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1.
Nat Food ; 4(12): 1075-1089, 2023 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-38053005

RESUMO

Knowledge-based nitrogen (N) management provides better synchronization of crop N demand with N supply to enhance crop production while reducing N losses. Yet, how these N management practices contribute to reducing N losses globally is unclear. Here we compiled 5,448 paired observations from 336 publications representing 286 sites to assess the impacts of four common knowledge-based N management practices, including balanced fertilization, organic fertilization, co-application of synthetic and organic fertilizers, and nitrification inhibitors, on global ecosystem N cycling. We found that organic and balanced fertilization rather than N-only fertilization stimulated soil nitrate retention by enhancing microbial biomass, but also stimulated soil N leaching and emissions relative to no fertilizer addition. Nitrification inhibitors, however, stimulated soil ammonium retention and plant N uptake while reducing N leaching and emissions. Therefore, integrative application of knowledge-based N management practices is imperative to stimulate ecosystem N retention and minimize the risk of N loss globally.


Assuntos
Compostos de Amônio , Nitrogênio , Nitrogênio/análise , Ecossistema , Solo , Plantas , Fertilizantes/análise
2.
Materials (Basel) ; 16(16)2023 Aug 17.
Artigo em Inglês | MEDLINE | ID: mdl-37629947

RESUMO

Li-rich manganese-based cathode materials (LRMs) are considered one of the most promising cathode materials for the next generation of lithium-ion batteries (LIBs) because of their high energy density. However, there are problems such as a capacity decay, poor rate performance, and continuous voltage drop, which seriously limit their large-scale commercial applications. In this work, Li1.2Mn0.54Co0.13Ni0.13O2 coated with Li2MoO4 with a unique spinel structure was prepared with the wet chemistry method and the subsequent calcination process. The Li2MoO4 coating layer with a spinel structure could provide a 3D Li+ transport channel, which is beneficial for improving rate performance, while protecting LRMs from electrolyte corrosion, suppressing interface side reactions, and improving cycling stability. The capacity retention rate of LRMs coated with 3 wt% Li2MoO4 increased from 69.25% to 81.85% after 100 cycles at 1 C, and the voltage attenuation decreased from 7.06 to 4.98 mV per cycle. The lower Rct also exhibited an improved rate performance. The results indicate that the Li2MoO4 coating effectively improves the cyclic stability and electrochemical performance of LRMs.

3.
Nat Food ; 4(1): 109-121, 2023 01.
Artigo em Inglês | MEDLINE | ID: mdl-37118576

RESUMO

The internal soil nitrogen (N) cycle supplies N to plants and microorganisms but may induce N pollution in the environment. Understanding the variability of gross N cycling rates resulting from the global spatial heterogeneity of climatic and edaphic variables is essential for estimating the potential risk of N loss. Here we compiled 4,032 observations from 398 published 15N pool dilution and tracing studies to analyse the interactions between soil internal potential N cycling and environmental effects. We observed that the global potential N cycle changes from a conservative cycle in forests to a less conservative one in grasslands and a leaky one in croplands. Structural equation modelling revealed that soil properties (soil pH, total N and carbon-to-N ratio) were more important than the climate factors in shaping the internal potential N cycle, but different patterns in the potential N cycle of terrestrial ecosystems across climatic zones were also determined. The high spatial variations in the global soil potential N cycle suggest that shifting cropland systems towards agroforestry systems can be a solution to improve N conservation.


Assuntos
Ecossistema , Nitratos , Ciclo do Nitrogênio , Solo/química , Compostos Orgânicos , Produtos Agrícolas
4.
Nat Commun ; 14(1): 223, 2023 01 14.
Artigo em Inglês | MEDLINE | ID: mdl-36641532

RESUMO

Consistent annotation transfer from reference dataset to query dataset is fundamental to the development and reproducibility of single-cell research. Compared with traditional annotation methods, deep learning based methods are faster and more automated. A series of useful single cell analysis tools based on autoencoder architecture have been developed but these struggle to strike a balance between depth and interpretability. Here, we present TOSICA, a multi-head self-attention deep learning model based on Transformer that enables interpretable cell type annotation using biologically understandable entities, such as pathways or regulons. We show that TOSICA achieves fast and accurate one-stop annotation and batch-insensitive integration while providing biologically interpretable insights for understanding cellular behavior during development and disease progressions. We demonstrate TOSICA's advantages by applying it to scRNA-seq data of tumor-infiltrating immune cells, and CD14+ monocytes in COVID-19 to reveal rare cell types, heterogeneity and dynamic trajectories associated with disease progression and severity.


