Comprehensive tissue deconvolution of cell-free DNA by deep learning for disease diagnosis and monitoring.

Plasma cell-free DNA (cfDNA) is a noninvasive biomarker for cell death of all organs. Deciphering the tissue origin of cfDNA can reveal abnormal cell death because of diseases, which has great clinical potential in disease detection and monitoring. Despite the great promise, the sensitive and accurate quantification of tissue-derived cfDNA remains challenging to existing methods due to the limited characterization of tissue methylation and the reliance on unsupervised methods. To fully exploit the clinical potential of tissue-derived cfDNA, here we present one of the largest comprehensive and high-resolution methylation atlas based on 521 noncancer tissue samples spanning 29 major types of human tissues. We systematically identified fragment-level tissue-specific methylation patterns and extensively validated them in orthogonal datasets. Based on the rich tissue methylation atlas, we develop the first supervised tissue deconvolution approach, a deep-learning-powered model, cfSort, for sensitive and accurate tissue deconvolution in cfDNA. On the benchmarking data, cfSort showed superior sensitivity and accuracy compared to the existing methods. We further demonstrated the clinical utilities of cfSort with two potential applications: aiding disease diagnosis and monitoring treatment side effects. The tissue-derived cfDNA fraction estimated from cfSort reflected the clinical outcomes of the patients. In summary, the tissue methylation atlas and cfSort enhanced the performance of tissue deconvolution in cfDNA, thus facilitating cfDNA-based disease detection and longitudinal treatment monitoring.

Cartilage stem/progenitor cells-derived exosomes facilitate knee cartilage repair in a subacute osteoarthritis rat model.

Cartilage defects in the knee are often associated with the progression of degenerative osteoarthritis (OA), and cartilage repair is a useful strategy for managing this disease. However, cartilage repair is challenging because of the unique environment within the tissue. Recently, stem cell-based therapies have shed new light on this issue. In this study, we prepared exosomes (EXOs) from cartilage stem/progenitor cells (CSPCs) and found that treatment with EXOs increased the viability, migration, and proliferation of cultured primary chondrocytes. In a subacute OA rat model, the application of EXOs facilitated cartilage regeneration as evidenced by histological staining. Exosomal protein analysis together with bioinformatics suggested that cyclin-dependent kinase 9 (CDK9) is a key factor for chondrocyte growth and migration. Functional studies confirmed this prediction, that is, inhibiting CDK9 reduced the beneficial effects induced by EXOs in primary chondrocytes; while overexpression of CDK9 recapitulated the EXOs-induced phenotypes. RNA-Seq data showed that a set of genes involved in cell growth and migration were up-regulated by EXOs in chondrocytes. These changes could be partially reproduced by CDK9 overexpression. Overall, our data suggest that EXOs derived from primary CSPCs hold great therapeutic potential for treating cartilage defect-associated disorders such as degenerative OA, and that CDK9 is a key factor in this process.

Comparison of unilateral and bilateral puncture percutaneous kyphoplasty in the treatment of osteoporotic vertebral compression fractures.

OBJECTIVES: To compare the clinical efficacy of unilateral and bilateral puncture PKP in the treatment of OVCFs and explored whether there is a difference in the efficacy of unilateral and bilateral puncture PKP after surgery. METHODS: A total of 98 patients with OVCFs treated by PKP from August 2016 to June 2018 were selected. There were 62 cases in the unilateral puncture group and 36 cases in the bilateral puncture group. The operation time, the amount of bone cement injection, the height of the anterior edge of the vertebral body and the visual analog scale (Visual Analog Scale, VAS) scores before and after the operation were analyzed, and whether the differences between the 2 groups were statistically significant was analyzed. RESULTS: All patients were followed up completely. The operation time and the number of X-ray fluoroscopies of the unilateral puncture group were significantly reduced compared to those of the bilateral group, and the difference was statistically significant (p<0.05). In terms of the bone cement injection volume, the average injection volume of the bilateral group was greater than that of the unilateral group, and the difference was statistically significant (p<0.05); the postoperative VAS scores of the 2 groups of patients were significantly improved, and the difference was statistically significant compared with that before surgery (p<0.05) but that of the unilateral group was not statistically significant compared with that of the bilateral group (p>0.05). The height of the anterior edge of the vertebral body in both groups was significantly improved compared with that before the operation, and the difference was statistically significant (p<0.05). CONCLUSION: Unilateral and bilateral puncture PKP can achieve good clinical efficacy in the treatment of osteoporotic vertebral compression fractures, but unilateral PKP has the advantages of short operation time and low X-ray exposure.

