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1.
Nucleic Acids Res ; 52(D1): D273-D284, 2024 Jan 05.
Artículo en Inglés | MEDLINE | ID: mdl-37956310

RESUMEN

Although over 170 chemical modifications have been identified, their prevalence, mechanism and function remain largely unknown. To enable integrated analysis of diverse RNA modification profiles, we have developed RMBase v3.0 (http://bioinformaticsscience.cn/rmbase/), a comprehensive platform consisting of eight modules. These modules facilitate the exploration of transcriptome-wide landscape, biogenesis, interactome and functions of RNA modifications. By mining thousands of epitranscriptome datasets with novel pipelines, the 'RNA Modifications' module reveals the map of 73 RNA modifications of 62 species. the 'Genes' module allows to retrieve RNA modification profiles and clusters by gene and transcript. The 'Mechanisms' module explores 23 382 enzyme-catalyzed or snoRNA-guided modified sites to elucidate their biogenesis mechanisms. The 'Co-localization' module systematically formulates potential correlations between 14 histone modifications and 6 RNA modifications in various cell-lines. The 'RMP' module investigates the differential expression profiles of 146 RNA-modifying proteins (RMPs) in 18 types of cancers. The 'Interactome' integrates the interactional relationships between 73 RNA modifications with RBP binding events, miRNA targets and SNPs. The 'Motif' illuminates the enriched motifs for 11 types of RNA modifications identified from epitranscriptome datasets. The 'Tools' introduces a novel web-based 'modGeneTool' for annotating modifications. Overall, RMBase v3.0 provides various resources and tools for studying RNA modifications.


Asunto(s)
MicroARNs , Conformación de Ácido Nucleico , MicroARNs/metabolismo , Procesamiento Postranscripcional del ARN , Análisis de Secuencia de ARN , Transcriptoma/genética , Bases de Datos Genéticas
2.
Nucleic Acids Res ; 51(D1): D46-D56, 2023 01 06.
Artículo en Inglés | MEDLINE | ID: mdl-36399495

RESUMEN

Non-coding RNAs (ncRNAs) are emerging as key regulators of various biological processes. Although thousands of ncRNAs have been discovered, the transcriptional mechanisms and networks of the majority of ncRNAs have not been fully investigated. In this study, we updated ChIPBase to version 3.0 (https://rnasysu.com/chipbase3/) to provide the most comprehensive transcriptional regulation atlas of ncRNAs and protein-coding genes (PCGs). ChIPBase has identified ∼151 187 000 regulatory relationships between ∼171 600 genes and ∼3000 regulators by analyzing ∼55 000 ChIP-seq datasets, which represent a 30-fold expansion. Moreover, we de novo identified ∼29 000 motif matrices of transcription factors. In addition, we constructed a novel 'Enhancer' module to predict ∼1 837 200 regulation regions functioning as poised, active or super enhancers under ∼1300 conditions. Importantly, we constructed exhaustive coexpression maps between regulators and their target genes by integrating expression profiles of ∼65 000 normal and ∼15 000 tumor samples. We built a 'Disease' module to obtain an atlas of the disease-associated variations in the regulation regions of genes. We also constructed an 'EpiInter' module to explore potential interactions between epitranscriptome and epigenome. Finally, we designed 'Network' module to provide extensive and gene-centred regulatory networks. ChIPBase will serve as a useful resource to facilitate integrative explorations and expand our understanding of transcriptional regulation.


Asunto(s)
Regulación de la Expresión Génica , ARN no Traducido , ARN no Traducido/genética , ARN no Traducido/metabolismo , Factores de Transcripción/metabolismo , Redes Reguladoras de Genes
3.
Genomics ; 116(1): 110779, 2024 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-38168627

RESUMEN

Meat quality is a critical aspect of pig breeding. In addition to genetics, meat quality is also influenced by nutritional and environmental factors. In this study, three pig breeds, Shengxianhua, Jiaxing, and Qinglian Black (SXH, JXB and QLB), were used as experimental animals. Transcriptional analysis was performed on the longissimus thoracis (LT) muscle to investigate variations in intramuscular fat (IMF), inosine monophosphate (IMP), amino acids, and muscle fiber morphology across different breeds. Ingenuity canonical pathway analysis (IPA) identified biological processes and key driver genes related to metabolism and muscle development. Additionally, weighted gene co-expression network analysis (WGCNA) revealed gene modules associated with IMP. KEGG and GO analyses identified specific biological processes and signaling pathways related to IMP, including the Oxidative Phosphorylation pathway and rRNA Metabolic Processes. These findings provide novel insights into the molecular regulatory mechanisms underlying meat quality variations among pig breeds.