Assuntos
COVID-19 , Humanos , Reprodutibilidade dos Testes , Análise de Célula Única/métodos , Progressão da Doença , Sequenciamento do Exoma , Análise de Sequência de RNA/métodos
5.
Glob Chang Biol ; 28(14): 4472-4488, 2022 07.
Artigo em Inglês | MEDLINE | ID: mdl-35445472

RESUMO

Microbial nitrogen (N) immobilization, which typically results in soil N retention but based on the balance of gross N immobilization over gross N production, affects the fate of the anthropogenic reactive N. However, global patterns and drivers of soil gross immobilization of ammonium (INH4 ) and nitrate (INO3 ) are still only tentatively known. Here, we provide a comprehensive analysis considering gross N production rates, soil properties, and climate and their interactions for a deeper understanding of the patterns and drivers of INH4 and INO3 . By compiling and analyzing 1966 observations from 274 15 N-labelled studies, we found a global average of INH4 and INO3 of 7.41 ± 0.72 and 2.03 ± 0.30 mg N kg-1  day-1 with a ratio of INO3 to INH4 (INO3 :INH4 ) of 0.79 ± 0.11. Soil INH4 and INO3 increased with increasing soil gross N mineralization (GNM) and nitrification (GN), microbial biomass, organic carbon, and total N and decreasing soil bulk density. Our analysis revealed that GNM and GN were the main stimulators for INH4 and INO3 , respectively. The structural equation modeling showed that higher soil microbial biomass, total N, pH, and precipitation stimulate INH4 and INO3 through enhancing GNM and GN. However, higher temperature and soil bulk density suppress INH4 and INO3 by reducing microbial biomass and total N. Soil INH4 varied with terrestrial ecosystems, being greater in grasslands and forests, which have higher rates of GNM, than in croplands. The highest INO3 :INH4 was observed in croplands, which had higher rates of GN. The global average of GN to INH4 was 2.86 ± 0.31, manifesting a high potential risk of N loss. We highlight that anthropogenic activities that influence soil properties and gross N production rates likely interact with future climate changes and land uses to affect soil N immobilization and, eventually, the fate of the anthropogenic reactive N.


Assuntos
Compostos de Amônio , Solo , Ecossistema , Nitratos , Nitrogênio/análise , Óxidos de Nitrogênio , Solo/química , Microbiologia do Solo
6.
Environ Sci Technol ; 56(6): 3791-3800, 2022 03 15.
Artigo em Inglês | MEDLINE | ID: mdl-35226464

RESUMO

Dissimilatory nitrate reduction to ammonium (DNRA), the nearly forgotten process in the terrestrial nitrogen (N) cycle, can conserve N by converting the mobile nitrate into non-mobile ammonium avoiding nitrate losses via denitrification, leaching, and runoff. However, global patterns and controlling factors of soil DNRA are still only rudimentarily known. By a meta-analysis of 231 observations from 85 published studies across terrestrial ecosystems, we find a global mean DNRA rate of 0.31 ± 0.05 mg N kg-1 day-1, being significantly greater in paddy soils (1.30 ± 0.59) than in forests (0.24 ± 0.03), grasslands (0.52 ± 0.15), and unfertilized croplands (0.18 ± 0.04). Soil DNRA was significantly enhanced at higher altitude and lower latitude. Soil DNRA was positively correlated with precipitation, temperature, pH, soil total carbon, and soil total N. Precipitation was the main stimulator for soil DNRA. Total carbon and pH were also important factors, but their effects were ecosystem-specific as total carbon stimulates DNRA in forest soils, whereas pH stimulates DNRA in unfertilized croplands and paddy soils. Higher temperatures inhibit soil DNRA via decreasing total carbon. Moreover, nitrous oxide (N2O) emissions were negatively related to soil DNRA. Thus, future changes in climate and land-use may interact with management practices that alter soil substrate availability and/or soil pH to enhance soil DNRA with positive effects on N conservation and lower N2O emissions.


Assuntos
Compostos de Amônio , Carbono , Desnitrificação , Ecossistema , Nitratos , Nitrogênio , Óxido Nitroso , Solo
7.
Life (Basel) ; 11(11)2021 Nov 16.
Artigo em Inglês | MEDLINE | ID: mdl-34833119

