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1.
Sci Rep ; 14(1): 14785, 2024 Jun 26.
Article in English | MEDLINE | ID: mdl-38926535

ABSTRACT

Direct laser acceleration (DLA) of electrons in plasmas of near-critical density (NCD) is a very advancing platform for high-energy PW-class lasers of moderate relativistic intensity supporting Inertial Confinement Fusion research. Experiments conducted at the PHELIX sub-PW Nd:glass laser demonstrated application-promising characteristics of DLA-based radiation and particle sources, such as ultra-high number, high directionality and high conversion efficiency. In this context, the bright synchrotron-like (betatron) radiation of DLA electrons, which arises from the interaction of a sub-ps PHELIX laser pulse with an intensity of 1019 W/cm2 with pre-ionized low-density polymer foam, was studied. The experimental results show that the betatron radiation produced by DLA electrons in NCD plasma is well directed with a half-angle of 100-200 mrad, yielding (3.4 ± 0.4)·1010 photons/keV/sr at 10 keV photon energy. The experimental photon fluence and the brilliance agree well with the particle-in-cell simulations. These results pave the way for innovative applications of the DLA regime using low-density pre-ionized foams in high energy density research.

3.
EBioMedicine ; 105: 105177, 2024 Jun 25.
Article in English | MEDLINE | ID: mdl-38924839

ABSTRACT

BACKGROUND: The 5-year survival rate of oesophageal squamous cell carcinoma (ESCC) is approximately 20%. The prognosis and drug response exhibit substantial heterogeneity in ESCC, impeding progress in survival outcomes. Our goal is to identify a signature for tumour subtype classification, enabling precise clinical treatments. METHODS: Utilising pre-treatment multi-omics data from an ESCC dataset (n = 310), an enhancer methylation-eRNA-target gene regulation network was constructed and validated by in vitro experiments. Four machine learning methods collectively identified core target genes, establishing an Enhancer Demethylation-Regulated Gene Score (EDRGS) model for classification. The molecular function of EDRGS subtyping was explored in scRNA-seq (n = 60) and bulk-seq (n = 310), and the EDRGS's potential to predict treatment response was assessed in datasets of various cancer types. FINDINGS: EDRGS stratified ESCCs into EDRGS-high/low subtypes, with EDRGS-high signifying a less favourable prognosis in ESCC and nine additional cancer types. EDRGS-high exhibited an immune-hot but immune-suppressive phenotype with elevated immune checkpoint expression, increased T cell infiltration, and IFNγ signalling in ESCC, suggesting a better response to immunotherapy. Notably, EDRGS outperformed PD-L1 in predicting anti-PD-1/L1 therapy effectiveness in ESCC (n = 42), kidney renal clear cell carcinoma (KIRC, n = 181), and bladder urothelial carcinoma (BLCA, n = 348) cohorts. EDRGS-low showed a cell cycle-activated phenotype with higher CDK4 and/or CDK6 expression, demonstrating a superior response to the CDK4/6 inhibitor palbociclib, validated in ESCC (n = 26), melanoma (n = 18), prostate cancer (n = 15) cells, and PDX models derived from patients with pancreatic cancer (n = 30). INTERPRETATION: Identification of EDRGS subtypes enlightens ESCC categorisation, offering clinical insights for patient management in immunotherapy (anti-PD-1/L1) and CDK4/6 inhibitor therapy across cancer types. FUNDING: This study was supported by funding from the National Key R&D Program of China (2021YFC2501000, 2020YFA0803300), the National Natural Science Foundation of China (82030089, 82188102), the CAMS Innovation Fund for Medical Sciences (2021-I2M-1-018, 2022-I2M-2-001, 2021-I2M-1-067), the Fundamental Research Funds for the Central Universities (3332021091).

