR-23a-3p, as confirmed by luciferase reporter assays. Lastly, HCC cells co-cultured with M2-derived exosomes secreted more GM-CSF, VEGF, G-CSF, MCP-1, and IL-4, which in turn further recruited M2 macrophages.

Conclusions
Our findings suggest that M2 macrophage-derived miR-23a-3p enhances HCC metastasis by promoting EMT and angiogenesis, as well as increasing vascular permeability.
LRRK2 is involved in the chemotaxis of neutrophils and differentiated HL-60 cells, and the inhibition of LRRK2 kinase activity increases fMLP-induced chemotactic activity
Authors: Mazaki Yuichi , Handa Haruka , Fumoto Yoshizuki , Horinouchi Takahiro , Onodera Yasuhito 
Published: October 2023

Abstract
Background
Neutrophils depend heavily on glycolysis for energy production under normal conditions. In contrast, neutrophils require energy supplied by mitochondrial oxidative phosphorylation (OXPHOS) during chemotaxis. However, the mechanism by which the energy supply changes from glycolysis to OXPHOS remains unknown. Leucine-rich repeat kinase 2 (LRRK2) is partially present in the outer mitochondrial membrane fraction. Lrrk2-deficient cells show mitochondrial fragmentation and reduced OXPHOS activity. We have previously reported that mitofusin (MFN) 2 is involved in chemotaxis and OXPHOS activation upon chemoattractant N-formyl-Met-Leu-Phe (fMLP) stimulation in differentiated HL-60 (dHL-60) cells. It has been previously reported that LRRK2 binds to MFN2 and partially colocalizes with MFN2 at the mitochondrial membranes. This study investigated the involvement of LRRK2 in chemotaxis and MFN2 activation in neutrophils and dHL-60 cells.

Methods
Lrrk2 knockout neutrophils and Lrrk2 knockdown dHL-60 cells were used to examine the possible involvement of LRRK2 in chemotaxis. Lrrk2 knockdown dHL-60 cells were used a tetracycline-inducible small hairpin RNA (shRNA) system to minimize the effects of LRRK2 knockdown during cell culture. The relationship between LRRK2 and MFN2 was investigated by measuring the GTP-binding activity of MFN2 in Lrrk2 knockdown dHL-60 cells. The effects of LRRK2 kinase activity on chemotaxis were examined using the LRRK2 kinase inhibitor MLi-2.

Results
fMLP-induced chemotactic activity was reduced in Lrrk2 knockout neutrophils in vitro and in vivo. Lrrk2 knockdown in dHL-60 cells expressing Lrrk2 shRNA also reduced fMLP-induced chemotactic activity. Lrrk2 knockdown dHL-60 cells showed reduced OXPHOS activity and suppressed mitochondrial morphological change, similar to Mfn2 knockdown dHL-60 cells. The amount of LRRK2 in the mitochondrial fraction and the GTP-binding activity of MFN2 increased upon fMLP stimulation, and the MFN2 GTP-binding activity was suppressed in Lrrk2 knockdown dHL-60 cells. Furthermore, the kinase activity of LRRK2 and Ser935 phosphorylation of LRRK2 were reduced upon fMLP stimulation, and LRRK2 kinase inhibition by MLi-2 increased the migration to fMLP.

Conclusions
LRRK2 is involved in neutrophil chemotaxis and the GTP-binding activity of MFN2 upon fMLP stimulation. On the other hand, the kinase activity of LRRK2 shows a negative regulatory effect on fMLP-induced chemotactic activity in dHL-60 cells.
Multipredictor risk models for predicting individual risk of Alzheimer’s disease
Authors: Hou Xiao-He , Suckling John , Shen Xue-Ning , Liu Yong , Zuo Chuan-Tao , Huang Yu-Yuan , Li Hong-Qi , Wang Hui-Fu , Tan Chen-Chen , Cui Mei , Dong Qiang , Tan Lan , Yu Jin-Tai ,   Alzheimer’s Disease Neuroimaging Initiative
Published: October 2023

Abstract
Background
Early prevention of Alzheimer’s disease (AD) is a feasible way to delay AD onset and progression. Information on AD prediction at the individual patient level will be useful in AD prevention. In this study, we aim to develop risk models for predicting AD onset at individual level using optimal set of predictors from multiple features.