RESUMO

Objectives In recent years; increasing evidence pointed out the clinical importance of adipose tissue (AT) distribution in various patient populations. In particular, visceral adipose tissue (VAT), when compared to subcutaneous adipose tissue (SAT), was found to play a pivotal role in the development of inflammatory reaction. The aim of the present study was to examine whether body fat distribution has an impact on the development of systemic inflammatory response syndrome (SIRS) in patients with polytrauma. Methods In our retrospective study; we filtered our institution records of the German Trauma Registry (Trauma Register DGU) from November 2018 to April 2021 and included 132 adult polytrauma patients with injury severity score (ISS) >16. Subsequently; we measured the visceral and subcutaneous adipose tissue area based on whole-body CT scan and calculated the ratio of VAT to SAT (VSr). Thereafter, the patient population was evenly divided into three groups; respectively VSr value less than 0.4 for the first group (low ratio), 0.4-0.84 for the second group (intermediate ratio), and greater than 0.84 for the third group (high ratio). Considering the other influencing factors; the groups were further divided into subgroups in the respective analysis according to gender (male/female), BMI (<25 or ≥25), and ISS (<26 or ≥26). Result VSr was an independent factor from body mass index (BMI) (r2 = 0.003; p = 0.553). VSr in male patients was significantly higher (p < 0.001). Patients with low VSr had higher ISS scores (p = 0.028). Polytrauma patients with higher VSr tended to have lower SIRS scores and significant differences of SIRS score were found on multiple days during the whole hospitalization period. In the low VAT/SAT group, male patients, and patients with BMI greater than 25, both exhibited higher SIRS scores during hospital stay (day 16: p = 0.01; day 22: p = 0.048 and p = 0.011; respectively). During hospitalization, patients with higher ISS score (≥26) in the low VSr group was found to have higher SIRS score (day 16; p = 0.007). Over the hospital stay; serum markers of CRP; CK; and leukocyte in patients with low VSr were higher than those in patients in the intermediate and high VSr groups; with significant difference discovered on multiple days (day 16: 0.014; day 22: p = 0.048). Conclusion Lower VSr is associated with increased inflammatory response and worse clinical outcome in patients with polytrauma. Furthermore; VSr is an independent factor providing additional information to BMI.

8.
Environ Pollut ; 288: 117721, 2021 Nov 01.
Artigo em Inglês | MEDLINE | ID: mdl-34247001

RESUMO

Both soil microbial nitrate (NO3--N) immobilization and denitrification are carbon (C)-limited; however, to what extent organic C addition may increase NO3--N immobilization while stimulate denitrification nitrogen (N) loss remains unclear. Here, 15N tracing coupled with acetylene inhibition methods were used to assess the effect of adding glucose, wheat straw and peanut straw on NO3--N immobilization and denitrification under aerobic conditions in an upland soil, in which NO3--N immobilization has been previously demonstrated to be negligible. The organic C sources (5 g C kg-1 soil) were added in a factorial experiment with 100, 500, and 1000 mg N kg-1 soil (as K15NO3) in a 12-d laboratory incubation. Microbial NO3--N immobilization in the 12-d incubation in the three N treatments was 5.5, 7.7, and 8.2 mg N kg-1 d-1, respectively, in the glucose-amended soil, 5.9, 4.2, and 2.4 mg N kg-1 d-1, respectively, in the wheat straw-amended soil, and 4.9, 5.1 and 4.4 mg N kg-1 d-1, respectively, in the peanut straw-amended soil. Therefore, under sufficient NO3--N substrate, the higher microbial NO3--N immobilization in the glucose than in the crop residue treatments was likely due to the slow decomposition of the latter that provided low available C. The 15N recovery in the N2O + N2 pool over the12-day incubation was <2% for all treatments, indicating negligible denitrification N loss due to low denitrification rates in the aerobic incubation in spite of increasing C availability. We conclude that external C addition can enhance microbial NO3--N immobilization without causing large N losses through denitrification. This has significant implications for reducing soil NO3--N accumulation by enhancing microbial NO3--N immobilization through increasing C inputs using organic materials and subsequently mitigating nitrate pollution of water bodies.


Assuntos
Nitrogênio , Solo , Desnitrificação , Nitratos , Nitrogênio/análise , Óxidos de Nitrogênio
9.
J Urol ; 206(4): 873-884, 2021 10.
Artigo em Inglês | MEDLINE | ID: mdl-34061567

RESUMO

PURPOSE: Next-generation sequencing (NGS)-based profiling of both urinary tumor DNA (utDNA) and circulating tumor DNA (ctDNA) shows promise for noninvasive detection and surveillance of urothelial bladder cancer (UBC). However, the analytical performance of these assays remains undefined in the real-world setting. Here, we sought to evaluate the concordance between tumor DNA (tDNA) profiling and utDNA or ctDNA assays using a UBC patient cohort from the intended-use population. MATERIALS AND METHODS: Fifty-nine cases with pathologically confirmed disease and matching tissue/urine pairs were prospectively enrolled. Baseline peripheral blood mononuclear cell and plasma specimens were collected during clinic visits. The PredicineCARETM NGS assay was applied for ultra-deep targeted sequencing and somatic alteration identification in tDNA, utDNA and ctDNA. RESULTS: Diverse quantitative metrics including cancer cell fraction, variant allele frequency and tumor mutation burden were invariably concordant between tDNA and utDNA, but not ctDNA. The mutational landscapes captured by tDNA or utDNA were highly similar, whereas a considerable proportion of ctDNA aberrations stemmed from clonal hematopoiesis. Using tDNA-informed somatic events as reference, utDNA assays achieved a specificity of 99.3%, a sensitivity of 86.7%, a positive predictive value of 67.2%, a negative predictive value of 99.8% and a diagnostic accuracy of 99.1%. Higher preoperative utDNA or tDNA abundance correlated with worse relapse-free survival. Actionable variants including FGFR3 alteration and ERBB2 amplification were identified in utDNA. CONCLUSIONS: Urine-based molecular pathology provides a valid and complete genetic profile of bladder cancer, and represents a faithful surrogate for genotyping and monitoring newly diagnosed UBC.