4.
Macromol Biosci ; : e2400027, 2024 Mar 11.
Article in English | MEDLINE | ID: mdl-38462911

ABSTRACT

Addressing complex tissue infections remains a challenging task because of the lack of effective means, and the limitations of traditional bioantimicrobial materials in single-application scenarios hinder their utility for complex infection sites. Hence, the development of a bioantimicrobial material with broad applicability and potent bactericidal activity is necessary to treat such infections. In this study, a layered lithium magnesium silicate nanoclay (LMS) is used to construct a nanobactericidal platform. This platform exhibits a sandwich-like structure, which is achieved through copper ion modification using a dopamine-mediated metallophenolic network. Moreover, the nanoclay is encapsulated within gelatin methacryloyl (GelMA) hydrogel microspheres for the treatment of complex tissue infections. The results demonstrate that the sandwich-like micro- and nanobactericidal hydrogel microspheres effectively eradicated Staphylococcus aureus (S. aureus) while exhibiting excellent biocompatibility with bone marrow-derived mesenchymal stem cells (BMSCs) and human umbilical vein endothelial cells (HUVECs). Furthermore, the hydrogel microspheres upregulated the expression levels of osteogenic differentiation and angiogenesis-related genes in these cells. In vivo experiments validated the efficacy of sandwich-like micro- and nanobactericidal hydrogel microspheres when injected into deep infected tissues, effectively eliminating bacteria and promoting robust vascular regeneration and tissue repair. Therefore, these innovative sandwich-like micro- and nanobacteriostatic hydrogel microspheres show great potential for treating complex tissue infections.

5.
Front Psychiatry ; 14: 1211684, 2023.
Article in English | MEDLINE | ID: mdl-37663609

ABSTRACT

Background: To explore the relationship between autistic clinical profiles and age at first concern and diagnosis among children with autism spectrum disorder. The clinical profiles included the severity of autism, cognition, adaptability, language development, and regression. Methods: The multivariate linear regression model was used to examine the association of diagnostic age and first-concern age with autistic clinical profiles and with further stratification analysis. Results: A total of 801 autistic children were included. Language delay and regression were associated with earlier diagnostic age (language delay: crudeß: -0.80, 95%CI%: -0.92--0.68; regression: crudeß: -0.21, 95%CI%: -0.43--0.00) and the age of first concern of autistic children (language delay: crudeß: -0.55, 95%CI%: -0.65--0.45; regression: crudeß: -0.17, 95%CI%: -0.34--0.00). After stratification by sex, language delay tended to be more associated with the earlier diagnostic age among boys (crudeß: -0.85, 95%CI%: -0.98--0.72) than among girls (crudeß: -0.46, 95%CI%: -0.77--0.16). After stratification by maternal education level or family income level, language delay was most associated with the earlier diagnostic age in autistic children from families with higher socioeconomic levels. Conclusion: Language delay, rather than other symptoms, promoted an earlier diagnostic age. Among male autistic children or children from families with higher socioeconomic levels, language delay was most significantly associated with an earlier age of diagnosis. Cognitive delay, or adaptive delay, was associated with a later age at diagnosis and presented only in autistic children from families with lower socioeconomic levels. There may be sex or socioeconomic inequality in the diagnostic age for autistic children. More publicity and public education about the diversity of autistic symptoms are urgently needed in the future, especially for low-socioeconomic families.

6.
Appl Opt ; 62(13): 3347-3356, 2023 May 01.
Article in English | MEDLINE | ID: mdl-37132835

ABSTRACT

The coefficient of thermal expansion (CTE) of ultra-low-expansion (ULE) glass is critical to the development of precision optical systems. Herein, an ultrasonic immersion pulse-reflection method is proposed to characterize the CTE of ULE glass. The ultrasonic longitudinal wave velocity of ULE-glass samples with significantly different CTE values was measured using a correlation algorithm combined with moving-average filtering, which can achieve 0.2 m/s precision with a contribution to the ultrasonic CTE measurement uncertainty of 0.47 ppb/°C. Furthermore, the established ultrasonic CTE measurement model predicted the 5°C-35°C mean CTE with a root-mean-square error of 0.9 ppb/°C. Notably, a complete uncertainty analysis methodology was established in this paper, which can provide directional guidance for the subsequent development of higher-performance measurement devices and the improvement of relevant signal processing procedures.