Methods
A total of 487 cognitively normal (CN) individuals and 796 mild cognitive impairment (MCI) patients were included from Alzheimer's Disease Neuroimaging Initiative. All the participants were assessed for clinical, cognitive, magnetic resonance imaging and cerebrospinal fluid (CSF) markers and followed for mean periods of 5.6 years for CN individuals and 4.6 years for MCI patients to ascertain progression from CN to incident prodromal stage of AD or from MCI to AD dementia. Least Absolute Shrinkage and Selection Operator Cox regression was applied for predictors selection and model construction.

Results
During the follow-up periods, 139 CN participants had progressed to prodromal AD (CDR ≥ 0.5) and 321 MCI patients had progressed to AD dementia. In the prediction of individual risk of incident prodromal stage of AD in CN individuals, the AUC of the final CN model was 0.81 within 5 years. The final MCI model predicted individual risk of AD dementia in MCI patients with an AUC of 0.92 within 5 years. The models were also associated with longitudinal change of Mini-Mental State Examination (p < 0.001 for CN and MCI models). An Alzheimer’s continuum model was developed which could predict the Alzheimer’s continuum for individuals with normal AD biomarkers within 3 years with high accuracy (AUC = 0.91).

Conclusions
The risk models were able to provide personalized risk for AD onset at each year after evaluation. The models may be useful for better prevention of AD.
Dose-effect relationship of linear accelerator based stereotactic radiotherapy for brain metastases
Authors: Wu Ning , Wang Zhiqiang , Guo Xin , Zhao Hongfu 
Published: October 2023

Abstract
Objective
The purpose of this study is to reveal the dose-effect relationship of linear accelerator (LINAC)-based stereotactic radiotherapy (SRT) in patients with brain metastases (BM).

Materials and methods
The PubMed, Cochrane, and Web of Science databases were used to identify studies that reported local tumour control after LINAC-based SRT in patients with BMs. Studies of other approaches that could affect local tumour control, such as whole brain radiotherapy, targeted therapy, and immunotherapy, were excluded from the dose-effect relationship analysis. Data extracted included patient and treatment characteristics and tumour local control. Probit model in XLSTAT 2016 was used for regression analysis, and P < 0.05 was set as the statistically significant level.

Results
After literature screening, 19 eligible studies involving 1523 patients were included in the probit model regression analysis. There was no significant dose-effect relationship between nominal BED10 and peripheral BED10 versus 12-month local control probability. There were significant dose effect relationships between the centre BED10 and the average BED10 versus the 12-month local control probability, with P values of 0.015 and 0.011, respectively. According to the model, the central BED10 and the average BED10 corresponding to probabilities of 90% 12-month local control were 109.2 GyBED10 (95% confidence interval (CI): 88.7–245.9 GyBED10) and 87.8 GyBED10 (95% CI: 74.3–161.5 GyBED10), respectively. A 12-month local control rate of 86.9% (95% CI: 81.7–89.7%) and 85.5% (95% CI: 81.2–89.2%) can be expected at a centre BED10 of 80 Gy and an average BED10 of 60 Gy, respectively.

Conclusion
For patients with BM treated with LINAC-based SRT, more attention should be given to the central and average doses of PTV. A clear definition of the dose prescription should be established to ensure the effectiveness and comparability of treatment.
Circulating small extracellular vesicle-derived splicing factor 3b subunit 4 as a non-invasive diagnostic biomarker of early hepatocellular carcinoma
Authors: Son Ju A , Weon Ji Hyang , Baek Geum Ok , Ahn Hye Ri , Choi Ji Yi , Yoon Moon Gyeong , Cho Hyo Jung , Cheong Jae Youn , Eun Jung Woo , Kim Soon Sun 
Published: October 2023

Abstract
Background
Hepatocellular carcinoma (HCC) accounts for a majority of primary liver cancer cases and related deaths. The purpose of this study was to assess the diagnostic value of splicing factor 3b subunit 4 (SF3B4) as a novel non-invasive biomarker for HCC and determine the association between SF3B4 expression and immune cell infiltration.

