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1.
Opt Express ; 30(24): 42875-42891, 2022 Nov 21.
Artigo em Inglês | MEDLINE | ID: mdl-36522998

RESUMO

In this paper, modal interference discrepancy in an all-fiber MZI is theoretically analyzed and experimentally verified. Theoretical analysis demonstrates that ambient refractive index (RI) response of core-cladding modal interference in an all-fiber MZI is blue-shift, while that of cladding-cladding modal interference is red-shift. Temperature response trends of the two kinds of modal interference are uniformly red-shift. The discrepancy is used to fabricate an improved Vernier sensor which is cascaded by two unit MZIs. One MZI is slightly core-offset fused to obtain core-cladding modal interference, and the other is obviously offset fused to get cladding-cladding modal interference. Ambient RI sensitivity of the cascaded sensor is improved with temperature cross-talk restrained. Ambient RI responses of the two unit MZIs are measured to be opposite, which are -54.009 nm/RIU (within RI range of 1.3362∼1.3811) for the slight and 142.581 nm/RIU for the obvious offset unit MZI. While, temperature response trends of them are consistent, which are 0.042 nm/°C for the slight and 0.025 nm/°C for the obvious offset unit MZI, respectively. For the cascaded Vernier sensor ambient RI sensitivity reaches -1788.160 nm/RIU, which is 33.1 and 12.5 folds improved over the two unit MZIs, respectively. Temperature sensitivity of the cascaded sensor is as low as 0.167 nm/°C and only causes a slight RI error of 9.339 × 10-5 RIU/°C. Due to the simple structure, ease of fabrication, and low temperature cross-talk, the modal interference discrepancy-based Vernier sensor is believed to have potential application prospects in biochemical sensing fields.

2.
Can Assoc Radiol J ; 72(4): 783-788, 2021 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-33023323

RESUMO

PURPOSE: We analyzed and compared the imaging characteristics of the vessel wall of the middle cerebral artery (MCA) in symptomatic and asymptomatic patients using a 3.0-T high-resolution magnetic resonance imaging (HR-MRI) protocol, including a 3-dimensional T1-sampling perfection with application-optimized contrasts using different flip angle evolutions sequence. METHODS: Fifty-three patients with atherosclerotic stenosis of the MCA underwent 3.0-T HR-MRI examinations. The characteristics of atherosclerotic plaques in 53 patients (28 symptomatic, 25 asymptomatic) were analyzed, including plaque distribution and signal intensity. Plaque burden (PB), stenosis degree, and the remodeling index were measured and compared between symptomatic and asymptomatic patients. RESULTS: The PB of the symptomatic group was significantly higher than that of the asymptomatic group (P = .006), and moderate-severe stenosis was more common (P = .01). The remodeling index of the symptomatic group was also lower (P = .015) and negative remodeling (NR) was more common (P = .043). Binary logistic regression analysis showed that stenosis degree was a risk factor in symptomatic patients (odds ratio = 135, P = .023). CONCLUSION: There is a trend that some characteristics of plaques and vessels, including the moderate-severe stenosis, larger PB, and NR, were observed more frequently among patients with symptomatic atherosclerotic stenosis of the MCA than among asymptomatic patients.


Assuntos
Aterosclerose/diagnóstico por imagem , Imageamento por Ressonância Magnética/métodos , Artéria Cerebral Média/diagnóstico por imagem , Constrição Patológica , Estudos de Avaliação como Assunto , Feminino , Humanos , Imageamento Tridimensional/métodos , Masculino , Pessoa de Meia-Idade , Reprodutibilidade dos Testes
3.
BMC Bioinformatics ; 16 Suppl 5: S7, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-25860335

RESUMO

We consider the emerging problem of comparing the similarity between (unlabeled) pedigrees. More specifically, we focus on the simplest pedigrees, namely, the 2-generation pedigrees. We show that the isomorphism testing for two 2-generation pedigrees is GI-hard. If the 2-generation pedigrees are monogamous (i.e., each individual at level-1 can mate with exactly one partner) then the isomorphism testing problem can be solved in polynomial time. We then consider the problem by relaxing it into an NP-complete decomposition problem which can be formulated as the Minimum Common Integer Pair Partition (MCIPP) problem, which we show to be FPT by exploiting a property of the optimal solution. While there is still some difficulty to overcome, this lays down a solid foundation for this research.