Ubiquitin conjugating enzyme E2 M promotes apoptosis in osteoarthritis chondrocytes via Wnt/ß-catenin signaling.

In this study, the role of ubiquitin conjugating enzyme E2 M (UBE2M) and molecular mechanisms associated with osteoarthritis (OA) were explored. Cartilage tissues and corresponding healthy tissues from OA patients were isolated. Our data suggested that the expression level of UBE2M in OA patients was significantly higher compared to that in healthy individuals (P < 0.01). The apoptosis of human OA chondrocytes was inhibited when silencing UBE2M and increased when overexpressing UBE2M. XAV939, as a tankyrase 1 inhibitor, could block the signaling pathway of Wnt/ß-catenin, which significantly reversed the change introduced by UBE2M. The expression level of cytoplasmic ß-catenin in siUBE2M cells dramatically increased, and the expression levels of nuclear ß-catenin, cleaved caspase-3 (C-caspase-3), and MMP13 remarkably downregulated. Moreover, the ubiquitination of Axin was enhanced by the overexpression of UBE2M. The expression level of Axin significantly decreased in OA chondrocytes with UBE2M overexpression and increased after MG132 treatment. Moreover, UBE2M enhanced the apoptosis of OA chondrocytes by activating the Axin-dependent Wnt/ß-catenin pathway. In this process, UBE2M downregulated Axin in an ubiquitination-dependent degradation pathway and subsequently activated Wnt/ß-catenin signaling.

Single-cell sequencing deciphers a convergent evolution of copy number alterations from primary to circulating tumor cells.

Copy number alteration (CNA) is a major contributor to genome instability, a hallmark of cancer. Here, we studied genomic alterations in single primary tumor cells and circulating tumor cells (CTCs) from the same patient. Single-nucleotide variants (SNVs) in single cells from both samples occurred sporadically, whereas CNAs among primary tumor cells emerged accumulatively rather than abruptly, converging toward the CNA in CTCs. Focal CNAs affecting the MYC gene and the PTEN gene were observed only in a minor portion of primary tumor cells but were present in all CTCs, suggesting a strong selection toward metastasis. Single-cell structural variant (SV) analyses revealed a two-step mechanism, a complex rearrangement followed by gene amplification, for the simultaneous formation of anomalous CNAs in multiple chromosome regions. Integrative CNA analyses of 97 CTCs from 23 patients confirmed the convergence of CNAs and revealed single, concurrent, and mutually exclusive CNAs that could be the driving events in cancer metastasis.

Variable Intra-Tumor Genomic Heterogeneity of Multiple Lesions in Patients With Hepatocellular Carcinoma.

BACKGROUND & AIMS: Many patients with hepatocellular carcinoma (HCC) have multiple lesions (primary tumors, intrahepatic metastases, multiple occurrences, satellite nodules, and tumor thrombi); these have been associated with a poor prognosis and tumor recurrence after surgery. We investigated the clonal relationship among these lesions on the basis of genetic features. METHODS: We collected 43 lesions and 10 matched control samples (blood or nontumorous liver) from 10 patients with hepatitis B virus-associated HCC treated at Tianjin Cancer Hospital (China) from January 2013 through May 2014. We performed exome and low-depth, whole-genome sequencing on these samples. Genomic aberrations, including somatic mutations and copy number variations, were identified using germline DNA as control. We compared the genetic features of different lesions from each patient and constructed phylogenetic trees to depict their evolutionary histories. RESULTS: In each patient, mutations shared by all the lesions were called ubiquitous mutations. The percentage of ubiquitous mutations varied from 8% to 97% among patients, indicating variation in the extent of intratumor heterogeneity. Branched evolution was evident, with somatic mutations, hepatitis B virus integrations, and copy number variations identified on both the trunks and branches of the phylogenetic trees. Intrahepatic metastases and tumor thrombi contained some, but not all, of the mutations detected in their matched primary lesions. By contrast, satellite nodules shared approximately 90% of mutations detected in primary lesions. In a patient with multicentric tumors, 6 lesions were assigned to 2 distinct groups, based on significant differences in genetic features. In another patient with combined hepatocellular and intrahepatic cholangiocarcinoma, the physically separate HCC and cholangiocarcinoma lesions shared 102 mutations. CONCLUSIONS: The extent of intratumor heterogeneity varies considerably among patients with HCC. Therefore, sequence analysis of a single lesion cannot completely characterize the genomic features of HCC in some patients. Genomic comparisons of multiple lesions associated with HCCs will provide important information on the genetic changes associated with tumor progression.