Asunto(s)
Perfilación de la Expresión Génica , Músculo Esquelético , Porcinos/genética , Animales , Músculo Esquelético/metabolismo , Carne/análisis , Redes Reguladoras de Genes , Aminoácidos
4.
FASEB J ; 37(10): e23177, 2023 10.
Artículo en Inglés | MEDLINE | ID: mdl-37688589

RESUMEN

Synovial inflammation and fibrosis are important pathological changes associated with osteoarthritis (OA). Herein, we investigated if nintedanib, a drug specific for pulmonary fibrosis, plays a positive role in osteoarthritic synovial inflammation and fibrosis. We assessed the effect of nintedanib on osteoarthritic synovial inflammation and fibrosis in a mouse model of OA created by destabilization of the medial meniscus and a macrophage M1 polarization model created by stimulating RAW264.7 cells with lipopolysaccharide. Histological staining showed that daily gavage administration of nintedanib significantly alleviated articular cartilage degeneration, reduced the OARSI score, upregulated matrix metalloproteinase-13 and downregulated collagen II expression, and significantly reduced the synovial score and synovial fibrosis in a mouse OA model. In addition, immunofluorescence staining showed that nintedanib significantly decreased the number of M1 macrophages in the synovium of a mouse model of OA. In vitro results showed that nintedanib downregulated the phosphorylation levels of ERK, JNK, p38, PI3K, and AKT while inhibiting the expression of macrophage M1 polarization marker proteins (CD86, CD80, and iNOS). In conclusion, this study suggests that nintedanib is a potential candidate for OA treatment. The mechanisms of action of nintedanib include the inhibition of M1 polarization in OA synovial macrophages via the MAPK/PI3K-AKT pathway, inhibition of synovial inflammation and fibrosis, and reduction of articular cartilage degeneration.


Asunto(s)
Osteoartritis , Fibrosis Pulmonar , Animales , Ratones , Fosfatidilinositol 3-Quinasas , Proteínas Proto-Oncogénicas c-akt , Osteoartritis/tratamiento farmacológico , Inflamación/tratamiento farmacológico , Macrófagos , Modelos Animales de Enfermedad
5.
Inorg Chem ; 63(1): 775-783, 2024 Jan 08.
Artículo en Inglés | MEDLINE | ID: mdl-38134353

RESUMEN

Polysulfide-based multilevel memorizers are promising as novel memorizers, in which the occurrence of Sn2- relaxation is key for their multilevel memory. However, the effects of crystal packing and the side group of organic ligands on Sn2- relaxation are still ambiguous. In this work, ionic [Zn(S6)2·Zn2(Bipy)2SO4 (1), Zn(S6)2·Zn(Pmbipy)3 (2)] and neutral [ZnS6(Ombipy) (3), ZnS6(Phen)2 (4)] Zn/polysulfide/organic complexes with different packing modes and structures of organic ligands have been synthesized and were fabricated as memory devices. In both ionic and neutral Zn complexes, the S62- relaxation will be blocked by steric hindrances due to the packing of counter-cations and hydrogen-bond restrictions. Consequently, only the binary memory performances can be seen in FTO/1/Ag, FTO/2/Ag, and FTO/4/Ag, which originate from the more condensed packing of conjugated ligands upon electrical stimulus. Interestingly, FTO/3/Ag illustrates the unique thermally triggered reversible binary-ternary switchable memory performance. In detail, after introducing a methyl group on the 6'-position of bipyridine in ZnS6(Ombipy) (3), the ring-to-chain relaxation of S62- anions at room temperature will be inhibited, but it can happen at a higher temperature of 120 °C, which has been verified by elongated S-S lengths and the strengthened C-H···S hydrogen bond upon heating. The rules drawn in this work will provide a useful guide for the design of stimulus-responsive memorizers that can be applied in special industries such as automobile, oil, and gas industries.