7.
Ecotoxicol Environ Saf ; 256: 114861, 2023 May.
Article in English | MEDLINE | ID: mdl-37027943

ABSTRACT

The brain barrier is an important structure for metal ion homeostasis. According to studies, lead (Pb) exposure disrupts the transportation of copper (Cu) through the brain barrier, which may cause impairment of the nervous system; however, the specific mechanism is unknown. The previous studies suggested the X-linked inhibitor of apoptosis (XIAP) is a sensor for cellular Cu level which mediate the degradation of the MURR1 domain-containing 1 (COMMD1) protein. XIAP/COMMD1 axis was thought to be an important regulator in Cu metabolism maintenance. In this study, the role of XIAP-regulated COMMD1 protein degradation in Pb-induced Cu disorders in brain barrier cells was investigated. Pb exposure significantly increased Cu levels in both cell types, according to atomic absorption technology testing. Western blotting and reverse transcription PCR (RT-PCR) showed that COMMD1 protein levels were significantly increased, whereas XIAP, ATP7A, and ATP7B protein levels were significantly decreased. However, there were no significant effects at the messenger RNA (mRNA) level (XIAP, ATP7A, and ATP7B). Pb-induced Cu accumulation and ATP7B expression were reduced when COMMD1 was knocked down by transient small interfering RNA (siRNA) transfection. In addition, transient plasmid transfection of XIAP before Pb exposure reduced Pb-induced Cu accumulation, increased COMMD1 protein levels, and decreased ATP7B levels. In conclusion, Pb exposure can reduce XIAP protein expression, increase COMMD1 protein levels, and specifically decrease ATP7B protein levels, resulting in Cu accumulation in brain barrier cells.


Subject(s)
Copper , Lead , Copper/metabolism , Lead/metabolism , Proteolysis , X-Linked Inhibitor of Apoptosis Protein/metabolism , Adaptor Proteins, Signal Transducing/genetics , Adenosine Triphosphatases/metabolism , RNA, Small Interfering/metabolism , Brain/metabolism
8.
J Colloid Interface Sci ; 642: 505-512, 2023 Jul 15.
Article in English | MEDLINE | ID: mdl-37028157

ABSTRACT

The electrochemical oxygen evolution reaction is a bottleneck reaction in hydrolysis and electrolysis because the four-step electron transfer leads to slow reaction kinetics and large overpotentials. This situation can be improved by fast charge transfer by optimizing the interfacial electronic structure and enhancing polarization. Herein, a unique metal (Ni) organic (diphenylalanine, DPA) framework Ni(DPA)2 (Ni-MOF) with tunable polarization is designed to bond with FeNi-LDH (layered double hydroxides) nanoflakes. The Ni-MOF@FeNi-LDH heterostructure delivers excellent oxygen evolution performance exemplified by an ultralow overpotential of 198 mV at 100 mA cm-2 compared to other (FeNi-LDH)-based catalysts. Experiments and theoretical calculations show that FeNi-LDH exists in an electron-rich state in Ni-MOF@FeNi-LDH due to polarization enhancement caused by interfacial bonding with Ni-MOF. This effectively changes the local electronic structure of the metal Fe/Ni active sites and optimizes adsorption of the oxygen-containing intermediates. Polarization and electron transfer of Ni-MOF are further enhanced by magnetoelectric coupling consequently giving rise to better electrocatalytic properties as a result of high-density electron transfer to active sites. These findings reveal a promising interface and polarization modulation strategy to improve electrocatalysis.

9.
Nano Lett ; 23(9): 3694-3700, 2023 May 10.
Article in English | MEDLINE | ID: mdl-37074399

ABSTRACT

Peroxide dianion (O22-) has strong oxidizing activity and ease of proton abstraction and is extremely unstable. Direct and controllable adsorption and release of O22- has large application implication and is a large challenge so far. Here, we use a unique metal (Ni)-organic (diphenylalanine, DPA) framework (MOF), Ni(DPA)2, as adsorbents for absorption and release of O22-. This MOF structure has room-temperature magnetoelectricity via distortion of the Ni-centered octahedron {NiN2O4} and thus possesses a tunable ferroelectric polarization under applied electric/magnetic fields. Controllable adsorption and release of O22- are realized in such a MOF system via electrochemical redox measurements. Structural/spectroscopic characterization and calculations reveal that a number of NH active sites in the nanopores of MOF can effectively adsorb O22- by hydrogen bonds and then tunable ferroelectric polarization induces controllable release of O22- under applied magnetic fields. This work presents a constructive way for controllable adsorption and release of reactive oxygen species.