Assuntos
Biomarcadores Tumorais/urina , Carcinoma de Células de Transição/diagnóstico , DNA Tumoral Circulante/urina , Técnicas de Genotipagem/métodos , Neoplasias da Bexiga Urinária/diagnóstico , Adulto , Idoso , Idoso de 80 Anos ou mais , Biomarcadores Tumorais/sangue , Biomarcadores Tumorais/genética , Carcinoma de Células de Transição/sangue , Carcinoma de Células de Transição/genética , Carcinoma de Células de Transição/urina , DNA Tumoral Circulante/sangue , DNA Tumoral Circulante/genética , Feminino , Frequência do Gene , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Biópsia Líquida/métodos , Masculino , Pessoa de Meia-Idade , Mutação , Recidiva Local de Neoplasia , Bexiga Urinária/patologia , Neoplasias da Bexiga Urinária/sangue , Neoplasias da Bexiga Urinária/genética , Neoplasias da Bexiga Urinária/urina
10.
Environ Pollut ; 284: 117176, 2021 Sep 01.
Artigo em Inglês | MEDLINE | ID: mdl-33901983

RESUMO

Although crop residue return increases upland soil emissions of nitrous oxide (N2O), a potent greenhouse gas, the mechanisms responsible for the increase remain unclear. Here, we investigate N2O emission pathways, gross nitrogen (N)-cycling rates, and associated N-cycling gene abundances in an upland soil following the addition of various organic material under aerobic incubation using a combination of 15N tracing technique, acetylene (C2H2) inhibition, and real-time PCR (qPCR) methods. Increased total N2O emissions following organic material amendment was attributed to both increased nitrification-derived N2O emissions, following increased ammonia-oxidizing bacteria (AOB)-amoA abundance, and denitrification-derived N2O emissions, following increased nirS and decreased nosZ abundance. Increasing plant residue carbon (C)/N ratio decreased total N2O emissions by decreasing the contribution of denitrification to N2O emissions, potentially due to higher proportions of denitrified N emitted as N2O than nitrified N emitted as N2O. We further propose a novel conceptual framework for organic material input effects on denitrification-derived N2O emissions based on the decomposable characteristics of the added organic material. For slowly decomposing organic materials (e.g., plant residue) with insufficient available C, NO3--N immobilization surpassed denitrification, resulting in gradual decrease in denitrification-derived N2O emissions with an increase in mineralization of plant residue C losses. In contrast, available C provided by readily available C sources (e.g., glucose) seemed sufficient to support the co-occurrence of NO3--N immobilization and denitrification. Overall, for the first time, we offer a microbial process perspective of N2O emissions following organic material input. The findings could facilitate the improvement of process-orientated models of N2O emissions and the formulation of appropriate N2O mitigation strategies for crop residue-amended soils.


Assuntos
Desnitrificação , Solo , Nitrificação , Óxido Nitroso/análise , Microbiologia do Solo
11.
Nucleic Acids Res ; 49(4): 1972-1986, 2021 02 26.
Artigo em Inglês | MEDLINE | ID: mdl-33503260

RESUMO

Maintenance of stem-cell identity requires proper regulation of enhancer activity. Both transcription factors OCT4/SOX2/NANOG and histone methyltransferase complexes MLL/SET1 were shown to regulate enhancer activity, but how they are regulated in embryonic stem cells (ESCs) remains further studies. Here, we report a transcription factor BACH1, which directly interacts with OCT4/SOX2/NANOG (OSN) and MLL/SET1 methyltransferase complexes and maintains pluripotency in mouse ESCs (mESCs). BTB domain and bZIP domain of BACH1 are required for these interactions and pluripotency maintenance. Loss of BACH1 reduced the interaction between NANOG and MLL1/SET1 complexes, and decreased their occupancy on chromatin, and further decreased H3 lysine 4 trimethylation (H3K4me3) level on gene promoters and (super-) enhancers, leading to decreased enhancer activity and transcription activity, especially on stemness-related genes. Moreover, BACH1 recruited NANOG through chromatin looping and regulated remote NANOG binding, fine-tuning enhancer-promoter activity and gene expression. Collectively, these observations suggest that BACH1 maintains pluripotency in ESCs by recruiting NANOG and MLL/SET1 complexes to chromatin and maintaining the trimethylated state of H3K4 and enhancer-promoter activity, especially on stemness-related genes.