6.
Clin Gastroenterol Hepatol ; 21(2): 328-336.e2, 2023 02.
Artículo en Inglés | MEDLINE | ID: mdl-35390509

RESUMEN

BACKGROUND & AIMS: Linked color imaging (LCI) is a novel technology that improves the color differences between colorectal lesions and the surrounding mucosa. The present study aims to compare the detection of colorectal sessile serrated lesions (SSL) using LCI with white light imaging (WLI). METHOD: A large-scale, multicenter, parallel prospective randomized controlled trial was conducted in 4 hospitals in China. The participants were randomly assigned to the LCI group and WLI group. The primary endpoint was the SSL detection rate (SDR). RESULTS: A total of 884 patients were involved in the intention-to-treat analysis, with 441 patients in the LCI group and 443 patients in the WLI group. The total polyp detection rate, adenoma detection rate, and SDR were 51.8%, 35.7%, and 8.6%, respectively. The SDR was significantly higher in the LCI group than in the WLI group (11.3% vs 5.9%, P = .004). Furthermore, LCI significantly increased the number of polyps and adenomas detected per patient, when compared with WLI (P < .05). In addition, there was higher detection rate of diminutive and flat lesions in the LCI group (P < .05). Multivariate analysis revealed that LCI is an independent factor associated with SDR (hazard ratio, 1.990; 95% confidence interval, 1.203-3.293; P = .007), along with withdrawal time (hazard ratio, 1.157; 95% confidence interval, 1.060-1.263; P = .001) and operator experience (hazard ratio, 1.850; 95% confidence interval, 1.045-3.273; P = .035). CONCLUSIONS: LCI is significantly superior to WLI for SSL detection, and may improve polyp and adenoma detection. LCI can be recommended as an appropriate method for routine inspection during colonoscopy (http://www.chictr.org.cn number, ChiCTR2000035705).


Asunto(s)
Adenoma , Pólipos del Colon , Neoplasias Colorrectales , Humanos , Pólipos del Colon/diagnóstico por imagen , Pólipos del Colon/patología , Neoplasias Colorrectales/diagnóstico por imagen , Neoplasias Colorrectales/patología , Estudios Prospectivos , Colonoscopía/métodos , Adenoma/diagnóstico por imagen , Adenoma/patología
7.
Brief Bioinform ; 22(4)2021 07 20.
Artículo en Inglés | MEDLINE | ID: mdl-33313674

RESUMEN

Although long noncoding RNAs (lncRNAs) have significant tissue specificity, their expression and variability in single cells remain unclear. Here, we developed ColorCells (http://rna.sysu.edu.cn/colorcells/), a resource for comparative analysis of lncRNAs expression, classification and functions in single-cell RNA-Seq data. ColorCells was applied to 167 913 publicly available scRNA-Seq datasets from six species, and identified a batch of cell-specific lncRNAs. These lncRNAs show surprising levels of expression variability between different cell clusters, and has the comparable cell classification ability as known marker genes. Cell-specific lncRNAs have been identified and further validated by in vitro experiments. We found that lncRNAs are typically co-expressed with the mRNAs in the same cell cluster, which can be used to uncover lncRNAs' functions. Our study emphasizes the need to uncover lncRNAs in all cell types and shows the power of lncRNAs as novel marker genes at single cell resolution.