10.
Front Bioeng Biotechnol ; 11: 1111449, 2023.
Article in English | MEDLINE | ID: mdl-36873369

ABSTRACT

Objectives: To study the mechanical sensitivity of different intervertebral disc and bone material parameters and ligaments under different force configurations and magnitudes in the scoliosis model. Methods: The finite element model of a 21-year-old female is built using computed tomography. Local range of motion testing and global bending simulations are performed for the model verification. Subsequently, Five force of different directions and configurations were applied to the finite element model applying the brace pad position. The material parameters of the model were related to different spinal flexibilities and included different material parameters of cortical bone, cancellous bone, nucleus and annulus. The virtual X-ray technique measured Cobb angle, thoracic Lordosis, and lumbar Kyphosis. Results: The difference in peak displacement is 9.28 mm, 19.99 mm, 27.06 mm, 43.99 mm, and 50.1 mm under five force configurations. The maximum Cobb angle difference due to material parameters are 4.7° and 6.2°, which are converted to thoracic and lumbar in-brace correction difference of 18% and 15.5%. The maximum difference in Kyphosis and Lordosis angle is 4.4° and 5.8°. The average thoracic and lumbar Cobb angle variation difference in intervertebral disc control group is larger than that in bone control group, while the average Kyphosis and Lordosis angle is inverse. The displacement distribution of models with or without ligaments is similar, with a peak displacement difference of 1.3 mm in C5. The peak stress occurred at the junction of the cortical bone and ribs. Conclusion: Spinal flexibility largely influences the treatment effect of the brace. The intervertebral disc has a greater effect on the Cobb angle, the bone has a greater effect on the Kyphosis and Lordosis angles, and the rotation is affected by both. Patient-specific material is the key to increasing accuracy in the personalized finite element model. This study provides a scientific basis for using controllable brace treatment for scoliosis.

11.
Phys Rev Lett ; 130(9): 095101, 2023 Mar 03.
Article in English | MEDLINE | ID: mdl-36930918

ABSTRACT

We report on charge state measurements of laser-accelerated carbon ions in the energy range of several MeV penetrating a dense partially ionized plasma. The plasma was generated by irradiation of a foam target with laser-induced hohlraum radiation in the soft x-ray regime. We use the tricellulose acetate (C_{9}H_{16}O_{8}) foam of 2 mg/cm^{3} density and 1 mm interaction length as target material. This kind of plasma is advantageous for high-precision measurements, due to good uniformity and long lifetime compared to the ion pulse length and the interaction duration. We diagnose the plasma parameters to be T_{e}=17 eV and n_{e}=4×10^{20} cm^{-3}. We observe the average charge states passing through the plasma to be higher than those predicted by the commonly used semiempirical formula. Through solving the rate equations, we attribute the enhancement to the target density effects, which will increase the ionization rates on one hand and reduce the electron capture rates on the other hand. The underlying physics is actually the balancing of the lifetime of excited states versus the collisional frequency. In previous measurement with partially ionized plasma from gas discharge and z pinch to laser direct irradiation, no target density effects were ever demonstrated. For the first time, we are able to experimentally prove that target density effects start to play a significant role in plasma near the critical density of Nd-glass laser radiation. The finding is important for heavy ion beam driven high-energy-density physics and fast ignitions. The method provides a new approach to precisely address the beam-plasma interaction issues with high-intensity short-pulse lasers in dense plasma regimes.

12.
Eur J Phys Rehabil Med ; 59(2): 212-221, 2023 Apr.
Article in English | MEDLINE | ID: mdl-36700244

ABSTRACT

BACKGROUND: Current guidelines for brace management of adolescent idiopathic scoliosis (AIS) are mostly recommended for curves between 25° to 40°. For AIS patients with curves >40°, surgery is often considered since bracing may be less effective; however, there are still some patients and families who refuse operation. Therefore, further research is necessary to determine optimal bracing management in this group. To date, few protocols for such have been reported in literature. AIM: The aim of this study was to introduce and evaluate the effectiveness of the treatment protocol comprising of intensive bracing management and physiotherapeutic scoliosis-specific exercises (PSSE) in AIS patients with a major curve of 40-60° who refuse surgery. DESIGN: This is a prospective cohort study. SETTING: The study was carried out in an outpatient clinic. POPULATION: 10-18-year-old AIS patients having 40-60°curves and a Risser grade of 0-3, but firmly refusing surgery were eligible. Patients who had a proximal thoracic curve or had undergone any other form of treatment previously were excluded from the study. METHODS: A total of 82 patients were recruited and received the treatment. The primary outcome was defined as "success" when the main curve was below 50° upon reaching skeletal maturity, and "failure" if otherwise. The secondary outcome was defined as improved (>5° reduction), unchanged (≤5° change) or progressed (>5° increase) based on the evolution of the main curve. The per protocol (PP) and intent to treat (ITT) analyses were performed to quantify success rates, while the dropouts were considered as failures. Risk factors associated with bracing failure were identified and a receiver operating characteristic (ROC) curve was used to determine the cut-off value. RESULTS: A total of 77 patients completed the treatment, while 5 dropped out. The average main curve was 47.40±5.93° at baseline and 38.56±11.85° at last follow-up (P<0.001). Our management was successful in 83% and 78% of patients based on the PP and ITT analyses, respectively. When compared with the curve magnitude at baseline, 65% patients improved, 30% remained unchanged, and 5% progressed when using a 5° threshold. Univariate comparison and logistic regression analysis demonstrated that patients with successful outcomes had a significantly smaller baseline curve, larger Risser Stage, and larger in-brace correction (IBC) rate. CONCLUSIONS: For AIS patients with 40-60° curves who refused surgery, our intensive bracing management along with PSSE was practical and effective, achieving success in 78% of patients based on an ITT analysis. A larger baseline curve, smaller Risser Stage, and smaller IBC rate were associated with treatment failure. CLINICAL REHABILITATION IMPACT: Our intensive management provides new insights into improving the effectiveness of bracing in patients with AIS who refuse surgery. This is a promising option for patients with 40-60° curves, since their scoliosis may be treated using a non-surgical technique instead of surgery in the future.