Reproducible copy number variation patterns among single circulating tumor cells of lung cancer patients.

Circulating tumor cells (CTCs) enter peripheral blood from primary tumors and seed metastases. The genome sequencing of CTCs could offer noninvasive prognosis or even diagnosis, but has been hampered by low single-cell genome coverage of scarce CTCs. Here, we report the use of the recently developed multiple annealing and looping-based amplification cycles for whole-genome amplification of single CTCs from lung cancer patients. We observed characteristic cancer-associated single-nucleotide variations and insertions/deletions in exomes of CTCs. These mutations provided information needed for individualized therapy, such as drug resistance and phenotypic transition, but were heterogeneous from cell to cell. In contrast, every CTC from an individual patient, regardless of the cancer subtypes, exhibited reproducible copy number variation (CNV) patterns, similar to those of the metastatic tumor of the same patient. Interestingly, different patients with the same lung cancer adenocarcinoma (ADC) shared similar CNV patterns in their CTCs. Even more interestingly, patients of small-cell lung cancer have CNV patterns distinctly different from those of ADC patients. Our finding suggests that CNVs at certain genomic loci are selected for the metastasis of cancer. The reproducibility of cancer-specific CNVs offers potential for CTC-based cancer diagnostics.

Infrared Spectrum Studies of Coatings under Irradiation of Sunlight and Ultraviolet.

Degradable resin- coated controlled release fertilizer is one of the hottest current research focuses in the field of fertilizer. In terms of practical application, the photodegradability characteristics of three kinds of coatings including polyethylene/hydrophilic nano-TiO2 composite, polyethylene/hydrophilic nano-TiO2 composite and pure polyethylene were analyzed under irradiation of sunlight and ultraviolet by ATR-FTIR, which was aimed to know their degradation behaviors under two conditions. The result showed that under irradiation of sunlight and ultraviolet, the type of functional group was not changed with the addition of the photo-catalyst, but the photo-catalyst just had an effect on intensity of functional groups. The trend was polyethylene/hydrophobic nano-TiO2 composite>polyethylene/hydrophilic nano-TiO2 composite>pure polyethylene. Furthermore, sunlight and ultraviolet had different effects on molecular structures of coatings. Under irradiation of sunlight, crosslinking reaction took place and ether bond was generated among the carbon chain of polyethylene except for the form of hydroperoxides. Then, carbon chain continued being oxidized to form carbonyl group. The existence of carbonyl group promoted the further degradation of coatings; under irradiation of ultraviolet, high local concentrations of reactive oxygen species were produced and the ability to attack the carbon chain of polymer was strong. Thus, the long alkyl chain of polyethylene was quickly oxidized to form intermediate products containing carbonyl groups. However, the irradiation experiment of ultraviolet didn't fully reveal the degradation behavior of coatings.

[Effects of Controlled-release Blended Fertilizer on Crop Yield and Greenhouse Gas Emissions in Wheat-maize Rotation System].