Assuntos
Algoritmos , Biologia Computacional/métodos , Simulação por Computador , Linhagem , Feminino , Humanos , Masculino
4.
BMC Bioinformatics ; 16: 340, 2015 Oct 23.
Artigo em Inglês | MEDLINE | ID: mdl-26498158

RESUMO

BACKGROUND: Despite ongoing reductions in the cost of sequencing technologies, whole genome SNP genotype imputation is often used as an alternative for obtaining abundant SNP genotypes for genome wide association studies. Several existing genotype imputation methods can be efficient for this purpose, while achieving various levels of imputation accuracy. Recent empirical results have shown that the two-step imputation may improve accuracy by imputing the low density genotyped study animals to a medium density array first and then to the target density. We are interested in building a series of staircase arrays that lead the low density array to the high density array or even the whole genome, such that genotype imputation along these staircases can achieve the highest accuracy. RESULTS: For genotype imputation from a lower density to a higher density, we first show how to select untyped SNPs to construct a medium density array. Subsequently, we determine for each selected SNP those untyped SNPs to be imputed in the add-one two-step imputation, and lastly how the clusters of imputed genotype are pieced together as the final imputation result. We design extensive empirical experiments using several hundred sequenced and genotyped animals to demonstrate that our novel two-step piecemeal imputation always achieves an improvement compared to the one-step imputation by the state-of-the-art methods Beagle and FImpute. Using the two-step piecemeal imputation, we present some preliminary success on whole genome SNP genotype imputation for genotyped animals via a series of staircase arrays. CONCLUSIONS: From a low SNP density to the whole genome, intermediate pseudo-arrays can be computationally constructed by selecting the most informative SNPs for untyped SNP genotype imputation. Such pseudo-array staircases are able to impute more accurately than the classic one-step imputation.


Assuntos
Estudo de Associação Genômica Ampla , Animais , Bovinos , Análise por Conglomerados , Genoma , Genótipo , Polimorfismo de Nucleotídeo Único , Software
5.
Anal Chem ; 87(19): 9838-45, 2015 Oct 06.
Artigo em Inglês | MEDLINE | ID: mdl-26327437

RESUMO

High-performance chemical isotope labeling (CIL) liquid chromatography-mass spectrometry (LC-MS) is an enabling technology based on rational design of labeling reagents to target a class of metabolites sharing the same functional group (e.g., all the amine-containing metabolites or the amine submetabolome) to provide concomitant improvements in metabolite separation, detection, and quantification. However, identification of labeled metabolites remains to be an analytical challenge. In this work, we describe a library of labeled standards and a search method for metabolite identification in CIL LC-MS. The current library consists of 273 unique metabolites, mainly amines and phenols that are individually labeled by dansylation (Dns). Some of them produced more than one Dns-derivative (isomers or multiple labeled products), resulting in a total of 315 dansyl compounds in the library. These metabolites cover 42 metabolic pathways, allowing the possibility of probing their changes in metabolomics studies. Each labeled metabolite contains three searchable parameters: molecular ion mass, MS/MS spectrum, and retention time (RT). To overcome RT variations caused by experimental conditions used, we have developed a calibration method to normalize RTs of labeled metabolites using a mixture of RT calibrants. A search program, DnsID, has been developed in www.MyCompoundID.org for automated identification of dansyl labeled metabolites in a sample based on matching one or more of the three parameters with those of the library standards. Using human urine as an example, we illustrate the workflow and analytical performance of this method for metabolite identification. This freely accessible resource is expandable by adding more amine and phenol standards in the future. In addition, the same strategy should be applicable for developing other labeled standards libraries to cover different classes of metabolites for comprehensive metabolomics using CIL LC-MS.


Assuntos
Aminas/análise , Compostos de Dansil/análise , Metabolômica/métodos , Fenol/análise , Aminas/metabolismo , Aminas/urina , Cromatografia Líquida/economia , Cromatografia Líquida/métodos , Compostos de Dansil/metabolismo , Humanos , Metaboloma , Metabolômica/economia , Fenol/metabolismo , Fenol/urina , Espectrometria de Massas em Tandem/economia , Espectrometria de Massas em Tandem/métodos , Fatores de Tempo , Urinálise/economia , Urinálise/métodos
6.
Anal Chem ; 87(20): 10619-26, 2015 Oct 20.
Artigo em Inglês | MEDLINE | ID: mdl-26415007