Subject(s)
Scoliosis , Humans , Adolescent , Child , Scoliosis/therapy , Prospective Studies , Braces , Exercise Therapy , Risk Factors , Treatment Outcome , Retrospective Studies
13.
Cancer Cell ; 41(1): 181-195.e9, 2023 01 09.
Article in English | MEDLINE | ID: mdl-36584672

ABSTRACT

Integrated molecular analysis of human cancer has yielded molecular classification for precise management of cancer patients. Here, we analyzed the whole genomic, epigenomic, transcriptomic, and proteomic data of 155 esophageal squamous cell carcinomas (ESCCs). Multi-omics analysis led to the classification of ESCCs into four subtypes: cell cycle pathway activation, NRF2 oncogenic activation, immune suppression (IS), and immune modulation (IM). IS and IM cases were highly immune infiltrated but differed in the type and distribution of immune cells. IM cases showed better response to immune checkpoint blockade therapy than other subtypes in a clinical trial. We further developed a classifier with 28 features to identify the IM subtype, which predicted anti-PD-1 therapy response with 85.7% sensitivity and 90% specificity. These results emphasize the clinical value of unbiased molecular classification based on multi-omics data and have the potential to further improve the understanding and treatment of ESCC.


Subject(s)
Carcinoma, Squamous Cell , Esophageal Neoplasms , Esophageal Squamous Cell Carcinoma , Humans , Esophageal Squamous Cell Carcinoma/genetics , Esophageal Squamous Cell Carcinoma/pathology , Esophageal Neoplasms/genetics , Esophageal Neoplasms/pathology , Carcinoma, Squamous Cell/genetics , Multiomics , Proteomics
14.
Signal Transduct Target Ther ; 7(1): 370, 2022 10 24.
Article in English | MEDLINE | ID: mdl-36274060

ABSTRACT

Whereas it is appreciated that cancer cells rewire lipid metabolism to survive and propagate, the roles of lipid metabolism in metastasis remain largely unknown. In this study, using esophageal squamous cell carcinoma (ESCC) as a pulmonary metastasis model, we find that the enzyme fatty acid 2-hydroxylase (FA2H), which catalyzes the hydroxylation of free fatty acids (FAs), is enriched in a subpopulation of ESCC cells with high metastatic potential, and that FA2H knockdown markedly mitigates metastatic lesions. Moreover, increased FA2H expression is positively associated with poor survival in patients with ESCC. Lipidomics analysis identifies that two dihydroceramides-Cer(d18:0/24:0) and Cer(d18:0/24:1)-are increased in FA2H-depleted metastasizing ESCC cells. Upon administration, Cer(d18:0/24:0) and Cer(d18:0/24:1) impair the formation of overt metastases in a mouse experimental metastasis model. Then, forkhead box protein C2 (FOXC2) and FA2H are found to be co-upregulated in metastatic ESCC cell populations and ESCC specimens, and FA2H expression is further experimentally verified to be transcriptionally induced by FOXC2, which is boosted per se by tumour necrosis factor α (TNFα), a critical pro-metastasis cytokine in the tumour microenvironment, in metastasizing cells. Together, these results demonstrate that TNFα-FOXC2-FA2H is a novel signaling axis to promote metastasis, and its downstream dihydroceramide products could be promising drugs to intervene in metastasis.