Assuntos
Fatores de Transcrição de Zíper de Leucina Básica/metabolismo , Células-Tronco Embrionárias/metabolismo , Elementos Facilitadores Genéticos , Histona-Lisina N-Metiltransferase/metabolismo , Proteína Homeobox Nanog/metabolismo , Regiões Promotoras Genéticas , Animais , Fatores de Transcrição de Zíper de Leucina Básica/química , Fatores de Transcrição de Zíper de Leucina Básica/fisiologia , Linhagem Celular , Células Cultivadas , Cromatina/metabolismo , Histonas/metabolismo , Camundongos , Fator 3 de Transcrição de Octâmero/metabolismo , Domínios Proteicos , Fatores de Transcrição SOXB1/metabolismo
12.
Biomed Res Int ; 2020: 9309134, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32550234

RESUMO

This study evaluated differences in outcome variables between dynamic stabilization adjacent to fusion (DATF) and posterior lumbar interbody fusion (PLIF) for the treatment of lumbar degenerative disease. A systematic review of PubMed, EMBASE, and Cochrane was performed. The variables of interest included clinical adjacent segment pathologies (CASPs), radiological adjacent segment pathologies (RASPs), lumbar lordosis (LL), visual analogue scale (VAS) of back (VAS-B) and leg (VAS-L), Oswestry disability index (ODI), Japanese Orthopaedic Association (JOA) score, duration of surgery (DS), estimated blood loss (EBL), complications, and reoperation rate. Nine articles identified as meeting all of the inclusion criteria. DATF was better than PLIF in proximal RASP, CASP, and ODI during 3 months follow-up, VAS-L. However, no significant difference between DATF and PLIF was found in distal RASP, LL, JOA score, VAS-B, ODI after 3 months follow-up, complication rates, and reoperation rate. These further confirmed that DATF could decrease the proximal ASP both symptomatically and radiographically as compared to fusion group; however, the influence of DATF on functional outcome was similar with PLIF. The differences between hybrid surgery and topping-off technique were located in DS and EBL in comparison with PLIF. Our study confirmed that DATF could decrease the proximal ASP both symptomatically and radiographically as compared to the fusion group; however, the influence of DATF on functional outcome was similar with PLIF. The difference between hybrid surgery and topping-off technique was not significant in treatment outcomes.


Assuntos
Degeneração do Disco Intervertebral/cirurgia , Vértebras Lombares/cirurgia , Região Lombossacral/cirurgia , Fusão Vertebral , Adulto , Idoso , Idoso de 80 Anos ou mais , Humanos , Pessoa de Meia-Idade , Complicações Pós-Operatórias , Reoperação , Fusão Vertebral/efeitos adversos , Fusão Vertebral/métodos , Fusão Vertebral/estatística & dados numéricos , Resultado do Tratamento
13.
BMC Musculoskelet Disord ; 21(1): 77, 2020 Feb 05.
Artigo em Inglês | MEDLINE | ID: mdl-32024487

RESUMO

BACKGROUND: The leptin receptor-deficient knockout (db/db) mouse is a well-established model for studying type II diabetes mellitus (T2DM). T2DM is an important risk factor of intervertebral disc degeneration (IVDD). Although the relationship between type I diabetes and IVDD has been reported by many studies, few studies have reported the effects of T2DM on IVDD in db/db mice model. METHODS: Mice were separated into 3 groups: wild-type (WT), db/db, and IGF-1 groups (leptin receptor-deficient mice were treated with insulin-like growth factor-1 (IGF-1). To observe the effects of T2DM and glucose-lowering treatment on IVDD, IGF-1 injection was used. The IVD phenotype was detected by H&E and safranin O fast green staining among db/db, WT and IGF-1 mice. The levels of blood glucose and weight in mice were also recorded. The changes in the mass of the trabecular bone in the fifth lumbar vertebra were documented by micro-computed tomography (micro-CT). Tunnel assays were used to detect cell apoptosis in each group. RESULTS: The weight of the mice were 27.68 ± 1.6 g in WT group, which was less than 57.56 ± 4.8 g in db/db group, and 52.17 ± 3.7 g in IGF-1 injected group (P < 0.05). The blood glucose levels were also significantly higher in the db/db mice group. T2DM caused by leptin receptor knockout showed an association with significantly decreased vertebral bone mass and increased IVDD when compared to WT mice. The db/db mice induced by leptin deletion showed a higher percentage of MMP3 expression as well as cell apoptosis in IVDD mice than WT mice (P < 0.05), while IGF-1 treatment reversed this situation (P < 0.05). CONCLUSIONS: T2DM induced by leptin receptor knockout led to IVDD by increasing the levels of MMP3 and promoting cell apoptosis. IGF-1 treatment partially rescue the phenotype of IVDD induced by leptin receptor knockout.