RESUMO

We report an analytical tool to facilitate metabolite identification based on an MS/MS spectral match of an unknown to a library of predicted MS/MS spectra of possible human metabolites. To construct the spectral library, the known endogenous human metabolites in the Human Metabolome Database (HMDB) (8,021 metabolites) and their predicted metabolic products via one metabolic reaction in the Evidence-based Metabolome Library (EML) (375,809 predicted metabolites) were subjected to in silico fragmentation to produce the predicted MS/MS spectra. This spectral library is hosted at the public MCID Web site ( www.MyCompoundID.org ), and a spectral search program, MCID MS/MS, has been developed to allow a user to search one or a batch of experimental MS/MS spectra against the library spectra for possible match(s). Using MS/MS spectra generated from standard metabolites and a human urine sample, we demonstrate that this tool is very useful for putative metabolite identification. It allows a user to narrow down many possible structures initially found by using an accurate mass search of an unknown metabolite to only one or a few candidates, thereby saving time and effort in selecting or synthesizing metabolite standard(s) for eventual positive metabolite identification.


Assuntos
Compostos Orgânicos/análise , Algoritmos , Bases de Dados Factuais , Humanos , Metabolômica , Estrutura Molecular , Compostos Orgânicos/metabolismo , Espectrometria de Massas em Tandem
7.
Zhongguo Zhong Yao Za Zhi ; 40(24): 4830-3, 2015 Dec.
Artigo em Chinês | MEDLINE | ID: mdl-27245030

RESUMO

This study aims to investigate whether the cultivation peony, can take the place of wild herbaceous peony by comparing the biological traits and paeoniflorin content between them. The result showed that the biomass of the stem, leaf, crown, fleshy root and fine root of wild plants were all smaller than that of bud asexual cultivated plants, while there was no significant differences in below-ground and aboveground biomass ratio between these two plants. The stele diameter, the proportion of stele, and the ratio of stele diameter to cortex thickness of wild plants were significantly higher than that of bud asexual cultivated plants, while the cortex thickness and the proportion of cortex were significantly smaller than bud asexual cultivated plants. Although the biological traits of bud asexual cultivated plants have changed significantly, the paeoniflorin content in fleshy roots has no significant difference between wild and bud asexual cultivated plants. Therefore, it is feasible to use the bud asexual cultivation to the conservation and large-scale cultivation of Paeonia laciflora, which is an endangered species.


Assuntos
Glucosídeos/análise , Monoterpenos/análise , Paeonia/química , Paeonia/anatomia & histologia , Paeonia/crescimento & desenvolvimento
8.
Anal Chem ; 86(7): 3568-74, 2014 Apr 01.
Artigo em Inglês | MEDLINE | ID: mdl-24635831

RESUMO

Small peptides, such as dipeptides and tripeptides, are naturally present in many biological samples (e.g., human biofluids and cell extracts). They have attracted great attention in many research fields because of their important biological functions as well as potential roles as disease biomarkers. Tandem mass spectrometry (MS/MS) can be used to profile these small peptides. However, the type and number of fragment ions generated in MS/MS are often limited for unambiguous identification. Herein we report a novel database-search strategy based on the use of MS/MS spectra of both unlabeled and dimethyl labeled peptides to identify and confirm amino acid sequences of di/tripeptides that are separated using hydrophilic interaction (HILIC) liquid chromatography (LC). To facilitate the di/tripeptide identification, a database consisting of all the predicted MS/MS spectra from 400 dipeptides and 8000 tripeptides was created, and a search tool, PEP Search, was developed and housed at the MyCompoundID website ( www.mycompoundid.org/PEP). To evaluate the identification specificity of this method, we used acid hydrolysis to degrade a standard protein, cytochrome c, to produce many di/tripeptides with known sequences for LC/MS/MS. The resultant MS/MS spectra were searched against the database to generate a list of matches which were compared to the known sequences. We correctly identified the di/tripeptides in the protein hydrolysate. We then applied this method to detect and identify di/tripeptides naturally present in human urine samples with high confidence. We envisage the use of this method as a complementary tool to various LC/MS techniques currently available for small molecule or metabolome profiling with an added benefit of covering all di/tripeptide chemical space.