Subject(s)
Esophageal Neoplasms , Esophageal Squamous Cell Carcinoma , Animals , Mice , Esophageal Squamous Cell Carcinoma/genetics , Tumor Necrosis Factor-alpha , Esophageal Neoplasms/genetics , Esophageal Neoplasms/pathology , Fatty Acids, Nonesterified , Ceramides/metabolism , Lipid Metabolism/genetics , Mixed Function Oxygenases/genetics , Mixed Function Oxygenases/metabolism , Forkhead Transcription Factors , Tumor Microenvironment
15.
NPJ Genom Med ; 7(1): 34, 2022 Jun 02.
Article in English | MEDLINE | ID: mdl-35654793

ABSTRACT

The 3' untranslated region (3'-UTR) is the vital element regulating gene expression, but most studies have focused on variations in RNA-binding proteins (RBPs), miRNAs, alternative polyadenylation (APA) and RNA modifications. To explore the posttranscriptional function of 3'-UTR somatic mutations in tumorigenesis, we collected whole-genome data from 2413 patients across 18 cancer types. Our updated algorithm, PIVar, revealed 25,216 3'-UTR posttranscriptional impairment-related SNVs (3'-UTR piSNVs) spanning 2930 genes; 24 related RBPs were significantly enriched. The somatic 3'-UTR piSNV ratio was markedly increased across all 18 cancer types, which was associated with worse survival for four cancer types. Several cancer-related genes appeared to facilitate tumorigenesis at the protein and posttranscriptional regulation levels, whereas some 3'-UTR piSNV-affected genes functioned mainly via posttranscriptional mechanisms. Moreover, we assessed immune cell and checkpoint characteristics between the high/low 3'-UTR piSNV ratio groups and predicted 80 compounds associated with the 3'-UTR piSNV-affected gene expression signature. In summary, our study revealed the prevalence and clinical relevance of 3'-UTR piSNVs in cancers, and also demonstrates that in addition to affecting miRNAs, 3'-UTR piSNVs perturb RBPs binding, APA and m6A RNA modification, which emphasized the importance of considering 3'-UTR piSNVs in cancer biology.

16.
Med Biol Eng Comput ; 60(4): 907-920, 2022 Apr.
Article in English | MEDLINE | ID: mdl-35157195

ABSTRACT

Adolescent idiopathic scoliosis (AIS) is a musculoskeletal disorder characterized as three-dimensional (3D) deformity, and bracing is a common conservative treatment for AIS. Finite element analysis (FEA) is a technique for numerically solving the differential equations arising in engineering and mathematical modeling and has been widely used in biomechanical studies. Recently, FEA has been under intensive focus to improve the clinical outcomes of brace treatment. This review focuses on using FEA to assist brace treatment for AIS and technique choices that may be encountered during the construction of the finite element model (FEM). The construction of geometric models, the mechanical property, element type, the boundary condition, and the observation items of FEA have been summarized while establishing FEM. In each technical aspect, different fields and limitations of FEA are discussed. The observation items based on FEA are collected in addition to the biomechanical value in clinical research. We also summarized the technical aspects of brace treatment by FEA and observation items and provided guidance and directions to improve the brace treatment.


Subject(s)
Kyphosis , Scoliosis , Adolescent , Braces , Finite Element Analysis , Humans , Scoliosis/therapy
17.
Brief Bioinform ; 23(2)2022 03 10.
Article in English | MEDLINE | ID: mdl-35037014

ABSTRACT

Optimal methods could effectively improve the accuracy of predicting and identifying candidate driver genes. Various computational methods based on mutational frequency, network and function approaches have been developed to identify mutation driver genes in cancer genomes. However, a comprehensive evaluation of the performance levels of network-, function- and frequency-based methods is lacking. In the present study, we assessed and compared eight performance criteria for eight network-based, one function-based and three frequency-based algorithms using eight benchmark datasets. Under different conditions, the performance of approaches varied in terms of network, measurement and sample size. The frequency-based driverMAPS and network-based HotNet2 methods showed the best overall performance. Network-based algorithms using protein-protein interaction networks outperformed the function- and the frequency-based approaches. Precision, F1 score and Matthews correlation coefficient were low for most approaches. Thus, most of these algorithms require stringent cutoffs to correctly distinguish driver and non-driver genes. We constructed a website named Cancer Driver Catalog (http://159.226.67.237/sun/cancer_driver/), wherein we integrated the gene scores predicted by the foregoing software programs. This resource provides valuable guidance for cancer researchers and clinical oncologists prioritizing cancer driver gene candidates by using an optimal tool.