Assuntos
Diabetes Mellitus Tipo 2/complicações , Fator de Crescimento Insulin-Like I/administração & dosagem , Degeneração do Disco Intervertebral/etiologia , Receptores para Leptina/deficiência , Animais , Apoptose , Glicemia/análise , Glicemia/efeitos dos fármacos , Diabetes Mellitus Tipo 2/sangue , Diabetes Mellitus Tipo 2/tratamento farmacológico , Diabetes Mellitus Tipo 2/genética , Modelos Animais de Doenças , Humanos , Disco Intervertebral/citologia , Disco Intervertebral/diagnóstico por imagem , Disco Intervertebral/patologia , Degeneração do Disco Intervertebral/sangue , Degeneração do Disco Intervertebral/diagnóstico , Vértebras Lombares/diagnóstico por imagem , Vértebras Lombares/patologia , Masculino , Camundongos , Camundongos Knockout , Receptores para Leptina/genética , Proteínas Recombinantes/administração & dosagem , Fatores de Risco , Microtomografia por Raio-X
14.
Bioinformatics ; 36(3): 666-675, 2020 02 01.
Artigo em Inglês | MEDLINE | ID: mdl-31504161

RESUMO

MOTIVATION: Sequencing-based 3D genome mapping technologies can identify loops formed by interactions between regulatory elements hundreds of kilobases apart. Existing loop-calling tools are mostly restricted to a single data type, with accuracy dependent on a predefined resolution contact matrix or called peaks, and can have prohibitive hardware costs. RESULTS: Here, we introduce cLoops ('see loops') to address these limitations. cLoops is based on the clustering algorithm cDBSCAN that directly analyzes the paired-end tags (PETs) to find candidate loops and uses a permuted local background to estimate statistical significance. These two data-type-independent processes enable loops to be reliably identified for both sharp and broad peak data, including but not limited to ChIA-PET, Hi-C, HiChIP and Trac-looping data. Loops identified by cLoops showed much less distance-dependent bias and higher enrichment relative to local regions than existing tools. Altogether, cLoops improves accuracy of detecting of 3D-genomic loops from sequencing data, is versatile, flexible, efficient, and has modest hardware requirements. AVAILABILITY AND IMPLEMENTATION: cLoops with documentation and example data are freely available at: https://github.com/YaqiangCao/cLoops. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Assuntos
Cromatina , Software , Algoritmos , Genoma , Genômica
15.
Int Orthop ; 43(6): 1521-1528, 2019 06.
Artigo em Inglês | MEDLINE | ID: mdl-30091068

RESUMO

PURPOSE: Accurate and comprehensive data on cervical endplates is essential for developing and improving cervical devices. However, current literature on vertebral disc geometry is scarce or not suitable. The aim of this study was to obtain quantitative parameters of cervical endplates and provide morphometric references for designing cervical devices. METHODS: In this study, 19 human cervical spine cadaveric specimens were considered. Employing a reverse engineering system, the surface information of each endplate was recorded in digital cloud and then 3D reconstructed. A measurement protocol that included three sagittal and three frontal surface curves was developed. The information of surface curves and endplate concavity were obtained and analyzed. The parametric equations of endplate surfaces were deduced based on coordinates of landmarks, and the reliability was verified. RESULTS: The cervical endplate surface had a trend that to be transversely elongated gradually. The concavity depths of inferior endplates (1.88 to 2.13 mm) were significantly larger than those of superior endplates (0.62 to 0.84 mm). The most-concave points in inferior endplates were concentrated in the central portion, while always located in post-median region in superior endplates. CONCLUSION: These results will give appropriate guidelines to design cervical prostheses without sacrificing valuable bone stock. The parametric equations applied for generating surface profile of cervical endplates may provide great convenience for subsequent studies.


Assuntos
Vértebras Cervicais/diagnóstico por imagem , Procedimentos de Cirurgia Plástica , Adulto , Membros Artificiais , Placas Ósseas , Vértebras Cervicais/cirurgia , Feminino , Humanos , Imageamento Tridimensional , Masculino , Pessoa de Meia-Idade , Reprodutibilidade dos Testes
16.
Genome Res ; 29(1): 40-52, 2019 01.
Artigo em Inglês | MEDLINE | ID: mdl-30455182

RESUMO

A few families of transposable elements (TEs) have been shown to evolve into cis-regulatory elements (CREs). Here, to extend these studies to all classes of TEs in the human genome, we identified widespread enhancer-like repeats (ELRs) and find that ELRs reliably mark cell identities, are enriched for lineage-specific master transcription factor binding sites, and are mostly primate-specific. In particular, elements of MIR and L2 TE families whose abundance co-evolved across chordate genomes, are found as ELRs in most human cell types examined. MIR and L2 elements frequently share long-range intra-chromosomal interactions and binding of physically interacting transcription factors. We validated that eight L2 and nine MIR elements function as enhancers in reporter assays, and among 20 MIR-L2 pairings, one MIR repressed and one boosted the enhancer activity of L2 elements. Our results reveal a previously unappreciated co-evolution and interaction between two TE families in shaping regulatory networks.