The increasing use of nitrogen fertilizers exerts extreme pressure on the environment (e.g., greenhouse gas emissions, GHGs) for winter wheat-summer maize rotation systems in the North China Plain. The application of controlled-release fertilizers is considered as an effective measure to improve crop yield and nitrogen fertilizer utilization efficiency. To explore the impact of one-time fertilization of controlled-release blended fertilizer on crop yield and GHGs of a wheat-maize rotation system, field experiments were carried out in Dezhou Modern Agricultural Science and Technology Park from 2020 to 2022. Five treatments were established for both winter wheat and summer maize, including no nitrogen control (CK), farmers' conventional nitrogen application (FFP), optimized nitrogen application (OPT), CRU1 (the blending ratio of coated urea and traditional urea on winter wheat and summer maize was 5:5 and 3:7, respectively), and CRU2 (the blending ratio of coated urea and traditional urea on winter wheat and summer maize was 7:3 and 5:5, respectively). The differences in yield, nitrogen fertilizer utilization efficiency, fertilization economic benefits, and GHGs among different treatments were compared and analyzed. The results showed that nitrogen application significantly increased the single season and annual crop yields of the wheat-maize rotation system (P < 0.05). Compared with those of FFP, the CRU1 and CRU2 treatments increased the yields of summer maize by 0.4% to 5.6%, winter wheat by -5.4% to 4.1%, and annual yields by -1.1% to 3.9% (P > 0.05). N recovery efficiency (NRE), N agronomic efficiency (NAE), and N partial factor productivity (NPFP) were increased by -8.6%-43.4%, 2.05-6.24 kg·kg-1, and 4.24-10.13 kg·kg-1, respectively. Annual net income increased by 0.2% to 6.3%. Nitrogen application significantly increased the annual emissions of soil N2O and CO2 in the rotation system (P < 0.05) but had no effect on the annual emissions of CH4 (except for in the FFP treatment in the first year). The annual total N2O emissions under the CRU1 and CRU2 treatments were significantly reduced by 23.4% to 30.2% compared to those under the FFP treatment (P < 0.05). Additionally, nitrogen application significantly increased the annual global warming potential (GWP) of the rotation system (P < 0.05), but the intensity of greenhouse gas emissions was reduced due to the increase in crop yields. Compared with that under FFP, the annual GWP under the CRU1 and CRU2 treatments decreased by 9.6% to 11.5% (P < 0.05), and the annual GHGs decreased by 11.2% to 13.8% (P > 0.05). In summary, the one-time application of controlled-release blended fertilizer had a positive role in improving crop yield and economic benefits, reducing nitrogen fertilizer input and labor costs, and GHGs, which is an effective nitrogen fertilizer management measure to promote cleaner production of food crops in the North China Plain.

Preparation and properties of composite manganese/fluorine coatings on metallic titanium.

Titanium is widely used in implants because of its good mechanical properties and biocompatibility. However, titanium has no biological activity and is prone to causing implant failure after implantation. In this study, we prepared a manganese- and fluorine-doped titanium dioxide coating on a titanium surface by microarc oxidation technology. The surface characteristics of the coating were evaluated by field emission scanning electron microscopy, X-ray diffraction, X-ray photoelectron spectroscopy, and atomic force microscopy and profiler, and the corrosion resistance and wear resistance of the coating were also evaluated. The bioactivity of the coating on bone marrow mesenchymal stem cells was evaluated by in vitro cell experiments, and the antibacterial properties of the coating were evaluated by in vitro bacterial experiments. The results confirmed that the manganese- and fluorine-doped titanium dioxide coating was successfully prepared on the titanium surface, and manganese and fluorine were successfully introduced into the coating. The doping of manganese and fluorine did not change the surface morphology of the coating, and the coating had good corrosion resistance and wear resistance. The results of the in vitro cell experiment showed that the titanium dioxide coating with manganese and fluoride could promote the proliferation, differentiation and mineralization of bone marrow mesenchymal stem cells. The results of the bacterial experiment in vitro showed that the coating material could inhibit the propagation of Staphylococcus aureus and had a good antibacterial effect. Conclusion: it is feasible to prepare a manganese- and fluorine-doped titanium dioxide coating on titanium surfaces by microarc oxidation. The coating not only has good surface characteristics but also has good bone-promoting and antibacterial properties and has potential for clinical application.

Clinical effects of 3D printing-assisted posterolateral incision in the treatment of ankle fractures involving the posterior malleolus.

Objective: To explore the clinical outcomes of a 3D printing-assisted posterolateral approach for the treatment of ankle fractures involving the posterior malleolus. Methods: A total of 51 patients with ankle fractures involving the posterior malleolus admitted to our hospital from January 2018 to December 2019 were selected. The patients were divided into 3D printing group (28 cases) and control group (23 cases). 3D printing was performed for ankle fractures, followed by printing of a solid model and simulation of the operation on the 3D model. The operation was then performed according to the preoperative plan, including open reduction and internal fixation via the posterolateral approach with the patient in the prone position. Routine x-ray and CT examinations of the ankle joint were performed, and ankle function was evaluated using the American Foot and Ankle Surgery Association (AOFAS) ankle-hindfoot score. Results: All patients underwent x-ray and CT examinations. All fractures healed clinically, without loss of reduction or failure of internal fixation. Good clinical effects were achieved in both groups of patients. The operation time, intraoperative blood loss and intraoperative fluoroscopy frequency in the 3D printing group were significantly less than those in the control group (p < 0.05). There was no significant difference between the two groups in the anatomical reduction rate of fractures or the incidence of surgical complications (p > 0.05). Conclusion: The 3D printing-assisted posterolateral approach is effective in the treatment of ankle fractures involving the posterior malleolus. The approach can be well planned before the operation, is simple to perform, yields good fracture reduction and fixation, and has good prospects for clinical application.