Asunto(s)
Bases de Datos de Ácidos Nucleicos , Regulación de la Expresión Génica , ARN Largo no Codificante , Análisis de la Célula Individual , Programas Informáticos , Animales , Humanos , Anotación de Secuencia Molecular , ARN Largo no Codificante/biosíntesis , ARN Largo no Codificante/genética
8.
Opt Lett ; 48(7): 1694-1697, 2023 Apr 01.
Artículo en Inglés | MEDLINE | ID: mdl-37221743

RESUMEN

We report ultralow-noise transmission over a 102-km single-mode fiber using a purely nonlinear amplification scheme consisting of a second-order distributed Raman amplifier (DRA) and a phase-sensitive amplifier (PSA) based on periodically poled LiNbO3 waveguides. The hybrid DRA/PSA features a broadband gain over the C and L bands and an ultralow-noise advantage, with a less than -6.3 dB effective noise figure in the DRA stage and a 1.6 dB optical signal-to-noise ratio (OSNR) improvement in the PSA stage. Compared with the unamplified link, the OSNR is improved by 10.2 dB for a 20-Gbaud 16QAM signal in the C band, resulting in error-free detection (a bit-error rate of less than 3.8 × 10-3) for the signal with a low link input power of -25 dBm. Mitigation of nonlinear distortion is also achieved by the proposed nonlinear amplified system due to the subsequent PSA.

9.
Compr Rev Food Sci Food Saf ; 22(2): 1030-1057, 2023 03.
Artículo en Inglés | MEDLINE | ID: mdl-36579838

RESUMEN

The problems with plastic materials and the good film-forming properties of polysaccharides motivated research in the development of polysaccharide-based films. In the last 5 years, there has been an explosion of publications on using green solvents, including ionic liquids (ILs), and deep eutectic solvents (DESs) as candidates to substitute the conventional solvents/plasticizers for preparations of desired polysaccharide-based films. This review summarizes related properties and recovery of ILs and DESs, a series of green preparation strategies (including pretreatment solvents/reaction media, ILs/DESs as components, extraction solvents of bioactive compounds added into films), and inherent properties of polysaccharide-based films with/without ILs and DESs. Major reported advantages of these new solvents are high dissolving capacity of certain ILs/DESs for polysaccharides (i.e., up to 30 wt% for cellulose) and better plasticizing ability than traditional plasticizers. In addition, they frequently display intrinsic antioxidant and antibacterial activities that facilitate ILs/DESs applications in the processing of polysaccharide-based films (especially active food packaging films). ILs/DESs in the film could also be further recycled by water or ethanol/methanol treatment followed by drying/evaporation. One particularly promising approach is to use bioactive cholinium-based ILs and DESs with good safety and plasticizing ability to improve the functional properties of prepared films. Whole extracts by ILs/DESs from various byproducts can also be directly used in films without separation/polishing of compounds from the extracting agents. Scaling-up, including costs and environmental footprint, as well as the safety and applications in real foods of polysaccharide-based film with ILs/DESs (extracts) deserves more studies.


Asunto(s)
Líquidos Iónicos , Solventes , Disolventes Eutécticos Profundos , Plastificantes , Polisacáridos
10.
Biomed Eng Online ; 21(1): 34, 2022 Jun 10.
Artículo en Inglés | MEDLINE | ID: mdl-35689282