Assuntos
Cromatografia Líquida/métodos , Oligopeptídeos/química , Espectrometria de Massas em Tandem/métodos , Citocromos c/metabolismo , Humanos , Hidrólise , Interações Hidrofóbicas e Hidrofílicas
9.
Front Neurol ; 15: 1365876, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38895698

RESUMO

Objective: Whether the efficacy of combined stent retriever and contact aspiration (S + A) is superior to stent retriever (S) alone for revascularisation in patients with large vessel occlusive stroke remains uncertain. The aim of this meta-analysis was to assess the safety and efficacy of combined stent retriever and contact aspiration for the treatment of acute ischaemic stroke with large vessel occlusion by comparing it with stent retriever alone. Methods: We systematically searched the PubMed, Embase, Web of Science, and The Cochrane Library databases for randomised controlled trials and observational studies (case-control and cohort studies) published before 1 October 2023 comparing the efficacy of combined stent retriever and contact aspiration versus tent retriever alone in patients with large vessel occlusive stroke. The end point of the primary efficacy observed in this meta-analysis study was the rate of first pass nearly complete or complete recanalisation (mTICI 2c-3). Secondary effectiveness nodes were: rate of first pass successful recanalisation (mTICI 2b-3), rate of near-complete or complete recanalisation of the postoperative vessel, rate of successful recanalisation of the postoperative vessel, and MRS 0-2 within 90 days. Safety endpoints were interoperative embolism, symptomatic intracranial haemorrhage, and mortality within 90 days. Results: A total of 16 studies were included in the literature for this meta-analysis, with a total of 7,320 patients (S + C group: 3,406, S group: 3,914). A comprehensive analysis of the included literature showed that combined stent retriever and contact aspiration had a higher rate of near-complete or complete recanalisation of the postoperative vessel [OR = 1.53, 95% CI (1.24, 1.88), p < 0.0001] and rate of successful recanalisation of the postoperative vessel compared to stent retriever alone [OR = 1.83, 95% CI (1.55, 2.17), p < 0.00001]; there were no statistically significant differences between the two groups in terms of the rate of first pass nearly complete or complete recanalisation [OR = 1.00, 95% CI (0.83, 1.19), p = 0.96], rate of first pass successful recanalisation [OR = 1.02, 95% CI (0.85, 1.24), p = 0.81], interoperative embolism [OR = 0.93, 95% CI (0.72, 1.20), p = 0.56], symptomatic intracranial haemorrhage [OR = 1.14, 95% CI (0.87, 1.48), p = 0.33], MRS 0-2 within 90 days [OR = 0.89, 95% CI (0.76, 1.04), p = 0.14] and mortality within 90 days [OR = 1.11, 95% CI (0.94, 1.31), p = 0.22]. Conclusion: Combined stent retriever and contact aspiration has a higher rate of postprocedural revascularisation (mTICI 2c-3/mTICI 2b-3) compared with stent retriever alone in patients with large vessel occlusion stroke. In addition, it was not superior to stenting alone in terms of the rate of first pass recanalisation (mTICI 2c-3/mTICI 2b-3), interoperative embolisation, symptomatic intracranial haemorrhage, good functional prognosis within 90 days and mortality within 90 days.

10.
Anal Chem ; 85(6): 3401-8, 2013 Mar 19.
Artigo em Inglês | MEDLINE | ID: mdl-23373753

RESUMO

Identification of unknown metabolites is a major challenge in metabolomics. Without the identities of the metabolites, the metabolome data generated from a biological sample cannot be readily linked with the proteomic and genomic information for studies in systems biology and medicine. We have developed a web-based metabolite identification tool ( http://www.mycompoundid.org ) that allows searching and interpreting mass spectrometry (MS) data against a newly constructed metabolome library composed of 8,021 known human endogenous metabolites and their predicted metabolic products (375,809 compounds from one metabolic reaction and 10,583,901 from two reactions). As an example, in the analysis of a simple extract of human urine or plasma and the whole human urine by liquid chromatography-mass spectrometry and MS/MS, we are able to identify at least two times more metabolites in these samples than by using a standard human metabolome library. In addition, it is shown that the evidence-based metabolome library (EML) provides a much superior performance in identifying putative metabolites from a human urine sample, compared to the use of the ChemPub and KEGG libraries.


Assuntos
Bibliotecas Digitais , Metaboloma/genética , Espectrometria de Massas em Tandem/métodos , Cromatografia Líquida/métodos , Bases de Dados Factuais , Humanos , Redes e Vias Metabólicas/genética
11.
Anal Chim Acta ; 1272: 341467, 2023 Sep 01.
Artigo em Inglês | MEDLINE | ID: mdl-37355326