The effect of reinforcement on the mechanical properties of veneered wood fiber/polypropylene composites assembled with chlorinated polypropylene.

Wood fiber/polypropylene (WF/PP) composites are environmentally friendly materials with high dimensional stability and mechanical properties. However, the applications of WF/PP composites are limited by an unattractive surface texture. In this study, the WF/PP composites were decorated with poplar wood veneer using chlorinated polypropylene (CPP) as a hot melt adhesive, the bonding strength is over 1.18 MPa. Surface bonding strength tests and scanning electron microscopy (SEM) were performed to analyze the quality of the CPP bonding layer. The physical and mechanical properties of the veneered WF/PP boards and unveneered controls were examined to determine the effects of reinforcement. The result shows that after veneered the tension strength and modulus of the whole composite board were increased over 30% and 10%; the flexural strength and modulus were increased over 10% and 20%. Low-velocity impact testing was performed to determine the impact resistance properties of the composites. Higher ratios of wood fiber in the WF/PP composite led to a higher surface bonding strength, which was evident in the SEM images. Wood veneer decoration increased the mechanical strength of the whole composite board. A tighter bond along the CPP layer would provide additional reinforcement of the veneered composite's mechanical properties.

Promotion of bone formation and antibacterial properties of titanium coated with porous Si/Ag-doped titanium dioxide.

Implant materials are mainly used to repair and replace defects in human hard tissue (bones and teeth). Titanium (Ti) and Ti alloys are widely used as implant materials because of their good mechanical properties and biocompatibilities, but they do not have the ability to induce new bone formation and have no antibacterial properties. Through surface modification, Ti and its alloys have certain osteogenic and antibacterial properties such that Ti implants can meet clinical needs and ensure integration between Ti implants and bone tissue, and this is currently an active research area. In this study, bioactive Si and Ag were introduced onto a Ti surface by plasma oxidation. The surface morphology, structure, elemental composition and valence, surface roughness, hydrophilicity and other physical and chemical properties of the coating were characterized by scanning electron microscopy (SEM), X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), a profiler and a contact angle meter (CA). Adhesion and extensions of osteoblasts on the surface of the material were observed by scanning electron microscopy, and mineralization of osteoblasts on the surface of the material were observed by alizarin red staining. The antibacterial properties of the material were tested by culturing Staphylococcus aureus on the surface of the material. The osteogenic properties of Ti implants with porous Si/Ag TiO2 (TCP-SA) coatings were evaluated with in vivo experiments in rats. The results showed that Si and Ag were successfully introduced onto the Ti surface by plasma oxidation, and doping with Si and Ag did not change the surface morphology of the coating. The osteoblasts showed good adhesion and extension on the surfaces of Si/Ag coated samples, and the porous Si/Ag TiO2 coating promoted cell proliferation and mineralization. The bacterial experiments showed that the porous TiO2 coatings containing Si/Ag had certain antibacterial properties. The animal experiments showed that Si/Ag-coated Ti implants promoted integration between the implants and the surrounding bone. It was concluded that the porous Si/Ag TiO2 coating on the Ti surface had good osteogenic and antibacterial properties and provides an optimal strategy for improving the osteogenic and antibacterial properties of Ti implants.

cfTrack: A Method of Exome-Wide Mutation Analysis of Cell-free DNA to Simultaneously Monitor the Full Spectrum of Cancer Treatment Outcomes Including MRD, Recurrence, and Evolution.