RESUMEN

BACKGROUND: There are a variety of internal fixation methods for unstable femoral neck fractures (FNFs), but the best method is still unclear. Femoral neck system (FNS) is a dynamic angular stabilization system with cross screws, and is a new internal fixation implant designed for minimally invasive fixation of FNFs. In this study, we conducted a biomechanical comparison of FNS, InterTan nail and three cannulated screws for the treatment of Pauwels III FNFs and investigate the biomechanical properties of FNS. METHODS: A total of 18 left artificial femurs were selected and randomly divide into Group A (fixation with FNS), Group B (fixation with InterTan nail) and Group C (fixation with three cannulated screws), with 6 specimens in each group. After creating Pauwels type III FNF models, the specimens in each were tested with non-destructive quasi-static tests, including torsion, A-P bending and axial compression tests. The average slope of the linear load-deformation curve obtained from quasi-static tests defines the initial torsional stiffness, A-P bending stiffness, and axial compression stiffness. After cyclic loading test was applied, the overall deformation of models and local deformation of implant holes in each group were assessed. The overall deformation was estimated as the displacement recorded by the software of the mechanical testing apparatus. Local deformation was defined as interfragmental displacement. Data were analyzed by one-way analysis of variance (ANOVA) followed by Bonferroni post hoc test using the SPSS software (version 24.0, IBM, New York, NY, USA). Correlation analysis was performed using Pearson's correlation analysis. RESULTS: Group B exhibited significantly higher axial stiffness and A-P bending stiffness than the other two groups (P < 0.01), while Group A had significantly higher axial stiffness and A-P bending stiffness than Group C (P < 0.01). Groups A and B exhibited significantly higher torsional stiffness than Group C (P < 0.01), no statistical significance was observed between Groups A and B (P > 0.05). Group B exhibited significantly lower overall and local deformations than the other two groups (P < 0.01), while Group A had significantly lower overall and local deformations than Group C (P < 0.01). Correlation analysis revealed positive correlation between axial stiffness and A-P bending stiffness (r = 0.925, P < 0.01), torsional stiffness (r = 0.727, P < 0.01), between torsional stiffness and A-P bending stiffness; negative correlation between overall, local deformations and axial stiffness (r = - 0.889, - 0.901, respectively, both P < 0.01), and positive correlation between the two deformations (r = - 0.978, P < 0.01). CONCLUSION: For fixation of unstable FNFs, InterTan nail showed the highest axial stiffness and A-P bending stiffness, followed by FNS, and then three cannulated screws. Torsional stiffness of FNS was comparable to that of the InterTan nail. FNS, as a novel minimally invasive implant, can create good mechanical environment for the healing of unstable FNFs. Clinical studies are needed to confirm the potential advantages of FNS observed in this biomechanical study.


Asunto(s)
Fracturas del Cuello Femoral , Fenómenos Biomecánicos , Tornillos Óseos , Fracturas del Cuello Femoral/cirugía , Cuello Femoral , Fijación Interna de Fracturas , Humanos
11.
Cytokine ; 143: 155546, 2021 07.
Artículo en Inglés | MEDLINE | ID: mdl-33895075

RESUMEN

OBJECTIVE: Osteoarthritis (OA) is a joint disease characterized by articular cartilage loss and afflicts many people worldwide. However, diagnostic methods and treatment options remain limited and are often characterized by low sensitivity and low efficacy. The focus of the present study was to identify proteomic biomarkers in synovial fluid to improve diagnosis and therapy of OA patients. METHODS: Antibody array technology was utilized for protein expression profiling of synovial fluid from 24 OA patients and 24 healthy persons. RESULTS: Compared with healthy persons, twenty proteins showed lower expression levels in OA patients, while thirty proteins had higher levels. Among these differential proteins, GITRL, CEACAM-1, FSH, EG-VEGF, FGF-4, PIGF, Cystatin EM and NT-4 were found for the first time to be differentially expressed in OA. Bioinformatics analysis showed that most of these differential proteins were involved leukocytes events, and some differentially expressed proteins including IL-18, CXCL1, CTLA4, MIP-3b, CD40, MMP-1, THBS1, CCL11, PAI-1, BAFF, aggrecan, angiogenin and follistatin were located in central positions of the protein-protein interaction (PPI) network. CONCLUSION: We speculate that leukocyte proliferation and migration to the joint may be an important pathogenesis of OA, which needs a further validation. The central proteins of the PPI network may play a more pivotal role in OA. The newly identified differentially expressed proteins may be novel biomarkers for OA diagnosis and targets for OA therapy.


Asunto(s)
Citocinas/metabolismo , Osteoartritis/metabolismo , Líquido Sinovial/metabolismo , Biomarcadores , Estudios de Casos y Controles , Análisis por Conglomerados , Biología Computacional , Femenino , Humanos , Masculino , Persona de Mediana Edad , Análisis de Componente Principal , Mapas de Interacción de Proteínas
12.
Angew Chem Int Ed Engl ; 60(31): 16911-16916, 2021 Jul 26.
Artículo en Inglés | MEDLINE | ID: mdl-34060186