Methods
An enzyme-linked immunosorbent assay (ELISA) was used to detect SF3B4 levels in plasma samples obtained from healthy controls (HCs) and patients with chronic hepatitis, liver cirrhosis, and HCC. The expression levels of autoantibodies that detect SF3B4 in the plasma samples of each group of patients were measured. Small extracellular vesicles (EVs) were isolated from patient sera, and the expression levels of EV-SF3B4 were measured using quantitative reverse transcription PCR.

Results
ELISA results confirmed that the expression levels of SF3B4 proteins and autoantibodies in the plasma of patients with HCC were higher than those in HCs. However, their diagnostic performance was not better than that of alpha-fetoprotein (AFP). The mRNA expression of SF3B4 in serum EV increased but not in the buffy coat or serum of patients with HCC. Serum EV-SF3B4 displayed better diagnostic power than AFP for all stages of HCC (AUC = 0.968 vs. 0.816), including early-stage HCC (AUC = 0.960 vs. 0.842), and this was consistent in the external cohort. Single-cell RNA sequencing indicated that SF3B4 expression was correlated with myeloid-derived suppressor cells. The Tumor Immune Estimation Resource database reconfirmed the correlation between SF3B4 expression and immune cell infiltration in HCC.

Conclusions
SF3B4 may be associated with tumor immune infiltration in HCC, and EV-SF3B4 shows potential as a novel non-invasive diagnostic biomarker of HCC.
CHESS 3: an improved, comprehensive catalog of human genes and transcripts based on large-scale expression data, phylogenetic analysis, and protein structure
Authors: Varabyou Ales , Sommer Markus J. , Erdogdu Beril , Shinder Ida , Minkin Ilia , Chao Kuan-Hao , Park Sukhwan , Heinz Jakob , Pockrandt Christopher , Shumate Alaina , Rincon Natalia , Puiu Daniela , Steinegger Martin , Salzberg Steven L. , Pertea Mihaela 
Published: October 2023

AbstractCHESS 3 represents an improved human gene catalog based on nearly 10,000 RNA-seq experiments across 54 body sites. It significantly improves current genome annotation by integrating the latest reference data and algorithms, machine learning techniques for noise filtering, and new protein structure prediction methods. CHESS 3 contains 41,356 genes, including 19,839 protein-coding genes and 158,377 transcripts, with 14,863 protein-coding transcripts not in other catalogs. It includes all MANE transcripts and at least one transcript for most RefSeq and GENCODE genes. On the CHM13 human genome, the CHESS 3 catalog contains an additional 129 protein-coding genes. CHESS 3 is available at http://ccb.jhu.edu/chess.
Identification of RNA reads encoding different channels in isolated rat ventricular myocytes and the effect of cell stretching on L-type Ca2+current
Authors: Kamkin Andre G. , Kamkina Olga V. , Kazansky Viktor E. , Mitrokhin Vadim M. , Bilichenko Andrey , Nasedkina Elizaveta A. , Shileiko Stanislav A. , Rodina Anastasia S. , Zolotareva Alexandra D. , Zolotarev Valentin I. , Sutyagin Pavel V. , Mladenov Mitko I. 
Published: October 2023

Abstract
Background
The study aimed to identify transcripts of specific ion channels in rat ventricular cardiomyocytes and determine their potential role in the regulation of ionic currents in response to mechanical stimulation. The gene expression levels of various ion channels in freshly isolated rat ventricular cardiomyocytes were investigated using the RNA-seq technique. We also measured changes in current through CaV1.2 channels under cell stretching using the whole-cell patch-clamp method.

Results
Among channels that showed mechanosensitivity, significant amounts of TRPM7, TRPC1, and TRPM4 transcripts were found. We suppose that the recorded L-type Ca2+ current is probably expressed through CaV1.2. Furthermore, stretching cells by 6, 8, and 10 μm, which increases ISAC through the TRPM7, TRPC1, and TRPM4 channels, also decreased ICa,L through the CaV1.2 channels in K+ in/K+ out, Cs+ in/K+ out, K+ in/Cs+ out, and Cs+ in/Cs+ out solutions. The application of a nonspecific ISAC blocker, Gd3+, during cell stretching eliminated ISAC through nonselective cation channels and ICa,L through CaV1.2 channels. Since the response to Gd3+ was maintained in Cs+ in/Cs+ out solutions, we suggest that voltage-gated CaV1.2 channels in the ventricular myocytes of adult rats also exhibit mechanosensitive properties.