Subject(s)
Neoplasms , Oncogenes , Algorithms , Computational Biology/methods , Gene Regulatory Networks , Humans , Mutation , Neoplasms/genetics , Software
18.
Comput Methods Biomech Biomed Engin ; 25(2): 132-139, 2022 Feb.
Article in English | MEDLINE | ID: mdl-34097549

ABSTRACT

In this study, the biomechanical differences among three internal fixation configurations for treatment of Pauwels type II and III femoral neck fractures were analyzed. Using finite element analysis, the femur displacement and stress distributions of the internal fixation device and fracture section were obtained for different patients and movement conditions. The results show that patients with osteoporosis are more prone to femoral varus and femoral neck shortening, and the fracture probability of the device for these patients is higher than that for patients with normal bone. The treatment effect of the inverted-triangle screw (ITS) fixation and proximal femoral nail anti-rotation (PFNA) fixation is better than that of dynamic hip screw (DHS) fixation. The ITS fixation is more suitable for the treatment of the normal bone patients with Pauwels II femur neck fracture. However, the PFNA fixation has better biomechanical advantages and better capability for anti-femoral neck shortening. Therefore, it is suitable for the treatment of femoral neck fracture patients with osteoporosis.


Subject(s)
Femoral Neck Fractures , Biomechanical Phenomena , Bone Screws , Femoral Neck Fractures/diagnostic imaging , Femoral Neck Fractures/surgery , Finite Element Analysis , Fracture Fixation, Internal , Humans
19.
J Pharm Sci ; 111(1): 116-123, 2022 01.
Article in English | MEDLINE | ID: mdl-34303671

ABSTRACT

This work aimed to use hot-melt extrusion (HME) and dual fused deposition modeling (FDM) 3D printing technology to develop a novel intragastric floating and sustained-release drug delivery system. The intragastric floating and sustained-release tablet was engineered by employing hydroxypropyl methylcellulose (AffinisolTM HPMC HME 15LV) for a drug-loaded core and polylactic acid (PLA) for an insoluble shell with an air chamber. Filaments for the drug-loaded core were compounded using a single-screw hot melt extruder. 3DMAX software was utilized to design a core with a complementary shell which consisted of a hollow chamber at the top and a drug-release window with different sizes (radius in 1.5, 2.5, 3, 3.5, 4.5 mm) at the bottom. Pharmaceutical characterization, solid dispersion evaluation, and drug release behavior were studied. The model drug in all formulations kept stable, and part of the drug in the extruded filaments and 3D printed tablets became amorphous. The introduction of an air chamber reduced the tablet density to below 0.9 g/cm3 and the 3D printed tablets floated immediately and continuously during the drug release process. The presence of the insoluble shell greatly prolonged the drug release time, and the drug release rate was positively correlated with the area of the release window. In addition, compared with shellless tablets, the 3D printed tablets with air chambers (radius in 4.5 mm) showed closer zero-order drug release for 24 h and released drug by diffusion-erosion combined mechanism. The developed intragastric floating and sustained-release tablets with air chambers could be applied to various drugs and provided a new way for the development of personalized drug delivery systems.


Subject(s)
Printing, Three-Dimensional , Technology, Pharmaceutical , Delayed-Action Preparations , Drug Liberation , Tablets
20.
Eng Life Sci ; 21(12): 825-831, 2021 Dec.
Article in English | MEDLINE | ID: mdl-34899119

ABSTRACT

Genome synthesis endows scientists the ability of de novo creating genomes absent in nature, by thorough redesigning DNA sequences and introducing numerous custom features. However, the genome synthesis is a labor- and time-consuming work, and thus it is a challenge to verify and quantify the synthetic genome rapidly and precisely. Thus, specific DNA sequences different from native genomic sequences are designed into synthetic genomes during synthesis, namely genomic markers. Genomic markers can be easily detected by PCR reaction, whole-genome sequencing (WGS) and a variety of methods to identify the synthetic genome from native one. Here, we review types and applications of genomic markers utilized in synthetic genomes, with the hope of providing a guidance for future works.

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