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Integrated analysis of public datasets for the discovery and validation of survival-associated genes in solid tumors

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The Innovation 2024年第3期5卷 129-137页

作者： Balázs Gyorffy department of Biophysics Medical SchoolUniversity of Pecs7624 PecsHungary department of Bioinformatics Semmelweis University1094 BudapestHungary Cancer biomarker research Group Institute of Molecular Life SciencesHUN-REN Research Centre for Natural Sciences1117 BudapestHungary

Identifying genes with prognostic significance that can act as biomarkers in solid tumors can help stratify patients and uncover novel therapy targets.Here,our goal was to expand our previous ranking analysis of survival-associated genes in various solid tumors to include colon cancer specimens with available transcriptomic and clinical data.A Gene Expression Omnibus search was performed to identify available datasets with clinical data and raw gene expression measurements.A combined database was set up and integrated into our Kaplan-Meier plotter,making it possible to identify genes with expression changes linked to altered survival.As a demonstration of the utility of the platform,the most powerful genes linked to overall survival in colon cancer were identified using uni-and multivariate Cox regression analysis.The combined colon cancer database includes 2,137 tumor samples from 17 independent cohorts.The most significant genes associated with relapse-free survival with a false discovery rate below 1%in colon cancer carcinoma were RBPMS(hazard rate[HR]=2.52),TIMP1(HR=2.44),and COL4A2(HR=2.36).The three strongest genes associated with shorter survival in stage II colon cancer include CSF1R(HR=2.86),FLNA(HR=2.88),and TPBG(HR=2.65).In summary,a new integrated database for colon cancer is presented.A colon cancer analysis subsystem was integrated into our Kaplan-Meier plotter that can be used to mine the entire database(https://***).The portal has the potential to be employed for the identification and prioritization of promising biomarkers and therapeutic target candidates in multiple solid tumors including,among others,breast,lung,ovarian,gastric,pancreatic,and colon cancers.

关键词： colon tumors analysis

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Application of Fusobacterium nucleatum as a biomarker in gastrointestinal malignancies

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World Journal of Gastrointestinal Oncology 2024年第6期16卷 2271-2283页

作者： Long-Chen Yu Ya-Ping Li Yue-Ming Xin Mai Mao Ya-Xin Pan Yi-Xuan Qu Zheng-Dong Luo Yi Zhang Xin Zhang department of Clinical Laboratory Qilu Hospital of Shandong UniversityShandong Engineering Research Center of Biomarker and Artificial Intelligence ApplicationJinan 250012Shandong ProvinceChina

The morbidity and mortality of gastrointestinal(GI)malignancies are among the highest in the world,posing a serious threat to human health.Because of the insidious onset of the cancer,it is difficult for patients to be diagnosed at an early stage,and it rapidly progresses to an advanced stage,resulting in poor treatment and prognosis.Fusobacterium nucleatum(F.nucleatum)is a gram-negative,sporefree anaerobic bacterium that primarily colonizes the oral cavity and is implicated in the development of colorectal,esophageal,gastric,and pancreatic cancers via various intricate mechanisms.Recent development in novel research suggests that F.nucleatum may function as a biomarker in GI malignancies.Detecting the abundance of F.nucleatum in stool,saliva,and serum samples of patients may aid in the diagnosis,risk assessment,and prognosis monitoring of GI malignancies.This editorial systematically describes the biological roles and mechanisms of F.nucleatum in GI malignancies focusing on the application of F.nucleatum as a biomarker in the diagnosis and prognosis of GI malignancies to promote the clinical translation of F.nucleatum and GI tumors-related research.

关键词： Gastrointestinal malignancies Fusobacterium nucleatum biomarker Diagnosis Prognosis

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Virus-like nanoparticle vaccines for inducing long-lasting immunity against infectious diseases

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National Science Review 2024年第4期11卷 13-15页

作者： Yi-Nan Zhang Sarah Auclair Jiang Zhu department of Integrative Structural and Computational Biology The Scripps Research Institute department of Immunology and Microbiology The Scripps Research Institute

Prophylactic vaccines that can generate long-lasting protective immune responses are needed for many infectious diseases. Efficient vaccination requires vaccine antigens to be retained and presented to B cells in lymp...