RESUMO

Liquid chromatography mass spectrometry (LC-MS) has been increasingly used for metabolome analysis. One of the critical steps in the LC-MS metabolome analysis workflow is related to metabolite identification. Among the measured parameters, peak mass is commonly used to search against a database for potential metabolite matches. Higher accuracy mass measurement allows the use of a narrower mass tolerance window for mass search. While various types of mass analyzers can routinely measure a peak mass with an error of less than a few ppm, mass measurement accuracy is not uniform for peaks with different intensities, particularly for quadrupole time-of-flight (QTOF) MS. Herein we present a simple and convenient method to determine the relation between peak intensity and mass error in LC-QTOF-MS-based metabolome analysis, followed by intensity-dependent mass search (IDMS) of a database for metabolite matches. This method is based on running a series of sodium formate mass calibrants, as part of the standard operating procedure (SOP) in LC-MS data acquisition, and then curve-fitting the measured mass errors and peak intensities. We show that, in two different quadrupole time-of-flight (QTOF) mass analyzers, mass accuracy is generally reduced as peak intensity decreases, which is independent of m/z values in the range commonly used for metabolite detection (e.g., m/z < 1000). We demonstrate the improvement in metabolite matches using IDMS in the analyses of dansyl labeled standards and human urine samples. We have implemented the IDMS method in the freely available MCID database at www.mycompoundid.org, which is composed of 8021 known human endogenous metabolites and their predicted metabolic products (375,809 compounds from one metabolic reaction and 10,583,901 compounds from two reactions).


Assuntos
Metaboloma , Metabolômica , Humanos , Marcação por Isótopo/métodos , Compostos de Dansil/química , Metabolômica/métodos , Cromatografia Líquida/métodos , Espectrometria de Massas/métodos
12.
Comput Struct Biotechnol J ; 21: 3183-3195, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-37333861

RESUMO

In order to mitigate the effects of a changing climate, agriculture requires more effective evaluation, selection, and production of crop cultivars in order to accelerate genotype-to-phenotype connections and the selection of beneficial traits. Critically, plant growth and development are highly dependent on sunlight, with light energy providing plants with the energy required to photosynthesize as well as a means to directly intersect with the environment in order to develop. In plant analyses, machine learning and deep learning techniques have a proven ability to learn plant growth patterns, including detection of disease, plant stress, and growth using a variety of image data. To date, however, studies have not assessed machine learning and deep learning algorithms for their ability to differentiate a large cohort of genotypes grown under several growth conditions using time-series data automatically acquired across multiple scales (daily and developmentally). Here, we extensively evaluate a wide range of machine learning and deep learning algorithms for their ability to differentiate 17 well-characterized photoreceptor deficient genotypes differing in their light detection capabilities grown under several different light conditions. Using algorithm performance measurements of precision, recall, F1-Score, and accuracy, we find that Suport Vector Machine (SVM) maintains the greatest classification accuracy, while a combined ConvLSTM2D deep learning model produces the best genotype classification results across the different growth conditions. Our successful integration of time-series growth data across multiple scales, genotypes and growth conditions sets a new foundational baseline from which more complex plant science traits can be assessed for genotype-to-phenotype connections.

13.
J Biomol NMR ; 53(3): 167-80, 2012 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-22678091

RESUMO

In protein X-ray crystallography, resolution is often used as a good indicator of structural quality. Diffraction resolution of protein crystals correlates well with the number of X-ray observables that are used in structure generation and, therefore, with protein coordinate errors. In protein NMR, there is no parameter identical to X-ray resolution. Instead, resolution is often used as a synonym of NMR model quality. Resolution of NMR structures is often deduced from ensemble precision, torsion angle normality and number of distance restraints per residue. The lack of common techniques to assess the resolution of X-ray and NMR structures complicates the comparison of structures solved by these two methods. This problem is sometimes approached by calculating "equivalent resolution" from structure quality metrics. However, existing protocols do not offer a comprehensive assessment of protein structure as they calculate equivalent resolution from a relatively small number (<5) of protein parameters. Here, we report a development of a protocol that calculates equivalent resolution from 25 measurable protein features. This new method offers better performance (correlation coefficient of 0.92, mean absolute error of 0.28 Å) than existing predictors of equivalent resolution. Because the method uses coordinate data as a proxy for X-ray diffraction data, we call this measure "Resolution-by-Proxy" or ResProx. We demonstrate that ResProx can be used to identify under-restrained, poorly refined or inaccurate NMR structures, and can discover structural defects that the other equivalent resolution methods cannot detect. The ResProx web server is available at http://www.resprox.ca.