PURPOSE: Cell-free DNA (cfDNA) offers a noninvasive approach to monitor cancer. Here we develop a method using whole-exome sequencing (WES) of cfDNA for simultaneously monitoring the full spectrum of cancer treatment outcomes, including minimal residual disease (MRD), recurrence, evolution, and second primary cancers. EXPERIMENTAL DESIGN: Three simulation datasets were generated from 26 patients with cancer to benchmark the detection performance of MRD/recurrence and second primary cancers. For further validation, cfDNA samples (n = 76) from patients with cancer (n = 35) with six different cancer types were used for performance validation during various treatments. RESULTS: We present a cfDNA-based cancer monitoring method, named cfTrack. Taking advantage of the broad genome coverage of WES data, cfTrack can sensitively detect MRD and cancer recurrence by integrating signals across known clonal tumor mutations of a patient. In addition, cfTrack detects tumor evolution and second primary cancers by de novo identifying emerging tumor mutations. A series of machine learning and statistical denoising techniques are applied to enhance the detection power. On the simulation data, cfTrack achieved an average AUC of 99% on the validation dataset and 100% on the independent dataset in detecting recurrence in samples with tumor fractions ≥0.05%. In addition, cfTrack yielded an average AUC of 88% in detecting second primary cancers in samples with tumor fractions ≥0.2%. On real data, cfTrack accurately monitors tumor evolution during treatment, which cannot be accomplished by previous methods. CONCLUSIONS: Our results demonstrated that cfTrack can sensitively and specifically monitor the full spectrum of cancer treatment outcomes using exome-wide mutation analysis of cfDNA.

Cost-effective methylome sequencing of cell-free DNA for accurately detecting and locating cancer.

Early cancer detection by cell-free DNA faces multiple challenges: low fraction of tumor cell-free DNA, molecular heterogeneity of cancer, and sample sizes that are not sufficient to reflect diverse patient populations. Here, we develop a cancer detection approach to address these challenges. It consists of an assay, cfMethyl-Seq, for cost-effective sequencing of the cell-free DNA methylome (with > 12-fold enrichment over whole genome bisulfite sequencing in CpG islands), and a computational method to extract methylation information and diagnose patients. Applying our approach to 408 colon, liver, lung, and stomach cancer patients and controls, at 97.9% specificity we achieve 80.7% and 74.5% sensitivity in detecting all-stage and early-stage cancer, and 89.1% and 85.0% accuracy for locating tissue-of-origin of all-stage and early-stage cancer, respectively. Our approach cost-effectively retains methylome profiles of cancer abnormalities, allowing us to learn new features and expand to other cancer types as training cohorts grow.

Osteoblast Response to Copper-Doped Microporous Coatings on Titanium for Improved Bone Integration.

Due to their excellent mechanical properties and good biocompatibility, titanium alloys have become a popular research topic in the field of medical metal implants. However, the surface of the titanium alloy does not exhibit biological activity, which may cause poor integration between the interface of the titanium implant and the interface of the bone tissue and subsequently may cause the implant to fall off. Therefore, surface biological inertness is one of the problems that titanium alloys must overcome to become an ideal orthopedic implant material. Surface modification can improve the biological properties of titanium, thereby enhancing its osseointegration effect. Copper is an essential trace element for the human body, can promote bone formation and plays an important role in maintaining the physiological structure and function of bone and bone growth and development. In this study, a microporous copper-titanium dioxide coating was prepared on the surface of titanium by microarc oxidation. Based on the evaluation of its surface characteristics, the adhesion, proliferation and differentiation of MC3T3-E1 cells were observed. A titanium rod was implanted into the rabbit femoral condyle, and the integration of the coating and bone tissue was evaluated. Our research results show that the microporous copper-titanium dioxide coating has a nearly three-dimensional porous structure, and copper is incorporated into the coating without changing the structure of the coating. In vitro experiments found that the coating can promote the adhesion, proliferation and differentiation of MC3T3-E1 cells. In vivo experiments further confirmed that the titanium copper-titanium dioxide microporous coating can promote the osseointegration of titanium implants. In conclusion, copper-titanium dioxide microporous coatings can be prepared by microarc oxidation, which can improve the biological activity and biocompatibility of titanium, promote new bone formation and demonstrate good osteoinductive properties. Therefore, the use of this coating in orthopedics has potential clinical application.

Sensitive detection of tumor mutations from blood and its application to immunotherapy prognosis.