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Microstructure and properties of coarse-grained WC-10Co cemented carbides with different carbon contents during heat treatments

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Rare Metals 2024年第4期43卷 1786-1792页

作者： Yuan-Feng Xie Xing-Cheng Xie Zhong-Wu Li Rui-Jun Cao Zhong-Kun Lin Qing Li Chen-Guang Lin Powder Metallurgy and Special Materials research department General Research Institute for Nonferrous Metals

The effects of cryogenic treatment（CT） and tempering-cryogenic treatment（TCT） on the microstructure and properties of coarse-grained WC-10Co cemented carbides with different carbon contents were researched.The binder phase,WC mean grain sizes,W solubility in the binder,relative magnetic s aturation,densities,hardness,wear resistance and second phase precipitation of cemented carbides with different heat treatments were discussed.The results show that there are significant changes of microstructure and properties in the samples with CT and TCT,especially due to the precipitation of metastable nanoparticles WxCoyCzin the binder during the heat treatments of CT and TCT.With the simultaneous combination of microstructure and nanoparticle-reinforced binder,a dramatically improved combination of hardness and wear resistance of the samples after TCT has been achieved.

关键词： Cryogenic treatment Tempering Coarse-grained cemented carbide Carbon content Nanoparticle-reinforced binder

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Combined Treatment with Bojungikgi-tang(Buzhong Yiqi Decoction) and Riluzole Attenuates Cell Death in TDP-43-Expressing Cells

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Chinese Journal of Integrative Medicine 2024年第7期30卷 616-622页

作者： Eun Jin Yang department of KM Science research Korea Institute of Oriental Medicine

Objective: To examine the effect of combined treatment with Bojungikgi-tang(BJIGT, Buzhong Yiqi Decoction) and riluzole(RZ) in transactive response DNA-binding protein 43(TDP-43) stress granule(SG) cells, a amyotrophic lateral sclerosis(ALS) cell line using transcriptomic and molecular techniques. Methods: TDP-43 SG cells were pretreated with BJIGT(100 μg/mL), RZ(50 μmol/L), and combined BJIGT(100 μg/mL)/RZ(50 μmol/L) for 6 h before treatment with lipopolysaccharide(LPS, 200 μmol/L). Cell viability assay was performed to elucidate cell toxicity in TDP-43 SC cells using a cell-counting kit-8(CCK8) assay kit. The expression levels of cell death-related proteins, including Bax, caspase 1, cleaved caspase 3 and DJ1 in TDP-43 SG cells were examined by Western blot analysis. The autophagy-related proteins, including pmTOR/mTOR, LC3b, P62, ATG7 and Bcl-2-associated athanogene 3(Bag3) were investigated using immunofluorescence and immunoblotting assays. Results: Cell viability assay and Western blot analysis showed that combined treatment with BJIGT and RZ suppressed LPS-induced cell death and expression of cell death-related proteins, including Bax, caspase 1, and DJ1(P<0.05 or P<0.01). Immunofluorescence and immunoblotting assays showed that combined treatment with BJIGT and RZ reduced LPS-induced formation of TDP-43 aggregates and regulated autophagy-related protein levels, including p62, light chain 3b, Bag3, and ATG7, in TDP-43-expressing cells(P<0.05 or P<0.01). Conclusion: The combined treatment of BJIGT and RZ might reduce inflammation and regulate autophagy dysfunction in TDP-43-induced ALS.

关键词： Bojungikgi-tang Buzhong Yiqi Decoction transactive response DNA-binding protein 43 autophagy oxidative stress amyotrophic lateral sclerosis

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The burden of upper motor neuron involvement is correlated with the bilateral limb involvement interval in patients with amyotrophic lateral sclerosis:a retrospective observational study

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Neural Regeneration research 2025年第5期20卷 1505-1512页

作者： Jieying Wu Shan Ye Xiangyi Liu Yingsheng Xu Dongsheng Fan department of Neurology Peking University Third HospitalBeijingChina Beijing Municipal Key Laboratory of biomarker and Translational research in Neurodegenerative Diseases BeijingChina Key Laboratory for Neuroscience National Health Commission/Ministry of EducationPeking UniversityBeijingChina