Assuntos
Algoritmos , Modelos Moleculares , Ressonância Magnética Nuclear Biomolecular , Proteínas/química , Cristalografia por Raios X , Conformação Proteica
14.
Nucleic Acids Res ; 38(Web Server issue): W633-40, 2010 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-20460469

RESUMO

PROSESS (PROtein Structure Evaluation Suite and Server) is a web server designed to evaluate and validate protein structures generated by X-ray crystallography, NMR spectroscopy or computational modeling. While many structure evaluation packages have been developed over the past 20 years, PROSESS is unique in its comprehensiveness, its capacity to evaluate X-ray, NMR and predicted structures as well as its ability to evaluate a variety of experimental NMR data. PROSESS integrates a variety of previously developed, well-known and thoroughly tested methods to evaluate both global and residue specific: (i) covalent and geometric quality; (ii) non-bonded/packing quality; (iii) torsion angle quality; (iv) chemical shift quality and (v) NOE quality. In particular, PROSESS uses VADAR for coordinate, packing, H-bond, secondary structure and geometric analysis, GeNMR for calculating folding, threading and solvent energetics, ShiftX for calculating chemical shift correlations, RCI for correlating structure mobility to chemical shift and PREDITOR for calculating torsion angle-chemical shifts agreement. PROSESS also incorporates several other programs including MolProbity to assess atomic clashes, Xplor-NIH to identify and quantify NOE restraint violations and NAMD to assess structure energetics. PROSESS produces detailed tables, explanations, structural images and graphs that summarize the results and compare them to values observed in high-quality or high-resolution protein structures. Using a simplified red-amber-green coloring scheme PROSESS also alerts users about both general and residue-specific structural problems. PROSESS is intended to serve as a tool that can be used by structure biologists as well as database curators to assess and validate newly determined protein structures. PROSESS is freely available at http://www.prosess.ca.


Assuntos
Conformação Proteica , Software , Cristalografia por Raios X , Internet , Modelos Moleculares , Ressonância Magnética Nuclear Biomolecular , Interface Usuário-Computador
15.
Front Neurol ; 13: 851910, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35572929

RESUMO

Introduction: The safety and efficacy of tirofiban in intravenous thrombolysis (IVT) bridging to mechanical thrombectomy in patients with acute ischemic stroke (AIS) is unknown. The purpose of this meta-analysis was to evaluate the safety and efficacy of tirofiban in IVT bridging to mechanical thrombectomy in acute ischemic stroke. Methods: We systematically searched PubMed, EMBASE, Web of Science, and The Cochrane Library, CNKI, and Wan Fang databases for randomized controlled trials and observational studies (case-control studies and cohort studies) comparing the tirofiban and non-tirofiban groups in AIS intravenous thrombolysis bridging to mechanical thrombectomy (Published by November 20, 2021). Our primary safety endpoints were symptomatic cerebral hemorrhage (sICH), intracranial hemorrhage (ICH), postoperative re-occlusion, and 3-month mortality; the efficacy endpoints were 3-month favorable functional outcome (MRS ≤ 2) and successful recanalization rate (modified thrombolytic therapy in cerebral infarction (mTICI) 2b or 3). Results: A total of 7 studies with 1,176 patients were included in this meta-analysis. A comprehensive analysis of the included literature showed that the difference between the tirofiban and non-tirofiban groups in terms of successful recanalization (OR = 1.19, 95% Cl [0.69, 2.03], p = 0.53, I 2 = 22%) and favorable functional outcome at 3 months (OR = 1.13, 95% Cl [0.81, 1.60], p = 0.47, I 2 = 17%) in patients with IVT bridging mechanical thrombectomy of AIS was not statistically significant. Also, the differences in the incidence of sICH (OR = 0.97, 95% Cl [0.58, 1.62], p = 0.89) and ICH (OR = 0.83, 95% Cl [0.55, 1.24], p = 0.36) between the two groups were not statistically significant. However, the use of tirofiban during IVT bridging mechanical thrombectomy reduced the rate of postoperative re-occlusion (OR = 0.36, 95% Cl [0.14, 0.91], p = 0.03) and mortality within 3 months (OR = 0.54, 95% Cl [0.33, 0.87], p = 0.01) in patients. Conclusion: The use of tirofiban during IVT bridging mechanical thrombectomy for AIS does not increase the risk of sICH and ICH in patients and reduces the risk of postoperative re-occlusion and mortality in patients within 3 months. However, this result needs to be further confirmed by additional large-sample, multicenter, prospective randomized controlled trials. Systematic Review Registration: http://www.crd.york.ac.uk/PROSPERO/, identifier: CRD42022297441.