Cell-free DNA (cfDNA) is attractive for many applications, including detecting cancer, identifying the tissue of origin, and monitoring. A fundamental task underlying these applications is SNV calling from cfDNA, which is hindered by the very low tumor content. Thus sensitive and accurate detection of low-frequency mutations (<5%) remains challenging for existing SNV callers. Here we present cfSNV, a method incorporating multi-layer error suppression and hierarchical mutation calling, to address this challenge. Furthermore, by leveraging cfDNA's comprehensive coverage of tumor clonal landscape, cfSNV can profile mutations in subclones. In both simulated and real patient data, cfSNV outperforms existing tools in sensitivity while maintaining high precision. cfSNV enhances the clinical utilities of cfDNA by improving mutation detection performance in medium-depth sequencing data, therefore making Whole-Exome Sequencing a viable option. As an example, we demonstrate that the tumor mutation profile from cfDNA WES data can provide an effective biomarker to predict immunotherapy outcomes.

GAB2 inhibits chondrocyte apoptosis through PI3K-AKT signaling in osteoarthritis.

Cartilage degeneration is considered the main pathologic feature of osteoarthritis (OA). Cumulative evidence indicates that chondrocyte apoptosis is associated with cartilage degradation. However, the underlying molecular mechanism of chondrocyte apoptosis remains unclear. Growth factor receptor-bound protein 2 (GAB2), an adaptor protein, belongs to the Gab family and is involved in various biologic processes. Here, we explored the role of GAB2 in the pathogenesis of osteoarthritis (OA). GAB2 expression was markedly increased in OA articular cartilage. GAB2 expression was also increased in an in vitro model of TNFα-induced apoptosis. GAB2 depletion by siRNA promoted expression of the apoptosis markers, PARP and caspase-3, and increased the number of apoptotic cells, indicating that GAB2 might have an anti-apoptotic effect in chondrocytes. Moreover, GAB2 knockdown inhibited AKT phosphorylation, increased BAX expression, and decreased BCL2 expression, which indicated that GAB2 regulates chondrocyte apoptosis through PI3K-AKT signaling. Taken together, our study indicates that GAB2 plays a vital role in chondrocyte apoptosis and provides a new therapeutic target for OA.

Electrospun cellulose nanocrystals/poly(methyl methacrylate) composite nanofibers: Morphology, thermal and mechanical properties.

An electrospinning process was utilized to fabricate composite nanofibers of poly(methyl methacrylate) (PMMA) reinforced with cellulose nanocrystals (CNCs). The effect of environmental relative humidity on the microstructure of CNC/PMMA nanofibers was investigated. Results showed that fiber surfaces of CNC/PMMA appeared smooth. Fibers had gradually decreasing diameters and lower diameter variations as CNC loading increased. The thermal property of CNC/PMMA nanofibers was also enhanced due to hydrogen bonding between PMMA molecular chains and CNC nanoparticles. Compared to pure PMMA fibers, the storage modulus and tensile strength of composite nanofibers were pronouncedly improved. By increasing relative humidity of the electrospinning environment, these nanofibers showed prominent nanoporous surfaces while the surface roughness and porosity of CNC/PMMA nanofibers increased. Furthermore, CNCs were critical to accelerating the evolution of pores and increasing surface roughness. Our findings can provide useful guidelines for the fabrication of nanofibers with desired properties and pore structure by electrospinning.

Migration of a double J stent into the inferior vena cava: A case report.

INTRODUCTION: Intravascular migration of a double J stent into the inferior vena cava is an uncommon complication. The management of such complication is less reported in the literature. This study aimed to reveal the diagnosis and treatment process of migration of a double J stent into the inferior vena cava. PATIENT CONCERNS: A 53-year-old male patients was transferred to our hospital because of migration of a double J stent into the inferior vena cava after left-side pyelolithotomy. DIAGNOSIS: In accordance with manifestations on computed tomography urography, the patient was diagnosed with migration of a double J stent into the inferior vena cava. INTERVENTIONS: Percutaneous nephroscope under C-arm guidance was performed to remove the migrated stent. After the operation, the patient was treated with continued anticoagulants and antibiotics. OUTCOMES: The migrated stent was removed successfully without any complications, and a new double J stent was placed and its location was confirmed under C-arm. The patient was discharged in good condition and the follow-up was uneventful. CONCLUSION: Intravascular migration of a double J stent into the inferior vena cava is an uncommon complication. Radiologic imaging after placement of ureteral stent is critical for prevention of this complication. Percutaneous nephroscope under C-arm guidance is a safe and effective approach to remove the migrated DJS in the IVC.