Amyotrophic lateral sclerosis is a rare neurodegenerative disease characterized by the involvement of both upper and lower motor neurons.Early bilateral limb involvement significantly affects patients'daily lives and may lead them to be confined to bed.However,the effect of upper and lower motor neuron impairment and other risk factors on bilateral limb involvement is unclear.To address this issue,we retrospectively collected data from 586 amyotrophic lateral sclerosis patients with limb onset diagnosed at Peking University Third Hospital between January 2020 and May 2022.A univariate analysis revealed no significant differences in the time intervals of spread in different directions between individuals with upper motor neuron-dominant amyotrophic lateral sclerosis and those with classic amyotrophic lateral sclerosis.We used causal directed acyclic graphs for risk factor determination and Cox proportional hazards models to investigate the association between the duration of bilateral limb involvement and clinical baseline characteristics in amyotrophic lateral sclerosis patients.Multiple factor analyses revealed that higher upper motor neuron scores(hazard ratio[HR]=1.05,95%confidence interval[CI]=1.01–1.09,P=0.018),onset in the left limb(HR=0.72,95%CI=0.58–0.89,P=0.002),and a horizontal pattern of progression(HR=0.46,95%CI=0.37–0.58,P<0.001)were risk factors for a shorter interval until bilateral limb involvement.The results demonstrated that a greater degree of upper motor neuron involvement might cause contralateral limb involvement to progress more quickly in limb-onset amyotrophic lateral sclerosis patients.These findings may improve the management of amyotrophic lateral sclerosis patients with limb onset and the prediction of patient prognosis.

关键词： amyotrophic lateral sclerosis bilateral limb involvement Cox proportional hazards regression model horizontal spread restricted cubic spline analysis time interval upper motor neuron vertical spread

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Comparative study between three carbonaceous nanoblades and nanodarts for antimicrobial applications

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Journal of Environmental Sciences 2024年第2期136卷 594-605页

作者： Mohamed S.Selim Ahmed M.Azzam Mohamed A.Shenashen Shimaa A.Higazy Bayaumy B.Mostafa Sherif A.El-Safty National Institute for Materials Science(NIMS) 1-2-1 SengenTsukuba-ShiIbaraki-Ken 305-0047Japan Petroleum Application department Egyptian Petroleum Research InstituteNasr City 11727Egypt department of Environmental research Theodor Bilharz Research InstituteGizaEgypt

The design of nanostructured materials occupies a privileged position in the development and management of affordable and effective technology in the antibacterial sector.Here,we discuss the antimicrobial properties of three carbonaceous nanoblades and nanodarts materials of graphene oxide(GO),reduced graphene oxide(RGO),and single-wall carbon nanotubes(SWCNTs)that have a mechano-bactericidal effect,and the ability to piercing or slicing bacterial membranes.To demonstrate the significance of size,morphology and composition on the antibacterial activity mechanism,the designed nanomaterials have been characterized.The minimum inhibitory concentration(MIC),standard agar well diffusion,and transmission electron microscopy were utilized to evaluate the antibacterial activity of GO,RGO,and SWCNTs.Based on the evidence obtained,the three carbonaceous materials exhibit activity against all microbial strains tested by completely encapsulating bacterial cells and causing morphological disruption by degrading the microbial cell membrane in the order of RGO>GO>SWCNTs.Because of the external cell wall structure and outer membrane proteins,the synthesized carbonaceous nanomaterials exhibited higher antibacterial activity against Gram-positive bacterial strains than Gram-negative and fungal microorganisms.RGO had the lowest MIC values(0.062,0.125,and 0.25 mg/mL against B.subtilis,S.aureus,and E.coli,respectively),as well as minimum fungal concentrations(0.5 mg/mL for both A.fumigatus and C.albicans).At 12 hr,the cell viability values against tested microbial strains were completely suppressed.Cell lysis and death occurred as a result of severe membrane damage caused by microorganisms perched on RGO nanoblades.Our work gives an insight into the design of effective graphene-based antimicrobial materials for water treatment and remediation.