16.
Front Mol Neurosci ; 15: 967174, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-36157076

RESUMO

Respirable fine particulate matter (PM2.5) has been one of the most widely publicized indicators of pollution in recent years. Epidemiological studies have established a strong association between PM2.5, lung disease, and cardiovascular disease. Recent studies have shown that PM2.5 is also strongly associated with brain damage, mainly cerebrovascular damage (stroke) and neurological damage to the brain (changes in cognitive function, dementia, psychiatric disorders, etc.). PM2.5 can pass through the lung-gas-blood barrier and the "gut-microbial-brain" axis to cause systemic oxidative stress and inflammation, or directly enter brain tissue via the olfactory nerve, eventually damaging the cerebral blood vessels and brain nerves. It is worth mentioning that there is a time window for PM2.5-induced brain damage to repair itself. However, the exact pathophysiological mechanisms of brain injury and brain repair are not yet fully understood. This article collects and discusses the mechanisms of PM2.5-induced brain injury and self-repair after injury, which may provide new ideas for the prevention and treatment of cerebrovascular and cerebral neurological diseases.

17.
Front Neurol ; 13: 968417, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-36188409

RESUMO

Purpose: For patients with symptomatic middle cerebral artery (MCA) atherosclerotic stenosis, identifying the potential stroke mechanisms may contribute to secondary prevention. The purpose of the study is to explore the relationship between stroke mechanisms and the characteristics of culprit plaques in patients with atherosclerotic ischemic stroke in the M1 segment of the middle cerebral artery (MCA) based on high-resolution vessel wall imaging (HR-VWI). Methods: We recruited 61 patients with acute ischemic stroke due to MCA atherosclerotic stenosis from Shenzhen Bao'an District People's Hospital. According to prespecified criteria based on infarct topography and magnetic resonance angiography, possible stroke mechanisms were divided into parent artery atherosclerosis occluding penetrating artery (P), artery-to-artery embolism (A), hypoperfusion (H), and mixed mechanisms (M). The correlation between the characteristics of MCA M1 culprit plaque and different stroke mechanisms was analyzed using HR-VWI. The indicators included plaque surface irregularity, T1 hyperintensity, location, plaque burden (PB), remodeling index (RI), enhancement rate, and stenosis rate. Results: Parental artery atherosclerosis occluding penetrating artery was the most common mechanism (37.7%). The proposed criteria showed substantial to excellent interrater reproducibility (κ, 0.728; 0.593-0.863). Compared with the P group, the surface irregularity, T1 hyperintensity, and obvious enhancement of the culprit plaque in the A group were more common (p < 0.0125). Compared with the other stroke mechanisms, positive remodeling of culprit plaques was more common (p < 0.0125), the RI was greater (p < 0.05), and the PB was the smallest (p < 0.05) in the P group. The enhancement ratio (ER) was smaller in the P group (p < 0.05). Compared with the A group, T1 hyperintensity of the culprit plaque was more common in the H group (p < 0.0125), and the stenosis rate was greater (p < 0.05). After adjustment for clinical demographic factors in the binary logistic regression analysis, the enhancement level (odds ratio [OR] 0.213, 95% CI (0.05-0.91), p = 0.037) and PB of culprit plaque (OR 0, 95% CI (0-0.477), p = 0.034) were negatively associated with P groups. Conclusion: The culprit plaque characteristics of patients with symptomatic MCA atherosclerotic in different stroke mechanisms may be evaluated using HR-VWI. The plaque characteristics of different stroke mechanisms may have clinical value for the selection of treatment strategies and prevention of stroke recurrence. Clinical trial registration: Identifier: ChiCTR1900028533.

18.
Nucleic Acids Res ; 37(Web Server issue): W670-7, 2009 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-19406927

RESUMO

GeNMR (GEnerate NMR structures) is a web server for rapidly generating accurate 3D protein structures using sequence data, NOE-based distance restraints and/or NMR chemical shifts as input. GeNMR accepts distance restraints in XPLOR or CYANA format as well as chemical shift files in either SHIFTY or BMRB formats. The web server produces an ensemble of PDB coordinates for the protein within 15-25 min, depending on model complexity and completeness of experimental restraints. GeNMR uses a pipeline of several pre-existing programs and servers to calculate the actual protein structure. In particular, GeNMR combines genetic algorithms for structure optimization along with homology modeling, chemical shift threading, torsion angle and distance predictions from chemical shifts/NOEs as well as ROSETTA-based structure generation and simulated annealing with XPLOR-NIH to generate and/or refine protein coordinates. GeNMR greatly simplifies the task of protein structure determination as users do not have to install or become familiar with complex stand-alone programs or obscure format conversion utilities. Tests conducted on a sample of 90 proteins from the BioMagResBank indicate that GeNMR produces high-quality models for all protein queries, regardless of the type of NMR input data. GeNMR was developed to facilitate rapid, user-friendly structure determination of protein structures via NMR spectroscopy. GeNMR is accessible at http://www.genmr.ca.