Conclusions
Our findings suggest that TRPM7, TRPC1, and TRPM4 channels represent stretch-activated nonselective cation channels in rat ventricular myocytes. Probably the CaV1.2 channels in these cells exhibit mechanosensitive properties. Our results provide insight into the molecular mechanisms underlying stretch-induced responses in rat ventricular myocytes, which may have implications for understanding cardiac physiology and pathophysiology.
Innovative and disruptive technologies to prescribe, encourage, and evaluate physical exercise in healthy adults: a protocol of exploratory study followed by a noninferiority, investigator-blinded randomized clinical trial
Authors: Loro Fernanda Laís , Martins Riane , de Araújo Cintia Laura Pereira , Prade Lucio Rene , do Rosário Denis Lima , da Rocha Seruffo Marcos César , de Freitas Italo Adriano Moraes , Nobre Jéferson , Both Cristiano Bonato , Dal Lago Pedro 
Published: October 2023

Abstract
Background
Cardiovascular diseases are a leading cause of mortality worldwide. A significant contributing factor to this mortality is the lack of engagement in preventive activities. Consequently, strategies for enhancing adherence to and duration of physical activity (PA) have become pivotal. This project aims to create and validate innovative, disruptive, and secure technologies that ensure appropriate exercise intensity, bolster adherence to PA, and monitor health biomarker responses pre-, during, and post-physical activity.

Methods
This exploratory study, followed by a noninferiority, investigator-blinded randomized clinical trial, will be divided into three phases: (1) development and validation of a sensor for real-time biofeedback during a functional assessment test; (2) integration of biofeedback and gamification into an app for the structured prescription of physical training within a controlled setting; and (3) implementation of biofeedback and gamification into an app for the prescription and monitoring of physical training in an uncontrolled setting. Phase 1 entails a validation test of a biosensor—monitoring heart rate (HR) and steps—during a modified shuttle walk test. In phase 2, the biosensor interfaces with a gamified smartphone application. The training regimen spans 6 weeks, 5 days weekly, with each session lasting 60 min: a five-min warm-up involving stationary gait, followed by 50 min of training at the target HR on the step and concluding with a five-min cool-down at a stationary pace. After 6 weeks of training, a new functional capacity test is conducted. Phase 3 involves an investigator-blinded, randomized clinical trial to demonstrate noninferiority. Participants are randomly assigned to either the intervention group (IG) or the control group (CG). IG participants practice exercise using the gamified application in an uncontrolled environment according to the prescribed method outlined in phase 2. CG participants receive PA practice guidelines exclusively.

Discussion
Anticipated outcomes include improved exercise adherence through the gamified application, better maintenance of prescribed exercise intensity, and enhanced health biomarkers. The results of this study will inform health-related decision-making.

Trial registration
The study protocol received approval from the Ethics Committee of Universidade Federal de Ciências da Saúde de Porto Alegre (54,492,221.80000.5345) and has been registered with the Brazilian Registry of Clinical Trials (ReBEC, RBR-359p69v).
Biochemical and structural characterization of a glucan synthase GFGLS2 from edible fungus Grifola frondosa to synthesize β-1, 3-glucan
Authors: Yang Yu-Meng , Fu Xin , Cui Feng-Jie , Sun Lei , Zan Xin-Yi , Sun Wen-Jing 
Published: October 2023

Abstract
Background
Grifola frondosa is a Basidiomycete fungus belonging to the family of Grifolaceae and the order of Polyporales. β-Glucans are the main polymers in G. frondosa, playing a crucial role in the physiology and representing the healthy benefits for humans. The membrane-integrated β-1, 3-glucan synthase (GLS) is responsible for glucan synthesis, cell wall assembly, differentiation and growth of the edible fungi. However, the structural/catalytic characteristics and mechanisms of β-1, 3-glucan synthases in G. frondosa are still unknown due to their extremely complex structures with multi-transmembranes and large molecular masses.