Assuntos
Cromossomos Humanos/genética , Elementos de DNA Transponíveis , Elementos Facilitadores Genéticos , Redes Reguladoras de Genes , Genoma Humano , Células HeLa , Humanos , Células K562
17.
Int J Nanomedicine ; 13: 3883-3896, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-30013342

RESUMO

INTRODUCTION: It is predicted that with increased life expectancy in the whole world, there will be a greater demand for synthetic biomedical materials to repair or regenerate lost, injured or diseased tissues. Natural polymers, as biomedical materials, have been widely applied in the field of regenerative medicine. MATERIALS AND METHODS: By incorporation of nanoporous diopside bioglass (nDPB) into glia-din (GL) matrix, macro-nanoporous scaffolds of nDPB/GL composites (DGC) were fabricated by method of solution compressing and particles leaching. RESULTS: The results revealed that the DGC scaffolds possessed well-interconnected macropores of 200-500 µm and nanopores of 4 nm, and the porosity and degradability of DGC scaffolds remarkably increased with the increase in nDPB content. In addition, in vitro cell experiments revealed that the adhesion and growth of MC3T3-E1 cells on DGC scaffolds were significantly promoted, which depended on nDPB content. Moreover, the results of histological evaluations confirmed that the osteogenic properties and degradability of DGC scaffolds in vivo significantly improved, which were nDPB content dependent. Furthermore, the results of immunohistochemical analysis demonstrated that, with the increase in nDPB content, the type I collagen expression in DGC scaffolds in vivo obviously enhanced, indicating excellent osteogenesis. DISCUSSION AND CONCLUSION: The results demonstrated that the DGC scaffolds containing 30 wt% nDPB (30nDGC) exhibited good biocompatibility and new bone formation ability, which might have a great potential for applications in bone regeneration.


Assuntos
Materiais Biocompatíveis/farmacologia , Gliadina/química , Nanoporos , Osteogênese/efeitos dos fármacos , Ácido Silícico/farmacologia , Alicerces Teciduais/química , Animais , Adesão Celular , Linhagem Celular , Proliferação de Células , Colágeno Tipo I/metabolismo , Humanos , Camundongos , Nanoporos/ultraestrutura , Espectroscopia de Infravermelho com Transformada de Fourier
18.
Int J Surg ; 53: 269-273, 2018 May.
Artigo em Inglês | MEDLINE | ID: mdl-29649666

RESUMO

OBJECTIVE: To investigate cigarette smoking's relevance with cervical disc degeneration. METHODS: We randomly selected 320 patients who came to our spine disease department outpatient clinic with chief complaint of neck-shoulder pain during June 2014-June 2016. According to the detailed smoking history, these patients were divided into 3 different groups, which were active smoker group (AS), passive smoking group (PS) and never-smoker group (NS). Each patient's Miyazaki's magnetic resonance imaging (MRI) classification of cervical disc degeneration was analyzed based on their cervical MRI films. In addition, VAS scores were applied to evaluate the degree of patients' neck-shoulder pain. With the help of statistical techniques, relevance between cigarette smoking, cervical disc degeneration and neck-shoulder pain were analyzed. RESULTS: In the NS group, the overall Miyazaki score, especially for C2/3, C3/4, C5,6 segments, are superior to those in the PS group, in addition, the Miyazaki scores for C1/2 - C6/7 segments in NS group beat the same segments in AS group with statistical significance (P < 0.05). In the AS and PS group, discs from C4/5 to C5/6 segments which score IV and V on Miyazaki classification account for a larger proportion than those discs from C1/2 to C3/4 segments with statistical significance (P < 0.05). In the AS group, male cases have larger proportion of Miyazaki level IV and V discs than female with statistical significance (P < 0.05). While in the AS and PS group, Miyazaki scores of patients whose smoking history ranges from 5 to 10 years are superior to those with smoking history longer than 10 years, with statistical significance (P < 0.05). In addition, VAS scores also vary among the three groups, in which, VAS scores in AS group are higher than those in the NS group. CONCLUSION: Smoking could accelerate the process of cervical disc degeneration, presenting with more severe neck-shoulder pain on the patients. In addition, the impact of smoking on the lower cervical discs is greater than the upper cervical discs.