Assuntos
Ressonância Magnética Nuclear Biomolecular , Conformação Proteica , Software , Algoritmos , Bases de Dados de Proteínas , Internet , Modelos Moleculares , Reprodutibilidade dos Testes
19.
Clin J Pain ; 38(4): 292-307, 2021 12 22.
Artigo em Inglês | MEDLINE | ID: mdl-34939973

RESUMO

OBJECTIVES: Sleep disturbance is prevalent among patients with chronic low back pain (CLBP). This systematic review aimed to summarize the evidence regarding the: (1) temporal relations between changes in sleep quality/quantity and the corresponding changes in pain and/or disability; and (2) role of baseline sleep quality/quantity in predicting future pain and/or disability in patients with CLBP. METHODS: Four databases were searched from their inception to February 2021. Two reviewers independently screened the abstract and full text, extracted data, assessed the methodological quality of the included studies, and evaluated the quality of evidence of the findings using the Grading of Recommendations Assessment Development and Evaluation (GRADE). RESULTS: Of 1995 identified references, 6 articles involving 1641 participants with CLBP were included. Moderate-quality evidence substantiated that improvements in self-reported sleep quality and total sleep time were significantly correlated with the corresponding LBP reduction. Low-quality evidence showed that self-reported improvements in sleep quality were related to the corresponding improvements in CLBP-related disability. There was conflicting evidence regarding the relation between baseline sleep quality/quantity and future pain/disability in patients with CLBP. DISCUSSION: This is the first systematic review to accentuate that improved self-reported sleep quality/quantity may be associated with improved pain/disability, although it remains unclear whether baseline sleep quality/quantity is a prognostic factor for CLBP. These findings highlight the importance of understanding the mechanisms underlying the relation between sleep and CLBP, which may inform the necessity of assessing or treating sleep disturbance in people with CLBP.


Assuntos
Dor Crônica , Dor Lombar , Transtornos do Sono-Vigília , Dor Crônica/complicações , Humanos , Dor Lombar/complicações , Dor Lombar/terapia , Autorrelato , Sono , Qualidade do Sono , Transtornos do Sono-Vigília/complicações
20.
Phys Ther Sport ; 52: 256-262, 2021 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-34662806

RESUMO

OBJECTIVE: To culturally adapt the VISA-A into a simplified Chinese version (VISA-A-CHN) and test its measurement properties. DESIGN: Methodological study; SETTING: Hospital and university laboratory. PARTICIPANTS: 240 subjects were divided into the healthy (n = 80), at-risk (n = 80), and tendinopathy groups (n = 80). MAIN OUTCOMES MEASURES: The internal consistency, test-retest reliability, construct validity, and the floor and ceiling effect of the VISA-A-CHN. RESULTS: The VISA-A-CHN showed adequate internal consistency (Cronbach's α = 0.73, 95% CI 0.63 to 0.81), excellent test-retest reliability (ICC3A,1 = 0.97, 95%CI = 0.95 to 0.98), standard error of measurement of 2.2 points, minimum detectable change of 6.0 points, with no floor and ceiling effects. Two factors (pain/symptoms and physical function/activity) were extracted in exploratory factor analysis. There were moderate associations of VISA-A-CHN score with scores of Lower Extremity Functional Scale and SF-36 physical components (rs = 0.53-0.74, P < 0.01) but low associations with SF-36 mental components (rs = 0.12-0.22, P > 0.05). VISA-A-CHN mean score of Achilles tendinopathy group was significantly lower than those of healthy and at-risk groups (P < 0.01). CONCLUSIONS: The VISA-A-CHN is equivalent to the original version in terms of language and measurement properties. It can be used as the outcome measure for Chinese patients with Achilles tendinopathy.


Assuntos
Tendão do Calcâneo , Tendinopatia , China , Comparação Transcultural , Humanos , Idioma , Psicometria , Reprodutibilidade dos Testes , Índice de Gravidade de Doença , Inquéritos e Questionários
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