Results
Herein, a β-1, 3-glucan synthase (GFGLS2) was purified and identified from the cultured mycelia with a specific activity of 60.01 pmol min−1 μg−1 for the first time. The GFGLS2 showed a strict specificity to UDP-glucose with a Vmax value of 1.29 ± 0.04 µM min−1 at pH 7.0 and synthesized β-1, 3-glucan with a maximum degree of polymerization (DP) of 62. Sequence Similarity Network (SSN) analysis revealed that GFGLS2 has a close relationship with others in Ganoderma sinense, Trametes coccinea, Polyporus brumalis, and Trametes pubescens. With the assistance of 3D structure modelling by AlphaFold 2, molecular docking and molecular dynamics simulations, the central hydrophilic domain (Class III) in GFGLS2 was the main active sites through binding the substrate UDP–glucose to 11 amino acid residues via hydrogen bonds, π-stacking and salt bridges.

Conclusions
The biochemical, 3D structural characterization and potential catalytic mechanism of a membrane-bound β-1, 3-glucan synthase GFGLS2 from cultured mycelia of G. frondosa were well investigated and would provide a reasonable full picture of β-1, 3-glucan synthesis in fungi.
Bacterial genome-wide association study substantiates papGII of Escherichia coli as a major risk factor for urosepsis
Authors: Cuénod Aline , Agnetti Jessica , Seth-Smith Helena M. B. , Roloff Tim , Wälchli Denise , Shcherbakov Dimitri , Akbergenov Rashid , Tschudin-Sutter Sarah , Bassetti Stefano , Siegemund Martin , Nickel Christian H. , Moran-Gilad Jacob , Keys Timothy G. , Pflüger Valentin , Thomson Nicholas R. , Egli Adrian 
Published: October 2023

AbstractBackgroundUrinary tract infections (UTIs) are among the most common bacterial infections worldwide, often caused by uropathogenicEscherichia coli. Multiple bacterial virulence factors or patient characteristics have been linked separately to progressive, more invasive infections. In this study, we aim to identify pathogen- and patient-specific factors that drive the progression to urosepsis by jointly analysing bacterial and host characteristics.MethodsWe analysed 1076E. colistrains isolated from 825 clinical cases with UTI and/or bacteraemia by whole-genome sequencing (Illumina). Sequence types (STs) were determined via srst2 and capsule loci via fastKaptive. We compared the isolates from urine and blood to confirm clonality. Furthermore, we performed a bacterial genome-wide association study (bGWAS) (pyseer) using bacteraemia as the primary clinical outcome. Clinical data were collected by an electronic patient chart review. We concurrently analysed the association of the most significant bGWAS hit and important patient characteristics with the clinical endpoint bacteraemia using a generalised linear model (GLM). Finally, we designed qPCR primers and probes to detectpapGII-positiveE. colistrains and prospectively screenedE. colifrom urine samples (n = 1657) at two healthcare centres.ResultsOur patient cohort had a median age of 75.3 years (range: 18.00–103.1) and was predominantly female (574/825, 69.6%). The bacterial phylogroups B2 (60.6%; 500/825) and D (16.6%; 137/825), which are associated with extraintestinal infections, represent the majority of the strains in our collection, many of which encode a polysaccharide capsule (63.4%; 525/825). The most frequently observed STs were ST131 (12.7%; 105/825), ST69 (11.0%; 91/825), and ST73 (10.2%; 84/825). Of interest, in 12.3% (13/106) of cases, theE. colipairs in urine and blood were only distantly related. In line with previous bGWAS studies, we identified the genepapGII(p-value < 0.001), which encodes the adhesin subunit of theE. coliP-pilus, to be associated with ‘bacteraemia’ in our bGWAS. In our GLM, correcting for patient characteristics,papGIIremained highly significant (odds ratio = 5.27, 95% confidence interval = [3.48, 7.97],p-value < 0.001). An independent cohort of cases which we screened forpapGII-carryingE. coliat two healthcare centres further confirmed the increased relative frequency ofpapGII-positive strains causing invasive infection, compared topapGII-negative strains (p-value = 0.033, chi-squared test).ConclusionsThis study builds on previous work linkingpapGIIwith invasive infection by showing that it is a major risk factor for progression from UTI to bacteraemia that has diagnostic potential.