Assuntos
Vértebras Cervicais/patologia , Fumar Cigarros/efeitos adversos , Degeneração do Disco Intervertebral/etiologia , Adulto , Idoso , Feminino , Humanos , Degeneração do Disco Intervertebral/patologia , Imageamento por Ressonância Magnética , Masculino , Pessoa de Meia-Idade , Cervicalgia/etiologia , Estudos Retrospectivos , Dor de Ombro/etiologia
19.
Sci Rep ; 7(1): 7403, 2017 08 07.
Artigo em Inglês | MEDLINE | ID: mdl-28785062

RESUMO

Epidemiological studies have concluded that hyperlipidemia and atherosclerosis were related to intervertebral disc degeneration (IVDD). The presence of oxidized low density lipoprotein (ox-LDL) and the expression of lectin-like oxidized low density lipoprotein receptor 1 (LOX-1) have not been explored in this tissue. In this study, we investigated the presence of ox-LDL and the expression of its receptor LOX-1 in non-degenerated, degenerated or herniated human intervertebral discs (IVDs). The expression of LOX-1 and matrix metalloproteinase 3 (MMP3) were studied after incubating nucleus pulposus cells (NPCs) with ox-LDL. The presence of ox-LDL and LOX-1 was positively related with the extent of IVDD in nucleus pulposus (NP), end-plate cartilage and outer annulus fibrous, but not with the extent of degeneration of inter annulus fibrous. Ox-LDL significantly reduced the viability of human NPCs in a dose and time-dependent manner, and increased the expression of MMP3 induced by LOX-1. Pretreatment with anti-human LOX-1 monoclonal antibody reversed these effects. Ox-LDL, principally mediated by LOX-1, enhanced MMP3 production in NPCs through the NF-κB signaling pathway. In conclusion, increased accumulation of ox-LDL and LOX-1 in IVDs indicates a specific role of the receptor-ligand interaction in degeneration or herniation of IVDs.


Assuntos
Degeneração do Disco Intervertebral/metabolismo , Deslocamento do Disco Intervertebral/metabolismo , Lipoproteínas LDL/metabolismo , Receptores Depuradores Classe E/metabolismo , Adulto , Idoso , Sobrevivência Celular , Células Cultivadas , Progressão da Doença , Humanos , Metaloproteinase 3 da Matriz/metabolismo , Pessoa de Meia-Idade , Núcleo Pulposo/metabolismo , Transdução de Sinais
20.
Int J Surg ; 44: 344-349, 2017 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-28711623

RESUMO

BACKGROUND CONTEXT: Single-stage surgery is usually applied to improving the symptoms of coexisting cervical and lumbar stenosis. In most cases, patients' willingness, surgery affordability, surgical trauma, surgical complications and patients' tolerance to surgery all limit the application of single-stage surgery. For patients who cannot receive single-stage surgery, we hope that we can find out by weighing up merits and flaws of the two surgical sites in order to make decision of prioritize one of the two surgery, so as to bring more benefits to the patients. OBJECTIVE: To confirm which one of prioritized cervical surgery and prioritized lumbar surgery has a better effect in alleviating the symptoms of patients with coexisting cervical and lumbar stenosis. STUDY DESIGN: A retrospective analysis and a cohort study for 15 years. PATIENT SAMPLE: The information of 222 patients who were diagnosed with coexisting cervical and lumbar stenosis over the past 15 years was collected, including 144 patients who underwent prioritized cervical surgery and 78 prioritized lumbar surgery, thereafter the changes in the patients' postoperative neurological functions were evaluated. OUTCOME MEASURES: Primary outcome variables are the clinical diagnosis event and the event of surgical site positioning. Secondary variables are the event of postoperative function changes and the symptom improvement event. METHODS: The information about 222 patients with coexisting cervical and lumbar stenosis who had a follow-up of more than 1 year during January 2000 and December 2014 was collected. The effects of prioritized staged cervical and lumbar surgeries on the prognosis for the above-mentioned patients were respectively evaluated via relevant evaluation indexes. RESULTS: The follow-up time was 18-156 months (58.0 ± 36.5). The lumbar reoperation rate after prioritized cervical surgery was lower than the cervical reoperation rate after prioritized lumbar surgery (22.91% < 57.69%) (P < 0.01). The JOA score and Nurick grade significantly improved (P < 0.01) and the ODI score improved (P < 0.05) after prioritized cervical surgery. No obvious improvement in the JOA score and Nurick grade (P > 0.05) was shown but the ODI score markedly improved (P < 0.01) after prioritized lumbar surgery. CONCLUSIONS: For patients with coexisting cervical and lumbar stenosis, prioritized cervical surgery is safe and effective and is superior to prioritized lumbar surgery on the improvement of cervical and lumbar symptoms, the postoperative recovery of limb function and the rate of reoperation on another site.


Assuntos
Vértebras Cervicais/cirurgia , Descompressão Cirúrgica/métodos , Vértebras Lombares/cirurgia , Estenose Espinal/cirurgia , Adulto , Idoso , Constrição Patológica/cirurgia , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Prognóstico , Reoperação , Estudos Retrospectivos , Adulto Jovem
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