RESUMEN

The development of new-type memristors with special performance is of great interest. Herein, an inorganic-organic hybrid crystalline polyoxometalate (POM) with usual dynamic structures is reported and used as active material for fabricating memristor with unique temperature-regulated resistive switching behaviors. The hybrid POM not only exhibits tunable thermochromic properties, but also thermal-induced reversible aggregation and disaggregation reactions, leading to reversible structural transformations in SCSC fashion. Further, the memory device using the hybrid POM as active layer exhibits uncommon performance, which can keep resistive switching silent in the low temperature range of 30-150 °C, but show nonvolatile memory behavior in the high temperature range of 150-270 °C. Particularly, the silent and working states at three special temperatures (30, 150 and 270 °C) can be monitored by chromism. The correlation between structure and resistive switching property of the material has been discussed. The work demonstrates that crystalline inorganic-organic hybrid POMs are promising materials for making memristors with superior performance.

13.
Small ; 16(13): e1906567, 2020 04.
Artículo en Inglés | MEDLINE | ID: mdl-32049432

RESUMEN

Sensors are of increasing interest since they can be applied to daily life in different areas from various industrial sectors. As a natural nanomaterial, nanocellulose plays a vital role in the development of novel sensors, particularly in the context of constructing multidimensional architectures. This review summarizes the utilization of nanocellulose including cellulose nanofibers, cellulose nanocrystals, and bacterial cellulose for sensor design, mainly focusing on the influence of nanocellulose on the sensing performance of these sensors. Special attention is paid to nanocellulose in different forms (1D, 2D, and 3D) to highlight the impact of nanocellulose constructed structures. The aim is to provide a critical review on the most recent progress (especially after 2017) related to nanocellulose-containing sensors, since there are significantly increasing research activities in this area. Moreover, the outlook for the development of nanocellulose-containing sensors is also provided at the end of this work.


Asunto(s)
Técnicas Biosensibles , Celulosa , Técnicas de Química Analítica , Nanofibras , Celulosa/química , Técnicas de Química Analítica/instrumentación , Nanofibras/química , Nanoestructuras/química
14.
Opt Lett ; 45(11): 3075-3078, 2020 Jun 01.
Artículo en Inglés | MEDLINE | ID: mdl-32479463

RESUMEN

We investigate the noise evolution of a hybrid fiber phase-sensitive amplifier (PSA) with an erbium-doped fiber amplifier (EDFA) as a function of the phase-sensitive gain. The noise performance of the hybrid amplifier with a large overall gain of 45.6 dB is experimentally evaluated in optical and electrical domains. The experimental results are in good agreement with theory, showing that significant improvement of the overall noise figure (NF) of the hybrid amplifier occurs in a low PSA gain region. A combined NF below 3 dB has been obtained in the hybrid amplifier with a PSA gain of 9 dB, which is 1.1 dB better than a conventional EDFA with an equivalent overall gain.

15.
Cryobiology ; 92: 151-160, 2020 02 01.
Artículo en Inglés | MEDLINE | ID: mdl-31917159

RESUMEN

Vitrification is a cryopreservation technique for the long-term storage of viable tissue, but the success of this technique relies on multiple factors. In 2012, our group published a working vitrification protocol for intact human articular cartilage and reported promising chondrocyte recovery after using a four-step multi-cryoprotectant (CPA) loading method that required 570 min. However, this protocol requires further optimization for clinical practice. Herein, we compared three multi-step CPA loading protocols to investigate their impact on chondrocyte recovery after vitrification of porcine articular cartilage on a bone base, including our previous four-step protocol (original: 570 min), and two shorter three-step protocols (optimized: 420 min, and minimally vitrifiable: 310 min). Four different CPAs were used including glycerol, dimethyl sulfoxide, ethylene glycol and propylene glycol. As vitrification containers, two conical tubes (50 ml and 15 ml) were evaluated for their heat transfer impact on chondrocyte recovery after vitrification. Osteochondral dowels were cored into two diameters of 10.0 mm and 6.9 mm with an approximately 10-mm thick bone base, and then allocated into the twelve experimental groups based on CPA loading protocol, osteochondral dowel size, and vitrification container size. After vitrification at -196 °C and tissue warming and CPA removal, samples in all groups were assessed for both chondrocyte viability and metabolic activity. The optimized protocol proposed based on mathematical modelling resulted in similar chondrocyte recovery to our original protocol and it was 150 min shorter. Furthermore, this study illustrated the role of CPA permeation (dowel size) and heat transfer (container size) on vitrification protocol outcome.