关键词： Antimicrobial properties Nanoblades Mechano-bactericidal effect RGO nanosheets Gram-positive bacteria Cell viability

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Seismic control of multi-degrees-of-freedom structures by vertical mass isolation method using MR dampers

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Earthquake Engineering and Engineering Vibration 2024年第2期23卷 503-510页

作者： Mohamad Shahrokh Abdi Masoud Nekooei Mohammad-Ali Jafari department of Civil Engineering Marivan BranchIslamic Azad UniversityMarivan ***Iran department of Civil Engineering Science and Research BranchIslamic Azad UniversityTehran ***Iran Structural department of Transmission and Distribution research Center Niroo Research Institute(NRI)Tehran ***Iran

Vertical mass isolation(VMI)is one of the novel methods for the seismic control of structures.In this method,the entire structure is assumed to consist of two mass and stiffness subsystems,and an isolated layer is located among them.In this study,the magnetorheological damper in three modes:passive-off,passive-on,and semi-active mode with variable voltage between zero and 9 volts was used as an isolated layer between two subsystems.Multi-degrees-of-freedom structures with 5,10,and 15 floors in two dimensions were examined under 11 pairs of near field earthquakes.On each level,the displacement of MR dampers was taken into account.The responses of maximum displacement,maximum inter-story drift,and maximum base shear in controlled and uncontrolled buildings were compared to assess the suggested approach for seismic control of the structures.According to the results,the semi-active control method can reduce the response by more than 12%compared to the uncontrolled mode in terms of maximum displacement of the mass subsystem of the structures.This method can reduce more than 16%and 20%of the responses compared to the uncontrolled mode in terms of maximum inter-story drift and base shear of the structure,respectively.

关键词： seismic control vertical mass isolation base shear magnetorheological damper semi-active control

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Damping capacity of Fe_(83)Ga_(17) magnetostrictive alloy under magnetic field

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Rare Metals 2024年第1期43卷 402-409页

作者： Shao-Wen Yan Xing Mu Bing-Jie Liu Li-Hong Xu Shi-Hai Guo Yan Qi Hong-Ping Zhang department of Functional Material research Central Iron and Steel Research InstituteBeijing 100081China

The damping performance of Fe_(83)Ga_(17) alloys has been investigated in the static magnetic field (H). The results demonstrate that the damping peak value can be adjusted between 0.020 and 0.085 under the magnetic f... 详细信息

关键词： alloy magnetic alloys

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Does topical vancomycin prevent fracture-related infections in closed fractures undergoing open reduction and internal fixation?A randomised controlled trial

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Chinese Journal of Traumatology 2024年第2期27卷 71-76页

作者： Mohit Gandhi Gopisankar Balaji Jagdish Menon Ruben Raj Thomas department of Orthopaedics Jawaharlal Institute of Postgraduate Medical Education and ResearchPondicherryIndia department of Preventive and Social Medicine Jawaharlal Institute of Postgraduate Medical Education and ResearchPondicherryIndia

Purpose:The role of topical vancomycin in fracture-related infection(FRI)is debatable.Very few studies have reported their efficacy in open and high-risk extremity fractures.This study aimed to assess topical vancomycin's role in reducing FRI in closed fractures undergoing open surgical intervention with an implant.Methods:This prospective randomized cohort study was carried out between February 2021 to January 2022.Patients with isolated closed fractures,who were planned for open reduction and internal fixation within 2 weeks from the time of injury were included for this study.The data collected included age,gender,socioeconomic status,mechanism of injury,diagnosis,Tscherne classification,and time interval to take up for surgery.Patients were randomized into the intervention and control groups using the block randomization technique.The control group received only systemic antibiotic prophylaxis,whereas the intervention group received topical application of vancomycin powder in the surgical wound alongside systemic antibiotic prophylaxis.The primary outcome measure was the incidence of FRI among these individuals.Clinical and radiological findings and culture reports(in cases with infection)were recorded during the post-operative period and at 6 weeks of follow-up.All relevant statistical calculations were done using STATA statistical/data analysis-parallel edition version 16.0(StataCorp LLC).The quantitative variables like age and duration of the surgery were assessed for normalcy by Shapiro-Wilk W test.An independent samples t-test with equal variances was applied to the age data.Fisher's exact test was used for the analysis of the primary outcome measure(presence of FRI following surgery),and"Risk of FRI"and"Risk difference"between the 2 groups was calculated.The strength of the association between qualitative variables was assessed using the Fisher's exact and Chi-square tests,respectively.Results:There were 88 patients included in this study.No statistical significance was found about FRI between both grou

关键词： Infections Antibiotics Vancomycin Fractures

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