Asunto(s)
Cartílago Articular/citología , Condrocitos/metabolismo , Criopreservación/métodos , Crioprotectores/farmacología , Vitrificación , Animales , Dimetilsulfóxido/metabolismo , Glicol de Etileno/metabolismo , Femenino , Glicerol/metabolismo , Humanos , Modelos Teóricos , Propilenglicol/metabolismo , Porcinos
16.
Cryobiology ; 92: 180-188, 2020 02 01.
Artículo en Inglés | MEDLINE | ID: mdl-31952947

RESUMEN

Osteochondral allograft transplantation can treat full thickness cartilage and bone lesions in the knee and other joints, but the lack of widespread articular cartilage banking limits the quantity of cartilage available for size and contour matching. To address the limited availability of cartilage, vitrification can be used to store harvested joint tissues indefinitely. Our group's reported vitrification protocol [Biomaterials 33 (2012) 6061-6068] takes 9.5 h to load cryoprotectants into intact articular cartilage on bone and achieves high cell viability, but further optimization is needed to shorten this protocol for clinical use. Herein, we use engineering models to calculate the spatial and temporal distributions of cryoprotectant concentration, solution vitrifiability, and freezing point for each step of the 9.5-h protocol. We then incorporate the following major design choices for developing a new shorter protocol: (i) all cryoprotectant loading solution concentrations are reduced, (ii) glycerol is removed as a cryoprotectant, and (iii) an equilibration step is introduced to flatten the final cryoprotectant concentration profiles. We also use a new criterion-the spatially and temporally resolved prediction of solution vitrifiability-to assess whether a protocol will be successful instead of requiring that each cryoprotectant individually reaches a certain concentration. A total cryoprotectant loading time of 7 h is targeted, and our new 7-h protocol is predicted to achieve a level of vitrifiability comparable to the proven 9.5-h protocol throughout the cartilage thickness.


Asunto(s)
Cartílago Articular/citología , Criopreservación/métodos , Crioprotectores/metabolismo , Glicerol/metabolismo , Articulación de la Rodilla/citología , Cartílago Articular/trasplante , Supervivencia Celular/efectos de los fármacos , Biología Computacional/métodos , Crioprotectores/farmacología , Glicerol/farmacología , Humanos , Vitrificación
17.
Nucleic Acids Res ; 46(D1): D85-D91, 2018 01 04.
Artículo en Inglés | MEDLINE | ID: mdl-29059382

RESUMEN

Although thousands of pseudogenes have been annotated in the human genome, their transcriptional regulation, expression profiles and functional mechanisms are largely unknown. In this study, we developed dreamBase (http://rna.sysu.edu.cn/dreamBase) to facilitate the investigation of DNA modification, RNA regulation and protein binding of potential expressed pseudogenes from multidimensional high-throughput sequencing data. Based on ∼5500 ChIP-seq and DNase-seq datasets, we identified genome-wide binding profiles of various transcription-associated factors around pseudogene loci. By integrating ∼18 000 RNA-seq data, we analysed the expression profiles of pseudogenes and explored their co-expression patterns with their parent genes in 32 cancers and 31 normal tissues. By combining microRNA binding sites, we demonstrated complex post-transcriptional regulation networks involving 275 microRNAs and 1201 pseudogenes. We generated ceRNA networks to illustrate the crosstalk between pseudogenes and their parent genes through competitive binding of microRNAs. In addition, we studied transcriptome-wide interactions between RNA binding proteins (RBPs) and pseudogenes based on 458 CLIP-seq datasets. In conjunction with epitranscriptome sequencing data, we also mapped 1039 RNA modification sites onto 635 pseudogenes. This database will provide insights into the transcriptional regulation, expression, functions and mechanisms of pseudogenes as well as their roles in biological processes and diseases.


Asunto(s)
Bases de Datos Genéticas , Seudogenes , ADN/genética , ADN/metabolismo , Expresión Génica , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , MicroARNs/genética , MicroARNs/metabolismo , Neoplasias/genética , Neoplasias/metabolismo , Unión Proteica/genética , ARN/genética , ARN/metabolismo , Procesamiento Postranscripcional del ARN , Proteínas de Unión al ARN/metabolismo , Análisis de Secuencia de ARN
18.
Opt Lett ; 44(7): 1848-1851, 2019 Apr 01.
Artículo en Inglés | MEDLINE | ID: mdl-30933163

RESUMEN

In this Letter, we report a wideband and low-error photonic instantaneous frequency measurement (IFM) system for microwave signals, which uses a nonlinear interferometer constructed with cascaded degenerate four-wave mixing (FWM) and in-between dispersion to introduce a tunable time delay. The microwave frequency is interpreted through interference of two idlers generated in cascaded FWM stages. This new approach allows parallel implementation of multiple IFMs without an overlap of idler wavelengths used for different IFMs, which is crucial to realize a wide frequency coverage and high accuracy without compromising the system practicality. A large, 40 GHz measurement bandwidth and a low measurement error of approximately 0.4% have been successfully achieved.

19.
Inorg Chem ; 58(20): 13862-13880, 2019 Oct 21.
Artículo en Inglés | MEDLINE | ID: mdl-31560205

RESUMEN

The encapsulation of guests into metal-organic frameworks (MOF) is an efficient strategy to generate novel multifunctional materials with enhanced properties. Herein, four halometallate@MOF composites with formulas of {(Pb2I4Br3)[(Pr(bpdo)4(H2O)2]·(H2O)}n (1), {[Pb3I10(H2O)2][Y2(bpdo)5(OH)2]·4(H2O)}n (2), {(Bi2I9)[(Pr(bpdo)3(H2O)]}n (3), {(Bi4I18)[(La(bpdo)4(H2O)2]2}n (4) (bpdo = 4,4'-bipyridine N,N'-dioxide) were prepared. In these composites, lanthanide-viologen MOF act as matrices, whose cavities were penetrated by halometallates. Consequently, the insertion of electron-rich halometallates into electron-deficient lanthanide-viologen matrices leads to the presence of strong room temperature charge transfer (CT) interactions. Importantly, these composites exhibit enhanced photo/thermal stabilities, controllable white emissions, reversible thermochromisms, and good photocurrent response performances. Specially, the memory devices based on these composites illustrate reversible electrical bistability behaviors, which can be assigned to ohmic and space-charge-limited conduction (SCLC) mechanisms. This kind of composite can be utilized as a multifunctional platform with enhanced stability.

20.
Nanotechnology ; 30(3): 034004, 2019 Jan 18.
Artículo en Inglés | MEDLINE | ID: mdl-30452391

RESUMEN

Phase transition from the semiconducting hexagonal (2H) phase to the metallic monoclinic (1T') phase in two-dimensional (2D) transition metal dichalcogenides like MoTe2 is not only of great importance in fundamental study but also of technological significance for broad device applications. Here we report a universal, facile, scalable and reversible phase engineering technique (between 2H and 1T' phases) for both monolayer and few-layer MoTe2 based on a soft hydrogen plasma treatment. The 2H â†’ 1T' transition was confirmed by a series of characterizations including Raman spectra and mapping studies, XPS analysis and FET device measurements at varying temperatures. We attribute the phase transition to the warping of Te-Mo bonds and the lateral sliding of the top Te-layer induced by the soft hydrogen ion bombardment according to both the structural and electronic characterizations as well as the horizontal comparison with the cases of Ar or O2 plasma treatment. We have also prepared a 2D heterostructure containing periodical 2H and 1T' MoTe2 and showed that such phase transition can be readily reversed by post annealing. These results thus provide a robust and efficient approach for the phase engineering of monolayer and few-layer MoTe2 and could aid the development of 2D optoelectronic, memory and reconfigurable devices.

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